Genomic Analysis of γ-Hexachlorocyclohexane-Degrading Sphingopyxis lindanitolerans WS5A3p Strain in the Context of the Pangenome of Sphingopyxis

Genes (Basel). 2019 Sep 6;10(9):688. doi: 10.3390/genes10090688.

Abstract

Sphingopyxis inhabit diverse environmental niches, including marine, freshwater, oceans, soil and anthropogenic sites. The genus includes 20 phylogenetically distinct, valid species, but only a few with a sequenced genome. In this work, we analyzed the nearly complete genome of the newly described species, Sphingopyxis lindanitolerans, and compared it to the other available Sphingopyxis genomes. The genome included 4.3 Mbp in total and consists of a circular chromosome, and two putative plasmids. Among the identified set of lin genes responsible for γ-hexachlorocyclohexane pesticide degradation, we discovered a gene coding for a new isoform of the LinA protein. The significant potential of this species in the remediation of contaminated soil is also correlated with the fact that its genome encodes a higher number of enzymes potentially involved in aromatic compound degradation than for most other Sphingopyxis strains. Additional analysis of 44 Sphingopyxis representatives provides insights into the pangenome of Sphingopyxis and revealed a core of 734 protein clusters and between four and 1667 unique proteins per genome.

Keywords: Sphingopyxis lindanitolerans; complete genome sequence; lin genes; pangenome; pesticide; γ-HCH degradation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Biodegradation, Environmental
  • Genome, Bacterial*
  • Hexachlorocyclohexane / metabolism*
  • Pesticides / metabolism*
  • Sphingomonadaceae / enzymology
  • Sphingomonadaceae / genetics*
  • Sphingomonadaceae / metabolism

Substances

  • Bacterial Proteins
  • Pesticides
  • Hexachlorocyclohexane

Supplementary concepts

  • Sphingopyxis lindanitolerans