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Journal of Bacteriology, March 2008, p. 2172-2182, Vol. 190, No. 6
0021-9193/08/$08.00+0     doi:10.1128/JB.01657-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Genomic Characterization of Mycobacteriophage Giles: Evidence for Phage Acquisition of Host DNA by Illegitimate Recombination ^,

Peter Morris, Laura J. Marinelli, Deborah Jacobs-Sera, Roger W. Hendrix, and Graham F. Hatfull^*

Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15241

Received 12 October 2007/ Accepted 22 December 2007

A characteristic feature of bacteriophage genomes is that they are architecturally mosaic, with each individual genome representing a unique assemblage of individual exchangeable modules. Plausible mechanisms for generating mosaicism include homologous recombination at shared boundary sequences of module junctions, illegitimate recombination in a non-sequence-directed process, and site-specific recombination. Analysis of the novel mycobacteriophage Giles genome not only extends our current perspective on bacteriophage genetic diversity, with more than 60% of the genes unrelated to other mycobacteriophages, but offers novel insights into how mosaic genomes are created. In one example, the integration/excision cassette is atypically situated within the structural gene operon and could have moved there either by illegitimate recombination or more plausibly via integrase-mediated site-specific recombination. In a second example, a DNA segment has been recently acquired from the host bacterial chromosome by illegitimate recombination, providing further evidence that phage genomic mosaicism is generated by nontargeted recombination processes.

Published ahead of print on 4 January 2008.

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

Present address: UG2, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom NR4 7TJ.