The complete genomic sequence of the marine phage Roseophage SIO1 shares homology with nonmarine phages

Rohwer, Forest, Anca Segall, Grieg Steward, Victor Seguritan, Mya Breitbart, Felise Wolven, Farooq Azam

Limnol. Oceanogr., 45(2), 2000, 408-418 | DOI: 10.4319/lo.2000.45.2.0408

ABSTRACT: Viruses are ubiquitous components of the marine environment, frequently reaching concentrations of 107 -108 viruses per milliliter of surface seawater. The majority of these viral particles are bacteriophages (phages). Although the oceans are probably the largest pool of bacteriophages on the planet, the evolutionary relationships of marine phages to phages from other environments are unknown. To address this issue, we have completely sequenced the genome of the lytic marine phage, Roseophage SIO1, that infects the heterotrophic marine bacterium Roseobacter SIO67. This phage has an isometric capsid with a diameter of approximately 43 nm, a short tail, a buoyant density of 1.49 g cm-3 in CsCl, and a 39,906-bp dsDNA genome. Sequence similarities and relative positions within the genome suggest that three of the open reading frames (ORFs) are homologous to the primase, DNA polymerase, and endodeoxyribonuclease I proteins of coliphages T3 and T7. The results are consistent with the mosaic theory of phage evolution and indicate a genetic link between marine and nonmarine phages. Additionally, basic life histories of marine phages can be elucidated by comparison of complete genomes to those of other extensively studied phages (e.g., lambda, T4, T7). The DNA replication machinery of Roseophage SIO1 shows a clear homology with that of coliphages T3 and T7, suggesting that the process of DNA replication may be similar among these phages. The Roseophage SIO1 genome also encodes four predicted proteins involved in phosphate metabolism (RP PhoH, RP ribonucleotide reductase, RP Thy1, and RP endodeoxyribonuclease I) suggesting that phosphate recycling is important to Roseophage SIO1’s life cycle. Other interesting clues about Roseophage SIO1’s life history come from the absence of certain expected protein regions. For example, we have not been able to identify the Roseophage SIO1 structural proteins (e.g., capsid proteins) by homology to other phages. It is also conspicuous that the Roseo-phage SIO1 genome lacks a recognizable RNA polymerase, an essential component of T3 and T7 life cycles. Analysis of the Roseophage SIO1 genome shows that marine and nonmarine phages are genetically related but basic life histories may be significantly different.

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