Journal Article

Genome Comparison <i>In Silico</i> in <i>Neisseria</i> Suggests Integration of Filamentous Bacteriophages by their Own Transposase

Mikihiko Kawai, Ikuo Uchiyama and Ichizo Kobayashi

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 12, issue 6, pages 389-401
Published in print February 2006 | ISSN: 1340-2838
Published online January 2005 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsi021

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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

Journal Article.  6967 words.  Illustrated.

Subjects: Genetics and Genomics

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