Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium

Yuji Nagata, Shunsuke Natsui, Ryo Endo, Yoshiyuki Ohtsubo, Natsuko Ichikawa, Akiho Ankai, Akio Oguchi, Shigehiro Fukui, Nobuyuki Fujita, Masataka Tsuda

    Research output: Contribution to journalArticlepeer-review

    37 Citations (Scopus)

    Abstract

    The complete genome sequencing of a γ-hexachlorocyclohexane-degrading strain, Sphingobium japonicum UT26, revealed that the genome consists of two circular chromosomes [with sizes of 3.5 Mb (Chr1) and 682. kb (Chr2)], a 191-kb large plasmid (pCHQ1), and two small plasmids with sizes of 32 and 5. kb. The lin genes are dispersed on Chr1, Chr2, and pCHQ1. Comparison of the UT26 genome with those of other sphingomonad strains demonstrated that the " specific" lin genes for conversion of γ-HCH to β-ketoadipate (linA, linB, linC, linRED, and linF) are located on the DNA regions unique to the UT26 genome, suggesting the acquisition of these lin genes by horizontal transfer events. On the other hand, linGHIJ and linKLMN are located on the regions conserved in the genomes of sphingomonads, suggesting that the linGHIJ-encoded β-ketoadipate pathway and the LinKLMN-type ABC transporter system are involved in core functions of sphingomonads. Based on these results, we propose a hypothesis that UT26 was created by recruiting the specific lin genes into a strain having core functions of sphingomonads. Most of the specific lin genes in UT26 are associated with IS. 6100. Our analysis of spontaneous linA-, linC-, and linRED-deletion mutants of UT26 revealed the involvement of IS. 6100 in their deduced genome rearrangements. These facts strongly suggest that IS. 6100 plays important roles both in the dissemination of the specific lin genes and in the genome rearrangements.

    Original languageEnglish
    Pages (from-to)499-508
    Number of pages10
    JournalEnzyme and Microbial Technology
    Volume49
    Issue number6-7
    DOIs
    Publication statusPublished - 2011 Dec 10

    Keywords

    • Biodegradation
    • Environmental pollutant
    • Genome
    • Insertion sequence
    • Sphingomonads
    • γ-Hexachlorocyclohexane

    ASJC Scopus subject areas

    • Biotechnology
    • Bioengineering
    • Biochemistry
    • Applied Microbiology and Biotechnology

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