High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection

被引:76
作者
Chattopadhyay, Sujay [1 ]
Weissman, Scott J. [2 ]
Minin, Vladimir N. [3 ]
Russo, Thomas A. [4 ,5 ,6 ]
Dykhuizen, Daniel E. [7 ]
Sokurenko, Evgeni V. [1 ]
机构
[1] Univ Washington, Dept Microbiol, Seattle, WA 98195 USA
[2] Univ Washington, Div Infect Dis, Dept Pediat, Seattle, WA 98195 USA
[3] Univ Washington, Dept Stat, Seattle, WA 98195 USA
[4] SUNY Buffalo, Vet Adm Western New York Healthcare Syst, Buffalo, NY 14260 USA
[5] SUNY Buffalo, Dept Med, Buffalo, NY 14260 USA
[6] SUNY Buffalo, Ctr Excellence Bioinformat & Life Sci, Buffalo, NY 14260 USA
[7] SUNY Stony Brook, Dept Ecol & Evolut, Stony Brook, NY 11794 USA
关键词
commensal; E. coli core genome; extra-intestinal; pathoadaptive evolution; Shigella; COMPARATIVE GENOMIC ANALYSIS; SOURCE-SINK DYNAMICS; PATHOADAPTIVE MUTATIONS; EVOLUTION; VIRULENCE; BACTERIAL; SEQUENCE; CONTINGENCY; UROPATHOGEN; ADAPTATION;
D O I
10.1073/pnas.0906217106
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];
摘要
Core genes comprising the ubiquitous backbone of bacterial genomes are not subject to frequent horizontal transfer and generally are not thought to contribute to the adaptive evolution of bacterial pathogens. We determined, however, that at least one-third and possibly more than one-half of the core genes in Escherichia coli genomes are targeted by repeated replacement substitutions in the same amino acid positions-hotspot mutations. Occurrence of hotspot mutations is driven by positive selection, as their rate is significantly higher than expected by random chance alone, and neither intragenic recombination nor increased mutability can explain the observed patterns. Also, commensal E. coli strains have a significantly lower frequency of mutated genes and mutations per genome than pathogenic strains. E. coli strains causing extra-intestinal infections accumulate hotspot mutations at the highest rate, whereas the highest total number of mutated genes has been found among Shigella isolates, suggesting the pathoadaptive nature of such mutations. The vast majority of hotspot mutations are of recent evolutionary origin, implying short-term positive selection, where adaptive mutations emerge repeatedly but are not sustained in natural circulation for long. Such pattern of dynamics is consistent with source-sink model of virulence evolution.
引用
收藏
页码:12412 / 12417
页数:6
相关论文
共 47 条
[1]
Lateral gene transfer in eukaryotes [J].
Andersson, JO .
CELLULAR AND MOLECULAR LIFE SCIENCES, 2005, 62 (11) :1182-1197
[2]
Phylogenomic analysis of natural selection pressure in Streptococcus genomes [J].
Anisimova, Maria ;
Bielawski, Joseph ;
Dunn, Katherine ;
Yang, Ziheng .
BMC EVOLUTIONARY BIOLOGY, 2007, 7 (1)
[3]
Barlow M, 2002, GENETICS, V160, P823
[4]
Molecular biology - DNA methylation de novo [J].
Bird, A .
SCIENCE, 1999, 286 (5448) :2287-2288
[5]
Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli [J].
Blount, Zachary D. ;
Borland, Christina Z. ;
Lenski, Richard E. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (23) :7899-7906
[6]
A simple and robust statistical test for detecting the presence of recombination [J].
Bruen, TC ;
Philippe, H ;
Bryant, D .
GENETICS, 2006, 172 (04) :2665-2681
[7]
How to become a uropathogen:: Comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains [J].
Brzuszkiewicz, Elzbieta ;
Brueggemann, Holger ;
Liesegang, Heiko ;
Emmerth, Melanie ;
Oeschlaeger, Tobias ;
Nagy, Gabor ;
Albermann, Kaj ;
Wagner, Christian ;
Buchrieser, Carmen ;
Emody, Levente ;
Gottschalk, Gerhard ;
Hackert, Joerg ;
Dobrindt, Ulrich .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (34) :12879-12884
[8]
Chan CX, 2007, S AFR COMPUT J, V38, P20
[9]
Haplotype diversity in "source-sink" dynamics of Escherichia coli urovirulence [J].
Chattopadhyay, Sujay ;
Feldgarden, Michael ;
Weissman, Scott J. ;
Dykhuizen, Daniel E. ;
van Belle, Gerald ;
Sokurenko, Evgeni V. .
JOURNAL OF MOLECULAR EVOLUTION, 2007, 64 (02) :204-214
[10]
ZPS: visualization of recent adaptive evolution of proteins [J].
Chattopadhyay, Sujay ;
Dykhuizen, Daniel E. ;
Sokurenko, Evgeni V. .
BMC BIOINFORMATICS, 2007, 8 (1)