Bacteriophage S-CRM01 has been isolated from a freshwater strain of Synechococcus and shown to
be present in the upper Klamath River valley in northern California and Oregon. The genome of this
lytic T4-like phage has a 178,563 bp circular genetic map with 297 predicted protein-coding genes
and 33 tRNA genes that represent all 20 amino acid specificities. Analyses based on gene sequence
and gene content indicate a close phylogenetic relationship to the “photosynthetic” marine
cyanomyophages infecting Synechococcus and Prochlorococcus. Such relatedness suggests that
freshwater and marine phages can draw on a common gene pool. The genome can be considered as
being comprised of three regions. Region 1 is populated predominantly with structural genes,
recognized as such by homology to other T4-like phages and by identification in a proteomic
analysis of purified virions. Region 2 contains most of the genes with roles in replication,
recombination, nucleotide metabolism and regulation of gene expression, as well as 5 of the 6
signature genes of the photosynthetic cyanomyophages (hli03, hsp20, mazG, phoH and psbA; cobS
is present in Region 3). Much of Regions 1 and 2 are syntenous with marine cyanomyophage
genomes, except that a segment encompassing Region 2 is inverted. Region 3 contains a high
proportion (85%) of genes that are unique to S-CRM01, as well as most of the tRNA genes. Regions
1 and 2 contain many predicted late promoters, with a combination of CTAAATA and ATAAATA
core sequences. Two predicted genes that are unusual in phage genomes are homologs of cellular
spoT and nusG.Keywords: Myoviridae, Phage tRNA, T4-like phage, Cyanomyophage, Freshwater phage, spoT, Klamath River, nus
