Three Prochlorococcus Cyanophage Genomes: Signature Features and Ecological Interpretations

Journal Article · 19 April 2005 · PLoS Biology (Online)

DOI: https://doi.org/10.1371/journal.pbio.0030144 · OSTI ID:1627138

Sullivan, Matthew B. ^[1]; Coleman, Maureen L. ^[2]; Weigele, Peter ^[3]; Rohwer, Forest ^[4]; Chisholm, Sallie W. ^[5]

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1. Woods Hole Oceanographic Institution, Woods Hole, MA (United States). Joint Program in Biological Oceanography; Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
2. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Civil and Environmental Engineering
3. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Biology
4. San Diego State Univ., CA (United States). Dept. of Biology
5. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States). Dept. of Civil and Environmental Engineering and Dept. of Biology

The oceanic cyanobacteria Prochlorococcus are globally important, ecologically diverse primary producers. It is thought that their viruses (phages) mediate population sizes and affect the evolutionary trajectories of their hosts. Here we present an analysis of genomes from three Prochlorococcus phages: a podovirus and two myoviruses. The morphology, overall genome features, and gene content of these phages suggest that they are quite similar to T7-like (P-SSP7) and T4-like (P-SSM2 and P-SSM4) phages. Using the existing phage taxonomic framework as a guideline, we examined genome sequences to establish ‘‘core’’ genes for each phage group. We found the podovirus contained 15 of 26 core T7-like genes and the two myoviruses contained 43 and 42 of 75 core T4-like genes. In addition to these core genes, each genome contains a significant number of ‘‘cyanobacterial’’ genes, i.e., genes with significant best BLAST hits to genes found in cyanobacteria. Some of these, we speculate, represent ‘‘signature’’ cyanophage genes. For example, all three phage genomes contain photosynthetic genes (psbA, hliP) that are thought to help maintain host photosynthetic activity during infection, as well as an aldolase family gene (talC) that could facilitate alternative routes of carbon metabolism during infection. The podovirus genome also contains an integrase gene (int) and other features that suggest it is capable of integrating into its host. If indeed it is, this would be unprecedented among cultured T7-like phages or marine cyanophages and would have significant evolutionary and ecological implications for phage and host. Further, both myoviruses contain phosphate-inducible genes (phoH and pstS) that are likely to be important for phage and host responses to phosphate stress, a commonly limiting nutrient in marine systems. Thus, these marine cyanophages appear to be variations of two well-known phages—T7 and T4—but contain genes that, if functional, reflect adaptations for infection of photosynthetic hosts in low-nutrient oceanic environments.

• Research Organization: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Stanford Univ., CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Science Foundation (NSF)
• Grant/Contract Number: AC02-05CH11231; W-7405-ENG-48; AC03-76SF00098; W-7405-ENG-36; FC02-99ER62873; FG02-99ER62814; FG02-02ER63445; OCE-9820035
• OSTI ID: 1627138
• Journal Information: PLoS Biology (Online), Vol. 3, Issue 5; ISSN 1545-7885
• Publisher: Public Library of ScienceCopyright Statement
• Country of Publication: United States
• Language: English