The Extinction Dynamics of Bacterial Pseudogenes
Chih-Horng Kuo¤, Howard Ochman*
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
Abstract
Pseudogenes are usually considered to be completely neutral sequences whose evolution is shaped by random mutations and chance events. It is possible, however, for disrupted genes to generate products that are deleterious due either to the energetic costs of their transcription and translation or to the formation of toxic proteins. We found that after their initial formation, the youngest pseudogenes in Salmonella genomes have a very high likelihood of being removed by deletional processes and are eliminated too rapidly to be governed by a strictly neutral model of stochastic loss. Those few highly degraded pseudogenes that have persisted in Salmonella genomes correspond to genes with low expression levels and low connectivity in gene networks, such that their inactivation and any initial deleterious effects associated with their inactivation are buffered. Although pseudogenes have long been considered the paradigm of neutral evolution, the distribution of pseudogenes among Salmonella strains indicates that removal of many of these apparently functionless regions is attributable to positive selection.
Author Summary
Pseudogenes have traditionally been viewed as evolving in a strictly neutral manner. In bacteria, however, pseudogenes are deleted rapidly from genomes, suggesting that their presence is somehow deleterious. The distribution of pseudogenes among sequenced strains of Salmonella indicates that removal of many of these apparently functionless regions is attributable to their deleterious effects in cell fitness, suggesting that a sizeable fraction of pseudogenes are under selection.
Citation: Kuo C-H, Ochman H (2010) The Extinction Dynamics of Bacterial Pseudogenes. PLoS Genet 6(8): e1001050. doi:10.1371/journal.pgen.1001050
Editor: Jianzhi Zhang, University of Michigan, United States of America
Received: May 4, 2010; Accepted: July 6, 2010; Published: August 5, 2010
Copyright: © 2010 Kuo, Ochman. 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 work was funded by NIH grants GM56130 and GM74738. The funder 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: howard.ochman@yale.edu
¤ Current address: Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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