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Protein structural domains, the Tree of Life and the evolution of
complexity
Graeme T. Lloyd, Philip C. J. Donoghue and Julian Gough
Protein Structural Domains
Folding
SCOP Protein Domain Classification
Domain
Family
Superfamily
Folds
(1445)
(2598)
(48)
Classes(7)
(75930)
Protein Domain Architectures
Protein 3:
Protein 2:
Protein 1: Architecture = A,A,C
Architecture = D,B
DCBA
Architecture = B
Protein 4:
Protein 5:
Architecture = C,A,A
Architecture = D,B,C
The Superfamily Databaseht
tp://
supf
am.o
rg
Protein Repertoire
Chothia et al. 2003, Science
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)
Phylogeny
The Tree of Life
Superfamilies FamiliesArchitectures
Function Trees
Complexity
(from B
oyiajian & Lutz 1992)
(from
Fus
co a
nd M
inel
li 20
00)
(from C
isne 1974)(from
McS
hea
1992
)
(from Valentine et al. 1994)
Cell Number and Complexity
(from Gregory 2005)
Genome Size and Complexity
Protein RepertoiresSuperfamilies Families Architectures
Tempo
‘Proteospace’
Genome size vs. Proteome size
Problems and Prospect
LUCA Genome vs. Proteome size
N Superfamilies
LUCA988
1. LUCA is a prokaryote2. Prokaryote genome size ~ N superfamilies3. LUCA genome size estimable using SCP (1404 kb)4. Therefore, LUCA superfamilies = 629
200 400 600 800 1000
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