TY - JOUR
T1 - The Evolutionary Mechanics of Domain Organization in Proteomes and the Rise of Modularity in the Protein World
AU - Wang, Minglei
AU - Caetano-Anollés, Gustavo
N1 - Funding Information:
We thank Jay E. Mittenthal for encouraging discussions and Liudmila S. Yafremava for comments on the manuscript. Research was supported in part by grants from the NSF (MCB-0343126 and MCB-0749836), the C-FAR Sentinel Program, and the USDA through HATCH Illu-802-314 and the Soybean Disease Biotechnology Center. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the funding agencies.
PY - 2009/1/14
Y1 - 2009/1/14
N2 - Protein domains are compact evolutionary units of structure and function that usually combine in proteins to produce complex domain arrangements. In order to study their evolution, we reconstructed genome-based phylogenetic trees of architectures from a census of domain structure and organization conducted at protein fold and fold-superfamily levels in hundreds of fully sequenced genomes. These trees defined timelines of architectural discovery and revealed remarkable evolutionary patterns, including the explosive appearance of domain combinations during the rise of organismal lineages, the dominance of domain fusion processes throughout evolution, and the late appearance of a new class of multifunctional modules in Eukarya by fission of domain combinations. Our study provides a detailed account of the history and diversification of a molecular interactome and shows how the interplay of domain fusions and fissions defines an evolutionary mechanics of domain organization that is fundamentally responsible for the complexity of the protein world.
AB - Protein domains are compact evolutionary units of structure and function that usually combine in proteins to produce complex domain arrangements. In order to study their evolution, we reconstructed genome-based phylogenetic trees of architectures from a census of domain structure and organization conducted at protein fold and fold-superfamily levels in hundreds of fully sequenced genomes. These trees defined timelines of architectural discovery and revealed remarkable evolutionary patterns, including the explosive appearance of domain combinations during the rise of organismal lineages, the dominance of domain fusion processes throughout evolution, and the late appearance of a new class of multifunctional modules in Eukarya by fission of domain combinations. Our study provides a detailed account of the history and diversification of a molecular interactome and shows how the interplay of domain fusions and fissions defines an evolutionary mechanics of domain organization that is fundamentally responsible for the complexity of the protein world.
KW - PROTEINS
UR - http://www.scopus.com/inward/record.url?scp=58149196295&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=58149196295&partnerID=8YFLogxK
U2 - 10.1016/j.str.2008.11.008
DO - 10.1016/j.str.2008.11.008
M3 - Article
C2 - 19141283
AN - SCOPUS:58149196295
SN - 0969-2126
VL - 17
SP - 66
EP - 78
JO - Structure
JF - Structure
IS - 1
ER -