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