phylogenetic distribution of potential cellulases in bacteria
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Phylogenetic distribution of potential cellulases in bacteria
R. Berlemont & A. Martiny
The cellulose degradation
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Project Goals
1) How do microbial taxa respond to environmental changes?2) How are extracellular enzyme genes distributed among microbial taxa?3) Can we predict enzyme function and litter decomposition rates by combining enzyme genedistributions with microbial taxa responses to environmental change?4) Are microbial communities and their functions resilient to environmental change?
4 main questions :
Analyze the Gene Content in Available sequenced bacterial
genomes
CAZy classification
• Endo/Exo-cellulases, -glucosidases
• Glycoside Hydrolases, GH
• >100 GH families (14 folds)
• >100 activities
• multifunctional enzymes contain catalytic domains that belong to different GH families
Mining the CAZy CAZy
GH
fam
ily
Str
uctu
re
Mec
hani
sm
Hit
s
Enz
ymes
ch
arac
teri
zed
*
End
ocel
lula
se
(3.2
.1.4
)
Exo
cell
ulas
e (3
.2.1
.74/
91/1
76)
-gl
ucos
idas
e (3
.2.1
.21)
Oth
er
char
acte
rize
d ac
tivi
ty (
hits
)
Cel
lulo
se
synt
hesi
s
GH1 (-)8 R 2890 87 1 48 5 (43) GH3 (-)8 R 3212 91 5 55 8 (50)
GH5 (-)8 R 1952 206
152 2 6 (63) (Berlemont et al, 2009)
GH6 Atypical
/ barrel
I 231 16 13 4 (de Jong et al, 2009)
GH8 (/)6 I 538 55 26 4 (33) (Romling,
2002) GH9 (/)6 I 468 75 66 6 1 1 (1)
GH12 β-jelly
roll R 144 22 21 1 (1)
GH44 (/)6 I 55 10 8 1 (4) GH45 (/)6 I 13 13 3 GH48 (/)6 I 128 13 4 11
-
End
o/ex
o -
Accessing the genomes• SEED environment
• PATRIC database
• GH : 1, 3, 5, 6, 8, 9, 12, 44, 45, 48
CAZy Vs. us CAZy
GH
fam
ily
Str
uctu
re
Mec
hani
sm
Hit
s
Enz
ymes
ch
arac
teri
zed
*
End
ocel
lula
se
(3.2
.1.4
)
Exo
cell
ulas
e (3
.2.1
.74/
91/1
76)
-gl
ucos
idas
e (3
.2.1
.21)
Oth
er
char
acte
rize
d ac
tivi
ty (
hits
)
Cel
lulo
se
synt
hesi
s
Iden
tifi
ed
orth
olog
s
(SE
ED
)
GH1 (-)8 R 2890 87 1 48 5 (43) 9071 GH3 (-)8 R 3212 91 5 55 8 (50) 7105
GH5 (-)8 R 1952 206
152 2 6 (63) (Berlemont et al, 2009)
1727
GH6 Atypical
/ barrel
I 231 16 13 4 (de Jong et al, 2009)
699
GH8 (/)6 I 538 55 26 4 (33) (Romling,
2002) 702 GH8 & 380 BcsZ
GH9 (/)6 I 468 75 66 6 1 1 (1) 160
GH12 β-jelly
roll R 144 22 21 1 (1)
2095
GH44 (/)6 I 55 10 8 1 (4) 1 GH45 (/)6 I 13 13 3 580 GH48 (/)6 I 128 13 4 11 3
-
End
o/ex
o -
CAZY : all the NCBI genomes (including genome fragments) – 9,631 genes
SEED : Only the sequenced genomes (3711) are considered - 22,523 genes
Variations across phylaGH rich:
Acidobacteria,
Bacteroidetes,
Digtyoglomi,
Fibrobacteres,
Thermotogae,
Verrucomicrobia
Lentisphaerae
(Actinobacteria,
Chloroflexi,
Firmicutes)
Variations across subphyla
• Actinobacteria
• 402 genomes
• Niches (soil : Streptomycetales)
• ‘GH-rich’
Str
ain
spec
ific
GH
di
strib
utio
n
0 GH1 GH>1 GH
16S rRNA phylogeny
GH associations
End
o/ex
o -
BcsZ
Spearman Correlation
Glycoside Hydrolase abundance
-
Synergistic model
Endocellulases
Exocellulases
-glucosidases
Com
plementarities
Redundancy
Group I
Group II
Group IIIa
Group IIIb
GH associations• Nothing ! (can’t degrade cellulose) (21%)
• No Group II – III : opportunists (Opp.) (44%)
• 100% Gr.I and 0% Gr.II:Gr.III
• putative Cellulose Degraders (pCD) (35%)
• 100% GII/III and GI (94%)
•pCD vs. Opp. ?
GH associations
Cellulose degraders and opportunists
put. cell. degr.Opportunists• Actinobacteria
+ Bacteroidetes
+ Proteobacteria
+ Firmicutes = 86 %
Sequenced strains
• putative Cell. Degr.,
Opportunists, in all phyla
• 35 % pCD [16-56%]
• G1pCD = (1.7-4.4) G1Opp.
Poor strains … and their life styles
RuBisCO
“Poor phyla, subphyla and strains” ?
e.g. : Cyanobacteria
Life-style vs. GH content
Autotrophs
Intracellular
Actinobacteria
Our first “delivrable”
• 16s rRNA Phylogeny (Neighbor Joining)• Glycoside hydrolases based-clustering (Bray Curtis)
• distance between the matrices, CADM (Mantel)
Phylogeny vs. GH content
Phylogeny vs. GH content16
s rR
NA
phy
loge
nyG
H – based clustering
402 Actinobacteria
?
Conclusions• No information concerning the Activity of these enzymes• 3711 sequenced genomes ≠ natural population (pathogens)
• Genomic perspectives – New “pipeline” for genes distribution/association– Tell me what is your GH content, I ‘ll tell you who you are!
• Ecological perspectives – Functional redundancy in sequenced genomes (substrate, pH, …), – 44% opportunists, 35% putative cellulose degraders
• Implications for ecosystems processes -glucosidases reveal nothing about the cellulose degradation !– More than 35% of the strains have endo/exo-cellulases !– Cellulose degraders have multiple copies of these genes !
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