Genome sequences characterizing five mutations in RNA polymerase and major capsid of phages ϕA318 and ϕAs51 of Vibrio alginolyticus with different burst efficiencies.

Wei-Hsien Wang,Ying-Rong Lin,Ming-Wei Lu,Wangta Liu,Chan-Shing Lin,Ping-Jyun Sung

doi:10.1186/1471-2164-15-505

Abstract

BackgroundThe burst size of a phage is important prior to phage therapy and probiotic usage. The efficiency for a phage to burst its host bacterium can result from molecular domino effects of the phage gene expressions which dominate to control host machinery after infection. We found two Podoviridae phages, ϕA318 and ϕAs51, burst a common host V. alginolyticus with different efficiencies of 72 and 10 PFU/bacterium, respectively. Presumably, the genome sequences can be compared to explain their differences in burst sizes.ResultsAmong genes in 42.5 kb genomes with a GC content of 43.5%, 16 out of 47 open-reading frames (ORFs) were annotated to known functions, including RNA polymerase (RNAP) and phage structure proteins. 11 strong phage promoters and three terminators were found. The consensus sequence for the new vibriophage promoters is AATAAAGTTGCCCTATA, where the AGTTG bases of −8 through −12 are important for the vibriophage specificity, especially a consensus T at −9 position eliminating RNAP of K1E, T7 and SP6 phages to transcribe the genes. ϕA318 and ϕAs51 RNAP shared their own specific promoters. In comparing ϕAs51 with ϕA318 genomes, only two nucleotides were deleted in the RNAP gene and three mutating nucleotides were found in the major capsid genes.ConclusionSubtle analyses on the residue alterations uncovered the effects of five nucleotide mutations on the functions of the RNAP and capsid proteins, which account for the host-bursting efficiency. The deletion of two nucleotides in RNAP gene truncates the primary translation due to early stop codon, while a second translational peptide starting from GTG just at deletion point can remediate the polymerase activity. Out of three nucleotide mutations in major capsid gene, H53N mutation weakens the subunit assembly between capsomeres for the phage head; E313K reduces the fold binding between β-sheet and Spine Helix inside the peptide.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-505) contains supplementary material, which is available to authorized users.

Highlights

The burst size of a phage is important prior to phage therapy and probiotic usage
Burst size, and thermal stability The plaques of φA318 that formed in 4 hours at 25°C were very clear at their center and at the margin of the edge; sizes of the plaques were about 3 mm in diameter, which increased to 5 mm overnight (Figure 1A)
Glu-313 residue of βJ in P-domain formed two hydrogen bonds with the O = C of Discussion This is the first Podoviridae genomes of Vibrio alginolyticus phages that are documented in GenBank. 16 out of 47 open-reading frames (ORFs) were annotated to known functions, while other ORFs were similar to enterobacteria phages K1E and SP6. 11 strong phage promoters and three terminators were predicted, which are located slightly differently from the closest partners, though genomic organizations were highly homologous [10,12]

Summary

Introduction

The burst size of a phage is important prior to phage therapy and probiotic usage. The efficiency for a phage to burst its host bacterium can result from molecular domino effects of the phage gene expressions which dominate to control host machinery after infection. Vibrio strains are reported to be fatal pathogens to humans and to aquaculture fish and shellfish. A Gram-negative halophilic bacterium that frequently occurs in the normal microbiota of marine environments, is a pathogen of epizootic outbreaks, which causes serious mortality of fish and shellfish and can transmit to humans. The disease caused by V. alginolyticus often has lethal consequences for fish larvae throughout the world, and it has become one of the major limiting factors in aquaculture in developing countries. It was a causal agent of vibriosis outbreaks in grouper sea bream Sparus aurata [2]. Neurotoxic effects caused by the supernates from diseased strains of Vibrio alginolyticus and Vibrio anguillarum caused several symptoms in trout, including convulsions, wriggling, contortive swimming and respiratory arrest [2]

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Discussion

Conclusion