Physiological Properties and Genome Structure of the Hyperthermophilic Filamentous Phage φOH3 Which Infects Thermus thermophilus HB8.

Yuko Nagayoshi,Kazuki Mori,Yasuhiro Fujino,Katsumi Doi,Kenta Kumagae,Ayano Nakamura,Takeo Iwamoto,Kosuke Tashiro,Yasuaki Hiromasa,Toshihisa Ohshima,Satoru Kuhara

doi:10.3389/fmicb.2016.00050

Abstract

A filamentous bacteriophage, φOH3, was isolated from hot spring sediment in Obama hot spring in Japan with the hyperthermophilic bacterium Thermus thermophilus HB8 as its host. Phage φOH3, which was classified into the Inoviridae family, consists of a flexible filamentous particle 830 nm long and 8 nm wide. φOH3 was stable at temperatures ranging from 70 to 90°C and at pHs ranging from 6 to 9. A one-step growth curve of the phage showed a 60-min latent period beginning immediately postinfection, followed by intracellular virus particle production during the subsequent 40 min. The released virion number of φOH3 was 109. During the latent period, both single stranded DNA (ssDNA) and the replicative form (RF) of phage DNA were multiplied from min 40 onward. During the release period, the copy numbers of both ssDNA and RF DNA increased sharply. The size of the φOH3 genome is 5688 bp, and eight putative open reading frames (ORFs) were annotated. These ORFs were encoded on the plus strand of RF DNA and showed no significant homology with any known phage genes, except ORF 5, which showed 60% identity with the gene VIII product of the Thermus filamentous phage PH75. All the ORFs were similar to predicted genes annotated in the Thermus aquaticus Y51MC23 and Meiothermus timidus DSM 17022 genomes at the amino acid sequence level. This is the first report of the whole genome structure and DNA multiplication of a filamentous T. thermophilus phage within its host cell.

Highlights

Thermophilic phages or viruses play extraordinarily important roles in the processes of evolution, biogeochemistry, ecology, and genetic exchange in extreme environments (Prangishvili et al, 2006)
We report the structure of the φOH3 genome the first example from a Thermus filamentous phage
Large numbers of plaques were formed from the enrichment culture of a geothermal water sample using T. thermophilus HB8 as the host

Summary

Introduction

Thermophilic phages or viruses play extraordinarily important roles in the processes of evolution, biogeochemistry, ecology, and genetic exchange in extreme environments (Prangishvili et al, 2006). Among these phages, those that infect Thermus species have been extensively studied (Liu et al, 2009), and complete genome sequences have been reported for myoviruses YS40. As a result of this structural arrangement, inoviruses are flexible filaments about 7 nm in diameter Inoviruses infect both gram-negative and gram-positive bacteria (Day, 2012), but are unusual among bacteriophages in that they do not lyse their host cells when new phage particles are produced. Inoviruses can undergo extensive recombination, often picking up new genes in the process, so that they may act as important vectors for gene transfer among hosts (Davis and Waldor, 2003; Faruque et al, 2005)

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