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 0 -CT and, at its right end, carries a transposase homologue (pivNM/irg) of RNaseH/Retroviral integrase superfamily. The

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... eny 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 0 -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 0 -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 0 -CTtat sequences. We concluded that the PivNM/Irg transposase on Nfs integrated their circular forms into the chromosomal 5 0 -CT-containing sequences and probably mediated the above rearrangements. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org CT tatat c a ggg 5'-attcccgc CT tatat gatgcgctctatcaaaggggcgcat-3' 5'-aaac CT tatat attgcgtccctaagaagggrygatt-3' 5'-CT tatat attgcrcyccat-aaggggcgcawr-3'