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J. Virol. doi:10.1128/JVI.00140-08
Copyright (c) 2008, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

The Temperate Marine Phage HAP-1 of Halomonas aquamarina Possesses a Linear Plasmid-like Prophage Genome

College of Marine Science, University of South Florida, 140 7^th Avenue South, Saint Petersburg, FL 33701; Department of Biology, San Diego State University, San Diego, California 92182-4614

^* To whom correspondence should be addressed. Email: jpaul{at}marine.usf.edu.

	Abstract

A myovirus-like temperate phage, HAP-1, was induced with Mitomycin C from an Halomonas aquamarina strain isolated from surface waters in the Gulf of Mexico. Induced cultures produced significantly more viral-like particles (3.73 x 10¹⁰ VLP ml^-1) than control cultures (3.83 x 10⁷ VLP ml^-1) when observed with epifluoresence microscopy. The induced phage was sequenced using linker-amplified shotgun libraries and contained a genome 39,245 nucleotides in length with a G+C content of 59 percent. The HAP-1 genome contained 46 putative open reading frames (ORFs), with 76 percent sharing significant similarity (e<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-adenine-DNA methyltransferase, and lysogeny-related genes. Although no integrase was found, the HAP-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 HAP-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 form. The linear plasmid prophage form of HAP-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 HAP-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.