Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages

Abstract

The genome of cyanophage P60, a lytic virus which infects marine Synechococcus WH7803, was completely sequenced. The P60 genome contained 47,872 bp with 80 potential open reading frames that were mostly similar to the genes found in lytic phages like T7, phi-YeO3-12, and SIO1. The DNA replication system, consisting of primase-helicase and DNA polymerase, appeared to be more conserved in podoviruses than in siphoviruses and myoviruses, suggesting that DNA replication genes could be the critical elements for lytic phages. Strikingly high sequence similarities in the regions coding for nucleotide metabolism were found between cyanophage P60 and marine unicellular cyanobacteria.

FIG. 1.

Electron micrograph of marine cyanophage 60. Bar, 50 nm.

FIG. 2.

Genomic arrangement of cyanophage P60. Nineteen ORFs were assigned putative functions, and they were RNA polymerase (ORF 6), endonuclease (ORFs 16 and 17), primase-helicase (ORF 18), DNA pol (ORF 20), exonuclease (ORF 22), ribonucleotide triphosphate reductase (ORFs 26 and 27), tail tubular protein (ORFs 34, 35, and 36), capsid protein (ORF 37), methionine codon (ORF 39), head-to-tail joining protein (ORF 41), proline-rich protein (ORF 42), thymidylate synthase (ORF 53), packaging protein (ORFs 54 and 55), and collagen alpha I chain precursor (ORF 57). The length of the arrow is proportional to the length of the predicated ORF.

FIG. 3.

Comparison of the genomic arrangements of four bacteriophages (Podoviridae): cyanophage P60, coliphages T7 and phi-YeO3-12, and roseophage SIO1.

FIG. 4.

Neighbor-joining tree constructed based on the aligned DNA pol amino acid sequences of 13 podoviruses. The alignment of whole sequences was used to construct the phylogenetic trees. Phage APSE-1 was used as an outgroup. Clusters are indicated on the right. The scale bar represents 0.1 fixed mutation per amino acid position. Bootstrap, 1,000.