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