Research ArticleEVOLUTION

Eukaryotic Protein Domains as Functional Units of Cellular Evolution

Science Signaling  24 Nov 2009:
Vol. 2, Issue 98, pp. ra76
DOI: 10.1126/scisignal.2000546

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Domains for Change

Protein domains endow proteins with specific activities and the ability to interact with specific partners. Most protein domains occur in many proteins and most proteins have multiple domains, but the combinations of domains are far fewer than would be predicted, suggesting that there is evolutionary pressure that preserves certain domain combinations. Jin et al. use a proteome-wide clustering method to identify eukaryotic protein domain combinations that correlate with evolutionary change. Their analysis suggests that reciprocal interactions between a protein and its microenvironment constrain the repertoire of domains that control specific cellular functions. They analyzed the proteins in seven eukaryotic species and organized the domains into 1245 “domain clubs,” with the majority of clubs containing proteins with multiple distinct domains and proteins with rich interrelationships among members of different clubs. They grouped proteins on the basis of their domain clubs into functional trees and were able to place domains of unknown function into functional groups, as well as make predictions about the role domain evolution contributes to the evolution of protein function within a molecular environment, as well as to the evolution of molecular environments.