Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes

• Autor: Treangen, Todd J ; Rocha, Eduardo P C
• Moran, Nancy A.
• Assuntos: Bacillus ; Bacillus - genetics ; Bacteria - genetics ; Bacterial proteins ; Bioinformatics ; Bradyrhizobiaceae - genetics ; Computational Biology ; Computational Biology/Comparative Sequence Analysis ; Computational Biology/Genomics ; Computational Biology/Population Genetics ; Computer Science ; Enterobacteriaceae ; Enterobacteriaceae - genetics ; Evolution ; Evolution, Molecular ; Evolutionary Biology/Evolutionary and Comparative Genetics ; Gene Duplication - genetics ; Gene Transfer, Horizontal ; Genes ; Genetic aspects ; Genetic transformation ; Genetics ; Genetics and Genomics/Genomics ; Genetics and Genomics/Microbial Evolution and Genomics ; Genome, Bacterial ; Genomics ; Helicobacter ; Helicobacter - genetics ; Life Sciences ; Multigene Family - genetics ; Natural history ; Neisseria ; Neisseria - genetics ; Phylogeny ; Prokaryotes ; Proteins ; Pseudomonas ; Pseudomonas - genetics ; Quantitative Methods ; Streptococcus ; Streptococcus - genetics ; Sulfolobus ; Sulfolobus - genetics
• É parte de: PLoS genetics, 2011-01, Vol.7 (1), p.e1001284
• Notas: ObjectType-Article-1
  SourceType-Scholarly Journals-1
  ObjectType-Feature-2
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  Current address: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
  Conceived and designed the experiments: TJT EPCR. Performed the experiments: TJT. Analyzed the data: TJT EPCR. Contributed reagents/materials/analysis tools: TJT. Wrote the paper: TJT EPCR.
  
• Descrição: 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 duplication leads to higher gene dosage. Accordingly, we show that paralogs share most protein-protein interactions and genetic regulators, whereas xenologs share very few of them. Prokaryotes invented most of life's biochemical diversity. Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families.
  
• Editor: United States: Public Library of Science
  
• Idioma: Inglês