Download Folie 1 - ERA-NET PathoGenoMics

Michael Wagner
Division of Microbial Ecology
www.microbial-ecology.net
Characterizing Uncultured Bacteria
University of Vienna
Vienna Roundtable Pathogenomics
• April 4
• 16 Scientists, 4 members of the bmbwk, 1
member of the FWF
• Introduction: ERA-NET
• Overview presentation by each scientist
• Identification of three major topics which are
suggested for the call
ERA-NET Partner Austria:
Key topic I: Host-Pathogen Interaction
Focus on obligate and facultative intracellular bacteria
and on pathogenic fungi
Decker, Horn, Müller, Kuchler
Toll-like receptors (TLR) and Interferons
(IFN) in Host-Pathogen Interaction
• TLR recognize bacteria and trigger an
antibacterial and inflammatory response.
• Stimulation of several TLR causes the
synthesis of type I IFN in infected cells.
• Antimicrobial gene expression results from
genes directly stimulated by TLR-derived
signals, by IFN signaling, or both.
 Interferons and TLR together determine the
gene expression signature of pathogeninfected cells.
Open Questions
• What are the signaling molecules
(signalosomes) linking the interferon genes to
extra- or intracellular nonviral pathogens
(similarities and differences between TLRmediated and intracellular recognition)?
• Is there a causal relationship between the
degree, timing, intensity of an IFN response
and the effect of IFN immune responses to
nonviral pathogenes?
• Can pathogen virulence be linked to IFN
synthesis (positively or negatively)?
Model System: Environmental chlamydiae which thrive in
protozoa, salmon, fruit bats etc.
Waddlia chondrophila WSU851044
Fritschea bemisiae
Fritschea eriococci
Waddlia chondrophila 2032
Waddlia sp. RLUH1
Simkania negevensis Z
Chlamydia trachomatis
Chlamydia muridarum
Chlamydia suis
Chlamydophila pneumoniae
Chlamydophila psittaci
Chlamydophila abortus
Chlamydophila caviae
Chlamydophila felis
Chlamydophila pecorum
Parachlamydia acanthamoebae Bn9
Endosymbiont of Acanthamoeba sp. Berg17
Parachlamydia sp. Hall's coccus
Parachlamydia sp. PL9
Candidatus
Rhabdochlamydia porcellionis
Endosymbiont von Acanthamoeba sp. TUME1
Endosymbiont von Acanthamoeba sp. UWC22
Neochlamydia hartmannellae
Endosymbiont von Acanthamoeba sp. UWE1
Protochlamydia amoebophila UWE25
Endosymbiont Kcont
Protochlamydia amoebophila UWE25
Endosymbiont von Acanthamoeba sp. TUMSJ61
Endosymbiont von Acanthamoeba sp. SS1
outgroup
0.10
Comparative genome analysis of
Protochlamydia amoebophila UWE25 –
Inferring the evolutionary history of chlamydiae
Horn et al. 2004. Science 304: 728
Environmental Chlamydia are ATP, NTP
and NAD+ parasites – a unique adaptation
to intracellular life
Wirtszelle
host
ATP
H
+
ADP
NAD+
N
T
T4
T2
NT
H+
NTT1
GTP
ATP
UTP
ADP
ATP ADP
ATP
GTP
Inklusion
inclusion
ADP
NAD+
ADP
UTP
ATP
CTP
NADP+
DNA/RNA Synthese
synthesis
Energie
energy
Redox-Coenzyme
electron carrier
Haferkamp et al. 2004. Nature 432: 622
Symbiont
symbiont
ERA-NET Partner Austria. Key topic II:
Regulatory Networks of Microbial Virulence
Bläsi, Charpentier, Kuchler,
Rosengarten
Virulence Genome of Candida glabrata
 C.g. 2nd most frequent human fungal pathogen - haploid
 Genome sequenced - closest in evolution to S. cerevisiae
 Virulence of C. glabrata - KNOCK-OUT ~ 6500 Genes
 Bar-Codes (Up-Down) of each C.g. knock-out as in S.c.
 Test & correlate pathogenicity of all knockouts in vivo & in vitro
 Pathogenicity genom/proteom of a fungal pathogen
• Cell-density dependent regulatory
systems (quorum sensing/auto-inducing
molecules) controlling virulence in
Salmonella typhimurium, Pseudomonas
aeruginosa and Streptococcus pyogenes
ERA-NET Partner Austria. Key topic III:
Metagenomics and postgenomics
of bacterial communities colonizing humans
Focus on oral cavity, skin, and gut system
Daims, Superti-Furga, Wagner
Metagenomics –
Reconstructing the ANAMMOX genome
substratum
N seq
three different BAC libraries
shotgun
library
140
120
100
N2
surface
80
NH4+
NO2NO2-
NH4+
60
40
20
0
0,200
0,300
0,400
0,500
0,600
0,700
BAC ends linked to ANAMMOX rRNA
• 200,000 shot gun reads
• 12,000 BAC end sequences
• 32 BAC full sequences
• 4.3 Mb in 4 contigs
0,800
ERA-NET Partner Austria:
Key topic I: Host-Pathogen Interaction
Key topic II: Regulatory Networks of
Microbial Virulence
Key topic III:
Metagenomics and postgenomics
of bacterial communities colonizing humans
Antimicrobial Action of Interferons
• Type II IFN (IFN-g) activates macrophages
and enhances immunity to predominantly
nonviral pathogens, particularly when
intracellular.
• Type I IFN (>10 genes) mediate antiviral
innate immunity. It is unclear why their
synthesis is an obligatory response to many
or even most nonviral pathogens.
• The immunological effect of type I IFN can be
benefitial or detrimental for the host,
depending on the pathogen and parameters
of infection. The underlying causes are not
known.
Approach
• Proteomics to identify the signaling molecules
(signalosomes) linking the interferon genes and
inflammatory genes to extra- or intracellular nonviral
pathogens.
• Gene expression patterns in mice with defined
mutations in IFN synthesis or response after infection
infection with pathogens stimulating different types of
immune responses. Link between gene expression
and protective or deterimental response.
• Infection of wildtype and mutant mice with microbial
mutants representing different degrees of virulence.
Virulence enhanced or reduced by defects in IFN
system?
Chlamydiae are …
… among the most important
bacterial pathogens of humans
Chlamydia trachomatis
Chlamydia muridarum
Chlamydia suis
Chlamydophila pneumoniae
Chlamydophila psittaci
Chlamydophila abortus
Chlamydophila caviae
Chlamydophila felis
Chlamydophila pecorum
… a phylogenetically well separated
group of closely related bacteria
… intracellular bacteria with a unique
biphasic developmental cycle
M.E. Ward (www.chlamydiae.com)