Complete Nucleotide Sequence and Organization of the Naphthalene Catabolic Plasmid pND6-1 From Pseudomonas Sp. Strain ND6

Gene. 2004 Jul 21;336(2):231-40. doi: 10.1016/j.gene.2004.03.027.

Abstract

Pseudomonas sp. strain ND6, which was isolated from industrial wastewater in Tianjin, China, was capable of dissimilating naphthalene as sole carbon and energy sources. We identified one plasmid, pND6-1, which was associated with the metabolism of naphthalene and determined the complete nucleotide sequence of pND6-1 (101,858 bp) using a whole-genome-shotgun approach. Computational analyses indicated that the naphthalene metabolism of the strain ND6 is associated with this plasmid. This is the first report of a complete sequence of naphthalene catabolic plasmid. pND6-1 encodes 102 putative coding sequences (CDSs). Among them, 23 CDSs were predicted to be involved in naphthalene catabolism, 14 were predicted to be involved in transposition and integration, 2 encoded putative transporters, 3 were putative transcriptional regulators, and 9 were proteins necessary for plasmid replication and partitioning. Most of the naphthalene catabolic genes of pND6-1 have 99-100% identity in amino acid sequences homologous to their nearest counterparts found in plasmid pDTG1, NAH7 and in a chromosome region in Pseudomonas stutzeri AN10 except for two duplicated genes (ND013 and ND016). Results of this study indicated that globally distributed naphthalene catabolic genes are highly conserved among different bacterial species.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • DNA Replication / genetics
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / genetics*
  • Gene Order
  • Genes, Bacterial / genetics
  • Genome, Bacterial
  • Integrases / genetics
  • Molecular Sequence Data
  • Naphthalenes / metabolism*
  • Operon / genetics
  • Plasmids / genetics*
  • Plasmids / metabolism
  • Pseudomonas / genetics*
  • Pseudomonas / metabolism
  • Pseudomonas putida / genetics
  • Sequence Analysis, DNA
  • Transcription Factors / genetics
  • Transposases / genetics

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • Naphthalenes
  • Transcription Factors
  • naphthalene
  • Integrases
  • Transposases

Associated data

  • GENBANK/AY208917