By Megan Scudellari
Gene swap key to evolution
Horizontal gene transfer accounts for the majority of prokaryotic protein evolution
[Published 27th January 2011 10:00 PM GMT]
Microbes evolve predominantly by acquiring genes from other microbes, new research suggests, challenging previous theories that gene duplication is the primary driver of protein evolution in prokaryotes.
Scanning electron micrograph of Helicobacter pylori
Janice Carr, Wikimedia
Janice Carr, Wikimedia
The finding, published today (January 27) in PLoS Genetics, could change the way scientists study and model biological networks and protein evolution.
"Even at a meeting last summer, there were those that thought that bacteria genomes expanded mostly through duplications and others that argued that it was due to gene acquisition," wrote Howard Ochman, an evolutionary biologist at Yale University who was not involved in the research, in an Email to The Scientist. "Now we all have a paper to point to that does a very good job of answering this question," he said. "Their conclusions are really robust."
Prokaryotes, including bacteria and archaea, thrive in diverse conditions thanks to their ability to rapidly modify their repertoire of proteins. This is achieved in two ways: by receiving genes from other prokaryotes, called horizontal gene transfer -- the nefarious way that bacteria acquire antibiotic resistance -- or by gene duplication, in which an existing gene is copied, taking on a new or enhanced function as mutations accumulate.
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Read more here/Leia mais aqui: The Scientist
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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, Département Génomes et Génétique, Paris, France, 2 CNRS, URA2171, Paris, France, 3 UPMC Université 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 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.
Author Summary
Prokaryotes can be found in the most diverse and severe ecological niches of the planet. Their rapid adaptation is, in part, the result of the ability to acquire genetic information horizontally. This means that prokaryotes utilize two major paths to expand their repertoire of protein families: they can duplicate a pre-existing gene or acquire it by horizontal transfer. In this study, we track family expansions among closely related strains of prokaryotic species. We find that the majority of gene expansions arrive via transfer not via duplication. Additionally, we find that duplicate genes tend be more transient and evolve slower than transferred ones, highlighting different roles with respect to adaptation and evolution. These results suggest that prevailing theories aimed at understanding the evolution of biological systems grounded on gene duplication might be poorly fit to explain the evolution of prokaryotic systems, which include the vast majority of life's biochemical diversity.
Citation: Treangen TJ, Rocha EPC (2011) Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes. PLoS Genet 7(1): e1001284. doi:10.1371/journal.pgen.1001284
Editor: Nancy A. Moran, Yale University, United States of America
Received: June 14, 2010; Accepted: December 20, 2010; Published: January 27, 2011
Copyright: © 2011 Treangen, Rocha. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This study was carried out with financial assistance from the Institut Pasteur and the Centre National de la Recherche Scientifique. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: treangen@pasteur.fr
¤ Current address: Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America.
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