title: Site-specific mobilization of vinyl chloride respiration islands by a mechanism common in Dehalococcoides.
abstract: BACKGROUND
  Vinyl 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: Department of Civil and Environmental Engineering, Stanford University, Stanford, California, USA. spormann@stanford.edu.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: McMurdie
authors.forename: Laura A
authors.initials: LA
authors.lastname: Hug
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Edwards
authors.forename: Susan
authors.initials: S
authors.lastname: Holmes
authors.forename: Alfred M
authors.initials: AM
authors.lastname: Spormann
mesh_terms: D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics; D041862:Chloroflexi / Q000235:genetics*; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D044404:Genomic Islands; D009876:Operon; D010088:Oxidoreductases / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment; D014752:Vinyl Chloride / Q000737:chemistry / Q000378:metabolism*; D014874:Water Pollutants, Chemical / Q000737:chemistry / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D014874:Water Pollutants, Chemical; C096222:tmRNA; D010088:Oxidoreductases; D014752:Vinyl Chloride