title: Genomic characterization of mycobacteriophage Giles: evidence for phage acquisition of host DNA by illegitimate recombination.
abstract: 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.
authors.affiliation: Department of Biological Sciences and Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Morris
authors.forename: Laura J
authors.initials: LJ
authors.lastname: Marinelli
authors.forename: Deborah
authors.initials: D
authors.lastname: Jacobs-Sera
authors.forename: Roger W
authors.initials: RW
authors.lastname: Hendrix
authors.forename: Graham F
authors.initials: GF
authors.lastname: Hatfull
mesh_terms: D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics*; D016679:Genome, Viral / Q000235:genetics*; D054884:Host-Pathogen Interactions; D008854:Microscopy, Electron; D008969:Molecular Sequence Data; D009160:Mycobacteriophages / Q000235:genetics* / Q000502:physiology / Q000648:ultrastructure; D020102:Mycobacterium smegmatis / Q000235:genetics / Q000821:virology; D009876:Operon / Q000235:genetics; D011995:Recombination, Genetic; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004269:DNA, Bacterial