enzyme evolution john mitchell, february 2010. theories of enzyme evolution

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  • Slide 1
  • Enzyme Evolution John Mitchell, February 2010
  • Slide 2
  • Theories of Enzyme Evolution
  • Slide 3
  • Overview (1) Divergent retrograde evolution, recruiting adjacent enzymes in pathway and constrained by binding similar molecules as substrates or products.
  • Slide 4
  • Overview (2) Divergent patchwork evolution, recruiting enzymes catalysing similar chemical reactions, typically from other pathways, constrained by supporting similar catalytic chemistry.
  • Slide 5
  • Overview (3) Convergent evolution, reinventing similar chemistry in a different evolutionary family.
  • Slide 6
  • Retrograde Evolution (Horowitz,1945) Pathways evolve backwards: the end product of the newly evolved reaction is the substrate of the existing one.
  • Slide 7
  • Picture adapted from Betts & Russell, 2009
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  • Slide 9
  • Successive reactions in the pathway would therefore be catalysed by homologous enzymes Picture adapted from Betts & Russell, 2009
  • Slide 10
  • Patchwork Evolution (Jensen,1976) Recruitment of enzymes for new reactions was based on similarity of reactions catalysed and possibly on substrate ambiguity. It did not necessarily require the sequential and backwardly evolving progression of steps.
  • Slide 11
  • Patchwork recruitment: Recruit an enzyme with a chemically similar catalytic function from a quite different pathway.
  • Slide 12
  • Picture from Betts & Russell, 2009
  • Slide 13
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  • Slide 15
  • The Importance of Moonlighting A moonlighting enzyme has a second job.
  • Slide 16
  • The Importance of Moonlighting Patchwork recruitment is most likely to occur when the original enzyme already has some low level of activity for catalysing a different reaction.
  • Slide 17
  • The Importance of Moonlighting This allows the enzyme to be recruited to carry out the new function.
  • Slide 18
  • Main reaction Minor side reaction
  • Slide 19
  • A starting point for evolving a new catalytic function! Main reaction Minor side reaction
  • Slide 20
  • How Might Divergent Evolution Occur? At the level of the gene, the most obvious idea is via gene duplication with one copy being free to mutate away from its original function
  • Slide 21
  • Picture adapted from Todd, Orengo & Thornton, 1999
  • Slide 22
  • Slide 23
  • Original functionNew function
  • Slide 24
  • Picture adapted from Todd, Orengo & Thornton, 1999 Original functionNew function This way, the original function is maintained and a new one evolved.
  • Slide 25
  • How Might Divergent Evolution Occur? There are other possible routes to diverged functions (Orengo, Thornton, Todd & others)
  • Slide 26
  • Picture adapted from Todd, Orengo & Thornton, 1999
  • Slide 27
  • Models for Divergent Enzyme Evolution Two main models of divergent enzyme evolution discussed by Gerlt and Babbitt: Chemistry is conserved, substrate specificity changes. Substrate binding is conserved, chemistry changes. Evidence for both models in different cases, but conserved chemistry is likely to be more common.
  • Slide 28
  • Models for Divergent Enzyme Evolution Two main models of divergent enzyme evolution discussed by Gerlt and Babbitt: Chemistry is conserved, substrate specificity changes. If true, implies that chemical reactions are harder to evolve than is substrate binding. Fits well with patchwork recruitment model.
  • Slide 29
  • Enzyme Nomenclature and Classification EC Classification Class Subclass Sub-subclass Serial number
  • Slide 30
  • Phylogeny of Enzymes (Caetano-Annols) Taking advantage of the genomic data now available, Caetano-Annols and group attempted to build a phylogeny of enzymes based on the occurrence of their folds in sequenced genomes.
  • Slide 31
  • Phylogeny of Enzymes (Caetano-Annols) In principle, this could age enzymes the more universal the older.
  • Slide 32
  • Picture from Caetano-Annols et al. (2007)
  • Slide 33
  • The diverse mix of ages within metabolic networks seems to support the patchwork model. Picture from Kim et al. (2006)
  • Slide 34
  • Using similar ideas of universality of superfamilies, tried to reconstruct proteome of LUCA. Interesting, but speculative?
  • Slide 35
  • Both Divergent & Convergent Evolution are Important Divergent evolution leads to one fold performing a plurality of functions. Convergent evolution leads to a plurality of folds performing the same function
  • Slide 36
  • Takes advantage of folds being both structural and evolutionary units of protein structure.
  • Slide 37
  • Slide 38
  • Divergence
  • Slide 39
  • Convergence
  • Slide 40
  • Those figures are based on available structures. As more become available, we will find more functions for existing folds, and more folds with existing functions. So these are underestimates! Convergent Divergent
  • Slide 41
  • Caveat: Our working definition of Convergent Evolution is dependent on the EC classification, which is not a perfect gold standard.
  • Slide 42
  • MACiE Mechanism, Annotation and Classification in Enzymes. http://www.ebi.ac.uk/thornton-srv/databases/MACiE/ The MACiE Database G.L. Holliday et al., Nucl. Acids Res., 35, D515-D520 (2007) Gemma Holliday, Daniel Almonacid, Noel OBoyle, Janet Thornton, Peter Murray-Rust, Gail Bartlett, James Torrance, John Mitchell
  • Slide 43
  • Slide 44
  • Enzyme Nomenclature and Classification EC Classification Class Subclass Sub-subclass Serial number
  • Slide 45
  • The EC Classification Deals with overall reaction, not mechanism Reaction direction arbitrary Cofactors and active site residues ignored Doesnt deal with structural and sequence information However, it was never intended to do so
  • Slide 46
  • A New Representation of Enzyme Reactions? Should be complementary to, but distinct from, the EC system Should take into account: Reaction Mechanism Structure Sequence Active Site residues Cofactors Need a database of enzyme mechanisms
  • Slide 47
  • MACiE Mechanism, Annotation and Classification in Enzymes. http://www.ebi.ac.uk/thornton-srv/databases/MACiE/ MACiE Database
  • Slide 48
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  • Slide 50
  • Difficulties of Hierarchical Classification Very similar mechanisms can end up in different first level classes. In the case of phosphoinositide-specific phospholipases C, this is due to a slow final hydrolysis step occurring in one of the two enzymes.
  • Slide 51
  • Classifying Related Enzymes: Phosphoinositide-specific Phospholipases C Eukaryotic (rat) Cell Signalling Multidomain Catalytic TIM Barrel EC 3.1.4.11 Hydrolase Final hydrolysis step Prefers bisphosphate Acid-base mechanism Calcium dependent Prokaryotic (B. cereus) Virulence factor Single domain Catalytic TIM Barrel EC 4.6.1.13 Lyase No/slow final hydrolysis Disfavours bisphosphate Acid-base mechanism Not calcium dependent Evolutionarily related
  • Slide 52
  • Similar reactions end up far apart EC 3.1.4.11 EC 4.6.1.13
  • Slide 53
  • Difficulties of Hierarchical Classification Different mechanisms can occur with exactly the same EC number. MACiE has six beta-lactamases, all with different mechanisms but the same overall reaction.
  • Slide 54
  • Slide 55
  • MACiE Mechanisms are Sourced from the Literature
  • Slide 56
  • Coverage of MACiE Representative based on a non-homologous dataset, and chosen to represent each available EC sub-subclass.
  • Slide 57
  • EC Coverage of MACiE Representative based on a non-homologous dataset, and chosen to represent each available EC sub-subclass. Structures exist for: 6 EC 1.-.-.- 57 EC 1.2.-.- 194 EC 1.2.3.- 1547 EC 1.2.3.4 MACiE covers: 6 EC 1.-.-.- 54 EC 1.2.-.- 165 EC 1.2.3.- 249 EC 1.2.3.4
  • Slide 58
  • Convergent Evolution of Enzyme Function D.E. Almonacid et al., PLoS Computational Biology, accepted N.M. OBoyle et al., J. Molec. Biol., 368, 1484-1499 (2007)
  • Slide 59
  • We use a combination of bioinformatics & chemoinformatics to identify similarities between enzyme-catalysed reaction mechanisms
  • Slide 60
  • Similarity of Overall Reactions: Compare Bond Changes
  • Slide 61
  • Similarity of Mechanisms: Compare Steps
  • Slide 62
  • Just like sequence alignment! We can measure their similarity Similarity of Mechanisms: Compare Steps
  • Slide 63
  • Carrying out an analysis of pairwise similarity of reactions in MACiE...

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