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GENERAL PRINCIPLES OF CELLULAR ORGANIZATION
IN THE GENOME-REDUCED BACTERIUM
MYCOPLASMA PNEUMONIAE
A dissertation submitted to the
SWISS FEDERAL INSTITUTE OF TECHNOLOGY ZURICH
for the degree
Doctor of Sciences
presented by
SEBASTIAN KÜHNER
Dipl. Biol., Ruprecht-Karls-University Heidelberg
born July 31, 1981
German citizen
Accepted on the recommendation of:
Prof. Dr. Ruedi Aebersold, examiner
Dr. Anne-Claude Gavin, co-examiner
Prof. Dr. Uwe Sauer, co-examiner
2010
Zusammenfassung
Eines der Ziele naturwissenschaftlicher Forschung ist es, eine selbstreplizierende Zelle in
ihrer Gesamtheit zu verstehen. Kennt man die organisatorischen Prinzipien, denen
grundlegende Bestandteile der Zelle, wie Transkriptom, Proteom und Metabolom unterliegen,
so ist man diesem Ziel einen bedeutenden Schritt näher. In den vergangenen Jahren haben
enorme technische Fortschritte bei analytischen Hochdurchsatzverfahren die systematische
Untersuchung dieser einzelnen „Ome“ ermöglicht. Dies wiederrum gibt uns heute die
Gelegenheit, in einem Organismus parallel das Transkriptom und seine Komplexität, die
Proteomorganisation in Proteinkomplexe sowie den Metabolismus und dessen Regulation
global zu analysieren. Die vorliegende Doktorarbeit beschreibt die systematische
Charakterisierung dieser zellulären Bestandteile in dem genomreduzierten Bakterium
Mycoplasma pneumoniae, das zu den kleinsten sich selbstständig fortpflanzenden
Lebensformen zählt. Der Fokus dieser Arbeit liegt auf der Analyse der Proteomorganisation,
der Studie zu der ich, im Vergleich aller drei Teilstudien, den mit Abstand größten Teil
beigetragen habe.
Zur Untersuchung der grundlegenden Prinzipien bakterieller Proteomorganisation führten wir
eine proteomweite, auf chromatographischer Aufreinigung sowie massenspektrometrischer
Analyse von Proteinkomplexen basierende Studie durch. Die Datenanalyse identifizierte 62
homopolymere und 116 heteropolymere, lösliche Proteinkomplexe, von denen die Mehrzahl
bisher uncharakterisiert ist. Etwa ein Drittel der heteropolymeren Komplexe ist an der
Bildung komplexerer Formen der Proteomorganisation beteiligt. Dazu zählt die Anordnung in
größere Multiproteinkomplexeinheiten, welche zum Teil die sequentiellen Schritte eines
biologischen Prozesses reflektieren. Des weiteren beobachten wir, dass ein und dasselbe
Protein
Bestandteil
mehrerer
verschiedener
Komplexe
sein
kann,
was
wir
als
Proteinmultifunktionalität interpretieren. Dies könnte eine mögliche Erklärung für die
Genomreduzierung
Proteinkomplexdaten
von
mit
elektronentomographischen
M.
pneumoniae
484
darstellen.
Proteinstrukturen,
Daten
liefert
Kombination
der
elektronenmikroskopischen
und
zusätzliche
Die
strukturelle
Details
der
Proteomorganisation dieses Bakteriums.
Um die grundlegenden Prinzipien des bakteriellen Metabolismus und seiner Regulation zu
verstehen, wurde ein metabolisches Netzwerk aus 129 Enzymen, die insgesamt 189
verschiedene Reaktionen katalysieren, konstruiert. Die Nutzung dieses biochemischen Atlas
ermöglichte es, ein Minimalmedium, bestehend aus 19 essentiellen Bestandteilen, zu
entwickeln. Das metabolische Netzwerk von M. pneumoniae hat im Vergleich zu
General principles of cellular organization in Mycoplasma pneumoniae
komplexeren Bakterien eine stärker lineare Topologie und enthält einen höheren Anteil an
multifunktionalen Enzymen. Allgemeine Eigenschaften wie die Konzentration von
Metaboliten, der zelluläre Energiehaushalt, die Anpassungsfähigkeit und die globale
Genexpression sind denen anderer Bakterien ähnlich.
Für die Transkriptionsanalyse wurde strangspezifische Mikrochiptechnologie „Tilingarrays“,
ergänzt durch die direkte Sequenzierung der Transkripte, mit mehr als 252 Spottedarrays
kombiniert. Es wurden 117 neue, meist nicht-codierende Transkripte, von denen 89 in
antisense Konfiguration zu bekannten Genen liegen, detektiert. Weiterhin wurden 202
monocistronische sowie 139 polycistronische Operons identifiziert, wobei fast die Hälfte der
letzteren
ein
stufenartiges
Transkriptionsprofil
aufweist.
Unter
variierenden
Wachstumsbedingungen können sich die Operons in bis zu 447 kleinere transkriptionelle
Einheiten aufteilen, was die Mannigfaltigkeit der alternativen Transkripte erklärt. Häufige
antisense und alternative Transkripte sowie unterschiedliche Regulationsmechanismen
verdeutlichen die hohe Dynamik dieses Transkriptoms.
Die Informationen in dieser Doktorarbeit können als kleiner Teil eines Bauplans für eine
minimale zelluläre Maschine angesehen werden. Die vier allgemeinen Schlußfolgerungen aus
dieser Arbeit sind:
1. M. pneumoniae weist besonders in seiner Proteomorganisation und in seinem
Metabolismus Aspekte der Multifunktionalität auf.
2. M. pneumoniae ist für einen nahezu minimalen Organismus, bezüglich seiner
regulatorischen Prozesse, deutlich komplexer als erwartet.
3. M. pneumoniae ähnelt Eukaryoten, hinsichtlich Komplexität seines Transkriptoms,
wesentlich stärker als erwartet.
4. M. pneumoniae ist auf Wirtsanpassung und nicht auf maximales Wachstum optimiert.
General principles of cellular organization in Mycoplasma pneumoniae
Summary
One aim of research in natural sciences is to understand a self-reproducing cell in its entity.
Transcriptome, proteome and metabolome are at the heart of cellular organization. To know
the general principles underlying these basic functional aspects of a cell is a key part on the
way to comprehensively understand cellular life. In recent years systematic analysis of the
individual “omes” has been facilitated via dramatically advancing analytical high-throughput
techniques. This opened opportunities to globally investigate the transcription and its
complexity, the proteome organization into protein complexes as well as the metabolism and
its regulation of an entire organism. In the presented PhD thesis I describe an effort to
systematically characterize these features for the genome-reduced organism Mycoplasma
pneumoniae, which is among the smallest self-replicating forms of life on earth. My work
hereby focuses on the analysis of the proteome organization, the part, among the three
investigations, to which I contributed most substantially.
In order to study basic principles of bacterial proteome organization, we used tandem affinity
purification followed by mass spectrometric analysis to investigate protein complexes in a
proteome-wide screen. The analysis revealed 62 homomultimeric and 116 heteromultimeric
soluble protein complexes, of which the majority are novel. About a third of the
heteromultimeric complexes show higher levels of proteome organization, including assembly
into larger, multi-protein complex entities, suggesting sequential steps in biological processes,
and extensive sharing of components implying protein multifunctionality. Incorporation of
structural models for 484 proteins, single particle EM and cellular electron tomograms
provided supporting structural details for this proteome organization.
To understand basic principles of bacterial metabolism and its regulation, a manually curated
metabolic network of 129 enzymes catalyzing 189 reactions was constructed. This metabolic
map allowed the design of a defined, minimal medium with 19 essential nutrients. In
summary, the M. pneumoniae metabolic network has a more linear topology and contains a
higher fraction of multifunctional enzymes compared to more complex bacteria; general
features such as metabolite concentrations, cellular energetics, adaptability and global gene
expression responses are similar though.
For the transcriptome analysis we combined strand-specific tiling arrays, complemented by
transcriptome sequencing, with more than 252 spotted arrays. We detected 117 previously undescribed, mostly non-coding transcripts, 89 of them in antisense configuration to known
genes. We identified 202 monocistronic and 139 polycistronic operons; almost half of the
latter show decaying expression in a staircase-like manner. Under various conditions, operons
General principles of cellular organization in Mycoplasma pneumoniae
could be divided into 447 smaller transcriptional units, resulting in many alternative
transcripts. Frequent antisense transcripts, alternative transcripts, and multiple regulators per
gene imply a highly dynamic transcriptome.
In essence this thesis dataset provides a blueprint of the minimal cellular machinery required
for life. The four general conclusions of this work are that:
1. M. pneumoniae shows aspects of multifunctionality particularly in its proteome
organization and metabolism.
2. M. pneumoniae, even though being an almost minimal organism, is more complex
than expected, particularly in its regulation.
3. M. pneumoniae resembles eukaryotes more than expected, particularly in its
transcription.
4. M. pneumoniae is optimized for host adaptation and not for growth.
General principles of cellular organization in Mycoplasma pneumoniae
Abbreviations
Ǻ:
Ångström (1×10−10 meters)
AARS:
Aminoacyl tRNA synthetase
AEBSF:
4-(2-Aminoethyl) benzenesulfonyl fluoride hydrochloride
AppppA:
5',5'''-P1, P4-diadenosine tetraphosphate
ATP:
Adenosine triphosphate
B. subtilis:
Bacillus subtilis
BCA:
Bicinchonic acid
bp:
Base pairs
°C:
Degree Celsius
CBPP:
Contagious bovine pleuropneumonia
c-di-AMP:
cyclic di(3'→5')-adenylic acid
CIRCE:
Controlling inverted repeat of chaperone expression
COG:
Clusters of orthologous groups of proteins
CRP:
Catabolite regulation protein
1D:
One dimensional
2D:
Two dimensional
Da:
Dalton
DNA:
Deoxyribonucleic acid
DSSS:
Direct strand specific sequencing
DTT:
Dithiothreitol
E. coli:
Escherichia coli
e.g.:
For example (exempli gratia)
EM:
Electron microscopy
et al.:
And others (et aliae)
FDR:
False discovery rate
fg:
Femto gram
FPInt:
False positive interaction
FT-MS:
Fourier transform-mass spectrometry
FWHM:
Full-Width Half-Maximum
g:
Gravity or gram
GC:
Guanine-cytosine
GE:
Glycolytic enzyme
GF:
Gel filtration
General principles of cellular organization in Mycoplasma pneumoniae
GO:
Gene ontology
h:
Hour
H. pylori:
Helicobacter pylori
HRP:
Horseradish peroxidase
i.e.:
That is (id est)
k:
Kilo
kbp:
Kilo base pairs
KEGG:
Kyoto Encyclopedia of Genes and Genomes
LC:
Liquid chromatography
L. lactis:
Lactococcus lactis
LTQ:
Linear trap quadrupole
LTQ-FT-ICR:
Linear trap quadrupole fourier transform ion cyclotron resonance
µ:
Micro
µRPLC:
Micro reversed phase liquid chromatography
m:
Milli
M:
Matrix component or Molar
MALDI:
Matrix assisted laser desorption ionization
MALDI-TOF:
Matrix assisted laser desorption ionization-time of flight
Mbp:
Mega base pairs
MI:
Multifunctionality index
NCBI:
National Center for Biotechnology Information
mRNA:
Messenger ribonucleic acid
MS:
Mass spectrometry
MW:
Molecular weight
M. genitalium:
Mycoplasma genitalium
M. pneumoniae:
Mycoplasma pneumoniae
m/z:
Mass to charge ratio
ncRNA:
Non-coding ribonucleic acid
ORF:
Open reading frame
PBS:
Phosphate buffered saline
PCR:
Polymerase chain reaction
PDB:
Protein Data Bank
(p)ppGpp:
Guanosine tetraphosphate (pentaphosphate)
General principles of cellular organization in Mycoplasma pneumoniae
pH:
Negative decadal logarithm of the H+ concentration
pI:
Isoelectric point
PMF:
Peptide mass fingerprint
PMSF:
Phenylmethanesulphonylfluoride
PPLO:
Pleuro pneumonia-like organisms
ppm:
Parts per million
PTM:
Post-translational modification
rRNA:
Ribosomal ribonucleic acid
S:
Spoke component or Svedberg
SA:
Socio-affinity
SDS-PAGE:
Sodium dodecyl sulfate-polyacylamide gel electrophoresis
TAP:
Tandem affinity purification
TAP-MS:
Tandem affinity purification-mass spectrometry
TCEP:
Tris(2-carboxyethyl)phosphine
TEV:
Tobacco etch virus
TF:
Transcription factor
TFA:
Trifluoroacetic acid
TPInt:
True positive interaction
TRIS:
Tris (hydroxymethyl) aminomethane
tRNA:
Transfer ribonucleic acid
General principles of cellular organization in Mycoplasma pneumoniae
Table of Contents
1. Introduction .............................................................................................................................1
1.1. M. pneumoniae – a genome reduced model organism .....................................................1
1.1.1. History of research in M. pneumoniae..................................................................... 1
1.1.2. Pathogenicity of M. pneumoniae.............................................................................. 4
1.1.3. Establishing M. pneumoniae as a model organism for systematic studies .............. 6
1.2. Studying M. pneumoniae at different levels.....................................................................9
1.2.1. Proteome of M. pneumoniae .................................................................................... 9
1.2.2. Metabolism of M. pneumoniae ............................................................................... 10
1.2.3. Transcriptome of M. pneumoniae .......................................................................... 12
1.3. Objectives of this PhD thesis .........................................................................................13
1.4. Research articles and reviews obtained during this PhD thesis .....................................14
2. Proteome organization in a genome-reduced bacterium .......................................................15
2.1. Authorship......................................................................................................................15
2.2. Abstract ..........................................................................................................................15
2.3. Introduction ....................................................................................................................16
2.4. Materials and methods ...................................................................................................17
2.4.1. Construction of a collection of M. pneumoniae strains expressing a TAP-fusion. 17
2.4.2. TAP purification of protein complexes and mass spectrometric analysis ............. 18
2.4.3. Sample preparation for PeptideAtlas data collection ............................................ 18
2.4.4. Protein digestion for PeptideAtlas data collection ................................................ 18
2.4.5. Directed mass spectrometry for PeptideAtlas data collection ............................... 19
2.4.5. Data processing and compilation of PeptideAtlas................................................. 19
2.4.6. Peptide Mass Fingerprinting ................................................................................. 20
2.4.7. Reproducibility ....................................................................................................... 20
2.4.8. Profilogs ................................................................................................................. 20
2.4.9. Consolidated scores ............................................................................................... 22
2.4.10. Socio-affinity scoring and integration of quantitative prey profiling across the
entire dataset .................................................................................................................... 26
2.4.11. Socio-affinity score benchmarking....................................................................... 29
2.4.12. Integration with predicted interactions................................................................ 29
2.4.13. Clustering ............................................................................................................. 29
2.4.14. Characterization of homomultimeric protein complexes ..................................... 30
2.4.15. Treatment of the extracts with RNase/DNase ...................................................... 30
General principles of cellular organization in Mycoplasma pneumoniae
2.4.16. Total RNA purification ......................................................................................... 30
2.4.17. Evaluating protein complexes by gel filtration chromatography and western blot
.......................................................................................................................................... 31
2.4.18. Multifunctionality index ....................................................................................... 32
2.4.19. Electron microscopy and image reconstruction of selected complexes............... 33
2.4.20. Cultivation of M. pneumoniae strain B176 for electron tomography .................. 33
2.4.21. Tilt series aquisition ............................................................................................. 34
2.4.22. Image processing.................................................................................................. 34
2.4.23. Mapping of complexes in cellular tomograms ..................................................... 35
2.4.24. Quantitative Western blotting .............................................................................. 37
2.4.25. Structural bioinformatics ..................................................................................... 39
2.5. Results ............................................................................................................................40
2.5.1. Genome-wide screen for protein complexes in M. pneumoniae ............................ 40
2.5.2. Systematic detection of homomultimeric protein complexes.................................. 42
2.5.3. Characteristics of M. pneumoniae protein complexes ........................................... 43
2.5.4. Comparison of methods for estimation of proteome organization......................... 44
2.5.5. The M. pneumoniae protein complex network reveals substantial cross-talk ....... 46
2.5.6. Functional reuse and modularity of protein complexes......................................... 46
2.5.7. Structural anatomy of M. pneumoniae................................................................... 48
2.6. Conclusions ....................................................................................................................50
3. Impact of genome reduction on bacterial metabolism and its regulation .............................52
3.1. Authorship......................................................................................................................52
3.2. Abstract ..........................................................................................................................52
3.3. Introduction ....................................................................................................................53
3.4. Results ............................................................................................................................53
3.4.1 Reconstruction of the metabolic network: verification by a defined, minimal
medium ............................................................................................................................. 53
3.4.2. Comparison of the metabolic network to those of more complex bacteria............ 56
3.4.3. Growth and energetics in comparison with larger bacteria. ................................. 58
3.4.4. Coordinated transcriptome dynamics along growth curve and under various
conditions ......................................................................................................................... 60
3.4.5. Complex metabolic regulation despite few transcription factors .......................... 63
3.5. Conclusions ....................................................................................................................64
4. Transcriptome complexity in a genome-reduced organism ..................................................65
General principles of cellular organization in Mycoplasma pneumoniae
4.1. Authorship......................................................................................................................65
4.2. Abstract ..........................................................................................................................65
4.3. Introduction ....................................................................................................................66
4.4. Results ............................................................................................................................66
4.5. Conclusions ....................................................................................................................71
5. Summary of results................................................................................................................72
6. Conclusions ...........................................................................................................................74
7. References .............................................................................................................................77
8. Acknowledgements ...............................................................................................................87
9. Curriculum vitae....................................................................................................................89
10. Supplement..........................................................................................................................94
10.1. Table S1: List of purifications and proteins identified.................................................94
10.2. Table S2: List of high confidence interactions and corresponding socio-affinity
scores...................................................................................................................................131
10.3. Table S3: List of protein complexes. .........................................................................174
10.4. Table S4: List of literature curated protein complexes. .............................................187
10.5. Table S5: List of modeled protein complexes............................................................195
10.6. Table S6: List of multifunctional proteins. ................................................................199
10.7. Table S7: List of literature curated multifunctional proteins. ....................................203
General principles of cellular organization in Mycoplasma pneumoniae
1. Introduction
1.1. M. pneumoniae – a genome reduced model organism
The following subchapters will first give an overview on the historic development of research
on M. pneumoniae. Secondly, its key pathogenic aspects are summarized and in a third part I
provide selected arguments as to why M. pneumoniae is a suitable model organism for
systematic studies.
1.1.1. History of research in M. pneumoniae
The history of the term “mycoplasma”, from the Greek “mykes”, which translates to fungus
and “plasma” meaning formed, dates back to the year 1889, when A. B. Frank illustrated the
special relationship between plant-invading fungi or other microorganisms and their host cells
(Frank 1889; Krass and Gardner 1973). The initial discovery of Mycoplasma, i.e. the first
isolation of the contagious bovine pleuropneumonia (CBPP) agent, to date known as
Mycoplasma mycoides subsp. mycoides, is credited to Nocard and Roux in the year 1898
(Nocard and Roux 1898; Razin, Yogev et al. 1998; Waites and Talkington 2004).
Subsequently, the nomenclature pleuro pneumonia-like organisms (PPLO) was chosen for
microorganisms in the genus Mycoplasma, referring to life forms similar to the causative
agent of CBPP (Edward, Meiklejohn et al. 1956). It has to be noted though that the fungus
like growth pattern described by the name “Mycoplasma” does only coincide with the growth
characteristics of Mycoplasma mycoides. Nevertheless the name Mycoplasma was adopted for
the entire genus (Razin, Yogev et al. 1998; Waites and Talkington 2004).
Since the 1960s Mycoplasmas are considered as members of a bacterial class named
Mollicutes. This name is derived form the Latin words “mollis” and “cutis” meaning soft skin
(Razin, Yogev et al. 1998) (Figure 1). Their soft skinned properties are the consequence of the
absence of a cell wall. The cellular membrane is however stiffened by the insertion of sterols.
In current taxonomy the class of Mollicutes is part of the phylum tenericutes within the
bacterial kingdom. It comprises 4 orders, 5 families, 8 genera and approximately 200 species
(Razin, Yogev et al. 1998; Waites and Talkington 2004).
General principles of cellular organization in Mycoplasma pneumoniae
1
Figure 1 M. pneumoniae amongst its bacterial relatives zoomed in from the tree of life (from http://itol.embl.de/) (Ciccarelli, Doerks et al. 2006). In blue the genome size (in number of genes) is shown next to each organism. The species highlighted in red are bacteria closely related to M. pneumoniae that are used as benchmarks within this work. Mycoplasma pneumoniae is a member of the family of Mycoplasmataceae and the order of
Mycoplasmatales. M. pneumoniae was originally isolated from the sputum of a patient with
primary atypical pneumoniae by Eaton, Meiklejohn and van Herick in 1944 and was hence
termed “Eaton’s agent” or “primary atypical pneumonia virus” (Eaton, Meiklejohn et al.
1944; Waites and Talkington 2004). In a concerted reclassification call in 1963 several
microbiological experts proposed to rename Eaton’s agent to Mycoplasma pneumoniae
(Chanock 1963). They did so because M. pneumoniae growth, although being unaffected by
microbial inhibitors such as thallium acetate, penicillin and amphotericin B, is sensitive to the
tetracycline group of antibiotics and therefore most likely of bacterial and not viral origin
(Chanock 1963).
In the following years the characterization of M. pneumoniae focused mainly on its
biochemical, cell biological as well as pathogenic properties.
In 1966 Prescott, Sobeslavsky and colleagues used chemical and chromatographic separation
techniques in two back to back studies reporting the isolation and characterization of different
cellular fractions of M. pneumoniae together with the investigation of their antigenic
properties (Prescott, Sobeslavsky et al. 1966; Sobeslavsky, Prescott et al. 1966). These studies
General principles of cellular organization in Mycoplasma pneumoniae
2
revealed a high immunogenicity of fractionated lipids combined with protein in complexes,
while lipids alone were only a weakly immunogenic (Prescott, Sobeslavsky et al. 1966;
Sobeslavsky, Prescott et al. 1966). In addition to such studies the ultra structure of M.
pneumoniae was investigated in detail using scanning and transmission electron microscopy
(Biberfeld and Biberfeld 1970; Kammer, Pollack et al. 1970; Knudson and MacLeod 1970;
Boatman and Kenny 1971; Wilson and Collier 1976). The three major messages of these
studies were that i) M. pneumoniae has a highly structured, basic protein rich, electron dense
rod structure at its thinner end (Tip region, attachment organelle), which is surrounded by
electron-lucent cytoplasm and the cell membrane (Biberfeld and Biberfeld 1970; Wilson and
Collier 1976) ii) M. pneumoniae undergoes an ordered and sequential metamorphosis during
its life cycle involving spherical and filamentous forms (Kammer, Pollack et al. 1970); M.
pneumoniae being pleomorph (Knudson and MacLeod 1970) iii) Nucleic acids present within
M. pneumoniae appear to be excluded from the tip region and mostly located in cytoplasmic
granules (Wilson and Collier 1976).
An important cell biological feature that enables M. pneumoniae to survive without a cell wall
is its internal cytoskeleton, which supports the integrity of the cellular membrane (Krause and
Balish 2001; Krause and Balish 2004; Balish and Krause 2006). The cytoskeleton is
structurally and compositionally novel in comparison to the cytoskeletons of other organisms,
including other bacteria, and it is involved in the cell division process (Balish and Krause
2006). Furthermore it is associated with the terminal attachment organelle, and proves to be
essential for colonization of the host as well as for gliding motility (Balish and Krause 2006).
Regarding M. pneumoniae cellular motility Radestock and Bredt observed that: “The cells
moved in an irregular pattern with numerous narrow bends and circles. They never changed
their leading end. The average speed was relatively constant between 0.2 and 0.5 µm/s. The
maximum speed was about 1.5 to 2.0 µm/s.” (Radestock and Bredt 1977). Furthermore it was
observed that the gliding motility of M. pneumoniae cells required an intact energy
metabolism and is susceptible to changes in pH, temperature, viscosity and various other
factors (Radestock and Bredt 1977). In recent years mutant analysis revealed requirement of
the protein P30 (Mpn453) in M. pneumoniae gliding motility (Hasselbring, Jordan et al.
2005); via a transposon mutagenesis approach additional genes associated with gliding
motility were identified (Hasselbring, Page et al. 2006). Just in the same year it was shown
that the separation of terminal organelles was impaired in a non motile mutant, indicating a
requirement for gliding motility in regular cell division (Hasselbring, Jordan et al. 2006)
General principles of cellular organization in Mycoplasma pneumoniae
3
With regard to understanding M. pneumoniae’s pathogenic properties two major advances
have been achieved towards in the mid 1980s. First, the involvement of the P1 surface protein
(Mpn141), that is located within the attachment organelle, in M. pneumoniae infection of
human host cells has been highlighted (Baseman, Cole et al. 1982; Feldner, Gobel et al. 1982;
Hu, Cole et al. 1982). Secondly, there was progress on the more detailed understanding of the
specificity of the interaction of M. pneumoniae with human erythrocytes. Here the lab of Ten
Feizi, a specialist on glycobiology and M. pneumoniae research, discovered that erythrocyte
receptors for M. pneumoniae are sialylated oligosaccharides (Loomes, Uemura et al. 1984).
In the late 1990s until the first decade of the 21st century M. pneumoniae research was
highly driven by technical advances on genome sequencing, which leveraged research in
virtually all aspects of the life sciences. In 1996 the genome of M. pneumoniae was amongst
the first to be completely sequenced. This work has been directed by Richard Herrmann, an
outspoken expert on M. pneumoniae biology (Himmelreich, Hilbert et al. 1996) who was also
involved in a re-annotation that followed four years later (Dandekar, Huynen et al. 2000).
Currently the M. pneumoniae genome contains 689 annotated genes and about 816kbp.
Finally, it seem worthwhile to notice that among the human mycoplasmas M. pneumoniae is
by far the best known and most carefully studied (Razin, Yogev et al. 1998; Waites and
Talkington 2004).
1.1.2. Pathogenicity of M. pneumoniae
Mycoplasmas in general are mucosal pathogens, which survive as parasites in close
association with their hosts (Waites and Talkington 2004). M. pneumoniae in particular is a
pathogenic bacterium exclusive to humans that colonizes lung epithelia (Waites and
Talkington 2004). It causes a respiratory illness that mainly affects children as well as
adolescents and during which cold agglutinins develop (Chanock 1963; Razin, Yogev et al.
1998; Hammerschlag 2001; Herrmann and Ruppert 2006). According to O’Donnell and
colleagues “the clinical syndrome is characterized by findings that are atypical for the usual
bacterial pneumonia: a lack of fever or systemic symptoms, negative cultures, unusual
radiographic features, or a combination of these” (O'Donnell, Kradin et al. 2004). Hence the
disease is termed “atypical pneumonia”. Also, in contrast to pneumonia caused by the more
traditional pathogens Streptococcus pneumoniae or Haemophilus influenzae, it does not
respond to the usual antibiotic treatment. It was already noted that M. pneumoniae growth is
unaffected by a number of antibiotics and that the bacterium is sensitive to gentamycin as well
as the tetracycline group of microbial inhibitors. To that end it is remarkable that the M.
General principles of cellular organization in Mycoplasma pneumoniae
4
pneumoniae RNA polymerase shows resistance to rifampin, due to a point mutation, whereas
other eubacteria can be successfully treated with this antibiotic.
Another striking feature of M. pneumoniae is that it fulfils all four of Koch’s postulates
(Rifkind, Chanock et al. 1962; Smith, Chanock et al. 1967; Clyde 1973). The postulates are
criteria, formulated by Robert Koch and Friedrich Loeffler in the late 19th century, which are
designed to establish a relationship between a causative microbe and a disease. The postulates
are as follows:
1. The bacteria must be present in every case of the disease.
2. The bacteria must be isolated from the host with the disease and grown in pure culture.
3. The specific disease must be reproduced when a pure culture of the bacteria is
inoculated into a healthy susceptible host.
4. The bacteria must be recoverable from the experimentally infected host.
A prerequisite for M. pneumoniae pathogenicity is the tight connection to epithelial host cells
via its attachment organelle. The attachment organelle mediating this adhesion is located in
the tip structure of the cell (Figures 10 &15). Consequence of such strong adhesion is the
impaired removal via the mucociliary clearance machinery of the host (Waites and Talkington
2004).
Within the last decades several reports were published that included microbiological-, animalas well as human volunteer tests, which have assessed the infectious properties of M.
pneumoniae (Smith, Chanock et al. 1967; Lipman, Clyde et al. 1969; Hansen, Wilson et al.
1979; Hansen, Wilson et al. 1979; Hansen, Wilson et al. 1981; Hansen, Wilson et al. 1981;
Leith, Hansen et al. 1983; Franzoso, Hu et al. 1993; Franzoso, Hu et al. 1994; Catrein,
Dumke et al. 2004; Dumke, Catrein et al. 2004). Lipman et al. derived pairs of virulent and
attenuated or avirulent M. pneumoniae strains and compared them in an effort to elucidate the
mechanisms of virulence (Lipman, Clyde et al. 1969). They found that variations in the
morphology as well as its cytadsorption characteristics closely correlated with avirulence in
the case of M. pneumoniae strain M129-B169 (where the 169 indicates the number of passage
in broth medium: B) (Lipman, Clyde et al. 1969). In a separate investigation Hansen and
colleagues report a similar strain derived from virulent M. pneumoniae M129 that is rapidly
cleared from lungs of infected hamsters (Hansen, Wilson et al. 1981). Subsequent studies
revealed that two proteins, a 40 and 90-kDa protein (Mpn142), which are present in
cytadsorbing, pathogenic wild-type strains are absent in the non-pathogenic strain M129B176 (Hu, Collier et al. 1977; Baseman, Cole et al. 1982; Hu, Cole et al. 1982). These two
General principles of cellular organization in Mycoplasma pneumoniae
5
proteins are surface exposed, localized on the terminal tip apparatus, and likely to be involved
in the attachment mechanism (Franzoso, Hu et al. 1993). These two proteins are products of
the mpn142 gene that encodes a membrane protein moiety, a leader signal, and a stop-transfer
sequence and produces the 90- and the 40-kDa protein instead of an expected 130-kDa protein
(Sperker, Hu et al. 1991; Franzoso, Hu et al. 1993). Another protein with major importance
for host recognition is the adhesin P1 (Mpn141). Until today there have been numerous
reports that highlight the major role of P1, which is concentrated in the tip structure and is a
major component of the virulence mediating interaction of M. pneumoniae with host cells
(Ruland, Wenzel et al. 1990; Layh-Schmitt and Herrmann 1992; Seto, Layh-Schmitt et al.
2001; Hasselbring, Page et al. 2006; Seybert, Herrmann et al. 2006).
To conclude this subchapter on pathogenicity, I want to remark that M. pneumoniae, although
being classified as an S2 (security standard) organism, is certainly not the most clinically
relevant organism causing acute pneumonia. Nevertheless it is essential to always perform
laboratory work according to good laboratory practices adjusted to S2 standards and with the
common sense of dealing with a pathogen. Yet the pathogenic aspects have not been the
major source of motivation for us to embark in a project with M. pneumoniae but rather the
idea to employ it as a model system for studying a “minimal organism” as depicted in the next
subchapter.
1.1.3. Establishing M. pneumoniae as a model organism for systematic studies
Mollicutes are, based on 16S RNA investigations classified as, gram-positive bacteria and are
generally characterized by their strikingly small genomes (Figure 1) (Fraser, Gocayne et al.
1995; Himmelreich, Hilbert et al. 1996). These genomes consist of a single circular
chromosome containing 0.58 to 2.2 Mbps and are thus the smallest known genomes of freeliving organisms. Therefore Mycoplasmas have attracted much attention as blueprints of
minimal cells. The M. pneumoniae genome for example encodes for 689 protein coding genes
and 44 ncRNAs. M. genitalium, which could be considered as a deletion mutant of M.
pneumoniae and is its phylogenetically closest relative, consists of only 485 protein coding
genes (Figure 1). In comparison to the standard model bacteria E. coli and B. subtilis the M.
pneumoniae genome is about 7 times smaller in terms of both base pairs and number of genes
(Table 1). The same holds true for its cellular volume, which is only 10% of that of E. coli
and less than 5% of that of a typical Bacillus like e.g. B. subtilis (Table 1) (Waites and
Talkington 2004). Similarly, the total number of mRNA molecules in E. coli is approximately
15 times larger than in M. pneumoniae (Table 1).
General principles of cellular organization in Mycoplasma pneumoniae
6
Other arguments as to why M. pneumoniae is an ideal near-minimal organism for systematic
studies are its minimal enzymatic toolbox. This reduced set suggests a controllable organism
complexity. For instance, the M. pneumoniae genome encodes for only one protein
phosphatase and two protein kinases creating an absolutely minimal phosphorylation
regulatory network. The same minimalism is evident for the current knowledge about other
PTMs. Apart from phosphorylation only three other PTMs are reported, which include two
variations of protein cleavage as well as modification with lipids.
On a genome regulatory level there are additional arguments underlining the parsimonious
way in which M. pneumoniae deals with its resources, e.g. genome annotations identified only
one sigma factor (Himmelreich, Hilbert et al. 1996; Dandekar, Huynen et al. 2000; Weiner,
Zimmerman et al. 2003).
Feature / cell
M. pneumoniae E. coli
# total DNA bp
816,394
4,639,675
# ORFs
689
4,132
# Ribosomes
140
18,000
# mRNAs
230
4,000
Cell volume [L]
6.7x10-17
6.7x10-16
Protein weight [fg]
10
165
Table 1 Benchmarking M. pneumoniae against the classic model bacterium E. coli. Data from this table originates from NCBI databases and (Guell, van Noort et al. 2009; Yus, Maier et al. 2009) Apart from all positive aspects that make M. pneumoniae an ideal model organism for
systematic studies there are also pitfalls to this bacterium. One major disadvantage is the
elongated generation time of 8 hours. Compared to E. coli, which divides every 20 minutes
this is considerably slower and makes research in M. pneumoniae more time-consuming.
Additionally this could severely hamper its applicability for biotechnological and engineering
purposes. A second drawback is the adherent life-style of M. pneumoniae, which enables the
growth of wild-type cells only in a two dimensional fashion. In consequence the amount of
cells that can be cultivated at once in comparison to bacterial suspension cultures is limited,
causing additional costs for culture equipment and manpower if larger cultures are to be
grown. However, the disadvantage of growing M. pneumoniae in an adherent fashion can be
circumvented by using non-adherent mutants such as the M. pneumoniae strain B176. This
mutant lacks parts of its attachment organelle causing the non-adherence and it has moreover
been reported to be avirulent.
General principles of cellular organization in Mycoplasma pneumoniae
7
Along the lines of using Mycoplasmas as a blueprint of minimal cells a team around John I.
Glass, Clyde A. Hutchison, Hamilton O. Smith and Craig Venter at the J. Craig Venter
Institute uses the close M. pneumoniae relative M. genitalium as a model organism for
synthetic biology. In a project that started more than 15 years ago they first sequenced the M.
genitalium genome (Fraser, Gocayne et al. 1995). In a following step transposon mutagenesis
was globally applied to identify nonessential genes in M. pneumoniae and M. genitalium.
Conversely this dataset then provides insight into the essential gene complement of the
minimal organism. In their first analysis Hutchison et al. report that about 265 to 350 of the
M. genitalium genes are essential under laboratory growth conditions, including about 100
proteins of unknown function (Hutchison, Peterson et al. 1999). In a second analysis of that
kind Glass et al. describe 382 of the protein coding genes as essential, with 28% of them
being of unknown function (Glass, Assad-Garcia et al. 2006). Just recently, the chemical
synthesis of a complete M. genitalium genome was reported (Gibson, Benders et al. 2008). In
another effort this team managed to perform a genome transplantation taking M. mycoides
genomic DNA and transplanting it into M. capricolum cells. The successful transplants were
phenotypically identical to the DNA donor cells of M. mycoides (Lartigue, Glass et al. 2007).
Following this transplantation report, the subsequent step was the transplantation of
Mycoplasma DNA into yeast to exploit its mechanism of homologous recombination for
highly efficient genetic modifications in order to create novel M. mycoides strains (Lartigue,
Vashee et al. 2009).
All mentioned technological advances above could most likely also be applied to M.
pneumoniae. Due to these advantageous characteristics and as M. pneumoniae is the best
studied species among the Mycoplasmas M. pneumoniae appears to be a suitable model
organism for systematic studies.
General principles of cellular organization in Mycoplasma pneumoniae
8
1.2. Studying M. pneumoniae at different levels
This subchapter introduces the state of the art of research prior to the studies that are
described in chapters 2 to 4. For that reason this part of the introduction is already structured
according to the research aspects of the individual studies focusing on the proteome, the
metabolism and the transcriptome of M. pneumoniae.
1.2.1. Proteome of M. pneumoniae
A proteome is the entire set of proteins that are expressed in an organism at a given condition
and time point. In the case of M. pneumoniae, proteomic studies have been conducted for
almost half a century. Initially these investigations focused mainly on one gene product at a
time. With the emergence of more sophisticated analytical tools, namely the use of mass
spectrometers for peptide and hence protein identification, global analysis of the M.
pneumoniae proteome became more widespread. The first of these studies by Regula and coworkers characterized the proteome via a two-dimensional gels electrophoresis (Regula,
Ueberle et al. 2000). Overall, 350 protein spots were analysed from various 1-D and 2-D gel
electrophoresis setups using diverse pH gradients as well as two different mass spectrometers
(Regula, Ueberle et al. 2000); they were assigned to 224 genes (Regula, Ueberle et al. 2000).
In a follow up effort this proteome map was extended to 305 gene products identified using
advanced chromatographic techniques (Ueberle, Frank et al. 2002). This new map
corresponded to 44% coverage of the at that time 688 annotated genes (Ueberle, Frank et al.
2002). Two years later Jaffe and colleagues increased the proteome coverage in M.
pneumoniae to 81% applying an approach called proteogenomic mapping (Jaffe, Berg et al.
2004). They mapped peptides detected in a whole-cell lysate of M. pneumoniae onto a
genomic scaffold and extended these hits into ORFs bound by traditional genetic signals to
generate the “proteogenomic map” (Jaffe, Berg et al. 2004). They detected 9,709 unique
peptides corresponding to 557 of the now 689 predicted ORFs (This includes annotated genes
with mpn numbers 1 to 688 and an additional gene called mpn528a) (Jaffe, Berg et al. 2004).
Subsequent to this study by Jaffe et al. a review by Herrmann and Ruppert summarized the
status of the M. pneumoniae proteome prior to the investigation described in this thesis
(Herrmann and Ruppert 2006). They counted a total of 565 proteins that were experimentally
identified out of 689 protein coding genes annotated (82% coverage) (Herrmann and Ruppert
2006). From the 689 protein coding genes annotated, by the NCBI via their system of COGs,
General principles of cellular organization in Mycoplasma pneumoniae
9
190 do not fit any COGs, while another 16 have an unknown function and 54 have a general
function prediction only (Herrmann and Ruppert 2006). This leaves 429 (of the 689)
annotated genes with a functional description according to COGs.
Another very important aspect of proteome research is that it benefits largely from integration
of additional data such as protein-protein interactions or protein structures in order to
functionally describe a cell.
Regarding the systematic characterization of protein complexes and the mapping of binary
protein-protein interactions major efforts have been reported for other bacteria such as
Campylobacter jejuni, E. coli or Helicobater pylori amongst others (Rain, Selig et al. 2001;
Butland, Peregrin-Alvarez et al. 2005; Arifuzzaman, Maeda et al. 2006; Parrish, Yu et al.
2007; Hu, Janga et al. 2009). For M. pneumoniae, a systematically derived binary proteinprotein interaction network and a global catalogue of protein complexes are yet missing.
Concerning the solution of protein structures considerable effort has been undertaken by the
Berkeley Structural Genomics Center to obtain a near-complete structural complement of the
minimal genomes of M. genitalium and M. pneumoniae. Altogether this initiative has
currently solved 90 structures from 59 targets, which are subject to various publications
(Chen, Yakunin et al. 2005; Shin, Kim et al. 2006; Das, Hyun et al. 2007). Taking into
account related structures from close orthologs brings the total number of M. pneumoniae
proteins for which a structure or model is available to ~350 (Kim, Shin et al. 2005; Chandonia
and Kim 2006). Thus the community is not that far away from a structurally solved organism.
Together with additional orthogonal initiatives this will assist in adding value to data
produced by classical proteomics experiments on the way to the systematic functional
description of this bacterial cell.
1.2.2. Metabolism of M. pneumoniae
In simple analogy to the genome of M. pneumoniae, its metabolism, the entity of all
biochemical reactions, which this organism can perform autonomously, is extremely reduced
and tailored towards the needs of a parasitic lifestyle closely associated with the host.
Therefore M. pneumoniae has a very limited enzymatic toolbox including for instance only
one protein phosphatase and two protein kinases. This might have a direct impact on the
regulatory capabilities via, e.g. phosphorylation.
As M. pneumoniae, like all mollicutes, misses enzymes for peptidoglycan synthesis encoded
in its genome it permanently lacks a cell wall (Razin, Yogev et al. 1998; Waites and
Talkington 2004). This confers pleomorphism and aggravates their taxonomical classification.
General principles of cellular organization in Mycoplasma pneumoniae
10
Another consequence of the absence of a cell wall is that the maintenance of osmotic stability
is especially important even though the pathogen stiffens its membrane with cholesterol
insertions (Razin, Yogev et al. 1998; Waites and Talkington 2004).
At yet another end of the M. pneumoniae biochemical pathways map it has been reported that
purine and pyrimidine metabolism is sufficient for enabling the synthesis of RNA and DNA
in this near-minimal cell based on nucleic acid precursors (Pachkov, Dandekar et al. 2007).
A review of the central carbohydrate metabolism revealed that M. pneumoniae possesses all
10 reactions of Glycolysis but tricarboxylic acid cycle and cytochrome mediated electron
transfer chains are however absent (Pollack, Myers et al. 2002; Waites and Talkington 2004).
Besides ATP generation via glycolysis M. pneumoniae is known to be capable of lactic acid
fermentation like various other bacteria (Razin, Yogev et al. 1998; Waites and Talkington
2004). This is a process of anaerobic respiration that converts sugars such as glucose,
fructose, or sucrose into cellularly amenable energy via substrate phosphorylation effected by
phosphoglycerate kinase (Mpn429) and pyruvate kinase (Mpn303), while the metabolic
product lactic acid is formed (Waites and Talkington 2004).
Other metabolic peculiarities that M. pneumoniae shares with most mollicutes lie within the
way these bacteria regulate translation. For instance, M. pneumoniae uses the universal stop
codon UGA as an alternative codon for tryptophan (Inamine, Ho et al. 1990). Additionally the
M. pneumoniae genome sequencing revealed the absence of generic Shine-Dalgarno
sequences, especially in comparison to other known, related genomes including e.g. B. subtilis
(Himmelreich, Hilbert et al. 1996; Osada, Saito et al. 1999; Sakai, Imamura et al. 2001).
These sequences are ribosomal binding sites to the mRNAs, generally located upstream of the
start codon AUG and show a characteristic consensus sequence among many other bacterial
classes.
Finally, a remark to the generic growth medium so called “Hayflick medium” that has been
used for M. pneumoniae research purposes in the last decades (Hayflick 1965). It provides
glucose as the major carbon source feeding the energy metabolism. Hayflick medium,
however is an undefined medium, as it contains horse serum. Furthermore it has not been
comprehensively characterized for its minimal components. From the point of view of
complete parameter control, which is prerequisite for optimal experimental reproducibility,
this is certainly a weakness of Hayflick medium especially in the analysis of the biochemical
properties of M. pneumoniae.
General principles of cellular organization in Mycoplasma pneumoniae
11
1.2.3. Transcriptome of M. pneumoniae
Besides their remarkably small sizes the Mollicutes genome’s are characterized by an
extremely low GC content (23 to 40%) (Razin, Yogev et al. 1998). This holds true for the
genome of M. pneumoniae (40%), too. Within the years following the completion of the M.
pneumoniae genome sequence, research has focused on the control of gene expression
(Weiner, Herrmann et al. 2000). From the analysis of the genomic sequences of M.
pneumoniae and M. genitalium it became obvious, that major regulators of gene expression in
other bacteria are missing (Fraser, Gocayne et al. 1995; Himmelreich, Plagens et al. 1997;
Weiner, Herrmann et al. 2000); this includes the absence of the two component system and
the Rho factor as well as the presence of a very limited number of σ factors (Himmelreich,
Hilbert et al. 1996; Himmelreich, Plagens et al. 1997; Bairoch and Apweiler 2000).
Interestingly, M. pneumoniae contains only one clearly identified σ factor (Mpn352), while a
second putative σ factor, suggested to induce mobility in M. pneumoniae, has been proposed
(Mpn626) (Bornberg-Bauer and Weiner 2002). The scarcity of σ factors in M. pneumoniae is
in contrast to the at least 14 σ factors of its close relative B. subtilis (Bairoch and Apweiler
2000). Despite this apparent lack of complexity regarding its transcriptional regulation, part of
the M. pneumoniae transcriptome, the entity of all RNAs (mRNA, rRNA, ncRNA) transcribed
under varying conditions, has been shown to be regulated, e.g. by heat-shock, significantly
increasing the expression of 47 genes including various known conserved heat shock genes
including clpB (Mpn531), dnaJ (Mpn021), dnaK (Mpn434), groES (Mpn574) and lon
(Mpn332) (Weiner, Zimmerman et al. 2003).
Yet the transcriptome in M. pneumoniae has not been comprehensively characterized. Even
though systematic gene expression studies have been reported for many other bacteria
(Selinger, Cheung et al. 2000; Tjaden, Saxena et al. 2002; Reppas, Wade et al. 2006;
McGrath, Lee et al. 2007; Nelson, Herron et al. 2008; Akama, Suzuki et al. 2009; ToledoArana, Dussurget et al. 2009), a complete dataset for M. pneumoniae is still missing. This
limits the current understanding of the entire transcriptome in terms of its operon structures
and regulation. Similarly, the number of classified ncRNAs in bacteria has recently been
expanded (Vogel and Wagner 2007), however a comprehensive and unbiased repertoire is still
missing and particularly underdeveloped in M. pneumoniae. To date the M. pneumoniae
transcriptome consists of 689 annotated protein coding genes and 44 ncRNAs.
General principles of cellular organization in Mycoplasma pneumoniae
12
1.3. Objectives of this PhD thesis
Although M. pneumoniae is considered as the best known and most carefully studied species
among the human mycoplasmas (Razin, Yogev et al. 1998; Waites and Talkington 2004)
there are still vast parts of its biology unaddressed i.e. not understood. Consequently, current
knowledge of the M. pneumoniae biology is lagging far behind that of other model organisms
like E. coli or S. cerevisiae, especially considering the knowledge of tools for genetic
engineering. However, as described in section 1.1.3, M. pneumoniae comes with the
advantage of an extremely reduced genome, which allows genome-wide functional studies to
be completed within the lifetime of a PhD thesis/student. This reduced genome size as well as
the significantly reduced cellular dimensions, from which we infer a reduced organism
complexity, are the main driving forces for us to globally investigate M. pneumoniae and
establish it as a model organism for systematic studies on near-minimal organisms.
In order to more systematically understand the general principles of cellular organization in
M. pneumoniae the objectives of this PhD thesis are to elucidate:
1. its proteome organization,
2. its metabolism as well as its regulation and
3. its transcriptome complexity.
Among these three projects, which are a combined effort of several research groups the focus
of my work will be on the analysis of the proteome organization in M. pneumoniae. This
includes the establishment of a library of M. pneumoniae strains in which all individual
proteins are labeled with a TAP-tag. Using this collection I will perform a genome-wide
screen for protein-protein interactions via TAP-MS to get an overview on the hetero- and
homomultimeric protein complexes in this near-minimal bacterium. By integration of other
datasets I want to address general questions like e.g. which molecular mechanisms must a
self-sufficient organism use to still survive with such a reduced-genome. Additionally I would
like to collaborate with experts on various structural biology techniques to exploit our proteinprotein interaction dataset in making the first steps towards solving the structural anatomy of
a cell.
General principles of cellular organization in Mycoplasma pneumoniae
13
1.4. Research articles and reviews obtained during this PhD thesis
1. Sebastian Kühner & Anne-Claude Gavin. Towards quantitative analysis of proteome
dynamics. Nat Biotechnol. 2007 Mar;25(3):298-300. [Review]
2. Samuel Bader, Sebastian Kühner & Anne-Claude Gavin. Interaction networks for
systems biology. FEBS Lett. 2008 Apr 9;582(8):1220-1224. Epub 2008 Feb 20. [Review]
3. Sebastian Kühner‡, Vera van Noort‡, Matthew J. Betts, Alejandra Leo-Macias, Claire
Batisse, Michaela Rode, Takuji Yamada, Tobias Maier, Samuel Bader, Pedro BeltranAlvarez, Daniel Castaño-Diez, Wei-Hua Chen, Damien Devos, Marc Güell, Tomas
Norambuena, Ines Racke, Vladimir Rybin, Alexander Schmidt, Eva Yus, Ruedi
Aebersold, Richard Herrmann, Bettina Böttcher, Achilleas S. Frangakis, Robert B.
Russell, Luis Serrano, Peer Bork, Anne-Claude Gavin. Proteome organization in a
genome-reduced bacterium. Science 326, 1235-1240 (2009).
4. Marc Güell, Vera van Noort, Eva Yus, Wei-Hua Chen, Justine Leigh-Bell, Konstantinos
Michalodimitrakis, Takuji Yamada, Manimozhiyan Arumugam, Tobias Doerks, Sebastian
Kühner, Michaela Rode, Mikita Suyama, Sabine Schmidt, Anne-Claude Gavin, Peer
Bork, Luis Serrano. Transcriptome complexity in a genome-reduced bacterium. Science
326, 1268-1271 (2009).
5. Eva Yus, Tobias Maier, Konstantinos Michalodimitrakis, Vera van Noort, Takuji Yamada,
Wei-Hua Chen, Judith A.H. Wodke, Marc Güell, Sira Martínez, Ronan Bourgeois,
Sebastian Kühner, Emanuele Raineri, Ivica Letunic, Olga V. Kalinina, Michaela Rode,
Richard Herrmann, Ricardo Gutiérrez-Gallego, Robert B. Russell, Anne-Claude Gavin,
Peer Bork, Luis Serrano. Impact of genome reduction on bacterial metabolism and its
regulation. Science 326, 1263-1268 (2009).
‡ Equal contribution
General principles of cellular organization in Mycoplasma pneumoniae
14
2. Proteome organization in a genome-reduced bacterium
2.1. Authorship
This chapter covers the systematic investigation of the proteome organization, i.e. the analysis
of protein-protein interactions and the structural anatomy, in M. pneumoniae. It represents the
major part of work during my time as a predoctoral fellow at EMBL Heidelberg and ETH
Zürich. This study has a shared first authorship with Vera van Noort, who contributed vast
parts of the bioinformatics analysis platform and managed major parts of the data integration.
Additionally there are numerous other co-authors who had their unique contributions. My
main contributions were the protein biochemistry and mass spectrometry, where I performed
most of the conducted experiments in this screen. I also organized and assisted in the
molecular biology and cell culture parts of the project. Additionally, I contributed major parts
to the data analysis and writing of the manuscripts and coordinated work between the various
collaborators. This chapter represents a reformatted version of a research article and its
supporting online material that has been published in Science.
2.2. Abstract
The genome of Mycoplasma pneumoniae is among the smallest found in self-replicating
organisms. To study the basic principles of bacterial proteome organization, we used TAPMS in a proteome-wide screen. The analysis revealed 62 homomultimeric and 116
heteromultimeric soluble protein complexes, of which the majority are novel. About a third of
the heteromultimeric complexes show higher levels of proteome organization, including
assembly into larger, multi-protein complex entities, suggesting sequential steps in biological
processes, and extensive sharing of components implying protein multifunctionality.
Incorporation of structural models for 484 proteins, single particle EM and cellular electron
tomograms provided supporting structural details for this proteome organization. The dataset
provides a blueprint of the minimal cellular machinery required for life.
General principles of cellular organization in Mycoplasma pneumoniae
15
2.3. Introduction
Biological function arises in part from the concerted actions of interacting proteins that
assemble into protein complexes and networks. Protein complexes are the first level of
cellular proteome organization: functional and structural units – often termed molecular
machines - that participate in all major cellular processes. Complexes are also highly dynamic
in the sense that their organization and composition varies in time and space (de Lichtenberg,
Jensen et al. 2005), and they interact to form higher level networks; this property is central to
whole-cell functioning. However, general rules concerning protein complex assembly and
dynamics remain elusive.
The combination of affinity purification with MS (Rigaut, Shevchenko et al. 1999) has been
applied to several organisms, providing a growing repertoire of molecular machines. Genomewide screens in Saccharomyces cerevisiae (Gavin, Aloy et al. 2006; Krogan, Cagney et al.
2006; Tarassov, Messier et al. 2008), captured discrete, dynamic proteome organization, and
revealed higher order assemblies with direct connections between complexes and frequent
sharing of common components. To date these exhaustive analyses have been applied only in
yeast. In bacteria, genome-wide yeast two-hybrid analyses have been reported (Rain, Selig et
al. 2001; Parrish, Yu et al. 2007), but only a few biochemical analyses on selected sets of
complexes are available (Terradot, Durnell et al. 2004; Butland, Peregrin-Alvarez et al. 2005;
Arifuzzaman, Maeda et al. 2006; Hu, Janga et al. 2009). The understanding of proteome
organization in these organisms concerns thus the binary interaction networks.
Here we report a genome-scale analysis of protein complexes in the bacterium, Mycoplasma
pneumoniae, a human pathogen that causes atypical pneumonia (Waites and Talkington
2004). This self-replicating organism has one of the smallest known genomes (689 proteinencoding genes) (Himmelreich, Hilbert et al. 1996; Dandekar, Huynen et al. 2000), making it
an ideal model organism for the investigation of absolute essentiality (Glass, Assad-Garcia et
al. 2006). This analysis and the integration with other consistently derived large-scale datasets
provide a blueprint of the proteome organization in a minimal cell and reveal principles
underlying adaptation to a reduced genome.
General principles of cellular organization in Mycoplasma pneumoniae
16
2.4. Materials and methods
2.4.1. Construction of a collection of M. pneumoniae strains expressing a TAP-fusion
TAP-fusions were expressed in M. pneumoniae M129 (ATTC29342 broth passage No. 31)
strains. Primers were designed for all 689 ORFs in M. pneumoniae. Each ORF was amplified
by PCR using cosmid DNA as template (Wenzel and Herrmann 1988; Wenzel and Herrmann
1989). PCR products were digested (NotI/ SfiI) and ligated into the pMT85-based pMT_ClpBTAP-tag vector (Zimmerman and Herrmann 2005), which carries the Staphylococcus aureus
transposon Tn4001 and the TAP cassette downstream of the SfiI site (Figure 2).
Transformation of M. pneumoniae was done by electroporation, following published
protocols (Hedreyda, Lee et al. 1993). Following transformation and recovery, cells were
plated out in modified Hayflick medium (Hayflick 1965), containing gentamycin (78 mg/l)
and incubated at 37ºC as described earlier (Catrein, Herrmann et al. 2005). Cell culture was
tested for expression by Western blot with a Peroxidase-Anti- Peroxidase antibody developed
in rabbit (Sigma, P1291).
TAPtag
SfiI (616)
tnp
SfiI (833)
NotI (854)
clpB
pMT clpB-TAPtag
5736 bp
o-Rep-ColE1
GMR
Figure 2 Generic TAP cassette vector used for M. pneumoniae transformation. After transformation, the transposase randomly integrates the construct including the gentamycin resistance into the genome. Form now on the TAP‐tagged allele of the gene of interested is expressed under control of the clpB promoter. General principles of cellular organization in Mycoplasma pneumoniae
17
2.4.2. TAP purification of protein complexes and mass spectrometric analysis
Two-liter cultures were incubated in ten 300 cm2 cell culture flasks (Sarstedt) and harvested
96 h after inoculation. Cells were washed twice with ice cold PBS and centrifuged at 9,860xg.
Pellets were resuspended in 2 ml lysis buffer (50 mM Tris pH 7.5, 5% glycerol, 1.5 mM
MgCl2, 100 mM NaCl, 0.2% NP40, 1 mM DTT, 1 mM AEBSF, 1 mM PMSF, 1 μg/ml
pepstatin A, 1 μg/ml antipain, 2 μg/ml aprotinin, 1 μg/ml leupeptin and 16 μg/ml benzamidin)
and lysed mechanically using a douncer. TAP purification was done following established
protocols (Rigaut, Shevchenko et al. 1999; Puig, Caspary et al. 2001). Protein samples were
then analyzed by SDS-PAGE (4-12% NuPage, Invitrogen). Sample preparation for mass
spectrometry was done essentially as described earlier (Shevchenko, Wilm et al. 1996; Gavin,
Bosche et al. 2002). Briefly, whole gel lanes were cut into 32 equal slices; the proteins were
then destained and digested (Trypsin, 12.5 mg/ml). Peptides were extracted in 1% formic acid
in acetonitrile, resuspended in 0.1% TFA in water, mixed (1:1) with matrix solution (0.1%
TFA in 50% acetonitrile and 50% methanol) and spotted on MALDI-TOF plates (Micromass,
Waters). The MS analyses were carried out on a MALDI Micro MXTM (Waters, Milford, MA,
USA). All data were acquired in positive ion mode over m/z range of 900-3,500 in reflectron
mode. Peak masses were extracted from the spectra and used for protein identification
(Supplementary CD).
2.4.3. Sample preparation for PeptideAtlas data collection
M. pneumoniae M129 (ATTC29342 broth passage No. 31) strain cells were washed twice in
ice cold PBS, harvested and pelleted by centrifugation at 9,860xg. Cells were resuspended in
100 µl denaturation buffer (100 mM ammoniumbicarbonate, 8 M urea, 0.1%
RapiGest™(Waters)), sonicated for 5 minutes and spun down for 5 minutes at 20,000xg at
4ºC. A small aliquot of the supernatant was taken to determine the protein concentration using
a commercially available BCA based protein assay kit (Pierce #23227).
2.4.4. Protein digestion for PeptideAtlas data collection
The proteins were reduced with 5 mM TCEP for 60 minutes at 37°C and alkylated with 10
mM iodoacetamide for 30 minutes in the dark before diluting the sample with 100 mM
ammoniumbicarbonate to a final urea concentration below 2 M. Proteins were digested by
incubation with trypsin (1/50, w/w) overnight at 37°C. The peptides were cleaned up by C18
reversed-phase spin columns according to the manufacturer’s instructions (Harvard
Apparatus).
General principles of cellular organization in Mycoplasma pneumoniae
18
2.4.5. Directed mass spectrometry for PeptideAtlas data collection
The setup of the μRPLC-MS system was as described previously (Schmidt, Gehlenborg et al.
2008). The hybrid LTQ-FT-ICR mass spectrometer was interfaced to a nanoelectrospray ion
source (both Thermo Electron, Bremen, Germany) coupled online to a Tempo 1D-plus
nanoLC (Applied Biosystems/MDS Sciex, Foster City, CA). Peptides were separated on a
RP-LC column (75 μm x 15 cm) packed in-house with C18 resin (Magic C18 AQ 3 μm;
Michrom BioResources, Auburn, CA, USA) using a linear gradient from 98% solvent A (98%
water, 2% acetonitrile, 0.15% formic acid) and 2% solvent B (98% acetonitrile, 2% water,
0.15% formic acid) to 30% solvent B over 120 minutes at a flow rate of 0.3 μl/minutes. Each
survey scan acquired in the ICR-cell at 100,000 FWHM was followed by MS/MS scans of the
three most intense precursor ions in the linear ion trap with enabled dynamic exclusion for 30
seconds. Charge state screening was employed to select for ions with at least two charges and
rejecting ions with undetermined charge state. The normalized collision energy was set to
32%, and one microscan was acquired for each spectrum.
For directed LC-MS/MS, two data-dependent LC-MS/MS runs, the SuperHirn peak extraction
and alignment algorithm (Mueller, Rinner et al. 2007) was used to extract all MS1 peaks.
After removing all features for which MS2-data was obtained, the remaining 24,461 masses
were divided in four lists and subsequently sequenced using directed LC-MS/MS analysis as
recently specified (Schmidt, Gehlenborg et al. 2008).
2.4.5. Data processing and compilation of PeptideAtlas
MS/MS spectra were searched using the SEQUEST search tool (Yates, Eng et al. 1995)
against a decoy database (consisting of forward and reverse protein sequences) of the
predicted proteome from M. pneumoniae strain M129 (ATTC29342), complete genome NCBI
genome number NC_000912 (http://www.ncbi.nlm.nih.gov/entrez), consisting of 689 proteins
as well as known contaminants such as porcine trypsin and human keratins (Non-Redundant
Protein Database, National Cancer Institute Advanced Biomedical Computing Center, 2004,
ftp://ftp.ncifcrf.gov/pub/nonredundant). The search was performed with semi-tryptic cleavage
specificity, mass tolerance of 15 ppm, methionine oxidation as variable modification and
cysteine carbamidomethylation as fixed modification. The database search results were
further processed using the PeptideProphet program (Keller, Nesvizhskii et al. 2002) with
decoy option. The peptide FDR was set to 1% (p=0.7).
General principles of cellular organization in Mycoplasma pneumoniae
19
2.4.6. Peptide Mass Fingerprinting
Mass intensity files were analyzed with MASCOT (Perkins, Pappin et al. 1999) and AlDente
(Tuloup, Hernandez et al. 2003; Gasteiger, Hoogland et al. 2005) to identify proteins (Figure
3, A and B). Parameter settings were 80 ppm and 0 missed cleavages for both programs. For
Aldente, shift was set at 0.20, slope at 200 and minimum number of peptides at two. For
MASCOT, identifications above PMF score 45 were always taken and above 30 only if the
consolidated score was at least 80 percent of the maximum consolidated score for that protein.
For AlDente the same files were used for PMF against a random database. All identifications
scoring lower than the random database were excluded. From these PMF identifications,
proteins scoring higher than 1.5 were always taken and higher than 0.5 only if the
consolidated score was at least 80 percent of the maximum consolidated score for that protein.
2.4.7. Reproducibility
To assess the quality of the entire approach, we first measured the reproducibility of the
overall experimental process, i.e. growth of adherent M. pneumoniae strains expressing TAPfusions, lysis of the cell pellets, TAP purification of protein complexes and mass
spectrometric identification of protein complex components. For this purpose, we ran this
entire procedure in duplicate for 18 strains expressing different TAP-fusions. We measure a
reproducibility rate of 73% for proteins involved in the high confidence interactions, which
are the ones that cluster in complexes in the dataset. This is comparable to most published
studies, including that of Sowa et al. that recently reported 80% reproducibility (derived from
four duplicated experiments) for high confidence interactions (Sowa, Bennett et al. 2009). We
also more specifically assess the quality of the MS and protein identification strategy. For this
purpose, 72 MS samples (see procedure above) were processed for MALDI-TOF analysis in
duplicate; the reproducibility for protein identification is 97%.
2.4.8. Profilogs
Proteins that have overlapping peptide mass profiles (we coined the term Profilogs) could lead
to spurious identifications. To detect spurious identifications of this sort we use the results
from the PeptideAtlas. The masses of sequenced peptides by FT-MS (PeptideAtlas) were
entered into MASCOT and AlDente to identify proteins by PMF. False positives (Profilogs)
are in this case identifications of proteins by PMF that were not the proteins sequenced in
MS2 (PeptideAtlas). Mascot scores of false positive identifications (Profilogs) were recorded
(Figure 3, C and D). For each protein identified by FT-MS, we identify all possible Profilogs
as false positive identifications by PMF. In the PMF results of the TAP purifications, all
General principles of cellular organization in Mycoplasma pneumoniae
20
identifications that were not the top-ranking proteins were considered as background if they
are Profilogs and they were not further considered.
Figure 3 Protein identification by MS. From all purifications, we processed 10,447 samples for MS. Proteins were identified using a refined approach that integrates both Mascot (Perkins, Pappin et al. 1999) and Aldente (Gasteiger, Hoogland et al. 2005) search algorithms. (A) This strategy increases the retrieval rate of true positives by 20% compared to only using Mascot. (B) The retrieval rate is calculated by comparing to known complexes. Of all the expected subunits that also belong to these known complexes, we retrieved 25%. The retrieval rate is used in the socio‐affinity scoring. (C) the PeptideAtlas was used to define profilogs; proteins that, in a MS experiment, give rise to overlapping peptide mass profiles. The masses of the sequenced peptides were used to do a PMF, if the actual sequenced protein is retrieved this is a true positive identification. If a different protein is retrieved this is a false positive identification resulting from the fact that the two proteins are profilogs. General principles of cellular organization in Mycoplasma pneumoniae
21
Black line: distribution of true positive identification scores. Red line: false positive identification scores. (D) Same as (C) however the Aldente scores are ordered to the maximum false positive score for each protein. In the screen, after using both Aldente and Mascot identifications to find significant proteins, the best‐scoring protein is always kept. Consecutive lower scoring hits are removed if a better‐scoring protein is a profilog of the lower scoring protein. 2.4.9. Consolidated scores
MASCOT and AlDente scores of overlapping identifications were used to re-scale all the
PMF scores, such that they have the same distribution. For PMF result, the maximum of the
two rescaled scores was taken as the consolidated score. These consolidated scores were used
in the subsequent analyses. Altogether, the set of successful redundant purifications comprises
259 purifications (Table S1) from 212 unique baits. In total 411 proteins were identified in the
consolidated set of identified proteins (Table S1; Figure 4, A, B, C, D, E; and 5).
General principles of cellular organization in Mycoplasma pneumoniae
22
General principles of cellular organization in Mycoplasma pneumoniae
23
Figure 4 Proteome coverage (functional & physicochemical). In (A) we represent the fraction of proteins identified per specified COG class (Tatusov, Koonin et al. 1997) in our TAP‐MS analysis (green), other proteomics analyses (Regula, Ueberle et al. 2000; Ueberle, Frank et al. 2002; Jaffe, Berg et al. 2004) including the PeptideAtlas (yellow), as well as those proteins predicted from the genome, but not yet observed (white). The M. pneumoniae genome contains 689 annotated protein coding genes, of which 564, corresponding to 82% of the genome, have been observed by MS‐based screens before our study. In the TAP‐MS analysis General principles of cellular organization in Mycoplasma pneumoniae
24
we detected 411 distinct M. pneumoniae proteins. Combining the results from the TAP‐MS screen, the PeptideAtlas as well as previous screens, a total of 622 proteins (90% of the genome) have been detected. (B) Virtual 2D gel where proteins are represented according to their size, y‐axis, and isoelectric point, x‐axis. The proteins identified in our dataset are colored red the ones not identified are seen in blue. The distribution of identified proteins covers molecular weights from 6 to 215 kDa and the pI range between 4 and 11.8. (C) The graph represents the fraction of proteins with a given molecular weight that were identified in the TAP‐MS analysis. MWs were extracted from UniProt. Proteins were grouped into different MW classes by exponential binning and subsequently counted. The plot shows that small proteins, e.g. below 20kDa, are significantly underrepresented (P = 0.000444). The R2 between the molecular weight and the fraction detected is 0.88 (correlation of 0.94). The table in panel (D) shows the five protein domains or motifs that were significantly underrepresented in the dataset. Proteins were classified according to their domain or motif composition according to SMART (Letunic, Doerks et al. 2009). The percentage of proteins with a given domain or a given motif that were identified in the TAP‐MS analysis was calculated. P‐values were calculated with the χ²‐test. (E) The graph represents the fraction of proteins with a given mRNA abundance that were identified in the TAP‐MS analysis. For abundance, we took the log2 signal of mRNA abundance on a spotted array measured under reference conditions and binned with a bin width of 0.5. Per bin, the number of proteins and the fraction detected was calculated. Low abundant proteins are underrepresented. There was no relation found between detection probability and hydrophobicity, when hydrophobicity scores were calculated using GRAVY. Figure 5 Screen saturation curve. The graph shows the cumulated number of non‐redundant proteins identified per TAP purifications as a function of increasing numbers of purifications performed. The 259 purifications are represented on the x‐axis in computationally randomized fashion, while the 411 identified proteins are depicted on the y‐axis. The average value, over ten randomization procedures, of proteins identified after a specific amount of purifications is shown in red. The maximal/minimal value, over ten randomization procedures, of proteins identified after a specific amount of purifications is shown in blue and yellow, respectively. General principles of cellular organization in Mycoplasma pneumoniae
25
2.4.10. Socio-affinity scoring and integration of quantitative prey profiling across the entire
dataset
The socio-affinity scoring was adapted from (Gavin, Aloy et al. 2006; Collins, Kemmeren et
al. 2007). To further discriminate contaminants from cognate complexes components we also
integrated systematic quantification of the preys across the entire dataset using spectral
counting. Our approach is very similar to what has been reported by Sowa et al. (Sowa,
Bennett et al. 2009) who originally integrated averaged spectral counts from technical
duplicates to the interaction scores. Their datasets, focused on a limited set of purifications,
contained only rare instances of reciprocal data (reverse tagging). In contrast, in genome-wide
datasets run to saturation (Figure 5), reciprocal interactions are frequent. Thus, for each
protein in the dataset, we could derive quantitative profiles across different purifications
where proteins were present as bait or preys (Figure 6A). We ranked all interactions according
to the quality of the MS data. This ranking is based on the PMF scores from MASCOT and
AlDente, which explicitly take into account spectral counts, further normalized for length of
the peptides and number of possible tryptic peptides per protein. Therefore, the PMF score
represents a more accurate measure than spectral counts alone.
More specifically, the approach is based on the principle that proteins present as contaminants
in a given purification often have low PMF scores (i.e. they are less abundant and they are
thus identified by a smaller number of peptides; they have lower spectral counts).
Reciprocally, the presence of such contaminant proteins with a high PMF score in a given
purification is usually indicative of a true interaction. Thus, we wanted to give a higher socioaffinity, if the PMF score was close to the maximum for that prey. We then sorted all
identified preys by PMF score across different purifications (using different baits), and use the
rank divided by the total number of times the prey was identified instead of the count divided
by the background frequency. In this way, we ensure that preys when identified with a higher
spectral count (reflected in the PMF score) receive a higher interaction score with this bait
than when they are identified with a lower spectral count (usually indicative of spurious
interactions).
Socio-affinity (SA) is build up of the Spokes component (S) where direct bait-prey relations
are counted and a Matrix component (M) where preys are counted that are seen together in a
purification (equation 1). S is a summation over the scores (s) of all purifications (k) where
the bait (i) was used and prey (j) was identified (equations 2 and 3) or prey (j) was not
identified (equation 4). The retrieval rate (r) is estimated to be 0.25 and the probability (pijk)
of finding a bait-prey interaction is estimated from a Poisson distribution (Collins, Kemmeren
General principles of cellular organization in Mycoplasma pneumoniae
26
et al. 2007) where nikprey is the number of preys identified in purification k with bait i, nibait is
the number of times protein i was used as bait, and fj is an estimate of the nonspecific
frequency of occurrence of prey j in the dataset, where we took a value of 1 for npseudo. We
computed fj as Bayesian posterior estimates based on the observed frequency of occurrence of
preys in the dataset and the prior hypothesis that all preys occur non-specifically with equal
frequency, for fj
,
we take only the prey frequency until the PMF score of the prey-
identification with bait i (Figure 6A). Similarly, for the Matrix component (M), m was
summed over all purifications where both prey (i) and prey (j) occur together. The value for
pijk is calculated using the Poisson distribution as in equation 9 where fi and fj are computed as
in equation 6, and ntotprey-prey is the total number of prey-prey pairs observed in the dataset.
Equations:
(1)
SA = S ij + S ji + M ij
(2)
S ij = ∑ sijk
k
r + (1 − r ) pijk
(3)
s ijk = log10
(4)
s ijk = log 10
(5)
p ijk = 1 − exp(− f i f j ntotprey − prey )
pijk
(1 − r )(1 − p ijk )
(1 − pijk )
= log 10 (1 − r )
n jpreyobs + n pseudo
(6)
fj =
(7)
M ijk = ∑ mijk
ntotpreyobs + (n distinct preys n pseudo )
k
r + (1 − r ) pijk
(8)
mijk = log10
(9)
pijk = 1 − exp(− f i nikprey nibait )
pijk
General principles of cellular organization in Mycoplasma pneumoniae
27
∑P ∑P
pc1
(10)
MI =
pc 2
N pc1 N pc 2
∑ Pc1c 2
N c1c 2
Figure 6 Refined socio‐affinity scoring, benchmarking & clustering. (A) Example of PMF scores for a protein that appears either as contaminant or as cognate interactor in different purifications. On the x‐axis is the MASCOT score of all identifications of Mpn004. On the y‐
axis is the cumulative frequency of identifications of Mpn004. This protein seems to be a contaminant in many purifications (low score). However, if the bait was Mpn003 (a known interactor), Mpn004 (red arrow) is identified with a very high MASCOT score (many identified peptides). This was also the case for other interactors within known complexes. Therefore, in the spoke component of the socio‐affinity, we take for fj only the cumulative prey frequency until the PMF score of the prey‐identification with bait i. (B) The socio‐
affinity scoring was adjusted from (Gavin, Aloy et al. 2006; Collins, Kemmeren et al. 2007). For every identified prey we ranked the PMF scores. The rank is now used instead of the frequency of the prey in the socio‐affinity scoring of bait‐prey relations. On the x‐axis is the normalized, refined socio‐affinity. Accuracy was estimated for each bin of socio‐affinity scores. Accuracy was measured by the golden standard set of known complexes (Table S4). TPInts are interactions between proteins of the same complex, whereas FPInts are interactions between proteins of different complexes. Accuracy is TPInt/(TPInt+FPInt), dots. A logistic is done and the logistic curve was used to estimate for each protein‐pair, the probability of an interaction. (C) During clustering the number of proteins clustering in complexes as well as the size of the largest complex was monitored. We chose a threshold to General principles of cellular organization in Mycoplasma pneumoniae
28
define complexes such that many proteins are in complexes but still the size of the largest cluster has not exploded yet. This is depicted in c where on the x‐axis the number of proteins in complexes and on the y‐axis the number of proteins in the largest complex is shown. We chose a threshold that includes 348 proteins into the complexes of our analysis. (D) Nomenclature and definition: classification of protein complex components into cores (ellipses) and attachments (diamonds). 2.4.11. Socio-affinity score benchmarking
A curated list of known complexes was inferred by homology to known complexes from the
literature (Table S4). The interactions between proteins in the same complexes form the
positive set. The interactions between proteins in different complexes form the negative set.
Reported accuracies for function prediction are always lower boundaries as there could be
true interactions also in the negative set. The protein-protein interactions were scored using
socio-affinity and classified in the positive or negative set (Figure 6B). Then we performed a
logistic regression on the socio-affinities and used the resulting logistic function to map the
socio-affinities to interaction probabilities.
2.4.12. Integration with predicted interactions
Predicted interactions were taken from STRING (COG mode) (Jensen, Kuhn et al. 2009);
predictions from databases and text mining were not taken into account. For every protein
pair, we now have an interaction probability from TAP and an interaction probability from
STRING (Jensen, Kuhn et al. 2009). These two probabilities were integrated the same way as
in STRING: P = 1- (1-p1)(1-p2). A weak score from TAP and a high score from STRING
could indicate physical interactions (van Noort, Snel et al. 2007) without predicting other
functional interactions.
For the clustering into complexes only those protein pairs were taken that were seen together
in purification at least once. From this we considered a set of 1,058 high confidence
interactions for clustering into complexes (Table S2).
2.4.13. Clustering
We adopted the clique percolation method from the CFinder method (Adamcsek, Palla et al.
2006). This is one of the clustering methods were proteins can belong to multiple complexes.
We used k=3 to find cliques and used overlapping cliques to define the cores of the
complexes. We took the high-confidence interactions (Table S2) and retrieved protein pairs
that have each other as highest scoring interaction partner (stable pairs). If these stable pairs
were part of a complex, they were also considered core members. If these stable pairs were
not part of a complex, they were added to the complex list as complex of size two. To the core
General principles of cellular organization in Mycoplasma pneumoniae
29
complexes, we added proteins with only one high-confidence interaction and call these
attachment proteins. We used different cut-offs for interaction probabilities to define
complexes and monitored the number of proteins clustering in complexes as well as the size
of the largest complex. We chose a threshold to define complexes such that many proteins
were in complexes but still the size of the largest cluster has not exploded yet (Figure 6C).
Altogether the study reports 116 heteromultimeric protein complexes (Table S3).
2.4.14. Characterization of homomultimeric protein complexes
The TAP-fusions were expressed from an exogenous locus and promoter. As a consequence
the TAP-fusions were present together with their untagged wild type allele. It was not rare
that in the same purification we could observe both TAP-tagged and untagged versions of the
bait, indicating homomultimerization. We manually inspected the 1D SDS-PAGE gel and MS
results for instances where the bait was present in more than one band. The bait was
considered homomultimeric, if we identified it in two distinct bands corresponding to the MW
of the tagged and the untagged versions. Altogether the study reports 62 homomultimeric
protein complexes (Table S3).
2.4.15. Treatment of the extracts with RNase/DNase
To digest DNA and RNA, some extracts were treated with RNase and DNase prior TAP. We
added 3 µl of RNase (Roche) and 1 spatula tip of DNase (Roche) to a cellular pellet in lysis
buffer before mechanical lysis with the douncer. TAP, SDS-PAGE and mass spectrometry
were then performed as described above. The association between RpoA-TAP and the
ribosome was unaffected by this DNA/RNA treatment indicating the interactions does not
imply RNA or DNA (Figure 7 A and B).
2.4.16. Total RNA purification
After growth, surface-attached cells are washed once with PBS at 37°C and immediately
lysed in the cultivation flask by adding RLT buffer from the QiagenTM RNeasy Plus Mini Kit
(Cat. Num. 74134). For cell lysis, 1.8 ml of RLT buffer in presence of 18 μl βmercaptoethanol was used per cultivation flask. RNA purification was done according to the
manufacturer’s protocol. Purification of RNA in presence of RNase inhibitors is also shown
in Figure 7A.
General principles of cellular organization in Mycoplasma pneumoniae
30
Figure 7 The association between the RNA polymerase and the ribosome (A) Ribosomal proteins copurify with RpoA‐TAP in extracts treated with RNase and DNase. Upper panels: Coomassie‐stained SDS‐PAGE gels of RpoA‐TAP and 30S ribosomal protein RpsF‐TAP purifications. Proteins identified by MS are indicated between gel images. Lower panel: Ethidium bromide stained 1% agarose gel of total extracted RNA. Cell extracts were treated either with RNase/RNase inhibitors or RNAse/DNAse. (B) RNA polymerase and ribosomal proteins copurify in various purifications. The matrix shows the different baits used in the top of each column and the preys identified by MS in each row underneath. This underlines ability to reversely purify the RNA polymerase with ribosomal entry points and vice versa. 2.4.17. Evaluating protein complexes by gel filtration chromatography and western blot
GF chromatography was performed at 10°C on a Pharmacia SMART system at a flow rate of
40 µl/minute by using a SuperoseTM 6 PC 3.2/30 column, equilibrated with lysis buffer. The
chromatographic profile was monitored at 280 nm by using the µPeak monitor (Pharmacia).
Volumes of 50 µl of M. pneumoniae lysates were loaded on a column and 60 µl fractions
were collected and analyzed by SDS-PAGE and Western blot (Figure 8B and 14A).
A peroxidase anti-peroxidase antibody (Sigma, P1291) was used to detect the TAP-fusions
(alpha subunit of DNA-directed RNA polymerase: RpoA-TAP and segregation and
condensation protein A: ScpA-TAP). Polyclonal antibodies produced in rabbits have been
used to detect the 30S ribosomal protein S4 (RpsD), the ATP-dependent protease La (Lon)
and the protein P115 homolog (P115); final detection was done using secondary antibodies
coupled to HRP (Sigma). For the quantification, total band intensity was integrated with
Photoshop software (Adobe) and normalized versus the highest detected peak (Figure 14A).
General principles of cellular organization in Mycoplasma pneumoniae
31
Figure 8 Novelties in protein complexes. (A) Mpn266 associates with the RNA polymerase as a homodimer. On the left, M. pneumoniae RNApol electron density (~17 nm) with a fitted structure modeled on T. aquaticus RNApol (PDB code: 1l9u). The model fits apart from an extra stalk (cyan arrow), which can be explained by a 200 amino‐acids N‐terminus insertion in M. pneumoniae RpoD. On the right, interaction with an Mpn266 homodimer modeled using a template of B. subtilis SPX interacting with RpoA C‐terminus (1z3e) and a template of an E. coli RpoA C‐terminus dimer interacting with DNA (1lb2). The RpoA C‐terminus dimer is separated by a distance (48Å) similar to that observed for the RpoA N‐terminus from the polymerase fitted on the EM (43Å) (B). The cohesin‐like protein complex. The components are color coded according to their belonging to expression clusters; the heat map illustrates some of these expression patterns (Yus, Maier et al. 2009). Core components are represented by circles, attachments by diamonds. The line attribute corresponds to socio‐
affinity indices: dashed lines, 0.5–0.86; plain lines, >0.86. The blots at the bottom show co‐
elution, during gel filtration chromatography, of ScpA (59kDa), Lon (90kDa) and P115 (111kDa) in extract over‐expressing (right) or not (left) ScpA‐TAP (79kDa). N.D.: not determined. 2.4.18. Multifunctionality index
For each set of two protein complexes and one protein, a multifunctionality index (MI) value
was calculated (Table S6). This index reflects the tendency for the protein to be part of both
complexes and corrects for the possibility that these two complexes should have been one
complex, but was separated due to the chosen threshold.
General principles of cellular organization in Mycoplasma pneumoniae
32
MI is calculated between each protein and each complex as above where the sums of the
interaction scores (P) between the protein under consideration and the members of protein
complex 1 (pc1) and protein complex 2 (pc2) are multiplied and divided by the product of the
Number of members (N) in complex 1 and complex 2 (equation 10). This is divided by the
sum over the interaction scores (Pc1c2) between members of complex 1 and complex 2 divided
by the total number of protein pairs (N c1c2) between complex 1 and complex 2, not taking into
account the protein for which the MI is being calculated (equation 10). To benchmark the
results from the MI a curated list of known multifunctional proteins from the literature was
used (Table S7).
2.4.19. Electron microscopy and image reconstruction of selected complexes
Selected protein complexes (DNA gyrase, DNA topoisomerase, RNA polymerase) were
purified according to the first step of the TAP-protocol (see above). The resulting TEV-eluate
was further purified on a glycerol-gradient and fixed by cross-linking following the GRAFIX
protocol (Kastner, Fischer et al. 2008). Fractions containing the bait were identified by dotblot using an antibody against calmodulin-binding domain. For electron microscopy, samples
were prepared from fractions containing the bait by sandwich negative staining (Golas,
Sander et al. 2003) (Figure 9). For DNA gyrase the first models were determined by random
conical tilt reconstruction (Radermacher, Wagenknecht et al. 1987). The first model of the
topoisomerase was determined by projection matching of class averages against the final map
of the gyrase. For RNA polymerase a low-pass filtered map of the polymerase from Thermus
aquaticus (1l9u) was used as first reference (Murakami, Masuda et al. 2002). Maps were
further refined by iterative projection matching against the current best map using SPIDER
(Frank, Radermacher et al. 1996).
2.4.20. Cultivation of M. pneumoniae strain B176 for electron tomography
The M. pneumoniae B176 avirulent, noncytadsorbing strain that lacks the 40- and 90-kDa
proteins, the products of the ORF6 gene (Mpn142), was used in this analysis (Ruland,
Himmelreich et al. 1994). In comparison to its parental strain, the virulent M. pneumoniae
M129, B176 does not grow in colonies and hence is more suitable to image individual cells by
electron tomography of plunge-frozen samples.
General principles of cellular organization in Mycoplasma pneumoniae
33
Figure 9 Electron microscopy particle selection. Electron microscopy and image analysis of negatively stained complexes fixed with glutaraldehyde on a glycerol density gradient. From left to right: DNA‐gyrase (Mpn003, Mpn004), RNA‐polymerase (Mpn191, Mpn352, Mpn515, Mpn516), DNA‐topoisomerase (Mpn122, Mpn123). Upper panel: Fractions of the glycerol gradient were tested by dot blot using an antibody against the calmodulin tag of the bait (fraction 1 is always at the bottom of the gradient). Arrowheads mark the fractions selected for further analysis by electron microscopy and image reconstruction. Representative micrographs of the fractions marked by arrowheads are shown below the dot blots. The samples were prepared by sandwich negative stain using 2% uranyl acetate for staining. The bottom panel shows results from the image analysis. Upper row: Selected class averages calculated by multivariate statistical analysis. The class averages match projections (central row) of the three‐dimensional image reconstructions of the respective complexes. Bottom row shows surface representations of the image reconstructions from the same direction as the projections above. The scale bars equal 10 nm. 2.4.21. Tilt series aquisition
Single-axis tilt-series were collected covering an angular range from -66° to +66° with 1.5
degrees of angular increment in a Tecnai G2 Polara microscope cooled to liquid nitrogen
temperature and equipped with a Gatan postcolumn GIF 2002 energy filter. Data acquisition
was carried out under low-dose conditions using the UCSF tomography software (Zheng,
Braunfeld et al. 2004). Images were recorded on a 2k x 2k pixel CCD camera at a defocus
level between -5 and -10 μm. The pixel size at the specimen level was 0.6 nm.
2.4.22. Image processing
The images were interactively aligned with respect to a common origin using 10 nm colloidal
gold particles distributed in the sample as fiducial markers. The reconstructions were
performed using weighted back-projection algorithm and visualized with the Amira package
(Pruggnaller, Mayr et al. 2008).
General principles of cellular organization in Mycoplasma pneumoniae
34
2.4.23. Mapping of complexes in cellular tomograms
We scanned 26 tomograms of whole M. pneumoniae cells (with sub-pixel alignment error),
with four templates: the ribosome (Gabashvili, Agrawal et al. 2000), GroEL (Forster,
Pruggnaller et al. 2008), the RNA polymerase, and the structural core of the pyruvate
dehydrogenase (PdhC, homomultimer) (Izard, Aevarsson et al. 1999), by means of locally
normalized cross-correlation (Frangakis, Bohm et al. 2002). We have developed a
classification method integrating knowledge on protein complexes networks for the detection
of putative complexes inside cellular tomograms that largely overcomes the problem of
template bias and significantly increases detection certainty (Figure 10). The principle here is
that a tomogram is scanned with a template resembling an incomplete complex. The part of
the complex, which is deliberately ignored, does not need to be structurally relevant.
Complexes are identified as such, when the ignored part is recovered after the classification.
Here, we illustrate the procedure on the example of the ribosome. The tomogram (Figure
10A) is scanned with a portion of the whole ribosome, in this case the large ribosomal subunit
(50S). The resulting probability map (Figure 10B) contains only the probabilities that the
large ribosomal subunit is located at particular positions in the electron tomogram. Most of
the ribosomes will most probably have the small ribosomal subunit (the 30S) attached to the
large one (Figure 10, C and D). Hence, when classifying the hits obtained for the 50S subunit,
we expect to identify classes which show the ribosome as a complete entity. We expect that
the sub-tomograms composing those classes will have significantly reduced false positive
rates, since the additional density resembles the structure of the small ribosomal subunit
increases our level of fidelity.
On each cell, the locally normalized cross-correlation (Frangakis, Bohm et al. 2002) produced
a list of putative particles, which were further classified using the missing wedge independent
procedure (Pascual-Montano, Donate et al. 2001; Forster, Pruggnaller et al. 2008) with a
network of 5x5 classification units (Figure 10E). Visual inspection of these classification units
reveals the presence of extra-density which was not included in the original template. The
similarity of this extra density to the 30S subunit is further asserted by normalized cross
correlation and Fourier Shell Correlation. As an effective decision criterion is considered a
high cross-correlation value and a Fourier Shell correlation extending into the higher
frequencies. The sub-tomograms classifying in classification units with high Fourier Shell
Correlation components are accounted as putative particles (Figure 10F). All other hits are
rejected.
General principles of cellular organization in Mycoplasma pneumoniae
35
Figure 10 Complex detection in M. pneumoniae cryoelectron tomograms by template‐
matching and protein complex‐based classification. Mapping the spatial distribution of four selected complexes in one of the cryo‐electron tomograms. (A) x‐y slice of a reconstruction. The protein density is visualized in dark intensity values. Some of the putative complexes after template matching have been highlighted with circles. (B) The same slice as in (A), in the normalized cross‐correlation map after scanning with the large ribosomal subunit. Higher cross‐correlation values are represented in the bright intensity values. High correlation values corresponding to putative complexes are highlighted with circle in (A) and (B). (C) Isosurface representation of four complexes present in the tomogram. Parts of these General principles of cellular organization in Mycoplasma pneumoniae
36
complexes only have been used as templates: the large subunit of the ribosome (yellow) only, half a RNA polymerase (purple), half the structural core of the pyruvate dehydrogenase (PdhC, homomultimer) (blue) and 10 out of the 14 apical and equatorial domains of GroEL (red). (D) The projection of the whole ribosome is visualized at the same view as the projection images in the classification units. (E) In the green overlay contour the 50S is indicated and in the purple the 30S small ribosomal subunit. The overlays are also superimposed to the classification units. (E) Protein complex‐based classification strategy using the ribosome as an example. In our methodology, the 50S subunit is used to search through the whole tomogram (in six degrees of freedom, three rotational and three translational). Sub‐Tomograms at all local maxima of the cross‐correlation map are extracted and subjected to missing wedge independent classification with KerDenSOM. A cropped region of the total output map of KerDenSOM is shown. A projection image of five out of the 25 classification units is presented. In the first row the Fourier shell correlation, visualized as the blue plot in the bottom right corner of the images, is at the high frequencies indicating high similarity of the density inside the green overlay region to the small ribosomal subunit. The Fourier shell correlation curves of all the other classification units are either close to zeros (showing no similarity) or even negative similarity (due to the inverted contrast). The visual inspection confirms this result. Hence only the sub‐tomograms classifying within the classes on the upper row are selected in this example to contain true hits for the ribosomes. The number of hits assigned to each class appears in the upper‐left corner of the classification unit. (F) Isosurface representation of the whole M. pneumoniae cell with the putative complexes mapped inside. Membrane (blue) and tip organelle (green) can also be visualized. The color mapping of the complexes is as in (C). 2.4.24. Quantitative Western blotting
To determine absolute quantities of GroEL and ribosomes in M. pneumoniae, levels of RpsD
and the GroEL monomer were quantified by Western blotting. M. pneumoniae recombinant
RpsD and GroEL genes used as standard were cloned into the pET19b vector, and proteins
carrying an N-terminal poly-histidine tag were expressed and purified from E. coli cells.
Protein concentrations were determined using a commercially available BCA based protein
assay kit (Pierce #23227) essentially following the instructions in the product manual.
Western blotting was carried out with polyclonal antibodies against RpsD and GroEL,
respectively. Western blot bands were quantified using the software “ImageJ”.
Relating band intensity values to known protein amounts of the purified standards and to the
experimentally determined protein per M. pneumoniae cell ratio (10 fg/cell), allowed the
calculation of copies of ribosomes and GroEL particles per cell, considering the homooligomeric state of the GroEL particle (Xu, Horwich et al. 1997) (Figure 11, A and B).
The value for the quantified Western blot band is divided by the slope of the standard curve
and multiplied by 1e-9 to obtain the amount of RpsD and GroEL in grams per gel lane.
General principles of cellular organization in Mycoplasma pneumoniae
37
Figure 11 Quantitative Western blots of GroEL and ribosomal protein S4 (RpsD) in whole cell extract (A) Top panels: 0‐100 ng affinity purified GroEL and RpsD protein was loaded next to a M. pneumoniae cell lysate and blotted with polyclonal antibodies (Antibodies: R. Herrmann). Bottom panels: Standard curves from quantified Western blots. The slope of the trend line was used to determine the amount of GroEL and RpsD protein in a M. pneumoniae cell lysates (red square). The error in quantifying the amount of GroEL in the M. pneumoniae sample is 2.1%, as judged from five measurements and 6.6% for RpsD, as judged from four measurements. (B) Estimation of the number of molecules of GroEL and RpsD proteins in a M. pneumonia cell. Determination of the protein concentration of the M. pneumoniae cell lysate (5.07 g/l) and the
amount of protein per M. pneumoniae cell (10 fg/cell) allows for calculating the number of
cells per gel lane, considering dilution factors and the amount of lysate loaded. Dividing the
amount of RpsD and GroEL per lane by the number of cells/lane gives a value for RpsD and
GroEL in grams per cell. This number is then transformed to moles by dividing it with the
molecular weight of the respective proteins in g/mol. The Avogadro constant determines 1
mol to contain 6.022e23 particles. Dividing the amount of protein per cell in moles by the
Avogadro constant allows the determination of molecules per cell. Since GroEL is a
General principles of cellular organization in Mycoplasma pneumoniae
38
homotetradecamer, this number has to be divided by 14 to obtain a number for GroEL
particles in a single cell. RpsD is believed to be in a 1:1 stochiometry with ribosomes; hence
the number of RpsD molecules directly reflects the number of ribosomes in a single M.
pneumoniae cell (Figure 11B).
2.4.25. Structural bioinformatics
Homologous proteins were collected using PSI-BLAST (Altschul, Madden et al. 1997) with
default parameters. Hidden-Markov Models were built and used to find homologues of known
structures from PDB (Berman, Henrick et al. 2003) using HHMake and HHSearch modules of
the HHPred suite (Soding 2005). Matches of at least 50 residues in the query and with an Evalue ≤ 0.01 were considered further. Two matches were considered to be in physical contact
when they did not overlap on the target sequence and each had at least 10 residues within 5.0
Å of the other. Overlaps between multiple interfaces on a single protein were calculated as the
number of such residues that they had in common, and the interfaces clustered in to groups
using these overlaps and the Markov Cluster algorithm ‘MCL’ (van Dongen 2000)(Table S5).
General principles of cellular organization in Mycoplasma pneumoniae
39
2.5. Results
2.5.1. Genome-wide screen for protein complexes in M. pneumoniae
We adapted the TAP-MS protocol (Rigaut, Shevchenko et al. 1999)to M. pneumoniae M129
(Figure 12). We processed all 689 M. pneumoniae protein-coding genes, of which 617 were
successfully cloned (90% of the genome (Dandekar, Huynen et al. 2000)). Using a
transposon-based expression system, we constructed a total of 456 M. pneumoniae strains.
They carry a stable genomic integration of carboxy-terminal TAP-fusions under
transcriptional control of the M. pneumoniae clpB (mpn531) promoter. From this collection,
all 352 individual strains expressing soluble TAP-fusions were grown to confluence in two
liters of adherent culture, leading to 212 successful purifications. The components of the
purified complex were separated by denaturing gel electrophoresis, and individual bands
trypsin-digested and analyzed by MS (Supplementary CD). We processed a total of 10,447
MS samples and identified proteins using a new approach that integrates the Mascot (Perkins,
Pappin et al. 1999) and Aldente (Gasteiger, Hoogland et al. 2005) search algorithms (Resing,
Meyer-Arendt et al. 2004). This increased the identification of known complex component by
~20% compared to either method alone (Figure 3, A and B). The procedure also scores the
quality of individual identifications considering all peptide profiles we observed for each
protein, including our purification dataset and a PeptideAtlas, a comprehensive set of tryptic
peptides (Desiere, Deutsch et al. 2006) measured with Fourier transform-MS from whole M.
pneumoniae lysates (Supplementary CD). We removed protein identifications with
overlapping peptide profiles (3%) (Figure 3, C and D). When applied to the entire purification
dataset, this approach uncovered 411 distinct proteins from 5,899 identifications (Table S1).
General principles of cellular organization in Mycoplasma pneumoniae
40
Figure 12 Synopsis of the genome‐wide screen of complexes in M. pneumoniae. The 411 proteins identified with 212 tagged proteins correspond to 60% of the
annotated ORFs and 85% of the predicted soluble proteome (Figure 4). They cover all cellular
functions, though low abundant, small or trans-membrane segment-containing proteins are
significantly underrepresented (Figure 4). Membrane proteins purification requires separate
biochemical protocols so they were not included in this screen. The proportion of new
proteins identified per purification dropped asymptotically as the screen progressed, implying
that the procedure was near saturation (Figure 5). This entails recurring protein complex
retrieval through reverse tagging, and is important both to confirm novel interactions and to
identify dynamic complexes (Gavin, Aloy et al. 2006).
To define complexes in a quantitative way, we first calculated socio-affinity indices
that measure the frequency with which pairs of proteins were found associated in our set of
biochemical purifications (Gavin, Aloy et al. 2006). We improved the concept by integrating
predicted interactions from the STRING database (Jensen, Kuhn et al. 2009) and the relative
abundance of a given prey when associated with different baits (i.e. across different
purifications (Sowa, Bennett et al. 2009)). We used the MS scores that measure the
probability for a peptide mass fingerprint to characterize each protein based on spectral
counting. A reduced score for a prey in a purification, when compared to the same prey in
other purifications, reflects identifications by a smaller number of peptides (lower spectral
counts) and is indicative of a spurious interaction; is therefore down-weighted (Figure 6A).
We applied this new scoring scheme to the entire dataset and calculated a list of 10,083
General principles of cellular organization in Mycoplasma pneumoniae
41
interactions. A cut-off was defined at an accuracy, i.e. fraction of true interactions (von
Mering, Krause et al. 2002), of more than 80%, which gave a set of 1,058 high-confidence
interactions (Figure 6, B and C; see also Table S2). We also measured the overall
experimental reproducibility on a set of 18 experiments that we performed twice; duplicates
included growth of adherent cultures, biochemical purifications and MS analyses. For protein
pairs with socio-affinity scores ≥ 0.8 the overall reproducibility is 73%; for those scoring
below it is 43% (P = 10-13, χ² test). For comparison, the reproducibility calculated on the
duplicated MS measurements of 72 MS samples is 97%. We then applied cluster analysis,
using a procedure called clique percolation that allows proteins to be part to different
complexes. We varied the clustering parameters over reasonable ranges. The best conditions
in terms of coverage (see below) generated a collection of 116 heteromultimeric complexes.
They are organized into densely (> one link) and loosely interconnected (one link)
components we called “core” and “attachment”, respectively (Figure 6D and Table S3).
Generally, M. pneumoniae proteins within complexes and cores are more often co-expressed
(Guell, van Noort et al. 2009) and conserved between species than average; protein within
complexes appear on average in 244 species compared to 173 for the entire proteome (median
= 190). Comparison to a set of 31 known complexes, described in other species (Table S4),
revealed a coverage of 61%, which is similar to results from previous screens in yeast and E.
coli (coverage ~60%) (Gavin, Bosche et al. 2002; Butland, Peregrin-Alvarez et al. 2005;
Gavin, Aloy et al. 2006; Krogan, Cagney et al. 2006).
2.5.2. Systematic detection of homomultimeric protein complexes
The TAP-fusions were expressed from exogenous loci and promoter and are therefore present
together with the untagged wild-type allele. It was thus common to observe both TAP-tagged
and untagged versions of the bait in the same purification, which is an indication of
homomultimerization (Figure 7). Careful scrutiny of the purification dataset revealed
evidence for 62 homomultimeric complexes (Table S3) covering 62% of those previously
seen either in M. pneumoniae or in another species by orthology (Table S4). Fourteen
homomultimeric complexes were novel, and for 12 of these we could find supporting
structural evidence from homologs of known structure (Berman, Henrick et al. 2003) (Table
S5). An example is Mpn266, a protein of previously unknown function that we found
associated to RNA polymerase (Complex 49; Table S3) as a dimer. Its binding to the
polymerase is consistent with its similarity to SpxA, an RNA polymerase-binding protein that
regulates transcription initiation in gram-positive bacteria (Zuber 2004; Yus, Maier et al.
General principles of cellular organization in Mycoplasma pneumoniae
42
2009). Comparative modeling of structure and single particle electron microscopy (Figure
8A) (Guell, van Noort et al. 2009) show M. pneumoniae RNA-polymerase resembles that of
Thermus aquaticus (Murakami, Masuda et al. 2002) with the exception of a substantially
bigger stalk at the position of the sigma factor, RpoD (Mpn352), consistent with M.
pneumoniae RpoD being 200 amino acids longer than its T. aquaticus ortholog (Figure 8A).
The models also further support the idea that each Mpn266 in the dimer binds one of the two
alpha subunits of the polymerase as do other transcription factors (Figure 8A). From the
number of baits used (212) and from the effectiveness of the method in recovering known
complexes (62% coverage), we estimate that as many as 47% of all soluble proteins form
homomultimers in M. pneumoniae. This is in agreement with a recent analysis of more than
5,000 protein structures (Levy, Boeri Erba et al. 2008). Finally, considering both homo- and
heteromultimers, almost 90% of soluble proteins were found to be part of at least one
complex, a figure similar to values estimated in yeast (Gavin, Aloy et al. 2006; Krogan,
Cagney et al. 2006). This further consolidates the view that exhaustive organization into
complexes is a general property of proteomes in bacteria and eukaryotes.
2.5.3. Characteristics of M. pneumoniae protein complexes
Overall, more than half of the identified complexes were not previously described. We also
found new components in previously known complexes: the dataset contains 126 proteins
with previously unknown or conflicting functional annotation. For example, complex
membership identifies Mpn426, previously annotated as a P115 homolog, as the missing Smc
(structural maintenance of chromosomes) DNA-binding subunit of the cohesin-like complex
(Complex 40; Figure 8B and Table S3) (Yus, Maier et al. 2009). This complex also contains
the ATP-dependent protease Lon (Mpn332) that binds DNA and regulates chromosome
replication (Wright, Stephens et al. 1996). The observed physical association between Lon
and Smc and the observation that Lon expression increases concomitant with Smc
degradation at the onset of the stationary phase (Figure 8B) suggest Smc might be a target of
this protease. The existence of a native complex including Lon, ScpA (Mpn300) and P115 is
further supported by the observation that these three proteins co-elute during gel filtration
chromatography (Figure 8B) (Yus, Maier et al. 2009). We also identified known eukaryotic
complexes such as those including several GEs that have been discovered at eukaryotic
plasma membrane, where they locally produce ATP (Table S4). We observed similar
assemblies in M. pneumoniae (Complexes 12 and 45; Table S3) suggesting that this function
is conserved in bacteria.
General principles of cellular organization in Mycoplasma pneumoniae
43
2.5.4. Comparison of methods for estimation of proteome organization
We overlaid the protein complex data with complementary large-scale datasets that have been
previously used to deduce physical interactions (Figure 13A). Only 48% of the TAP
interactions within complexes were found in any existing dataset; 359 associations were only
identified by TAP-MS (Figure 13A). Even in the worst-case scenario, where we consider the
upper limit of the estimated false-positives rate (20% = 100%-80% accuracy) and assume that
false positives are completely excluded from the other datasets, we estimate at least 220 new
true associations were identified here. Overlap with interactions inferred from genome
organization or gene expression was particularly low: only 7% of the high confidence
interactions are between gene products from the same operon and only 18% were consistently
co-expressed (Guell, van Noort et al. 2009). This implies that temporal or conditional
regulation of complex formation is analogous to that for eukaryotes, in which different
components are expressed at different times (de Lichtenberg, Jensen et al. 2005). For
example, the four known subunits of the RNA polymerase are in three operons and their
transcription profiles correlate with two different gene expression groups along the growth
curve (Guell, van Noort et al. 2009; Yus, Maier et al. 2009). With current knowledge, only a
small fraction of proteome organization can be inferred from analysis of the genomes or
transcriptional data making proteomics studies critical for understanding prokaryotic systems.
General principles of cellular organization in Mycoplasma pneumoniae
44
Figure 13 Proteome organization is only partially reflected by other biological datasets. (A) General overlap between TAP and interactions inferred from other datasets: co‐expression, operons (Guell, van Noort et al. 2009; Yus, Maier et al. 2009), STRING (Jensen, Kuhn et al. 2009) and pathways (Kanehisa, Araki et al. 2008). Numbers refer to the interacting pairs within the different datasets. The fraction of TAP‐interactions that cluster into complexes and are covered by other datasets is given in between brackets. For TAP interacting protein pairs the cut‐off was set at 80% accuracy. Cut offs for other datasets were optimized for coverage (accuracies 40 to 100%). (B) Frequent functional cross‐talk in the protein complex dataset. All proteins within high confidence pairs were functionally annotated according to COG (Tatusov, Koonin et al. 1997). Boxed areas are colored proportionally to the number of interactions linking two functional classes. The scales represent the total (upper panel) and normalized (lower panel) number of interactions (von Mering, Krause et al. 2002). Category Q (secondary metabolites) contains only two proteins. The category most frequently linked is J (Translation) with itself; it however contains the highest number of proteins. The highest proportion of interactions is between proteins within category K (Transcription). General principles of cellular organization in Mycoplasma pneumoniae
45
2.5.5. The M. pneumoniae protein complex network reveals substantial cross-talk
About a third of the heteromultimeric complexes in M. pneumoniae have extensive physical
interconnections that suggest proteins participate in different cellular processes (Figure 13B).
These reflect protein multifunctionality (see below) and organization into at least 35 larger
assemblies, sometimes hinting at physical, possibly temporal associations of sequential steps
in biological processes (Table S3). For example, we reconstituted major parts of the ribosome
from the interaction screen and saw extensive cross-talk with RNA polymerase (Figure 14A).
This higher level association was unaffected by RNAse and DNAse treatments suggesting
protein-protein rather than protein-nucleic acid interactions were involved (Figure 7). The
TAP-MS data were consistent with gel filtration results showing the RNA polymerase alphasubunit, RpoA (Mpn191), and the ribosomal protein RpsD (Mpn446) co-elute with high
apparent molecular sizes (Figure 14A). These observations are further supported by the
genome organization, where the rpoA gene is localized in and co-regulated with a ribosomal
operon (Guell, van Noort et al. 2009). This network provides a molecular model for the
coupling of transcription and translation proposed in bacteria (Gowrishankar and
Harinarayanan 2004) and the direct involvement of ribosomal proteins in transcriptional
regulation (Torres, Condon et al. 2001). The same assembly also includes translational
initiation factors InfA (Mpn187), InfB (Mpn155) and InfC (Mpn115), which are part of the
30S initiation complex, as well as elongation factors Tuf (Mpn665) and Tsf (Mpn631),
suggesting that we have captured sequential steps in a pathway running from transcription to
translation.
2.5.6. Functional reuse and modularity of protein complexes
Genome-wide screens in eukaryotes show that proteins often participate in more than one
complex, an attribute that has been proposed to account for protein multifunctionality,
pleiotropy or moonlighting (Hodgkin 1998). We defined a multifunctionality index that
measures the tendency of proteins to associate with more than one complex. This is based on
frequency with which pairs of proteins were found associated in our set of purifications and is
insensitive to the clustering parameters. We found 156 multifunctional proteins (Table S6),
covering 54% of M. pneumoniae proteins that are currently known to be multifunctional in the
literature (Table S7). We also compared to a set of multifunctional enzymes that catalyze
different enzymatic reactions (Yus, Maier et al. 2009) and the overlap was smaller (32%). Our
analysis captured distinct mechanisms for multifunctionality that imply the combinatorial use
of gene products in different contexts, for different functions.
General principles of cellular organization in Mycoplasma pneumoniae
46
Figure 14 Higher level of proteome organization. (A) The RNA polymerase‐ribosome assembly. Core components are represented by circles, attachments by diamonds. The line attribute corresponds to socio‐affinity indices: dashed lines, 0.5–0.86; plain lines, > 0.86. Color code and shaded yellow circles around groups of proteins refer to individual complexes: RNA polymerase (pink), ribosome (purple) and translation elongation factor (green). The lower panel shows the ribosomal protein RpsD (23kDa) and the α subunit of the RNA polymerase, RpoA‐TAP (57kDa) co‐elute in high molecular weight fractions (MDa range) during gel filtration chromatography. (B) DNA topoisomerase (diameter ~12 nm) is a heterodimer in bacteria: ParE, (ATPase and DNA‐binding domains), and ParC (cleavage and C‐terminal domains). The interaction between ParE‐DNA‐binding and ParC‐cleavage domains was modeled using yeast topoisomerase II as a template (PDB code 2rgr) and ParE‐ATPase and ParC C‐terminal domains were modeled separately on structures of gyrase homologs (1kij & 1suu). All four domains were fitted into the EM density. Gyrase (~12 nm) is similarly split in bacteria, into GyrA/GyrB, which are paralogs of ParE/ParC, and was modeled and fitted using 1bjt as a template for the GyrB‐DNA‐binding and GyrA‐cleavage domains interaction. (C) Protein multifunctionality in M. pneumoniae illustrated with the aminoacyl‐
tRNA synthetase complexes. For example, GyrA (Mpn004) is a component of the DNA gyrase complex that
introduces negative supercoils into DNA, and ParE (Mpn122), is a member of the
topoisomerase IV complex which decatenates DNA (Zechiedrich and Cozzarelli 1995).
Besides well documented interactions within their respective complexes (Complexes 17 and
82; Table S3), GyrA and ParE were also found to stably associate with each other (Complex
102; Table S3). Single particle electron microscopy and comparative modeling (Figure 8 and
General principles of cellular organization in Mycoplasma pneumoniae
47
9) showed that DNA-topoisomerase and DNA-gyrase have related overall shapes, as expected
from their functional similarity, and also supports the notion that they might be able to
interchange subunits (Figure 14B). In eukaryotes ParE and ParC (Mpn123) are fused into one
single polypeptide. In bacteria, the possibility for the split ParE and ParC to contribute to
different complexes might represent a parsimonious way of generating functional diversity
and also robustness to mutations with a set of paralogous proteins.
Another example is a complex containing a cluster of five different AARSs (Complex
10; Figure 14C and Table S3). In eukaryotes and archaea, AARSs form macromolecular
complexes that improve aminoacylation efficiency by channeling substrates to ribosome
(Praetorius-Ibba, Hausmann et al. 2007; Kyriacou and Deutscher 2008). These assemblies
also act as reservoirs of AARSs that additionally exert a range of non-canonical regulatory
functions in transcription, metabolism and signaling (Park, Schimmel et al. 2008). The
existence in bacteria of big multi-AARS complexes is controversial; the most recent review
advocates assembly in binary complexes that are functionally involved in tRNA metabolism
and editing (Hausmann and Ibba 2008). Our results suggest that higher order multi-AARS
complexes might also exist in bacteria. We also found several AARSs in other complexes
involved in functions as diverse as translation, transcription, DNA replication, and
metabolism (Figure 14C).
2.5.7. Structural anatomy of M. pneumoniae
Because of their small genome size, bacteria from the genus Mycoplasma have attracted
attention as model organisms for structural genomics (Kim, Shin et al. 2005). We used these
data to populate our protein complex network with structural information. Sequence similarity
searches and comparative modeling provided structures for 484 M. pneumoniae proteins (70%
of the genome), and 340 proteins in the network. There were also structural templates to
construct models for 153 binary interactions (Figure 12) covering 29 heteromultimeric and 57
homomultimeric complexes (Table S5). These data can be used both to study particular
interactions or complexes (Figure 14B and 8A) and to infer general correlations. Structural
interfaces are particularly illuminating for the multifunctional proteins. When structural
models are available for multiple interactions with a common protein, analysis of the
interfaces can suggest whether the interactions are mutually exclusive (same binding sites), or
compatible (different sites) (Kim, Lu et al. 2006). We observed that multifunctional proteins
generally tend to accommodate more ligands per interacting interface (P = 0.003), consistent
with the view that multifunctionality engages mutually exclusive interactions. For example,
General principles of cellular organization in Mycoplasma pneumoniae
48
the protein P115 (Mpn426) has six distinct interfaces, each of which has several mutually
exclusive interaction partners.
Figure 15 From proteomics to the cell. By a combination of pattern recognition and classification algorithms the following TAP‐identified complexes from M. pneumoniae, matching to existing EM, X‐ray and tomogram structures (A), were placed in a whole‐cell tomogram (B): the structural core of pyruvate dehydrogenase in blue (~23 nm), the ribosome in yellow (~26 nm), RNA polymerase in purple (~17 nm), and GroEL homomultimer in red (~20 nm). Cell dimensions are ~300 nm by 700 nm. The cell‐membrane is shown in light‐blue. The rod, a prominent structure filling the space of the tip region is depicted in green. Its major structural elements are HMW2 (Mpn310) in the core and HMW3 (Mpn452) in the periphery stabilizing the rod (Seybert, Herrmann et al. 2006). The individual complexes (A) are not to scale, but they are shown to scale within the bacterial cell (B). Having assembled a repertoire of structural information, the next logical step is to map
these networks and protein complexes in their native environment, the cell. For this purpose,
we performed cryo-electron tomography of 26 entire M. pneumoniae cells (Seybert,
Herrmann et al. 2006) (Figure 10). We used pattern recognition techniques to generate
General principles of cellular organization in Mycoplasma pneumoniae
49
probability maps for complexes selected from the larger ones in M. pneumoniae (Figure 15),
as they are more likely to be identified. After a thorough classification considering missing
data, low signal-to-noise ratio and known spatial proximities of different sub-complexes we
generated maps for the ribosome, the chaperone GroEL (Mpn573), the structural core of the
pyruvate dehydrogenase (PdhC, Mpn391, homomultimer), and RNA polymerase, with a
minimal number of false positives (Figure 15). These large complexes are excluded from the
tip, an organelle required for the attachment to epithelial cells, illustrating that even in a
simple, minimal bacteria the proteome is spatially organized (Seybert, Herrmann et al. 2006).
Within the cell bodies, we could not find significant proximities or patterns among the
different complexes. In contrast to E. coli that contain a compact nucleoid forming an
exclusion area in the cell center (Thanbichler and Shapiro 2008), circular DNA in M.
pneumoniae is apparently uniformly distributed (Seto, Layh-Schmitt et al. 2001). We
estimated the average number of complexes per cell to 140 for the ribosome, 100 for GroELs,
100 for pyruvate dehydrogenase and 300 for RNA polymerase. For the ribosome and GroEL,
we also quantified complex abundances by Western blotting (Figure 11). For both, the
numbers derived from Western blot were in the range of those estimated from the tomograms.
This adds to the emerging view that the mapping of macromolecular structures into entire cell
tomograms (Al-Amoudi, Diez et al. 2007), even though still challenging, is a powerful
strategy when combined with unbiased large-scale complex purification. It opens the way to
more general charting of cellular networks in entire cell tomograms.
2.6. Conclusions
Our genome-scale screen for soluble complexes in a bacterium provides a valuable resource
for the functional annotation of many genes whose biological roles in prokaryotic or parasitic
cells are elusive. The coverage of known complexes leads to an estimate of some 200
molecular machines in M. pneumoniae. The study allows estimation of unanticipated
proteome complexity for an apparently minimal organism that could not be directly inferred
from its genome composition and organization or from extensive transcriptional analysis.
Organisms with small genomes are the most tractable for systems biology, and the
biochemical dataset, proteome-wide spectra, ORFome and collection of TAP-expressing M.
pneumoniae strains will provide an extremely useful resource for this community.
Comparison to both more complex bacteria and to even smaller ones, such as M. genitalium
with 485 annotated protein coding genes (Gibson, Benders et al. 2008), should reveal
additional systemic features associated with genome streamlining.
General principles of cellular organization in Mycoplasma pneumoniae
50
With protein structures available for about three quarter of its ORFs, either directly
from structural genomics efforts (Kim, Shin et al. 2005) or indirectly inferred by homology,
M. pneumoniae has been extensively studied. We demonstrated that we can integrate datasets
of biochemically determined complexes with structural information to approximate the threedimensional organization of proteins into functional molecular machines. These models can
then be mapped in entire cell tomograms, providing a three-dimensional view of cellular
proteomes and interactomes (Bork and Serrano 2005); ultimately whole cell models will
benefit studies of biological function and disease.
General principles of cellular organization in Mycoplasma pneumoniae
51
3. Impact of genome reduction on bacterial metabolism and
its regulation
3.1. Authorship
This chapter covers the systematic investigation of the metabolism and its regulation in M.
pneumoniae. It represents a minor part of work during my time as a predoctoral fellow at
EMBL Heidelberg and ETH Zürich. This study has a first authorship by Eva Yus, who
performed the minimal medium experiments, contributed to the reconstructed the metabolic
network, generated expression data, did major parts of the cell culture work and majorly
contributed editing manuscript and figures. Additionally there are numerous other co-authors
who had their unique contributions. My main contributions were providing comparative data
and reagents from the proteome analysis and participating in cell culture work. Additionally, I
prepared and edited figures as well as the manuscript of this study. This chapter represents a
reformatted version of a report that has been published in Science.
3.2. Abstract
To understand basic principles of bacterial metabolism organization and regulation, but also
the impact of genome-size thereon, we systematically studied one of the smallest bacteria,
Mycoplasma pneumoniae. A manually curated metabolic network of 189 reactions catalyzed
by 129 enzymes allowed the design of a defined, minimal medium with 19 essential nutrients.
More than 1,300 growth curves were recorded in the presence of various nutrient
concentrations. Measurements of biomass indicators, metabolites and
13
C-glucose provided
information on directionality, fluxes and energetics; integration with transcription profiling
enabled global analysis of metabolic regulation. Compared to more complex bacteria, the M.
pneumoniae metabolic network has a more linear topology and contains a higher fraction of
multifunctional enzymes; general features such as metabolite concentrations, cellular
energetics, adaptability and global gene expression responses are similar though.
General principles of cellular organization in Mycoplasma pneumoniae
52
3.3. Introduction
Accurate representation of cellular networks by mathematical models is a central goal of
integrative systems biology. For this purpose, all components and reactions of a target system
should be listed and validated, and their quantitative relations should be determined and
analyzed in the context of the physiology of the organism (Feist and Palsson 2008). We have
selected M. pneumoniae, a human pathogen causing atypical pneumonia (Waites and
Talkington 2004) as a model organism for bacterial and archebacterial systems biology. Like
other mollicutes, M. pneumoniae has undergone a massive genome reduction to include only
689 protein coding genes, 231 of which have unknown function (Supplementary CD Yus et
al. Table S1) (Dandekar, Huynen et al. 2000); yet it can be cultivated in vitro without helper
cells (Proft and Herrmann 1994). The genome reduction of M. pneumoniae favors its
suitability as a systems biology model because it largely follows genome size scaling
principles (Supplementary CD Yus et al. Figure S1) (van Nimwegen 2003). We manually
reconstructed and validated the metabolic network of M. pneumoniae and studied its
regulation, thereby complementing analyses of the transcriptome (Guell, van Noort et al.
2009) and the proteome organization (Kuhner, van Noort et al. 2009).
3.4. Results
3.4.1 Reconstruction of the metabolic network: verification by a defined, minimal medium
The metabolism of M. pneumoniae has been studied biochemically (Pollack 1997) and
computationally (Pachkov, Dandekar et al. 2007). We integrated these approaches in a
framework that maximized coverage and accuracy (Supplementary CD Yus et al.). To build a
comprehensive metabolic network, we complemented the reactions from KEGG
(www.genome.jp/kegg) with activities obtained manually from the literature and new
annotations (Supplementary CD Yus et al. e.g. in Tables S1 to S5 and Figure S2) (Pollack,
Williams et al. 1997). We also considered other genomic (co-occurance in one operon),
sequence (homology to known enzymes) and structural information (identification of catalytic
residues to ensure enzyme functionality) (Figure 16A and Supplementary CD Yus et al.
Figure S2 and S3). For example, we identified an incomplete ascorbate pathway by sequence
analyses and filled the gap by assigning a critical enzyme (L-ascorbate-6-phosphate lactonase,
mpn497) based on sequence homology, predicted activity (metal-dependent hydrolase) and its
position in the ascorbate operon (mpn492 to 497). For pathways where only one enzyme was
General principles of cellular organization in Mycoplasma pneumoniae
53
missing we closed the gap by adding an unassigned reaction (e.g. transketolase activity in the
pentose pathway). Putative enzymes missing conserved catalytic residues were discarded (e.g.
Mpn255 and Mpn673 enzymes of the terpenoid pathway). Finally, for enzymes that could
carry out more than one reaction, we removed the reactions that were decoupled from
pathways and those for which the substrate was unavailable. The final result was a map
without gaps, isolated reactions, or open metabolic loops (Figure 17).
A number of alternative pathways interactions between pathways as well as missing
enzymes still needed to be validated, and reaction directionalities had to be inferred. For this,
we used two different experimental strategies. We first used the rich medium (Supplementary
CD Yus et al. Figure S4) to validate the pathway functionality in various carbon sources. As
expected from the map (Figure 17), all known carbon sources but mannitol supported growth
to various extents (Supplementary CD Yus et al. Figure S5 and S6) (Halbedel, Hames et al.
2004). By using
13
C-glucose labeling we validated, for examples, the predicted connection
between glycolysis, the pentose phosphate pathway and lipid synthesis (Supplementary CD
Yus et al. Figure S3 and Table S6), and ruled out the proposed production of aspartate from
pyruvate (Manolukas, Barile et al. 1988). For our second strategy we developed, based on the
metabolic map, a defined medium (Figure 16A and Supplementary CD Yus et al. Table S7)
with which we could validate other pathways (e.g. vitamin metabolism, Supplementary CD
Yus et al. Figure S10) and reaction directionalities that could not be studied in rich medium
(e.g. synthesis of uracyl and thymine nucleotides from cytosine; Supplementary CD Yus et al.
Figure S7 and S8). The low number of amino acid permeases and transporters and the
existence of a peptide importer (oppB-F cluster, Table S1) suggested a requirement for
peptides in the medium, which we confirmed experimentally (Supplementary CD Yus et al.
Figure S9).
General principles of cellular organization in Mycoplasma pneumoniae
54
Figure 16 Metabolic network development and properties, and minimal medium design. (A) Schematic diagram of the process leading to M. pneumoniae metabolic network reconstruction and design of a minimal medium. (B) Comparison of M. pneumoniae metabolic network properties with the ones of other model bacteria, (C) quantification of enzyme multifuntionality among prokaryotic genomes: M. pneumoniae (red), L. lactis (yellow), B. subtilis (green) and E. coli (blue), other bacterial species (grey). We systematically tested the defined medium in more than 1,300 experiments to properly
assess all the components necessary for survival. We replaced these components with simpler
building blocks to obtain a defined, minimal medium that contains only 26 components (19 of
which are essential; Figure 16A). This medium, as predicted from our metabolic map and
comparative analysis also supports growth of Mycoplasma genitalium (Supplementary CD
Yus et al. Figure S11 and S12). Based on these experiments we estimated the upper flux
limits for the utilization of the various nutrients (Supplementary CD Yus et al. Figure S13).
The medium implicitly validates the reconstructed metabolic map (Figure 17) which consists
of 189 reactions (Supplementary CD Yus et al. Table S2): 169 are catalyzed by the products
of 140 known genes, and 20 are not yet assigned to any gene (Supplementary CD Yus et al.
Table S4). It includes 74 essential metabolic genes and 34 conditionally essential ones
(depending on medium composition), which is in agreement with essentiality determined by
transposon mutagenesis analyses (96% overlap; Supplementary CD Yus et al. Figure S14 and
Table S8) (Hutchison, Peterson et al. 1999). A total of 32 enzymes (25%) are multifunctional,
i.e. have more than one activity and together catalyze 91 reactions (48% of the total;
Supplementary CD Yus et al. Table S3). With respect to previous genome annotations
(Himmelreich, Hilbert et al. 1996; Dandekar, Huynen et al. 2000), we assigned new or refined
functions to 57 metabolic genes (plus 30 non-metabolic genes, Supplementary CD Yus et al.
see new annotations in Table S1). The above strategy could more generally be used to design
General principles of cellular organization in Mycoplasma pneumoniae
55
media to grow anexically, hard-to-culture bacteria as was done for the recalcitrant
Tropheryma whipplei (Renesto, Crapoulet et al. 2003) and might be applicable in the context
of increasing metagenomics efforts.
3.4.2. Comparison of the metabolic network to those of more complex bacteria
Analysis of the metabolism of M. pneumoniae reveals that it is more linear than that of larger
bacteria such as B. subtilis (Figure 16B). Furthermore, M. pneumoniae has a wider metabolic
network diameter (shortest biochemical pathway averaged over all pairs of substrates)
although the diameter has been reported to increase with the logarithm of the network size
(Zientz, Dandekar et al. 2004). The greater linearity and the wider diameter of the network
suggest that it is less interconnected and contains fewer parallel paths. Thus, the M.
pneumoniae network is less redundant both in terms of enzyme paralogy and in network
topology. Yet, the distribution of the number of metabolites per reaction is similar to other
organisms (Supplementary CD Yus et al. Figure S14). This is partly achieved by an increased
fraction of multifunctional enzymes compared to that in larger bacteria, as happens in
endosymbionts (Zientz, Dandekar et al. 2004). We did not find any evidence of M.
pneumoniae multifunctional enzymes being more conserved than others. This suggests the
larger number could be due to function acquisition not present (or detected) in their homologs.
This might represent a more general mechanism expected to facilitate further genome
reduction (Figure 16B and C). The increased linearity and limited redundancy in the
metabolic network suggest limited robustness and adaptability to external factors (Pipe and
Grimson 2008): 60% of the metabolic enzymes are essential (Glass, Assad-Garcia et al.
2006), in contrast to only 15% in E. coli (www.shigen.nig.ac.jp/ecoli/pec/index.jsp).
General principles of cellular organization in Mycoplasma pneumoniae
56
Figure 17 Metabolic map of M. pneumoniae. Main metabolites are shown as boxes and enzymes and transporters as pentagons. In blue, input metabolites, in red, output products. New enzymatic activities determined in this study are displayed in yellow, enzymes catalyzing multiple reactions are bold. Essential enzymes (according to the mutagenesis study in M. genitalium) are marked with a black triangle. Minimal medium components have General principles of cellular organization in Mycoplasma pneumoniae
57
been encircled in blue. See right hand bottom legend for details, Supplementary CD Yus et al. Figure S12 and Table S2 for description of the enzymatic reactions and enzymes and Supplementary CD Yus et al. Table S25 for metabolite abbreviations. aaRS stands for aminoacyl‐tRNA synthase. 3.4.3. Growth and energetics in comparison with larger bacteria.
M. pneumoniae has a relatively long duplication time (at least 8 hours) in comparison with E.
coli or L. lactis (20 min), both in culture (Hasselbring, Jordan et al. 2006) and in the presence
of host cells (Dallo and Baseman 2000). Slow growth in genome-reduced, parasitic bacteria
has been proposed to be the result of i) less efficient enzymatic activity that is explained by
the accumulation of mutations resulting from genetic drift (Smart and Thomas 1987), ii) a
reduced number of rRNA operons and/or iii) other mechanisms related to the adaptation to a
parasitic lifestyle. To understand the causes of slow growth it is necessary to measure the
overall energetics of the metabolic network (Figure 17), as well as the changes in
macromolecules (Figure 18A) and metabolites along the growth curve (Figure 18B).
We used the metabolic map, the measured protein concentration (10 fg protein per cell) and
the estimated turnover rates of macromolecules (~20 hours for proteins and ~7 min for
mRNA; Supplementary CD Yus et al. Table S9 and Figure S15) to estimate the rate of
glucose uptake required to duplicate a cell every 8 h at 18,000-24,000 glucose molecules per
second (assuming that the majority of ATP is used for biomass production) (Supplementary
CD Yus et al.). This figure closely matched the experimentally determined value under
exponential growth: ~19,000 glucose molecules per cell per second (Figure 18C)
(Supplementary CD Yus et al.). When cultures approached stationary phase (Figure 18A), the
rate increased to ~45,000 glucose molecules per cell per second (Figure 18C), concomitantly
with the increased transcription of many glycolytic and fermentation genes (Figure 18D and
Supplementary CD Yus et al. Table S10 and S11). In both cases at least 95% of the glucose
carbon was found in lactate and acetate (Figure 18B and Supplementary CD Yus et al. Figure
S16), implying that the glucose is used primarily for energy production. At the fastest glucose
consumption rate, assuming all ATP were devoted to biomass production, M. pneumoniae
could divide about every 3 hours. However, most of the energetic parameters (i.e.
concentration of glycolytic intermediates: fructose-1,6-biphosphate, glycerol-3-phosphate,
phosphoenolpyruvate, glucose-6-phosphate, fructose-6-phosphate, ribose-5-phosphate and
glycerone phosphate, and glucose uptake) that we measured were similar to those of larger
bacteria (Supplementary CD Yus et al. Table S9), suggesting comparable enzyme
efficiencies. This similarity extended to regulatory processes seen in L. lactis (Moran 2002).
General principles of cellular organization in Mycoplasma pneumoniae
58
For example, as in L. lactis, we observe both a shift from mostly mixed-acid to homolactic
fermentation and an acceleration of glycolysis when the medium acidifies (Figure 18A and
B); the drop in O2 concentration relieves inhibition of lactate dehydrogenase (Supplementary
CD Yus et al.) (Smart and Thomas 1987; Cocaign-Bousquet, Even et al. 2002). Also, the ATP
yield per fermented glucose (2 to 4 ATP, depending of lactate or acetate fermentation), is the
same as in L. lactis (Supplementary CD Yus et al. Table S9).
Figure 18 Determination of various metabolic parameters in growing cultures. Consistently generated heterogeneous data, all derived using a rich medium, are compared using time in hours (X‐axis). (A) M. pneumoniae growth determined by monitoring the decrease in extracellular pH and the concomitant changes in the amount of protein, DNA and total RNA. (B) Determination of glucose consumption and its fermentation to lactate and acetate. (C) Changes in the number of glucose molecules imported by a cell per second and comparison with the biomass doubling time. (D) Changes in gene expression of a representative ribosomal protein (rplX), and two enzymes: ldh, and a component of the pyruvate dehydrogenase complex (pdhA), enzymes from the two fermentation branches and the relation with the shift from acetate to lactate production (ratio between acetate and lactate General principles of cellular organization in Mycoplasma pneumoniae
59
is shown in green, which can be compared to that of cells grown in the presence of oxygen in magenta). Given all the above we cannot explain the slow growth of M. pneumoniae on the basis of
glycolytic efficiency or ATP yield. One of the main differences compared to fast dividing
bacteria is the number of rRNA operons per genome (just one in M. pneumoniae and 6 in L.
lactis) (Supplementary CD Yus et al. Figure S17); and 5 to 10 times proportionally fewer
ribosomes compared to E. coli (Supplementary CD Yus et al. Table S10) (Kuhner, van Noort
et al. 2009). In many bacteria the number of ribosomes correlates with the division rate
(Nomura 1999). For M. pneumoniae, we see a correlation of changes in biomass duplication
speed with the number of ribosomes, but not with the glycolytic rate (Figure 18C and D and
Supplementary CD Yus et al. Figure S17). We thus suggest that the slow division rate of M.
pneumoniae is not due to less efficient energy production but to the limit in protein
biosynthesis capacity. This small parasitic bacterium does not appear to be optimized for
biomass production. Instead, more complex strategies for fitness, such as suppression of
growth by other microorganisms (Teusink, Wiersma et al. 2006) or optimization of
interactions with host-cells might determine growth-rate in small organisms.
3.4.4. Coordinated transcriptome dynamics along growth curve and under various
conditions
It has been suggested that genome-reduced organisms have limited adaptability to external
factors (Cocaign-Bousquet, Even et al. 2002). To determine the capacity of M. pneumoniae to
respond to environmental changes we performed three types of experiments. First, we
followed the changes in gene expression from the exponential growth phase to the stationary
phase (Figure 19A). Analysis of changes in gene expression (validated by tiling arrays and
quantitative PCR; Supplementary CD Yus et al. Figure S18) at different points along the
growth curve showed that a large part of the transcriptome can be grouped into four timedependent expression clusters (Figure 19A and Supplementary CD Yus et al. Figure. S19 and
S20, Table S11 and S12). These clusters can be regarded as two pairs of anti-correlating
patterns, indicating a complex regulation. Subsequent analysis by mass spectrometry for a
subset of enzymes showed correlation between changes in mRNA and protein abundance
(Supplementary CD Yus et al. Figure S18 and Table S10). For example, the production of
lactate by lactate dehydrogenase (Mpn674|Ldh) revealed the close temporal coordination of
General principles of cellular organization in Mycoplasma pneumoniae
60
gene and protein expression, and metabolite turnover (Figure 18B and D and Supplementary
CD Yus et al. Table S10).
Second, we analyzed the response of M. pneumoniae to specific individual metabolic
perturbations encountered as the population grows, such as low pH, accumulation of
fermentation end-products, and sugar and amino acid starvation, as well as to more complex
stimuli like entry into the stationary phase (Figure 19 B to D and Supplementary CD Yus et
al. Tables S13 to S16),. We found coordinated changes in gene expression specific to each
condition (Figure 19B and Supplementary CD Yus et al. Figure S21). For example, we see a
general inhibition of transcription and translation upon glucose deprivation, and an increase of
ATP proton pump genes at pH 6.5 (Figure 19B and C). Induction of the stringent response (a
global response to the absence of amino acids) results in upregulation of peptide and amino
acid transporters (Figure 19D). Also a specific repression of the Thr-tRNA synthetase gene
(mpn553) (Supplementary CD Yus et al. Table S17), which is a core component of a tRNA
synthetase complex (Kuhner, van Noort et al. 2009), suggests its possible regulatory role in
complex assembly and therefore, in regulation of translation. Interestingly, we found some
common responses to multiple stresses. Some were known as was the down-regulation of
ribosomal proteins or peptide importers, common to all stresses. Others, like the up-regulation
of ldh and glycerol-3-P dehydrogenase (mpn051), were unexpected suggesting additional
functions for these proteins during stress (Figure 19B). Third, we adapted the cells by serial
passage (15 passages) to efficient growth in other carbon sources (fructose, mannose, and
glycerol) (Supplementary CD Yus et al. Tables S18 to S20). Fructose adaptation resulted in
over-expression of fruA and fruK (>3 Log2), and mannose-adapted cells over-expressed the
mannitol importer (>5 Log2) (Supplementary CD Yus et al. Tables S19 and S20). Thus M.
pneumoniae shows surprising adaptation capability similar to that reported for E. coli
(Oxman, Alon et al. 2008).
The coordinated changes in gene expression along the growth curve, the specific
responses to many various metabolic perturbations and the adaptability of the cells to various
carbon sources indicate that M. pneumoniae retains some robustness and adaptability despite
its extreme genome reduction.
General principles of cellular organization in Mycoplasma pneumoniae
61
Figure 19 Regulation of metabolism. (A) Representative plot of the four main gene co‐
expression clusters identified along the growth curve, named after the main functional classes of the genes involved. (B) Upper panel: overlap between changes in gene expression under various stresses, i.e.: lactate (80 mM buffered lactate), low pH (pH 6.5), glucose or amino acid starvation (stringent response) and the entry into stationary phase. Lower panel: heatmap of the genes found to be commonly up‐ or down regulated under stress and growth inhibition. (C) GO functional classification of genes significantly regulated during exponential growth and glucose deprivation in M. pneumoniae (Mpn) or L. lactis (Lla). The average of the significant changes within each category is depicted. C Energy production and conversion, D Cell division and chromosome partitioning, E Amino acid transport and metabolism, F Nucleotide transport and metabolism, G Carbohydrate transport and metabolism, H Coenzyme metabolism, I Lipid metabolism, J Translation, ribosomal structure and biogenesis, K Transcription, L DNA replication, recombination and repair, M Cell envelope biogenesis, outer membrane, O Posttranslational modification, protein turnover, chaperones, P Inorganic ion transport and metabolism, R General function, T Signal transduction mechanisms. (D) Stringent response expression pattern was compared with that of L. lactis and B. subtilis (Bsu). The average of the significant changes upon stringent response induction (with norvaline) is shown. (E) Venn diagrams showing the overlap in M. pneumoniae and L. lactis of ortholog genes under various metabolic conditions. High P‐value General principles of cellular organization in Mycoplasma pneumoniae
62
in the case of the stringent response indicates that it is not statistically significant. (F) Upper panel: growth curve of cells growing in minimal medium plus increasing amounts of glycerol. Lower panel: glucose titration in Hayflick is shown for comparison. 3.4.5. Complex metabolic regulation despite few transcription factors
Compared to more complex bacteria, M. pneumoniae lacks the majority of TFs regulating
metabolic genes factors (such as the CRP), major sigma factors and other regulators (Goebel
and Lory 2006). Gene assignment based on sequence analysis (Supplementary CD Yus et al.
Table S1), in some cases validated by co-purification with the RNA polymerase complex (e.g.
mpn266|spxA) (Kuhner, van Noort et al. 2009), revealed four transcription factors
(mpn239|gntR; mpn329|fur; mpn124|hrcA), the general sigma 70 (mpn352|sigA) factor, two
putative sigma-like factors (mpn626|sigD; mpn424|ylxM) and a putative DNA-binding protein
(mpn241|whiA) (see Supplementary CD Yus et al. Table S1 and Figure S2). Despite this
apparently reduced gene regulatory toolbox, both environmental stresses (Guell, van Noort et
al. 2009) and metabolic insults induced complex, specific transcriptional responses;
comparison with more complex bacteria showed similarities, but also some specific
differences in regulation of gene expression (Supplementary CD Yus et al. Table S21 to S23).
For example, we observed an increase in mRNA and protein expression of glycolytic
enzymes concomitant with the increase of glycolytic rate upon medium acidification (Figure
18C and D and Supplementary CD Yus et al. Figure S20 and Table S15), very similar to what
has been described in L. lactis cultures (Even, Lindley et al. 2003). Response to glucose
starvation was also similar to that of L. lactis (Figure 19C and E and Supplementary CD Yus
et al. Table S21) (Even, Lindley et al. 2002). Part of the stringent response, e.g. induction of
peptide and amino acid transporters and down-regulation of carbohydrate catabolism
(Potrykus and Cashel 2008), was conserved in M. pneumoniae (Supplementary CD Yus et al.
Table S22); other mechanisms such as the repression of ribosomal protein operons or rRNA
synthesis were not observed (Figure 19D and Supplementary CD Yus et al. Figure S22). This
is in agreement with the proposed involvement of the RNA polymerase omega subunit
(missing in M. pneumoniae) in sensing guanosine pentaphosphate/tetraphosphate [(p)ppGpp]
and thus arresting rRNA biosynthesis (Vrentas, Gaal et al. 2005).
We believe it is unlikely that the conserved responses, and the specific differences in
regulation, can be caused only by combinations of the few TFs that regulate operons and
suboperons, even if one includes regulation by antisense RNA (Guell, van Noort et al. 2009).
The presence of genes for synthesis or degradation of a number of chemical messengers, such
as (p)ppGpp (mpn397|spoT), AppppA (mpn273|hit1), or c-di-AMP (mpn244|disA)
General principles of cellular organization in Mycoplasma pneumoniae
63
(Supplementary CD Yus et al. see Table S1 and Figure S2) (Su, Hutchison et al. 2007),
implies that signaling mechanisms has been preserved despite genome reduction. For
example, over-expression of the spoT gene that regulates (p)ppGpp levels (Potrykus and
Cashel 2008) results in significant changes in gene expression, mainly related to the stringent
response (Supplementary CD Yus et al. Table S24). The presence of genes coding for a
Ser/Thr phosphatase (mpn247|ptc1) and two protein kinases (Ser/Thr/Tyr kinase:
mpn248|prkC, mpn223|hrpK, an HPr kinase) and the differential phosphorylation of key
metabolic enzymes under various growth conditions (Su, Hutchison et al. 2007) suggest posttranslational control. Also metabolites like glycerol regulate gene expression at the base of the
fermentation branches in M. pneumoniae (Halbedel, Eilers et al. 2007), as well as glucose
import (Halbedel, Hames et al. 2007). This explains why glycerol is essential in the minimal
medium in a concentration-independent manner (Figure 19F).
3.5. Conclusions
Our results suggest that complex metabolic regulation can be achieved in a streamlined
genome despite the absence of the respective TFs, probably by a combination of
transcriptional regulators, post-translational modifications and small molecules including
chemical messengers and metabolites.
Taken together, our newly established M. pneumoniae resource, containing a manually
annotated metabolic map, full annotations, reactome, consistently measured growth curves
and gene expression profiles corresponding to an extensive list of metabolites, should
facilitate integrative systems biology studies at a high resolution. Comparison to more
complex bacteria revealed systemic features associated with genome streamlining, which
should be examined in other small bacteria. Despite its apparently simplicity, we have shown
that M. pneumoniae shows metabolic responses and adaptation similar to more complex
bacteria, providing hints that other, unknown regulatory mechanisms might exist.
General principles of cellular organization in Mycoplasma pneumoniae
64
4. Transcriptome complexity in a genome-reduced organism
4.1. Authorship
This chapter covers the systematic investigation of the transcriptome and its complexity in M.
pneumoniae. It represents a minor part of work during my time as a predoctoral fellow at
EMBL Heidelberg and ETH Zürich. This study has a first authorship by Marc Güell, who
performed most of the tiling and microarray experiments, identified new transcripts, defined
operons and suboperons, contributed to the correlation analysis, did major parts of the cell
culture and mainly contributed to editing manuscript and figures. Additionally there are
several other co-authors who had their substantial contributions. My main contributions were
providing comparative data and reagents from the proteome organization analysis and
participating in cell culture work. Additionally, I edited figures as well as the manuscript of
this study. This chapter represents a reformatted version of a report that has been published in
Science.
4.2. Abstract
To study basic principles of transcriptome organization in bacteria, we analyzed one of the
smallest self-replicating organisms, Mycoplasma pneumoniae. We combined strand-specific
tiling arrays, complemented by transcriptome sequencing, with more than 252 spotted arrays.
We detected 117 previously un-described, mostly non-coding transcripts, 89 of them in
antisense configuration to known genes. We identified 341 operons, of which 139 are
polycistronic; almost half of the latter show decaying expression in a staircase-like manner.
Under various conditions, operons could be divided into 447 smaller transcriptional units,
resulting in many alternative transcripts. Frequent antisense transcripts, alternative transcripts,
and multiple regulators per gene imply a highly dynamic transcriptome, more similar to that
of eukaryotes than previously thought.
General principles of cellular organization in Mycoplasma pneumoniae
65
4.3. Introduction
Although large-scale gene expression studies have been reported for various bacteria
(Selinger, Cheung et al. 2000; Tjaden, Saxena et al. 2002; Reppas, Wade et al. 2006;
McGrath, Lee et al. 2007; Nelson, Herron et al. 2008; Akama, Suzuki et al. 2009; ToledoArana, Dussurget et al. 2009), comprehensive strand-specific data sets are still missing,
limiting our understanding of operon structure and regulation. Similarly, the number of
classified non-coding RNAs in bacteria has recently been expanded (Vogel and Wagner
2007), but a complete and unbiased repertoire is still not available. To obtain a blueprint of
bacterial transcription, we combined the robustness and versatility of spotted arrays (62
independent conditions and 252 array experiments) (Supplementary CD Güell et al.), the
superior resolution of strand specific tiling arrays (Figure 20A) (designed after genome resequencing, Supplementary CD Güell et al. Table S1) and the mapping capacity of RNA deep
sequencing (DSSS) (Fig 20A and Supplementary CD Güell et al. Figure S1) in one of the
smallest bacteria that can live outside a host cell, M. pneumoniae, with annotated 689 protein
coding genes and 44 non coding RNAs (ncRNAs).
4.4. Results
Considering DSSS under reference conditions (Supplementary CD Güell et al.) and 43 tiling
arrays from four time series (growth-curve, heat shock, DNA damage and cell cycle arrest)
(Supplementary CD Güell et al. Table S8), we observed the expression of all genes. Using a
segmentation algorithm for the tiling arrays (Huber, Toedling et al. 2006), we identified
additional 117 regions with no previous annotation (Supplementary CD Güell et al. Table S2).
These regions were further confirmed by DSSS (Figure 20B and Supplementary CD Güell et
al. Figure S1) and in four cases by quantitative polymerase chain reaction (Supplementary CD
Güell et al. Table S3). Sequence similarity with known proteins revealed the presence of two
new protein-coding genes, a pseudogene, one N-terminal truncation, and five 5’-extensions of
known genes (Supplementary CD Güell et al. Table S2). The remaining 108 transcripts are
probably regulatory rather than structural RNAs, because comparison of their predicted
secondary structures with the ones of coding genes does not show any substantial difference
(Supplementary CD Güell et al.). Eighty-nine of them are antisense with respect to previously
annotated genes. Out of the non-overlapping ones, two of them (NEW87 and NEW8) are
General principles of cellular organization in Mycoplasma pneumoniae
66
conserved in M. genitalium and could be involved in DNA replication and repair, and in
peptide transport, respectively (Supplementary CD Güell et al. Figure S3 to S5). In total, 13%
of the coding genes are covered by antisense; this is twice more than in yeast (7%) (Xu, Wei
et al. 2009), and about half of what was reported for plants (22.2%) (Wang, Gaasterland et al.
2005; Henz, Cumbie et al. 2007), or humans (22.6%) (Ge, Wu et al. 2006). Antisense
transcripts may affect expression of the overlapping functional sense transcripts through
several mechanisms (Lapidot and Pilpel 2006): double-stranded RNA-dependent mechanisms
require coexpression with their target (Brantl and Wagner 1994), whereas transcriptional
interference rather implies mutual exclusion of sense and antisense transcripts (Brantl 2007;
Andre, Even et al. 2008). In M. pneumoniae, we observed a predominance of double-stranded
RNA mechanism as in mammals (Katayama, Tomaru et al. 2005) (47% positive correlation
versus 2% negative correlation). In addition, we detected a reduced expression level of genes
targeted by antisense transcripts, as reported in some prokaryotes (Brantl 2007)
(Supplementary CD Güell et al. Figure S6).
Figure 20 Transcriptome feature in the reference condition. (A) The first operon in the genome on the forward strand has a staircase behavior, meaning that the consecutive genes have lower and steady expression levels. (B) Example of an anti‐sense RNA transcript. (C) Analysis of staircase operons. Left: all reference operons subdivided by the number of protein coding genes they contain. Right: all reference operons subdivided by their staircase behavior (see bottom graphs). (D) Left: overlap of operon starts and single gene starts with previously identified ‐10 promoter sequence motifs in M. pneumoniae (Weiner, Herrmann et al. 2000) and predicted promoters based on hexamers. Right, Overlap of operon ends and single gene ends with predicted transcription termination hairpins. General principles of cellular organization in Mycoplasma pneumoniae
67
We identified operon boundaries through sharp transcription changes in the tiling reference
condition by using local convolution methods (Figure 20A) (Supplementary CD Güell et al.)
(Hooper, Boue et al. 2007). More than 90% of the operons (139 polycistronic and 202
monocistronic operons; Supplementary CD Güell et al. Table S4) were well supported by
DSSS reads (DSSS alone was not sufficient to unambiguously characterize operons;
Supplementary CD Güell et al. Figure S2). Most polycistronic operons contain two or three
genes (Figure 20C and Supplementary CD Güell et al. Figure S7, Table S4); the largest one is
the ribosomal operon containing 20 genes. For the majority of operons, we observed a
canonical or slightly altered version of a standard sigma 70 promoter region (Supplementary
CD Güell et al. Figure S8), with transcription starts located within 60 bp (Supplementary CD
Güell et al. Figure S9) upstream of the translation start (McGrath, Lee et al. 2007). In contrast
to previous suggestions (Washio, Sasayama et al. 1998), we observe, as proposed by others
(de Hoon, Makita et al. 2005), a preferential use of termination hairpins for tight regulation of
gene expression (Figure 20A and D and Supplementary CD Güell et al. Table S5). Moreover,
we found that almost half of the consecutive genes within polycistronic operons show a decay
behaviour (Figure 20A and Supplementary CD Güell et al. Figure S1), indicating that such
‘staircase’-like expression is a widespread phenomenon in bacteria (Supplementary CD Güell
et al.).
Analysis of the 43 tiling arrays and integration with 252 spotted arrays representing 173
independent conditions, some of them from time-series, revealed context-dependent
modulation of operon structures involving repression or activation of operon internal genes, as
well as of genes located at the beginning, or end (Figure 21A and B and Supplementary CD
Güell et al. Figure S10 and Table S5). In some cases this modulation can be assigned to
specific environmental changes. Down regulation of the four first genes of the ftsZ operon
involved in initiation of cell division corresponds to entry into stationary phase (Figure 21B,
lower panel). Increase in expression of arginine fermentation genes (arcA, arcI, arcC) (Figure
21B) in stationary phase could be a mechanism to cope with acidification (Budin-Verneuila,
Maguin et al. 2004). We found formal evidence for a total of 447 transcriptional units (336
monocistronic and 111 polycistronic), implying a high rate of alternative transcripts (42%) in
this bacterium in the conditions studied, similar to that in eukaryotes (40%, although still
under debate) (Boue, Letunic et al. 2003) and archea (40% in H. salinarum) (Koide, Reiss et
al. 2009). Interestingly we found that genes that are split into different suboperons tend to
belong to different functional categories (Supplementary CD Güell et al.). Thus, although
General principles of cellular organization in Mycoplasma pneumoniae
68
genome reduction leads to longer operons accommodating genes with different functions
(Yus, Maier et al. 2009), the latter can still retain internal transcription and termination sites
under certain conditions.
The high frequency of alternative transcripts of M. pneumoniae genes hints at a situation
similar to that in eukaryotes where many factors contribute to the regulation of gene
expression. To further support this hypothesis, we used gene expression clustering under the
62 distinct conditions (Supplementary CD Güell et al. Table S7) to identify groups of coexpressed genes and their possible common regulatory motifs. Using a correlation cut-off of
0.65 we identified 94 co-expression groups (Supplementary CD Güell et al. Table S6 and
Figure S11), encompassing 416 genes. Thirty of the clusters contained genes from more than
two operons. Of these, 14 share a unique sequence motif in their upstream region and another
8 have a unique combination of motifs (Supplementary CD Güell et al. Figure S12), which
might drive the co-expression (e.g. 4 of the 14 motifs are found at splitting sites inside
operons). This is exemplified by the five heat shock induced genes containing a regulatory
CIRCE element (Chang, Chen et al. 2008) (Figure 21C). Not all of them clustered together
indicating at least another regulatory element. Similarly, over expression of a transcription
factor (mpn329; Fur, ferric uptake regulator) reveals a common motif in all genes
significantly changing expression, although they belong to different co expression clusters
(Supplementary CD Güell et al. Figure S13 and Table S6).
General principles of cellular organization in Mycoplasma pneumoniae
69
Figure 21 Alternative operon structure. The continuous lines in A and B indicate expression level measured with tiling arrays. (A), Alternative transcripts discovery pipeline . Reference operon 001 is splitted into 3 suboperons. (Top) Tiling and DSSS under reference conditions. (Middle) Specific expression changes for genes dnaA and xdj1 involved in DNA repair and replication. (Bottom) The coexpression matrices correspond to the final conditional operon splitting by 252 arrays. (B) Two examples of conditional operons are presented. (Top) Specific induction of the middle genes in the operon 126 when the cells reach stationary phase. (Bottom) Repression of the first 4 genes of the operon 129 involved in cell division when the cells reach stationary phase. (C), Example of heat shock induced genes sharing the known CIRCE element. The calculated consensus sequence is represented below. General principles of cellular organization in Mycoplasma pneumoniae
70
4.5. Conclusions
Our work revealed an unanticipated complexity in the transcriptome of a genomereduced bacterium. This complexity cannot be explained by the presence of 8 predicted TFs
(Yus, Maier et al. 2009). Furthermore, the fact that the proteome organization is not
explainable by the genome organization (Kuhner, van Noort et al. 2009) indicates the
existence of other regulatory processes. The surprisingly frequent expression heterogeneity
within operons, the change of operon structures leading to alternative transcripts in response
to environmental perturbations and the frequency of antisense RNA which might explain
some of these expression changes suggest that transcriptional regulation in bacteria resemble
that of eukaryotes more than previously thought.
General principles of cellular organization in Mycoplasma pneumoniae
71
5. Summary of results
The systematic investigation of cellular organization on different levels and the integration of
this acquired information into other orthogonal datasets can leverage the creation of biological
knowledge. This was one of the main tasks and is one of the major results of this thesis, which
aims at describing general principles of cellular organization in the genome-reduced
bacterium M. pneumoniae.
Altogether there are three major studies described in this thesis which aim at the
characterization of the:
1. proteome organization,
2. metabolism and its regulation,
3. transcriptome and its complexity in M. pneumoniae.
In chapter 2, I describe the results of the investigation of the proteome organization in M.
pneumoniae. The analysis revealed 62 homomultimeric and 116 heteromultimeric soluble
protein complexes, of which the majority are novel. About a third of the heteromultimeric
complexes show higher levels of proteome organization, including assembly into larger,
multi-protein complex entities, suggesting sequential steps in biological processes, and
extensive sharing of components implying protein multifunctionality. Incorporation of
structural models for 484 proteins, single particle EM and cellular electron tomograms
provided supporting structural details for this proteome organization. The dataset provides a
blueprint of the minimal cellular machinery required for life.
Chapter 3 outlines the results of the investigation of the metabolism and its regulation in M.
pneumoniae. In order to understand basic principles of its metabolic organization and
regulation, but also the impact of genome-size thereon a manually curated metabolic network
of 189 reactions catalyzed by 129 enzymes was created. This allowed the design of a defined,
minimal medium with 19 essential nutrients. More than 1,300 growth curves were recorded in
the presence of various nutrient concentrations. Measurements of biomass indicators,
metabolites and
13
C-glucose provided information on directionality, fluxes and energetics.
The integration of transcriptional profiles enabled global analysis of metabolic regulation.
Compared to more complex bacteria, the M. pneumoniae metabolic network has a more linear
topology and contains a higher fraction of multifunctional enzymes; general features such as
metabolite concentrations, cellular energetics, adaptability and global gene expression
responses are similar though.
General principles of cellular organization in Mycoplasma pneumoniae
72
Chapter 4 highlights the results of the investigation of the transcriptome complexity in M.
pneumoniae. Here, we combined strand-specific tiling arrays, complemented by transcriptome
sequencing, with more than 252 spotted arrays. We detected 117 previously un-described,
mostly non-coding transcripts, 89 of them in antisense configuration to known genes. We
identified 341 operons, of which 139 are polycistronic; almost half of the latter show decaying
expression in a staircase-like manner. Under various conditions, operons could be divided into
447 smaller transcriptional units, resulting in many alternative transcripts. Frequent antisense
transcripts, alternative transcripts, and multiple regulators per gene imply a highly dynamic
transcriptome, more similar to that of eukaryotes than previously thought.
In a more conceptual summary there are four major messages, which the three studies, of
which my PhD thesis is part of, have produced:
1. M. pneumoniae shows aspects of multifunctionality particularly in its proteome
organization and metabolism.
2. M. pneumoniae, even though being an almost minimal organism, is more complex
than expected, particularly in its regulation.
3. M. pneumoniae resembles eukaryotes more than expected, particularly in its
transcription.
4. M. pneumoniae is optimized for host adaptation and not for growth.
General principles of cellular organization in Mycoplasma pneumoniae
73
6. Conclusions
The work on the proteome organization, the metabolism and its regulation as well as on the
transcriptional complexity in M. pneumoniae provided in this thesis adds to previous research
and will certainly strengthen the interest in this genome-reduced organism (Ochman and
Raghavan 2009). Furthermore, it will help to establish M. pneumoniae as a near-minimal
model organism (Glass, Hutchison et al. 2009). As such this work will provide a useful
ground for further systematic biological investigations in M. pneumoniae as well as related
species and maybe even for its use in synthetic biology (Marshall 2009).
In the following paragraphs I will therefore briefly express my personal view on i) the next
possible directions of research in M. pneumoniae, ii) medically relevant aspects to be
addressed, iii) necessary steps to make M. pneumoniae a candidate for biotechnological use as
well as iv) possible biotechnological and synthetic biological applications of minimal cells.
There are various scientific challenges and next steps of systematic research in M.
pneumoniae focusing again on the basic understanding of this organism. In analogy to work
performed in Leptospira interrogans useful insights could be derived from measuring
proteome-wide cellular protein concentrations in M. pneumoniae as well as half-life of
proteins and RNA (Malmstrom, Beck et al. 2009). In the best case scenario this would be
performed investigating various relevant growth conditions. Similarly the protein interactions
should also be charted in various conditions and along different stages of the cell cycle of M.
pneumoniae. Along these lines it is also essential to get a better understanding of the global
use of PTMs in these near-minimal cells. Currently only two types of protein cleavage,
protein phosphorylation as well as protein acetylation are reported while others remain to be
discovered (Herrmann and Ruppert 2006). Another rather neglected aspect is the membrane
biology in M. pneumoniae and here especially the membrane proteome, which currently
consists of about 100 proteins many of which are only vaguely annotated. At this end
comprehensive mapping of the membrane proteome would further advance the understanding
of M. pneumoniae. In addition to that the topology of all membrane proteins should also be
looked at. Experiments using MS/MS analysis for membrane protein identification could be
validated by orthogonal approaches e.g. immunogold labelling of membrane proteins and
detection via EM, which could moreover add spatial information on the distribution patterns
of membrane proteins. The relative or even absolute quantification via heavy isotope labelling
would yet add another level of detail and could also help assess false positive hits from a nonGeneral principles of cellular organization in Mycoplasma pneumoniae
74
quantitative mapping approach. Finally the combination of these results and the integration of
additional datasets like the ones provided in this thesis could help elucidate regulatory
patterns of the extracellular membrane proteome in single- or multi-conditional analysis.
Eventually these combined datasets could then be used for entire cell modelling in order to
better understand the M. pneumoniae lifestyle and growth behaviour.
From a therapeutic point of view an intensified investigation of the growth on host cells and a
more thorough understanding of the pathogenicity of M. pneumoniae are the most urgent
questions. Although numerous advanced have been made in the last 25 years in the
elucidation of the attachment process and the proteins as well as oligosaccharides involved
(chapters 1.1.1 & 1.1.2.) there still many regulatory details not understood. These ask for an in
detail investigation of the attachment process to host cells as well as its regulation and a more
systematic charting of the host-pathogen interaction network. Inhibitors with antibacterial
function could be derived from exhaustive insights into the involved target molecules at
various stages of the attachment process. These could be M. pneumoniae specific or in a best
case scenario also amenable for other pathogens with a similarly regulated host cell
recognition process.
In order to make M. pneumoniae available for biotechnological applications there are a few
limitations to tackle (chapter 1.1.3). Among them is the rather long generation time of 8h
which severely slows down the growth potential of this pathogen and probably reflects its
adaptive lifestyle to the host, which should not be killed. Trying to accelerate the M.
pneumoniae generation time to 2h or less via genetic modifications seems a necessary
prerequisite for industrial use. To that end it also seems required to use a non-adherent M.
pneumoniae M129 strain like, e.g. B169/176 (Lipman, Clyde et al. 1969). This strain comes
with the advantage of being able to grow in a three-dimensional fashion batch mode so that
the biomass production can be increased. Additionally this strain appears to be avirulent and
could possibly be reclassified to S1 security level, which would dramatically decrease the
growth costs for a weight unit of cells. Another aspect that needs to be addressed is the
growth medium. In this thesis a minimal medium for M. pneumoniae growth has been
proposed (Yus, Maier et al. 2009). It seems worthwhile to check whether the defined minimal
medium or the defined non-minimal medium are optimal also for long term batch culture
growth of a modified bacterium that has the desired growth characteristics. From a genetic
manipulation point of view the above proposed modifications seem to be achievable,
especially considering the progress that has been accomplished by the synthetic biology &
General principles of cellular organization in Mycoplasma pneumoniae
75
bioenergy group at the J. Craig Venter Institute (see chapter 1.1.3. for details) (Lartigue, Glass
et al. 2007; Gibson, Benders et al. 2008; Lartigue, Vashee et al. 2009).
Finally a short glimpse at potential applications for a controllable minimal organism in
biotechnology and synthetic biology as reviewed (Serrano 2007). Such an organism could be
used as a source for growing initial compounds for chemical synthesis, which are either
impossible to produce in a chemical way or their chemical synthesis is simply uneconomic.
Feasibility of such an approach was e.g. demonstrated for the production of terpenoid
compounds in E. coli and S. cerevisiae, which have been used as precursors in the synthesis of
antimalarial drugs (Martin, Pitera et al. 2003; Lindahl, Olsson et al. 2006; Ro, Paradise et al.
2006; Serrano 2007). Controllable minimal cells could also be exploited as a source for
energy supply and research towards that aim appears to accelerate (Marshall 2009). Even
more than for pure chemical synthesis, controllable cellular systems seem to be predestined
for the production of a wide range of biologics, a market that is still growing according to a
recent analysis (Aggarwal 2009).
The above discussed points clearly show that there are still many questions of M. pneumoniae
biology unanswered. Therefore future projects will help to further understand this nearminimal organism. The exact social benefit for the support of academic research towards that
direction cannot be exactly estimated; however the odds are not too long that further
investigations turn out to be extremely valuable.
General principles of cellular organization in Mycoplasma pneumoniae
76
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8. Acknowledgements
To say “Thank you” to many great individuals who helped me in one way or another over the
past few years and in some cases life-long is not a compulsory task here but is something I do
with the greatest pleasure and gratitude towards all my supporters, friends and family.
First and most important for the successful completion of my PhD thesis I want to thank my
supervisor at EMBL Heidelberg Dr. Anne-Claude Gavin, who was always extremely
motivated, incredibly supportive and a great person to work with. I want to thank you AnneClaude for the great time I had in the lab, the invaluable lessons I learned form you as well as
the great degrees of freedom I had during my work and the confidence you always had and
have in our fascinating projects. Secondly, I would like to thank Prof. Dr. Ruedi Aebersold for
giving me the opportunity and the support to perform my PhD thesis as an external PhD
student in his laboratory at ETH Zürich and for the reliably great input during our meetings. I
am especially thankful to you Ruedi for the very warm welcome in Zürich and all your open
mindedness that I will also always forward in life.
In order to perform a lot of high quality work it is of priceless to be in a lab with a great
atmosphere, where interesting and very smart personalities from various countries gather to
address interesting research questions. I found this working atmosphere in our lab at EMBL
and enjoyed spending lots of time with all of you. I especially enjoyed speaking different
languages, though mostly our beloved English, having so many diverse cultural backgrounds
around and I took pleasure from the fact that all of you are great characters. Therefore I want
to thank all lab members for the very good time I had. This includes: Dr. Anne-Claude Gavin,
Michaela Rode, Dr. Pedro Beltran, Ines Racké, Emma Dalton, Christian Matetzki, Jamie
Trott, Jelena Gvozdenovic-Jeremic, Carmen Gurrieri Aguilar, Tomás Norambuena, Samuel
Bader, Dr. Sebastian Charbonnier, Dr. Stefan Bonn, Dr. Oriol Gallego, Evelyn Sawa, Tatjana
Schneidt, Dr. Emmanuel Poilpré, Dr. Kenji Maeda, Dr. Arun Kumar, Dr. Emmanuel Saliba,
Dr. Jan Seebacher, Lisa Lirussi and Mattia Poletto.
For the scientific input to the projects mentioned within this PhD thesis I am also grateful to
Dr. Matthias Wilm, Dr. Sven Fraterman, Frank Thommen, Emma Dalton, Michael Schulz,
Evely Sawa, Dr. Meikel Diepholz, Elisabeth Pirkl, Dr. Anja Seybert, all the members of the
Gavin group as well as the Bork group, Dr. Thomas Franz, Dr. Jeroen Krijgsveld, Stefan
Leicht, Sabrina Rüggeberg, Kristina Dzeyk from the EMBL Proteomics core facility and Dr.
Vladimir Benes, Sabine Schmidt, Jos de Graaf, Tomi Bähr-Ivacevic and Jens Stolte from the
EMBL Genomics Core facility for expert help and discussion as well as all authors of the
General principles of cellular organization in Mycoplasma pneumoniae
87
studies. Especially, I also want to thank Prof. Dr. Richard Herrmann, who is the groups
external Mycoplasma pneumoniae expert and who shares all his knowledge and materials
with us, for his great support with manuscripts, intensive suggestions for improvements of this
thesis as well as for countless valuable discussions.
For the record, the protein-protein interaction data set has been submitted to the International
Molecular Exchange Consortium (http://imex.sf.net) through IntAct (pmid is 17145710;
identifier is IM-11644). The electron microscopy maps have been submitted to the Electron
Microscopy Data Bank (www.ebi.ac.uk/pdbe-srv/emsearch/) (identification codes EMD1637, EMD-1638, and EMD-1639).
At EMBL everybody knows about the great advice you get from your TAC (Thesis advisory
committee) members. Therefore I would like to thank the members of my TAC for all their
efforts: So thanks to Dr. Lars Steinmetz, Dr. Toby Gibson, Dr. Anne-Claude Gavin & Prof.
Dr. Ruedi Aebersold. Furthermore I would like to thank all the people at our administration at
EMBL Heidelberg and ETH Zürich for their great support. This includes in particular, Tamara
Kantzos-Marinkovic, Nelly van der Jagt González, Milanka Stojkovic, Dr. Helke Hillebrand
and Dr. Lars Steinmetz from EMBL Heidelberg and Dominic Dähler and the entire
Doktoratsadministration from ETH Zürich.
To spend a lot of time at EMBL means to spend less time elsewhere. For being so patient
when I came late to countless occasions e.g. Fussballmittwoch, poker nights, occasional
cooking sessions etc. and for being wonderful friends I want to thank: Alexander, Sebastian,
Christoph, Jochen, Jens, Thiemo, Mathias, Philipp, Jochen, Kathrin, Nina, Alicja, Katharina,
Patricia, Petra, Matthias, Tim, Boris, Stefan, David, Patrick, Christian, Christoph, Felix,
Niklas, Tillman, Tobias & Evelyn. I am looking forward to the next years!
Finally, I want to thank my parents Ingrid and Heinz Werner, my sister Julia, my grand and
great grand parents and all family members for their continuous and enduring support.
General principles of cellular organization in Mycoplasma pneumoniae
88
9. Curriculum vitae
Sebastian Kühner, Dipl. Biol. & cand. oec.
Address:
Phone:
E-Mail:
Date of Birth:
Place of Birth:
Nationality:
Martial Status:
Kirschenstraße 49
68519 Viernheim
0179/4767031
[email protected]
July 31st 1981
Heidelberg
German
Single
Studies & PhD thesis
October 2006
February 2010
Predoctoral fellow in biochemistry at the European Molecular Biology
Laboratory, Heidelberg & ETH Zürich with Dr. Anne-Claude Gavin
PhD thesis title: „General principles of cellular organization in the
genome-reduced bacterium Mycoplasma pneumoniae”
Since October 2005
Second degree studies in economics at Ruprecht-Karls-Universität
Heidelberg, prediploma exam passed in winter semester 2007,
presumable end of studies summer semester 2010.
October 2001 July 2006
Studies of biochemistry & molecular biology in Heidelberg & Oxford,
UK as an Erasmus fellow, Diploma grade average: 1,0
Diploma thesis on: „ATP induced Myosin unbinding of Actin“
Internships & working experience
Since August 2008
Project member & share holder of Klein, Kühner, Tussing & Woertge
GbR a company organizing an entire intranet relaunch for a german
subsidiary of an international electronic- & industrial multicorporate
enterprise
August 2008 November 2008
Project leader & share holder of Doganov, Ksienzyk, Kühner, Lang &
Ritter GbR a company that analyzed mechanical engineering and
construction markets for a medium sized investment good producer
July 2006 October 2006
Bayer AG, Bayer Business Services GmbH, business
consulting segment with Dr. Alexander Moscho. Analysis, calculation
and successful presentation of a business case for partial restructuring
of the information technology landscape at all corporations of Bayer
AG
November 2005 June 2006
Interdisciplinary Center of Scientific Computing Heidelberg,
Computational Biochemistry Group of Dr. Stefan Fischer, Diploma
thesis in computational biochemistry investigating conformational
transitions between protein crystal structures using simulation
techniques
General principles of cellular organization in Mycoplasma pneumoniae
89
April 2005 June 2005
BASF AG Ludwigshafen, Agricultural products unit in Limburgerhof
Germany, Laboratory of Dr. B. Navé, In vitro investigation of the
molecular mode of action of fungicides targeting agriculturally
relevant pathogenic fungi
July 2004 January 2005
Biochemistry Center Heidelberg, Dr. Elisabeth Davioud Charvet.
In vitro characterization of glutathione-reductase inhibitors as potent
anti-malarial drugs.
January 2004 July 2004
Plant Cell Biology & Microscopy Group Prof. Dr. C. Hawes
Oxford Brookes University: Investigation of the dynamics of
protein localization in the membrane of the endoplasmic reticulum
October 2002 March 2005
Ruprecht-Karls-Universität Heidelberg, teaching tutorials in
inorganic and biological chemistry for molecular cell biology students
Since 1996
Working experience in parental owned business in staffing, logistics,
financial and budgetary planning as well as accounting
School education
1992 - 2001
Albertus-Magnus-Secondary school, Viernheim
A-Levels / Majors: Maths and Chemistry, Grade: 1,4
1999
Brother Rice High School, Bloomfield Hills, Michigan U.S.A.
Language skills
German:
English:
French:
Chinese:
Latin:
native language
Fluent communication and written skills
written and spoken on an advanced level
basic communication skills in mandarin
good translation and reading abilities (Latinum)
Awards & Honours
July 2009
Finn Wold Travel award from the U.S. Protein Society for the 23rd
annual protein society symposium in Boston, MA, U.S.A.
July 2008
Travel award from the German science foundation (DFG) for an oral
presentation at the HUPO conference in Amsterdam, Netherlands 2008
July 2008
Hoffmann la Roche travel award for an oral presentation at the HUPO
conference in Amsterdam, Netherlands 2008 (declined)
Since 2008
E-fellows scholar
October 2007
Awarded with the diploma & master prize of the German Society of
biochemistry & molecular biology (GBM) for the best thesis at the
Ruprecht-Karls University Heidelberg in 2006/2007
General principles of cellular organization in Mycoplasma pneumoniae
Since 2007
“Capstone” Fellow in the mentoring programme of McKinsey &
Company Inc.
Since October 2006
Predoctoral fellow at the European molecular biology laboratory in
Heidelberg, Germany enrolled as PhD student at ETH Zürich
Since 2006
“Join the Best” Scholar in the fellow program of MLP AG
January 2004 July 2004
Erasmus fellow for studies and research at Oxford Brookes
University, Oxford UK
Memberships & additional qualifications
Since 2006
Member of consulting society GalileiConsult e.V. of the University of
Heidelberg, department of information technology
Since 2004
Member of the Oxford Union debating society, member of the German
Society of Biochemistry and Molecular Biology (GBM) and their
international associations FEBS and IUBMB
Since 2004
Member of the Initiative Wertpapier Heidelberg (IWH), the capital
market and stock exchange society of the University of Heidelberg
2002-2006
Member of the Biological Union of the Ruprecht-Karls University
Heidelberg, involved in consultancy, administration and organising
tutorials
Since 1999
Treasurer and active organizer of summer camps and trips of the
Catholic Youth Society St. Hildegard, Viernheim
Since 1999
Full and clean driving licence, various motorboat and sailing licences
Publications
1. Runions J., Brach T., Kühner S. & Hawes C. Photoactivation of GFP reveals protein
dynamics within the endoplasmic reticulum membrane; Journal of Experimental Botany,
2006 57(1):43-50.
2. Bauer H., Fritz-Wolf K., Winzer A., Kühner S., Little S., Yardley V., Verzin H., Palfey
B., Schirmer R. H. & Davioud-Charvet E. A Fluoro Analogue of the Menadione
Derivative 6-[2'-(3'-Methyl)-1',4'-naphthoquinolyl]hexanoic Acid Is a Suicide Substrate of
Glutathione Reductase. Crystal Structure of the Alkylated Human Enzyme; J. Am. Chem.
Soc., 128 (33), 10784 -10794, 2006.
3. Kühner S. ATP induced Myosin unbinding of Actin. Diploma Thesis in Computational
Biochemistry at the Ruprecht-Karls-Universität Heidelberg 2006. download available:
http://www.embl-heidelberg.de/~kuehner/publications/thesis.pdf
4. Kühner S. & Gavin A.-C.. Towards quantitative analysis of proteome dynamics, Nature
Biotechnology, 2007, 25, 298-300.
5. Bader S., Kühner S. & Gavin A.-C. Interaction networks for systems biology. FEBS Lett.
2008, 582(8):1220-1224.
General principles of cellular organization in Mycoplasma pneumoniae
91
6. Kühner S., van Noort V., ..., Aebersold R., ..., Gavin AC. Proteome organization in a
genome-reduced bacterium. Science, 2009, 326, 1235-1240.
7. Güell M., ..., Kühner S., ..., Gavin A.C., ..., Serrano L. Transcriptome complexity in a
genome-reduced bacterium. Science, 2009, 326, 1268-1271.
8. Yus E., ..., Kühner S., ..., Gavin A.C., ..., Serrano L. Impact of genome reduction on
bacterial metabolism and its regulation. Science, 2009, 326, 1263-1268.
9. Kühner S., & Fischer S. Structural Mechanism of ATP-triggered Myosin release from
Actin in muscle contraction. “Manuscript in preparation.”
Invited Talks, Poster presentations, workshops & teaching
November 2009
11th EMBL International PhD symposium Heidelberg – talk
November 2009
EMBL Biochemical PhD student course - teaching
September 2009
EMBL PhD student retreat Marseille/France - talk
July 2009
23rd Protein Society Meeting Boston/U.S. – poster presentation
March 2009
MBTI Workshop “Power of Personality” Berlin
November 2008
„Capstone Communication Skills Workshop“ Düsseldorf
September 2008
EMBL PhD student retreat Lisbon, Portugal - talk
September 2008
CSHL/WT Network Biology meeting Hinxton/Cambridge, UK poster presentation
August 2008
HUPO annual meeting Amsterdam, Netherlands- talk
Juli 2008
Proteomics course ETH Zürich, Schweiz
March 2008
Computational proteomics workshop Schloss Dagstuhl, Saarland
November 2007
Organization of the 9th EMBL International PhD symposium
“Patterns in Biology” in Heidelberg
November 2007
EMBL Biochemical PhD student practical - teaching
October 2007
EBI Bioinformatics course in Hinxton/Cambridge, UK
September 2007
EMBL PhD Student retreat Barcelona, Spain - talk
September 2007
Biomolecular mass spectrometry course in Utrecht, Netherlands
October 2006 December 2006
EMBL International PhD Program starting course in Heidelberg
and Grenoble, France
Hobbies
Tennis, Soccer, Cooking & Eating, Literature, Skiing, Sailing etc.
General principles of cellular organization in Mycoplasma pneumoniae
92
References
Dr. Anne-Claude Gavin, Head of Gavin Group, European Molecular
Biology Laboratory , 69117 Heidelberg; Phone: +49 (0)6221 387-8816
E-Mail: [email protected]
Dr. Alexander Moscho, Head of Business Consulting, Bayer Business
Services GmbH, 51368 Leverkusen; Phone: +49 (0)214 30 71070
E-Mail: [email protected]
Dr. Elisabeth Davioud-Charvet, Antiparasitic Drug Design, Biochemie
Zentrum Heidelberg, 69120 Heidelberg; Phone: +49 (0)6221 544188
E-Mail: [email protected]
General principles of cellular organization in Mycoplasma pneumoniae
93
10. Supplement
10.1. Table S1: List of purifications and proteins identified.
In total 259 successful purifications were performed using 212 distinct TAP-fusion proteins.
i) Is the list of TAP purifications. The first column gives the purification ID. The second and
third columns provide the annotated systematic and protein names of the TAP-protein used as
entry point, respectively. The last column gives the list of prey proteins that co-purify with the
bait. ii) Is the list of proteins identified in the PeptideAtlas by FT-MS/MS. The first column
provides the annotated systematic name of each identified protein. The second column gives
the protein name.
i) List of purifications
Bait
Bait
Purification
(systematic (protein
ID
name)
name)
EMBL001
Mpn025
Preys
Fba
Mpn025 Mpn434 Mpn067 Mpn573 Mpn118 Mpn034 Mpn003
EMBL002
Mpn025
Fba
Mpn025 Mpn390 Mpn516 Mpn430 Mpn315 Mpn665 Mpn261 Mpn365
Mpn034 Mpn141 Mpn669 Mpn210 Mpn434 Mpn573 Mpn207 Mpn515
Mpn426 Mpn546 Mpn608 Mpn191 Mpn020 Mpn252 Mpn452 Mpn621
Mpn004
EMBL003
Mpn567
P200
Mpn210 Mpn434 Mpn095 Mpn567 Mpn390 Mpn295 Mpn003 Mpn393
Mpn004
Mpn390 Mpn230 Mpn516 Mpn394 Mpn440 Mpn354 Mpn258 Mpn658
Mpn228 Mpn556 Mpn166 Mpn573 Mpn515 Mpn686 Mpn191 Mpn020
Mpn452 Mpn621 Mpn004 Mpn619 Mpn303 Mpn179 Mpn430 Mpn665
Mpn261 Mpn685 Mpn044 Mpn574 Mpn019 Mpn660 Mpn210 Mpn434
Mpn226 Mpn280 Mpn426 Mpn050 Mpn189
EMBL004
Mpn230
RpsR
EMBL005
Mpn051
Mpn051 Mpn210 Mpn627 Mpn361 Mpn573 Mpn051 Mpn042 Mpn034
EMBL006
Mpn516
RpoB
Mpn434 Mpn352 Mpn191 Mpn020 Mpn516 Mpn228 Mpn515
General principles of cellular organization in Mycoplasma pneumoniae
94
EMBL007
Mpn516
RpoB
Mpn328 Mpn352 Mpn516 Mpn665 Mpn171 Mpn330 Mpn571 Mpn228
Mpn210 Mpn226 Mpn024 Mpn515 Mpn673 Mpn239 Mpn191 Mpn020
Mpn004
EMBL008
Mpn379
PolA
Mpn210 Mpn621
EMBL009
Mpn379
PolA
Mpn684 Mpn390 Mpn665 Mpn261 Mpn379 Mpn258 Mpn141 Mpn210
Mpn434 Mpn573 Mpn310 Mpn207 Mpn032 Mpn515 Mpn426 Mpn050
Mpn020 Mpn621 Mpn004
EMBL010
Mpn006
Tmk
Mpn372 Mpn210 Mpn134 Mpn434 Mpn390 Mpn280 Mpn516 Mpn665
Mpn515 Mpn006 Mpn191 Mpn258 Mpn452 Mpn621
EMBL011
Mpn006
Tmk
Mpn210 Mpn434 Mpn204 Mpn390 Mpn118 Mpn665 Mpn426 Mpn006
Mpn034 Mpn040 Mpn452 Mpn213
EMBL012
Mpn006
Tmk
Mpn134 Mpn025 Mpn619 Mpn390 Mpn303 Mpn118 Mpn516 Mpn430
Mpn197 Mpn665 Mpn394 Mpn261 Mpn378 Mpn006 Mpn393 Mpn258
Mpn141 Mpn210 Mpn553 Mpn434 Mpn322 Mpn573 Mpn280 Mpn515
Mpn191 Mpn452 Mpn106 Mpn621 Mpn004
EMBL013
Mpn416
P29
Mpn623 Mpn434 Mpn656 Mpn674 Mpn665 Mpn108 Mpn314 Mpn392
Mpn416 Mpn393 Mpn034 Mpn337
EMBL014
Mpn320
ThyA
Mpn563 Mpn210 Mpn434 Mpn573 Mpn324 Mpn516 Mpn515 Mpn426
Mpn320
EMBL015
Mpn320
ThyA
Mpn284 Mpn434 Mpn320 Mpn573 Mpn555 Mpn076 Mpn032
EMBL016
Mpn493
UlaD
Mpn596 Mpn434 Mpn555 Mpn674 Mpn665 Mpn314 Mpn392 Mpn034
General principles of cellular organization in Mycoplasma pneumoniae
95
EMBL017
Mpn327
RpmA
Mpn390 Mpn516 Mpn430 Mpn261 Mpn615 Mpn658 Mpn574 Mpn228
Mpn165 Mpn322 Mpn434 Mpn166 Mpn226 Mpn676 Mpn032 Mpn314
Mpn239 Mpn549 Mpn081 Mpn621
EMBL018
Mpn228
RpsF
Mpn352 Mpn230 Mpn516 Mpn103 Mpn518 Mpn169 Mpn115 Mpn228
Mpn553 Mpn616 Mpn515 Mpn178 Mpn020 Mpn191 Mpn621 Mpn004
Mpn446 Mpn480 Mpn179 Mpn295 Mpn520 Mpn665 Mpn171 Mpn182
Mpn465 Mpn685 Mpn660 Mpn035 Mpn210 Mpn434 Mpn226 Mpn622
Mpn280 Mpn239 Mpn189 Mpn252 Mpn561
EMBL019
Mpn389
LplA
Mpn389 Mpn434 Mpn295
EMBL020
Mpn553
ThrS
Mpn210 Mpn553 Mpn204 Mpn573 Mpn595 Mpn034
EMBL021
Mpn322
NrdF
Mpn210 Mpn434 Mpn322 Mpn573 Mpn390 Mpn419 Mpn261 Mpn034
Mpn365 Mpn004
EMBL022
Mpn322
NrdF
Mpn454 Mpn210 Mpn434 Mpn322 Mpn059 Mpn324
EMBL023
Mpn550
ThiI
Mpn210 Mpn434 Mpn550 Mpn573 Mpn295 Mpn003 Mpn515
EMBL024
Mpn573
GroL
Mpn062 Mpn392 Mpn573 Mpn264 Mpn194 Mpn430 Mpn008
Mpn269 Mpn430 Mpn315 Mpn665 Mpn309 Mpn365 Mpn019 Mpn228
Mpn210 Mpn434 Mpn324 Mpn495 Mpn515 Mpn426 Mpn050 Mpn345
Mpn004 Mpn621
EMBL025
Mpn495
UlaB
EMBL026
Mpn668
Mpn668 Mpn563 Mpn391 Mpn203 Mpn514 Mpn118 Mpn665 Mpn668
General principles of cellular organization in Mycoplasma pneumoniae
96
Mpn111
Mpn390 Mpn340 Mpn303 Mpn555 Mpn516 Mpn430 Mpn315 Mpn665
Mpn261 Mpn658 Mpn574 Mpn669 Mpn210 Mpn434 Mpn573 Mpn032
Mpn111 Mpn314 Mpn515 Mpn111 Mpn050 Mpn547 Mpn621 Mpn004
EMBL028
Mpn663
Mpn671 Mpn390 Mpn342 Mpn516 Mpn430 Mpn003 Mpn536 Mpn438
Mpn246 Mpn034 Mpn210 Mpn185 Mpn434 Mpn573 Mpn515 Mpn452
Mpn663 Mpn621 Mpn004
EMBL029
Mpn686
DnaA
EMBL030
Mpn509
Mpn210 Mpn434 Mpn390 Mpn516 Mpn430 Mpn295 Mpn003 Mpn665
Mpn509 Mpn281 Mpn034 Mpn599 Mpn509 Mpn452
EMBL031
Mpn079
FruK
EMBL032
Mpn013
Mpn390 Mpn665 Mpn258 Mpn210 Mpn556 Mpn434 Mpn553 Mpn280
Mpn013 Mpn207 Mpn346 Mpn515 Mpn426 Mpn050 Mpn452 Mpn004 Mpn621
EMBL033
Mpn075
Mpn210 Mpn075 Mpn434 Mpn322 Mpn573 Mpn324 Mpn665 Mpn261
Mpn075 Mpn426 Mpn020 Mpn258 Mpn228 Mpn399
EMBL034
Mpn328
Nfo
Mpn525 Mpn300 Mpn328 Mpn567 Mpn390 Mpn042 Mpn516 Mpn665
Mpn261 Mpn258 Mpn574 Mpn141 Mpn210 Mpn434 Mpn226 Mpn573
Mpn192 Mpn388 Mpn110 Mpn515 Mpn314 Mpn426 Mpn050 Mpn621
Mpn004
EMBL035
Mpn328
Nfo
Mpn210 Mpn434 Mpn328 Mpn573 Mpn118 Mpn516 Mpn515 Mpn034
Mpn072
RbfA
Mpn390 Mpn555 Mpn156 Mpn516 Mpn430 Mpn665 Mpn261 Mpn033
Mpn034 Mpn228 Mpn210 Mpn434 Mpn226 Mpn063 Mpn515 Mpn593
Mpn191 Mpn621 Mpn004
EMBL027
EMBL036
Mpn156
Mpn210 Mpn434 Mpn686 Mpn516 Mpn452 Mpn376 Mpn141
Mpn434 Mpn062 Mpn573 Mpn390 Mpn295 Mpn665 Mpn079
General principles of cellular organization in Mycoplasma pneumoniae
97
EMBL037
Mpn269 Mpn390 Mpn555 Mpn516 Mpn430 Mpn315 Mpn665 Mpn536
Mpn436 Mpn261 Mpn115 Mpn574 Mpn072 Mpn210 Mpn434 Mpn550
Mpn573 Mpn524 Mpn515 Mpn050 Mpn020 Mpn345 Mpn452 Mpn621
Mpn536
RuvB
EMBL038
Mpn002
Mpn397 Mpn134 Mpn303 Mpn352 Mpn516 Mpn430 Mpn295 Mpn665
Mpn261 Mpn002 Mpn034 Mpn165 Mpn210 Mpn553 Mpn434 Mpn573
Mpn002 Mpn280 Mpn310 Mpn674 Mpn515 Mpn050 Mpn191 Mpn621 Mpn004
EMBL039
Mpn638
Mpn638 Mpn434
EMBL040
Mpn638
Mpn210 Mpn434 Mpn366 Mpn295 Mpn474 Mpn518 Mpn273 Mpn638
Mpn638 Mpn004 Mpn072
EMBL041
Mpn393
PdhA
Mpn210 Mpn434 Mpn280 Mpn516 Mpn665 Mpn662 Mpn515 Mpn426
Mpn392 Mpn050 Mpn393 Mpn020 Mpn258 Mpn621 Mpn004
EMBL042
Mpn246
Def
Mpn434 Mpn573 Mpn390 Mpn246 Mpn155 Mpn245
EMBL043
Mpn168
RplB
Mpn210 Mpn434 Mpn390 Mpn315 Mpn295 Mpn665 Mpn261 Mpn207
Mpn060 Mpn252 Mpn621 Mpn004
Mpn275
Mpn596 Mpn568 Mpn390 Mpn118 Mpn520 Mpn516 Mpn430 Mpn315
Mpn665 Mpn394 Mpn261 Mpn275 Mpn556 Mpn210 Mpn434 Mpn676
Mpn275 Mpn036 Mpn515 Mpn392 Mpn050 Mpn621 Mpn004
EMBL045
Mpn172
RplP
Mpn642 Mpn390 Mpn430 Mpn211 Mpn103 Mpn665 Mpn261 Mpn658
Mpn228 Mpn210 Mpn418 Mpn434 Mpn166 Mpn063 Mpn032 Mpn426
Mpn050 Mpn020 Mpn252 Mpn452 Mpn621
EMBL046
Mpn268
Mpn062 Mpn671 Mpn390 Mpn516 Mpn665 Mpn261 Mpn379 Mpn259
Mpn268 Mpn258 Mpn210 Mpn322 Mpn434 Mpn268 Mpn207 Mpn252 Mpn452
EMBL044
General principles of cellular organization in Mycoplasma pneumoniae
98
EMBL047
Mpn268
Mpn210 Mpn434 Mpn268 Mpn390 Mpn555 Mpn295 Mpn003 Mpn665
Mpn268 Mpn261 Mpn314 Mpn426 Mpn489 Mpn034 Mpn040 Mpn452
EMBL048
Mpn192
RplQ
EMBL049
Mpn559
Mpn210 Mpn434 Mpn516 Mpn430 Mpn665 Mpn436 Mpn640 Mpn559
Mpn559 Mpn426 Mpn514 Mpn452 Mpn072
EMBL050
Mpn472
Mpn210 Mpn434 Mpn429 Mpn390 Mpn516 Mpn430 Mpn665 Mpn261
Mpn472 Mpn472 Mpn317 Mpn426 Mpn034 Mpn452
EMBL051
Mpn479
AzoR
EMBL052
Mpn461
Mpn461 Mpn434 Mpn390 Mpn034 Mpn295 Mpn476
Mpn253 Mpn434 Mpn034 Mpn665 Mpn108
Mpn390 Mpn479 Mpn040
EMBL053
Mpn208
RpsB
Mpn390 Mpn555 Mpn516 Mpn430 Mpn315 Mpn665 Mpn261 Mpn169
Mpn115 Mpn034 Mpn658 Mpn228 Mpn210 Mpn434 Mpn226 Mpn622
Mpn674 Mpn515 Mpn314 Mpn426 Mpn239 Mpn050 Mpn191 Mpn208
Mpn621 Mpn004
EMBL054
Mpn558
GidB
Mpn558 Mpn434 Mpn573 Mpn390 Mpn280 Mpn562 Mpn059 Mpn452
Mpn621
EMBL055
Mpn117
RplT
Mpn210 Mpn434 Mpn269 Mpn303 Mpn180 Mpn430 Mpn665 Mpn050
Mpn222 Mpn034 Mpn658 Mpn574 Mpn452 Mpn650 Mpn621 Mpn004
EMBL056
Mpn117
RplT
Mpn165 Mpn423 Mpn390 Mpn436 Mpn515 Mpn034 Mpn191 Mpn658
Mpn189 Mpn228 Mpn332 Mpn167
General principles of cellular organization in Mycoplasma pneumoniae
99
EMBL057
Mpn390
PdhD
Mpn210 Mpn390
EMBL058
Mpn245
Gmk
Mpn434
EMBL059
Mpn419
AlaS
Mpn434 Mpn011 Mpn573 Mpn118 Mpn555 Mpn516 Mpn419 Mpn003
Mpn582
EMBL060
Mpn100
Mpn210 Mpn434 Mpn390 Mpn118 Mpn295 Mpn100 Mpn547 Mpn034
Mpn100 Mpn509 Mpn650 Mpn004
EMBL061
Mpn108
Mpn390 Mpn516 Mpn430 Mpn665 Mpn261 Mpn108 Mpn529 Mpn210
Mpn434 Mpn124 Mpn524 Mpn346 Mpn515 Mpn426 Mpn452 Mpn646
Mpn108 Mpn004 Mpn621
EMBL062
Mpn108
Mpn210 Mpn434 Mpn619 Mpn155 Mpn430 Mpn665 Mpn640 Mpn032
Mpn108 Mpn034 Mpn004 Mpn072
EMBL063
Mpn471
Mpn390 Mpn555 Mpn516 Mpn430 Mpn261 Mpn115 Mpn228 Mpn210
Mpn462 Mpn434 Mpn207 Mpn294 Mpn515 Mpn020 Mpn252 Mpn004
RpmG1 Mpn621
EMBL064
Mpn631
Tsf
EMBL065
Mpn521
Mpn521 Mpn573
EMBL066
Mpn023
MetG
Mpn631 Mpn434 Mpn295 Mpn665
Mpn025 Mpn619 Mpn390 Mpn303 Mpn118 Mpn516 Mpn430 Mpn401
Mpn315 Mpn665 Mpn261 Mpn354 Mpn638 Mpn393 Mpn023 Mpn141
Mpn061 Mpn210 Mpn434 Mpn322 Mpn007 Mpn280 Mpn324 Mpn515
Mpn032 Mpn426 Mpn347 Mpn191 Mpn106 Mpn621 Mpn004
General principles of cellular organization in Mycoplasma pneumoniae
100
EMBL067
Mpn001
DnaN
Mpn434 Mpn001
EMBL068
Mpn001
DnaN
Mpn434 Mpn001 Mpn516 Mpn621
EMBL069
Mpn064
DeoA
Mpn210 Mpn033 Mpn434 Mpn064
Efp
Mpn555 Mpn516 Mpn430 Mpn295 Mpn665 Mpn261 Mpn321 Mpn393
Mpn258 Mpn029 Mpn586 Mpn210 Mpn322 Mpn434 Mpn573 Mpn280
Mpn207 Mpn314 Mpn515 Mpn621 Mpn004
ParE
Mpn402 Mpn390 Mpn516 Mpn665 Mpn436 Mpn006 Mpn060 Mpn351
Mpn122 Mpn141 Mpn210 Mpn434 Mpn424 Mpn674 Mpn426 Mpn123
Mpn392 Mpn050 Mpn266 Mpn191 Mpn452 Mpn252 Mpn387 Mpn621
Mpn282
Mpn062 Mpn516 Mpn430 Mpn665 Mpn262 Mpn044 Mpn034 Mpn658
Mpn122 Mpn210 Mpn434 Mpn573 Mpn515 Mpn050 Mpn549 Mpn191
Mpn020 Mpn345 Mpn621 Mpn004
EMBL070
EMBL071
Mpn029
Mpn122
EMBL072
Mpn122
ParE
EMBL073
Mpn563
Mpn563 Mpn210 Mpn434 Mpn486 Mpn573 Mpn390 Mpn251 Mpn665
Mpn563 Mpn006 Mpn125 Mpn034 Mpn658 Mpn650 Mpn399
EMBL074
Mpn165
RplC
Mpn390 Mpn430 Mpn261 Mpn228 Mpn141 Mpn165 Mpn210 Mpn475
Mpn434 Mpn166 Mpn226 Mpn487 Mpn207 Mpn515 Mpn426 Mpn050
Mpn191 Mpn020 Mpn252 Mpn413 Mpn452 Mpn621 Mpn004
EMBL075
Mpn251
Rpe
Mpn434 Mpn390 Mpn555 Mpn315 Mpn251 Mpn674 Mpn665 Mpn261
Mpn640 Mpn034 Mpn040 Mpn660
EMBL076
Mpn223
HprK
Mpn341 Mpn434 Mpn573 Mpn044 Mpn555 Mpn658 Mpn223
General principles of cellular organization in Mycoplasma pneumoniae
101
EMBL077
Mpn067
Mpn067 Mpn210 Mpn434 Mpn067 Mpn550 Mpn504 Mpn516 Mpn248 Mpn261
EMBL078
Mpn067
Mpn210 Mpn434 Mpn595 Mpn545 Mpn516 Mpn003 Mpn261 Mpn008
Mpn067 Mpn515 Mpn426 Mpn067 Mpn452 Mpn678
EMBL079
Mpn067
Mpn430 Mpn315 Mpn665 Mpn261 Mpn258 Mpn210 Mpn322 Mpn434
Mpn067 Mpn573 Mpn324 Mpn426 Mpn472 Mpn067 Mpn050 Mpn191 Mpn020
EMBL080
Mpn392
PdhB
EMBL081
Mpn266
Mpn352 Mpn516 Mpn665 Mpn261 Mpn247 Mpn228 Mpn210 Mpn669
Mpn434 Mpn280 Mpn515 Mpn673 Mpn266 Mpn191 Mpn020 Mpn004
Mpn266 Mpn621
EMBL082
Mpn266
Mpn434 Mpn226 Mpn352 Mpn516 Mpn665 Mpn515 Mpn266 Mpn020
Mpn266 Mpn191 Mpn658 Mpn509 Mpn621 Mpn004
EMBL083
Mpn427
Mpn210 Mpn434 Mpn573 Mpn516 Mpn419 Mpn003 Mpn034 Mpn427
Mpn427 Mpn004
Mpn020
Mpn025 Mpn062 Mpn352 Mpn516 Mpn394 Mpn354 Mpn386 Mpn258
Mpn141 Mpn669 Mpn553 Mpn322 Mpn573 Mpn598 Mpn515 Mpn392
Mpn020 Mpn191 Mpn106 Mpn153 Mpn621 Mpn004 Mpn014 Mpn303
Mpn315 Mpn430 Mpn520 Mpn665 Mpn261 Mpn393 Mpn034 Mpn061
Mpn020 Mpn210 Mpn434 Mpn280 Mpn324 Mpn688
EMBL085
Mpn020
Mpn390 Mpn555 Mpn352 Mpn264 Mpn516 Mpn003 Mpn665 Mpn394
Mpn261 Mpn571 Mpn228 Mpn476 Mpn072 Mpn210 Mpn429 Mpn434
Mpn226 Mpn592 Mpn674 Mpn515 Mpn032 Mpn314 Mpn673 Mpn191
Mpn020 Mpn020 Mpn509 Mpn004
EMBL086
Mpn191
RpoA
EMBL084
Mpn434 Mpn392 Mpn306 Mpn393
Mpn437 Mpn352 Mpn191 Mpn516 Mpn515
General principles of cellular organization in Mycoplasma pneumoniae
102
EMBL087
Mpn191
RpoA
Mpn118 Mpn352 Mpn516 Mpn443 Mpn171 Mpn228 Mpn210 Mpn265
Mpn434 Mpn226 Mpn640 Mpn362 Mpn515 Mpn673 Mpn239 Mpn191
Mpn020 Mpn621 Mpn004
EMBL088
Mpn106
PheT
Mpn210 Mpn434 Mpn322 Mpn516 Mpn295 Mpn665 Mpn261 Mpn034
Mpn106 Mpn141
PheT
Mpn269 Mpn390 Mpn470 Mpn516 Mpn430 Mpn295 Mpn665 Mpn394
Mpn261 Mpn141 Mpn165 Mpn434 Mpn573 Mpn324 Mpn515 Mpn608
Mpn191 Mpn466 Mpn106 Mpn621
RpsL
Mpn390 Mpn516 Mpn430 Mpn100 Mpn665 Mpn034 Mpn228 Mpn277
Mpn210 Mpn434 Mpn280 Mpn515 Mpn173 Mpn050 Mpn191 Mpn040
Mpn345 Mpn452 Mpn621 Mpn004
EMBL089
EMBL090
Mpn106
Mpn225
EMBL091
Mpn397
SpoT
Mpn397 Mpn062 Mpn390 Mpn142 Mpn555 Mpn430 Mpn665 Mpn171
Mpn297 Mpn354 Mpn441 Mpn021 Mpn434 Mpn573 Mpn559 Mpn538
Mpn546 Mpn547 Mpn079
EMBL092
Mpn300
ScpA
Mpn300 Mpn210 Mpn434 Mpn423 Mpn573 Mpn390 Mpn211 Mpn665
Mpn551 Mpn032 Mpn301 Mpn426 Mpn508 Mpn040
RplI
Mpn231 Mpn390 Mpn303 Mpn118 Mpn516 Mpn430 Mpn154 Mpn665
Mpn261 Mpn365 Mpn658 Mpn574 Mpn228 Mpn210 Mpn434 Mpn063
Mpn515 Mpn426 Mpn173 Mpn050 Mpn020 Mpn452 Mpn621
EMBL093
Mpn231
EMBL094
Mpn231
RplI
Mpn231 Mpn352 Mpn516 Mpn665 Mpn365 Mpn034 Mpn658 Mpn574
Mpn210 Mpn434 Mpn166 Mpn515 Mpn640 Mpn020 Mpn252 Mpn452
Mpn004
EMBL095
Mpn303
Pyk
Mpn303 Mpn191 Mpn430
EMBL096
Mpn118
Mpn563 Mpn298 Mpn269 Mpn390 Mpn155 Mpn124 Mpn430 Mpn346
Mpn118 Mpn041 Mpn050 Mpn331 Mpn400
General principles of cellular organization in Mycoplasma pneumoniae
103
EMBL097
Mpn470
PepP
EMBL098
Mpn381
Mpn381 Mpn434 Mpn573 Mpn656 Mpn324 Mpn034 Mpn381 Mpn665
EMBL099
Mpn295
Mpn295 Mpn434
EMBL100
Mpn120
GrpE
Mpn210 Mpn434 Mpn390 Mpn430 Mpn295 Mpn120 Mpn032 Mpn452
Mpn621 Mpn004
Mpn171
RpsC
Mpn558 Mpn390 Mpn555 Mpn516 Mpn430 Mpn315 Mpn665 Mpn261
Mpn309 Mpn297 Mpn169 Mpn034 Mpn574 Mpn228 Mpn165 Mpn210
Mpn265 Mpn434 Mpn166 Mpn226 Mpn573 Mpn280 Mpn380 Mpn008
Mpn515 Mpn426 Mpn191 Mpn020 Mpn621 Mpn004
EMBL102
Mpn330
Mpn303 Mpn352 Mpn516 Mpn315 Mpn665 Mpn330 Mpn115 Mpn258
Mpn658 Mpn574 Mpn228 Mpn141 Mpn660 Mpn210 Mpn434 Mpn226
Mpn063 Mpn622 Mpn280 Mpn380 Mpn515 Mpn032 Mpn294 Mpn426
Mpn330 Mpn445 Mpn050 Mpn191 Mpn020 Mpn252 Mpn621 Mpn004
EMBL103
Mpn677
Mpn677 Mpn434 Mpn677 Mpn573 Mpn034 Mpn658 Mpn223 Mpn665
EMBL104
Mpn351
Mpn351 Mpn351 Mpn034
Mpn009
Mpn619 Mpn390 Mpn516 Mpn430 Mpn665 Mpn261 Mpn141 Mpn210
Mpn434 Mpn573 Mpn310 Mpn380 Mpn515 Mpn426 Mpn191 Mpn452
Mpn009 Mpn004
Mpn009
Mpn619 Mpn390 Mpn516 Mpn430 Mpn665 Mpn261 Mpn009 Mpn141
Mpn210 Mpn434 Mpn573 Mpn515 Mpn426 Mpn050 Mpn191 Mpn452
Mpn009 Mpn004
EMBL101
EMBL105
EMBL106
Mpn210 Mpn434 Mpn470 Mpn004
General principles of cellular organization in Mycoplasma pneumoniae
104
EMBL107
Mpn365
Mpn365 Mpn210 Mpn434 Mpn615 Mpn343 Mpn365 Mpn040 Mpn034 Mpn665
EMBL108
Mpn278
Glf
Mpn210 Mpn434 Mpn573 Mpn555 Mpn324 Mpn430 Mpn665 Mpn314
Mpn050 Mpn278 Mpn542 Mpn228 Mpn621 Mpn004
EMBL109
Mpn061
Ffh
Mpn390 Mpn516 Mpn665 Mpn261 Mpn600 Mpn258 Mpn228 Mpn210
Mpn434 Mpn226 Mpn280 Mpn032 Mpn515 Mpn191 Mpn004 Mpn621
EMBL110
Mpn618
DnaX
Mpn684 Mpn516 Mpn430 Mpn665 Mpn465 Mpn169 Mpn685 Mpn258
Mpn658 Mpn141 Mpn618 Mpn322 Mpn434 Mpn573 Mpn280 Mpn515
Mpn032 Mpn317 Mpn426 Mpn514 Mpn191 Mpn020 Mpn252 Mpn452
Mpn153
EMBL111
Mpn429
Pgk
Mpn210 Mpn434 Mpn429
EMBL112
Mpn185
Adk
Mpn210 Mpn434 Mpn185 Mpn034
EMBL113
Mpn595
RpiB
Mpn269 Mpn595 Mpn295
EMBL114
Mpn324
NrdE
Mpn434 Mpn322 Mpn573 Mpn390 Mpn555 Mpn324 Mpn516 Mpn430
Mpn003 Mpn665 Mpn515 Mpn050 Mpn222 Mpn621
EMBL115
Mpn007
Mpn618 Mpn434 Mpn573 Mpn007 Mpn665 Mpn032 Mpn351 Mpn034
Mpn007 Mpn040 Mpn629
EMBL116
Mpn007
Mpn618 Mpn210 Mpn434 Mpn280 Mpn007 Mpn516 Mpn430 Mpn665
Mpn007 Mpn515 Mpn258 Mpn621
General principles of cellular organization in Mycoplasma pneumoniae
105
EMBL117
Mpn007
Mpn303 Mpn516 Mpn430 Mpn665 Mpn171 Mpn440 Mpn246 Mpn258
Mpn034 Mpn148 Mpn618 Mpn556 Mpn210 Mpn434 Mpn011 Mpn573
Mpn007 Mpn140 Mpn207 Mpn598 Mpn515 Mpn392 Mpn311 Mpn466
Mpn007 Mpn020 Mpn450 Mpn452 Mpn153 Mpn621 Mpn004
EMBL118
Mpn545
Rnc
Mpn434
EMBL119
Mpn257
GalE
Mpn210 Mpn497 Mpn434 Mpn089 Mpn269 Mpn390 Mpn118 Mpn656
Mpn516 Mpn257 Mpn207 Mpn034 Mpn040 Mpn621 Mpn004
Mpn329
Mpn099 Mpn390 Mpn303 Mpn516 Mpn430 Mpn665 Mpn261 Mpn440
Mpn609 Mpn258 Mpn658 Mpn228 Mpn210 Mpn434 Mpn573 Mpn324
Mpn207 Mpn329 Mpn515 Mpn314 Mpn050 Mpn191 Mpn020 Mpn452
Mpn329 Mpn252 Mpn621 Mpn004
Mpn317
FtsZ
Mpn062 Mpn390 Mpn516 Mpn430 Mpn315 Mpn665 Mpn261 Mpn258
Mpn141 Mpn228 Mpn210 Mpn434 Mpn322 Mpn573 Mpn066 Mpn515
Mpn032 Mpn317 Mpn426 Mpn546 Mpn191 Mpn020 Mpn621 Mpn004
Mpn062 Mpn118 Mpn555 Mpn516 Mpn430 Mpn003 Mpn665 Mpn361
Mpn685 Mpn258 Mpn210 Mpn434 Mpn071 Mpn573 Mpn008 Mpn032
Mpn515 Mpn317 Mpn426 Mpn273 Mpn020
EMBL120
EMBL121
EMBL122
Mpn317
FtsZ
EMBL123
Mpn483
Mpn210 Mpn434 Mpn573 Mpn430 Mpn665 Mpn515 Mpn483 Mpn609
Mpn483 Mpn050 Mpn258 Mpn141 Mpn004
EMBL124
Mpn483
Mpn210 Mpn497 Mpn434 Mpn306 Mpn390 Mpn430 Mpn665 Mpn515
Mpn483 Mpn032 Mpn027 Mpn483 Mpn452
EMBL125
Mpn158
RibF
Mpn292
Mpn210 Mpn434 Mpn573 Mpn390 Mpn516 Mpn003 Mpn665 Mpn515
Mpn426 Mpn292 Mpn094 Mpn547 Mpn034 Mpn106 Mpn221 Mpn305
Mpn292 Mpn678
EMBL126
Mpn158 Mpn390 Mpn295 Mpn665
General principles of cellular organization in Mycoplasma pneumoniae
106
Mpn273
Mpn210 Mpn434 Mpn390 Mpn261 Mpn207 Mpn515 Mpn273 Mpn050
Mpn273 Mpn040 Mpn658 Mpn452 Mpn153 Mpn621 Mpn004
EMBL128
Mpn526
Mpn340 Mpn516 Mpn003 Mpn141 Mpn228 Mpn210 Mpn434 Mpn592
Mpn573 Mpn116 Mpn324 Mpn257 Mpn674 Mpn346 Mpn515 Mpn347
Mpn526 Mpn254 Mpn526 Mpn232 Mpn004
EMBL129
Mpn387
Mpn387 Mpn434 Mpn390 Mpn387 Mpn293
EMBL130
Mpn221
Pth
Mpn434 Mpn226 Mpn340 Mpn430 Mpn665 Mpn649 Mpn034 Mpn658
Mpn221 Mpn228 Mpn004 Mpn621
Mpn390 Mpn516 Mpn430 Mpn574 Mpn228 Mpn434 Mpn226 Mpn063
Mpn280 Mpn207 Mpn032 Mpn515 Mpn239 Mpn191 Mpn020 Mpn452
Mpn621 Mpn004
EMBL127
EMBL131
Mpn541
RpsT
EMBL132
Mpn089
Mpn089 Mpn210 Mpn497 Mpn434 Mpn089 Mpn573 Mpn003 Mpn674 Mpn665
EMBL133
Mpn269
Mpn210 Mpn434 Mpn684 Mpn269 Mpn573 Mpn207 Mpn114 Mpn341
Mpn269 Mpn262 Mpn050 Mpn547 Mpn258 Mpn241 Mpn004 Mpn277
EMBL134
Mpn568
Era
EMBL135
Mpn307
Mpn210 Mpn434 Mpn063 Mpn516 Mpn430 Mpn207 Mpn515 Mpn346
Mpn307 Mpn472 Mpn040 Mpn621 Mpn004
EMBL136
Mpn307
Mpn307 Mpn027 Mpn434 Mpn034 Mpn665
Mpn210 Mpn434 Mpn573 Mpn568 Mpn390 Mpn665 Mpn640 Mpn663
Mpn034
General principles of cellular organization in Mycoplasma pneumoniae
107
EMBL137
Mpn628
GpmI
Mpn218 Mpn210 Mpn390 Mpn516 Mpn430 Mpn628 Mpn027 Mpn350
Mpn191 Mpn599 Mpn252
EMBL138
Mpn378
DnaE
Mpn434 Mpn353 Mpn573 Mpn118 Mpn003 Mpn665 Mpn551 Mpn108
Mpn378 Mpn034 Mpn141
EMBL139
Mpn533
AckA
Mpn210 Mpn533 Mpn434 Mpn516
EMBL140
Mpn321
FolA
Mpn210 Mpn434 Mpn573 Mpn390 Mpn555 Mpn516 Mpn430 Mpn457
Mpn207 Mpn321 Mpn050 Mpn034 Mpn252 Mpn621 Mpn004
EMBL141
Mpn361
PrfA
Mpn210 Mpn434 Mpn361 Mpn034 Mpn419 Mpn003
EMBL142
Mpn499
Mpn210 Mpn645 Mpn434 Mpn674 Mpn665 Mpn314 Mpn200 Mpn392
Mpn499 Mpn514 Mpn499 Mpn034 Mpn367
Mpn187
InfA
Mpn099 Mpn352 Mpn516 Mpn665 Mpn536 Mpn171 Mpn416 Mpn685
Mpn034 Mpn187 Mpn660 Mpn078 Mpn210 Mpn429 Mpn434 Mpn226
Mpn515 Mpn559 Mpn191 Mpn189 Mpn252 Mpn621 Mpn004
EMBL143
EMBL144
Mpn155
InfB
Mpn179 Mpn042 Mpn516 Mpn171 Mpn685 Mpn571 Mpn115 Mpn034
Mpn658 Mpn228 Mpn226 Mpn155 Mpn515 Mpn616 Mpn191 Mpn189
Mpn621 Mpn167 Mpn004
EMBL145
Mpn124
HrcA
Mpn210 Mpn434 Mpn573 Mpn390 Mpn124 Mpn516 Mpn515 Mpn452
Mpn621 Mpn004
EMBL146
Mpn229
Ssb
Mpn034 Mpn229 Mpn665
General principles of cellular organization in Mycoplasma pneumoniae
108
EMBL147
Mpn487
Csd
EMBL148
Mpn349
Mpn210 Mpn434 Mpn573 Mpn063 Mpn656 Mpn555 Mpn665 Mpn349
Mpn349 Mpn044 Mpn034
EMBL149
Mpn220
RplA
Mpn390 Mpn516 Mpn430 Mpn315 Mpn103 Mpn665 Mpn261 Mpn115
Mpn258 Mpn034 Mpn658 Mpn574 Mpn228 Mpn210 Mpn434 Mpn226
Mpn063 Mpn357 Mpn280 Mpn310 Mpn515 Mpn294 Mpn426 Mpn050
Mpn191 Mpn020 Mpn452 Mpn621 Mpn004
EMBL150
Mpn081
Mpn081 Mpn434 Mpn573 Mpn295 Mpn081 Mpn665 Mpn515 Mpn505
EMBL151
Mpn446
Mpn210 Mpn434 Mpn390 Mpn034 Mpn436 Mpn399
RpsD
Mpn390 Mpn118 Mpn295 Mpn261 Mpn456 Mpn258 Mpn228 Mpn210
Mpn434 Mpn524 Mpn487 Mpn294 Mpn426 Mpn222 Mpn050 Mpn020
Mpn252 Mpn621 Mpn004
Mpn353 Mpn142 Mpn118 Mpn555 Mpn516 Mpn003 Mpn665 Mpn551
Mpn378 Mpn034 Mpn258 Mpn141 Mpn434 Mpn083 Mpn686 Mpn040
Mpn582
EMBL152
Mpn353
DnaG
EMBL153
Mpn340
Mpn340 Mpn005 Mpn521 Mpn340 Mpn034 Mpn674 Mpn108
Mpn042
Mpn390 Mpn042 Mpn516 Mpn430 Mpn315 Mpn665 Mpn261 Mpn354
Mpn115 Mpn258 Mpn574 Mpn046 Mpn228 Mpn210 Mpn434 Mpn063
Mpn207 Mpn515 Mpn294 Mpn426 Mpn445 Mpn050 Mpn040 Mpn252
Mpn042 Mpn621 Mpn004
EMBL155
Mpn126
Mpn390 Mpn303 Mpn126 Mpn516 Mpn430 Mpn665 Mpn394 Mpn365
Mpn034 Mpn658 Mpn574 Mpn019 Mpn210 Mpn434 Mpn573 Mpn398
Mpn126 Mpn515 Mpn050 Mpn040 Mpn452 Mpn621 Mpn004
EMBL156
Mpn126
Mpn210 Mpn434 Mpn269 Mpn573 Mpn390 Mpn126 Mpn516 Mpn665
Mpn126 Mpn580 Mpn346 Mpn034
EMBL154
General principles of cellular organization in Mycoplasma pneumoniae
109
EMBL157
Mpn430
GapA
Mpn390 Mpn516 Mpn430 Mpn665 Mpn379 Mpn258 Mpn019 Mpn141
Mpn210 Mpn434 Mpn280 Mpn207 Mpn515 Mpn426 Mpn546 Mpn050
Mpn020 Mpn252 Mpn621 Mpn004
EMBL158
Mpn430
GapA
Mpn210 Mpn434 Mpn619 Mpn390 Mpn555 Mpn516 Mpn430 Mpn683
Mpn426 Mpn361 Mpn542 Mpn034 Mpn452 Mpn072
EMBL159
Mpn401
GreA
Mpn210 Mpn434 Mpn063 Mpn352 Mpn516 Mpn401 Mpn665 Mpn515
Mpn673 Mpn321 Mpn350 Mpn191 Mpn621 Mpn004
EMBL160
Mpn003
GyrB
Mpn210 Mpn434 Mpn486 Mpn516 Mpn003 Mpn020 Mpn004 Mpn621
EMBL161
Mpn003
GyrB
Mpn210 Mpn434 Mpn486 Mpn573 Mpn390 Mpn280 Mpn003 Mpn665
Mpn426 Mpn677 Mpn020 Mpn258 Mpn004
EMBL162
Mpn665
Tuf
Mpn434 Mpn137 Mpn658 Mpn665
EMBL163
Mpn177
RplE
Mpn623 Mpn434 Mpn573 Mpn665
EMBL164
Mpn033
Upp
Mpn210 Mpn133 Mpn434 Mpn155 Mpn295 Mpn665 Mpn346 Mpn635
Mpn016 Mpn072
Mpn390 Mpn516 Mpn430 Mpn315 Mpn295 Mpn665 Mpn261 Mpn456
Mpn034 Mpn133 Mpn210 Mpn434 Mpn155 Mpn515 Mpn346 Mpn426
Mpn635 Mpn050 Mpn191 Mpn020 Mpn016 Mpn621 Mpn004
EMBL165
Mpn033
Upp
EMBL166
Mpn297
Mpn297 Mpn297 Mpn210 Mpn434 Mpn042 Mpn034
General principles of cellular organization in Mycoplasma pneumoniae
110
EMBL167
Mpn606
Eno
Mpn210 Mpn612 Mpn434 Mpn390 Mpn118 Mpn516 Mpn003 Mpn606
Mpn629 Mpn316 Mpn452 Mpn569
EMBL168
Mpn235
Ung
Mpn210 Mpn434 Mpn390 Mpn014 Mpn674 Mpn515 Mpn222 Mpn235
Mpn034 Mpn678
EMBL169
Mpn494
UlaC
Mpn390 Mpn555 Mpn352 Mpn516 Mpn430 Mpn665 Mpn261 Mpn494
Mpn210 Mpn434 Mpn314 Mpn515 Mpn426 Mpn050 Mpn191 Mpn452
Mpn621 Mpn004
EMBL170
Mpn574
GroS
Mpn434 Mpn226 Mpn535 Mpn352 Mpn280 Mpn516 Mpn024 Mpn665
Mpn515 Mpn191 Mpn658 Mpn228 Mpn621
EMBL171
Mpn653
MtlF
Mpn210 Mpn434 Mpn042 Mpn516 Mpn295 Mpn665 Mpn551 Mpn653
EMBL172
Mpn544
Mpn544 Mpn210 Mpn544 Mpn434 Mpn361 Mpn390 Mpn295 Mpn003 Mpn665
EMBL173
Mpn539
RplL
Mpn480 Mpn516 Mpn430 Mpn003 Mpn665 Mpn551 Mpn261 Mpn065
Mpn658 Mpn210 Mpn434 Mpn643 Mpn207 Mpn515 Mpn426 Mpn073
Mpn191 Mpn020 Mpn621 Mpn004
EMBL174
Mpn066
ManB
Mpn434 Mpn118 Mpn066 Mpn042 Mpn295 Mpn674 Mpn564 Mpn394
Mpn048 Mpn365
EMBL175
Mpn280
Mpn430 Mpn103 Mpn665 Mpn261 Mpn562 Mpn278 Mpn228 Mpn434
Mpn280 Mpn573 Mpn280 Mpn239 Mpn549 Mpn191 Mpn686 Mpn345 Mpn621
EMBL176
Mpn492
UlaE
Mpn210 Mpn434 Mpn573 Mpn390 Mpn283 Mpn665 Mpn436 Mpn492
Mpn034 Mpn277
General principles of cellular organization in Mycoplasma pneumoniae
111
EMBL177
Mpn602
AtpF
Mpn665 Mpn261 Mpn600 Mpn258 Mpn072 Mpn210 Mpn434 Mpn207
Mpn515 Mpn598 Mpn426 Mpn020 Mpn452 Mpn153 Mpn004 Mpn621
EMBL178
Mpn073
Prs
Mpn210 Mpn434 Mpn573 Mpn404 Mpn674 Mpn515 Mpn073 Mpn034
Mpn004
EMBL179
Mpn050
GlpK
Mpn210 Mpn434 Mpn322 Mpn324 Mpn516 Mpn419 Mpn295 Mpn665
Mpn261 Mpn050 Mpn266
Mpn050
GlpK
Mpn062 Mpn269 Mpn390 Mpn555 Mpn516 Mpn430 Mpn665 Mpn141
Mpn210 Mpn434 Mpn032 Mpn515 Mpn426 Mpn483 Mpn050 Mpn020
Mpn452 Mpn079
EMBL181
Mpn107
Mpn390 Mpn555 Mpn516 Mpn665 Mpn261 Mpn379 Mpn258 Mpn556
Mpn210 Mpn434 Mpn573 Mpn207 Mpn032 Mpn515 Mpn426 Mpn444
Mpn107 Mpn107 Mpn050 Mpn608 Mpn020 Mpn452 Mpn621 Mpn004
EMBL182
Mpn107
Mpn434 Mpn573 Mpn118 Mpn555 Mpn003 Mpn665 Mpn032 Mpn426
Mpn107 Mpn107 Mpn141
EMBL183
Mpn222
TilS
Mpn623 Mpn434 Mpn222 Mpn516 Mpn430 Mpn665 Mpn621 Mpn515
Mpn004
EMBL180
EMBL184
Mpn323
NrdI
Mpn407 Mpn390 Mpn118 Mpn516 Mpn430 Mpn261 Mpn034 Mpn072
Mpn210 Mpn322 Mpn434 Mpn573 Mpn515 Mpn323 Mpn050 Mpn452
Mpn621 Mpn004
EMBL185
Mpn395
Apt
Mpn434 Mpn514 Mpn388 Mpn042 Mpn001 Mpn395 Mpn367 Mpn295
Mpn195
EMBL186
Mpn652
MtlD
Mpn210 Mpn434 Mpn573 Mpn516 Mpn515 Mpn032 Mpn426 Mpn191
Mpn652 Mpn228 Mpn004
General principles of cellular organization in Mycoplasma pneumoniae
112
Mpn383
Mpn210 Mpn434 Mpn656 Mpn674 Mpn665 Mpn314 Mpn533 Mpn034
Mpn383 Mpn383
EMBL188
Mpn167
RplW
Mpn390 Mpn516 Mpn665 Mpn261 Mpn428 Mpn115 Mpn034 Mpn658
Mpn574 Mpn228 Mpn399 Mpn165 Mpn210 Mpn434 Mpn226 Mpn063
Mpn515 Mpn426 Mpn191 Mpn020 Mpn621 Mpn167 Mpn004
EMBL189
Mpn105
PheS
Mpn210 Mpn105 Mpn434 Mpn322 Mpn062 Mpn573 Mpn568 Mpn516
Mpn665 Mpn515 Mpn472 Mpn426 Mpn247 Mpn020 Mpn106 Mpn141
EMBL190
Mpn105
PheS
Mpn105 Mpn434 Mpn573 Mpn555 Mpn516 Mpn106 Mpn329 Mpn141
Mpn515
EMBL191
Mpn504
Mpn504 Mpn434 Mpn555 Mpn331 Mpn295 Mpn674 Mpn665
EMBL192
Mpn180
RplF
EMBL193
Mpn555
Mpn390 Mpn555 Mpn516 Mpn665 Mpn261 Mpn141 Mpn210 Mpn434
Mpn555 Mpn324 Mpn515 Mpn426 Mpn020 Mpn452 Mpn153 Mpn652 Mpn004
EMBL194
Mpn555
Mpn555 Mpn210 Mpn434 Mpn555 Mpn324 Mpn665 Mpn261 Mpn072
EMBL195
Mpn531
ClpB
Mpn434 Mpn686 Mpn531 Mpn280 Mpn258 Mpn516 Mpn621
ClpB
Mpn531 Mpn352 Mpn516 Mpn665 Mpn182 Mpn171 Mpn571 Mpn228
Mpn434 Mpn226 Mpn515 Mpn616 Mpn640 Mpn673 Mpn239 Mpn191
Mpn020 Mpn189
EMBL187
EMBL196
Mpn531
Mpn434 Mpn180 Mpn658
General principles of cellular organization in Mycoplasma pneumoniae
113
EMBL197
Mpn283
Mpn470 Mpn352 Mpn283 Mpn516 Mpn430 Mpn315 Mpn665 Mpn394
Mpn261 Mpn354 Mpn258 Mpn556 Mpn210 Mpn434 Mpn007 Mpn380
Mpn283 Mpn515 Mpn050 Mpn191 Mpn020 Mpn621 Mpn004
EMBL198
Mpn283
Mpn283 Mpn210 Mpn434 Mpn118 Mpn643 Mpn283 Mpn216 Mpn003 Mpn665
EMBL199
Mpn517
Mpn517 Mpn434 Mpn226 Mpn517
EMBL200
Mpn551
Mpn210 Mpn434 Mpn573 Mpn295 Mpn003 Mpn551 Mpn683 Mpn059
Mpn551 Mpn034 Mpn452
EMBL201
Mpn562
NadE
EMBL202
Mpn247
Mpn210 Mpn434 Mpn429 Mpn619 Mpn390 Mpn665 Mpn426 Mpn247
Mpn247 Mpn094 Mpn461 Mpn004
EMBL203
Mpn169
RpsS
Mpn269 Mpn390 Mpn516 Mpn430 Mpn665 Mpn261 Mpn171 Mpn363
Mpn341 Mpn571 Mpn115 Mpn228 Mpn210 Mpn434 Mpn226 Mpn280
Mpn515 Mpn426 Mpn191 Mpn020 Mpn452 Mpn621 Mpn004
EMBL204
Mpn658
RplS
Mpn573 Mpn571 Mpn034 Mpn665 Mpn536
RplS
Mpn568 Mpn516 Mpn034 Mpn658 Mpn574 Mpn228 Mpn078 Mpn165
Mpn210 Mpn434 Mpn226 Mpn515 Mpn292 Mpn222 Mpn020 Mpn547
Mpn252 Mpn189 Mpn004
Pip
Mpn062 Mpn619 Mpn303 Mpn516 Mpn430 Mpn665 Mpn261 Mpn321
Mpn393 Mpn023 Mpn365 Mpn034 Mpn022 Mpn141 Mpn210 Mpn322
Mpn573 Mpn388 Mpn324 Mpn310 Mpn598 Mpn515 Mpn472 Mpn426
Mpn050 Mpn191 Mpn452 Mpn106 Mpn621 Mpn004
EMBL205
EMBL206
Mpn658
Mpn022
Mpn426 Mpn210 Mpn562 Mpn434 Mpn573 Mpn516 Mpn515 Mpn097
General principles of cellular organization in Mycoplasma pneumoniae
114
EMBL207
Mpn556
ArgS
Mpn556 Mpn361 Mpn073 Mpn665
EMBL208
Mpn265
TrpS
Mpn300 Mpn390 Mpn555 Mpn516 Mpn430 Mpn665 Mpn320 Mpn210
Mpn265 Mpn322 Mpn434 Mpn573 Mpn207 Mpn644 Mpn515 Mpn191
Mpn020 Mpn452 Mpn621 Mpn004
EMBL209
Mpn265
TrpS
Mpn265 Mpn434 Mpn573 Mpn118 Mpn003 Mpn665
EMBL210
Mpn063
DeoC
Mpn210 Mpn434 Mpn063 Mpn047 Mpn555 Mpn516 Mpn430 Mpn665
Mpn515 Mpn426 Mpn392 Mpn191 Mpn658 Mpn621 Mpn004
EMBL211
Mpn656
Mpn516 Mpn665 Mpn536 Mpn034 Mpn658 Mpn210 Mpn434 Mpn573
Mpn674 Mpn515 Mpn426 Mpn392 Mpn050 Mpn663 Mpn452 Mpn243
Mpn656 Mpn004 Mpn621
EMBL212
Mpn557
GidA
Mpn210 Mpn434 Mpn573 Mpn390 Mpn155 Mpn118 Mpn557 Mpn042
Mpn516 Mpn295 Mpn003 Mpn665 Mpn515 Mpn621
EMBL213
Mpn219
RplK
Mpn555 Mpn516 Mpn430 Mpn665 Mpn394 Mpn261 Mpn606 Mpn533
Mpn574 Mpn141 Mpn228 Mpn078 Mpn556 Mpn210 Mpn389 Mpn289
Mpn434 Mpn573 Mpn324 Mpn674 Mpn668 Mpn314 Mpn426 Mpn020
Mpn479 Mpn621 Mpn004
EMBL214
Mpn598
AtpD
Mpn602 Mpn516 Mpn598
EMBL215
Mpn032
Mpn556 Mpn434 Mpn573 Mpn555 Mpn516 Mpn665 Mpn515 Mpn032
Mpn032 Mpn191 Mpn574 Mpn621
EMBL216
Mpn314
MraZ
Mpn210 Mpn434 Mpn390 Mpn516 Mpn430 Mpn339 Mpn314 Mpn032
Mpn521 Mpn034 Mpn040 Mpn633 Mpn621 Mpn004
General principles of cellular organization in Mycoplasma pneumoniae
115
EMBL217
Mpn109
Mpn596 Mpn390 Mpn516 Mpn430 Mpn665 Mpn261 Mpn309 Mpn169
Mpn115 Mpn658 Mpn574 Mpn210 Mpn434 Mpn550 Mpn578 Mpn032
Mpn314 Mpn515 Mpn426 Mpn444 Mpn635 Mpn109 Mpn073 Mpn050
Mpn109 Mpn191 Mpn020 Mpn621 Mpn004
EMBL218
Mpn109
Mpn109 Mpn210 Mpn434 Mpn118 Mpn109 Mpn034 Mpn516
EMBL219
Mpn360
RpmE
Mpn390 Mpn531 Mpn516 Mpn430 Mpn401 Mpn307 Mpn261 Mpn177
Mpn297 Mpn365 Mpn658 Mpn228 Mpn669 Mpn210 Mpn434 Mpn590
Mpn226 Mpn063 Mpn280 Mpn207 Mpn329 Mpn515 Mpn426 Mpn050
Mpn020 Mpn452 Mpn252 Mpn621
EMBL220
Mpn332
Lon
Mpn269 Mpn390 Mpn555 Mpn516 Mpn443 Mpn430 Mpn665 Mpn606
Mpn210 Mpn434 Mpn207 Mpn515 Mpn040 Mpn452 Mpn332 Mpn004
Mpn621
EMBL221
Mpn332
Lon
Mpn210 Mpn434 Mpn390 Mpn034 Mpn665
EMBL222
Mpn560
Mpn560 Mpn560 Mpn434 Mpn573 Mpn555
Mpn480 Mpn118 Mpn516 Mpn295 Mpn003 Mpn665 Mpn551 Mpn034
Mpn228 Mpn210 Mpn434 Mpn226 Mpn573 Mpn032 Mpn515 Mpn454
Mpn004
EMBL223
Mpn480
ValS
EMBL224
Mpn342
Mpn210 Mpn089 Mpn507 Mpn390 Mpn342 Mpn295 Mpn003 Mpn551
Mpn342 Mpn361 Mpn034
EMBL225
Mpn182
RpsE
Mpn516 Mpn295 Mpn182 Mpn171 Mpn518 Mpn571 Mpn441 Mpn228
Mpn210 Mpn434 Mpn226 Mpn573 Mpn032 Mpn515 Mpn547 Mpn191
Mpn020 Mpn189 Mpn252 Mpn621 Mpn004
EMBL226
Mpn662
MsrB
Mpn434 Mpn555 Mpn537 Mpn516 Mpn665 Mpn662
General principles of cellular organization in Mycoplasma pneumoniae
116
EMBL227
Mpn540
RpmF
Mpn390 Mpn470 Mpn051 Mpn516 Mpn430 Mpn315 Mpn665 Mpn261
Mpn571 Mpn115 Mpn658 Mpn228 Mpn210 Mpn434 Mpn226 Mpn535
Mpn515 Mpn032 Mpn294 Mpn426 Mpn191 Mpn020 Mpn621 Mpn004
EMBL228
Mpn391
PdhC
Mpn391
EMBL229
Mpn060
MetK
Mpn048 Mpn434 Mpn060 Mpn034
EMBL230
Mpn508
Mpn508 Mpn426 Mpn210 Mpn434 Mpn034 Mpn516 Mpn452 Mpn430 Mpn665
EMBL231
Mpn034
PolC
Mpn336 Mpn210 Mpn434 Mpn390 Mpn324 Mpn034 Mpn516 Mpn261
Mpn207 Mpn004
EMBL232
Mpn034
PolC
Mpn210 Mpn612 Mpn434 Mpn573 Mpn280 Mpn516 Mpn008 Mpn145
Mpn620 Mpn677 Mpn514 Mpn526 Mpn034 Mpn088 Mpn621
PolC
Mpn218 Mpn269 Mpn352 Mpn516 Mpn609 Mpn258 Mpn228 Mpn141
Mpn553 Mpn598 Mpn515 Mpn358 Mpn238 Mpn250 Mpn392 Mpn611
Mpn452 Mpn572 Mpn153 Mpn004 Mpn671 Mpn303 Mpn470 Mpn197
Mpn295 Mpn315 Mpn430 Mpn261 Mpn665 Mpn393 Mpn034 Mpn210
Mpn372 Mpn434 Mpn207
EMBL233
Mpn034
EMBL234
Mpn034
PolC
Mpn645 Mpn390 Mpn516 Mpn430 Mpn665 Mpn261 Mpn034 Mpn258
Mpn210 Mpn434 Mpn573 Mpn280 Mpn207 Mpn515 Mpn426 Mpn546
Mpn050 Mpn490 Mpn191 Mpn020 Mpn621 Mpn004
EMBL235
Mpn331
Tig
Mpn210 Mpn165 Mpn434 Mpn209 Mpn516 Mpn003 Mpn665 Mpn158
Mpn331 Mpn452 Mpn228 Mpn004
EMBL236
Mpn302
PfkA
Mpn210 Mpn434 Mpn034 Mpn302 Mpn665 Mpn644 Mpn097
General principles of cellular organization in Mycoplasma pneumoniae
117
EMBL237
Mpn263
TrxA
Mpn321 Mpn034 Mpn452 Mpn263 Mpn314
EMBL238
Mpn188
RpmJ
Mpn434 Mpn390 Mpn665
EMBL239
Mpn072
Mpn210 Mpn434 Mpn042 Mpn516 Mpn295 Mpn177 Mpn515 Mpn059
Mpn072 Mpn191 Mpn599 Mpn004 Mpn072
Mpn226
RpsG
Mpn390 Mpn555 Mpn516 Mpn430 Mpn003 Mpn665 Mpn428 Mpn034
Mpn658 Mpn228 Mpn210 Mpn434 Mpn226 Mpn324 Mpn294 Mpn314
Mpn452 Mpn621 Mpn004
EMBL241
Mpn110
Mpn062 Mpn390 Mpn555 Mpn516 Mpn430 Mpn419 Mpn315 Mpn665
Mpn261 Mpn297 Mpn169 Mpn115 Mpn034 Mpn574 Mpn660 Mpn210
Mpn434 Mpn226 Mpn524 Mpn110 Mpn280 Mpn515 Mpn426 Mpn239
Mpn110 Mpn050 Mpn191 Mpn020 Mpn452 Mpn252 Mpn621 Mpn004
EMBL242
Mpn267
PpnK
Mpn210 Mpn434 Mpn573 Mpn280 Mpn264 Mpn516 Mpn267 Mpn515
Mpn050 Mpn621
EMBL243
Mpn674
Ldh
Mpn210 Mpn434 Mpn516 Mpn674 Mpn621
EMBL244
Mpn380
MutM
Mpn434 Mpn555 Mpn295 Mpn665 Mpn380
EMBL240
EMBL245
Mpn008
TrmE
Mpn390 Mpn516 Mpn430 Mpn665 Mpn261 Mpn258 Mpn228 Mpn210
Mpn322 Mpn434 Mpn553 Mpn573 Mpn008 Mpn515 Mpn317 Mpn050
Mpn191 Mpn547
EMBL246
Mpn008
TrmE
Mpn210 Mpn434 Mpn573 Mpn516 Mpn665 Mpn261 Mpn008 Mpn050
General principles of cellular organization in Mycoplasma pneumoniae
118
Mpn434 Mpn226 Mpn390 Mpn430 Mpn295 Mpn665 Mpn174 Mpn386
Mpn020 Mpn191 Mpn228
EMBL247
Mpn174
RpsQ
EMBL248
Mpn362
Mpn362 Mpn434 Mpn573 Mpn555 Mpn516 Mpn665 Mpn108 Mpn362
EMBL249
Mpn121
Mpn210 Mpn434 Mpn366 Mpn390 Mpn135 Mpn430 Mpn346 Mpn121
Mpn121 Mpn050 Mpn034
EMBL250
Mpn377
Mpn377 Mpn377 Mpn434 Mpn014 Mpn034
EMBL251
Mpn490
RecA
Mpn210 Mpn434 Mpn402 Mpn490 Mpn034 Mpn252 Mpn079 Mpn621
EMBL252
Mpn490
RecA
Mpn284 Mpn210 Mpn480 Mpn434 Mpn573 Mpn003 Mpn490 Mpn034
Mpn452
EMBL253
Mpn420
Mpn210 Mpn434 Mpn573 Mpn555 Mpn516 Mpn419 Mpn394 Mpn668
Mpn420 Mpn515 Mpn314 Mpn420 Mpn034
EMBL254
Mpn232
DnaB
Mpn210 Mpn434 Mpn390 Mpn665 Mpn415 Mpn207 Mpn232 Mpn258
Mpn141 Mpn241
EMBL255
Mpn232
DnaB
Mpn298 Mpn210 Mpn390 Mpn118 Mpn295 Mpn108 Mpn521 Mpn526
Mpn232 Mpn034 Mpn452
EMBL256
Mpn311
Mpn210 Mpn434 Mpn204 Mpn095 Mpn390 Mpn324 Mpn280 Mpn516
Mpn311 Mpn430 Mpn665 Mpn261 Mpn621 Mpn004
General principles of cellular organization in Mycoplasma pneumoniae
119
EMBL257
Mpn176
RplX
Mpn210 Mpn434 Mpn665 Mpn615 Mpn220 Mpn685 Mpn034 Mpn658
Mpn189 Mpn091 Mpn228 Mpn004 Mpn097
EMBL258
Mpn189
RpsM
Mpn434 Mpn629 Mpn034 Mpn228
Mpn316
Mpn390 Mpn555 Mpn516 Mpn430 Mpn665 Mpn261 Mpn440 Mpn258
Mpn141 Mpn556 Mpn210 Mpn553 Mpn434 Mpn573 Mpn192 Mpn636
Mpn329 Mpn515 Mpn546 Mpn549 Mpn050 Mpn191 Mpn252 Mpn316
Mpn316 Mpn452 Mpn621
EMBL259
ii) Proteins identified in the
PeptideAtlas by FT-MS/MS
Systematic name
Protein name
Mpn001
DnaN
Mpn002
Mpn002
Mpn003
GyrB
Mpn004
GyrA
Mpn005
SerS
Mpn006
Tmk
Mpn007
Mpn007
Mpn008
TrmE
Mpn009
Mpn009
Mpn011
Mpn011
Mpn012
Mpn012
Mpn013
Mpn013
Mpn015
Mpn015
Mpn016
Mpn016
Mpn017
FolD
Mpn018
Mpn018
Mpn019
Mpn019
Mpn020
Mpn020
Mpn021
DnaJ
Mpn022
Pip
Mpn023
MetG
Mpn024
RpoE
Mpn025
Fba
Mpn026
Mpn026
Mpn027
Mpn027
Mpn029
Efp
Mpn030
Mpn030
Mpn031
Mpn031
Mpn033
Upp
Mpn034
PolC
Mpn035
Mpn035
General principles of cellular organization in Mycoplasma pneumoniae
120
Mpn036
Mpn043
Mpn044
Mpn045
Mpn046
Mpn047
Mpn050
Mpn051
Mpn052
Mpn053
Mpn055
Mpn058
Mpn059
Mpn060
Mpn061
Mpn062
Mpn063
Mpn064
Mpn065
Mpn066
Mpn067
Mpn068
Mpn070
Mpn071
Mpn072
Mpn073
Mpn075
Mpn076
Mpn077
Mpn078
Mpn079
Mpn080
Mpn081
Mpn082
Mpn083
Mpn084
Mpn090
Mpn099
Mpn105
Mpn106
Mpn109
Mpn115
Mpn116
Mpn117
Mpn118
Mpn119
Mpn120
Mpn121
Mpn122
Mpn123
Mpn036
GlpF
Tdk
HisS
AspS
Mpn047
GlpK
Mpn051
Mpn052
PtsH
PotA
Mpn058
Gcp
MetK
Ffh
DeoD
DeoC
DeoA
Cdd
ManB
Mpn067
Mpn068
Mpn070
Mpn071
Mpn072
Prs
Mpn075
Mpn076
Mpn077
FruA
FruK
Mpn080
Mpn081
Tkt
Mpn083
Mpn084
Mpn090
Mpn099
PheS
PheT
Mpn109
InfC
RpmI
RplT
Mpn118
Mpn119
GrpE
Mpn121
ParE
ParC
General principles of cellular organization in Mycoplasma pneumoniae
121
Mpn124
Mpn125
Mpn126
Mpn131
Mpn132
Mpn133
Mpn134
Mpn135
Mpn136
Mpn140
Mpn141
Mpn142
Mpn144
Mpn149
Mpn152
Mpn153
Mpn154
Mpn155
Mpn156
Mpn157
Mpn158
Mpn159
Mpn160
Mpn161
Mpn162
Mpn163
Mpn164
Mpn165
Mpn166
Mpn167
Mpn168
Mpn169
Mpn170
Mpn171
Mpn172
Mpn173
Mpn174
Mpn175
Mpn176
Mpn177
Mpn178
Mpn179
Mpn180
Mpn181
Mpn182
Mpn183
Mpn184
Mpn185
Mpn186
Mpn187
HrcA
UvrC
Mpn126
Mpn131
Mpn132
Mpn133
Mpn134
Mpn135
Mpn136
Mpn140
MgpA
Mpn142
Mpn144
Mpn149
Mpn152
Mpn153
NusA
InfB
RbfA
Mpn157
RibF
Mpn159
Mpn160
Mpn161
Mpn162
Mpn163
RpsJ
RplC
RplD
RplW
RplB
RpsS
RplV
RpsC
RplP
RpmC
RpsQ
RplN
RplX
RplE
RpsZ
RpsH
RplF
RplR
RpsE
RplO
SecY
Adk
Map
InfA
General principles of cellular organization in Mycoplasma pneumoniae
122
Mpn188
Mpn189
Mpn190
Mpn191
Mpn192
Mpn193
Mpn194
Mpn195
Mpn196
Mpn197
Mpn199
Mpn200
Mpn202
Mpn205
Mpn207
Mpn208
Mpn209
Mpn210
Mpn211
Mpn213
Mpn214
Mpn215
Mpn216
Mpn217
Mpn218
Mpn219
Mpn220
Mpn221
Mpn222
Mpn223
Mpn224
Mpn225
Mpn226
Mpn227
Mpn228
Mpn229
Mpn230
Mpn231
Mpn232
Mpn233
Mpn235
Mpn236
Mpn237
Mpn238
Mpn239
Mpn240
Mpn241
Mpn243
Mpn244
Mpn245
RpmJ
RpsM
RpsK
RpoA
RplQ
CbiO1
CbiO2
Mpn195
TruA
PepF
Mpn199
Mpn200
Mpn202
Mpn205
PtsG
RpsB
PacL
SecA
UvrB
Mpn213
Mpn214
OppB
OppC
OppD
OppF
RplK
RplA
Pth
TilS
HprK
Lgt
RpsL
RpsG
FusA
RpsF
Ssb
RpsR
RplI
DnaB
Mpn233
Ung
Mpn236
GatA
GatB
Mpn239
TrxB
Mpn241
RnR
Mpn244
Gmk
General principles of cellular organization in Mycoplasma pneumoniae
123
Mpn246
Mpn247
Mpn248
Mpn250
Mpn251
Mpn252
Mpn255
Mpn256
Mpn257
Mpn258
Mpn259
Mpn260
Mpn261
Mpn262
Mpn263
Mpn264
Mpn265
Mpn266
Mpn267
Mpn268
Mpn269
Mpn271
Mpn273
Mpn275
Mpn276
Mpn277
Mpn278
Mpn279
Mpn280
Mpn284
Mpn286
Mpn288
Mpn291
Mpn292
Mpn293
Mpn294
Mpn295
Mpn296
Mpn297
Mpn298
Mpn299
Mpn300
Mpn301
Mpn302
Mpn303
Mpn307
Mpn308
Mpn309
Mpn310
Mpn311
Def
Mpn247
Mpn248
Pgi
Rpe
AsnS
Mpn255
Mpn256
GalE
Mpn258
Mpn259
Mpn260
TopA
Mpn262
TrxA
Mpn264
TrpS
Mpn266
PpnK
Mpn268
Mpn269
Mpn271
Mpn273
Mpn275
Mpn276
LysS
Glf
LepA
Mpn280
Mpn284
Mpn286
Mpn288
Mpn291
Mpn292
LspA
Mpn294
Mpn295
RpsU
Mpn297
AcpS
PlsC
ScpA
ScpB
PfkA
Pyk
Mpn307
Mpn308
P65
Hmw2
Mpn311
General principles of cellular organization in Mycoplasma pneumoniae
124
Mpn312
Mpn314
Mpn315
Mpn316
Mpn317
Mpn318
Mpn319
Mpn320
Mpn321
Mpn322
Mpn323
Mpn324
Mpn325
Mpn326
Mpn327
Mpn328
Mpn329
Mpn330
Mpn331
Mpn332
Mpn336
Mpn337
Mpn338
Mpn339
Mpn340
Mpn342
Mpn343
Mpn346
Mpn349
Mpn352
Mpn353
Mpn354
Mpn355
Mpn356
Mpn357
Mpn358
Mpn359
Mpn360
Mpn361
Mpn362
Mpn366
Mpn370
Mpn372
Mpn376
Mpn378
Mpn379
Mpn380
Mpn381
Mpn383
Mpn384
Mpn312
MraZ
MraW
Mpn316
FtsZ
Mpn318
Mpn319
ThyA
FolA
NrdF
NrdI
NrdE
RplU
Mpn326
RpmA
Nfo
Mpn329
Mpn330
Tig
Lon
Mpn336
Mpn337
Mpn338
Mpn339
Mpn340
Mpn342
Mpn343
Mpn346
Mpn349
RpoD
DnaG
GlyQS
Mpn355
CysS
LigA
Mpn358
Mpn359
RpmE
PrfA
Mpn362
Mpn366
Mpn370
Mpn372
Mpn376
DnaE
PolA
MutM
Mpn381
Mpn383
LeuS
General principles of cellular organization in Mycoplasma pneumoniae
125
Mpn386
Mpn387
Mpn389
Mpn390
Mpn391
Mpn392
Mpn393
Mpn394
Mpn395
Mpn396
Mpn397
Mpn398
Mpn399
Mpn400
Mpn401
Mpn402
Mpn406
Mpn407
Mpn408
Mpn409
Mpn415
Mpn419
Mpn420
Mpn421
Mpn422
Mpn423
Mpn425
Mpn426
Mpn427
Mpn428
Mpn429
Mpn430
Mpn432
Mpn434
Mpn436
Mpn438
Mpn443
Mpn444
Mpn445
Mpn446
Mpn447
Mpn449
Mpn452
Mpn453
Mpn454
Mpn456
Mpn459
Mpn460
Mpn461
Mpn469
Mpn386
Mpn387
LplA
PdhD
PdhC
PdhB
PdhA
Nox
Apt
Mpn396
SpoT
Mpn398
Mpn399
Mpn400
GreA
ProS
Mpn406
Mpn407
Mpn408
Mpn409
P37
AlaS
Mpn420
Mpn421
TrmU
Mpn423
FtsY
P115
Mpn427
Pta
Pgk
GapA
Mpn432
DnaK
Mpn436
Mpn438
Mpn443
Mpn444
Mpn445
RpsD
Hmw1
Mpn449
Hmw3
P30
Mpn454
Mpn456
Mpn459
Mpn460
Mpn461
Mpn469
General principles of cellular organization in Mycoplasma pneumoniae
126
Mpn470
Mpn471
Mpn472
Mpn473
Mpn474
Mpn475
Mpn476
Mpn477
Mpn478
Mpn479
Mpn480
Mpn481
Mpn483
Mpn487
Mpn488
Mpn489
Mpn490
Mpn491
Mpn492
Mpn493
Mpn494
Mpn496
Mpn497
Mpn499
Mpn500
Mpn505
Mpn506
Mpn509
Mpn512
Mpn514
Mpn515
Mpn516
Mpn517
Mpn518
Mpn519
Mpn520
Mpn521
Mpn522
Mpn523
Mpn524
Mpn525
Mpn526
Mpn528
Mpn529
Mpn530
Mpn531
Mpn532
Mpn533
Mpn538
Mpn539
PepP
RpmG1
Mpn472
Mpn473
Mpn474
EngA
Cmk
Mpn477
Mpn478
AzoR
ValS
EngB
Mpn483
Csd
Mpn488
Mpn489
RecA
Mpn491
UlaE
UlaD
UlaC
UlaA
Mpn497
Mpn499
Mpn500
Mpn505
Mpn506
Mpn509
Mpn512
Mpn514
RpoC
RpoB
Mpn517
Mpn518
Mpn519
IleS
Mpn521
TrmB
Mpn523
Mpn524
Mpn525
Mpn526
Ppa
Mpn529
Mpn530
ClpB
Mpn532
AckA
RplJ
RplL
General principles of cellular organization in Mycoplasma pneumoniae
127
Mpn540
Mpn541
Mpn542
Mpn543
Mpn544
Mpn545
Mpn546
Mpn547
Mpn548
Mpn549
Mpn550
Mpn551
Mpn552
Mpn553
Mpn554
Mpn555
Mpn556
Mpn557
Mpn558
Mpn560
Mpn561
Mpn562
Mpn563
Mpn564
Mpn566
Mpn567
Mpn568
Mpn572
Mpn573
Mpn574
Mpn576
Mpn578
Mpn591
Mpn592
Mpn593
Mpn595
Mpn597
Mpn598
Mpn599
Mpn600
Mpn601
Mpn602
Mpn603
Mpn604
Mpn606
Mpn607
Mpn608
Mpn609
Mpn610
Mpn611
RpmF
RpsT
Mpn542
Fmt
Mpn544
Rnc
PlsX
Mpn547
Mpn548
Mpn549
ThiI
Mpn551
Mpn552
ThrS
Mpn554
Mpn555
ArgS
GidA
GidB
Mpn560
Udk
NadE
Mpn563
Adh
Mpn566
P200
Era
PepA
GroL
GroS
GlyA
Mpn578
Mpn591
Mpn592
Mpn593
RpiB
AtpC
AtpD
AtpG
AtpA
AtpH
AtpF
AtpE
AtpB
Eno
MsrA
Mpn608
PstB
PstA
Mpn611
General principles of cellular organization in Mycoplasma pneumoniae
128
Mpn612
Mpn616
Mpn617
Mpn618
Mpn619
Mpn620
Mpn621
Mpn622
Mpn623
Mpn624
Mpn625
Mpn627
Mpn628
Mpn629
Mpn630
Mpn631
Mpn632
Mpn636
Mpn638
Mpn639
Mpn641
Mpn642
Mpn643
Mpn652
Mpn653
Mpn655
Mpn658
Mpn659
Mpn660
Mpn661
Mpn662
Mpn663
Mpn664
Mpn665
Mpn666
Mpn667
Mpn668
Mpn669
Mpn670
Mpn671
Mpn672
Mpn673
Mpn674
Mpn677
Mpn678
Mpn679
Mpn680
Mpn682
Mpn683
Mpn684
Mpn612
RpsI
RplM
DnaX
UvrA
Mpn620
Mpn621
RpsO
Mpn623
RpmB
Mpn625
PtsI
GpmI
TpiA
Mpn630
Tsf
PyrH
Frr
Mpn638
Mpn639
Mpn641
Mpn642
Mpn643
MtlD
MtlF
Mpn655
RplS
TrmD
RpsP
Mpn661
MsrB
Mpn663
Mpn664
Tuf
Mpn666
GalU
Mpn668
TyrS
Mpn670
FtsH
Hpt
Mpn673
Ldh
Mpn677
GltX
KsgA
OxaA
RpmH
Mpn683
Mpn684
General principles of cellular organization in Mycoplasma pneumoniae
129
Mpn685
Mpn686
Mpn687
Mpn688
Mpn685
DnaA
Mpn687
Mpn688
General principles of cellular organization in Mycoplasma pneumoniae
130
10.2. Table S2: List of high confidence interactions and corresponding socio-affinity
scores.
In total 2,116 redundant high confidence interactions, i.e. 1,058 non-redundant interactions,
are reported in this list. The first two columns give the proteins involved in these interactions.
The third column provides the socio-affinity score attributed to this interaction.
Protein 1
Mpn230
Mpn230
Mpn230
Mpn230
Mpn230
Mpn516
Mpn516
Mpn322
Mpn573
Mpn178
Mpn178
Mpn178
Mpn178
Mpn178
Mpn178
Mpn023
Mpn122
Mpn122
Mpn392
Mpn106
Mpn106
Mpn171
Mpn171
Mpn171
Mpn171
Mpn171
Mpn622
Mpn622
Mpn622
Mpn622
Mpn622
Mpn622
Mpn622
Mpn622
Mpn622
Mpn207
Mpn089
Mpn378
Mpn515
Mpn515
Protein 2
Mpn178
Mpn228
Mpn660
Mpn179
Mpn616
Mpn515
Mpn191
Mpn324
Mpn574
Mpn230
Mpn171
Mpn446
Mpn182
Mpn179
Mpn169
Mpn106
Mpn004
Mpn123
Mpn393
Mpn023
Mpn105
Mpn178
Mpn182
Mpn189
Mpn169
Mpn226
Mpn446
Mpn182
Mpn228
Mpn660
Mpn208
Mpn179
Mpn169
Mpn616
Mpn226
Mpn268
Mpn342
Mpn353
Mpn516
Mpn191
Socio-affinity score x1000
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
General principles of cellular organization in Mycoplasma pneumoniae
131
Mpn611
Mpn446
Mpn446
Mpn446
Mpn446
Mpn446
Mpn446
Mpn446
Mpn446
Mpn446
Mpn003
Mpn602
Mpn602
Mpn167
Mpn167
Mpn166
Mpn166
Mpn598
Mpn598
Mpn182
Mpn182
Mpn182
Mpn182
Mpn182
Mpn182
Mpn182
Mpn182
Mpn182
Mpn182
Mpn189
Mpn189
Mpn189
Mpn189
Mpn189
Mpn189
Mpn189
Mpn352
Mpn600
Mpn600
Mpn609
Mpn228
Mpn228
Mpn228
Mpn228
Mpn228
Mpn228
Mpn004
Mpn004
Mpn393
Mpn172
Mpn609
Mpn178
Mpn622
Mpn182
Mpn189
Mpn228
Mpn179
Mpn169
Mpn616
Mpn226
Mpn004
Mpn598
Mpn600
Mpn165
Mpn179
Mpn172
Mpn165
Mpn602
Mpn600
Mpn178
Mpn171
Mpn622
Mpn446
Mpn189
Mpn228
Mpn179
Mpn169
Mpn616
Mpn226
Mpn171
Mpn446
Mpn182
Mpn179
Mpn169
Mpn616
Mpn226
Mpn191
Mpn602
Mpn598
Mpn611
Mpn230
Mpn622
Mpn446
Mpn182
Mpn660
Mpn616
Mpn122
Mpn003
Mpn392
Mpn166
General principles of cellular organization in Mycoplasma pneumoniae
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
132
Mpn660
Mpn660
Mpn660
Mpn660
Mpn268
Mpn123
Mpn208
Mpn208
Mpn208
Mpn165
Mpn165
Mpn165
Mpn191
Mpn191
Mpn191
Mpn507
Mpn618
Mpn618
Mpn007
Mpn324
Mpn450
Mpn353
Mpn179
Mpn179
Mpn179
Mpn179
Mpn179
Mpn179
Mpn179
Mpn179
Mpn179
Mpn179
Mpn179
Mpn574
Mpn105
Mpn169
Mpn169
Mpn169
Mpn169
Mpn169
Mpn169
Mpn169
Mpn169
Mpn169
Mpn169
Mpn169
Mpn616
Mpn616
Mpn616
Mpn616
Mpn230
Mpn622
Mpn228
Mpn179
Mpn207
Mpn122
Mpn622
Mpn169
Mpn226
Mpn167
Mpn166
Mpn169
Mpn516
Mpn515
Mpn352
Mpn342
Mpn007
Mpn450
Mpn618
Mpn322
Mpn618
Mpn378
Mpn230
Mpn178
Mpn622
Mpn446
Mpn167
Mpn182
Mpn189
Mpn660
Mpn169
Mpn616
Mpn226
Mpn573
Mpn106
Mpn178
Mpn171
Mpn622
Mpn446
Mpn182
Mpn189
Mpn208
Mpn165
Mpn179
Mpn616
Mpn226
Mpn230
Mpn622
Mpn446
Mpn182
General principles of cellular organization in Mycoplasma pneumoniae
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
133
Mpn616
Mpn616
Mpn616
Mpn616
Mpn342
Mpn342
Mpn226
Mpn226
Mpn226
Mpn226
Mpn226
Mpn226
Mpn226
Mpn226
Mpn226
Mpn174
Mpn230
Mpn141
Mpn106
Mpn171
Mpn171
Mpn171
Mpn446
Mpn434
Mpn434
Mpn166
Mpn166
Mpn189
Mpn189
Mpn327
Mpn228
Mpn660
Mpn660
Mpn165
Mpn165
Mpn120
Mpn220
Mpn179
Mpn658
Mpn658
Mpn021
Mpn616
Mpn616
Mpn226
Mpn230
Mpn230
Mpn178
Mpn178
Mpn178
Mpn106
Mpn189
Mpn228
Mpn179
Mpn169
Mpn089
Mpn507
Mpn171
Mpn622
Mpn446
Mpn182
Mpn189
Mpn208
Mpn179
Mpn169
Mpn174
Mpn226
Mpn189
Mpn106
Mpn141
Mpn166
Mpn165
Mpn179
Mpn660
Mpn120
Mpn021
Mpn171
Mpn327
Mpn230
Mpn228
Mpn166
Mpn189
Mpn446
Mpn616
Mpn171
Mpn658
Mpn434
Mpn658
Mpn171
Mpn165
Mpn220
Mpn434
Mpn660
Mpn226
Mpn616
Mpn622
Mpn446
Mpn622
Mpn616
Mpn226
Mpn678
General principles of cellular organization in Mycoplasma pneumoniae
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
999
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
998
997
997
997
997
997
997
134
Mpn171
Mpn171
Mpn171
Mpn622
Mpn622
Mpn538
Mpn446
Mpn446
Mpn167
Mpn167
Mpn678
Mpn182
Mpn189
Mpn660
Mpn660
Mpn631
Mpn429
Mpn430
Mpn665
Mpn180
Mpn658
Mpn616
Mpn226
Mpn226
Mpn230
Mpn516
Mpn178
Mpn003
Mpn182
Mpn182
Mpn034
Mpn490
Mpn189
Mpn352
Mpn327
Mpn228
Mpn228
Mpn228
Mpn208
Mpn165
Mpn191
Mpn007
Mpn450
Mpn179
Mpn486
Mpn658
Mpn226
Mpn226
Mpn638
Mpn171
Mpn538
Mpn446
Mpn167
Mpn230
Mpn178
Mpn171
Mpn230
Mpn171
Mpn171
Mpn189
Mpn106
Mpn660
Mpn167
Mpn182
Mpn226
Mpn665
Mpn430
Mpn429
Mpn631
Mpn658
Mpn180
Mpn178
Mpn178
Mpn660
Mpn182
Mpn352
Mpn189
Mpn486
Mpn230
Mpn191
Mpn490
Mpn034
Mpn178
Mpn516
Mpn658
Mpn208
Mpn179
Mpn226
Mpn228
Mpn226
Mpn182
Mpn450
Mpn007
Mpn228
Mpn003
Mpn327
Mpn228
Mpn165
Mpn347
Mpn616
General principles of cellular organization in Mycoplasma pneumoniae
997
997
997
997
997
997
997
997
997
997
997
997
997
997
997
997
997
997
997
997
997
997
997
997
996
996
996
996
996
996
996
996
996
996
996
996
996
996
996
996
996
996
996
996
996
996
996
996
995
995
135
Mpn347
Mpn089
Mpn177
Mpn258
Mpn166
Mpn166
Mpn182
Mpn176
Mpn327
Mpn518
Mpn165
Mpn259
Mpn497
Mpn220
Mpn179
Mpn169
Mpn658
Mpn616
Mpn230
Mpn606
Mpn025
Mpn320
Mpn133
Mpn115
Mpn300
Mpn629
Mpn430
Mpn169
Mpn016
Mpn226
Mpn230
Mpn392
Mpn166
Mpn390
Mpn115
Mpn658
Mpn230
Mpn178
Mpn177
Mpn176
Mpn189
Mpn228
Mpn228
Mpn402
Mpn169
Mpn060
Mpn226
Mpn226
Mpn516
Mpn020
Mpn638
Mpn497
Mpn658
Mpn259
Mpn179
Mpn169
Mpn518
Mpn220
Mpn165
Mpn182
Mpn327
Mpn258
Mpn089
Mpn176
Mpn166
Mpn166
Mpn177
Mpn171
Mpn169
Mpn629
Mpn430
Mpn300
Mpn016
Mpn226
Mpn320
Mpn606
Mpn025
Mpn230
Mpn133
Mpn115
Mpn115
Mpn390
Mpn658
Mpn392
Mpn230
Mpn166
Mpn226
Mpn228
Mpn226
Mpn189
Mpn176
Mpn178
Mpn169
Mpn060
Mpn228
Mpn402
Mpn230
Mpn177
Mpn020
Mpn516
General principles of cellular organization in Mycoplasma pneumoniae
995
995
995
995
995
995
995
995
995
995
995
995
995
995
995
995
995
995
994
994
994
994
994
994
994
994
994
994
994
994
993
993
993
993
993
993
992
992
992
992
992
992
992
992
992
992
992
992
991
991
136
Mpn177
Mpn115
Mpn191
Mpn220
Mpn169
Mpn226
Mpn171
Mpn515
Mpn352
Mpn191
Mpn192
Mpn166
Mpn426
Mpn191
Mpn300
Mpn226
Mpn166
Mpn191
Mpn178
Mpn329
Mpn434
Mpn551
Mpn079
Mpn172
Mpn660
Mpn133
Mpn062
Mpn440
Mpn353
Mpn635
Mpn635
Mpn531
Mpn658
Mpn016
Mpn322
Mpn306
Mpn392
Mpn106
Mpn387
Mpn293
Mpn191
Mpn137
Mpn179
Mpn665
Mpn167
Mpn226
Mpn165
Mpn191
Mpn232
Mpn225
Mpn191
Mpn169
Mpn177
Mpn226
Mpn115
Mpn220
Mpn191
Mpn352
Mpn515
Mpn171
Mpn191
Mpn226
Mpn300
Mpn192
Mpn426
Mpn166
Mpn191
Mpn166
Mpn660
Mpn440
Mpn531
Mpn353
Mpn062
Mpn658
Mpn178
Mpn635
Mpn079
Mpn329
Mpn551
Mpn133
Mpn016
Mpn434
Mpn172
Mpn635
Mpn106
Mpn392
Mpn306
Mpn322
Mpn293
Mpn387
Mpn179
Mpn665
Mpn191
Mpn137
Mpn226
Mpn167
Mpn191
Mpn165
Mpn526
Mpn173
General principles of cellular organization in Mycoplasma pneumoniae
991
991
991
991
991
991
990
990
990
990
989
989
989
989
989
989
988
988
986
986
986
986
986
986
986
986
986
986
986
986
986
986
986
986
985
985
985
985
985
985
985
985
985
985
984
984
983
983
982
982
137
Mpn173
Mpn526
Mpn298
Mpn118
Mpn446
Mpn191
Mpn246
Mpn365
Mpn189
Mpn245
Mpn191
Mpn345
Mpn002
Mpn023
Mpn434
Mpn619
Mpn537
Mpn033
Mpn033
Mpn189
Mpn133
Mpn220
Mpn016
Mpn662
Mpn192
Mpn253
Mpn005
Mpn340
Mpn228
Mpn231
Mpn177
Mpn167
Mpn623
Mpn191
Mpn573
Mpn192
Mpn171
Mpn009
Mpn606
Mpn228
Mpn292
Mpn430
Mpn547
Mpn226
Mpn516
Mpn064
Mpn033
Mpn678
Mpn189
Mpn660
Mpn225
Mpn232
Mpn118
Mpn298
Mpn191
Mpn446
Mpn245
Mpn345
Mpn191
Mpn246
Mpn189
Mpn365
Mpn434
Mpn619
Mpn002
Mpn023
Mpn662
Mpn133
Mpn016
Mpn220
Mpn033
Mpn189
Mpn033
Mpn537
Mpn253
Mpn192
Mpn340
Mpn005
Mpn231
Mpn228
Mpn623
Mpn191
Mpn177
Mpn167
Mpn009
Mpn226
Mpn228
Mpn573
Mpn430
Mpn171
Mpn547
Mpn606
Mpn292
Mpn192
Mpn678
Mpn033
Mpn064
Mpn516
Mpn660
Mpn189
General principles of cellular organization in Mycoplasma pneumoniae
982
982
981
981
981
981
980
980
980
980
980
980
979
979
979
979
978
978
978
978
978
978
978
978
977
977
977
977
977
977
976
976
976
976
975
975
975
975
975
975
975
975
975
975
974
974
974
974
974
974
138
Mpn179
Mpn685
Mpn171
Mpn187
Mpn340
Mpn166
Mpn189
Mpn521
Mpn434
Mpn598
Mpn476
Mpn189
Mpn352
Mpn153
Mpn461
Mpn165
Mpn573
Mpn573
Mpn194
Mpn008
Mpn023
Mpn182
Mpn393
Mpn571
Mpn061
Mpn025
Mpn660
Mpn361
Mpn169
Mpn556
Mpn051
Mpn668
Mpn341
Mpn376
Mpn203
Mpn014
Mpn228
Mpn686
Mpn223
Mpn048
Mpn627
Mpn505
Mpn644
Mpn081
Mpn060
Mpn302
Mpn174
Mpn377
Mpn515
Mpn261
Mpn685
Mpn179
Mpn187
Mpn171
Mpn521
Mpn189
Mpn166
Mpn340
Mpn352
Mpn153
Mpn461
Mpn165
Mpn434
Mpn598
Mpn476
Mpn189
Mpn194
Mpn008
Mpn573
Mpn573
Mpn393
Mpn571
Mpn023
Mpn182
Mpn025
Mpn061
Mpn169
Mpn556
Mpn660
Mpn361
Mpn627
Mpn203
Mpn223
Mpn686
Mpn668
Mpn377
Mpn174
Mpn376
Mpn341
Mpn060
Mpn051
Mpn081
Mpn302
Mpn505
Mpn048
Mpn644
Mpn228
Mpn014
Mpn261
Mpn515
General principles of cellular organization in Mycoplasma pneumoniae
974
974
973
973
973
973
973
973
972
972
972
972
972
972
972
972
971
971
971
971
969
969
969
969
968
968
967
967
967
967
966
966
966
966
966
966
966
966
966
966
966
966
966
966
966
966
966
966
965
965
139
Mpn341
Mpn622
Mpn221
Mpn269
Mpn189
Mpn228
Mpn020
Mpn572
Mpn515
Mpn611
Mpn191
Mpn169
Mpn573
Mpn573
Mpn668
Mpn178
Mpn392
Mpn391
Mpn191
Mpn665
Mpn006
Mpn178
Mpn572
Mpn561
Mpn378
Mpn538
Mpn222
Mpn551
Mpn250
Mpn623
Mpn663
Mpn536
Mpn665
Mpn021
Mpn615
Mpn365
Mpn365
Mpn343
Mpn097
Mpn562
Mpn573
Mpn606
Mpn434
Mpn264
Mpn665
Mpn539
Mpn014
Mpn066
Mpn167
Mpn564
Mpn269
Mpn189
Mpn228
Mpn341
Mpn622
Mpn221
Mpn515
Mpn611
Mpn020
Mpn572
Mpn169
Mpn191
Mpn392
Mpn665
Mpn391
Mpn191
Mpn573
Mpn668
Mpn178
Mpn573
Mpn665
Mpn561
Mpn250
Mpn178
Mpn551
Mpn021
Mpn623
Mpn378
Mpn572
Mpn222
Mpn536
Mpn663
Mpn006
Mpn538
Mpn365
Mpn615
Mpn343
Mpn365
Mpn562
Mpn097
Mpn264
Mpn434
Mpn606
Mpn573
Mpn539
Mpn665
Mpn352
Mpn564
Mpn616
Mpn066
General principles of cellular organization in Mycoplasma pneumoniae
963
963
963
963
963
963
962
962
962
962
962
962
961
961
961
961
961
961
961
961
960
960
960
960
960
960
960
960
960
960
960
960
960
960
959
959
959
959
959
959
958
958
958
958
958
958
957
957
957
957
140
Mpn352
Mpn660
Mpn658
Mpn616
Mpn176
Mpn658
Mpn014
Mpn235
Mpn573
Mpn167
Mpn025
Mpn115
Mpn191
Mpn191
Mpn226
Mpn174
Mpn191
Mpn220
Mpn424
Mpn424
Mpn238
Mpn238
Mpn238
Mpn238
Mpn178
Mpn419
Mpn341
Mpn088
Mpn088
Mpn358
Mpn358
Mpn358
Mpn358
Mpn020
Mpn572
Mpn572
Mpn035
Mpn035
Mpn145
Mpn145
Mpn561
Mpn339
Mpn611
Mpn611
Mpn611
Mpn282
Mpn282
Mpn140
Mpn140
Mpn395
Mpn014
Mpn658
Mpn660
Mpn167
Mpn658
Mpn176
Mpn235
Mpn014
Mpn025
Mpn115
Mpn573
Mpn167
Mpn226
Mpn174
Mpn191
Mpn191
Mpn220
Mpn191
Mpn282
Mpn123
Mpn358
Mpn572
Mpn611
Mpn250
Mpn035
Mpn582
Mpn020
Mpn145
Mpn620
Mpn238
Mpn572
Mpn611
Mpn250
Mpn341
Mpn238
Mpn358
Mpn178
Mpn561
Mpn088
Mpn620
Mpn035
Mpn633
Mpn238
Mpn358
Mpn250
Mpn424
Mpn123
Mpn450
Mpn148
Mpn195
General principles of cellular organization in Mycoplasma pneumoniae
957
957
957
957
956
956
955
955
954
954
954
954
954
954
954
954
953
953
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
141
Mpn646
Mpn642
Mpn404
Mpn633
Mpn529
Mpn041
Mpn250
Mpn250
Mpn250
Mpn418
Mpn189
Mpn400
Mpn254
Mpn123
Mpn123
Mpn475
Mpn582
Mpn450
Mpn450
Mpn629
Mpn073
Mpn073
Mpn556
Mpn620
Mpn620
Mpn413
Mpn148
Mpn148
Mpn195
Mpn116
Mpn192
Mpn665
Mpn516
Mpn027
Mpn033
Mpn033
Mpn346
Mpn125
Mpn563
Mpn628
Mpn635
Mpn226
Mpn230
Mpn393
Mpn390
Mpn685
Mpn251
Mpn606
Mpn125
Mpn569
Mpn529
Mpn418
Mpn073
Mpn339
Mpn646
Mpn400
Mpn238
Mpn358
Mpn611
Mpn642
Mpn629
Mpn041
Mpn116
Mpn424
Mpn282
Mpn413
Mpn419
Mpn140
Mpn148
Mpn189
Mpn404
Mpn556
Mpn073
Mpn088
Mpn145
Mpn475
Mpn140
Mpn450
Mpn395
Mpn254
Mpn665
Mpn192
Mpn226
Mpn628
Mpn346
Mpn635
Mpn033
Mpn563
Mpn125
Mpn027
Mpn033
Mpn516
Mpn685
Mpn390
Mpn393
Mpn230
Mpn125
Mpn569
Mpn251
Mpn606
General principles of cellular organization in Mycoplasma pneumoniae
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
952
950
950
949
949
949
949
949
949
949
949
949
949
948
948
948
948
947
947
947
947
142
Mpn135
Mpn187
Mpn187
Mpn235
Mpn066
Mpn492
Mpn492
Mpn551
Mpn366
Mpn678
Mpn189
Mpn436
Mpn277
Mpn191
Mpn300
Mpn211
Mpn048
Mpn059
Mpn665
Mpn574
Mpn032
Mpn226
Mpn121
Mpn121
Mpn232
Mpn116
Mpn246
Mpn257
Mpn257
Mpn561
Mpn155
Mpn446
Mpn418
Mpn254
Mpn211
Mpn158
Mpn209
Mpn116
Mpn006
Mpn134
Mpn171
Mpn622
Mpn320
Mpn076
Mpn573
Mpn367
Mpn426
Mpn514
Mpn100
Mpn228
Mpn121
Mpn189
Mpn191
Mpn678
Mpn048
Mpn436
Mpn277
Mpn059
Mpn121
Mpn235
Mpn187
Mpn492
Mpn492
Mpn187
Mpn211
Mpn300
Mpn066
Mpn551
Mpn226
Mpn032
Mpn574
Mpn665
Mpn135
Mpn366
Mpn116
Mpn232
Mpn155
Mpn254
Mpn116
Mpn446
Mpn246
Mpn561
Mpn211
Mpn257
Mpn418
Mpn209
Mpn158
Mpn257
Mpn134
Mpn006
Mpn622
Mpn171
Mpn076
Mpn320
Mpn426
Mpn514
Mpn573
Mpn367
Mpn650
Mpn225
General principles of cellular organization in Mycoplasma pneumoniae
946
946
946
946
946
946
946
946
946
946
946
946
946
946
946
946
946
946
946
946
946
946
946
946
945
945
944
944
944
944
944
944
944
944
944
944
944
944
943
943
942
942
941
941
940
940
940
940
939
939
143
Mpn225
Mpn650
Mpn303
Mpn269
Mpn301
Mpn258
Mpn025
Mpn300
Mpn009
Mpn619
Mpn232
Mpn254
Mpn573
Mpn321
Mpn103
Mpn352
Mpn673
Mpn280
Mpn020
Mpn061
Mpn561
Mpn437
Mpn490
Mpn553
Mpn663
Mpn191
Mpn568
Mpn280
Mpn567
Mpn230
Mpn230
Mpn424
Mpn479
Mpn141
Mpn035
Mpn035
Mpn185
Mpn350
Mpn561
Mpn387
Mpn387
Mpn387
Mpn221
Mpn378
Mpn515
Mpn282
Mpn446
Mpn203
Mpn401
Mpn301
Mpn228
Mpn100
Mpn025
Mpn258
Mpn300
Mpn269
Mpn303
Mpn301
Mpn619
Mpn009
Mpn254
Mpn232
Mpn321
Mpn573
Mpn280
Mpn673
Mpn352
Mpn103
Mpn490
Mpn280
Mpn553
Mpn191
Mpn020
Mpn561
Mpn568
Mpn437
Mpn663
Mpn061
Mpn525
Mpn035
Mpn561
Mpn387
Mpn289
Mpn378
Mpn230
Mpn446
Mpn438
Mpn401
Mpn230
Mpn424
Mpn282
Mpn123
Mpn305
Mpn141
Mpn539
Mpn387
Mpn035
Mpn391
Mpn350
Mpn508
General principles of cellular organization in Mycoplasma pneumoniae
939
939
937
937
937
937
937
937
936
936
936
936
935
935
935
935
935
935
934
934
934
934
934
934
934
934
934
934
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
144
Mpn140
Mpn504
Mpn438
Mpn438
Mpn391
Mpn508
Mpn311
Mpn311
Mpn311
Mpn311
Mpn316
Mpn389
Mpn248
Mpn123
Mpn569
Mpn095
Mpn091
Mpn220
Mpn450
Mpn305
Mpn525
Mpn525
Mpn539
Mpn289
Mpn289
Mpn342
Mpn148
Mpn110
Mpn416
Mpn251
Mpn221
Mpn301
Mpn367
Mpn211
Mpn209
Mpn200
Mpn499
Mpn499
Mpn337
Mpn640
Mpn649
Mpn331
Mpn354
Mpn061
Mpn402
Mpn252
Mpn317
Mpn685
Mpn269
Mpn241
Mpn311
Mpn248
Mpn185
Mpn342
Mpn203
Mpn301
Mpn140
Mpn095
Mpn450
Mpn148
Mpn569
Mpn289
Mpn504
Mpn387
Mpn316
Mpn311
Mpn220
Mpn091
Mpn311
Mpn221
Mpn567
Mpn110
Mpn515
Mpn479
Mpn389
Mpn438
Mpn311
Mpn525
Mpn337
Mpn640
Mpn649
Mpn211
Mpn499
Mpn301
Mpn331
Mpn499
Mpn367
Mpn200
Mpn416
Mpn251
Mpn221
Mpn209
Mpn061
Mpn354
Mpn252
Mpn402
Mpn685
Mpn317
Mpn241
Mpn269
General principles of cellular organization in Mycoplasma pneumoniae
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
933
932
932
932
932
932
932
932
932
932
932
932
932
932
932
931
931
931
931
930
930
929
929
145
Mpn379
Mpn210
Mpn379
Mpn020
Mpn020
Mpn261
Mpn397
Mpn021
Mpn509
Mpn509
Mpn315
Mpn218
Mpn572
Mpn118
Mpn118
Mpn097
Mpn041
Mpn400
Mpn281
Mpn536
Mpn225
Mpn599
Mpn665
Mpn658
Mpn314
Mpn302
Mpn006
Mpn549
Mpn452
Mpn232
Mpn228
Mpn665
Mpn280
Mpn219
Mpn516
Mpn219
Mpn573
Mpn020
Mpn265
Mpn189
Mpn390
Mpn191
Mpn225
Mpn220
Mpn665
Mpn685
Mpn315
Mpn611
Mpn197
Mpn317
Mpn210
Mpn379
Mpn020
Mpn379
Mpn261
Mpn020
Mpn021
Mpn397
Mpn281
Mpn599
Mpn314
Mpn572
Mpn218
Mpn041
Mpn400
Mpn302
Mpn118
Mpn118
Mpn509
Mpn658
Mpn665
Mpn509
Mpn225
Mpn536
Mpn315
Mpn097
Mpn452
Mpn280
Mpn006
Mpn228
Mpn232
Mpn219
Mpn549
Mpn665
Mpn219
Mpn516
Mpn390
Mpn265
Mpn020
Mpn685
Mpn573
Mpn225
Mpn191
Mpn665
Mpn220
Mpn189
Mpn317
Mpn197
Mpn611
Mpn315
General principles of cellular organization in Mycoplasma pneumoniae
928
928
927
927
926
926
926
926
925
925
925
925
925
925
925
925
925
925
925
925
925
925
925
925
925
925
923
923
923
923
923
923
923
923
922
922
921
921
921
921
921
921
921
921
921
921
920
920
920
920
146
Mpn238
Mpn306
Mpn192
Mpn218
Mpn636
Mpn497
Mpn294
Mpn399
Mpn118
Mpn677
Mpn009
Mpn339
Mpn633
Mpn557
Mpn445
Mpn261
Mpn423
Mpn311
Mpn176
Mpn563
Mpn223
Mpn300
Mpn465
Mpn091
Mpn024
Mpn574
Mpn204
Mpn314
Mpn314
Mpn685
Mpn155
Mpn155
Mpn155
Mpn103
Mpn228
Mpn133
Mpn465
Mpn158
Mpn179
Mpn169
Mpn016
Mpn331
Mpn168
Mpn118
Mpn172
Mpn191
Mpn173
Mpn353
Mpn665
Mpn665
Mpn218
Mpn497
Mpn636
Mpn238
Mpn192
Mpn306
Mpn445
Mpn563
Mpn557
Mpn223
Mpn261
Mpn314
Mpn314
Mpn118
Mpn294
Mpn009
Mpn300
Mpn204
Mpn091
Mpn399
Mpn677
Mpn423
Mpn685
Mpn176
Mpn574
Mpn024
Mpn311
Mpn339
Mpn633
Mpn465
Mpn133
Mpn179
Mpn016
Mpn228
Mpn103
Mpn155
Mpn169
Mpn331
Mpn155
Mpn465
Mpn155
Mpn158
Mpn665
Mpn353
Mpn665
Mpn173
Mpn191
Mpn118
Mpn168
Mpn172
General principles of cellular organization in Mycoplasma pneumoniae
919
919
919
919
919
919
918
918
918
918
918
918
918
918
918
918
918
918
918
918
918
918
918
918
918
918
918
918
918
918
917
917
917
917
917
917
917
917
917
917
917
917
916
916
916
916
916
916
916
916
147
Mpn354
Mpn322
Mpn023
Mpn454
Mpn461
Mpn247
Mpn218
Mpn218
Mpn572
Mpn611
Mpn688
Mpn250
Mpn197
Mpn386
Mpn280
Mpn562
Mpn424
Mpn154
Mpn310
Mpn426
Mpn173
Mpn402
Mpn516
Mpn243
Mpn310
Mpn688
Mpn022
Mpn598
Mpn663
Mpn225
Mpn457
Mpn269
Mpn269
Mpn262
Mpn321
Mpn063
Mpn176
Mpn665
Mpn114
Mpn047
Mpn182
Mpn665
Mpn516
Mpn428
Mpn539
Mpn226
Mpn538
Mpn179
Mpn665
Mpn665
Mpn023
Mpn454
Mpn354
Mpn322
Mpn247
Mpn461
Mpn611
Mpn250
Mpn197
Mpn218
Mpn386
Mpn218
Mpn572
Mpn688
Mpn562
Mpn280
Mpn402
Mpn173
Mpn426
Mpn310
Mpn154
Mpn424
Mpn225
Mpn663
Mpn022
Mpn598
Mpn310
Mpn688
Mpn243
Mpn516
Mpn321
Mpn262
Mpn114
Mpn269
Mpn457
Mpn047
Mpn665
Mpn176
Mpn269
Mpn063
Mpn665
Mpn182
Mpn539
Mpn226
Mpn516
Mpn428
Mpn665
Mpn665
Mpn538
Mpn179
General principles of cellular organization in Mycoplasma pneumoniae
915
915
915
915
915
915
914
914
914
914
914
914
914
914
914
914
913
913
913
913
913
913
912
912
912
912
912
912
912
912
911
911
911
911
911
911
911
911
911
911
910
910
909
909
909
909
908
908
908
908
148
Mpn567
Mpn479
Mpn001
Mpn185
Mpn307
Mpn155
Mpn515
Mpn167
Mpn590
Mpn590
Mpn389
Mpn165
Mpn220
Mpn665
Mpn531
Mpn342
Mpn195
Mpn110
Mpn177
Mpn553
Mpn115
Mpn618
Mpn685
Mpn072
Mpn516
Mpn118
Mpn563
Mpn220
Mpn671
Mpn246
Mpn611
Mpn553
Mpn450
Mpn204
Mpn106
Mpn303
Mpn025
Mpn430
Mpn243
Mpn328
Mpn656
Mpn330
Mpn665
Mpn174
Mpn020
Mpn020
Mpn177
Mpn434
Mpn264
Mpn191
Mpn110
Mpn389
Mpn195
Mpn342
Mpn590
Mpn167
Mpn220
Mpn155
Mpn307
Mpn531
Mpn479
Mpn665
Mpn515
Mpn165
Mpn590
Mpn185
Mpn001
Mpn567
Mpn072
Mpn115
Mpn553
Mpn685
Mpn618
Mpn177
Mpn220
Mpn563
Mpn118
Mpn516
Mpn611
Mpn450
Mpn671
Mpn204
Mpn246
Mpn553
Mpn025
Mpn430
Mpn106
Mpn303
Mpn656
Mpn330
Mpn243
Mpn328
Mpn174
Mpn665
Mpn434
Mpn264
Mpn665
Mpn020
Mpn020
Mpn665
General principles of cellular organization in Mycoplasma pneumoniae
907
907
907
907
907
907
907
907
907
907
907
907
907
907
907
907
907
907
906
906
906
906
906
906
905
905
905
905
904
904
904
904
904
904
903
903
903
903
901
901
901
901
901
901
900
900
900
900
900
900
149
Mpn665
Mpn665
Mpn006
Mpn515
Mpn182
Mpn490
Mpn390
Mpn402
Mpn567
Mpn011
Mpn083
Mpn419
Mpn321
Mpn177
Mpn434
Mpn094
Mpn395
Mpn395
Mpn367
Mpn142
Mpn388
Mpn025
Mpn095
Mpn292
Mpn292
Mpn669
Mpn305
Mpn353
Mpn353
Mpn263
Mpn178
Mpn171
Mpn320
Mpn665
Mpn665
Mpn284
Mpn612
Mpn612
Mpn612
Mpn612
Mpn298
Mpn298
Mpn011
Mpn011
Mpn011
Mpn135
Mpn238
Mpn238
Mpn178
Mpn083
Mpn177
Mpn191
Mpn390
Mpn182
Mpn515
Mpn402
Mpn006
Mpn490
Mpn095
Mpn419
Mpn353
Mpn011
Mpn263
Mpn434
Mpn177
Mpn292
Mpn367
Mpn388
Mpn395
Mpn353
Mpn395
Mpn669
Mpn567
Mpn094
Mpn305
Mpn025
Mpn292
Mpn083
Mpn142
Mpn321
Mpn665
Mpn665
Mpn284
Mpn178
Mpn171
Mpn320
Mpn088
Mpn145
Mpn569
Mpn620
Mpn041
Mpn400
Mpn140
Mpn450
Mpn148
Mpn366
Mpn197
Mpn372
Mpn465
Mpn142
General principles of cellular organization in Mycoplasma pneumoniae
900
900
899
899
899
899
899
899
898
898
898
898
898
898
898
898
898
898
898
898
898
898
898
898
898
898
898
898
898
898
897
897
897
897
897
897
896
896
896
896
896
896
896
896
896
896
896
896
896
896
150
Mpn083
Mpn578
Mpn676
Mpn218
Mpn046
Mpn088
Mpn358
Mpn358
Mpn358
Mpn572
Mpn035
Mpn347
Mpn347
Mpn145
Mpn561
Mpn262
Mpn592
Mpn592
Mpn538
Mpn538
Mpn611
Mpn282
Mpn301
Mpn643
Mpn643
Mpn140
Mpn140
Mpn094
Mpn367
Mpn367
Mpn642
Mpn142
Mpn142
Mpn142
Mpn366
Mpn366
Mpn564
Mpn041
Mpn250
Mpn250
Mpn445
Mpn197
Mpn197
Mpn197
Mpn441
Mpn441
Mpn372
Mpn372
Mpn372
Mpn372
Mpn582
Mpn444
Mpn036
Mpn358
Mpn445
Mpn612
Mpn218
Mpn197
Mpn372
Mpn372
Mpn465
Mpn254
Mpn116
Mpn612
Mpn465
Mpn114
Mpn254
Mpn116
Mpn142
Mpn441
Mpn372
Mpn402
Mpn423
Mpn065
Mpn216
Mpn011
Mpn466
Mpn305
Mpn200
Mpn195
Mpn211
Mpn083
Mpn538
Mpn021
Mpn135
Mpn474
Mpn048
Mpn298
Mpn197
Mpn372
Mpn046
Mpn238
Mpn358
Mpn250
Mpn538
Mpn021
Mpn238
Mpn358
Mpn572
Mpn611
General principles of cellular organization in Mycoplasma pneumoniae
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
151
Mpn372
Mpn423
Mpn400
Mpn254
Mpn254
Mpn065
Mpn474
Mpn123
Mpn241
Mpn241
Mpn415
Mpn211
Mpn048
Mpn465
Mpn465
Mpn465
Mpn569
Mpn582
Mpn200
Mpn200
Mpn076
Mpn444
Mpn450
Mpn450
Mpn305
Mpn665
Mpn665
Mpn114
Mpn114
Mpn466
Mpn466
Mpn466
Mpn402
Mpn402
Mpn645
Mpn169
Mpn021
Mpn021
Mpn036
Mpn620
Mpn216
Mpn284
Mpn148
Mpn148
Mpn195
Mpn188
Mpn116
Mpn116
Mpn167
Mpn166
Mpn250
Mpn301
Mpn298
Mpn347
Mpn592
Mpn643
Mpn366
Mpn402
Mpn415
Mpn114
Mpn241
Mpn642
Mpn564
Mpn178
Mpn035
Mpn561
Mpn612
Mpn083
Mpn367
Mpn645
Mpn284
Mpn578
Mpn011
Mpn466
Mpn094
Mpn169
Mpn188
Mpn262
Mpn241
Mpn140
Mpn450
Mpn148
Mpn282
Mpn123
Mpn200
Mpn665
Mpn142
Mpn441
Mpn676
Mpn612
Mpn643
Mpn076
Mpn011
Mpn466
Mpn367
Mpn665
Mpn347
Mpn592
Mpn665
Mpn665
General principles of cellular organization in Mycoplasma pneumoniae
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
896
895
895
152
Mpn665
Mpn665
Mpn515
Mpn441
Mpn225
Mpn547
Mpn573
Mpn606
Mpn418
Mpn172
Mpn178
Mpn561
Mpn538
Mpn434
Mpn386
Mpn520
Mpn520
Mpn174
Mpn595
Mpn462
Mpn553
Mpn471
Mpn231
Mpn407
Mpn665
Mpn574
Mpn323
Mpn180
Mpn191
Mpn443
Mpn516
Mpn416
Mpn154
Mpn067
Mpn515
Mpn555
Mpn623
Mpn324
Mpn434
Mpn394
Mpn622
Mpn508
Mpn115
Mpn300
Mpn567
Mpn424
Mpn351
Mpn365
Mpn155
Mpn515
Mpn167
Mpn166
Mpn225
Mpn547
Mpn515
Mpn441
Mpn606
Mpn573
Mpn172
Mpn418
Mpn520
Mpn520
Mpn434
Mpn538
Mpn174
Mpn178
Mpn561
Mpn386
Mpn553
Mpn471
Mpn595
Mpn462
Mpn574
Mpn323
Mpn180
Mpn231
Mpn407
Mpn665
Mpn443
Mpn191
Mpn067
Mpn623
Mpn515
Mpn516
Mpn154
Mpn324
Mpn416
Mpn555
Mpn394
Mpn434
Mpn115
Mpn300
Mpn622
Mpn508
Mpn390
Mpn351
Mpn424
Mpn040
Mpn515
Mpn155
General principles of cellular organization in Mycoplasma pneumoniae
895
895
894
894
894
894
893
893
893
893
892
892
892
892
892
892
892
892
891
891
891
891
891
891
891
891
891
891
890
890
889
889
889
889
889
889
889
889
888
888
887
887
887
887
886
886
886
886
886
886
153
Mpn390
Mpn040
Mpn516
Mpn003
Mpn189
Mpn686
Mpn179
Mpn665
Mpn156
Mpn156
Mpn479
Mpn541
Mpn538
Mpn446
Mpn033
Mpn683
Mpn551
Mpn438
Mpn663
Mpn593
Mpn397
Mpn569
Mpn040
Mpn629
Mpn226
Mpn252
Mpn424
Mpn246
Mpn266
Mpn622
Mpn257
Mpn347
Mpn561
Mpn515
Mpn140
Mpn352
Mpn060
Mpn226
Mpn516
Mpn178
Mpn061
Mpn434
Mpn688
Mpn362
Mpn430
Mpn443
Mpn428
Mpn187
Mpn167
Mpn656
Mpn567
Mpn365
Mpn179
Mpn686
Mpn665
Mpn003
Mpn516
Mpn189
Mpn033
Mpn593
Mpn040
Mpn226
Mpn397
Mpn252
Mpn156
Mpn551
Mpn683
Mpn663
Mpn438
Mpn156
Mpn538
Mpn629
Mpn479
Mpn569
Mpn541
Mpn446
Mpn060
Mpn140
Mpn352
Mpn561
Mpn347
Mpn257
Mpn622
Mpn226
Mpn246
Mpn266
Mpn424
Mpn515
Mpn178
Mpn516
Mpn688
Mpn430
Mpn061
Mpn443
Mpn434
Mpn362
Mpn167
Mpn660
Mpn428
Mpn381
General principles of cellular organization in Mycoplasma pneumoniae
886
886
885
885
885
885
885
885
884
884
884
884
884
884
884
884
884
884
884
884
884
884
884
884
884
884
883
883
883
883
883
883
883
883
883
883
883
883
882
882
882
882
882
882
882
882
881
881
881
881
154
Mpn660
Mpn165
Mpn475
Mpn381
Mpn516
Mpn154
Mpn067
Mpn020
Mpn009
Mpn515
Mpn210
Mpn008
Mpn025
Mpn248
Mpn007
Mpn317
Mpn574
Mpn535
Mpn434
Mpn194
Mpn264
Mpn247
Mpn322
Mpn671
Mpn106
Mpn118
Mpn185
Mpn257
Mpn378
Mpn656
Mpn426
Mpn553
Mpn173
Mpn665
Mpn283
Mpn216
Mpn524
Mpn572
Mpn347
Mpn592
Mpn446
Mpn434
Mpn265
Mpn362
Mpn609
Mpn254
Mpn429
Mpn526
Mpn526
Mpn526
Mpn187
Mpn475
Mpn165
Mpn656
Mpn154
Mpn516
Mpn248
Mpn007
Mpn210
Mpn025
Mpn009
Mpn317
Mpn515
Mpn067
Mpn020
Mpn008
Mpn535
Mpn574
Mpn247
Mpn264
Mpn194
Mpn434
Mpn426
Mpn185
Mpn553
Mpn378
Mpn671
Mpn656
Mpn118
Mpn257
Mpn322
Mpn106
Mpn665
Mpn173
Mpn216
Mpn283
Mpn446
Mpn609
Mpn526
Mpn526
Mpn524
Mpn429
Mpn362
Mpn265
Mpn572
Mpn526
Mpn434
Mpn347
Mpn592
Mpn254
General principles of cellular organization in Mycoplasma pneumoniae
881
881
881
881
880
880
880
880
880
880
880
880
880
880
880
880
880
880
879
879
879
879
878
878
878
878
878
878
878
878
878
878
878
878
878
878
877
877
877
877
877
877
877
877
877
877
877
877
877
877
155
Mpn526
Mpn116
Mpn002
Mpn553
Mpn002
Mpn660
Mpn191
Mpn685
Mpn020
Mpn106
Mpn257
Mpn232
Mpn153
Mpn669
Mpn182
Mpn008
Mpn558
Mpn252
Mpn668
Mpn479
Mpn022
Mpn619
Mpn586
Mpn676
Mpn218
Mpn218
Mpn001
Mpn029
Mpn350
Mpn434
Mpn643
Mpn094
Mpn395
Mpn656
Mpn197
Mpn182
Mpn441
Mpn327
Mpn065
Mpn558
Mpn059
Mpn628
Mpn628
Mpn124
Mpn349
Mpn539
Mpn539
Mpn247
Mpn671
Mpn419
Mpn116
Mpn526
Mpn553
Mpn002
Mpn191
Mpn685
Mpn002
Mpn660
Mpn153
Mpn669
Mpn232
Mpn257
Mpn020
Mpn106
Mpn252
Mpn558
Mpn008
Mpn182
Mpn479
Mpn668
Mpn619
Mpn022
Mpn029
Mpn327
Mpn197
Mpn628
Mpn395
Mpn586
Mpn628
Mpn124
Mpn539
Mpn247
Mpn001
Mpn349
Mpn218
Mpn441
Mpn182
Mpn676
Mpn539
Mpn059
Mpn558
Mpn218
Mpn350
Mpn434
Mpn656
Mpn643
Mpn065
Mpn094
Mpn259
Mpn361
General principles of cellular organization in Mycoplasma pneumoniae
877
877
876
876
875
875
875
875
873
873
873
873
873
873
872
872
872
872
871
871
871
871
870
870
870
870
870
870
870
870
870
870
870
870
870
870
870
870
870
870
870
870
870
870
870
870
870
870
869
869
156
Mpn341
Mpn259
Mpn361
Mpn114
Mpn516
Mpn549
Mpn020
Mpn171
Mpn561
Mpn346
Mpn346
Mpn540
Mpn636
Mpn133
Mpn191
Mpn535
Mpn616
Mpn016
Mpn171
Mpn265
Mpn446
Mpn665
Mpn573
Mpn275
Mpn003
Mpn544
Mpn642
Mpn172
Mpn021
Mpn036
Mpn616
Mpn685
Mpn354
Mpn668
Mpn434
Mpn420
Mpn189
Mpn115
Mpn434
Mpn025
Mpn393
Mpn220
Mpn354
Mpn483
Mpn497
Mpn520
Mpn567
Mpn573
Mpn187
Mpn553
Mpn114
Mpn671
Mpn419
Mpn341
Mpn171
Mpn636
Mpn191
Mpn516
Mpn616
Mpn133
Mpn016
Mpn535
Mpn549
Mpn346
Mpn020
Mpn540
Mpn561
Mpn346
Mpn265
Mpn171
Mpn665
Mpn446
Mpn021
Mpn036
Mpn544
Mpn003
Mpn172
Mpn642
Mpn573
Mpn275
Mpn685
Mpn616
Mpn434
Mpn420
Mpn354
Mpn668
Mpn115
Mpn189
Mpn220
Mpn393
Mpn025
Mpn434
Mpn520
Mpn497
Mpn483
Mpn354
Mpn295
Mpn553
Mpn226
Mpn573
General principles of cellular organization in Mycoplasma pneumoniae
869
869
869
869
868
868
868
868
868
868
868
868
868
868
868
868
868
868
867
867
865
865
864
864
864
864
864
864
864
864
864
864
863
863
863
863
863
863
862
862
862
862
861
861
861
861
860
860
860
860
157
Mpn295
Mpn226
Mpn322
Mpn269
Mpn555
Mpn362
Mpn277
Mpn108
Mpn223
Mpn323
Mpn612
Mpn230
Mpn051
Mpn354
Mpn416
Mpn011
Mpn668
Mpn246
Mpn246
Mpn192
Mpn083
Mpn676
Mpn559
Mpn559
Mpn100
Mpn088
Mpn088
Mpn099
Mpn677
Mpn677
Mpn677
Mpn351
Mpn351
Mpn035
Mpn257
Mpn145
Mpn145
Mpn561
Mpn387
Mpn221
Mpn089
Mpn378
Mpn533
Mpn071
Mpn592
Mpn487
Mpn487
Mpn538
Mpn282
Mpn282
Mpn567
Mpn187
Mpn323
Mpn277
Mpn223
Mpn108
Mpn269
Mpn362
Mpn555
Mpn322
Mpn316
Mpn465
Mpn535
Mpn252
Mpn099
Mpn311
Mpn289
Mpn438
Mpn148
Mpn525
Mpn378
Mpn081
Mpn538
Mpn021
Mpn173
Mpn677
Mpn526
Mpn416
Mpn088
Mpn145
Mpn620
Mpn282
Mpn123
Mpn182
Mpn592
Mpn677
Mpn526
Mpn182
Mpn402
Mpn094
Mpn507
Mpn083
Mpn289
Mpn273
Mpn257
Mpn475
Mpn413
Mpn559
Mpn351
Mpn060
General principles of cellular organization in Mycoplasma pneumoniae
860
860
859
859
859
859
859
859
859
859
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
158
Mpn446
Mpn446
Mpn401
Mpn177
Mpn606
Mpn094
Mpn094
Mpn646
Mpn529
Mpn041
Mpn041
Mpn480
Mpn182
Mpn182
Mpn438
Mpn508
Mpn508
Mpn423
Mpn590
Mpn590
Mpn311
Mpn311
Mpn316
Mpn400
Mpn400
Mpn474
Mpn123
Mpn123
Mpn461
Mpn475
Mpn300
Mpn507
Mpn211
Mpn465
Mpn465
Mpn330
Mpn173
Mpn273
Mpn273
Mpn526
Mpn526
Mpn526
Mpn124
Mpn124
Mpn124
Mpn124
Mpn024
Mpn081
Mpn525
Mpn525
Mpn480
Mpn465
Mpn590
Mpn590
Mpn289
Mpn221
Mpn461
Mpn124
Mpn124
Mpn124
Mpn331
Mpn446
Mpn035
Mpn561
Mpn246
Mpn423
Mpn211
Mpn508
Mpn401
Mpn177
Mpn011
Mpn466
Mpn612
Mpn124
Mpn331
Mpn273
Mpn351
Mpn060
Mpn094
Mpn487
Mpn525
Mpn089
Mpn508
Mpn230
Mpn446
Mpn024
Mpn100
Mpn071
Mpn474
Mpn088
Mpn145
Mpn620
Mpn646
Mpn529
Mpn041
Mpn400
Mpn330
Mpn676
Mpn192
Mpn300
General principles of cellular organization in Mycoplasma pneumoniae
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
159
Mpn535
Mpn466
Mpn402
Mpn021
Mpn289
Mpn289
Mpn289
Mpn620
Mpn620
Mpn413
Mpn060
Mpn060
Mpn331
Mpn331
Mpn148
Mpn252
Mpn612
Mpn516
Mpn559
Mpn099
Mpn307
Mpn187
Mpn340
Mpn606
Mpn078
Mpn674
Mpn674
Mpn165
Mpn292
Mpn599
Mpn499
Mpn499
Mpn640
Mpn645
Mpn531
Mpn413
Mpn072
Mpn514
Mpn533
Mpn197
Mpn389
Mpn553
Mpn652
Mpn032
Mpn516
Mpn182
Mpn264
Mpn267
Mpn303
Mpn434
Mpn051
Mpn311
Mpn387
Mpn559
Mpn668
Mpn533
Mpn606
Mpn677
Mpn526
Mpn487
Mpn282
Mpn123
Mpn041
Mpn400
Mpn246
Mpn354
Mpn606
Mpn674
Mpn640
Mpn187
Mpn531
Mpn099
Mpn674
Mpn612
Mpn292
Mpn516
Mpn340
Mpn413
Mpn078
Mpn072
Mpn645
Mpn514
Mpn559
Mpn499
Mpn307
Mpn165
Mpn599
Mpn499
Mpn389
Mpn553
Mpn533
Mpn197
Mpn032
Mpn652
Mpn182
Mpn516
Mpn267
Mpn264
Mpn434
Mpn303
General principles of cellular organization in Mycoplasma pneumoniae
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
858
857
857
857
857
857
857
857
857
857
857
857
857
857
857
857
857
857
857
857
857
857
857
856
856
856
856
856
856
854
854
854
854
852
852
160
Mpn208
Mpn191
Mpn516
Mpn002
Mpn002
Mpn002
Mpn446
Mpn452
Mpn261
Mpn686
Mpn363
Mpn165
Mpn571
Mpn169
Mpn169
Mpn520
Mpn428
Mpn354
Mpn298
Mpn322
Mpn322
Mpn424
Mpn549
Mpn549
Mpn549
Mpn621
Mpn621
Mpn621
Mpn621
Mpn621
Mpn002
Mpn246
Mpn294
Mpn294
Mpn218
Mpn023
Mpn023
Mpn141
Mpn251
Mpn392
Mpn020
Mpn020
Mpn020
Mpn303
Mpn303
Mpn009
Mpn185
Mpn622
Mpn350
Mpn221
Mpn191
Mpn208
Mpn002
Mpn516
Mpn261
Mpn165
Mpn520
Mpn686
Mpn002
Mpn452
Mpn169
Mpn002
Mpn169
Mpn363
Mpn571
Mpn446
Mpn430
Mpn352
Mpn295
Mpn321
Mpn320
Mpn426
Mpn555
Mpn553
Mpn556
Mpn622
Mpn619
Mpn618
Mpn616
Mpn620
Mpn004
Mpn258
Mpn303
Mpn295
Mpn228
Mpn022
Mpn025
Mpn142
Mpn261
Mpn394
Mpn025
Mpn024
Mpn019
Mpn294
Mpn295
Mpn004
Mpn663
Mpn621
Mpn352
Mpn226
General principles of cellular organization in Mycoplasma pneumoniae
852
852
851
851
851
851
851
851
851
851
851
851
851
851
851
851
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
161
Mpn262
Mpn321
Mpn321
Mpn003
Mpn033
Mpn434
Mpn066
Mpn222
Mpn222
Mpn142
Mpn555
Mpn555
Mpn555
Mpn555
Mpn555
Mpn551
Mpn258
Mpn258
Mpn258
Mpn258
Mpn258
Mpn022
Mpn656
Mpn656
Mpn656
Mpn250
Mpn250
Mpn452
Mpn619
Mpn684
Mpn197
Mpn261
Mpn261
Mpn261
Mpn261
Mpn261
Mpn261
Mpn261
Mpn261
Mpn034
Mpn034
Mpn210
Mpn210
Mpn210
Mpn423
Mpn008
Mpn008
Mpn426
Mpn426
Mpn025
Mpn258
Mpn322
Mpn324
Mpn008
Mpn034
Mpn436
Mpn062
Mpn228
Mpn226
Mpn141
Mpn549
Mpn551
Mpn553
Mpn550
Mpn556
Mpn555
Mpn246
Mpn262
Mpn250
Mpn261
Mpn252
Mpn023
Mpn663
Mpn665
Mpn658
Mpn258
Mpn261
Mpn450
Mpn621
Mpn685
Mpn191
Mpn251
Mpn258
Mpn250
Mpn264
Mpn248
Mpn259
Mpn247
Mpn252
Mpn033
Mpn032
Mpn208
Mpn211
Mpn209
Mpn426
Mpn003
Mpn004
Mpn424
Mpn423
Mpn023
General principles of cellular organization in Mycoplasma pneumoniae
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
162
Mpn025
Mpn352
Mpn352
Mpn264
Mpn320
Mpn320
Mpn228
Mpn228
Mpn228
Mpn228
Mpn553
Mpn553
Mpn553
Mpn550
Mpn663
Mpn663
Mpn663
Mpn663
Mpn686
Mpn004
Mpn004
Mpn004
Mpn004
Mpn248
Mpn436
Mpn393
Mpn660
Mpn208
Mpn062
Mpn191
Mpn295
Mpn295
Mpn295
Mpn211
Mpn259
Mpn259
Mpn618
Mpn007
Mpn324
Mpn324
Mpn209
Mpn024
Mpn546
Mpn220
Mpn450
Mpn430
Mpn665
Mpn665
Mpn665
Mpn665
Mpn020
Mpn354
Mpn350
Mpn261
Mpn322
Mpn324
Mpn218
Mpn222
Mpn220
Mpn219
Mpn549
Mpn555
Mpn556
Mpn555
Mpn185
Mpn656
Mpn665
Mpn658
Mpn685
Mpn002
Mpn009
Mpn008
Mpn007
Mpn261
Mpn434
Mpn394
Mpn665
Mpn210
Mpn066
Mpn197
Mpn298
Mpn294
Mpn303
Mpn210
Mpn261
Mpn252
Mpn621
Mpn004
Mpn321
Mpn320
Mpn210
Mpn020
Mpn547
Mpn228
Mpn452
Mpn428
Mpn656
Mpn663
Mpn660
Mpn658
General principles of cellular organization in Mycoplasma pneumoniae
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
163
Mpn665
Mpn019
Mpn547
Mpn394
Mpn394
Mpn247
Mpn658
Mpn658
Mpn658
Mpn556
Mpn556
Mpn556
Mpn219
Mpn032
Mpn616
Mpn620
Mpn662
Mpn685
Mpn685
Mpn226
Mpn226
Mpn252
Mpn252
Mpn252
Mpn424
Mpn266
Mpn434
Mpn434
Mpn674
Mpn191
Mpn023
Mpn303
Mpn155
Mpn033
Mpn440
Mpn556
Mpn472
Mpn207
Mpn602
Mpn542
Mpn429
Mpn430
Mpn426
Mpn317
Mpn354
Mpn487
Mpn515
Mpn222
Mpn007
Mpn169
Mpn662
Mpn020
Mpn546
Mpn392
Mpn393
Mpn261
Mpn656
Mpn663
Mpn665
Mpn549
Mpn555
Mpn553
Mpn228
Mpn034
Mpn621
Mpn621
Mpn665
Mpn684
Mpn686
Mpn221
Mpn222
Mpn258
Mpn261
Mpn259
Mpn266
Mpn424
Mpn674
Mpn191
Mpn434
Mpn434
Mpn303
Mpn023
Mpn033
Mpn155
Mpn556
Mpn440
Mpn429
Mpn602
Mpn207
Mpn430
Mpn472
Mpn542
Mpn317
Mpn426
Mpn007
Mpn222
Mpn169
Mpn487
Mpn354
Mpn515
General principles of cellular organization in Mycoplasma pneumoniae
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
850
849
849
849
849
849
849
848
848
848
848
848
848
847
847
847
847
847
847
846
846
845
845
845
845
845
845
164
Mpn168
Mpn294
Mpn399
Mpn533
Mpn487
Mpn044
Mpn383
Mpn517
Mpn596
Mpn684
Mpn540
Mpn493
Mpn223
Mpn618
Mpn618
Mpn060
Mpn226
Mpn252
Mpn638
Mpn365
Mpn297
Mpn078
Mpn066
Mpn504
Mpn232
Mpn389
Mpn474
Mpn415
Mpn397
Mpn331
Mpn416
Mpn573
Mpn238
Mpn238
Mpn178
Mpn671
Mpn671
Mpn671
Mpn671
Mpn671
Mpn578
Mpn578
Mpn578
Mpn341
Mpn615
Mpn615
Mpn358
Mpn358
Mpn266
Mpn572
Mpn060
Mpn540
Mpn487
Mpn383
Mpn399
Mpn223
Mpn533
Mpn226
Mpn493
Mpn618
Mpn294
Mpn596
Mpn044
Mpn684
Mpn252
Mpn168
Mpn517
Mpn618
Mpn474
Mpn066
Mpn397
Mpn389
Mpn365
Mpn331
Mpn415
Mpn078
Mpn638
Mpn232
Mpn297
Mpn504
Mpn656
Mpn663
Mpn671
Mpn609
Mpn518
Mpn238
Mpn358
Mpn572
Mpn250
Mpn438
Mpn596
Mpn309
Mpn635
Mpn363
Mpn343
Mpn091
Mpn671
Mpn609
Mpn123
Mpn671
General principles of cellular organization in Mycoplasma pneumoniae
844
844
844
844
844
844
844
844
844
844
844
844
844
844
844
844
844
844
843
843
843
843
843
843
843
843
843
843
843
843
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
165
Mpn213
Mpn035
Mpn035
Mpn035
Mpn035
Mpn035
Mpn622
Mpn561
Mpn561
Mpn343
Mpn097
Mpn014
Mpn078
Mpn688
Mpn688
Mpn656
Mpn250
Mpn250
Mpn678
Mpn623
Mpn596
Mpn596
Mpn684
Mpn438
Mpn388
Mpn388
Mpn609
Mpn609
Mpn609
Mpn281
Mpn663
Mpn363
Mpn277
Mpn474
Mpn123
Mpn518
Mpn518
Mpn518
Mpn518
Mpn125
Mpn125
Mpn599
Mpn309
Mpn337
Mpn091
Mpn091
Mpn305
Mpn525
Mpn179
Mpn179
Mpn204
Mpn622
Mpn518
Mpn179
Mpn616
Mpn520
Mpn035
Mpn518
Mpn179
Mpn615
Mpn091
Mpn688
Mpn289
Mpn014
Mpn520
Mpn416
Mpn671
Mpn609
Mpn305
Mpn337
Mpn578
Mpn036
Mpn114
Mpn671
Mpn525
Mpn195
Mpn238
Mpn358
Mpn250
Mpn599
Mpn573
Mpn341
Mpn114
Mpn518
Mpn266
Mpn178
Mpn035
Mpn561
Mpn474
Mpn486
Mpn650
Mpn281
Mpn578
Mpn623
Mpn615
Mpn097
Mpn678
Mpn388
Mpn035
Mpn561
General principles of cellular organization in Mycoplasma pneumoniae
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
842
166
Mpn114
Mpn114
Mpn204
Mpn635
Mpn486
Mpn289
Mpn036
Mpn036
Mpn616
Mpn520
Mpn520
Mpn520
Mpn195
Mpn650
Mpn549
Mpn187
Mpn515
Mpn345
Mpn020
Mpn606
Mpn352
Mpn443
Mpn061
Mpn155
Mpn434
Mpn600
Mpn327
Mpn208
Mpn081
Mpn616
Mpn315
Mpn046
Mpn445
Mpn316
Mpn636
Mpn208
Mpn115
Mpn042
Mpn042
Mpn042
Mpn615
Mpn118
Mpn307
Mpn155
Mpn383
Mpn063
Mpn480
Mpn674
Mpn189
Mpn025
Mpn684
Mpn277
Mpn213
Mpn578
Mpn125
Mpn078
Mpn596
Mpn520
Mpn035
Mpn035
Mpn688
Mpn036
Mpn388
Mpn125
Mpn345
Mpn515
Mpn187
Mpn549
Mpn352
Mpn443
Mpn020
Mpn606
Mpn600
Mpn616
Mpn208
Mpn061
Mpn081
Mpn434
Mpn327
Mpn155
Mpn042
Mpn042
Mpn042
Mpn636
Mpn316
Mpn115
Mpn208
Mpn315
Mpn046
Mpn445
Mpn081
Mpn025
Mpn063
Mpn189
Mpn674
Mpn307
Mpn520
Mpn383
Mpn155
Mpn118
General principles of cellular organization in Mycoplasma pneumoniae
842
842
842
842
842
842
842
842
842
842
842
842
842
842
841
841
841
841
840
840
840
840
839
839
839
839
839
839
839
839
838
838
838
838
838
838
838
838
838
838
836
836
836
836
836
836
836
836
836
836
167
Mpn004
Mpn081
Mpn520
Mpn072
Mpn573
Mpn023
Mpn106
Mpn683
Mpn324
Mpn430
Mpn516
Mpn487
Mpn446
Mpn177
Mpn674
Mpn526
Mpn479
Mpn615
Mpn278
Mpn155
Mpn078
Mpn176
Mpn542
Mpn563
Mpn042
Mpn650
Mpn020
Mpn106
Mpn394
Mpn520
Mpn178
Mpn218
Mpn350
Mpn480
Mpn153
Mpn618
Mpn516
Mpn171
Mpn166
Mpn571
Mpn354
Mpn021
Mpn306
Mpn020
Mpn378
Mpn140
Mpn619
Mpn618
Mpn483
Mpn430
Mpn072
Mpn615
Mpn480
Mpn004
Mpn106
Mpn324
Mpn573
Mpn430
Mpn023
Mpn683
Mpn177
Mpn446
Mpn487
Mpn516
Mpn526
Mpn674
Mpn078
Mpn176
Mpn542
Mpn042
Mpn479
Mpn615
Mpn278
Mpn650
Mpn155
Mpn563
Mpn394
Mpn520
Mpn020
Mpn106
Mpn480
Mpn350
Mpn218
Mpn178
Mpn618
Mpn153
Mpn166
Mpn571
Mpn516
Mpn171
Mpn021
Mpn354
Mpn483
Mpn430
Mpn619
Mpn618
Mpn378
Mpn140
Mpn306
Mpn020
General principles of cellular organization in Mycoplasma pneumoniae
836
836
836
836
835
835
835
835
835
835
834
834
834
834
834
834
831
831
831
831
831
831
831
831
831
831
830
830
830
830
829
829
829
829
829
829
828
828
828
828
827
827
826
826
826
826
826
826
826
826
168
Mpn516
Mpn668
Mpn671
Mpn580
Mpn329
Mpn492
Mpn636
Mpn173
Mpn126
Mpn283
Mpn556
Mpn289
Mpn219
Mpn219
Mpn342
Mpn520
Mpn230
Mpn117
Mpn029
Mpn561
Mpn221
Mpn005
Mpn321
Mpn515
Mpn678
Mpn480
Mpn420
Mpn065
Mpn521
Mpn165
Mpn191
Mpn239
Mpn073
Mpn394
Mpn658
Mpn520
Mpn573
Mpn573
Mpn340
Mpn490
Mpn430
Mpn050
Mpn105
Mpn116
Mpn516
Mpn155
Mpn656
Mpn346
Mpn623
Mpn197
Mpn173
Mpn219
Mpn342
Mpn126
Mpn636
Mpn283
Mpn329
Mpn516
Mpn580
Mpn492
Mpn520
Mpn219
Mpn668
Mpn289
Mpn671
Mpn556
Mpn520
Mpn658
Mpn321
Mpn480
Mpn678
Mpn521
Mpn029
Mpn165
Mpn221
Mpn561
Mpn394
Mpn073
Mpn005
Mpn515
Mpn239
Mpn191
Mpn065
Mpn420
Mpn117
Mpn230
Mpn050
Mpn105
Mpn116
Mpn430
Mpn490
Mpn573
Mpn573
Mpn340
Mpn165
Mpn635
Mpn623
Mpn124
Mpn656
Mpn393
General principles of cellular organization in Mycoplasma pneumoniae
825
825
825
825
825
825
825
825
825
825
825
825
825
825
825
825
824
824
824
824
824
824
824
824
824
824
824
824
824
824
824
824
824
824
824
824
823
823
823
823
823
823
823
823
822
822
822
822
822
822
169
Mpn182
Mpn393
Mpn165
Mpn239
Mpn309
Mpn124
Mpn635
Mpn169
Mpn221
Mpn515
Mpn340
Mpn434
Mpn167
Mpn508
Mpn426
Mpn571
Mpn283
Mpn658
Mpn551
Mpn480
Mpn379
Mpn257
Mpn207
Mpn307
Mpn340
Mpn653
Mpn544
Mpn551
Mpn590
Mpn254
Mpn686
Mpn361
Mpn497
Mpn280
Mpn360
Mpn360
Mpn243
Mpn278
Mpn515
Mpn636
Mpn546
Mpn280
Mpn165
Mpn331
Mpn006
Mpn294
Mpn171
Mpn515
Mpn123
Mpn115
Mpn239
Mpn197
Mpn516
Mpn182
Mpn169
Mpn346
Mpn155
Mpn309
Mpn340
Mpn167
Mpn221
Mpn283
Mpn515
Mpn426
Mpn508
Mpn658
Mpn434
Mpn571
Mpn480
Mpn551
Mpn207
Mpn497
Mpn379
Mpn360
Mpn254
Mpn551
Mpn361
Mpn653
Mpn360
Mpn340
Mpn280
Mpn544
Mpn257
Mpn686
Mpn307
Mpn590
Mpn515
Mpn280
Mpn243
Mpn546
Mpn636
Mpn278
Mpn331
Mpn165
Mpn123
Mpn115
Mpn515
Mpn171
Mpn006
Mpn294
General principles of cellular organization in Mycoplasma pneumoniae
822
822
822
822
822
822
822
822
821
821
821
821
821
821
821
821
821
821
820
820
819
819
819
819
819
819
819
819
819
819
819
819
819
819
819
819
817
817
817
817
817
817
816
816
815
815
815
815
815
815
170
Mpn315
Mpn023
Mpn061
Mpn357
Mpn393
Mpn662
Mpn222
Mpn324
Mpn357
Mpn142
Mpn022
Mpn656
Mpn388
Mpn674
Mpn397
Mpn220
Mpn061
Mpn515
Mpn167
Mpn228
Mpn179
Mpn032
Mpn567
Mpn567
Mpn416
Mpn668
Mpn328
Mpn246
Mpn246
Mpn246
Mpn192
Mpn192
Mpn559
Mpn479
Mpn479
Mpn001
Mpn266
Mpn351
Mpn278
Mpn185
Mpn595
Mpn347
Mpn387
Mpn387
Mpn533
Mpn592
Mpn282
Mpn033
Mpn606
Mpn606
Mpn357
Mpn061
Mpn023
Mpn315
Mpn662
Mpn393
Mpn324
Mpn222
Mpn220
Mpn397
Mpn388
Mpn674
Mpn022
Mpn656
Mpn142
Mpn357
Mpn032
Mpn179
Mpn228
Mpn167
Mpn515
Mpn061
Mpn192
Mpn300
Mpn559
Mpn389
Mpn024
Mpn185
Mpn311
Mpn342
Mpn567
Mpn110
Mpn416
Mpn533
Mpn606
Mpn367
Mpn282
Mpn387
Mpn562
Mpn246
Mpn545
Mpn232
Mpn351
Mpn060
Mpn479
Mpn232
Mpn266
Mpn593
Mpn479
Mpn389
General principles of cellular organization in Mycoplasma pneumoniae
814
814
814
814
814
814
813
813
812
812
812
812
812
812
812
812
811
811
811
811
811
811
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
171
Mpn367
Mpn423
Mpn311
Mpn232
Mpn232
Mpn490
Mpn320
Mpn389
Mpn389
Mpn593
Mpn300
Mpn300
Mpn545
Mpn024
Mpn644
Mpn645
Mpn562
Mpn332
Mpn342
Mpn060
Mpn110
Mpn110
Mpn401
Mpn434
Mpn383
Mpn656
Mpn678
Mpn352
Mpn292
Mpn629
Mpn595
Mpn269
Mpn515
Mpn606
Mpn166
Mpn316
Mpn178
Mpn677
Mpn515
Mpn034
Mpn191
Mpn556
Mpn616
Mpn252
Mpn229
Mpn003
Mpn434
Mpn034
Mpn599
Mpn628
Mpn001
Mpn332
Mpn246
Mpn347
Mpn592
Mpn645
Mpn644
Mpn668
Mpn606
Mpn033
Mpn567
Mpn110
Mpn595
Mpn328
Mpn320
Mpn490
Mpn278
Mpn423
Mpn246
Mpn387
Mpn192
Mpn300
Mpn352
Mpn629
Mpn656
Mpn383
Mpn292
Mpn401
Mpn678
Mpn434
Mpn269
Mpn595
Mpn166
Mpn316
Mpn515
Mpn606
Mpn515
Mpn034
Mpn178
Mpn677
Mpn616
Mpn252
Mpn191
Mpn556
Mpn034
Mpn434
Mpn003
Mpn229
Mpn628
Mpn599
General principles of cellular organization in Mycoplasma pneumoniae
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
810
809
809
809
809
809
809
809
809
808
808
808
808
808
808
807
807
807
807
807
807
807
807
806
806
806
806
806
806
172
Mpn192
Mpn100
Mpn515
Mpn515
Mpn177
Mpn434
Mpn061
Mpn393
Mpn268
Mpn259
Mpn638
Mpn061
Mpn257
Mpn089
Mpn166
Mpn228
Mpn207
Mpn027
Mpn321
Mpn483
Mpn243
Mpn020
Mpn003
Mpn426
Mpn324
Mpn050
Mpn515
Mpn434
Mpn192
Mpn177
Mpn515
Mpn100
Mpn393
Mpn061
Mpn259
Mpn268
Mpn061
Mpn638
Mpn089
Mpn257
Mpn228
Mpn166
Mpn321
Mpn483
Mpn207
Mpn027
Mpn426
Mpn003
Mpn020
Mpn243
Mpn050
Mpn324
General principles of cellular organization in Mycoplasma pneumoniae
805
805
805
805
805
805
804
804
804
804
803
803
803
803
803
803
802
802
802
802
801
801
801
801
801
801
173
10.3. Table S3: List of protein complexes.
This table is a repository of all protein complexes that have been observed in this study. It is divided into i) a set of 116
heteromultimeric complexes and ii) a set of 62 homomultimeric complexes. In part i) the first column gives the assembly ID that
specifies the higher order molecular assembly in which a heteromultimeric protein complex clusters. The second column
specifies the unique complex ID for each protein complex. Columns 3 and 4 provide complex name and complex function,
respectively. In columns 5-8 the systematic name, protein name, UniProt protein name and subunit type of each protein
component of a complex are indicated. In part ii) the first column on the left shows the complex ID of the homomultimeric protein
complexes. The second column indicates the complex name. Columns 3 and 4 give the annotated systematic and protein name
of each homomultimer.
Assemb
ly ID
Comple
x ID
Complex
name
Complex
function
Systema
tic name
Protein
name
UniProt protein name
Subunit
type
i) Heteromultimeric complexes
XXVIII
XXX
40
42
Cohesin like
complex
Complex 42
Cell division
and
chromosome
partitioning
Cell division
and
chromosome
partitioning
XXX
43
Complex 43
Cell division
and
chromosome
partitioning
III
3
DNA
Polymerase III
γ complex
DNA
replication,
recombination
and repair
XX
29
DNA
Polymerase III
core complex
59
DnaA complex
82
DNA Gyrase
complex
DNA
replication,
recombination
and repair
DNA
replication,
recombination
and repair
DNA
replication,
recombination
and repair
Mpn300
ScpA
Segregation and condensation protein A
core
Mpn301
ScpB
Segregation and condensation protein B
core
Mpn426
P115
Protein P115 homolog
core
Mpn423
Mpn423
Uncharacterized protein MG296 homolog
core
Mpn211
UvrB
UvrABC system protein B
core
Mpn508
Mpn508
Uncharacterized protein MPN508
Mpn332
Lon
ATP-dependent protease La
core
attachm
ent
attachm
ent
Mpn573
GroL
60 kDa chaperonin
Mpn314
MraZ
Protein MraZ
core
Mpn339
Mpn339
Uncharacterized protein MG243 homolog
core
Mpn633
Mpn633
Uncharacterized protein Mpn633
core
S-adenosyl-L-methionine-dependent
methyltransferase
attachm
ent
Mpn315
MraW
Mpn314
MraZ
Protein MraZ
core
Mpn315
MraW
S-adenosyl-L-methionine-dependent
methyltransferase
core
Mpn007
Mpn007
Uncharacterized protein MG007 homolog
core
Mpn618
DnaX
DNA polymerase III subunit γ/τ
core
Mpn450
Mpn450
Uncharacterized protein MG315 homolog
core
Mpn353
DnaG
DNA primase
core
Mpn378
DnaE
DNA polymerase III subunit α
core
Mpn551
Mpn551
Uncharacterized protein MG373 homolog
core
Mpn118
Mpn118
Uncharacterized protein MG199 homolog
core
Mannitol-specific phosphotransferase enzyme IIA
component
Putative ABC transporter ATP-binding protein MG467
homolog
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
Mpn563
Mpn563
Uncharacterized GTP-binding protein MG384 homolog
Mpn557
GidA
tRNA uridine 5-carboxymethylaminomethyl
modification enzyme
Mpn141
MgpA
Adhesin P1 precursor
Mpn059
Gcp
Probable O-sialoglycoprotein endopeptidase
Mpn653
MtlF
Mpn683
Mpn683
Mpn376
Mpn376
Uncharacterized protein Mpn376
core
Mpn686
DnaA
Chromosomal replication initiator protein dnaA
core
Mpn003
GyrB
DNA gyrase subunit B
core
Mpn004
GyrA
DNA gyrase subunit A
core
General principles of cellular organization in Mycoplasma pneumoniae
174
XI
ParE-GyrA
complex
DNA
replication,
recombination
and repair
Mpn122
ParE
DNA topoisomerase 4 subunit B
core
102
Mpn004
GyrA
DNA gyrase subunit A
core
DNA
Topoisomeras
e IV complex
DNA
replication,
recombination
and repair
Mpn123
ParC
DNA topoisomerase 4 subunit A
core
17
Mpn122
ParE
DNA topoisomerase 4 subunit B
core
DNA
Recombinatio
n complex
DNA
replication,
recombination
and repair
Mpn034
PolC
DNA polymerase III PolC-type
core
Mpn490
RecA
Protein RecA
core
DNA
replication,
recombination
and repair
DNA
replication,
recombination
and repair
DNA
replication,
recombination
and repair
DNA
replication,
recombination
and repair
DNA
replication,
recombination
and repair
DNA
replication,
recombination
and repair
DNA
replication,
recombination
and repair
Mpn003
GyrB
DNA gyrase subunit B
core
Mpn486
Mpn486
Uncharacterized protein Mpn486
core
Mpn014
Mpn014
Uncharacterized protein MG010 homolog
core
Mpn377
Mpn377
Uncharacterized protein Mpn377
core
Mpn014
Mpn014
Uncharacterized protein MG010 homolog
core
Mpn235
Ung
Uracil-DNA glycosylase
core
Mpn125
UvrC
UvrABC system protein C
core
Mpn563
Mpn563
Uncharacterized GTP-binding protein MG384 homolog
core
Mpn023
MetG
Methionyl-tRNA synthetase
core
Mpn619
UvrA
UvrABC system protein A
core
Mpn536
RuvB
Holliday junction ATP-dependent DNA helicase RuvB
core
Mpn663
Mpn663
Uncharacterized protein MG449 homolog
core
Mpn020
Mpn020
Uncharacterized ATP-dependent helicase MPN020
core
Mpn341
UvrD
Probable DNA helicase II homolog
core
86
XI
XXXV
101
GyrB-Mpn486
complex
84
DNA Primase
complex
103
DNA Primase
complex
90
Complex 90
105
Complex 105
100
Complex 100
104
Helicase
complex
15
DNA
Recombinatio
n complex
DNA
replication,
recombination
and repair
114
Complex 114
Transcription
49
RNA
polymerase
complex
Transcription
Mpn123
ParC
DNA topoisomerase 4 subunit A
core
Mpn282
Mpn282
Uncharacterized protein Mpn282
core
Mpn424
Mpn424
UPF0122 protein Mpn424
core
Mpn060
MetK
S-adenosylmethionine synthetase
core
Mpn402
ProS
Prolyl-tRNA synthetase
core
Mpn351
Mpn351
Uncharacterized protein MG248 homolog
core
Mpn387
Mpn387
Uncharacterized protein MG269 homolog
Mpn293
LspA
Lipoprotein signal peptidase
Mpn490
RecA
Protein RecA
Mpn122
ParE
DNA topoisomerase 4 subunit B
core
attachm
ent
attachm
ent
attachm
ent
Mpn352
RpoD
RNA polymerase σ factor RpoD
core
Mpn434
DnaK
Chaperone protein DnaK
core
Mpn020
Mpn020
Uncharacterized ATP-dependent helicase Mpn020
core
Mpn261
TopA
DNA topoisomerase 1
core
Mpn352
RpoD
RNA polymerase σ factor RpoD σ-A)
core
Mpn515
RpoC
DNA-directed RNA polymerase β' chain
core
Mpn516
RpoB
DNA-directed RNA polymerase β chain
core
Mpn191
RpoA
DNA-directed RNA polymerase α chain
core
Mpn178
RpsZ
30S ribosomal protein S14 type Z
core
Mpn154
NusA
Transcription elongation protein NusA
core
Mpn002
Mpn002
DnaJ-like protein MG002 homolog
core
Mpn539
RplL
50S ribosomal protein L7/L12
core
Uncharacterized protein MG010 homolog
attachm
ent
Mpn014
Mpn014
General principles of cellular organization in Mycoplasma pneumoniae
175
V
VII
VII
XXXV
7
10
11
51
Complex 7
AminoacyltRNA
synthetase
complex
PhenylalaninetRNA
synthetase
complex
Complex 51
Translation,
ribosomal
structure and
biogenesis
Translation,
ribosomal
structure and
biogenesis
Translation,
ribosomal
structure and
biogenesis
Translation,
ribosomal
structure and
biogenesis
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
Mpn673
Mpn673
Uncharacterized protein MG459 homolog
Mpn437
Mpn437
Uncharacterized protein Mpn437
Mpn067
Mpn067
Protein MG054 homolog
Mpn265
TrpS
Tryptophanyl-tRNA synthetase
Mpn678
GltX
Glutamyl-tRNA synthetase
Mpn379
PolA
Probable 5'-3' exonuclease
Mpn153
Mpn153
Uncharacterized ATP-dependent helicase MG140
homolog
Mpn490
RecA
Protein RecA
Mpn266
Mpn266
Uncharacterized protein MG127 homolog
Mpn009
Mpn009
Uncharacterized deoxyribonuclease MG009 homolog
Mpn443
Mpn443
Probable ATP-dependent RNA helicase MG308
homolog
Mpn155
InfB
Translation initiation factor IF-2
Mpn187
InfA
Translation initiation factor IF-1
Mpn252
AsnS
Asparaginyl-tRNA synthetase
Mpn354
GlyQS
Glycyl-tRNA synthetase
Mpn219
RplK
50S ribosomal protein L11
Mpn173
RpmC
50S ribosomal protein L29
Mpn016
Mpn016
Uncharacterized protein MG012 homolog
core
Mpn033
Upp
Uracil phosphoribosyltransferase
core
Mpn133
Mpn133
Uncharacterized lipoprotein MG186 homolog
precursor
core
Mpn635
Mpn635
Uncharacterized protein Mpn635
core
Mpn155
InfB
Translation initiation factor IF-2
core
Mpn346
Mpn346
Uncharacterized protein Mpn346
Mpn064
DeoA
Thymidine phosphorylase
Mpn156
RbfA
Ribosome-binding factor A
core
attachm
ent
attachm
ent
Mpn025
Fba
Fructose-bisphosphate aldolase
core
Mpn105
PheS
Phenylalanyl-tRNA synthetase α chain
core
Mpn669
TyrS
Tyrosyl-tRNA synthetase
core
Mpn061
Ffh
Signal recognition particle protein
core
Mpn023
MetG
Methionyl-tRNA synthetase
core
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
Mpn678
GltX
Glutamyl-tRNA synthetase
Mpn106
PheT
Phenylalanyl-tRNA synthetase β chain
Mpn322
NrdF
Ribonucleoside-diphosphate reductase subunit β
Mpn141
MgpA
Adhesin P1 precursor
Mpn553
ThrS
Threonyl-tRNA synthetase
Mpn106
PheT
Phenylalanyl-tRNA synthetase β chain
core
Mpn105
PheS
Phenylalanyl-tRNA synthetase α chain
core
Mpn035
Mpn035
Uncharacterized protein Mpn035
core
Mpn561
Udk
Uridine kinase
core
Mpn178
RpsZ
30S ribosomal protein S14 type Z
core
Mpn553
ThrS
Threonyl-tRNA synthetase
attachm
ent
General principles of cellular organization in Mycoplasma pneumoniae
176
XXXV
XXXV
XII
XXXV
52
Translation
elongation
factor complex
Translation,
ribosomal
structure and
biogenesis
Translation,
ribosomal
structure and
biogenesis
Translation,
ribosomal
structure and
biogenesis
53
L29-S12
complex
96
Complex 96
18
Cytidine
deaminationribosome
complex
Translation,
ribosomal
structure and
biogenesis
Ribosomecom
plex
Translation,
ribosomal
structure and
biogenesis
50
Mpn631
Tsf
Elongation factor Ts
Mpn665
Tuf
Elongation factor Tu
core
core
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
Mpn006
Tmk
Thymidylate kinase
Mpn137
Mpn137
UPF0134 protein Mpn137
Mpn219
RplK
50S ribosomal protein L11
Mpn168
RplB
50S ribosomal protein L2
Mpn173
RpmC
50S ribosomal protein L29
Mpn225
RpsL
30S ribosomal protein S12
Mpn173
RpmC
50S ribosomal protein L29
core
Mpn225
RpsL
30S ribosomal protein S12
core
Mpn361
PrfA
Peptide chain release factor 1
core
Mpn556
ArgS
Arginyl-tRNA synthetase
core
Mpn065
Cdd
Cytidine deaminase
core
Mpn643
Mpn643
Uncharacterized lipoprotein MG440 homolog 2
precursor
core
Mpn539
RplL
50S ribosomal protein L7/L12
core
Mpn216
OppC
Oligopeptide transport system permease protein OppC
attachm
ent
Mpn616
RpsI
30S ribosomal protein S9
core
Mpn622
RpsO
30S ribosomal protein S15
core
Mpn115
InfC
Translation initiation factor IF-3
core
Mpn165
RplC
50S ribosomal protein L3
core
Mpn166
RplD
50S ribosomal protein L4
core
Mpn167
RplW
50S ribosomal protein L23
core
Mpn169
RpsS
30S ribosomal protein S19
core
Mpn171
RpsC
30S ribosomal protein S3
core
Mpn172
RplP
50S ribosomal protein L16
core
Mpn174
RpsQ
30S ribosomal protein S17
core
Mpn176
RplX
50S ribosomal protein L24
core
Mpn177
RplE
50S ribosomal protein L5
core
Mpn179
RpsH
30S ribosomal protein S8
core
Mpn182
RpsE
30S ribosomal protein S5
core
Mpn189
RpsM
30S ribosomal protein S13
core
Mpn192
RplQ
50S ribosomal protein L17
core
Mpn208
RpsB
30S ribosomal protein S2
core
Mpn220
RplA
50S ribosomal protein L1
core
Mpn226
RpsG
30S ribosomal protein S7
core
Mpn228
RpsF
30S ribosomal protein S6
core
Mpn230
RpsR
30S ribosomal protein S18
core
Mpn327
RpmA
50S ribosomal protein L27
core
Mpn446
RpsD
30S ribosomal protein S4
core
Mpn658
RplS
50S ribosomal protein L19
core
Mpn221
Pth
Peptidyl-tRNA hydrolase
core
Mpn660
RpsP
30S ribosomal protein S16
core
Mpn685
Putative ABC transporter ATP-binding protein
MG468.1 homolog
core
Mpn685
Mpn518
Mpn518
Uncharacterized protein MG343 homolog
core
Mpn571
Mpn571
Putative ABC transporter ATP-binding MG390
homolog
core
Mpn665
Tuf
Elongation factor Tu
core
Mpn178
RpsZ
30S ribosomal protein S14 type Z
core
General principles of cellular organization in Mycoplasma pneumoniae
177
XXV &
XXXI
37
VI &
XXXII
9
VI
8
GroEL-GroES
complex
Dnak-GrpE
complex
Protein
chaperone
complex
Posttranslatio
nal
modification,
protein
turnover,
chaperones
Posttranslatio
nal
modification,
protein
turnover,
chaperones
Posttranslatio
nal
modification,
protein
turnover,
chaperones
Mpn155
InfB
Translation initiation factor IF-2
core
Mpn520
IleS
Isoleucyl-tRNA synthetase
core
Mpn091
Mpn091
Uncharacterized protein Mpn091
core
Mpn428
Pta
Phosphate acetyltransferase
core
Mpn465
Mpn465
Uncharacterized protein Mpn465
core
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
Mpn541
RpsT
30S ribosomal protein S20
Mpn154
NusA
Transcription elongation protein NusA
Mpn517
Mpn517
Uncharacterized protein MG342 homolog
Mpn538
RplJ
50S ribosomal protein L10
Mpn231
RplI
50S ribosomal protein L9
Mpn180
RplF
50S ribosomal protein L6
Mpn117
RplT
50S ribosomal protein L20
Mpn475
EngA
GTP-binding protein EngA
Mpn636
Frr
Ribosome recycling factor
Mpn676
Mpn676
Uncharacterized protein Mpn676
Mpn103
Mpn103
Uncharacterized protein Mpn103
Mpn386
Mpn386
Uncharacterized protein MG268 homolog
Mpn536
RuvB
Holliday junction ATP-dependent DNA helicase RuvB
Mpn623
Mpn623
Mpn253
PgsA
Mpn524
Mpn524
UPF0134 protein Mpn524
Mpn539
RplL
50S ribosomal protein L7/L12
Mpn553
ThrS
Threonyl-tRNA synthetase
Mpn072
Mpn072
Uncharacterized protein MG057 homolog
Mpn219
RplK
50S ribosomal protein L11
Mpn006
Tmk
Thymidylate kinase
Mpn137
Mpn137
UPF0134 protein Mpn137
Mpn188
RpmJ
50S ribosomal protein L36
Mpn168
RplB
50S ribosomal protein L2
Mpn317
FtsZ
Cell division protein FtsZ
Mpn225
RpsL
30S ribosomal protein S12
Mpn573
GroL
60 kDa chaperonin
core
Mpn574
GroS
10 kDa chaperonin
core
Mpn120
GrpE
Protein GrpE
core
Mpn434
DnaK
Chaperone protein DnaK
core
Mpn538
RplJ
50S ribosomal protein L10
core
Mpn434
DnaK
Chaperone protein DnaK
core
Mpn021
DnaJ
Chaperone protein DnaJ
core
Mpn142
Mpn142
Mgp-operon protein 3 precursor
core
SpoT
Probable guanosine-3',5'-bis(diphosphate) 3'pyrophosphohydrolase
core
Mpn397
Probable ATP-dependent RNA helicase MG425
homolog
CDP-diacylglycerol-glycerol-3-phosphate 3phosphatidyltransferase
General principles of cellular organization in Mycoplasma pneumoniae
178
Mpn441
VIII
XXXIII
12
46
92
XXXII
45
Glycolytic
enzyme
complex 1
Complex 46
Complex 92
Glycolytic
enzyme
complex 2
Carbohydrate
transport and
metabolism
Carbohydrate
transport and
metabolism
Carbohydrate
transport and
metabolism
Carbohydrate
transport and
metabolism
38
Peptidase
complex
Amino acid
transport and
metabolism
Mpn297
Uncharacterized protein MG211 homolog
Mpn002
Mpn002
DnaJ-like protein MG002 homolog
Mpn531
ClpB
Chaperone ClpB
Mpn124
HrcA
Heat-inducible transcription repressor HrcA
Mpn247
Mpn247
Putative protein phosphatase
Mpn354
GlyQS
Glycyl-tRNA synthetase
Mpn394
Nox
Probable NADH oxidase
Mpn429
Pgk
Phosphoglycerate kinase
Mpn120
GrpE
Protein GrpE
Mpn547
Mpn547
Uncharacterized protein MG369 homolog
39
Complex 39
Metabolism
core
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
Mpn025
Fba
Fructose-bisphosphate aldolase
core
Mpn430
GapA
Glyceraldehyde-3-phosphate dehydrogenase
core
Mpn303
Pyk
Pyruvate kinase
core
Mpn606
Eno
Enolase
core
Mpn629
TpiA
Triosephosphate isomerase
core
Mpn569
Mpn569
Putative metalloprotease Mpn569
core
Mpn316
Mpn316
Uncharacterized protein MG223 homolog
core
Mpn258
Mpn258
Putative carbohydrate transport ATP-binding protein
Mpn258
core
Mpn259
Mpn259
Uncharacterized protein MG120 homolog
core
Mpn430
GapA
Glyceraldehyde-3-phosphate dehydrogenase
core
Mpn429
Pgk
Phosphoglycerate kinase
core
core
Mpn606
Eno
Enolase
Mpn434
DnaK
Chaperone protein DnaK
core
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
Mpn120
GrpE
Protein GrpE
Mpn002
Mpn002
DnaJ-like protein MG002 homolog
Mpn531
ClpB
Chaperone ClpB
Mpn124
HrcA
Heat-inducible transcription repressor
Mpn247
Mpn247
Putative protein phosphatase
Mpn354
GlyQS
Glycyl-tRNA synthetase
Mpn394
Nox
Probable NADH oxidase
GatB
Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase
subunit B
core
Mpn250
Pgi
Glucose-6-phosphate isomerase
core
Mpn358
Mpn358
Uncharacterized protein MG255 homolog
core
Mpn572
PepA
Probable cytosol aminopeptidase
core
Mpn609
PstB
Phosphate import ATP-binding protein PstB
core
Mpn611
Mpn611
Uncharacterized lipoprotein MG412 homolog
precursor
core
Mpn197
PepF
Oligoendopeptidase F homolog
core
Mpn218
OppF
Oligopeptide transport ATP-binding protein OppF
core
Mpn372
Mpn372
ADP-ribosylating toxin CARDS
core
Mpn671
FtsH
Cell division protease FtsH homolog
core
GpmI
2,3-bisphosphoglycerate-independent
phosphoglycerate mutase
attachm
ent
Mpn628
XXVII
Uncharacterized protein Mpn441
Mpn297
Mpn238
XXVI
Mpn441
Mpn203
Mpn203
Putative adhesin P1-like protein Mpn203
core
Mpn668
Mpn668
Organic hydroperoxide resistance protein-like
core
Mpn391
PdhC
Dihydrolipoyllysine-residue acetyltransferase
core
General principles of cellular organization in Mycoplasma pneumoniae
179
94
XXXI
44
54
93
XXXIV
XIX
XXIV
XXIV
47
28
34
35
95
109
Ribonucleosid
e-diphosphate
reductase
complex
Pyruvate
dehydrogenas
e complex
Phosphotransf
er system
complex
ScpA-ThyA
complex
ATP synthase
complex
Restriction
enzyme
complex
Restriction
enzyme
complex
Restriction
enzyme
complex
Mpn420
Mpn420
Uncharacterized protein MG293 homolog
attachm
ent
Mpn322
NrdF
Ribonucleoside-diphosphate reductase subunit β
core
Mpn324
NrdE
Ribonucleoside-diphosphate reductase α subunit
core
Mpn392
PdhB
Pyruvate dehydrogenase E1 component subunit β
core
Mpn393
PdhA
Pyruvate dehydrogenase E1 component subunit α
core
Mpn573
GroL
60 kDa chaperonin
core
Mpn390
PdhD
Dihydrolipoyl dehydrogenase
Mpn574
GroS
10 kDa chaperonin
Mpn006
Tmk
Thymidylate kinase
Mpn306
ArcB
Ornithine carbamoyltransferase, catabolic
Mpn023
MetG
Methionyl-tRNA synthetase
Mpn008
TrmE
Probable tRNA modification GTPase TrmE
Mpn009
Mpn009
Uncharacterized deoxyribonuclease MG009 homolog
Mpn321
FolA
Dihydrofolate reductase
Mpn426
P115
Protein P115 homolog
Metabolism
Metabolism
Metabolism
Metabolism
Energy
production
and
conversion
Defense
mechanisms
Defense
mechanisms
Defense
mechanisms
Restriction
enzyme
complex
Defense
mechanisms
Restriction
enzyme
complex
Defense
mechanisms
core
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
Mpn553
ThrS
Threonyl-tRNA synthetase
Mpn207
PtsG
PTS system glucose-specific EIICBA component
core
Mpn268
Mpn268
Putative phosphotransferase enzyme IIB component
core
Mpn300
ScpA
Segregation and condensation protein A
core
Mpn320
ThyA
Thymidylate synthase
core
Mpn598
AtpD
ATP synthase subunit β
core
Mpn600
AtpA
ATP synthase subunit α
core
Mpn602
AtpF
ATP synthase B chain precursor
core
Mpn153
Mpn153
Uncharacterized ATP-dependent helicase MG140
homolog
Mpn688
Mpn688
ParA family protein Mpn688
attachm
ent
attachm
ent
Mpn347
Mpn347
Mpn638
Mpn638
Putative type I restriction enzyme MpnORFDP R
protein part 1
Putative type I restriction enzyme specificity protein
Mpn638 (S protein)
core
core
Mpn185
Adk
Adenylate kinase
core
Mpn438
Mpn438
Uncharacterized protein Mpn438
core
Mpn342
Mpn342
Putative type I restriction enzyme MpnORFDP M
protein
core
Mpn663
Mpn663
Uncharacterized protein MG449 homolog
core
Cell division protease FtsH homolog
core
Mpn671
FtsH
Mpn342
Mpn342
Mpn507
Mpn507
Mpn089
Mpn089
Mpn345
Mpn345
Putative type-1 restriction enzyme MpnORFDP R
protein part 2
core
Mpn365
Mpn365
Putative type I restriction enzyme specificity protein
Mpn365 (S protein)
core
Mpn089
Mpn089
Putative type I restriction enzyme specificity protein
Mpn089 (S protein)
core
Mpn497
Mpn497
Uncharacterized protein Mpn497
core
Putative type I restriction enzyme MpnORFDP M
protein
Putative type I restriction enzyme specificity protein
Mpn507 (S protein)
Putative type I restriction enzyme specificity protein
Mpn089 (S protein)
General principles of cellular organization in Mycoplasma pneumoniae
core
core
core
180
113
115
XIX
II
27
2
81
IV
IV
IV
IX
X
XIII
4
5
6
13
14
19
Restriction
enzyme
complex
Defense
mechanisms
Restriction
enzyme
complex
Defense
mechanisms
Restriction
enzyme
complex
Complex 2
Complex 81
Complex 4
Complex 5
Complex 6
Complex 13
Complex 14
Complex 19
Defense
mechanisms
Cell envelope
biogenesis,
outer
membrane
Cell envelope
biogenesis,
outer
membrane
Function
unknown
Function
unknown
Function
unknown
Function
unknown
Function
unknown
Function
Mpn365
Mpn365
Putative type I restriction enzyme specificity protein
Mpn365 (S protein)
core
Mpn343
Mpn343
Putative type I restriction enzyme specificity protein
Mpn343 (S protein)
core
Mpn365
Mpn365
Putative type I restriction enzyme specificity protein
Mpn365 (S protein)
core
Mpn615
Mpn615
Putative type I restriction enzyme specificity protein
Mpn615 (S protein)
core
Mpn116
RpmI
50S ribosomal protein L35
core
Mpn254
Mpn254
Protein MG115 homolog
core
Mpn232
DnaB
Replicative DNA helicase
core
Mpn526
Mpn526
Uncharacterized protein MG350 homolog
core
Mpn347
Mpn347
Putative type I restriction enzyme MpnORFDP R
protein part 1
core
Mpn257
GalE
UDP-glucose 4-epimerase
core
Mpn592
Mpn592
Uncharacterized lipoprotein Mpn592 precursor
core
Mpn638
Mpn638
Putative type I restriction enzyme specificity protein
Mpn638 (S protein)
Mpn656
Mpn656
Uncharacterized protein MG442 homolog
attachm
ent
attachm
ent
Mpn367
Mpn367
Putative mgpC-like protein Mpn367
core
Mpn514
Mpn514
Uncharacterized protein Mpn514
core
Mpn200
Mpn200
Uncharacterized lipoprotein Mpn200 precursor
core
Mpn499
Mpn499
Uncharacterized protein Mpn499
core
Mpn645
Mpn645
Uncharacterized lipoprotein MG439 homolog 2
precursor
core
Mpn100
Mpn100
UPF0134 protein Mpn100
core
Mpn650
Mpn650
Uncharacterized lipoprotein Mpn650 precursor
core
Mpn140
Mpn140
Mgp-operon protein 1
core
Mpn148
Mpn148
Uncharacterized protein Mpn148
core
Mpn450
Mpn450
Uncharacterized protein MG315 homolog
core
Mpn311
Mpn311
Uncharacterized protein MG218.1 homolog
core
Mpn246
Def
Peptide deformylase
core
Mpn011
Mpn011
Uncharacterized lipoprotein Mpn011 precursor
core
Mpn466
Mpn466
Uncharacterized protein Mpn466
core
attachm
ent
attachm
ent
attachm
ent
attachm
ent
Mpn204
Mpn204
UPF0134 protein Mpn204
Mpn245
Gmk
Guanylate kinase
Mpn419
AlaS
Alanyl-tRNA synthetase
Mpn095
Mpn095
Uncharacterized protein Mpn095
Mpn246
Def
Peptide deformylase
core
Mpn245
Gmk
Guanylate kinase
core
Mpn095
Mpn095
Uncharacterized protein Mpn095
core
Mpn311
Mpn311
Uncharacterized protein MG218.1 homolog
core
Mpn041
Mpn041
Uncharacterized protein Mpn041
core
Mpn400
Mpn400
Uncharacterized protein MG281 homolog
core
Mpn118
Mpn118
Uncharacterized protein MG199 homolog
core
Mpn298
AcpS
Holo-[acyl carrier protein] synthase
Mpn563
Mpn563
Uncharacterized GTP-binding protein MG384 homolog
Mpn557
GidA
tRNA uridine 5-carboxymethylaminomethyl
modification enzyme
attachm
ent
attachm
ent
core
Mpn066
ManB
Phosphomannomutase
core
Mpn564
Adh
Probable NADP-dependent alcohol dehydrogenase
core
Mpn048
Mpn048
Uncharacterized protein Mpn048
core
Mpn320
ThyA
Thymidylate synthase
core
General principles of cellular organization in Mycoplasma pneumoniae
181
unknown
XIV
20
Complex 20
Function
unknown
Mpn076
Mpn076
Uncharacterized protein MG061 homolog 1
core
Mpn284
Mpn284
Uncharacterized lipoprotein Mpn284 precursor
core
Mpn353
DnaG
DNA primase
core
Mpn083
Mpn083
Uncharacterized lipoprotein Mpn083 precursor
core
Mpn142
Mpn142
Mgp-operon protein 3 precursor
core
Mpn582
Uncharacterized lipoprotein Mpn582 precursor
attachm
ent
Mpn088
Mpn088
Uncharacterized protein Mpn088
core
Mpn145
Mpn145
UPF0134 protein Mpn145
core
Mpn620
Mpn620
Uncharacterized protein MG422 homolog
core
Mpn612
Mpn612
Uncharacterized protein MG414 homolog
core
Mpn221
Pth
Peptidyl-tRNA hydrolase
core
Mpn292
Mpn292
Uncharacterized RNA pseudouridine synthase MG209
homolog
core
Mpn094
Mpn094
UPF0134 protein Mpn094
core
Mpn305
ArcA
Putative arginine deiminase
Mpn582
XV
XVI
XVI
XVII
XVIII
XVIII
XXI
21
22
23
24
25
26
31
Complex 21
Complex 22
Complex 23
Complex 24
Complex 25
Complex 26
Complex 31
Function
unknown
Function
unknown
Function
unknown
Function
unknown
Function
unknown
Function
unknown
Function
unknown
Mpn547
Mpn547
Mpn247
Mpn247
Putative protein phosphatase
Mpn292
Mpn292
Uncharacterized RNA pseudouridine synthase MG209
homolog
core
Mpn547
Mpn547
Uncharacterized protein MG369 homolog
core
Mpn525
Mpn525
Uncharacterized protein MG349 homolog
core
Mpn567
P200
Protein P200
core
Mpn110
Mpn110
Uncharacterized protein Mpn110
32
Complex 32
Function
unknown
XXIII
33
Complex 33
Function
unknown
XXV
36
Complex 36
Function
unknown
core
attachm
ent
attachm
ent
Mpn295
Mpn295
Uncharacterized protein MG210.1 homolog
Mpn095
Mpn095
Uncharacterized protein Mpn095
Mpn258
Mpn258
Putative carbohydrate transport ATP-binding protein
core
Mpn341
UvrD
Probable DNA helicase II homolog
core
Mpn114
Mpn114
Putative acetyltransferase
core
Mpn241
Mpn241
Uncharacterized protein MG103 homolog
core
Mpn262
Mpn262
Uncharacterized protein MG123 homolog
core
Mpn269
Mpn269
UPF0144 protein MG130 homolog
core
attachm
ent
attachm
ent
Mpn223
HprK
HPr kinase/phosphorylase
Mpn415
P37
High affinity transport system protein p37 precursor
Mpn341
UvrD
Probable DNA helicase II homolog
core
Mpn223
HprK
HPr kinase/phosphorylase
core
Mpn121
Mpn121
Uncharacterized protein MG202 homolog
core
Mpn135
Mpn135
Probable ABC transporter permease protein MG188
homolog
core
Mpn366
Mpn366
Putative mgpC-like protein Mpn366
core
Uncharacterized protein MG328 homolog
attachm
ent
Mpn474
XXII
Uncharacterized protein MG369 homolog
core
attachm
ent
attachm
ent
Mpn474
Mpn158
RibF
Putative riboflavin biosynthesis protein
core
Mpn209
PacL
Probable cation-transporting P-type ATPase
core
Mpn331
Tig
Trigger factor
core
Mpn172
RplP
50S ribosomal protein L16
core
Mpn418
Mpn418
Putative Holliday junction resolvase
core
Mpn642
Uncharacterized lipoprotein MG439 homolog 4
precursor
core
Mpn211
UvrB
UvrABC system protein B
core
Mpn573
GroL
60 kDa chaperonin
core
Mpn194
CbiO2
Cobalt import ATP-binding protein CbiO 2
core
Mpn264
Mpn264
Uncharacterized protein MG125 homolog
core
Mpn642
General principles of cellular organization in Mycoplasma pneumoniae
182
XI
XXIX
XXXIV
I
XX
16
41
48
1
Complex 16
Complex 41
Complex 48
Complex 1
Function
unknown
Function
unknown
Function
unknown
Function
unknown
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
attachm
ent
Mpn574
GroS
10 kDa chaperonin
Mpn267
PpnK
Probable inorganic polyphosphate/ATP-NAD kinase
Mpn008
TrmE
Probable tRNA modification GTPase TrmE
Mpn009
Mpn009
Uncharacterized deoxyribonuclease MG009 homolog
Mpn321
FolA
Dihydrofolate reductase
Mpn426
P115
Protein P115 homolog
Mpn553
ThrS
Threonyl-tRNA synthetase
Mpn387
Mpn387
Uncharacterized protein MG269 homolog
core
Mpn293
LspA
Lipoprotein signal peptidase
core
Mpn289
Mpn289
Putative type I restriction enzyme specificity protein
Mpn289 (S protein)
core
Mpn479
AzoR
FMN-dependent NADH-azoreductase
core
Mpn389
LplA
Probable lipoate-protein ligase A
core
Uncharacterized protein Mpn040
attachm
ent
Mpn040
Mpn040
Mpn602
AtpF
ATP synthase B chain precursor
core
Mpn153
Mpn153
Uncharacterized ATP-dependent helicase MG140
homolog
core
Mpn195
Mpn195
Uncharacterized protein MG181 homolog
core
Mpn395
Apt
Adenine phosphoribosyltransferase
core
Mpn367
Mpn367
Putative mgpC-like protein Mpn367
core
Mpn001
DnaN
DNA polymerase III subunit β
core
Mpn388
Mpn388
Uncharacterized protein MG269.1 homolog
core
Mpn551
Mpn551
Uncharacterized protein MG373 homolog
core
MtlF
Mannitol-specific phosphotransferase enzyme IIA
component
core
30
Complex 30
Function
unknown
55
Complex 55
Function
unknown
Mpn444
Mpn444
Putative esterase/lipase 1
core
Mpn578
Mpn578
Uncharacterized protein Mpn578
core
56
Complex 56
Function
unknown
Mpn071
Mpn071
UPF0011 protein MG056 homolog
core
Mpn273
Mpn273
Uncharacterized 16.1 kDa HIT-like protein
core
Function
unknown
Mpn462
Mpn462
Uncharacterized protein Mpn462
core
Mpn471
RpmG1
50S ribosomal protein L33 1
core
Mpn281
Mpn281
Uncharacterized lipoprotein Mpn281 precursor
core
Mpn509
Mpn509
Uncharacterized protein Mpn509
core
Mpn294
Mpn294
Uncharacterized protein Mpn294
core
Mpn445
Uncharacterized lipoprotein MG309 homolog
precursor
core
57
Complex 57
Mpn653
58
Complex 58
Function
unknown
60
Complex 60
Function
unknown
61
Complex 61
Function
unknown
Mpn328
Nfo
Probable endonuclease 4
core
Mpn330
Mpn330
Uncharacterized protein MG237 homolog
core
Function
unknown
Mpn062
DeoD
Purine nucleoside phosphorylase DeoD-type
core
Mpn079
FruK
Putative 1-phosphofructokinase
core
NrdI
Protein NrdI
core
Mpn407
Mpn407
Uncharacterized protein Mpn407
core
62
Complex 62
Mpn445
63
Complex 63
Function
unknown
Mpn323
64
Complex 64
Function
unknown
Mpn029
Efp
Elongation factor P
core
Mpn586
Mpn586
Uncharacterized protein Mpn586
core
65
Complex 65
Function
unknown
Mpn248
Mpn248
Putative serine/threonine-protein kinase
core
Mpn504
Mpn504
UPF0134 protein Mpn504
core
core
66
67
Complex 66
Complex 67
Function
unknown
Mpn493
UlaD
Probable 3-keto-L-gulonate-6-phosphate
decarboxylase
Mpn596
Mpn596
Uncharacterized protein MG397 homolog
core
Function
unknown
Mpn350
Mpn350
UPF0078 membrane protein Mpn350
core
Mpn401
GreA
Transcription elongation factor GreA
core
General principles of cellular organization in Mycoplasma pneumoniae
183
Mpn329
Mpn329
Uncharacterized protein MG236 homolog
core
Mpn440
Mpn440
Uncharacterized protein Mpn440
core
Mpn302
PfkA
6-phosphofructokinase
core
Mpn644
Mpn644
Uncharacterized lipoprotein MG439 homolog 3
precursor
core
Function
unknown
Mpn097
Mpn097
Uncharacterized lipoprotein Mpn097 precursor
core
Mpn562
NadE
Probable NH3-dependent NAD synthetase
core
Mpn337
Uncharacterized protein MG241 homolog
core
68
Complex 68
Function
unknown
69
Complex 69
Function
unknown
70
Complex 70
+
71
Complex 71
Function
unknown
Mpn337
Mpn416
P29
Probable ABC transporter ATP-binding protein p29
core
72
Complex 72
Function
unknown
Mpn047
Mpn047
Uncharacterized protein MG037 homolog
core
Mpn063
DeoC
Deoxyribose-phosphate aldolase
core
73
Complex 73
Function
unknown
74
Complex 74
75
76
77
Complex 75
Complex 76
Complex 77
Mpn529
Mpn529
Uncharacterized protein MG353 homolog
core
Mpn646
Mpn646
Uncharacterized lipoprotein MG440 homolog 1
precursor
core
Function
unknown
Mpn051
Mpn051
Uncharacterized protein MG039 homolog
core
Mpn627
PtsI
Phosphoenolpyruvate-protein phosphotransferase
core
Function
unknown
Mpn461
Mpn461
Uncharacterized protein MG323 homolog
core
Mpn476
Cmk
Cytidylate kinase
core
Mpn436
Uncharacterized lipoprotein MG307 homolog
precursor
core
Function
unknown
Mpn436
Mpn492
UlaE
Probable L-ribulose-5-phosphate 3-epimerase
core
Function
unknown
Mpn126
Mpn126
Putative metallophosphoesterase MG207 homolog
core
Mpn580
Mpn580
Uncharacterized protein Mpn580
core
Mpn537
Uncharacterized protein MG360 homolog
core
Peptide methionine sulfoxide reductase
core
78
Complex 78
Function
unknown
Mpn537
Mpn662
MsrB
79
Complex 79
Function
unknown
Mpn307
Mpn307
Carbamate kinase-like protein
core
Mpn590
Mpn590
Uncharacterized lipoprotein Mpn590 precursor
core
core
80
83
Complex 80
Complex 83
Function
unknown
Mpn081
Mpn081
Putative ABC transporter ATP-binding protein MG065
homolog
Mpn505
Mpn505
Uncharacterized protein Mpn505
core
Function
unknown
Mpn005
SerS
Seryl-tRNA synthetase
core
Mpn340
Mpn340
Probable DNA helicase
core
Mpn027
Mpn027
Uncharacterized protein Mpn027.
core
Mpn628
GpmI
2,3-bisphosphoglycerate-independent
phosphoglycerate mutase
core
85
Complex 85
Function
unknown
87
Complex 87
Function
unknown
Mpn036
Mpn036
Uncharacterized protein Mpn036
core
Mpn676
Mpn676
Uncharacterized protein Mpn676
core
Function
unknown
Mpn073
Prs
Ribose-phosphate pyrophosphokinase
core
Mpn404
Mpn404
Uncharacterized protein MG285 homolog
core
Mpn103
Uncharacterized protein Mpn103
core
88
Complex 88
89
Complex 89
Function
unknown
Mpn103
Mpn280
Mpn280
UPF0036 protein MG139 homolog
core
91
Complex 91
Function
unknown
Mpn210
SecA
Preprotein translocase subunit SecA
core
Mpn379
PolA
Probable 5'-3' exonuclease
core
Complex 97
Function
unknown
Mpn386
Mpn386
Uncharacterized protein MG268 homolog
core
Mpn688
Mpn688
ParA family protein Mpn688
core
Mpn413
Uncharacterized protein Mpn413
core
Mpn475
EngA
GTP-binding protein EngA
core
97
98
Complex 98
Function
unknown
Mpn413
99
Complex 99
Function
unknown
Mpn419
AlaS
Alanyl-tRNA synthetase
core
Mpn582
Mpn582
Uncharacterized lipoprotein Mpn582 precursor
core
106
Complex 106
Function
unknown
Mpn025
Fba
Fructose-bisphosphate aldolase
core
Mpn573
GroL
60 kDa chaperonin
core
Function
unknown
Mpn060
MetK
S-adenosylmethionine synthetase
core
Mpn048
Mpn048
Uncharacterized protein Mpn048
core
107
Complex 107
General principles of cellular organization in Mycoplasma pneumoniae
184
108
Complex 108
Function
unknown
Mpn073
Prs
Ribose-phosphate pyrophosphokinase
core
Mpn556
ArgS
Arginyl-tRNA synthetase
core
110
Complex 110
Function
unknown
Mpn189
RpsM
30S ribosomal protein S13
core
Mpn629
TpiA
Triosephosphate isomerase
core
Mpn623
Probable ATP-dependent RNA helicase MG425
homolog
core
111
Function
unknown
112
Complex 112
Function
unknown
116
Complex 116
Function
unknown
Complex
ID
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
Complex 111
Mpn623
Mpn222
TilS
tRNA(Ile)-lysidine synthase
core
Mpn340
Mpn340
Probable DNA helicase Mpn340
core
Mpn521
Mpn521
Uncharacterized tRNA/rRNA methyltransferase
MG346 homolog
core
Mpn573
GroL
60 kDa chaperonin
core
Mpn665
Tuf
Elongation factor Tu
core
Systematicname
Protein
name
ii) Homomultimeric complexes
DNA polymerase III subunit β
DNA gyrase subunit B
Thymidylate kinase
Uncharacterized protein MG007 homolog
Mpn001
Mpn003
Mpn006
Mpn007
DnaN
GyrB
Tmk
Mpn007
Uncharacterized ATP-dependent helicase Mpn020
Putative proline iminopeptidase
Methionyl-tRNA synthetase
Fructose-biphosphate aldolase
DNA polymerase III PolC-type
Glycerol kinase
Mpn020
Mpn022
Mpn023
Mpn025
Mpn034
Mpn050
Mpn020
Pip
MetG
Fba
PolC
GlpK
Uncharacterized protein MG039 homolog
Deoxyribose-phosphate aldolase
Phosphomannomutase
Putative 1-phosphofructokinase
Phenylalanyl-tRNA synthetase α chain
Phenylalanyl-tRNA synthetase β chain
Mpn051
Mpn063
Mpn066
Mpn079
Mpn105
Mpn106
Mpn051
DeoC
ManB
FruK
PheS
PheT
Uncharacterized protein MG202 homolog
Putative Metallophosphoesterase
DNA-directed RNA polymerase subunit α
HPr kinase/phosphorylase
Single stranded DNA binding protein
Replicative DNA helicase
Uncharacterized protein MG127 homolog
Probable inorganic polyphosphate/ATP-NAD kinase
2',3'-cyclic-nucleotide 2'-phosphodiesterase
Mpn121
Mpn126
Mpn191
Mpn223
Mpn229
Mpn232
Mpn266
Mpn267
Mpn269
Mpn121
Mpn126
RpoA
HprK
Ssb
DnaB
Mpn266
PpnK
Mpn269
Uncharacterized protein MG134 homolog
6-phosphofructokinase /Phosphohexokinase
Pyruvate kinase
Protein MraZ
Cell division protein
Thymidylate synthase
Ribonucleoside-diphosphate reductase subunit β
Ribonucleoside-diphosphate reductase subunit α
Probable endonuclease 4
Mpn275
Mpn302
Mpn303
Mpn314
Mpn317
Mpn320
Mpn322
Mpn324
Mpn328
Mpn275
PfkA
Pyk
MraZ
FtsZ
ThyA
NrdF
NrdE
Nfo
Uncharacterized protein MG236 homolog
Mpn329
Mpn329
Complex name
General principles of cellular organization in Mycoplasma pneumoniae
185
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
Uncharacterized protein MG246 homolog
Uncharacterized protein MG259 homolog
Uncharacterized protein MG263 homolog
Dihydrolipoyl lysine-residue acetyltransferase
Pyruvate dehydrogenase E1 component subunit β
Pyruvate dehydrogenase E1 component subunit α
Alanyl-tRNA synthetase
Mpn349
Mpn362
Mpn381
Mpn391
Mpn392
Mpn393
Mpn419
Mpn349
Mpn362
Mpn381
PdhC
PdhB
PdhA
AlaS
Uncharacterized protein MG293 homolog
Glyceraldehyde-3-phosphate-dehydrogenase
Putative Xaa-Pro aminopeptidase
FMN-dependent NADH-azoreductase
Recombinase A
Probable L-ribulose-5-phosphate 3-epimerase UlaE
Mpn420
Mpn430
Mpn470
Mpn479
Mpn490
Mpn492
Mpn420
GapA
PepP
AzoR
RecA
UlaE
Uncharacterized protein MG350 homolog
Chaperone protein ClpB
Acetate kinase
Probable thiamine biosynthesis protein
Mpn526
Mpn531
Mpn533
Mpn550
Mpn526
ClpB
AckA
ThiL
Uncharacterized protein MG377 homolog
Ribosomal RNA small subunit methyltransferase G
Arginine deiminase-like protein
Probable NH3-dependent NAD+ synthetase
60 kDa chaperonin
Enolase
Putative type I restriction enzyme specificity protein
Elongation factor Tu
L-lactate dehydrogenase
Mpn555
Mpn558
Mpn560
Mpn562
Mpn573
Mpn606
Mpn638
Mpn665
Mpn674
Mpn555
RsmG
Mpn560
NadE
GroL
Eno
Mpn638
Tuf
Ldh
Uncharacterized protein MG461 homolog
Mpn677
Mpn677
General principles of cellular organization in Mycoplasma pneumoniae
186
10.4. Table S4: List of literature curated protein complexes.
This table is a repository of literature evidence for i) 31 heteromultimeric and ii) 78 homomultimeric protein complexes that may
exist in M. pneumoniae based on observed homologs in other species. In i) the first column states complex name. In columns
2-4 the table describes the protein components present in each complex, with their annotated systematic name, protein name
and subunit/function, if known. In column 5, the PubMed ID or database evidence is highlighted. Column 6 specifies the
organism for which the complex is observed. In ii) the first column provides the complex name. Columns 2 and 3 give the
systematic and protein name of a homomultimer. Column 4 states the multimerization state of each complex. In column 5, the
PubMed ID or database evidence is highlighted. Column 6 specifies the organism for which the complex is observed.
Components
Complex name
Systematic
name
Protein
name
Mpn003
GyrB
B-subunit
Mpn004
GyrA
A-subunit
Mpn105
SyfA
a-subunit
Mpn106
SyfB
b-subunit
Mpn024
RpoE
Probable δ-factor
Mpn191
RpoA
a-subunit
Mpn352
RpoD
σ-factor
Mpn516
RpoB
b-subunit
PubMed ID
or source
Genus/
species
Expasy
M. pneumoniae
Expasy
M. pneumoniae by
similarity
Expasy
M. pneumoniae by
similarity
Expasy
by homology to
Bacillus subtilis
Expasy
M. pneumoniae by
similarity
Expasy
M. pneumoniae by
similarity
Expasy
M. pneumoniae
Expasy
M. pneumoniae by
similarity
Expasy
M. pneumoniae
Subunit/function
i) Heteromultimeric complexes
DNA Gyrase complex
Phenylalanine-tRNA
synthetase complex
RNA polymerase
complex
Transcription
antitermination factor
complex
Pyruvate
dehydrogenase
complex
Mpn515
RpoC
b'-subunit
Mpn067
NusG
Transcription antitermination
Mpn024
RpoE
Probable δ-factor
Mpn191
RpoA
a-subunit
Mpn352
RpoD
σ-factor
Mpn516
RpoB
b-subunit
Mpn515
RpoC
b'-subunit
Mpn390
PdhD
E3 component Dihydrolipoyl
dehydrogenase
Mpn391
PdhC
E2 component Dihydrolipoamide
acetyltransferase
Mpn392
PdhB
E1 component b-subunit
Mpn393
PdhA
E1 component a-subunit
Ribonucleosidediphosphate
reductase complex
Mpn322
NrdF
a-subunit
Mpn324
NrdE
b-subunit
DNA Topoisomerase
IV complex
Mpn122
ParE
b-subunit
Mpn123
ParC
a-subunit
Mpn001
DnaN
b-subunit
Mpn007
Mpn007
d-subunit
Mpn034
PolC
Mpn378
DnaE
a-subunit
Mpn450
Mpn450
d'-subunit
Mpn618
DnaX
g/t-subunit
Mpn631
Tsf
DNA polymerase III
complex
Translation elongation
General principles of cellular organization in Mycoplasma pneumoniae
187
factor complex
Mpn665
GroEL-GroES
complex
Mpn573
GroL
Mpn574
GroS
Mpn089
Mpn089
S protein
Mpn201
Mpn201
S protein
Mpn285
Mpn285
S protein
Mpn289
Mpn289
S protein
Mpn290
Mpn290
S protein
Mpn342
Mpn342
M protein
Mpn343
Mpn343
S protein
Mpn345
Mpn345
R protein
Mpn347
Mpn347
R protein
Mpn365
Mpn365
S protein
Mpn507
Mpn507
S protein
Restriction enzyme
complexes
Ribosome complex
Tuf
Mpn615
Mpn615
S protein
Mpn638
Mpn638
S protein
Mpn069
RpmG2
50S ribosomal protein L33 2
Mpn116
RpmI
50S ribosomal protein L35
Mpn117
RplT
50S ribosomal protein L20
Mpn164
RpsJ
30S ribosomal protein S10
Mpn165
RplC
50S ribosomal protein L3
Mpn166
RplD
50S ribosomal protein L4
Mpn167
RplW
50S ribosomal protein L23
Mpn168
RplB
50S ribosomal protein L2
Mpn169
RpsS
30S ribosomal protein S19
Mpn170
RplV
50S ribosomal protein L22
Mpn171
RpsC
30S ribosomal protein S3
Mpn172
RplP
50S ribosomal protein L16
Mpn173
RpmC
50S ribosomal protein L29
Mpn174
RpsQ
30S ribosomal protein S17
Mpn175
RplN
50S ribosomal protein L14
Mpn176
RplX
50S ribosomal protein L24
Mpn177
RplE
50S ribosomal protein L5
Mpn178
RpsZ/RpsN
30S ribosomal protein S14 type Z
Mpn179
RpsH
30S ribosomal protein S8
Mpn180
RplF
50S ribosomal protein L6
Mpn181
RplR
50S ribosomal protein L18
Mpn182
RpsE
30S ribosomal protein S5
Mpn183
RplO
50S ribosomal protein L15
Mpn188
RpmJ
50S ribosomal protein L36
Mpn189
RpsM
30S ribosomal protein S13
Mpn190
RpsK
30S ribosomal protein S11
Mpn192
RplQ
50S ribosomal protein L17
Mpn208
RpsB
30S ribosomal protein S2
Mpn219
RplK
50S ribosomal protein L11
Mpn220
RplA
50S ribosomal protein L1
Mpn225
RpsL
30S ribosomal protein S12
Mpn226
RpsG
30S ribosomal protein S7
General principles of cellular organization in Mycoplasma pneumoniae
Expasy
M. pneumoniae by
similarity
Expasy
M. pneumoniae by
similarity
Expasy
M. pneumoniae
188
Translation initiation
factor 1-Ribosome
complex
Translation initiation
factor 2-Ribosome
complex
Cohesin-like complex
RbfA-30S-ribosomal
subunit complex
Glycolytic enzyme
complex 1
Dnak-GrpE-DnaJ
complex
Glycolytic enzyme
complex 2
Era-30S-ribosomal
Mpn228
RpsF
30S ribosomal protein S6
Mpn230
RpsR
30S ribosomal protein S18
Mpn231
RplI
50S ribosomal protein L9
Mpn296
RpsU
30S ribosomal protein S21
Mpn325
RplU
50S ribosomal protein L21
Mpn327
RpmA
50S ribosomal protein L27
Mpn360
RpmE
50S ribosomal protein L31
Mpn446
RpsD
30S ribosomal protein S4
Mpn471
RpmG1
50S ribosomal protein L33 1
Mpn538
RplJ
50S ribosomal protein L10
Mpn539
RplL
50S ribosomal protein L7/L12
Mpn540
RpmF
50S ribosomal protein L32
Mpn541
RpsT
30S ribosomal protein S20
Mpn616
RpsI
30S ribosomal protein S9
Mpn617
RplM
50S ribosomal protein L13
Mpn622
RpsO
30S ribosomal protein S15
Mpn624
RpmB
50S ribosomal protein L28
Mpn658
RplS
50S ribosomal protein L19
Mpn660
RpsP
30S ribosomal protein S16
Mpn682
RpmH
50S ribosomal protein L34
Mpn187
InfA
Translation initiation factor IF-1
Ribosome
Ribosome
Mpn155
InfB
Ribosome
Ribosome
Mpn300
ScpA
Mpn301
ScpB
Mpn426
Smc
Mpn156
RbfA
30S ribosomal
subunit
30S ribosomal
subunit
Mpn430
GapA
Glyceraldehyde-3-phosphate
dehydrogenase
Mpn025
Fba
Fructose-bisphosphate aldolase
Mpn674
Ldh
L-lactate dehydrogenase
Translation initiation factor IF-2
17329809,
11959450
by homology to
Mycobacterium
tuberculosis
Expasy
M. pneumoniae by
similarity
Expasy
M. pneumoniae by
similarity
15866174
by homology to
Thermus
thermophilus
15701694
by homology to
Mus musculus
15632130
By homology to
Escherichia coli
8613464
by homology to
MCF-7 cells
(eukaryotes)
15866174
by homology to
Ribosome-binding factor A
Mpn303
Pyk
Pyruvate kinase
Mpn302
PfkA
6-phosphofructokinase
Mpn120
GrpE
Protein GrpE
Mpn434
DnaK
Chaperone protein DnaK
Mpn021
DnaJ
Chaperone protein dnaJ
Mpn430
GapA
Glyceraldehyde-3-phosphate
dehydrogenase
Mpn429
Fba
Phosphoglycerate kinase
Mpn606
Ldh
Enolase
Mpn303
Pyk
Pyruvate kinase
Mpn568
Era
General principles of cellular organization in Mycoplasma pneumoniae
189
subunit complex
Thermus
thermophilus
30S ribosomal
subunit
30S ribosomal
subunit
Mpn401
GreA
Transcription elongation factor
Mpn024
RpoE
probable δ-factor
Mpn191
RpoA
a-subunit
Mpn352
RpoD
σ-factor
Mpn516
RpoB
b-subunit
Mpn515
RpoC
b'-subunit
Dihydrofolate
reductase-thymidylate
synthase complex
Mpn321
FolA
Mpn320
ThyA
Holliday junction ATPdependent helicase
complex
Mpn536
RuvB
Mpn535
RuvA
Aspartyl-glutamyltRNA(Asn/Gln)
amidotransferase
complex
Mpn238
GatB
Mpn237
GatA
Mpn236
GatC
Mpn125
UvrC
Mpn619
UvrA
GreA-RNA
polymerase complex
UvrABC complex
Phosphotransfer
system maltose
complex
DnaB-DnaG complex
Phosphotransfer
system glucose
complex
Phosphotransfer
system fructose
complex
Phosphotransfer
system maltose
complex
tRNA modification
complex
Mpn211
UvrB
Mpn053
PtsH
Mpn651
MtlA
Mpn653
MtlF
Mpn232
DnaB
Mpn353
DnaG
Mpn053
PtsH
Mpn207
PtsG
Mpn053
PtsH
Mpn078
FruA
Mpn053
PtsH
Mpn494
UlaC
Mpn495
UlaB
Mpn496
UlaA
Mpn557
MnmG
Mpn008
TrmE
Protein function
17207814
M. pneumoniae by
similarity
Expasy
other
Expasy
M. pneumoniae
Expasy
M. pneumoniae by
similarity
Expasy
M. pneumoniae by
similarity
17803963
by homology to
Escherichia coli
17947583
by homology to
Escherichia coli
Expasy
M. pneumoniae by
similarity
Expasy
M. pneumoniae by
similarity
Expasy
M. pneumoniae by
similarity
17062623
by homology to
Escherichia coli
Subunits
PubMed
per
ID or
complex
source
ii) Homomultimeric complexes
Systematic Protein
name
name
Cell division MraZ
Mpn314
MraZ
8
Expasy
Pyruvate kinase
Mpn303
Pyk
4
Expasy
Thymidylate synthase
Mpn320
ThyA
2
Expasy
L-lactate dehydrogenase
Mpn674
Ldh
4
Expasy
General principles of cellular organization in Mycoplasma pneumoniae
Genus/
species
M. pneumoniae
M. pneumoniae by
similarity
M. pneumoniae by
similarity
M. pneumoniae by
similarity
190
Fructose-biphosphate
aldolase
Fba
2
Expasy
M. pneumoniae by
similarity
Mpn317
FtsZ
multiple/
aggregates
to form a
ring-like
structure
17977836
M. pneumoniae by
similarity
Mpn223
HprK
6
Expasy
M. pneumoniae
Mpn302
PfkA
multiple
Mpn479
AzoR
2
Mpn430
GapA
4
Acetate kinase
Mpn533
AckA
2/4
Alanyl-tRNA synthetase
Mpn419
AlaS
2
Cell division FtsZ
HPr kinase/
phosphorylase
6-phosphofructokinase
/Phosphohexokinase
FMN-dependent NADHazoreductase
Glyceraldehyde-3phosphate-dehydrogenase
Mpn025
by homology to
Escherichia coli
by homology to
16684776
Escherichia coli
M. pneumoniae by
Expasy
similarity
216674,
by homology to
29037,
Veillonella
230181
alcalescens
by homology to
9207019
Thermus thermophilus
16289704
Probable inorganic
polyphosphate/ATP-NAD
kinase
Mpn267
PpnK
2
11006082
by homology to
Micrococcus flavus &
Mycobacterium
tuberculosis
Recombinase A
Mpn490
RecA
6
17955055
by homology to
Escherichia coli
Chaperone protein ClpB
Mpn531
ClpB
6
Expasy
M. pneumoniae by
similarity
Replicative DNA helicase
Mpn232
DnaB
6
17947583
by homology to
Escherichia coli
Glycerol kinase
Mpn050
GlpK
2/4
9930671
by homology to
Escherichia coli
Putative proline
iminopeptidase
Mpn022
Pip
multiple
8885412
by homology
Xanthomonas
campestris pv. citri
Methionyl-tRNA
synthetase
Mpn023
MetG
Enolase
Mpn606
Eno
2
Expasy
Putative
Metallophosphoesterase
Mpn126
Mpn126
4
17586769
Single stranded DNA
binding protein
Mpn229
Ssb
4
16041080
by homology to
Mycobacterium
smegmatis
Arginine deiminase-like
protein
Mpn560
Mpn560
2/3
17223359,
11911465
by homology to
Lactococcus lactis
DNA polymerase III
subunit β
Mpn001
DnaN
2
Expasy
by homology to
Streptococcus
pneumoniae
2126467
General principles of cellular organization in Mycoplasma pneumoniae
by homology to
Escherichia coli
M. pneumoniae by
similarity
by homology to
Escherichia coli
191
by homology to
Thermus thermophilus
by homology to Homo
11071809
sapiens
by homology to
11545747
Pyrococcus furiosus
M. pneumoniae by
Expasy
similarity
DNA gyrase subunit B
Mpn003
GyrB
2
Thymidylate kinase
Mpn006
Tmk
2
Mpn007
Mpn007
6
Mpn034
PolC
2
Deoxyribose-phosphate
aldolase
Mpn063
DeoC
1/2
Phosphomannomutase
Mpn066
ManB
2
Putative 1phosphofructokinase
Mpn079
FruK
8
Mpn105
PheS
2
Mpn106
PheT
2
Mpn191
RpoA
2
Mpn322
NrdF
2
Mpn324
NrdE
2
Mpn328
Nfo
2
Mpn391
PdhC
60
Mpn392
PdhB
2
Mpn393
PdhA
2
Putative Xaa-Pro
aminopeptidase
Mpn470
PepP
2
12377124
by homology to
Pyrococcus horikoshii
Probable L-ribulose-5phosphate 3-epimerase
UlaE
Mpn492
UlaE
4
11732895
by homology to
Pseudomonas cichorii
Probable thiamine
biosynthesis protein
Mpn550
ThiL
2
16343540
by homology to
Bacillus anthracis
Ribosomal RNA small
subunit methyltransferase
G
Mpn558
RsmG
2
18667428
by homology to
Geobacter
sulfurreducens
Probable NH(3)-dependent
NAD(+) synthetase
Mpn562
NadE
2
15645437
60 kDa chaperonin
Mpn573
GroL
2x7
Expasy
Putative type I restriction
enzyme specificity protein
Mpn638
Mpn638
2
16038930
Uncharacterized protein
MG007 homolog
DNA polymerase III polCtype
Phenylalanyl-tRNA
synthetase α chain
Phenylalanyl-tRNA
synthetase β chain
DNA-directed RNA
polymerase subunit α
Ribonucleosidediphosphate reductase
subunit β
Ribonucleosidediphosphate reductase
subunit α
Probable endonuclease 4
Dihydrolipoyllysine-residue
acetyltransferase
Pyruvate dehydrogenase
E1 component subunit β
Pyruvate dehydrogenase
E1 component subunit α
General principles of cellular organization in Mycoplasma pneumoniae
11850422
by homology to
Escherichia coli
by homology to
16540464
Sulfolobus Tokodaii
by homology to Homo
2527305
sapiens
by homology to
7664121
Thermus thermophilus
by homology to
7664121
Thermus thermophilus
M. pneumoniae by
Expasy
similarity
by homology to
16301799
Salmonella
typhimurium
by homology to
8052308
Salmonella
typhimurium
by homology to
10458614
Escherichia coli
M. pneumoniae by
9990008
similarity
M. pneumoniae by
Expasy
similarity
M. pneumoniae by
Expasy
similarity
7675789
by homology to
Bacillus subtilis
M. pneumoniae by
similarity
by homology to
Methanocaldococcus
jannaschii
192
by homology to
Escherichia coli
M. pneumoniae by
similarity
Elongation factor Tu
Mpn665
Tuf
2
16257965
Dihydrolipoyl
dehydrogenase
Mpn390
PdhD
2
Expasy
10 kDa chaperonin
Mpn574
GroS
7
Expasy
DNA topoisomerase 4
subunit B
Mpn122
ParE
2
Expasy
Mpn332
Lon
4
Expasy
Mpn008
TrmE
2
Expasy
Mpn278
Glf
2
10089346
Mpn632
PyrH
6
17297917
Mpn595
RpiB
4
15162497
Mpn186
Map
2
12297034
FAD synthetase
Mpn158
RibF
2
15468322
GMP kinase
Mpn245
Def
2
17012781
Mpn298
AcpS
2
16788183
M. pneumoniae
Mpn395
Apt
2
10393170,
11535055
Threonyl-tRNA synthetase
Mpn553
ThrS
2
Expasy
Thymidine phosphorylase
Mpn064
DeoA
multiple
Expasy
Ribose-phosphate
pyrophosphokinase
Mpn073
Prs
multiple
2169413
Protein GrpE
Mpn120
GrpE
2
Expasy
UDP-glucose 4-epimerase
Mpn257
GalE
2
Expasy
Mpn265
TrpS
2
Expasy
Mpn686
DnaA
multiple
16829961
Mpn629
TpiA
2
Expasy
Mpn576
GlyA
4
Expasy
Mpn627
PtsL
2
Expasy
by homology to
Leishmania donovani
M. pneumoniae by
similarity
M. pneumoniae by
similarity
by homology to
Bacillus subtilis
M. pneumoniae by
similarity
M. pneumoniae by
similarity
M. pneumoniae by
similarity
by homology to
Aquifex aeolicus
M. pneumoniae by
similarity
M. pneumoniae by
similarity
M. pneumoniae by
similarity
ATP-dependent protease
Lon
Probable tRNA
modification GTPase
UDP-galactopyranose
mutase
Uridylate Kinase Mpn632
Ribose-5-phosphateisomerase-B
Methionine
aminopeptidase,
Peptidase M
Acyl carrier protein (ACP)
synthase
Adenine
phosphoribosyltransferase
Tryptophanyl-tRNA
synthetase
Replication initiator protein
DnaA
Triosephosphate
isomerase
Serine
hydroxymethyltransferase
Phosphoenolpyruvateprotein transferase
General principles of cellular organization in Mycoplasma pneumoniae
M. pneumoniae by
similarity
M. pneumoniae by
similarity
M. pneumoniae by
similarity
by homology to
Thermotoga maritima
by homology to
Escherichia coli
by homology to
Sulfolobus solfataricus
by homology to
Thermotoga maritima
by homology to
Bacillus
stearothermophilus
by homology to
Thermotoga maritima
by homology to
Staphylococcus
aureus
193
Glycyl-tRNA synthetase
Mpn354
GlyqS
2
Expasy
Seryl-tRNA synthetase
Mpn005
SerS
2
Expasy
Bifunctional protein FolD
Mpn017
FolD
2
Expasy
Lysyl-tRNA synthase
Mpn277
LysS
2
Expasy
Histidyl-tRNA synthase
Mpn045
HisS
2
Expasy
Thioredoxin reductase
Mpn240
TrxB
2
Expasy
Chaperone protein dnaJ
Mpn021
DnaJ
2
Expasy
General principles of cellular organization in Mycoplasma pneumoniae
M. pneumoniae by
similarity
M. pneumoniae by
similarity
M. pneumoniae by
similarity
M. pneumoniae by
similarity
M. pneumoniae by
similarity
M. pneumoniae by
similarity
M. pneumoniae by
similarity
194
10.5. Table S5: List of modeled protein complexes.
This table is a list of binary interactions that can be modeled for all protein complexes in this study. It
is divided into i) a set of 29 heteromultimeric complexes and ii) a set of 57 homomultimeric
complexes. In part i) the first column gives the unique complex ID for each protein complex modeled.
Column 2 provides the complex name. In columns 3 and 4 give the systematic name and protein
name of the first interactor modeled, columns 5 and 6 give the systematic name and protein name of
the second interactor modeled. Columns 7 and 8 give the PDB ID and the species this information
was obtained from. In part ii) the first column on the left shows the complex ID of the homomultimeric
protein complexes modeled. The second column indicates the complex name. Columns 3 and 4 give
the annotated systematic and protein name of each homomultimer. Columns 5 and 6 give the PDB ID
and the species this information was obtained from. (* novel homomultimers supported by structural
models)
Interactor 1
Interactor 2
ComComplex
PDB
PDB species
plex
Systematic Protein Systematic Protein
name
ID
ID
name
name
name
name
i) Heteromultimeric complexes
Mpn007
Mpn007 Mpn450
Mpn450 1sxj S. cerevisiae
DNA Polymerase
3
Mpn007
Mpn007 Mpn618
DnaX
1njf
E. coli
III γ complex
Mpn450
Mpn450 Mpn618
DnaX
1iqp P. furiosus
Mpn002
Mpn002 Mpn434
DnaK
2qwq B. taurus
Mpn021
DnaJ
Mpn002
Mpn002
2och C. elegans
Protein
8
chaperone
Mpn021
DnaJ
Mpn434
DnaK
2qwq B. taurus
complex
Mpn120
GrpE
Mpn434
DnaK
1dkg E. coli
Mpn120
GrpE
Mpn531
ClpB
2tma O. cuniculus
9
Dnak-GrpE
complex
Mpn120
GrpE
Mpn434
DnaK
1dkg
E. coli
10
Mpn023
Aminoacyl-tRNA Mpn105
synthetase
Mpn105
complex
Mpn106
MetG
PheS
PheS
PheT
Mpn678
Mpn106
Mpn553
Mpn553
GltX
PheT
ThrS
ThrS
1g59
2rhs
2zcd
2e3c
T. thermophilus
S. haemolyticus
M. mazei
M. mazei
11
PhenylalaninetRNA synthetase Mpn105
complex
PheS
Mpn106
PheT
2rhs
S. haemolyticus
15
DNA
Recombination
complex
Mpn122
ParE
Mpn123
ParC
1bjt
S. cerevisiae
17
DNA
Topoisomerase
IV complex
Mpn122
ParE
Mpn123
ParC
1bjt
S. cerevisiae
19
25
Complex 19
Complex 25
Mpn076
Mpn223
Mpn076 Mpn284
HprK
Mpn258
Mpn284 2r6g E. coli
Mpn258 1kkm L. casei
Adk
FtsH
34
Restriction
Mpn185
enzyme complex
Mpn671
General principles of cellular organization in Mycoplasma pneumoniae
2rhm C. aurantiacus
195
35
Restriction
Mpn089
enzyme complex
36
Mpn089 Mpn507
Mpn507 1yf2
Complex 36
Mpn008
Mpn194
Mpn574
TrmE
CbiO2
GroS
Mpn426
Mpn426
Mpn573
P115
P115
GroL
2ocy S. cerevisiae
1mv5 L. lactis
1gru E. coli
37
GroEL-GroES
complex
Mpn574
GroS
Mpn573
GroL
1gru
E. coli
38
Peptidase
complex
Mpn218
OppF
Mpn609
PstB
2ouk
G.
stearothermophilus
40
Cohesin like
complex
Mpn426
P115
Mpn508
Mpn508 3bat
Mpn008
TrmE
Mpn426
P115
44
Pyruvate
dehydrogenase
complex
Mpn392
PdhB
Mpn393
PdhA
GroS
Mpn002
GrpE
GrpE
Mpn573
Mpn434
Mpn434
Mpn531
GroL
DnaK
DnaK
ClpB
S. cerevisiae
G.
1w85
stearothermophilus
1gru E. coli
2qwq B. taurus
1dkg E. coli
2tma O. cuniculus
AtpD
Mpn600
AtpA
2jj1
B. taurus
Mpn020
Mpn020
Mpn153
Mpn153
RpoA
RpoA
RpoA
AsnS
TopA
TopA
RpoD
RpoD
RpoC
Tmk
Tmk
Mpn137
Mpn137
Mpn137
InfB
InfB
InfB
RplC
RplW
RpsS
RplE
RpsZ
RpsH
RpsH
Mpn153
Mpn443
Mpn443
Mpn490
Mpn266
Mpn515
Mpn516
Mpn354
Mpn515
Mpn516
Mpn515
Mpn516
Mpn516
Mpn386
Mpn536
Mpn155
Mpn475
Mpn524
Mpn475
Mpn524
Mpn665
Mpn658
Mpn174
Mpn189
Mpn446
Mpn171
Mpn182
Mpn208
Mpn153
Mpn443
Mpn443
RecA
Mpn266
RpoC
RpoB
GlyQS
RpoC
RpoB
RpoC
RpoB
RpoB
Mpn386
RuvB
InfB
EngA
Mpn524
EngA
Mpn524
Tuf
RplS
RpsQ
RpsM
RpsD
RpsC
RpsE
RpsB
2qeq
8ohm
2qeq
2gbl
1z3e
2a69
1ynj
3bju
2nvq
2r7z
2a69
1smy
1ynn
2ccg
2ar7
2ocy
2ocy
2ba2
2zej
2eqb
2qmu
1voy
1ml5
2vqe
1ml5
2i2p
2avy
1s1h
Kunjin virus
Hepatitis C virus
Kunjin virus
S. elongatus
B. subtilis
T. thermophilus
T. aquaticus
H. sapiens
S. cerevisiae
S. cerevisiae
T. thermophilus
T. thermophilus
T. aquaticus
S. aureus
H. sapiens
S. cerevisiae
S. cerevisiae
M. pneumoniae
H. sapiens
S. cerevisiae
S. solfataricus
E. coli
E. coli
T. thermophilus
E. coli
E. coli
E. coli
S. cerevisiae
45
47
49
50
Mpn574
Mpn002
Glycolytic
enzyme complex Mpn120
2
Mpn120
ATP synthase
complex
Mpn598
Mpn020
Mpn020
Mpn153
Mpn153
Mpn191
Mpn191
RNA polymerase
Mpn191
complex
Mpn252
Mpn261
Mpn261
Mpn352
Mpn352
Mpn515
Ribosome
Mpn006
complex
Mpn006
Mpn137
Mpn137
Mpn137
Mpn155
Mpn155
Mpn155
Mpn165
Mpn167
Mpn169
Mpn177
Mpn178
Mpn179
Mpn179
General principles of cellular organization in Mycoplasma pneumoniae
M. jannaschii
A. irradians
2ocy
196
Mpn182
Mpn230
Mpn386
Mpn475
Mpn475
Mpn536
RpsE
RpsR
Mpn386
EngA
EngA
RuvB
Mpn446
Mpn228
Mpn536
Mpn524
Mpn665
Mpn571
RpsD
RpsF
RuvB
Mpn524
Tuf
Mpn571
1fjg
2vho
1sxj
2eqb
2zej
2chg
Mpn571
Mpn571 Mpn685
Mpn685 2olk
T. thermophilus
E. coli
S. cerevisiae
S. cerevisiae
H. sapiens
A. fulgidus
G.
stearothermophilus
52
Translation
elongation factor Mpn631
complex
Tsf
Mpn665
Tuf
54
Phosphotransfer
Mpn207
system complex
PtsG
Mpn268
Mpn268 1o2f
E. coli
Mpn004
GyrA
S. cerevisiae
1xb2
B. taurus
82
DNA Gyrase
complex
Mpn003
GyrB
92
Complex 92
Mpn258
Mpn258 Mpn259
Mpn259 2onk
A. fulgidus
93
ScpA-ThyA
complex
Mpn300
ScpA
Mpn320
ThyA
2oip
C. hominis
94
Ribonucleosidediphosphate
reductase
complex
Mpn322
NrdF
Mpn324
NrdE
2bq1
S. typhimurium
102
ParE-GyrA
complex
Mpn004
GyrA
Mpn122
ParE
1bjt
S. cerevisiae
1bjt
113
Restriction
Mpn343
enzyme complex
Mpn343 Mpn365
Mpn365 1yf2
M. jannaschii
115
Restriction
Mpn365
enzyme complex
Mpn365 Mpn615
Mpn615 1yf2
M. jannaschii
Com
plex
ID
Complex name
Systematic
name
Protein
name
PDB
ID
PDB species
DnaN
GyrB
Tmk
Mpn007
Mpn020
Pip
Fba
PolC
GlpK
Mpn051
DeoC
ManB
FruK
PheS
PheT
1mmi
1kij
2uvq
1njf
2qeq
1xkt
1rv8
2p1j
2dpn
1ryi
1jcj
2f7l
1gqt
1eqr
3bu2
E. coli
T. thermophilus
H. sapiens
E. coli
Kunjin virus
H. sapiens
T. aquaticus
T. maritima
T. thermophilus
B. subtilis
E. coli
S. tokodaii
E. coli
E. coli
S. saprophyticus
ii) Homomultimeric complexes
117
118
119
120
121*
122
124
125
126
127*
128
129
130
131
132
DNA polymerase III subunit β
DNA gyrase subunit B
Thymidylate kinase
Uncharacterized protein MG007 homolog
Uncharacterized ATP-dependent helicase Mpn020
Putative proline iminopeptidase
Fructose-biphosphate aldolase
DNA polymerase III PolC-type
Glycerol kinase
Uncharacterized protein MG039 homolog
Deoxyribose-phosphate aldolase
Phosphomannomutase
Putative 1-phosphofructokinase
Phenylalanyl-tRNA synthetase α chain
Phenylalanyl-tRNA synthetase β chain
Mpn001
Mpn003
Mpn006
Mpn007
Mpn020
Mpn022
Mpn025
Mpn034
Mpn050
Mpn051
Mpn063
Mpn066
Mpn079
Mpn105
Mpn106
General principles of cellular organization in Mycoplasma pneumoniae
197
134
135
136
137
139*
140
141*
142*
143
Putative Metallophosphoesterase
DNA-directed RNA polymerase subunit α
HPr kinase/phosphorylase
Single stranded DNA binding protein
Uncharacterized protein MG127 homolog
Probable inorganic polyphosphate/ATP-NAD kinase
2',3'-cyclic-nucleotide 2'-phosphodiesterase
Uncharacterized protein MG134 homolog
6-phosphofructokinase /Phosphohexokinase
Mpn126
Mpn191
Mpn223
Mpn229
Mpn266
Mpn267
Mpn269
Mpn275
Mpn302
Mpn126
RpoA
HprK
Ssb
Mpn266
PpnK
Mpn269
Mpn275
PfkA
1z2w
2cw0
1knx
1s3o
1r7h
1y3h
2pau
1j8b
1pfk
144
146
147
148
149
Pyruvate kinase
Cell division protein
Thymidylate synthase
Ribonucleoside-diphosphate reductase subunit β
Ribonucleoside-diphosphate reductase subunit α
Mpn303
Mpn317
Mpn320
Mpn322
Mpn324
Pyk
FtsZ
ThyA
NrdF
NrdE
2e28
1w58
1hw4
2bq1
2bq1
150
151*
152*
153*
154*
155
Probable endonuclease 4
Uncharacterized protein MG236 homolog
Uncharacterized protein MG246 homolog
Uncharacterized protein MG259 homolog
Uncharacterized protein MG263 homolog
Dihydrolipoyl lysine-residue acetyltransferase
Mpn328
Mpn329
Mpn349
Mpn362
Mpn381
Mpn391
Nfo
Mpn329
Mpn349
Mpn362
Mpn381
PdhC
1did
2fe3
1t71
2ipx
2p9j
1c4t
156
157
158
159*
Pyruvate dehydrogenase E1 component subunit β
Pyruvate dehydrogenase E1 component subunit α
Alanyl-tRNA synthetase
Uncharacterized protein MG293 homolog
Mpn392
Mpn393
Mpn419
Mpn420
PdhB
PdhA
AlaS
Mpn420
1w85
2r8p
1vhx
2pz0
160
161
162
163
164
166
167
168
169*
170
171
172
173
174
175
176
177
Glyceraldehyde-3-phosphate-dehydrogenase
Putative Xaa-Pro aminopeptidase
FMN-dependent NADH-azoreductase
Recombinase A
Probable L-ribulose-5-phosphate 3-epimerase UlaE
Chaperone protein ClpB
Acetate kinase
Probable thiamine biosynthesis protein
Uncharacterized protein MG377 homolog
Ribosomal RNA small subunit methyltransferase G
Arginine deiminase-like protein
Probable NH3-dependent NAD+ synthetase
60 kDa chaperonin
Enolase
Putative type I restriction enzyme specificity protein
Elongation factor Tu
L-lactate dehydrogenase
Mpn430
Mpn470
Mpn479
Mpn490
Mpn492
Mpn531
Mpn533
Mpn550
Mpn555
Mpn558
Mpn560
Mpn562
Mpn573
Mpn606
Mpn638
Mpn665
Mpn674
GapA
PepP
AzoR
RecA
UlaE
ClpB
AckA
ThiI
Mpn555
GidB
Mpn560
NadE
GroL
Eno
Mpn638
Tuf
Ldh
1nqa
1wn1
2z9c
1oft
1k77
2tma
1g99
1vbk
1zxj
1ne2
2ci5
1wxe
2nwc
1pdz
1yf2
2bvn
1uxg
M. musculus
T. thermophilus
M. pneumoniae
H. sapiens
C. ammoniagenes
M. tuberculosis
E. coli
H. Influenzae
E. coli
G.
stearothermophilus
M. jannaschii
H. sapiens
S. typhimurium
S. typhimurium
Arthrobacter sp.
nrrl
B. subtilis
M. pneumoniae
H. sapiens
A. aeolicus
E. coli
G.
stearothermophilus
E. coli
B. subtilis
T. tengcongensis
G.
stearothermophilus
P. horikoshii
E. coli
P. aeruginosa
E. coli
O. cuniculus
M. thermophila
P. horikoshii
M. pneumoniae
T. acidophilum
B. taurus
E. coli
E. coli
H. gammarus
M. jannaschii
E. coli
C. aurantiacus
Mpn677
Mpn677
2q14
B. thetaiotaomicron
178* Uncharacterized protein MG461 homolog
General principles of cellular organization in Mycoplasma pneumoniae
198
10.6. Table S6: List of multifunctional proteins.
This table gives a list of all multifunctional proteins. The first column indicates the annotated
systematic name. The second column provides the protein name.The third column gives all
complexes a multifunctional protein clusters to.
Systematic
name
Protein
name
Complexes
Mpn003
GyrB
35
83
58
59
112
99
34
46
56
101
96
29
Mpn004
GyrA
104
67
102
26
17
106
105
100
82
6
75
83
36
3
94
111
47
Mpn006
Tmk
90
17
15
Mpn007
Mpn007
28
3
10
105
Mpn011
Mpn011
6
4
99
3
5
Mpn014
Mpn014
84
103
106
97
10
12
Mpn020
Mpn020
104
11
26
17
48
93
106
3
97
61
94
108
98
101
43
10
86
Mpn025
Fba
28
106
97
9
105
Mpn027
Mpn027
109
85
79
Mpn034
PolC
112
90
21
83
86
Mpn042
Mpn042
74
60
1
24
14
Mpn048
Mpn048
14
107
62
54
10
105
82
105
110
Mpn060
MetK
16
17
15
107
Mpn061
Ffh
28
97
105
47
Mpn062
DeoD
92
11
56
97
10
Mpn063
DeoC
67
72
79
Mpn067
Mpn067
Mpn073
Prs
108
96
55
12
22
20
33
60
106
65
88
18
Mpn078
FruA
71
23
41
Mpn081
Mpn081
87
80
115
Mpn089
Mpn089
35
109
Mpn094
Mpn094
22
75
Mpn097
Mpn097
69
70
Mpn100
Mpn100
81
53
95
Mpn103
Mpn103
33
89
51
Mpn106
PheT
Mpn108
Mpn108
Mpn115
InfC
11
28
94
97
112
71
83
73
60
51
55
110
Mpn118
Mpn118
99
106
13
105
29
Mpn122
ParE
104
95
102
17
82
Mpn124
HrcA
73
13
Mpn141
MgpA
59
11
Mpn142
Mpn142
62
20
Mpn153
Mpn153
38
4
97
48
59
112
37
101
73
20
3
Mpn155
InfB
7
13
5
110
Mpn165
RplC
52
98
32
116
23
Mpn166
RplD
52
98
33
116
110
Mpn169
RpsS
51
110
55
Mpn177
RplE
111
79
Mpn189
RpsM
51
23
110
Mpn191
RpoA
67
53
51
18
106
Mpn192
RplQ
24
68
110
10
General principles of cellular organization in Mycoplasma pneumoniae
199
Mpn207
PtsG
3
64
68
12
47
79
48
98
18
93
86
54
Mpn210
SecA
74
67
33
32
90
91
98
103
56
24
43
86
Mpn211
UvrB
33
93
Mpn218
OppF
38
67
Mpn221
Pth
112
22
83
Mpn222
TilS
103
94
23
111
51
110
105
100
85
Mpn228
RpsF
33
53
57
Mpn230
RpsR
59
51
105
Mpn246
Def
6
4
34
3
100
Mpn257
GalE
112
27
109
28
83
Mpn258
Mpn258
25
92
3
68
86
Mpn264
Mpn264
36
75
Mpn269
Mpn269
25
77
Mpn277
LysS
25
53
76
Mpn280
Mpn280
53
64
89
Mpn284
Mpn284
19
86
Mpn294
Mpn294
60
57
Mpn300
ScpA
69
93
Mpn307
Mpn307
85
79
Mpn311
Mpn311
6
Mpn314
MraZ
42
Mpn315
MraW
43
105
Mpn316
Mpn316
46
68
Mpn320
ThyA
69
Mpn321
FolA
Mpn322
Mpn324
40
24
4
3
68
5
71
66
68
43
104
93
94
19
67
64
105
NrdF
11
63
94
NrdE
94
41
Mpn328
Nfo
61
24
Mpn329
Mpn329
11
67
Mpn330
Mpn330
60
61
Mpn331
Tig
32
90
13
65
Mpn340
Mpn340
112
27
28
83
68
5
47
48
102
82
79
101
Mpn341
UvrD
25
104
102
26
82
Mpn342
Mpn342
109
35
34
30
100
5
Mpn345
Mpn345
81
95
100
17
Mpn346
Mpn346
27
77
73
7
13
31
79
Mpn347
Mpn347
112
27
67
28
83
10
105
Mpn350
Mpn350
67
85
61
51
Mpn352
RpoD
84
103
67
37
Mpn354
GlyQS
60
28
97
105
Mpn361
PrfA
35
74
99
56
108
96
Mpn365
Mpn365
95
105
115
79
113
14
Mpn366
Mpn366
28
56
31
Mpn378
DnaE
105
20
Mpn379
PolA
116
91
Mpn387
Mpn387
76
16
17
15
107
Mpn388
Mpn388
1
24
105
Mpn390
PdhD
75
44
Mpn392
PdhB
106
36
71
66
37
Mpn393
PdhA
64
71
97
10
105
97
17
General principles of cellular organization in Mycoplasma pneumoniae
200
Mpn394
Nox
97
41
14
Mpn401
GreA
67
28
10
68
105
79
Mpn402
ProS
86
17
Mpn416
P29
71
100
Mpn419
AlaS
99
96
Mpn426
P115
93
86
Mpn430
GapA
12
33
85
53
56
106
67
33
32
7
80
26
17
99
88
100
110
28
75
40
95
108
112
69
49
10
104
11
53
78
107
93
106
46
23
96
65
50
3
51
111
9
114
58
12
15
8
52
81
34
45
86
19
5
10
105
110
36
108
112
34
37
10
19
86
5
Mpn434
DnaK
56
37
101
Mpn436
Mpn436
76
17
15
3
Mpn440
Mpn440
6
4
Mpn461
Mpn461
75
105
68
Mpn476
Cmk
75
58
Mpn480
ValS
18
30
51
Mpn486
Mpn486
90
101
82
Mpn487
Csd
98
76
111
Mpn497
Mpn497
109
85
Mpn509
Mpn509
81
58
Mpn514
Mpn514
1
39
21
2
Mpn515
RpoC
67
53
57
61
111
48
18
106
110
Mpn516
RpoB
53
57
61
111
51
17
47
107
106
87
106
43
44
96
29
20
44
Mpn520
IleS
Mpn526
Mpn526
11
97
108
51
112
27
28
21
Mpn531
ClpB
79
110
Mpn536
RuvB
95
71
100
Mpn547
Mpn547
81
25
23
Mpn550
ThiI
65
55
Mpn551
Mpn551
35
18
40
30
Mpn553
ThrS
11
97
51
12
38
106
37
Mpn556
ArgS
4
87
3
68
108
41
96
Mpn562
NadE
59
70
89
Mpn563
Mpn563
81
39
90
Mpn567
P200
6
24
Mpn568
Era
87
23
100
88
93
106
105
100
48
38
4
106
105
Mpn573
GroL
11
90
80
Mpn574
GroS
60
37
9
Mpn582
Mpn582
99
20
13
26
Mpn592
Mpn592
27
75
Mpn596
Mpn596
87
66
108
55
Mpn598
AtpD
3
97
12
47
Mpn599
AtpG
67
85
58
Mpn606
Eno
46
41
110
Mpn609
PstB
38
68
Mpn612
Mpn612
21
46
110
Mpn615
Mpn615
87
80
115
Mpn619
UvrA
75
105
Mpn622
RpsO
60
51
Mpn623
Mpn623
71
111
Mpn629
TpiA
3
46
113
110
General principles of cellular organization in Mycoplasma pneumoniae
201
Mpn635
Mpn635
7
55
Mpn644
Mpn644
69
93
Mpn650
Mpn650
81
90
Mpn656
Mpn656
109
71
100
Mpn658
RplS
33
23
26
100
Mpn662
MsrB
78
44
90
53
100
54
Mpn665
Tuf
Mpn668
Mpn668
104
33
32
39
90
41
Mpn669
TyrS
106
97
79
Mpn671
FtsH
Mpn673
Mpn673
38
92
34
67
61
Mpn676
Mpn676
87
80
Mpn677
Mpn677
21
26
Mpn678
GltX
22
103
23
Mpn685
Mpn685
56
37
51
110
Mpn686
DnaA
70
102
20
59
48
116
18
101
29
82
106
23
96
110
50
36
51
111
47
52
49
37
54
115
89
General principles of cellular organization in Mycoplasma pneumoniae
202
10.7. Table S7: List of literature curated multifunctional proteins.
This table is a repository of literature evidence for multifunctional proteins that may exist in M.
pneumoniae based on observed homologs in other species. In total 50 multifunctional proteins are
reported in this list. The first column on the left gives the annotated systematic name of each
multifunctional protein. The second and third column provide the protein name and protein functions.
The last column gives the PubMed ID or database, in which this evidence is reported.
PMID or
Systematic
Protein description
Functions, enzymatic activities
other
name
source:
Mpn002
DnaJ-like protein
17919282
Mpn008
tRNA modification
GTPase mnmE
DnaJ has a function as co-chaperone of dnaK,
but is also reported to be involved in DNA
replication in Escherichia coli
DNA gyrase catalyzes the interconversion of
various topological isomers of double-stranded
DNA rings, including catenanes and knotted
rings
DNA gyrase catalyzes the interconversion of
various topological isomers of double-stranded
DNA rings, including catenanes and knotted
rings
Thymidylate kinase can use purine and
pyrimidine nucleosides as substrates
Has both GTPase and tRNA modification
activities
Mpn003
DNA gyrase subunit B
Mpn004
DNA gyrase subunit A
Mpn006
Thymidylate kinase
Mpn025
Fructose-bisphosphate Glycolytic enzyme.
aldolase
In eukaryotes associates with vacuolar H+ATPase; contribute to its assembly, activity.
Aldolase interacts with the endocytic proteins
sorting nexin 9 (SNX9)
Role in actin cytoskeleton assembly; bind Factin.
Also binds g-tubuline, heparin, phospholipase
Dand the glucose transporter Glut4.
Histidyl-tRNA
Is a class-II aminoacyl-tRNA synthetase and is
synthetase
reported to interact with translation elongation
factors in mammals
Aspartyl-tRNA
Is a class-II aminoacyl-tRNA synthetase and is
synthetase
reported to interact with translation elongation
factors in mammals
Signal recognition
Respond to acid stress
particle protein
Protein export and membrane biogenesis
18453690
15299020
Mpn045
Mpn046
Mpn061
Mpn105
Phenylalanyl-tRNA
synthetase α-chain
Mpn106
Phenylalanyl-tRNA
synthetase β-chain
Mpn155
Translation initiation
factor IF-2.
Expasy
Expasy
18477629
12730230
12362348
12362348
11274114
Is a class-II aminoacyl-tRNA synthetase and is
12362348
reported to interact with translation elongation
factors in mammals
Is a aminoacyl-tRNA synthetase and is reported 12362348
to interact with translation elongation factors in
mammals
Is involved in the hydrolysis of GTP during the
Expasy
formation of the 70S ribosomal complex
Protects formylmethionyl-tRNA from
spontaneous hydrolysis and promotes its
binding to the 30S ribosomal
General principles of cellular organization in Mycoplasma pneumoniae
203
Mpn164
Mpn166
30S ribosomal protein
S10
50S ribosomal protein
L4
Mpn171
30S ribosomal protein
S3
Mpn172
50S ribosomal protein
L16
Mpn177
50S ribosomal protein
L5
Mpn178
50S ribosomal protein
S14 type Z
Mpn179
30S ribosomal protein
S8
Mpn189
30S ribosomal protein
S13
Mpn211
UvrABC system
protein B
50S ribosomal protein
L1
Mpn220
Involved in translation and NusB mediated
antitermination of transcription
Suppresses translation of S10 operon mRNA
also inhibits transcription of the s10 operon,
binds to L4 mRNA and inhibits translation
Is involved in translation and has an
endonuclease activity in Homo sapiens &
Escherichia coli and a lyase function in
Drosophila melanogaster
Is involved in translation; It is also seems to
make contacts with the A and possibly P site
tRNAs
Is involved in translation and L5-5S rRNA
complex stimulates aminoacyl-tRNA
synthetases
Is involved in translation, binds to S14 gene and
inhibits transcription
8871397
Is involved in translation and inhibits translation
by binding to mRNAs in specific ribosomal
cistrons
Is involved in translation and it associates with
the ribosomal protein S19 and RNA fragments
16S rRNA recognition though its C-terminal
domain
Helicase, nuclease and hydrolase activities
8871397
8871397
8871397
Expasy
8871397
8871397
8193163
GO
Is involved in translation and inhibits translation
by binding to mRNAs in specific ribosomal
cistrons
Peptidyl-tRNA
Releases tRNA from peptidyl-tRNAs by
hydrolase
cleavage of ester bond
Pth is also capable of hydrolysing an amide
bond between the peptide and the 3'-amino
group of the modified ribose at the end of the
tRNA. It also associates with the 30S ribosomal
subunit
30S ribosomal protein Is involved in translation and inhibits translation
S7
by binding to mRNAs in specific ribosomal
cistrons
Uracil-DNA
Glyceraldehyde-3-phosphate dehydrogenase
glycosylase
and transcriptional activation
Thioredoxin
Thioredoxin activity; synthesis of
deoxyribonucleotides. Also binds to the
Escherichia coli the T7 DNA polymerase
Segregation and
Chromosome segregation and condensation
condensation protein A DNA repair and transcription regulation
8871397
Mpn303
Pyruvate Kinase
15877277
Mpn320
Mpn332
Thymidylate synthase
ATP-dependent
protease La
Mpn221
Mpn226
Mpn235
Mpn263
Mpn300
Final step of glycolysis—the conversion of
phosphoenolpyruvate to pyruvate.
In mammalian muscle it binds thyroid hormone.
It regulates the transcriptional responses of the
thyroid-hormone receptor.
In bacteria, it can synthesize nucleotide
triphosphate (NTP) under anaerobic conditions
Pyrimidine metabolism. Translation inhibitor
Chaperone
General principles of cellular organization in Mycoplasma pneumoniae
16849786
8871397
1924305
768986
15009890
1924359
9149530
204
Mpn345
Mpn347
Mpn356
Putative type-1
restriction enzyme
MpnORFDP R protein
part 2
Putative type I
restriction enzyme
MpnORFDP R protein
part 1
Cysteinyl-tRNA
synthetase
Mpn379
DNA polymerase
(PolA)
Mpn384
Leucyl-tRNA
synthetase
Mpn430
Glyceraldehyde-3phosphate
dehydrogenase
Chaperone protein
dnaK
Mpn434
Mpn446
30S ribosomal protein
S4
Mpn480
Valyl-tRNA synthetase
Mpn520
Isoleucyl-tRNA
synthetase
Mpn538
50S ribosomal protein
L10
Mpn539
50S ribosomal protein
L7/L12
Mpn541
30S ribosomal protein
S20
Enolase
Mpn606
Mpn616
30S ribosomal protein
S9
Mpn622
30S ribosomal protein
S15
It has an ATP dependent nuclease as well as
DNA translocation function
16126220
It has an ATP dependent nuclease as well as
DNA translocation function
16126220
Is a class-I aminoacyl-tRNA synthetase and is
reported to interact with translation elongation
factors
5'-3' exonuclease, but also reverse transcriptase
activity in Streptomyces; part of the
Streptomyces telomere complex
Is a class-I aminoacyl-tRNA synthetase and is
reported to interact with translation elongation
factors in mammals
Converts glyceraldehyde-3-phosphate to 1,3diphosphoglycerate, but also binds RNA, RNA
polymerase and HPr in Bacillus subtilis
Besides its role as protein chaperone dnaK was
also shown to be involved in DNA replication
Escherichia coli
Is involved in translation, nucleats assembly of
the body of 30S ribosome by binding directly to
the 16S rRNA and inhibits translation by binding
to mRNAs in specific ribosomal cistrons in
Homo sapiens
Is a class-I aminoacyl-tRNA synthetase and has
two distinct active sites: one for aminoacylation
and one for editing.Additionally it is reported to
interact with translation elongation factors in
mammals
Is a class-I aminoacyl-tRNA synthetase and has
two distinct active sites: one for aminoacylation
and one for editing. Additionally it is reported to
specifically interact with HSP90 in mammals
Is involved in translation and inhibits translation
by binding to mRNAs in specific ribosomal
cistrons in Escherichia coli
Inhibits the translation of specific mRNAs
including its own in Homo sapiens
12362348
Is involved in translation and polyamine
biosynthesis in Saccharomyces cerevisiae
Catalyzes the conversion of 2-phosphoglycerate
to phosphoenolpyruvate in glycolysis, but further
it is reported to function also as heat-shock
protein, to bind cytoskeleton and chromatin
structures
Is involved in translation and participates in the
error prone SOS repair process in Escherichia
coli
Is involved in translation and seems to
selectively stabilize the temperature sensitive
cap-binding subunit of eIF-4E in
Saccharomyces cerevisiae
General principles of cellular organization in Mycoplasma pneumoniae
15353591
12362348
17142398
15877277
17919282
2470510
Uniprot
12362348
12362348
2470510
8871397
2470510
7539334
15877277
8871397
8871397
205
Mpn623
ATP-dependent RNA
helicase
Mpn665
Elongation factor Tu
Mpn671
Cell division protease
ftsH homolog
Mpn678
Glutamyl-tRNA
synthetase
Some members of the same family are involved
in RNA transcription, mRNA transport,
translation initiation and cell cycle regulation in
Homo sapiens
Elongation factor Tu promotes the GTPdependent binding of aminoacyl-tRNA to the Asite of ribosomes during protein biosynthesis, in
addition it has a direct function in host cell
adherence in M. pneumoniae
Metalloprotease, but has also chaperone
function in Escherichia coli
Is a class-I aminoacyl-tRNA synthetase and is
reported to specifically interact with HSP90 in
mammals
General principles of cellular organization in Mycoplasma pneumoniae
17979704
17709513
9149530
12362348
206