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

Dimitrios Skliros,Panos G Kalatzis,Pantelis Katharios,Emmanouil Flemetakis

doi:10.3389/fmicb.2016.01807

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.

Highlights

The ever growing demand for fishery products and seafood has led to intensification of aquaculture
This suggests that whereas dUTP pyrophosphatase is absent in V. alginolyticus, lytic Vibrio bacteriophages carry it to possibly satisfy the need for quick uracil hydrolysis, which can interfere during the rolling circle replication if misused by DNA polymerase as a building block
It is noteworthy that dUTP pyrophosphatase is found in most sequenced bacterial genomes, with Escherichia coli knock-out mutants resulting in accretion of putative short Okazaki fragments and subsequent errors in DNA replication (Tye and Lehman, 1977; Shlomai and Kornberg, 1978), while the T4 phage carries a bifunctional homologous dCTPase-dUTPase gene, which takes part in forming 5-hydroxy-methyl-cytosine (Gary et al, 1998)

Summary

Introduction

The ever growing demand for fishery products and seafood has led to intensification of aquaculture. Bacteriophage therapy has been suggested as a potential alternative method for both treatment and prophylaxis of bacterial infections, including aquaculture, showing very promising results (Stone, 2002; Sulakvelidze, 2011; Jassim and Limoges, 2014). The advancement of sequencing technology has boosted the genomic characterization of isolated phages providing fascinating insights to their biology and interaction with their host. The T4 bacteriophage’s genome has been fully sequenced, annotated, and characterized for many years (Miller et al, 2003b), the need for T4-like phages genomic characterization from a varied host range remains high, with the number of newly isolated bacteriophages and their genomic characterization increasing (Klumpp et al, 2012)

Methods

Results

Conclusion