Electronic versions

  • Olivia Molenda
    University of Toronto
  • Shuiquan Tang
    Zymo Research
  • Line Lomheim
    University of Toronto
  • Vasu K Gautam
    University of Toronto
  • Sofia Lemak
    University of Toronto
  • Alexander F Yakunin
    University of Toronto
  • Karen L Maxwell
    University of Toronto
  • Elizabeth A Edwards
    University of Toronto

Dehalococcoides mccartyi are obligate organohalide-respiring bacteria that play an important detoxifying role in the environment. They have small genomes (~1.4 Mb) with a core region interrupted by two high plasticity regions (HPRs) containing dozens of genes encoding reductive dehalogenases involved in organohalide respiration. The genomes of eight new strains of D. mccartyi were closed from metagenomic data from a related set of enrichment cultures, bringing the total number of genomes to 24. Two of the newly sequenced strains and three previously sequenced strains contain CRISPR-Cas systems. These D. mccartyi CRISPR-Cas systems were found to primarily target prophages and genomic islands. The genomic islands were identified either as integrated into D. mccartyi genomes or as circular extrachromosomal elements. We observed active circularization of the integrated genomic island containing vcrABC operon encoding the dehalogenase (VcrA) responsible for the transformation of vinyl chloride to non-toxic ethene. We interrogated archived DNA from established enrichment cultures and found that the CRISPR array acquired three new spacers in 11 years. These data provide a glimpse into dynamic processes operating on the genomes distinct to D. mccartyi strains found in enrichment cultures and provide the first insights into possible mechanisms of lateral DNA exchange in D. mccartyi.

Keywords

  • Bacteria/enzymology, Biodegradation, Environmental, CRISPR-Cas Systems, DNA, Bacterial/genetics, DNA, Circular/genetics, Gene Expression Regulation, Bacterial, Gene Expression Regulation, Enzymologic/genetics, Genome, Bacterial, Genomic Islands/genetics, Halogenation
Original languageEnglish
Pages (from-to)24-38
Number of pages15
JournalThe ISME Journal
Volume13
Issue number1
Early online date13 Aug 2018
DOIs
Publication statusPublished - 1 Jan 2019
Externally publishedYes
View graph of relations