Genomic analysis of Pseudomonas sp. Strain SCT, an iodate-reducing bacterium isolated from marine sediment, reveals a possible use for bioremediation

Masafumi Harada, Kohei Ito, Nobuyoshi Nakajima, Shigeki Yamamura, Masaru Tomita, Haruo Suzuki, Seigo Amachi

Research output: Contribution to journalArticle

Abstract

Strain SCT is an iodate-reducing bacterium isolated from marine sediment in Kanagawa Prefecture, Japan. In this study, we determined the draft genome sequence of strain SCT and compared it to complete genome sequences of other closely related bacteria, including Pseudomonas stutzeri. A phylogeny inferred from concatenation of core genes revealed that strain SCT was closely related to marine isolates of P. stutzeri. Genes present in the SCT genome but absent from the other analyzed P. stutzeri genomes comprised clusters corresponding to putative prophage regions and possible operons. They included pil genes, which encode type IV pili for natural transformation; the mer operon, which encodes resistance systems for mercury; and the pst operon, which encodes a Pi-specific transport system for phosphate uptake. We found that strain SCT had more prophage-like genes than the other P. stutzeri strains and that the majority (70%) of them were SCT strain-specific. These genes, encoded on distinct prophage regions, may have been acquired after branching from a common ancestor following independent phage transfer events. Thus, the genome sequence of Pseudomonas sp. strain SCT can provide detailed insights into its metabolic potential and the evolution of genetic elements associated with its unique phenotype.

Original languageEnglish
Pages (from-to)1321-1329
Number of pages9
JournalG3: Genes, Genomes, Genetics
Volume9
Issue number5
DOIs
Publication statusPublished - 2019 May 1

Fingerprint

Iodates
Geologic Sediments
Environmental Biodegradation
Pseudomonas stutzeri
Pseudomonas
Prophages
Genome
Bacteria
Operon
Genes
Molecular Evolution
Phylogeny
Mercury
Bacteriophages
Japan
Phosphates
Phenotype

Keywords

  • Comparative genomics
  • Gene conservation
  • Genome analysis
  • Iodate-reducing bacterium
  • Marine sediment
  • Phylogeny
  • Pseudomonas stutzeri
  • Strain SCT

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

Genomic analysis of Pseudomonas sp. Strain SCT, an iodate-reducing bacterium isolated from marine sediment, reveals a possible use for bioremediation. / Harada, Masafumi; Ito, Kohei; Nakajima, Nobuyoshi; Yamamura, Shigeki; Tomita, Masaru; Suzuki, Haruo; Amachi, Seigo.

In: G3: Genes, Genomes, Genetics, Vol. 9, No. 5, 01.05.2019, p. 1321-1329.

Research output: Contribution to journalArticle

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