1. Protein structural domains, the
Tree of Life and the evolution of
complexity
Graeme T. Lloyd, Philip C. J. Donoghue and
Julian Gough

2. Protein Structural Domains
Folding

3. SCOP Protein Domain Classification
Classes
(7)
Folds
(48)
Superfamily
(1445)
Family
(2598)
Domain
(75930)

4. Protein Domain Architectures
A B C D
Protein 1: Architecture = A,A,C
Protein 2: Architecture = D,B
Protein 3: Architecture = B
Protein 4: Architecture = C,A,A
Protein 5: Architecture = D,B,C

5. http://supfam.org The Superfamily Database

6. Protein Repertoire
Chothia et al. 2003, Science

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. Phylogeny

9. The Tree of Life
Architectures
Superfamilies Families

10. Function Trees

11. Complexity

12. (from Fusco and Minelli 2000) (from McShea 1992)
(from Boyiajian & Lutz 1992) (from Cisne 1974)

13. Cell Number and Complexity
(from Valentine et al. 1994)

14. Genome Size and Complexity
(from Gregory 2005)

15. Protein Repertoires
Superfamilies Families Architectures

16. Tempo

17. ‘Proteospace’

18. Genome size vs. Proteome size

19. Problems and Prospect

20. LUCA Genome vs. Proteome size
LUCA
988
200 400 600 800 1000
N Superfamilies
1. LUCA is a prokaryote
2. Prokaryote genome size ~ N superfamilies
3. LUCA genome size estimable using SCP (1404 kb)
4. Therefore, LUCA superfamilies = 629

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