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Diversité métabolique des micro-organismes majoritaires
d’un écosystème riche en arsenic décrypté par protéo- et
méta-génomique
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P. Bertin
L’arsenic dans l’environnement
Lièvremont et al., Biochimie, 2009
Sources hydrothermales
Eaux souterraines
Industries
Agriculture
Origine naturelle Activités humaines
As
Géochimie
Volcanisme
As-org
As !
Microorganismes
Formes immobilisées As[III] As[V]
Feux de forêts
Activités minières
P. Bertin - ECL2011
Séquençage Protéines Gènes
Collection d’objets
Post- séquençage Protéome
Transcriptome
Relations Entre objets
Image intégrée des systèmes biologiques
Physiologie
Génétique
Des microbes aux écosystèmes et vice versa!
P. Bertin - ECL2011
Herminiimonas arsenicoxydans: une référence
Muller et al., PLoS Genetics, 2007
P. Bertin - ECL2011
Carapito et al., Biochimie, 2006 Protéomique / Transcriptomique
-As[III]
IEF!pI = 4! pI = 7!
21!
9!
10!
22!
11!12!
1!
2!
13! 14!15!
18!
3!19!
16!17!
4!5!6!
7!
8!20!
+As[III]
IEF!pI = 4! pI = 7!
21!
9!
10!
22!
11!12!
1!
2!
13! 14!15!
18!
3!19!16!17!
4!5!6!
7!20!
8!
Weiss et al., Biochimie, 2009
P. Bertin - ECL2011
ArsC AsIII AsV
arsC2a arsB2 arsH arsR arsC2b
arsR4 arsC4 arsH4
arsB1 arsR1 arsC1
I II
III
AsIII AsV
AsIII
MCP
FliC
ArsB
AsV
AsIII
tar
EPS
2 O2.- + 2H+ = O2 + H2O2
SodB
O2 + 2 H2O
KatA
Glutathione disulfide + 2 H2O
Glutathione
Gpo
GshB
ATP
?
pstS2 pstC2 pstA2 pstB2
aoxA aoxB aoxC aoxD
phoU pstB1 pstS1a
AsIII
FlgE
PilQ PilT
PilH ATP
ADP
+ ?
1
2 3
4
5
FliD
FliH CheW
CheY
CapP
6
Cytc oxidase
Cyt bc1
complex
NADH NAD+
2H+
4H+ 2 X 2H+ 2H+
Pi ADP ATP
3 H+
PetA PetC
NuoG NuoD
SdhB
CtaC
7
8
AtpD
AtpF AtpE
AtpA
Na+
DnaJ
DnaK
GrpE GroL
GroS UspA
Hsp
SurA
HtpG
ClpB
Koechler et al., BMC Microbiol., 2010 Cleiss-Arnold et al., BMC Genomics, 2010
P. Bertin - ECL2011
As
Cu
K Cl
I.
Cu II.
Motilité et biofilm Muller et al., PLoS Genetics, 2007
Marchal et al. Microbiology, 2010
P. Bertin - ECL2011
- As
+ As
General Acid
Oxidative
Carboxysomes
AoxAB
Phosphate/Phosphite
import
Fructose
Che proteins
ATP ArsC As(III)
ArsB
As(III)
As(V)
ArsA
Cd
Cd, Zn, Co
Hg2+
Hg2+ Hg0
Hg0
MerTP
Cr Ag
FruAB PtsHI
Ethanol
Glycerol
Fructose-P
Amino acid transporters
Ala Asp Glu Gln Gly His Ser Lys Pro
Fe(II)
Fe(II) FeoC
Bfr (storage)
Fur (regulation)
EMP Entner-Doudoroff pathway
Rubisco shunt
NADH NAD+ "O2 H2O 2H+
4H+
Succinate Fumarate
UQ Cyt bc1
complex Cyt.
oxidase ATP synthase
2H+
Sox
Thiosulfate, S0, Sulfite or
H2S
SO42- SorAB
Sqr
Sulfite SO42-
H2S S0
Cyt c552
Sil
Czc Cad Chr
MerAB
MntH
Nitrate reductase
1,3-Biphosphoglycerate
Glyceraldehyde 3-phosphate
ribulose 5-biphosphate
ribulose 1,5-biphosphate
phosphoglycerate
rubisco
Fe(II) trafficking
protein YggX
L-lysine cadaverine + CO2
LDC
Urea + H2O CO2 + 2 NH3 UreA-G
O2 H2O2 "O2 + H2O SodB PerA
2 R‘-SH +ROOH R‘-S-S-R‘+ H2O+ROH Ahp, TrX
2 GSH+H2O2 GSSG+ 2H2O Gpo
Glu+Cys GshAB
Peptide-L-Met-R-S-oxide + thioredoxin
Peptide-L-Met + H2O+ thioredoxin disulfide
MsrB
PHB
PO43-
As(V) PO4
3-
TCA pathway
Flagellum
FccAB
H2S S0
DNA repair (radA, recQ, ruvA, recA, xseA, polA,
holB-like, dinB-like, parC)
ATP Poly-P
KdpABC
ClcAB cus
Cu, Zn, Co
Porin
Pilus (pil genes)
FeoAB
Glycogen/Starch
Fructose-6-P/ Glucose 6-P
Acetyl-CoA citrate
isocitrate
!-ketoglutarate succinate
malate
Thiomonas
Bryan et al., BMC Microbiol., 2009
Arsène-Ploetze et al., PLoS Genetics, 2010 P. Bertin - ECL2011
deletion duplication
Tm. perometabolis Ynys1 CB6 CB1 Tm. arsenivorans CB2 CB3
O P J I B F GH C A E K Q R S
Arsène-Ploetze et al. PLoS Genet., 2010 Génomique comparée (CGH)
P. Bertin - ECL2011
AMD
Génomique environnementale
P. Bertin - ECL2011
5("6789:";<"=>"
#?@7:@AB6C?@D"EF:GE:D":@"6BD:@87H"I:B":A"D?JIB:"
1.2 megatonnes de déchets ;6BD:@?5KB8A:>"
!"#$%&'
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/ 01/'2/'
L4DM"N"OPQ"RSTF"
4D)))T4DU"N"QHVP"
L4DM"N"PW"RSTF"
4D)))T4DU"N"QHOQ"
L4DM"N"OXP"RSTF"
4D)))T4DU"N"QHWV"
Atténuation naturelle de [As]
P. Bertin - ECL2011
Phyloprotéomique
Bruneel et al. Microb. Ecol., 2011
CARN 1
CARN 2
CARN 4
CARN 3 + 5
CARN 6 + 7
• 550 920 runs Sanger -> 366.4 Mb • 281 758 runs GSFlex -> 63.9 Mb
Metaprotéogénomique
Coverage
GC
P. Bertin - ECL2011
Bertin et al., ISME J. 2011
Synécologie
Bertin et al., ISME J., 2011 P. Bertin - ECL2011
Acidic pH
H2O
O2 Inorganic precipitation of Fe colloids
pHi 5.0 to 6.4
H+
PSII
SOD, peroxiredoxin, hydroperoxyde reductase, Ascorbate peroxidase
Oxidative stress
vacuole V/F/A-ATPases
wat
er
sedi
men
ts
Organic matter deposit
Bacteria
Cell division/Motility Actin Tubulin
Articulin Kinesin Fibrillarin
Hsps Proteasome
P-ATPases
H+
H+
Cation transport
ATPase
Glutamate
Glutamine synthetase
Glutamate deshydrogenase
Alpha cetoglutarate
H+
Serine amino hydroxytransferase
Glycine deshydrogenase
Malate synthase
Glycine catabolism
Alpha ketoglutarate Lysine
Saccharopine
Saccharopine deshydrogenase
serine
HCO3-
CO2
Carbonic anhydrase
H+
H2O
Ornithine
Ornithine carbamoyl
transferase
Arginine
Arginine deiminase
Arginosuccinate synthase
Citrulline
Glutamine
Photosynthesis
N assimilation
Asparagine Aspartate Asparagine synthetase
Alpha ketoglutarate
Aspartate aminotransferase
PSI
Photons
ATP synthase
Cyt b6-f
Chlorophyll
metabolism
Fatty acid metabolism
Carbon fixation Rubisco
Glycolyse Krebs cycle
Biosynthesis branched-chain amino acids
Aminoacids Fatty acids Carbon
Protéométabolomique
glycine glyoxylate malate
Halter et al., ISME J., in press
P. Bertin - ECL2011
Conclusions
P. Bertin - Colloque GE - Lyon - Novembre 2011
Génomique
Transcriptomique
Protéomique
Environnement
Physiologie
Taxonomie
Biologie moléculaire
Genomics Microbiology, Ecotoxicology
Microbiology, Proteomics
Genomics
Ecotechnology
Microbial ecology
Geochemistry Microbial ecology
Microbiology, Biochemistry Microbial ecology
Bioremediation
http://gdr2909.u-strasbg.fr
CNRS Research Group - GDR2909
P. Bertin - Colloque GE - Lyon - Novembre 2011