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Nucleic Acids Research Advance Access originally published online on February 16, 2008
Nucleic Acids Research 2008 36(6):2094-2105; doi:10.1093/nar/gkn053
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Nucleic Acids Research, 2008, Vol. 36, No. 6 2094-2105
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Nucleic Acids Enzyme

Phage T4 SegB protein is a homing endonuclease required for the preferred inheritance of T4 tRNA gene region occurring in co-infection with a related phage

Vera S. Brok-Volchanskaya1, Farid A. Kadyrov1, Dmitry E. Sivogrivov1, Peter M. Kolosov1, Andrey S. Sokolov1, Michael G. Shlyapnikov1, Valentine M. Kryukov2 and Igor E. Granovsky1,*

1Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Nauki ave., 5, Pushchino and 2Institute of Cell Biophysics, Russian Academy of Sciences, Nauki ave., 3, Pushchino, Moscow Region, 142290, Russia

*To whom correspondence should be addressed. Tel: +7 4967 730479; Fax: +7 495 9563370; Email: granovsky{at}ibpm.pushchino.ru

Received January 23, 2008. Revised January 25, 2008. Accepted January 25, 2008.

Homing endonucleases initiate nonreciprocal transfer of DNA segments containing their own genes and the flanking sequences by cleaving the recipient DNA. Bacteriophage T4 segB gene, which is located in a cluster of tRNA genes, encodes a protein of unknown function, homologous to homing endonucleases of the GIY-YIG family. We demonstrate that SegB protein is a site-specific endonuclease, which produces mostly 3' 2-nt protruding ends at its DNA cleavage site. Analysis of SegB cleavage sites suggests that SegB recognizes a 27-bp sequence. It contains 11-bp conserved sequence, which corresponds to a conserved motif of tRNA T{psi}C stem-loop, whereas the remainder of the recognition site is rather degenerate. T4-related phages T2L, RB1 and RB3 contain tRNA gene regions that are homologous to that of phage T4 but lack segB gene and several tRNA genes. In co-infections of phages T4 and T2L, segB gene is inherited with nearly 100% of efficiency. The preferred inheritance depends absolutely on the segB gene integrity and is accompanied by the loss of the T2L tRNA gene region markers. We suggest that SegB is a homing endonuclease that functions to ensure spreading of its own gene and the surrounding tRNA genes among T4-related phages.

Present addresses: Farid A. Kadyrov, Department of Biochemistry, Box 3711, Duke University Medical Center, Durham, NC 27710, USA Peter M. Kolosov, Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya st., 16/10, 117997 GSP, Moscow V-437, Russia


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