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Protein structural domains, the Tree of Life and the evolution of complexity

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Protein structural domains, the Tree of Life and the evolution of complexity

  1. 1. Protein structural domains, the Tree of Life and the evolution of complexityGraeme T. Lloyd, Philip C. J. Donoghue and Julian Gough
  2. 2. Protein Structural DomainsFolding
  3. 3. SCOP Protein Domain ClassificationClasses(7)Folds(48)Superfamily(1445)Family(2598)Domain(75930)
  4. 4. Protein Domain Architectures 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
  5. 5. http://supfam.org The Superfamily Database
  6. 6. Protein Repertoire Chothia et al. 2003, Science
  7. 7. Potential Use• Data occur as presences in genomes• Phylogenetic utility: – Tree searches – Synapomorphies of ancient clades• Complexity metric: – “The complexity of a system is some increasing function of the number of different types of parts or interactions it has” (McShea 1996)
  8. 8. Phylogeny
  9. 9. The Tree of Life ArchitecturesSuperfamilies Families
  10. 10. Function Trees
  11. 11. Complexity
  12. 12. (from Fusco and Minelli 2000) (from McShea 1992) (from Boyiajian & Lutz 1992) (from Cisne 1974)
  13. 13. Cell Number and Complexity (from Valentine et al. 1994)
  14. 14. Genome Size and Complexity (from Gregory 2005)
  15. 15. Protein RepertoiresSuperfamilies Families Architectures
  16. 16. Tempo
  17. 17. ‘Proteospace’
  18. 18. Genome size vs. Proteome size
  19. 19. Problems and Prospect
  20. 20. LUCA Genome vs. Proteome size LUCA 988 200 400 600 800 1000 N Superfamilies1. LUCA is a prokaryote2. Prokaryote genome size ~ N superfamilies3. LUCA genome size estimable using SCP (1404 kb)4. Therefore, LUCA superfamilies = 629
  21. 21. Summary• Protein domains are ancient characters• Phylogenetic utility still to be fully realised• They offer a useful complexity metric• Protein evolution switches between creation of novel domains to shuffling and recombining existing ones

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