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Journal of Virology, July 2008, p. 6618-6630, Vol. 82, No. 13
0022-538X/08/$08.00+0     doi:10.1128/JVI.00140-08
Copyright © 2008, American Society for Microbiology. 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 7th Avenue South, Saint Petersburg, Florida 33701,¹ Department of Biology, San Diego State University, San Diego, California 92182-4614²

Received 18 January 2008/ Accepted 21 April 2008

A myovirus-like temperate phage, HAP-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 10¹⁰ VLP ml^–1) than control cultures (3.83 x 10⁷ 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 HAP-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 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 forms. 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.

Published ahead of print on 30 April 2008.