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
Graeme T. Lloyd, Philip C. J. Donoghue and Julian Gough
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Protein Structural Domains
Folding
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SCOP Protein Domain Classification
Domain
Family
Superfamily
Folds
(1445)
(2598)
(48)
Classes(7)
(75930)
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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
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The Superfamily Databaseht
tp://
supf
am.o
rg
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Protein Repertoire
Chothia et al. 2003, Science
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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)
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Phylogeny
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The Tree of Life
Superfamilies FamiliesArchitectures
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Function Trees
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Complexity
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(from B
oyiajian & Lutz 1992)
(from
Fus
co a
nd M
inel
li 20
00)
(from C
isne 1974)(from
McS
hea
1992
)
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(from Valentine et al. 1994)
Cell Number and Complexity
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(from Gregory 2005)
Genome Size and Complexity
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Protein RepertoiresSuperfamilies Families Architectures
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Tempo
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‘Proteospace’
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Genome size vs. Proteome size
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Problems and Prospect
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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
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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