Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes

Chan, Jacqueline; Millard, Andrew; Mann, Nicholas H.; Schäfer, Hendrik

doi:10.3389/fmicb.2014.00506

Cited by 43 publications

(66 citation statements)

References 61 publications

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“…None of these analyses showed any match between R5C and viral spacer sequences within CRISPRs. When the R5C genes were searched against the POV and GOS databases, we found that their homologs were widespread from coastal regions to open oceans, similar to the previously shown genomic recruitment of N4-like roseophages [29]. A more detailed analysis showed that similar levels of identity (coastal, 22.2–90.0%; intermediate, 22.0–81.8%; open ocean, 22.6–83.3%) were found in different kinds of environment in the POV.…”

Section: Resultssupporting

confidence: 74%

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A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea

Yang

Cai

et al. 2017

Viruses

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The Roseobacter clade is abundant and widespread in marine environments and plays an important role in oceanic biogeochemical cycling. In this present study, a lytic siphophage (labeled vB_DshS-R5C) infecting the strain type of Dinoroseobacter shibae named DFL12T, which is part of the Roseobacter clade, was isolated from the oligotrophic South China Sea. Phage R5C showed a narrow host range, short latent period and low burst size. The genome length of phage R5C was 77, 874 bp with a G+C content of 61.5%. Genomic comparisons detected no genome matches in the GenBank database and phylogenetic analysis based on DNA polymerase I revealed phylogenetic features that were distinct to other phages, suggesting the novelty of R5C. Several auxiliary metabolic genes (e.g., phoH gene, heat shock protein and queuosine biosynthesis genes) were identified in the R5C genome that may be beneficial to the host and/or offer a competitive advantage for the phage. Among siphophages infecting the Roseobacter clade (roseosiphophages), four gene transfer agent-like genes were commonly located with close proximity to structural genes, suggesting that their function may be related to the tail of siphoviruses. The isolation and characterization of R5C demonstrated the high genomic and physiological diversity of roseophages as well as improved our understanding of host–phage interactions and the ecology of the marine Roseobacter.

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Section: Resultssupporting

confidence: 74%

“…It has been shown that roseophages contain a considerable degree of genomic variability [29,33]. However, compared with the biogeographical, physiological and ecological diversity of Roseobacter , the range of roseophages studied so far remains relatively narrow.…”

Section: Introductionmentioning

confidence: 99%

A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea

Yang

Cai

et al. 2017

Viruses

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“…also cluster with the host species. Overall, the phylogeny of N4-like phage genotypes based on the DNA pol gene is concordant with that previously reported based on concatenated core genes of N4-like phages (24). The congruency between the DNA pol phylogeny and the host taxonomy suggests N4 phages originated from a common ancestor and coevolved with their hosts.…”

Section: Resultssupporting

confidence: 71%

“…To do this, we screened a library of viral concentrates collected from the Chesapeake Bay over the course of 2 years (2004 and 2005) through the Microbial Observatory for Virioplankton Ecology Project (http://www.virusecology.org/MOVE/Home.html) using a PCR primer set targeting conserved regions of the DNA pol genes of N4-like phages. The DNA pol gene is one of the 14 conserved core genes of N4-like phages (24), making it a valuable diagnostic marker for culture-independent surveys. A total of 56 viral samples, which cover four seasons and the full transect of the Bay, were tested.…”

Section: Resultsmentioning

confidence: 99%

“…(17)(18)(19)(20)(21)(22)(23). With the exception of Enterobacter phage EcP1 (NC_019485), which has a relatively small capsid and genome, all N4-like phages characterized to date share morphologies, genome sizes, and genomic architectures similar to those of coliphage N4 (24). Given the recent successes in isolating N4-like phages from phylogenetically diverse bacterial taxa, we were motivated to better understand the distribution of this phage group in natural systems.…”

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confidence: 99%

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Novel N4 Bacteriophages Prevail in the Cold Biosphere

Zhan

Buchan

Chen

2015

Appl Environ Microbiol

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bColiphage N4 is a lytic bacteriophage discovered nearly half a century ago, and it was considered to be a "genetic orphan" until very recently, when several additional N4-like phages were discovered to infect nonenteric bacterial hosts. Interest in this genus of phages is stimulated by their unique genetic features and propagation strategies. To better understand the ecology of N4-like phages, we investigated the diversity and geographic patterns of N4-like phages by examining 56 Chesapeake Bay viral communities, using a PCR-clone library approach targeting a diagnostic N4-like DNA polymerase gene. Many new lineages of N4-like phages were found in the bay, and their genotypes shift from the lower to the upper bay. Interestingly, signature sequences of N4-like phages were recovered only from winter month samples, when water temperatures were below 4°C. An analysis of existing metagenomic libraries from various aquatic environments supports the hypothesis that N4-like phages are most prolific in colder waters. In particular, a high number of N4-like phages were detected in Organic Lake, Antarctica, a cold and hypersaline system. The prevalence of N4-like phages in the cold biosphere suggests these viruses possess yet-to-be-determined mechanisms that facilitate lytic infections under cold conditions. A s the most abundant microbial form, viruses play important roles in shaping host population structures, mediating genetic exchange between hosts, and modulating trophic transfer in marine food webs (1-3). Marine viral metagenomic studies suggest that viruses encompass the largest genetic repertoire in the ocean (4, 5), yet the functions of ϳ70% of the putative genes identified in viral metagenomic studies remain unknown (6). Recently, several novel phages infecting dominant marine bacteria have been isolated from the ocean (7,8). Both cultivation techniques and molecular approaches suggest that a great many marine viruses await discovery.Bacteriophage N4 was first isolated from sewer waters using Escherichia coli as a host nearly half a century ago (9) and remained a "genetic orphan" for decades, as no other genetically similar phages were characterized. Phage N4 has several unique features with regard to its morphology, physiology, and genome that have made it a focus of study. It has a 70-nm isocahedral capsid, and its genome size is 70 kb. More remarkably, N4 is the only known phage that does not rely on host RNA polymerase for early transcription (10, 11). Instead, it contains a DNA-dependent virionencapsidated RNA polymerase (vRNAP), which is coinjected with viral DNA into its host and initiates transcription (12). The phage also exhibits a lysis-inhibited infection cycle and an extremely large burst size (ca. 3,000 phages per cell), suggestive of a novel mechanism of cell lysis regulation (13,14).The recent renewed interest in the ecology of N4 was prompted by the isolation from a coastal estuary of two new N4-like phages, which infect bacteria of the marine Roseobacter lineage (15). Roseobacters are a widely ...

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Characterization and Complete Genome Sequences of Three N4-Like Roseobacter Phages Isolated from the South China Sea

Zhang

Long

et al. 2016

Curr Microbiol

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Three bacteriophages (RD-1410W1-01, RD-1410Ws-07, and DS-1410Ws-06) were isolated from the surface water of Sanya Bay, northern South China Sea, on two marine bacteria type strains of the Roseobacter lineage. These phages have an isometric head and a short tail, morphologically belonging to the Podoviridae family. Two of these phages can infect four of seven marine roseobacter strains tested and the other one can infect three of them, showing relatively broader host ranges compared to known N4-like roseophages. One-step growth curves showed that these phages have similar short latent periods (1-2 h) but highly variable burst sizes (27-341 pfu cell(-1)). Their complete genomes show high level of similarities to known N4-like roseophages in terms of genome size, G + C content, gene content, and arrangement. The morphological and genomic features of these phages indicate that they belong to the N4likevirus genus. Moreover, comparative genomic analysis based on 43 N4-like phages (10 roseobacter phages and 33 phages infecting other lineages of bacteria) revealed a core genome of 18 genes shared by all the 43 phages and 38 genes shared by all the ten roseophages. The 38 core genes of N4-like roseophages nearly make up 70 % of each genome in length. Phylogenetic analysis based on the concatenated core gene products showed that our phage isolates represent two new phyletic branches, suggesting the broad genetic diversity of marine N4-like roseophages remains.

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Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes

Cited by 43 publications

References 61 publications

A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea

A Novel Roseosiphophage Isolated from the Oligotrophic South China Sea

Novel N4 Bacteriophages Prevail in the Cold Biosphere

Characterization and Complete Genome Sequences of Three N4-Like Roseobacter Phages Isolated from the South China Sea

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