title: Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6.
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.
authors.affiliation: Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.forename: Jiandang
authors.initials: J
authors.lastname: Shi
authors.forename: Xuegang
authors.initials: X
authors.lastname: Wang
authors.forename: Yuning
authors.initials: Y
authors.lastname: Han
authors.forename: Wei
authors.initials: W
authors.lastname: Tong
authors.forename: Lin
authors.initials: L
authors.lastname: Ma
authors.forename: Bin
authors.initials: B
authors.lastname: Liu
authors.forename: Baoli
authors.initials: B
authors.lastname: Cai
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D023061:Gene Order; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D019426:Integrases / Q000235:genetics; D008969:Molecular Sequence Data; D009281:Naphthalenes / Q000378:metabolism*; D009876:Operon / Q000235:genetics; D010957:Plasmids / Q000235:genetics* / Q000378:metabolism; D011549:Pseudomonas / Q000235:genetics* / Q000378:metabolism; D016958:Pseudomonas putida / Q000235:genetics; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics; D019895:Transposases / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D009281:Naphthalenes; D014157:Transcription Factors; C031721:naphthalene; D019426:Integrases; D019895:Transposases