cohesive versus flexible evolution of functional modules in eukaryotes有凝聚力和灵活的功能模块在真核生物的进化.pdfVIP

Cohesive versus Flexible Evolution of Functional Modules in Eukaryotes Like Fokkens1,2*, Berend Snel1,2 1Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands, 2 Academic Biomedical Centre, Utrecht University, Utrecht, The Netherlands Abstract Although functionally related proteins can be reliably predicted from phylogenetic profiles, many functional modules do not seem to evolve cohesively according to case studies and systematic analyses in prokaryotes. In this study we quantify the extent of evolutionary cohesiveness of functional modules in eukaryotes and probe the biological and methodological factors influencing our estimates. We have collected various datasets of protein complexes and pathways in Saccheromyces cerevisiae. We define orthologous groups on 34 eukaryotic genomes and measure the extent of cohesive evolution of sets of orthologous groups of which members constitute a known complex or pathway. Within this framework it appears that most functional modules evolve flexibly rather than cohesively. Even after correcting for uncertain module definitions and potentially problematic orthologous groups, only 46% of pathways and complexes evolve more cohesively than random modules. This flexibility seems partly coupled to the nature of the functional module because biochemical pathways are generally more cohesively evolving than complexes. Citation: Fokkens L, Snel B (2009) Cohesive versus Flexible Evolution of Functional Modules in Eukaryotes. PLoS Comput Biol 5(1): e1000276. doi:10.1371/ journal.pcbi.1000276 Editor: Christian von Mering, University of Zurich, Switzerland Received September 12, 2008; Accepted December 16, 2008; Published January 30, 2009 Copyright: 2009 Fokkens, Snel. This is an open-access article distributed under the terms of the Creative Commons Attribution License