The evolution and structural anatomy of small molecule metabolism pathways in Escherichia coli.

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The evolution and structural anatomy of small
molecule metabolism pathways in Escherichia coli.

• Of Pathways and Proteins
• Stuart Rison and Sarah Teichmann

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Questions

• How are homologous proteins (enzymes) distributed
  in E. coli metabolism?
  
• How does this distribution fit with theories of
  pathway evolution?
  

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Pathway evolution

• Norman Horowitz, 1945 On the evolution of
  biochemical syntheses, Proc. Nat. Acc. Sci.
  31153-157.
  
• Retrograde evolution
• Roy Jensen, 1976 Enzyme recruitment in
  evolution of new function, Ann. Rev. Microbiol
  30409-425.
  
• Patchwork evolution

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Retrograde evolution
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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

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Patchwork evolution
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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

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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

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Methods
E. coli
IMPALA
HMM
Y-BLAST


Y-BLAST
(75aa)
Evolutionary Relationships
Pathways
Proteins
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Domain assignments
566 SMM proteins
124 unassigned proteins
442 proteins assigned to 1 families (78)
169 PDB-D families
31 sequence domain families
200 domain families
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Glycogen Catabolism
glycogen phosphorylase
a-amylase, 3.2.1.1
a-amylase, 3.2.1.1
malS
glgP
amyA
phosphoglucomutase, 5.4.2.2
malodextrin phosphorylase
pgm
malP
malodextrin glucosidase
amylomaltase, 2.4.1.25
malQ
malZ
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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)

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Duplications within and across Pathways

• 710 domains in 200 families
• 510 domains have arisen by duplication
• 232 duplications within pathways to 278
  duplications across pathways
  
• (Assumption duplication within pathways wherever
  possible.)
  

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Type of conservation
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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
  

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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

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Conclusions Pathway evolution

• Data support a patchwork evolution model
• Little evidence of retrograde evolution

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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
  

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Future

• Identification and analysis of novel pathway
  duplication events
  
• Focus on order in pathways
• Stepwise analysis
• Doublet/triplet analysis
• Analysis domain combination in SMM

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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