TY - JOUR

T1 - Extrachromosomal circular elements targeted by CRISPR-Cas in Dehalococcoides mccartyi are linked to mobilization of reductive dehalogenase genes

AU - Molenda, Olivia

AU - Tang, Shuiquan

AU - Lomheim, Line

AU - Gautam, Vasu K

AU - Lemak, Sofia

AU - Yakunin, Alexander F

AU - Maxwell, Karen L

AU - Edwards, Elizabeth A

PY - 2019/1/1

Y1 - 2019/1/1

N2 - 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.

AB - 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.

KW - Bacteria/enzymology

KW - Biodegradation, Environmental

KW - CRISPR-Cas Systems

KW - DNA, Bacterial/genetics

KW - DNA, Circular/genetics

KW - Gene Expression Regulation, Bacterial

KW - Gene Expression Regulation, Enzymologic/genetics

KW - Genome, Bacterial

KW - Genomic Islands/genetics

KW - Halogenation

U2 - 10.1038/s41396-018-0254-2

DO - 10.1038/s41396-018-0254-2

M3 - Article

C2 - 30104577

VL - 13

SP - 24

EP - 38

JO - The ISME Journal

JF - The ISME Journal

SN - 1751-7362

IS - 1

ER -