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Journal of Bacteriology, June 2006, p. 4057-4067, Vol. 188, No. 11
0021-9193/06/$08.00+0     doi:10.1128/JB.00185-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Genomic and Functional Analysis of the IncP-9 Naphthalene-Catabolic Plasmid NAH7 and Its Transposon Tn4655 Suggests Catabolic Gene Spread by a Tyrosine Recombinase{dagger}

Masahiro Sota,1,2,3* Hirokazu Yano,2 Akira Ono,2 Ryo Miyazaki,2 Hidenori Ishii,2 Hiroyuki Genka,2 Eva M. Top,3 and Masataka Tsuda2

Department of Environmental Simulation, Institute for Environmental Sciences, Rokkasho, Aomori 039-3212,1 Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Katahira, Sendai 980-8577, Japan,2 Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844-30513

Received 3 February 2006/ Accepted 23 March 2006

The naphthalene-catabolic (nah) genes on the incompatibility group P-9 (IncP-9) self-transmissible plasmid NAH7 from Pseudomonas putida G7 are some of the most extensively characterized genetic determinants for bacterial aerobic catabolism of aromatic hydrocarbons. In contrast to the detailed studies of its catabolic cascade and enzymatic functions, the biological characteristics of plasmid NAH7 have remained unclear. Our sequence determination in this study together with the previously deposited sequences revealed the entire structure of NAH7 (82,232 bp). Comparison of NAH7 with two other completely sequenced IncP-9 catabolic plasmids, pDTG1 and pWW0, revealed that the three plasmids share very high nucleotide similarities in a 39-kb region encoding the basic plasmid functions (the IncP-9 backbone). The backbone of NAH7 is phylogenetically more related to that of pDTG1 than that of pWW0. These three plasmids carry their catabolic gene clusters at different positions on the IncP-9 backbone. All of the NAH7-specified nah genes are located on a class II transposon, Tn4655. Our analysis of the Tn4655-encoded site-specific recombination system revealed that (i) a novel tyrosine recombinase, TnpI, catalyzed both the intra- and intermolecular recombination between two copies of the attI site, (ii) the functional attI site was located within a 119-bp segment, and (iii) the site-specific strand exchange occurred within a 30-bp segment in the 41-bp CORE site. Our results and the sequence data of other naphthalene-catabolic plasmids, pDTG1 and pND6-1, suggest a potential role of the TnpI-attI recombination system in the establishment of these catabolic plasmids.

* Corresponding author. Mailing address: Department of Biological Sciences, 252 Life Science South, University of Idaho, Moscow, ID 83844-3051. Phone: (208) 885-4031. Fax: (208) 885-7905. E-mail: sota{at}uidaho.edu.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

Journal of Bacteriology, June 2006, p. 4057-4067, Vol. 188, No. 11
0021-9193/06/$08.00+0     doi:10.1128/JB.00185-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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