title: The temperate marine phage PhiHAP-1 of Halomonas aquamarina possesses a linear plasmid-like prophage genome.
abstract: A myovirus-like temperate phage, PhiHAP-1, was induced with mitomycin C from a Halomonas aquamarina strain isolated from surface waters in the Gulf of Mexico. The induced cultures produced significantly more virus-like particles (VLPs) (3.73 x 10(10) VLP ml(-1)) than control cultures (3.83 x 10(7) VLP ml(-1)) when observed with epifluorescence microscopy. The induced phage was sequenced by using linker-amplified shotgun libraries and contained a genome 39,245 nucleotides in length with a G+C content of 59%. The PhiHAP-1 genome contained 46 putative open reading frames (ORFs), with 76% sharing significant similarity (E value of <10(-3)) at the protein level with other sequences in GenBank. Putative functional gene assignments included small and large terminase subunits, capsid and tail genes, an N6-DNA adenine methyltransferase, and lysogeny-related genes. Although no integrase was found, the PhiHAP-1 genome contained ORFs similar to protelomerase and parA genes found in linear plasmid-like phages with telomeric ends. Southern probing and PCR analysis of host genomic, plasmid, and PhiHAP-1 DNA indicated a lack of integration of the prophage with the host chromosome and a difference in genome arrangement between the prophage and virion forms. The linear plasmid prophage form of PhiHAP-1 begins with the protelomerase gene, presumably due to the activity of the protelomerase, while the induced phage particle has a circularly permuted genome that begins with the terminase genes. The PhiHAP-1 genome shares synteny and gene similarity with coliphage N15 and vibriophages VP882 and VHML, suggesting an evolutionary heritage from an N15-like linear plasmid prophage ancestor.
authors.affiliation: University of South Florida, College of Marine Science, 140 7th Avenue South, Saint Petersburg, FL 33701, USA.
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Mobberley
authors.forename: R Nathan
authors.initials: RN
authors.lastname: Authement
authors.forename: Anca M
authors.initials: AM
authors.lastname: Segall
authors.forename: John H
authors.initials: JH
authors.lastname: Paul
mesh_terms: D001435:Bacteriophages / Q000235:genetics* / Q000648:ultrastructure*; D001482:Base Composition; D001483:Base Sequence; D015139:Blotting, Southern; D017931:DNA Primers / Q000235:genetics; D016521:Electrophoresis, Gel, Pulsed-Field; D005431:Florida; D016679:Genome, Viral / Q000235:genetics*; D020632:Halomonas / Q000821:virology*; D013058:Mass Spectrometry; D046529:Microscopy, Electron, Transmission; D008856:Microscopy, Fluorescence; D016685:Mitomycin; D008969:Molecular Sequence Data; D009792:Oceans and Seas; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D026801:Synteny / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D017931:DNA Primers; D014764:Viral Proteins; D016685:Mitomycin