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DNA Research Advance Access published online on February 22, 2006
DNA Research, doi:10.1093/dnares/dsi021
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© The Author 2006. Kazusa DNA Research Institute.
Received August 24, 2005
Revised November 24, 2005

Full Papers

Genome Comparison In Silico in Neisseria Suggests Integration of Filamentous Bacteriophages by their Own Transposase

Mikihiko Kawai 1, Ikuo Uchiyama 2, and Ichizo Kobayashi 3 *

1 Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Japan; Institute of Medical Science, The University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Division of Pathology, Immunology and Microbiology, Graduate School of Medicine, The University of Tokyo, Japan
2 Research Center for Computational Science, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan
3 Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Japan; Institute of Medical Science, The University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan; Graduate Program in Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Japan

* To whom correspondence should be addressed.
Ichizo Kobayashi, E-mail: ikobaya{at}ims.u-tokyo.ac.jp


  Abstract

We have identified filamentous prophages, Nf (Neisserial filamentous phages), during an in silico genome comparison in Neisseria. Comparison of three genomes of Neisseria meningitidis and one of Neisseria gonorrhoeae revealed four subtypes of Nf. Eleven intact copies are located at different loci in the four genomes. Each intact copy of Nf is flanked by duplication of 5'-CT and, at its right end, carries a transposase homologue (pivNM/irg) of RNaseH/Retroviral integrase superfamily. The phylogeny of these putative transposases and that of phage-related proteins on Nfs are congruent. Following circularization of Nfs, a promoter-like sequence forms. The sequence at the junction of these predicted circular forms (5'-atCTtatat) was found in a related plasmid (pMU1) at a corresponding locus. Several structural variants of Nfs--partially inverted, internally deleted and truncated--were also identified. The partial inversion seems to be a product of site-specific recombination between two 5'-CTtat sequences that are in inverse orientation, one at its end and the other upstream of pivNM/irg. Formation of internally deleted variants probably proceeded through replicative transposition that also involved two 5'-CTtat sequences. We concluded that the PivNM/Irg transposase on Nfs integrated their circular forms into the chromosomal 5'-CT-containing sequences and probably mediated the above rearrangements.

Keywords: transposase; filamentous bacteriophage; integration; prophage; genome comparison.
Communicated by Kenta Nakai
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