Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage

Abstract

The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G؉C content of 42.6%. It encodes 386 putative proteinencoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the KVP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to KVP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from KVP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. KVP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synthesize the modified cytosine (hydroxymethyl glucose) present in T-even phages, and lacks group I introns. KVP40 likely utilizes the T4-type sigma-55 late transcription apparatus, but features of early-or middle-mode transcription were not identified. There are 26 CDSs that have no viral homolog, and many did not necessarily originate from Vibrio spp., suggesting an even broader host range for KVP40. From these latter CDSs, an NAD salvage pathway was inferred that appears to be unique among bacteriophages. Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved.Bacteriophage KVP40 and similar Vibrio phages were isolated from polluted seawater off the coast of Japan with a strain of Vibrio parahaemolyticus as the host (41). KVP40 differs from many described vibriophages in having a broad host range; it has been reported to infect eight Vibrio species, including Vibrio cholerae and Vibrio parahaemolyticus, the nonpathogenic species Vibrio natriegens, and Photobacterium leiognathi (41). Additional studies have implicated the Vibrio OmpK outer membrane protein as the phage receptor (23).Vibriophage KVP40, like the well-studied phage T4 (27, 44), belongs to the Myoviridae family of viruses. This family is characterized by having a double-stranded DNA genome, a prolate icosahedral capsid, and a contractile tail with associated baseplate and extended tail fibers (1). However, there are morphological differences between phage T4 and KVP40. For example, the head of KVP40 is longer (140 nm long and 70 nm wide) than that of T4. Due to the constraints of head size on DNA packaging, this observation suggested that the genome of KVP40 is larger than the 168,903-bp genome of T4.Beyond morphological similarities, major and minor capsid genes of KVP40 have been sequenced and are related to and functionally conserved with those of T4 (39). However, phylogenetic analysis of Myoviridae capsid genes suggests that the vibriophages, along with ...

The NAD Biosynthesis Pathway Mediated by Nicotinamide Phosphoribosyltransferase Regulates Sir2 Activity in Mammalian Cells

“…The gene encoding Haemophilus Nampt, nadV, is carried on a plasmid called pNAD1 (30), which has recently been found to contain homologs of the genes originated from a single-stranded bacteriophage (45). Most surprisingly, the entire pyridine nucleotide salvage cycle containing genes homologous to Nampt, Nmnat, and Sir2 has been found in the T4-like, broad host range vibriophage KVP40 (46). Based on these findings, the functional connection between NAD biosynthesis mediated by Nampt and Sir2 seems ancient and fundamental.…”

Bacteriophages of Ralstonia solanacearum: Their Diversity and Utilization as Biocontrol Agents in Agriculture

“…These include Pseudomonas aeruginosa phage KZ (280 kbp, Mesyanzhinov et al, 2002), EL (211 kbp, Herveldt et al, 2005), and PA3 (309 kbp, Monson et al, 2011), Vibrio parahaemolyticus phage KVP40 (245 kbp, Miller et al, 2003), Stenotrophomonas maltophila phage SMA5 (250 kbp, Chang et al, 2005), and Yersinia enterocolitica phage R1-37 (270 kbp, Kiljunen et al, 2005). Jumbo phages were also reported for Sinorhizobium meliloti (phage N3, 207 kbp, Martin and Long, 1984) and Bacillus megaterium (phage G, 670 kbp, Sun and Serwer, 1997).…”

Characterization of Polynucleotide Kinase/Phosphatase Enzymes from Mycobacteriophages Omega and Cjw1 and Vibriophage KVP40

“…The role of T4 Rnl2 in vivo is unclear. Vibriophage KVP40, which we show specifies a Pnkp enzyme, encodes its own homologs of both Rnl1 and Rnl2 (41,54). The provocative correlation is that Omega and Cjw1, which are distinguished from other mycobacteriophages by their possession of a Pnkp enzyme, are also unique among the mycobacteriophages in their specification of putative Rnl2-like ligases (Fig.…”

“…1). The conservation of Pnkp in KVP40 is notable given that only 26% of the predicted KVP40 proteins have homologs in phage T4 and only 36% of T4 proteins have homologs in KVP40 (41). The genome sequences of 10 mycobacteriophages isolated from diverse niches by selection for lytic growth in Mycobacterium smegmatis (40) revealed that two of these DNA viruses, Omega and Cjw1, also encoded putative homologs of T4 Pnkp.…”

“…By analogy to the T4 tRNA restriction and eukaryal RNase L systems, it is conceivable that many viruses trigger the incision of an essential host or viral RNA molecule, thereby impeding virus replication or pathogenesis, in which case such viruses might encode T4-like RNA repair functions. Here we identify and characterize homologs of T4 Pnkp from two mycobacteriophages, Omega and Cjw1 (40), and the vibriophage KVP40 (41). The recurrence of Pnkp enzymes in disparate viral pathogens suggests that RNA damage-based responses to virus infection may be widespread.…”