Comparative Functional Genomic Analysis of Two Vibrio Phages Reveals Complex Metabolic Interactions with the Host Cell

Abstract

Sequencing and annotation was performed for two large double stranded DNA bacteriophages, φGrn1 and φSt2 of the Myoviridae family, considered to be of great interest for phage therapy against Vibrios in aquaculture live feeds. In addition, phage–host metabolic interactions and exploitation was studied by transcript profiling of selected viral and host genes. Comparative genomic analysis with other large Vibrio phages was also performed to establish the presence and location of homing endonucleases highlighting distinct features for both phages. Phylogenetic analysis revealed that they belong to the “schizoT4like” clade. Although many reports of newly sequenced viruses have provided a large set of information, basic research related to the shift of the bacterial metabolism during infection remains stagnant. The function of many viral protein products in the process of infection is still unknown. Genome annotation identified the presence of several viral open reading frames (ORFs) participating in metabolism, including a Sir2/cobB (sirtuin) protein and a number of genes involved in auxiliary NAD+ and nucleotide biosynthesis, necessary for phage DNA replication. Key genes were subsequently selected for detail study of their expression levels during infection. This work suggests a complex metabolic interaction and exploitation of the host metabolic pathways and biochemical processes, including a possible post-translational protein modification, by the virus during infection.

The Development of Bacteriophage Resistance in Vibrio alginolyticus Depends on a Complex Metabolic Adaptation Strategy

“…In comparison, bacteriophage phiSt2 affected the metabolic state of the cells more radically and caused a more complicated adaptive metabolism in the cells ( Figure 6 and Figure 7 ), a possible fact that may be a result of a combined fast and efficient lytic activity contrary to the other phages [ 30 ], rendered by its complicated genetic “armory” [ 31 ].…”

“…Two of them belong to the Myoviridae family and one to Siphoviridae . phiSt2 was isolated in Crete, Greece [ 30 ], and belongs to the Schizotequatrovirus phage genus according to the International Committee on Taxonomy of Viruses (ICTV) as detailed described in [ 31 ]. Aphrodite1 belongs to the Aphroditevirus genus according to ICTV and was isolated from the aquatic area of North Euboea Greece.…”

“…Bacteriophage DNA extraction and sequencing for Aphrodite1 and Ares1 were done as previously described [ 31 ]. Briefly, liquid bacterial cultures of V. alginolyticus strain V1 at the exponential phase of growth (grown in LB medium), were infected separately by bacteriophages Aphrodite1 and Ares1 with an MOI of 10.…”

Genomic characterization of three novel Basilisk-like phages infecting Bacillus anthracis

“…The B. anthracis nrdE gene also contains a phage-like group I intron generating two exons for this gene [ 56 ]. Phage-derived RNRs have previously been proposed to modulate alterations in host DNA metabolism [ 57 ]. The RNR genes of Bacillus prophages are also targets of parasitic genetic elements [ 58 ] and have been associated with targets of phage resistance.…”

Degradation of host translational machinery drives tRNA acquisition in viruses

“…Then, why do some phages carry tRNAs? This question is now more puzzling, as the recent explosion in phage genome sequencing has revealed many more cases of "jumbo phage" that carry tRNA and other translation-associated genes (Hatfull, 2008;Skliros et al, 2016).…”