Get access

Sequence analysis of three plasmids harboured in Rhodococcus erythropolis strain PR4

Authors

  • Mitsuo Sekine,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Satoshi Tanikawa,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Seiha Omata,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Mika Saito,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Takatomo Fujisawa,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Naofumi Tsukatani,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Takahisa Tajima,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Tomohiro Sekigawa,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Hiroki Kosugi,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Yasunori Matsuo,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Rika Nishiko,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Kohsuke Imamura,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Mio Ito,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Hitomi Narita,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Shinichi Tago,

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author
  • Nobuyuki Fujita,

    Corresponding author
    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
      *E-mail fujita-nobuyuki@nite.go.jp; Tel. (+81) 3 3481 1972; Fax (+81) 3 3481 8424.
    Search for more papers by this author
  • Shigeaki Harayama

    1. NITE Genome Analysis Center, Department of Biotechnology, National Institute of Technology and Evaluation (NITE), 2-10-49 Nishihara, Shibuya-ku, Tokyo 151-0066, Japan.
    Search for more papers by this author

*E-mail fujita-nobuyuki@nite.go.jp; Tel. (+81) 3 3481 1972; Fax (+81) 3 3481 8424.

Summary

Rhodococcus erythropolis strain PR4 has been isolated as an alkane-degrading bacterium. The strain harbours one linear plasmid, pREL1 (271 577 bp) and two circular plasmids, pREC1 (104 014 bp) and pREC2 (3637 bp), all with some sequence similarities to other Rhodococcus plasmids. For pREL1, pREC1 and pREC2, 298, 102 and 3 open reading frames, respectively, were predicted. Linear plasmid pREL1 has several regions homologous to plasmid pBD2 found in R. erythropolis BD2. Sequence analysis of pREL1 and pBD2 identified common metal-resistance genes on both, but pREL1 also encodes alkane-degradation genes not found on pBD2, with enzyme constituents some of which are quite different from those of other organisms. The alkane hydroxylase consisted of a cytochrome P450 monooxygenase, a 2Fe-2S ferredoxin, and a ferredoxin reductase. The ferredoxin reductase amino acid sequence resembles the AlkT (rubredoxin reductase) sequence. A zinc-containing alcohol dehydrogenase further oxydizes alkanols, alkane oxidation products catalysed by alkane hydroxylase. Of the circular plasmids, the pREC1 sequence is partially similar to the sequence of pREAT701, the virulence plasmid found in Rhodococcus equi. pREC1 has no pREAT701 virulence genes and encodes genes for β-oxidation of fatty acids. Thus, joint actions of enzymes encoded by pREL1 and pREC1 may enable efficient mineralization of alkanes.

Get access to the full text of this article

Ancillary