horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes横向转移,而不是重复,导致原核生物蛋白质家族的扩张.pdfVIP

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes Todd J. Treangen1,2,3¤*, Eduardo P. C. Rocha1,2,3 ´ ´ ´ ´ ´ 1 Institut Pasteur, Microbial Evolutionary Genomics, Departement Genomes et Genetique, Paris, France, 2 CNRS, URA2171, Paris, France, 3 UPMC Universite Pierre et Marie Curie, Atelier de Bioinformatique, Paris, France Abstract Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. While there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. We analyzed closely related prokaryote strains or species with small genomes (Helicobacter, Neisseria, Streptococcus, Sulfolobus), average-sized genomes (Bacillus, Enterobacteriaceae), and large genomes (Pseudomonas, Bradyrhizobiaceae) to untangle the effects of duplication and horizontal transfer. After removing the effects of transposable elements and phages, we show that the vast majority of expansions of protein families are due to transfer, even among large genomes. Transferred genes—xenologs—persist longer in prokaryotic lineages possibly due to a higher/longer adaptive role. On the other hand, duplicated genes—paralogs—are expressed more, and, when persistent, they evolve slower. This suggests that gene transfer and gene duplication have very different roles in shaping the evolution of biological systems: transfer allows the acquisition of new functions and