Adventures in protein world reveal the Tree of Life and the evolution of complexity
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Adventures in protein world reveal the Tree of Life and the evolution of complexity

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Adventures in protein world reveal the Tree of Life and the evolution of complexity Presentation Transcript

  • 1. Adventures in protein world revealthe Tree of Life and the evolution of complexityGraeme T. Lloyd, Philip C. J. Donoghue and Julian Gough
  • 2. Scala Naturae
  • 3. The Problem“Complexity is hard to define or measure…” Maynard Smith and Szathmáry, 1995
  • 4. Genome Size and the Scala Naturae (from Gregory 2005)
  • 5. Cell Number and the Scala Naturae (from Valentine et al. 1994)
  • 6. Proteome Size and the Scala Naturae ?
  • 7. Protein Structural DomainsFolding
  • 8. Protein Domain Classification IFoldSuperfamily(1445)Family(2598)Domain
  • 9. Protein Domain Classification II A B C DProtein 1: Architecture = A,A,CProtein 2: Architecture = D,BProtein 3: Architecture = BProtein 4: Architecture = C,A,AProtein 5: Architecture = D,B,C
  • 10. http://supfam.org Protein Domain Database I
  • 11. Protein Domain Database II238 Bacteria 26 Basal 53 Fungi 8 Arthropods Eukaryotes27 Archaea 9 Plants 5 Invertebrates 19 Chordates (excl. Arthropods)
  • 12. Superfamily Number and the Scala Naturae
  • 13. Family Number and the Scala Naturae
  • 14. Architecture Number and the Scala Naturae
  • 15. The Tree of Life I ArchitecturesSuperfamilies Families
  • 16. The Tree of Life II
  • 17. The Tree of Life III
  • 18. The Tree of Life IV
  • 19. Protein Space I
  • 20. Protein Space IIPrincipal Coordinate Analysis – A Very Brief Introduction PC1 Variable 2 PC 2 Variable 1
  • 21. Protein Space III - Superfamilies
  • 22. Protein Space IV - Families
  • 23. Protein Space V - Architectures
  • 24. Tempo and Protein Evolution I
  • 25. Tempo and Protein Evolution II - SuperfamiliesLUCA
  • 26. Tempo and Protein Evolution III - FamiliesLUCA
  • 27. Tempo and Protein Evolution IV - ArchitecturesLUCA
  • 28. Conclusions• Protein domains can help us reconstruct the tree of life and offer a promising new metric for biologic complexity• Novel domain families and superfamilies have appeared at a roughly constant rate over the history of life and across different groups• By contrast, novel architectures (new proteins) are acquired at a faster rate in animals, and vertebrates in particular