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Supplementary Information
Understanding the antimicrobial mechanism of TiO2-based nanocomposite films in a
pathogenic bacterium
Anna Kubacka1, María Suárez Diez2, David Rojo3, Rafael Bargiela1, Sergio Ciordia4, Inés
Zapico4, Juan P. Albar4, Coral Barbas3, Vitor A.P. Martins dos Santos2,5, Marcos FernándezGarcía1,* & Manuel Ferrer1,*
1
Institute of Catalysis, CSIC, 28049 Madrid, Spain, 2Chair of Systems and Synthetic Biology,
Wageningen University, 6703 HB Wageningen, The Netherlands, 3Center for Metabolomics and
Bioanalysis, University CEU San Pablo, Boadilla del Monte, 28668 Madrid, Spain, 4Proteomic
Facility, CNB-National Centre for Biotechnology, CSIC, 28049 Madrid, Spain, 5LifeGlimmer GmbH,
12163 Berlin, Germany.
1
Supplementary Methods
Gene chip experiments. The microarray analysis was performed with the Affymetrix P.
aeruginosa GeneChip. Each condition was performed in triplicate, and each biological
replicate was used for one GeneChip. In total, nine microarrays were used, which allowed
changes in gene expression to be determined with a confidence value of P < 0.001. The data
analyses were performed with applications belonging to the appropriate software packages
from the Bioconductor microarray analysis suite59. The quality of all of the chips was
assessed by fitting a linear model to the probe level data using the function fitPLM from the
affyPLM package. The expression values were computed using the Robust Multichip Average
algorithm60. The computations were performed using function “gc rma” from the package
“affy”. The Rank Products algorithm was used to identify differentially expressed genes 61. A
percentage of false positives (pfp) value of 0.05 was accepted.
Protein mass spectrometric analysis. The samples were centrifuged for 1 min at 16,000 x g
and 4°C. The supernatant was discarded, and the bacterial cell pellet was lysed in 1.2 ml of
BugBuster® Protein Extraction Reagent (Novagen, Darmstadt, Germany) for 30 min at 4°C
with further disruption by sonication (using a pin Sonicator® 3000; Misonix) for 2.5 min (10
watts) on ice (5 cycles x 0.5 min). The extracts were then centrifuged for 5 min at 12,000 x g
to separate the cell debris and intact cells. Finally, the supernatants were carefully aspirated
(to avoid disturbing the pellet) and transferred to a new tube.
Protein digestion and tagging with iTRAQ-4-plex® reagent: The total protein
concentration was determined using RC/DC protein assay (Bio-Rad, Madrid, Spain). For
digestion, 20 μg of protein from each condition (UV+EVOH and UV-TiO2-coated EVOH)
was precipitated by the methanol/chloroform method. Protein pellets were resuspended and
denatured in 20 µl of 6 M guanidine hydrochloride/100 mM 4-(2-hydroxyethyl)piperazine-1ethanesulphonic acid (HEPES), pH 7.5, (SERVA Electrophoresis GmbH), reduced with 1 µl
of 50 mM Tris(2-carboxyethyl) phosphine (TCEP, AB SCIEX, Foster City, CA, USA), pH
8.0, at 60°C for 30 min and then treated with 2 µl of 200 mM cysteine-blocking reagent
(methyl methanethiosulphonate (MMTS; Pierce, IL, USA) for 10 min at room temperature.
Samples were diluted up to 120 µl with 50 mM TEAB to reduce guanidine concentration.
Digestions were initiated by adding 1.5 µl (1 µg/µl) sequence grade-modified trypsin (Sigma
Chemical Co.; St. Louis, MO, USA) to each sample in a ratio 1/10 (w/w), which were then
incubated at 37°C overnight on a shaker. The digested samples were evaporated to dryness.
Each peptide solution was labelled at room temperature for 2 hours with a half unit of iTRAQ
2
Reagent Multi-plex kit (AB SCIEX, Foster City, CA, USA) that had been previously
reconstituted with 80 μl of 70% ethanol/50 mM TEAB. In iTRAQ labelling, tags 114 and 115
were used to label UV+EVOH and UV-TiO2-coated EVOH condition, respectively.
Afterwards, both labelled samples were combined and the labelling reaction was stopped by
the addition of 100 µl of 50% acetonitrile (ACN) and evaporation in a Speed Vac. The
digested, labelled and pooled peptide mixture was desalted using a Sep-PAK C18 Cartridge
(Waters, MA, USA), the following manufacturer’s instructions. Lastly, the cleaned tryptic
peptides were evaporated to dryness and stored at -20°C for further analysis.
Liquid chromatography and mass spectrometer analysis: A 2.5-µg aliquot of the resulting
mixture was subjected to 2D-nano LC ESI-MSMS analysis using a nano liquid
chromatography system (Eksigent Technologies nanoLC Ultra 1D plus, AB SCIEX, Foster
City, CA) coupled to high speed Triple TOF 5600 mass spectrometer (AB SCIEX, Foster
City, CA) with a duo spray ionisation source. The analytical column used was a silica-based
reversed phase column C18 ChromXP (75 µm × 15 cm) with a 3-µm particle size and a 120Å pore size (Eksigent Technologies, AB SCIEX, Foster City, CA). The trap column was a
C18 ChromXP (Eksigent Technologies, AB SCIEX, Foster City, CA) with a 3-µm particle
diameter and a 120-Å pore size, and it was switched on-line with the analytical column. The
loading pump delivered a solution of 0.1% formic acid in water at 2 µl/min. The nano-pump
provided a flow-rate of 300 nl/min and was operated under gradient elution conditions, using
0.1% formic acid in water as mobile phase A and 0.1% formic acid in ACN as mobile phase
B. Gradient elution was performed according the following scheme: isocratic conditions of
98% A: 2% B for 1 minutes, a linear increase to 30% B in 210 minutes, a linear increase to
40% B in 10 minutes, a linear increase to 90% B in 5 minutes, isocratic conditions of 90% B
for 5 minutes and a return to the initial conditions in 2 min. The injection volume was 5 µl.
Data acquisition was performed with a TripleTOF 5600 System (AB SCIEX, Concord, ON).
Data were acquired using an ion spray voltage floating (ISVF) 2800 V, curtain gas (CUR) 20,
interface heater temperature (IHT) 150, ion source gas 1 (GS1) 20, declustering potential
(DP) 85 V. All data were acquired using information-dependent acquisition (IDA) mode with
Analyst TF 1.5 software (AB SCIEX, Foster City, CA, USA). For the IDA parameters, 0.25 s
MS survey scan in the mass range of 350–1250 Da were followed by 15 MS/MS scans of 250
ms in the mass range of 100–1800 (total cycle time: 4.04 s). The switching criteria were set to
ions with mass to charge ratio (m/z) greater than 350 and smaller than 1250 with a charge
state of 2–5 and an abundance threshold of more than 90 counts (cps). Former target ions
3
were excluded for 20 s. IDA rolling collision energy (CE) parameters script was used for
automatically controlling the CE.
Data analysis: MS and MS/MS data obtained for pooled samples were processed using
Analyst® TF 1.5.1 Software (AB SCIEX, Foster City, CA, USA). Raw data file conversion
tools
generated
mgf
files,
which
were
also
searched
against
a
customised
UniProtKB/SwissProt database from P. aeruginosa (taxonid:208964), containing 5,572
protein coding genes and their corresponding reversed entries using the Mascot Server v.
2.3.02 (Matrix Science, London, UK). Search parameters were set as follows: enzyme,
trypsin; allowed missed cleavages, 1; fixed modifications, iTRAQ4plex (N-term and K) and
beta-methylthiolation of cysteine; variable modifications, oxidation of methionine. The
peptide mass tolerance was set to ± 20 ppm for precursors and 0.05 Da for fragment masses.
The confidence interval for protein identification was set to ≥ 95% (p<0.05), and only
peptides with an individual ion score above the 1% false discovery rate (FDR) threshold were
considered correctly identified. Only proteins having at least two quantified peptides and pvalues of ≤ 0.1 were considered in the quantitation62.
Metabolomic analysis by CE-TOF-MS. The samples were centrifuged for 1 min at 16,000 x
g and 4°C, and the cell pellets immediately mixed with 1.2 ml of cold (-80ºC) HPLC-grade
methanol (Sigma Chemical Co.; St. Louis, MO, USA). The samples were then stored at -80ºC
for 60 min. Then, the samples were vortex-mixed (for 10 seg) and sonicated for 30 s (10
watts) on ice (5 cycles x 0.5 min). After sonication, the pellet was removed by centrifugation
at 16,000 g for 20 min at 4ºC and the methanol solution was stored at -80ºC until use.
Immediately, 1.2 ml milli-Q H2O was added to the cell pellet, and, after re-suspension, the
samples were sonicated for 30 s (10 watts) on ice (5 cycles x 0.5 min). After sonication, the
pellet was removed by centrifugation at 16,000 x g for 20 min at 4ºC and the water solution
was separated. Finally, equal volumes (1 ml) of each of the methanol and H2O solutions were
mixed and stored at -80ºC until analysis. The analysis was performed as follows: Samples for
CE-MS analysis were prepared from a volume of 100 µl by evaporating to dryness using a
Speedvac Concentrator (Thermo Fisher Scientific Inc., Waltham, MA). Each sample was then
reconstituted in 100 µl of MilliQ® water with the internal standard (0.4 mM L-methionine
sulphone) and 0.1 M formic acid. A capillary electrophoresis system (7100 Agilent) coupled
with a TOF Mass Spectrometer (6224 Agilent) was employed for the CE-MS analysis of the
samples. The CE mode was controlled by ChemStation software (B.04.03, Agilent) and MS
mode by Mass Hunter Workstation Data Analysis (B.02.01, Agilent). The separation occurred
4
in a fused-silica capillary (Agilent) (total length, 100 cm; i.d., 50 μm). All separations were
carried out in normal polarity with a background electrolyte containing a 0.8 M formic acid
solution in 10% methanol (v/v) at 20ºC. New capillaries were pre-conditioned with a flush of
1.0 M NaOH for 30 min followed by MilliQ® water for 30 min and background electrolyte for
30 min. Before each analysis, the capillary was conditioned with a flush of background
electrolyte for 5 min. The sheath liquid (6 µl/min) was MeOH:H2O (1:1) containing 1.0 mM
formic acid with two reference masses: m/z 121.0509 ([C5H4N4+H]+) and m/z 922.0098
([C18H18O6N3P3F24+H]+), which allowed correction and higher mass accuracy in the MS. The
samples were hydrodynamically injected at 50 mBar for 50 s. The stacking was carried out by
applying background electrolytes at 100 mBar for 20 s. The separation voltage was 30 kV, the
internal pressure was 25 mBar and the analyses were carried out for 35 min. The MS
parameters were as follows: fragmentor, 100 V; skimmer, 65 V; octopole, 750 V; drying gas
temperature, 200 ºC; flow rate, 10 l/min; and capillary voltage, 3500 V. The data were
acquired in positive mode with a full scan from m/z 85 to 1000 at a rate of 1.41 scan/s. The
resulting data files were cleaned of background noise and unrelated ions by Mass Hunter
Qualitative Analysis software (B.05.00, Agilent). This tool was used to look for the target list
of the compounds (±20 ppm) that were interesting for the project in the corresponding
electropherograms. The identity of each compound was confirmed in a second analysis by
adding the corresponding standard (10 ppm) to the samples. Then, each sample was checked
for an increase in the peak; the result was positive in all cases. The following reagents have
been used for the metabolomic analysis: formic acid (MS grade - Sigma-Aldrich, Steinheim,
Germany), L-methionine sulphone (Sigma-Aldrich, Taufkirchen, Germany), sodium
hydroxide (Panreac-Montcada I Reixac, Spain), and the reference masses were purine and
hexakis (1H,1H,3H-tetrafluoropropoxy)phosphazine (HP)) from Agilent (API-TOF reference
mass solution kit). All solutions were prepared using MilliQ® water (Millipore, Billerica, MA,
USA).
Supplementray references
59.
Gentleman, R. C. et al. Bioconductor: open software development for computational
biology and bioinformatics. Genome Biol. 5, R80 (2004).
60.
Irizarry, R. A., Ooi, S. L., Wu, Z. & Boeke, J. D. Use of mixture models in a
microarray-based screening procedure for detecting differentially represented yeast
mutants. Stat. Appl. Genet. Mol. Biol. 2, 1544-6115 (2003).
5
61.
Breitling, R., Amtmann, A. & Herzyk, P. Graph-based iterative group analysis enhances
microarray interpretation. BMC Bioinformatics 5, 100 (2004).
62.
Matallana-Surget, S. et al. Shotgun redox proteomics: identification and quantitation of
carbonylated proteins in the UVB-resistant marine bacterium, Photobacterium angustum
S14. PLoS One 8, e68112 (2013).
63.
Benjamin, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and
powerful approach to multiple testing. J. R. Statist. Soc. 57, 289-300 (1995).
6
Supplementary Fig. S1 Upper panel: EPR spectra obtained in presence of the
nanocomposite film and DMPO spin trapping molecule under light excitation in water
or ethanol. Signals from the solvent were subtracted. Lower panel: Evolution of the
DMPO-OH• signal intensity obtained in water as a function of the irradiation time.
Ti-EVOH nanocomposite
DMPO/C2H5OH
20 min. UV
5 min. UV
1 min. UV
DMPO/H2O
g = 2.0056
20 min. UV
5 min. UV
1 min. UV
no UV
3430
3440
3450
3460
3470
3480
3490
DMPO-OH intensity / a.u.
Magnetic field / G
DMPO/H2O
0
5
10
15
20
25
UV irradiation time / min.
7
30
Supplementary Fig. S2 Expression level of genes encoding enzymes involved in the
catabolic pathway of glycine to the one carbon pool and related reactions under TiO2
photocatalysis. The genes encoding enzymes implicated in each particular reaction and their
expression levels are specifically indicated. Gene code as follows: gbcA, glycine betaine
demethylase subunit A (Rieske subunit); gbcB, glycine betaine catabolism protein; dgcB,
Dimethylglycine catabolism protein; soxABC, sarcosine oxidase subunits; katA and katB,
catalases; glyA2, serine hydroxymethyltransferase/glycine hydroxymethyltransferase; gcvP2,
glycine dehydrogenase (decarboxylating); gcvT2, aminomethyltransferase (glycine cleavage
system aminomethyltransferase); gcvH2, glycine cleavage system H protein; sdaB, L-serine
dehydratase. Colour code as follows: green, genes expressed (and thus reaction active) at
higher level; red, genes expressed (and thus reaction active) at lower level. The numbers in
parentheses are expression fold changes.
sdaB
(13.2)
NH3
Serine
Lower expression
NH3
Pyruvate
Tetrahydrofolate
Higher expression
glyA2
(50.5)
DimethylGlycine betaine
Sarcosine
glycine
soxA (6.8)
gbcA (19.5)
dgcB (7.8)
soxB (13.2)
gbcB (17.0)
O2
5,10-methylenetetrahydrofolate
Glycine
soxD (11.7)
H2O2
katA (6.6)
katB (59.7)
gcvP2 (39.1)
S-Amino-methydihydrolipoylprotein
8
gcvT2 (7.7)
gcvH2 (10.0)
Supplementary Fig. S3 Cartoon representing the major effects in cells of P. aeruginosa
when confronted to TiO2 photocatalysis. Colour code as follows: green, genes expressed
(and thus reaction active) at higher level; red, genes expressed (and thus reaction active) at
lower level. Abbreviations used: LPS, lipopolysaccharide; HSL, homo-serinelactone; THF,
tetrahydrofolate; 5,10-MTHF, 5,10-methylenetetrahydrofolate.
O2
H+ (out)
O2
Pi (out)
Iron homeostasis
H2O
Siderophore
Pho
regulon
Iron (in)
H+ (in)
Coenzymedepedent
e- transfer
Pi uptake
Acetyl CoA
Heme synthesis
& degradation
Sugar (out)
Serine
AccD
THF
Folding
Putrescine
HPr
Spermidine
Peptidoglycan
Chaperones
Cat/Perox
Pho
PvdR
Dnr
3’
Cell wall
Glycine
Sarcosine
5,10-MTHF
Transcription
system
GntR
Detoxification
system
5’
Cell
membrane
Ammonia (in)
PchR, GntR
FiuI, RsaL
5’
LPS
Coenzymeindepedent
e- transfer
H2O2
Glycine betaine
O2
One carbon
pool by folate
Glycolysis
Spermidine
synthase
Dissimilatory nitrate
respiration
H2O
Pyruvate
Malonyl-CoA
Sugar(in)
NO3- (out)
Ubiquinol
Iron (out)
RecANX
Lipid
metabolism
Lower expression
Higher expression
9
Signaling
system
Pyocianin
HpaR
DNA/RNA
repair System
HSL
Homoserine
lactone
AA
AA
AA
Supplementary Table S1 Cell inactivation rates and time for 50% reduction in
experiment concerning the elimination of several microorganisms with initial
concentration 8 x 108 cell ml-1.
Microorganism
Rate / 10-7 CFU ml-1 s-1 a
T1/2 / min a
Pseudomonas aeruginosa
63.1
5.5
Escherichia coli
1.9
10.1
Staphylococcus aureus
3.3
7.4
Enterococcus faecalis
1.7
19.1
Pichia jadinii
0.5
19.4
a) Standard error; ± 8; 0.5 min.
10
Supplementary Table S2 List of P. aeruginosa PAO1 genes most strongly induced in response to OH radicals. Data were statistically scored, using the
Student´s t-test. p-values were then adjusted for multiple testing, using the False Discovery Rate procedure of Benjamini and Hochberg63. Statistical analyses
were performed in R using the mulltest package. The data represent the mean of three independent experiments, with each chip experiment performed in
triplicate.
Gene
name
PA1540
PA0140
PA2850
Gene
name
ahpF
ohr
EC number
PA1982
exaA
EC 1.1.2.8
PA1541
PA3183
PA3584
PA4613
PA2825
PA4623
PA2444
zwf
glpD
katB
ospR
glyA2
PA3283
PA2826
PA1332
PA3182
PA2445
PA4714
PA0567_i
PA0848
PA3195
PA0069
PA1983
pgl
gcvP2
ahpB
gapA
exaB
EC 1.6.4.-
EC 1.1.1.49
EC 1.1.1.8
EC 2.1.2.1
EC 1.11.1.9
EC 3.1.1.31
EC 1.4.4.2
EC 1.6.4.EC 1.2.1.12
EC 1.9.3.1
Gene product
Biological category
FC:(class1/class2)
P value
Putative uncharacterized protein
Alkyl hydroperoxide reductase subunit F
Organic hydroperoxide reductase (Ohr subfamily
peroxiredoxin)
Quinoprotein ethanol dehydrogenase/ Glucose
dehydrogenase
Drug efflux transporter
Glucose-6-phosphate 1-dehydrogenase
Glycerol-3-phosphate dehydrogenase
Catalase
Transcriptional regulator
Putative uncharacterized protein
Serine hydroxymethyltransferase 2 / glycine
hydroxymethyltransferase
Putative uncharacterized protein
Glutathione peroxidase
Putative uncharacterized protein
6-Phosphogluconolactonase
Glycine dehydrogenase (decarboxylating] 1
Putative uncharacterized protein
Putative uncharacterized protein
Alkyl hydroperoxide reductase
Glyceraldehyde-3-phosphate dehydrogenase
Putative uncharacterized protein
Cytochrome c550
Unknown
Detoxification
Detoxification
224.2408
145.2743
74.0643
0
0
Central metabolic reaction (carbohydrate metabolism)
73.7251
Transport (ABC/Efflux pump transport)
Central metabolic reaction (carbohydrate metabolism)
Central metabolic reaction (carbohydrate metabolism)
Detoxification
Regulation (transcription regulation)
Unknown
Central metabolic reaction (amino acid metabolism)
73.374
67.3921
64.1499
59.7164
58.0861
56.1644
50.5342
Unknown
Detoxification
Unknown
Central metabolic reaction (carbohydrate metabolism)
Central metabolic reaction (amino acid metabolism)
Unknown
Unknown
Detoxification
Central metabolic reaction (carbohydrate metabolism)
Unknown
central metabolic reactions (energy production and conversion)
48.9415
46.5293
44.4957
42.3234
39.1214
35.7571
33.6694
33.1195
32.107
31.8945
31.8417
0
11
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
PA0849
PA4763
PA3282
PA3181
PA3126
PA1981
PA4356
PA2000
trxB2
recN
ibpA
xenB
dhcB
PA3281
PA0506
PA2288
PA0671
PA0922
PA2001
PA0613
PA3194
PA4994
PA4354
PA4881
PA1999
atoB
edd
dhcA
PA3007
PA0670
PA3284
PA0565
PA1736
PA5053
PA3930
PA1737
lexA
hslV
cioA
-
EC 1.8.1.9
EC 3.1.-.EC 4.1.2.14
EC 1.6.99.1
EC 2.8.3.8
EC 1.3.99.3
EC 2.3.1.9
EC 4.2.1.12
EC 1.3.99.3
EC 2.8.3.8
EC 2.3.1.9
EC 1.10.3.EC 1.1.1.35
Thioredoxin reductase
DNA repair protein RecN
Putative uncharacterized protein
2-Dehydro-3-deoxy-phosphogluconate aldolase
Heat-shock protein IbpA
Putative uncharacterized protein
NADH:flavin oxidoreductases (Old Yellow enzyme family)
3-Oxoacid CoA-transferase B subunit (Acyl
CoA:acetate/3-ketoacid CoA transferase, beta subunit )
Putative uncharacterized protein
Acyl-CoA dehydrogenase
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Acetyl-CoA acetyltransferase
Putative uncharacterized protein
Phosphogluconate dehydratase
Acyl-CoA dehydrogenase
Putative uncharacterized protein
Putative uncharacterized protein
3-Oxoacid CoA-transferase, A subunit (Acyl
CoA:acetate/3-ketoacid CoA transferase, alpha subunit )
Peptidase S24 LexA-like repressor
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Acetyl-CoA acetyltransferase or acyl-CoA thiolase
ATP-dependent protease hslV
Cytochrome Ubiquinol Oxidase
3-Hydroxyacyl-CoA dehydrogenase, NAD binding
domain (Crotonase/Enoyl-Coenzyme A (CoA) hydratase
superfamily)
Posttranslational modification, protein turnover, chaperones
DNA replication, recombination, modification and repair
Unknown
Central metabolic reaction (carbohydrate metabolism)
Posttranslational modification, protein turnover, chaperones
Unknown
central metabolic reactions (energy production and conversion)
Cell membrane structure (lipid metabolism)
31.7961
30.4606
29.8014
27.5867
24.9903
24.9542
24.0298
22.9917
Unknown
Cell membrane structure (lipid metabolism)
Unknown
Unknown
Unknown
Cell membrane structure (lipid metabolism)
Unknown
Central metabolic reaction (carbohydrate metabolism)
Cell membrane structure (lipid metabolism)
Unknown
Unknown
Cell membrane structure (lipid metabolism)
22.1633
21.3395
20.6712
20.2575
20.0785
19.5771
19.2665
19.1734
19.0445
18.7651
18.284
17.1444
Regulation (transcription regulation)
Unknown
Unknown
Unknown
Cell membrane structure (lipid metabolism)
Posttranslational modification, protein turnover, chaperones
central metabolic reactions (energy production and conversion)
Cell membrane structure (lipid metabolism)
16.9571
16.8393
16.7417
16.4815
16.4216
16.1266
15.9921
15.7455
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
12
PA4542
PA2116
PA4612
PA3616
PA4202
PA5023
PA2759
PA2830
PA5523
clpB
ankB
recX
htpX
hemL
PA1420
PA3008
PA0779
PA0132
PA2597
PA5106
bauA
-
PA4762
PA1847
PA3014
grpE
faoA
PA3951
PA1984
exaC
PA3531
PA0830
PA2486
PA2598
PA5314
PA4387
bfrB
-
EC 2.6.1.-
EC 3.5.3.13
EC 1.1.1.-
EC 1.2.1.3
Chaperone protein clpB
Putative uncharacterized protein
Ankyrin-like protein AnkB
Recombination regulator RecX
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Protease HtpX (heat shock protein)
Pyridoxal phosphate dependent aminotransferase (acetyl
ornithine aminotransferase / glutamate-1-semialdehyde
aminotransferase / 4-aminobutyrate aminotransferase)
Putative uncharacterized protein
Putative uncharacterized protein
ATP-dependent Lon protease (S16)
Beta-alanine-pyruvate transaminase
Putative uncharacterized protein
Metallo-dependent hydrolase or N-formimino-L-glutamate
deiminase
Heat shock protein GrpE
Putative uncharacterized protein
Fatty acid oxidation complex subunit alpha
(crotonase/Enoyl-Coenzyme A (CoA) hydratase
superfamily or 3-hydroxyacyl-CoA dehydrogenase)
Putative uncharacterized protein
NAD+ dependent aldehyde dehydrogenase ExaC /
NAD+-dependent acetaldehyde dehydrogenase II-like
protein
Bacterioferritin
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Posttranslational modification, protein turnover, chaperones
Unknown
Detoxification
DNA replication, recombination, modification and repair
Unknown
Unknown
Unknown
Posttranslational modification, protein turnover, chaperones
Central metabolic reaction (unclear: amino acid metabolism /
cofactor metabolism)
14.8436
14.7732
14.6468
14.3783
14.019
14.0036
13.8818
13.666
13.3908
Unknown
Unknown
Posttranslational modification, protein turnover, chaperones
Central metabolic reaction (amino acid metabolism)
Unknown
Central metabolic reaction (amino acid metabolism)
13.3016
13.2319
13.0406
13.013
12.954
12.8775
Posttranslational modification, protein turnover, chaperones
Unknown
Cell membrane structure (lipid metabolism)
12.8368
12.7353
12.7
Unknown
central metabolic reactions (energy production and conversion)
12.6763
11.9168
Transport (metal ion homeostasis)
Unknown
Unknown
Unknown
Unknown
Unknown
11.6399
11.3009
11.2703
11.1247
11.0667
11.0082
13
0
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
2,00E-004
2,00E-004
PA3952
PA4761
PA0635
PA3815
PA3287
PA0276
PA1970
PA2600
PA5522
PA0737
PA3416
PA3928
PA3193
PA2446
PA3441
PA5054
PA3811
PA0048
PA4355
PA4786
dnaK
ankB
pauA6
glk
gcvH2
hslU
hscB
-
PA2601
PA1596
PA0911
PA2483
PA5055
PA2112
PA4691
PA3814
PA0627
htpG
iscS
-
EC 6.3.1.2
EC 1.2.4.1
EC 2.7.1.2
EC 1.1.1.100
EC 1.8.3.1
EC 2.8.1.7
Putative uncharacterized protein
Chaperone protein dnaK
Putative uncharacterized protein
Putative uncharacterized protein
Ankyrin-like protein AnkB
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Glutamine synthetase
Putative uncharacterized protein
Pyruvate dehydrogenase E1 component, beta chain
Putative uncharacterized protein
Glucokinase
Glycine cleavage system H protein 1
Molybdopterin-binding protein
ATP-dependent hsl protease ATP-binding subunit hslU
Co-chaperone protein hscB
Transcriptional regulator
Major facilitator superfamily (MFS) transporter
Short-chain dehydrogenase/reductase SDR (3-ketoacyl(acyl-carrier-protein) reductase, sugar dehydrogenase,
etc.)
LysR-type transcriptional regulator
Chaperone protein htpG
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Sulfite oxidase subunit
Cysteine desulfurase
P2-like prophage tail protein X
Unknown
Posttranslational modification, protein turnover, chaperones
Unknown
Unknown
Detoxification
Unknown
Unknown
Unknown
Central metabolic reaction (amino acid metabolism)
Unknown
central metabolic reactions (energy production and conversion)
Unknown
Central metabolic reaction (carbohydrate metabolism)
Central metabolic reaction (carbohydrate metabolism)
General function prediction only
Posttranslational modification, protein turnover, chaperones
Posttranslational modification, protein turnover, chaperones
Regulation (transcription regulation)
Transport (ABC/Efflux pump transport)
Cell membrane structure (lipid metabolism)
10.9442
10.7914
10.7138
10.5915
10.4683
10.3728
10.2922
10.2393
10.1246
10.1134
10.0868
10.0327
9.9996
9.9929
9.8722
9.8313
9.8125
9.7966
9.7842
9.6656
Regulation (transcription regulation)
Posttranslational modification, protein turnover, chaperones
Unknown
Unknown
Unknown
Unknown
General function prediction only
Central metabolic reaction (amino acid metabolism)
Genomic prophage-mediated cell lysis
9.5104
9.3887
9.347
9.2023
9.1462
9.113
8.8159
8.8044
8.7973
14
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
3,00E-004
3,00E-004
3,00E-004
3,00E-004
3,00E-004
3,00E-004
3,00E-004
3,00E-004
PA5525
-
PA3971
PA3013
foaB
PA3617
PA0738
PA1865
PA5105
PA2665
recA
hutC
fhpR
EC 2.3.1.16
PA1333
PA0493
PA0449
PA5312
pauC
PA5546
PA2111
PA0131
PA5524
-
PA0610
PA2442
prtN
gcvT2
PA5104
PA2002
PA3237
PA5313
gabT2
EC 2.6.1.-
PA3929
cioB
EC 1.10.3.-
EC 6.4.1.2
EC 1.2.1.10
EC 1.1.1.100
EC 2.1.2.10
DNA-binding domain of the GntR family of transcriptional
regulator
Putative uncharacterized protein
Fatty-acid oxidation complex beta-subunit (3-ketoacylCoA thiolase / acetyl-CoA acetyltransferase)
DNA recombination protein recA
Putative uncharacterized protein
Putative uncharacterized protein
GntR family transcriptional regulator
Transcriptional regulator containing GAF, AAA-type
ATPase
Putative uncharacterized protein
Biotin carboxyl carrier protein of acetyl-CoA carboxylase
Putative uncharacterized protein
NAD(P)+-dependent aldehyde dehydrogenase (gammaglutamyl-gamma-aminobutyraldehyde dehydrogenase;
10-formyltetrahydrofolate dehydrogenase, etc.)
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Short-chain dehydrogenase/reductase SDR (3-ketoacyl(acyl-carrier-protein) reductase, sugar dehydrogenase,
etc.)
Pyocin activator protein PrtN
Aminomethyltransferase (glycine cleavage system
aminomethyltransferase)
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Pyridoxal phosphate dependent aminotransferase (acetyl
ornithine aminotransferase / glutamate-1-semialdehyde
aminotransferase / 4-aminobutyrate aminotransferase)
Cytochrome bd-type quinol oxidase, subunit 2
(respiratory pathway)
Regulation (transcription regulation)
8.6621
Unknown
Cell membrane structure (lipid metabolism)
8.5293
8.5124
DNA replication, recombination, modification and repair
Unknown
Unknown
Regulation (transcription regulation)
Regulation (transcription regulation)
8.4985
8.4728
8.4397
8.134
8.1306
Unknown
Cell membrane structure (lipid metabolism)
Unknown
central metabolic reactions (energy production and conversion)
8.0429
7.9763
7.973
7.9368
Unknown
Unknown
Unknown
General function prediction only
7.8819
7.8739
7.8687
7.8608
Regulation (transcription regulation)
Central metabolic reaction (amino acid metabolism)
7.8316
7.7727
Unknown
Unknown
Unknown
Central metabolic reaction (unclear: amino acid metabolism /
cofactor metabolism)
7.7471
7.7215
7.7123
7.577
central metabolic reactions (energy production and conversion)
7.5209
4,00E-004
4,00E-004
4,00E-004
4,00E-004
4,00E-004
4,00E-004
4,00E-004
4,00E-004
5,00E-004
5,00E-004
5,00E-004
5,00E-004
5,00E-004
5,00E-004
5,00E-004
5,00E-004
5,00E-004
5,00E-004
5,00E-004
5,00E-004
6,00E-004
6,00E-004
6,00E-004
15
PA0249
PA0839
PA3969
PA4435
PA2788
-
PA3414
PA0612
ptrB
PA0624
PA1744
PA4692
PA2849
PA1535
PA0907
PA4236
PA3676
PA4841
PA0623
PA2776
PA0130
PA0665
PA3092
ohrR
katA
bauC
erpA
fadH1
PA1551
PA4353
PA2943
PA1550
PA0622
PA1743
PA5026
-
EC 1.3.99.3
EC 1.8.3.1
EC 1.3.99.3
EC 1.2.1.EC 1.3.1.34
EC 2.5.1.54
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Long chain acyl-CoA dehydrogenase
Type IV pili Methyl-accepting chemotaxis protein
Putative uncharacterized protein
Phage/conjugal plasmid C-4 type zinc finger protein,
TraR family
Putative uncharacterized protein
Putative uncharacterized protein
Sulfite oxidase (SO) family protein
DNA-binding transcriptional repressor MarR
Long chain acyl-CoA dehydrogenase
Putative uncharacterized protein
Catalase
Cation/multidrug efflux pump AcrB/AcrD/AcrF family
Nudix hydrolase superfamily protein
Phage contractile tail tube protein, P2 family
Putative uncharacterized protein
NAD(P)+ dependent aldehyde dehydrogenase
Iron-sulfur cluster assembly accessory protein erpA
NADH:flavin oxidoreductases, Old Yellow Enzyme family
(2.4-dienoyl-CoA reductase (DCR) FMN-binding domain
FadH1)
Polyferredoxin
Putative uncharacterized protein
Phospho-2-dehydro-3-deoxyheptonate aldolase
Putative uncharacterized protein
Phage tail sheath protein FI
Putative uncharacterized protein
Putative uncharacterized protein
Unknown
Unknown
Unknown
Cell membrane structure (lipid metabolism)
Chemotaxis (Cell motility and secretion / Signal transduction
mechanisms)
Unknown
Regulation (transcription regulation)
7.4387
7.4093
7.3242
7.3023
7.2161
Unknown
Unknown
General function prediction only
Regulation (transcription regulation)
Cell membrane structure (lipid metabolism)
Unknown
Detoxification
Transport (ABC/Efflux pump transport)
General function prediction only
Genomic prophage-mediated cell lysis
Unknown
central metabolic reactions (energy production and conversion)
Posttranslational modification, protein turnover, chaperones
central metabolic reactions (energy production and conversion)
6.9589
6.945
6.7923
6.7138
6.7125
6.6848
6.6672
6.6595
6.5451
6.5013
6.4245
6.2767
6.272
6.2164
central metabolic reactions (energy production and conversion)
Unknown
Central metabolic reaction (amino acid metabolism)
Unknown
Genomic prophage-mediated cell lysis
Unknown
Unknown
16
7.1379
6.9723
6.1362
6.0699
5.98
5.9741
5.9251
5.9092
5.8808
6,00E-004
6,00E-004
6,00E-004
6,00E-004
6,00E-004
7,00E-004
7,00E-004
7,00E-004
7,00E-004
8,00E-004
8,00E-004
8,00E-004
8,00E-004
8,00E-004
9,00E-004
9,00E-004
9,00E-004
0,001
0,001
0,001
0,001
0,001
0,0011
0,0011
0,0012
0,0012
0,0012
0,0012
PA2692
PA0910
PA0634
PA5528
PA4760
PA4385
PA3577
PA0492
dnaJ
groEL
PA0887
PA4359
PA1606
PA5367
acsA
PA4358
PA2426
lamB
pstA
pvdS
PA5369
PA0921
PA5368
PA5475
PA2119
pstS
PA1546
PA5366
hemN
pstB
PA2762
PA2428
PA5361
PA1673
PA5360
PA4357
EC 6.2.1.1
pstC
phoR
phoB
EC 1.1.1.2 or
EC 1.2.1.46
EC 1.3.3.3
Iron-responsive transcriptional regulator rrf2
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Chaperone protein dnaJ
Molecular chaperone GroEL (60 kDa chaperonin)
Putative uncharacterized protein
Putative lactam utilization protein LamB
Regulation (transcription regulation)
Unknown
Unknown
Unknown
Posttranslational modification, protein turnover, chaperones
Posttranslational modification, protein turnover, chaperones
Unknown
General function prediction only
5.8456
5.7712
5.7583
5.7228
5.6662
5.6106
5.6009
5.5611
Acyl-coenzyme A synthetase/AMP-(fatty) acid ligase
Putative uncharacterized protein
Putative uncharacterized protein
Membrane protein component of ABC phosphate
transporter
Ferrous iron transport protein
RNA polymerase sigma-70 factor controlling pyoverdine
biosynthesis
Phosphate ABC transporter substrate-binding protein
Putative uncharacterized protein
Phosphate ABC transporter permease
Putative uncharacterized protein
Threonine dehydrogenase and related Zn-dependent
dehydrogenases
Oxygen-independent coproporphyrinogen III oxidase
PstB ATP-binding component of ABC phosphate
transporter
Putative uncharacterized protein
Putative uncharacterized protein
Phosphate regulon sensor protein PhoR
Hemerythrin-like non-heme diiron oxygen transport
protein
Phosphate regulon transcriptional regulatory protein
PhoB
Putative uncharacterized protein
Cell membrane structure (lipid metabolism)
Unknown
Unknown
Inorganic phosphate (Pi) uptake
5.5524
0.0086
0.0134
0.0141
Transport (metal ion homeostasis)
Pyoverdine siderophore biosynthesis
0.0175
0.0206
Inorganic phosphate (Pi) uptake
Unknown
Inorganic phosphate (Pi) uptake
Unknown
Central metabolic reaction (amino acid metabolism)
0.0236
0.0249
0.0261
0.028
0.0286
Central metabolic reaction (cofactor metabolism (porphyrin))
Inorganic phosphate (Pi) uptake
0.0289
0.0304
Unknown
Unknown
Inorganic phosphate (Pi) uptake
Transport (metal ion homeostasis)
0.0376
0.0387
0.0406
0.0416
Inorganic phosphate (Pi) uptake
0.0419
Unknown
0.0452
0,0012
0,0012
0,0013
0,0013
0,0013
0,0014
0,0014
0,0014
0,0014
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
17
0
0
PA5170
PA5232
PA5396
PA5410
PA0200
PA3904
PA3309
PA5411
PA2425
PA3530
PA1557
arcD
gbcA
gbcB
pvdG
EC 3.1.2.14
ccoN2
EC 1.9.3.1
PA3556
PA5365
PA3236
arnT
phoU
EC 2.4.2.43
PA2394
PA1431
PA0527
PA1746
PA5427
PA3250
PA2398
PA2384
PA4577
PA2396
PA5379
PA2513
PA2392
PA3558
PA5397
pvdN
rsaL
dnr
EC 2.8.1.7
adhA
EC 1.1.1.1
fpvA
pvdF
sdaB
antB
pvdP
EC 6.3.2EC 4.3.1.17
EC 1.14.12.1
Arginine/ornithine antiporter permease
Putative uncharacterized protein
Putative uncharacterized protein
Glycine betaine demethylase subunit A (Rieske subunit)
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Glycine betaine catabolism protein
Pyoverdine synthetase PvdG
Putative uncharacterized protein
cbb3-type cytochrome C oxidase subunit I (CcoN
subunit)
4-Amino-4-deoxy-L-arabinose transferase
Phosphate uptake regulator
ABC-type proline/glycine betaine transport system
protein
Pyoverdine synthetase PvdN
Virulence gene repressor RsaL
Catabolite gene activator protein (CAP)
Putative uncharacterized protein
Alcohol (sugar) dehydrogenase
Putative uncharacterized protein
TonB-like ferripyoverdine receptor
Putative uncharacterized protein
Putative uncharacterized protein
Pyoverdine synthetase PvdF
L-serine dehydratase
Anthranilate dioxygenase small subunit
Pyoverdine synthetase PvdP
Putative uncharacterized protein
Putative uncharacterized protein
Transport (ABC/Efflux pump transport)
Unknown
Unknown
Central metabolic reaction (amino acid metabolism)
Unknown
Unknown
Unknown
Central metabolic reaction (amino acid metabolism)
Pyoverdine siderophore biosynthesis
Unknown
central metabolic reactions (energy production and conversion)
0.0477
0.0499
0.0512
0.0514
0.0525
0.0532
0.056
0.0591
0.0596
0.0613
0.0617
Cell wall structure (lipopolysaccharide metabolism)
Inorganic phosphate (Pi) uptake
Transport (ABC/Efflux pump transport)
0.0639
0.0639
0.0642
Pyoverdine siderophore biosynthesis
Regulation (transcription regulation)
Regulation (transcription regulation)
Unknown
central metabolic reactions (energy production and conversion)
Unknown
Pyoverdine siderophore biosynthesis
Unknown
Unknown
Pyoverdine siderophore biosynthesis
Central metabolic reaction (amino acid metabolism)
General function prediction only
Pyoverdine siderophore biosynthesis
Unknown
Unknown
0.0647
0.0664
0.0675
0.068
0.0699
0.0704
0.0716
0.0742
0.0746
0.0748
0.0758
0.0759
0.0782
0.0783
0.0816
18
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
1,00E-004
1,00E-004
PA4300
PA3557
PA4844
PA2393
PA5417
PA2395
PA3249
PA4610
PA4227
PA4348
PA2413
PA4299
PA5416
PA5027
PA4350
PA2397
PA3880
PA4067
PA3476
PA2358
PA5231
PA2427
PA4773
PA3278
PA2386
PA3572
PA5398
PA3280
PA3337
Putative uncharacterized protein
Putative uncharacterized protein
Methyl-accepting chemotaxis protein
soxD
pvdO
gntR
EC 3.4.13.EC 1.5.3.1
EC 1.8.99.-
pchR
pvdH
tadD
soxB
EC 2.6.1.76
EC 1.5.3.1
pvdE
oprG
rhlL
EC 2.3.1.184
speD
EC 4.1.1.50
pvdA
EC 1.13.12.-
dgcA
oprO
rafD
EC 1.5.1.29
EC 5.1.3.20
Zn-dependent dipeptidase or amidohydrolase
Sarcosine oxidase delta subunit
Pyoverdine biosynthesis protein PvdO
GntR family of transcriptional regulator
Putative uncharacterized protein
Transcriptional regulator pchR containing an amidase
domain and an AraC-type DNA-binding
Putative uncharacterized protein
Aspartate beta-semialdehyde dehydrogenase
Flp pilus assembly protein TadD
Sarcosine oxidase beta subunit
Putative uncharacterized protein
Putative uncharacterized protein
Pyoverdine biosynthesis protein PvdE
Putative uncharacterized protein
Outer membrane protein OprG
N-acyl-L-homoserine lactone synthetase rhlI
Putative uncharacterized protein
Probable ATP-binding/permease fusion ABC transporter
Putative uncharacterized protein
S-adenosylmethionine decarboxylase
Putative uncharacterized protein
L-ornithine 5-monooxygenase
Putative uncharacterized protein
NADH:flavin oxidoreductase (Old Yellow Enzyme family)
Phosphate-specific outer membrane porin OprO
ADP-L-glycero-D-manno-heptose-6-epimerase
Unknown
Unknown
Chemotaxis (Cell motility and secretion / Signal transduction
mechanisms)
Pyoverdine siderophore biosynthesis
Central metabolic reaction (amino acid metabolism)
Pyoverdine siderophore biosynthesis
Regulation (transcription regulation)
Unknown
Regulation (transcription regulation)
0.0818
0.0819
0.0847
Unknown
Pyoverdine siderophore biosynthesis
Cell wall structure (pilus biosynthesis)
Central metabolic reaction (amino acid metabolism)
Unknown
Unknown
Pyoverdine siderophore biosynthesis
Unknown
Cell wall structure (protein insertion)
Signaling (synthesis of quorum-sensing signal molecules
(homoserine lactone))
Unknown
Transport (ABC/Efflux pump transport)
Unknown
Spermidine biosynthesis
Unknown
Pyoverdine siderophore biosynthesis
Unknown
central metabolic reactions (energy production and conversion)
Inorganic phosphate (Pi) uptake
Cell wall structure (lipopolysaccharide metabolism)
0.0894
0.0897
0.0905
0.0912
0.0913
0.0914
0.0917
0.0944
0.0973
0.0983
19
0.0853
0.0856
0.0879
0.0889
0.089
0.0894
0.0991
0.1012
0.1031
0.1046
0.1047
0.105
0.1055
0.106
0.1082
0.109
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
1,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
PA2391
PA3906
PA3254
PA4775
PA2804
PA2385
PA4774
PA0929
PA0802
PA2389
PA0028
PA0674
PA0111
PA1300
PA0105
PA4782
PA4135
opmQ
pvdQ
speE
phoB
pvdR
vreA
coxB
EC 1.9.3.1
hpaR
PA4710
phuR
PA4370
PA2862
icmP
lipA
PA4298
PA0842
PA5399
PA2365
PA4776
PA4351
PA2939
PA0540
EC 3.5.1.97
EC 2.5.1.16
EC 3.1.1.3
EC 2.4.2.dgcB
pmrA
olsA
EC 3.4.11.-
ATP-dependent efflux pump
Putative uncharacterized protein
ATP-binding cassette domain of the carbohydrate and
solute transporter-like ABC transporter
Putative uncharacterized protein
Putative uncharacterized protein
Pyoverdine synthetase PvdQ
Spermidine synthase 2
Phosphate regulon transcriptional regulatory protein
Putative uncharacterized protein
Pyoverdine regulatory protein PvdR
Putative uncharacterized protein
TonB-like ferripyoverdine receptor
Cytochrome c oxidase subunit
RNA polymerase sigma-70 factor (ECF subfamily)
Cytochrome c oxidase subunit 2
Putative uncharacterized protein
Homoprotocatechuate degradation operon regulator
HpaR
TonB-dependent hemoglobin/transferrin/lactoferrin
receptor family protein
Uncharacterized iron-regulated membrane protein
Lactonizing lipase
Pyoverdine siderophore biosynthesis
Unknown
Transport (ABC/Efflux pump transport)
0.1098
0.1117
0.1132
Unknown
Unknown
Pyoverdine siderophore biosynthesis
Spermidine biosynthesis
Inorganic phosphate (Pi) uptake
Unknown
Pyoverdine siderophore biosynthesis
Unknown
Transport (metal ion homeostasis)
central metabolic reactions (energy production and conversion)
Regulation (transcription regulation)
central metabolic reactions (energy production and conversion)
Unknown
Regulation (transcription regulation)
0.1134
0.1134
0.1165
0.1175
0.1182
0.1192
0.1194
0.1205
0.1208
0.1211
0.1222
0.1236
0.1239
0.1244
Transport (metal ion homeostasis)
0.1245
Transport (metal ion homeostasis)
Signaling (synthesis of quorum-sensing signal molecules
(homoserine lactone))
Unknown
Cell wall structure (lipopolysaccharide metabolism)
Central metabolic reaction (amino acid metabolism)
Unknown
Regulation (transcription regulation)
Cell membrane structure (lipid metabolism)
General function prediction only
Unknown
0.1246
0.1249
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
2,00E-004
3,00E-004
3,00E-004
3,00E-004
3,00E-004
3,00E-004
3,00E-004
3,00E-004
3,00E-004
3,00E-004
3,00E-004
3,00E-004
Putative uncharacterized protein
Glycosyl transferase family 1 protein
Dimethylglycine catabolism protein
Putative uncharacterized protein
Two-component transcriptional regulator PmrA
Lysophospholipid acyltransferase (LPLATs)
Zn-peptidase (aminopeptidase / carboxypeptidase)
Putative uncharacterized protein
20
0.1253
0.1275
0.1284
0.1296
0.1333
0.1345
0.1364
0.1367
3,00E-004
3,00E-004
3,00E-004
4,00E-004
4,00E-004
4,00E-004
4,00E-004
4,00E-004
4,00E-004
5,00E-004
5,00E-004
PA3907
PA2305
ambB
PA3153
wzx
PA0052
PA0526
PA2803
PA1812
PA1353
PA5418
PA4709
PA3910
PA1199
PA5058
PA3559
PA3296
PA0107
PA3905
PA3477
PA3252
PA4777
PA3467
PA3253
PA4675
PA5400
PA4302
PA2411
PA4479
EC 6.2.1.3
mltD
EC 4.2.2.-
soxA
EC 1.5.3.1
phaC2
EC 1.1.1phoA
rhlR
pmrB
tadA
mreD
Putative uncharacterized protein
Nonribosomal peptide synthase (pyocyanin synthesis
protein)
Membrane protein (involved in the export of Oantigen/lipopolysaccharides)
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Membrane-bound lytic murein transglycosylase D
Putative uncharacterized protein
Sarcosine oxidase alpha subunit
Heme degradation protein
Putative uncharacterized protein
Cell wall peptidase (lipoprotein)
Poly(3-hydroxyalkanoic acid) synthase 2
Nucleotide sugar dehydrogenase (catalyze the NADdependent 2-fold oxidation of an alcohol to an acid
without the release of an aldehyde intermediate)
Periplasmic alkaline phosphatase
Cytochrome c oxidase subunit
Putative uncharacterized protein
Transcriptional regulatory protein with autoinducer
binding domain
ABC transporter permease
Two-component regulator system signal sensor kinase
PmrB (or histidine kinase-like ATPase)
Major facilitator superfamily (MFS) transporter
ABC transporter permease
TonB-like ferripyoverdine receptor
Electron transfer flavoprotein alpha subunit
Flp pilus assembly protein, ATPase CpaF
Pyoverdine synthetase
Cell shape-determining protein MreD
Unknown
Signaling (synthesis of quorum-sensing signal molecules
(pyocianin))
Cell wall structure (lipopolysaccharide metabolism)
0.1388
0.141
Unknown
Unknown
Unknown
Cell wall structure (peptidoglycan metabolism)
Unknown
Central metabolic reaction (amino acid metabolism)
Transport (metal ion homeostasis)
Unknown
Cell wall structure (protein insertion)
Central metabolic reaction (carbohydrate metabolism)
Cell wall structure (lipopolysaccharide metabolism)
0.1421
0.1432
0.1441
0.1455
0.1455
0.1456
0.1456
0.1456
0.1463
0.1476
0.1479
Inorganic phosphate (Pi) uptake
central metabolic reactions (energy production and conversion)
Unknown
Regulation (transcription regulation)
0.1482
0.1483
0.1497
0.1499
Transport (ABC/Efflux pump transport)
Regulation (transcription regulation)
0.15
0.1501
Transport (ABC/Efflux pump transport)
Transport (ABC/Efflux pump transport)
Transport (metal ion homeostasis)
central metabolic reactions (energy production and conversion)
Cell wall structure (pilus biosynthesis)
Pyoverdine siderophore biosynthesis
Cell wall structure (peptidoglycan metabolism)
0.1508
0.1517
0.1517
0.1536
0.1544
0.1574
0.1638
21
5,00E-004
5,00E-004
0.1418
5,00E-004
5,00E-004
5,00E-004
6,00E-004
6,00E-004
6,00E-004
6,00E-004
6,00E-004
6,00E-004
6,00E-004
6,00E-004
6,00E-004
6,00E-004
6,00E-004
7,00E-004
7,00E-004
7,00E-004
8,00E-004
8,00E-004
8,00E-004
8,00E-004
8,00E-004
8,00E-004
9,00E-004
9,00E-004
PA0108
PA4471
PA4497
PA0106
PA0594
PA4306
PA4496
PA4677
PA5456
PA0377
PA3724
coIII
EC 1.9.3.1
coxA
surA
EC 1.9.3.1
EC 5.2.1.8
PA4778
cueR
PA1200
PA3112
PA0938
PA3648
PA5568
PA0472
PA5340
PA2371
lasB
accD
opr86
oxaA
fiuI
EC 6.4.1.2
Cytochrome c oxidase, subunit III
Putative uncharacterized protein
ABC transporter
Cytochrome c oxidase, subunit I
Chaperone peptidyl-prolyl cis-trans isomerase SurA
Putative uncharacterized protein
ABC transporter
Putative uncharacterized protein
Putative uncharacterized protein
Putative uncharacterized protein
Peptidase M4 family protein (thermolysin, protealysin,
aureolysin and neutral protease)
Helix-Turn-Helix DNA binding domain of CueR-like
transcription regulator
Putative uncharacterized protein
Acetyl-CoA carboxylase beta subunit
Putative uncharacterized protein
Probable outer membrane protein
Inner membrane translocase protein oxaA
RNA polymerase sigma-70 factor (ECF subfamily)
Putative uncharacterized protein
ClpA/B-type protease
central metabolic reactions (energy production and conversion)
Unknown
Transport (ABC/Efflux pump transport)
central metabolic reactions (energy production and conversion)
Posttranslational modification, protein turnover, chaperones
Unknown
Transport (ABC/Efflux pump transport)
Unknown
Unknown
Unknown
Posttranslational modification, protein turnover, chaperones
0.164
0.1647
0.1669
0.1673
0.1674
0.1675
0.1723
0.1743
0.1764
0.1764
0.1794
Regulation (transcription regulation)
0.1804
Unknown
Cell membrane structure (lipid metabolism)
Unknown
Cell wall structure (protein insertion)
Cell wall structure (protein insertion)
Regulation (transcription regulation)
Unknown
Posttranslational modification, protein turnover, chaperones
0.1809
0.1818
0.1839
0.184
0.1854
0.186
0.1868
0.1891
9,00E-004
9,00E-004
9,00E-004
9,00E-004
9,00E-004
0,001
0,001
0,001
0,001
0,001
0,001
22
0,0011
0,0011
0,0011
0,0012
0,0012
0,0012
0,0012
0,0013
0,0013
Supplementary Table S3 List of proteins whose expression level is most strongly affected
in response to OH radicals. MASCOT searching details for protein identification are
shown.
ID
Protein name
PA2395
PA0672
PA0973
PA4710
PA2398
PA4168
PA2394
PA1151
PA2001
PA5060
PvdO
Heme oxygenase
OprL
PhuR
FpvA
FpvB
PvdN
Pyocin S2 protein
AtoB
PhaF
Protein Coverage Nr. peptides
score
338
31
7
1180
89
19
735
58
11
1638
48
30
795
25
15
426
15
8
199
12
4
150
35
3
1250
75
21
368
25
8
23