The genome of S-PM2, a "photosynthetic" T4-type bacteriophage that infects marine Synechococcus strains

Abstract

Bacteriophage S-PM2 infects several strains of the abundant and ecologically important marine cyanobacterium Synechococcus. A large lytic phage with an isometric icosahedral head, S-PM2 has a contractile tail and by this criterion is classified as a myovirus (1). The linear, circularly permuted, 196,280-bp double-stranded DNA genome of S-PM2 contains 37.8% G+C residues. It encodes 239 open reading frames (ORFs) and 25 tRNAs. Of these ORFs, 19 appear to encode proteins associated with the cell envelope, including a putative S-layer-associated protein. Twenty additional S-PM2 ORFs have homologues in the genomes of their cyanobacterial hosts. There is a group I self-splicing intron within the gene encoding the D1 protein. A total of 40 ORFs, organized into discrete clusters, encode homologues of T4 proteins involved in virion morphogenesis, nucleotide metabolism, gene regulation, and DNA replication and repair. The S-PM2 genome encodes a few surprisingly large (e.g., 3,779 amino acids) ORFs of unknown function. Our analysis of the S-PM2 genome suggests that many of the unknown S-PM2 functions may be involved in the adaptation of the metabolism of the host cell to the requirements of phage infection. This hypothesis originates from the identification of multiple phage-mediated modifications of the host's photosynthetic apparatus that appear to be essential for maintaining energy production during the lytic cycle.

FIG. 1.

Organization of the genome of phage S-PM2. The circles from outside to inside indicate the following: 1 to 6 represent the six reading frames, 7 is the scale bar (in kilobases), 8 is G+C content (smoothed with a sigma = 200 bp; Gaussian; range is 28.2 to 60.4%, with a mean of 37.8%), and 9 shows homology with other organisms. Labels show ORF numbers and gene designations where a putative homologue in T4 has been identified. MS indicates that presence of protein in the virion has been established by mass spectrometry and is shown in parentheses if the ORF has already been shown to encode a virion structural protein on the basis of proposed homology. The following color scheme has been used: green, ORFs encoding proteins exhibiting similarity to cyanobacterial proteins; blue, phage structural proteins; red, other phage proteins; purple, tRNA genes; and black, unidentified ORFs. The four clusters of T4-like genes are shaded in gray.

FIG. 2.

Consensus features of S-PM2 putative early (A) and late (B) promoters. The features were calculated by using WebLogo (12). The height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of each symbol within the stack reflects the relative frequency of the corresponding base at that position. The consensus promoter features of phages T4 and RB49 (15) are shown for comparison.