Genomic Analysis of Freshwater Cyanophage Pf-WMP3 Infecting Cyanobacterium Phormidium foveolarum: The Conserved Elements for a Phage

Abstract

Cyanophages are ecologically abundant, genetically diverse in aquatic environments, and affect the population and evolutionary trajectories of their hosts. After reporting the cyanophage Pf-WMP4 genome (Liu et al. in Virology 366:28-39, 2007), we hereby present a related cyanophage, Pf-WMP3, which also infects the freshwater cyanobacterium Phormidium foveolarum. The Pf-WMP3 genome contains 43,249 bp with 234 bp direct terminal repeats. The overall genome organization and core genes of the two phages are comparable to those of the T7 supergroup phages. Compared with Pf-WMP4, cyanophage Pf-WMP3 has diverged extensively at the DNA level; however, they are closely related at the protein level and genome architecture. The left arm genes for the two phages, which mainly encode the DNA replication machinery, are not conserved in the gene order. Whereas the right arm genes of the two phages coding for structural proteins show high similarity in amino acid sequences and modular architecture, indicating that they have retained similar development strategies. The differences in similarity levels between the left and right arm genes suggest that the structural genes are the most conserved elements for a phage.

Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages

“…Of the five sequenced cyanophages that infect Microcystis aeruginosa (Yoshida et al, 2008), Phormidium foveolarum (Liu et al, 2007(Liu et al, , 2008, Planktothrix agardhii (Gao et al, 2012) and Synechococcus spp. (Dreher et al, 2011), only the myovirus S-CRM01 that infects the latter is related to myoviruses infecting marine Synechococcus spp.…”

Unraveling the genome structure of cyanobacterial podovirus A-4L with long direct terminal repeats

“…As a preface to gain insight into the biological properties of cyanophages and their interactions with cyanobacterial hosts at the molecular level, it is necessary to obtain their complete genome sequences. Since the first total genome sequence of a Synechococcus cyanophage P60 was reported in 2002, more than 40 cyanophages from different species of cyanobacteria have been characterized at the genome level (Chen and Lu, 2002;Liu et al, 2008;Huang et al, 2012;Dreher et al, 2011;Gao et al, 2012;Labrie et al, 2013). Furthermore, some cyanophages have been reported to contain special genes, such as photosynthesis-related genes, carbon metabolism genes and phosphate stress genes, and these genes are speculated to play defining functional roles in cyanobacterial virus-host interactions (Lindell et al, 2004(Lindell et al, , 2005Sullivan et al, 2005;Gao et al, 2012).…”

“…In order to investigate the phylogenetic relationships of A-4L and other cyanobacterial podoviruses, all freshwater cyanobacterial podoviruses with published genomes (Pf-WMP3, PP, and Pf-WMP4) and three marine representatives (P60, Syn5, and P-SSP7) were selected for comparison of genome organization and phylogenetic analysis (Chen and Lu, 2002;Sullivan et al, 2005;Pope et al, 2007;Liu et al, 2007Liu et al, , 2008Zhou et al, 2013). As shown in Fig.…”

Sequence and Structural Characterization of Great Salt Lake Bacteriophage CW02, a Member of the T7-Like Supergroup

“…PSI-BLAST analysis of putative CW02 ORFs resulted in matches to T7-like phages, including Pseudomonas phage PA11 (34), roseophage SIO1 (46), cyanophage Pf-WMP3 (38), and vibriophage VpV262 (23). The genomes of CW02 and PA11 have at least 24 homologous ORFs in common (Table 1), though the functions of the PA11 gene products have not yet been determined.…”

“…Based on negative stain transmission electron microscopy, CW02 is morphologically similar to viruses of the Podoviridae family. Genomic analysis and mass spectrometry (MS) of CW02 genes and proteins revealed the strongest sequence similarities to Pseudomonas phage PA11 (34), roseophage SIO1 (46), vibriophage VpV262 (23), and cyanophage Pf-WMP3 (38), all of which are distant relatives of bacteriophage T7 but members of the T7 supergroup. The 16-Å resolution structure of CW02, solved by cryogenic electron microscopy (cryo-EM) and three-dimensional (3D) reconstruction, permitted fitting of the HK97-like fold into the capsid density, thereby supporting the observation that the capsid proteins of tailed ds-DNA phages adopt a common ancestral fold.…”