Phylogenomic Network and Comparative Genomics Reveal a Diverged Member of the ϕKZ-Related Group, Marine Vibrio Phage ϕJM-2012

Abstract

bBacteriophages are the largest reservoir of genetic diversity. Here we describe the novel phage JM-2012. This natural isolate from marine Vibrio cyclitrophicus possesses very few gene contents relevant to other well-studied marine Vibrio phages. To better understand its evolutionary history, we built a mathematical model of pairwise relationships among 1,221 phage genomes, in which the genomes (nodes) are linked by edges representing the normalized number of shared orthologous protein families. This weighted network revealed that JM-2012 was connected to only five members of the Pseudomonas KZ-like phage family in an isolated network, strongly indicating that it belongs to this phage group. However, comparative genomic analyses highlighted an almost complete loss of colinearity with the KZ-related genomes and little conservation of gene order, probably reflecting the action of distinct evolutionary forces on the genome of JM-2012. In this phage, typical conserved core genes, including six RNA polymerase genes, were frequently displaced and the hyperplastic regions were rich in both unique genes and predicted unidirectional promoters with highly correlated orientations. Further, analysis of the JM-2012 genome showed that segments of the conserved N-terminal parts of KZ tail fiber paralogs exhibited evidence of combinatorial assortment, having switched transcriptional orientation, and there was recruitment and/or structural changes among phage endolysins and tail spike protein. Thus, this naturally occurring phage appears to have branched from a common ancestor of the KZ-related groups, showing a distinct genomic architecture and unique genes that most likely reflect adaptation to its chosen host and environment.

Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly

“…Further searches showed that the 10 proteins encoded by these genes in SPN3US also have homologs in other recently identified ϕKZ-related phages, such as Vibrio phage JM2012 (25) and Erwinia phage Ea35-70 (46), and other giant phages (Table 6), supporting the broader relevance of utilizing a genetic system to study SPN3US. Examples of several proteins well conserved in all myoviruses (major head, sheath, and terminase proteins [47]) are also included in Table 6 to illustrate the intrinsically divergent nature of homologous proteins in these phages.…”

“…Recent studies have demonstrated that extraordinarily large bacterial viruses (giant phages) are abundant in a variety of environments (9, 17, 24, 25, 35, 43). The ability to define such giant phages at the genome level has been limited due to the fact that a large proportion of their proteins have not been characterized.…”

“…These questions are not straightforward to address, as the genomes of the giant phages related to ϕKZ range in length from approximately 167 kb (JM-2012) to 316 kb (201ϕ2-1) and include many genes that are highly divergent in nature compared to those of other phage groups (17, 25). This divergence makes functional annotation of proteins very difficult, even for proteins that are essential and well conserved in many tailed phage types and whose identification is normally straightforward—for instance, it was 10 years after ϕKZ was first sequenced that its portal protein and split subunit DNA polymerase were identified (22), as well as its prohead protease (15).…”

“…This divergence makes functional annotation of proteins very difficult, even for proteins that are essential and well conserved in many tailed phage types and whose identification is normally straightforward—for instance, it was 10 years after ϕKZ was first sequenced that its portal protein and split subunit DNA polymerase were identified (22), as well as its prohead protease (15). Comparative genome analyses have revealed an unusually high degree of genome rearrangement, especially inversions, between different members of the ϕKZ-related phages (17, 22, 25). Obviously, with many genes whose functions remain undetermined, the ϕKZ-related phages are likely to encode many novel molecular mechanisms, and the challenge is how to unravel them.…”

Integrative omics analysis ofPseudomonas aeruginosavirus PA5oct highlights the molecular complexity of jumbo phages

“…Bacillus phages 0305phi8-36Figure 3A and Table S5) can support evolutionary links between jumbo phages and smaller-genome phages (Hendrix, 2009;Adriaenssens et al, 2012;Jang et al, 2013). Together, the visualization and analysis of gene content relationships of the jumbo phages as a network revealed the global distribution of genetically diverse groups of jumbo phages across 2,259 viruses, in which most of them together with smaller-genome phage(s) are placed into two major groups comprising viruses belonging to the Tevenvirinae as well as the Phikzvirus/Elvirus/Agrican357virus/Rsl2virus, respectively, and others form evolutionary distinct clades (Gill et al, 2012;Yamada et al, 2010) (Table S5).…”