Site-Specific Mobilization of Vinyl Chloride Respiration Islands by a Mechanism Common in Dehalococcoides

BMC Genomics

Research Article

Laura A Hug¹  Elizabeth A Edwards²  Paul J McMurdie³  Alfred M Spormann⁴  Susan Holmes⁵ 

[1] Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada;Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada;Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada;Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA;Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA;Department of Chemical Engineering, Stanford University, Stanford, California, USA;Department of Statistics, Stanford University, Stanford, California, USA;

关键词: Additional Data File;    Vinyl Chloride;    Direct Repeat;    Genomic Island;    Protein Encode Gene;   

DOI  :  10.1186/1471-2164-12-287

 received in 2011-01-31, accepted in 2011-06-02,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundVinyl chloride is a widespread groundwater pollutant and Group 1 carcinogen. A previous comparative genomic analysis revealed that the vinyl chloride reductase operon, vcrABC, of Dehalococcoides sp. strain VS is embedded in a horizontally-acquired genomic island that integrated at the single-copy tmRNA gene, ssrA.ResultsWe targeted conserved positions in available genomic islands to amplify and sequence four additional vcrABC -containing genomic islands from previously-unsequenced vinyl chloride respiring Dehalococcoides enrichments. We identified a total of 31 ssrA-specific genomic islands from Dehalococcoides genomic data, accounting for 47 reductive dehalogenase homologous genes and many other non-core genes. Sixteen of these genomic islands contain a syntenic module of integration-associated genes located adjacent to the predicted site of integration, and among these islands, eight contain vcrABC as genetic 'cargo'. These eight vcrABC -containing genomic islands are syntenic across their ~12 kbp length, but have two phylogenetically discordant segments that unambiguously differentiate the integration module from the vcrABC cargo. Using available Dehalococcoides phylogenomic data we estimate that these ssrA-specific genomic islands are at least as old as the Dehalococcoides group itself, which in turn is much older than human civilization.ConclusionsThe vcrABC -containing genomic islands are a recently-acquired subset of a diverse collection of ssrA-specific mobile elements that are a major contributor to strain-level diversity in Dehalococcoides, and may have been throughout its evolution. The high similarity between vcrABC sequences is quantitatively consistent with recent horizontal acquisition driven by ~100 years of industrial pollution with chlorinated ethenes.

【 授权许可】

Unknown   
© McMurdie et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.