The evolution and structural anatomy of small molecule metabolism pathways in Escherichia coli. Of...
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Transcript of The evolution and structural anatomy of small molecule metabolism pathways in Escherichia coli. Of...
The evolution and structural anatomy of
small molecule metabolism pathways in
Escherichia coli.Of Pathways and ProteinsStuart Rison and Sarah
Teichmann
Questions
• How are homologous proteins (enzymes) distributed in E. coli metabolism?
• How does this distribution fit with theories of pathway evolution?
Pathway evolution
• Norman Horowitz, 1945: ‘On the evolution of biochemical syntheses’, Proc. Nat. Acc. Sci. 31:153-157.
“Retrograde evolution”• Roy Jensen, 1976: ‘Enzyme
recruitment in evolution of new function’, Ann. Rev. Microbiol 30:409-425.
“Patchwork evolution”
Retrograde evolution
[ ]
[ ]
[ ]
Jensen, 1976: Substrate ambiguity
• ‘Original pool’ of unregulated and enzymatically versatile proteins
• Enzymes recruited from the pool• Ad hoc pathways• Gene duplication and
specialisation leads to regulated, specific and efficient pathways
Patchwork evolution
Why E. coli?
• An extensively studied model organism
• Complete genome available• Most Small Molecule Metabolism
pathways well known and empirically characterised
• A manageable size
• Good associated databases
Strategy
• Identify all SMM proteins and the pathway(s) in which they belong
• Detect homologous proteins by structure or sequence
• Combine these data to analyse homologous protein distribution in SMM
Methods
E. coli
IMPALA
HMM
-BLAST
-BLAST (>75aa)
+ =
EvolutionaryRelationships
PathwaysProteins
566 SMM proteins
442 proteins assignedto 1+ families (78%)
124 unassignedproteins
169 PDB-D families 31 ‘sequence’ domainfamilies
200 domain families
Domain assignments
Chemistry andclose substrateChemistry and
substrate
Glycogen Catabolism
malQ
malS
malZ
pgmmalP
glgPamyA
-amylase, 3.2.1.1
phosphoglucomutase, 5.4.2.2
amylomaltase, 2.4.1.25
-amylase, 3.2.1.1 glycogen phosphorylase
malodextrin phosphorylase
malodextrin glucosidase
-glucosyltransferase
Phosphoglucomutase
-amylase, C-term
Glycosyltransferases
Domains
Internal duplicationIsozymes
Duplications Across Pathways
• 110 out of 200 families occur in more than one pathway
• Can exhibit conservation of chemistry, shared cofactor or minor substrate similarity
• 36 families have close conservation of EC number (Chemistry conserved)
• 74 families conserve 1 or no EC number; 11 are cofactor-binding families (cofactor, minor substrate)
Duplications within and across Pathways
• 710 domains in 200 families510 domains have arisen by
duplication
• 232 duplications within pathways to 278 duplications across pathways
(Assumption: duplication within pathways wherever possible.)
0
10
20
30
40
50
60
70
80
90
100
Num
ber o
f pro
tein
s in
volv
ed
Cofactor ChemistryIsozymesInternal
Dup.Substrate
Type of conservation
Conclusion: Structural Anatomy
• 710 domains in 442 proteins of the 566 proteins in E. coli SMM pathways
• 200 families (3.5 members/family)
• Most sizeable families are distributed in several pathways
Conclusion: Recruitment and Conservation
• Duplications have taken place between and within pathways to roughly the same degree
• Duplications occur within most longer pathways:– Isozymes, internal duplications and co-
factor binding most common– Chemistry common– Conservation of substrate binding with
modified chemistry is rare
Conclusions: Pathway evolution
• Data support a “patchwork evolution” model
• Little evidence of “retrograde evolution”
Conclusions: hum…
• Recruitment, duplication and evolution of enzymes are constantly taking place so we are always observing a dynamic system
• Likely to be other evolutionary mechanisms and combinations thereof
Future
• Identification and analysis of novel pathway duplication events
• Focus on order in pathways:– Stepwise analysis– Doublet/triplet analysis
• Analysis domain combination in SMM
Acknowledgements
• Sarah A. Teichmann, Dept. Biochemistry, University College London
• Janet M. Thornton, David Lee, Dept. Crystallography, Birkbeck College and Dept. Biochemistry, University College London
• Monica Riley, Alida Pelegrini-Toole, Marine Biology Laboratory, Woods Hole, USA
• Cyrus Chothia, Julian Gough, MRC Laboratory of Molecular Biology, Cambridge, UK