Genome sequences of two novel phages infecting marine roseobacters

Zhao, Yanlin; Wang, Kui; Jiao, Nianzhi; Chen, Feng

doi:10.1111/j.1462-2920.2009.01927.x

Cited by 63 publications

(76 citation statements)

References 40 publications

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“…28, 29), and again Cellulophaga phages do not. Marine cyanophages share 16 (podoviruses) and 38 (myoviruses) genes with nonmarine enterophages (28), and roseophage DSS3ϕ2 shares 26 genes with enterophage N4 (29). In contrast, most Cellulophaga phages share few genes (average, n = 3; range, n = 1-6) with any non-Cellulophaga phage.…”

Section: Resultsmentioning

confidence: 99%

Twelve previously unknown phage genera are ubiquitous in global oceans

Holmfeldt

Solonenko

Shah

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

168

173

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Viruses are fundamental to ecosystems ranging from oceans to humans, yet our ability to study them is bottlenecked by the lack of ecologically relevant isolates, resulting in "unknowns" dominating culture-independent surveys. Here we present genomes from 31 phages infecting multiple strains of the aquatic bacterium Cellulophaga baltica (Bacteroidetes) to provide data for an underrepresented and environmentally abundant bacterial lineage. Comparative genomics delineated 12 phage groups that (i) each represent a new genus, and (ii) represent one novel and four wellknown viral families. This diversity contrasts the few well-studied marine phage systems, but parallels the diversity of phages infecting human-associated bacteria. Although all 12 Cellulophaga phages represent new genera, the podoviruses and icosahedral, nontailed ssDNA phages were exceptional, with genomes up to twice as large as those previously observed for each phage type. Structural novelty was also substantial, requiring experimental phage proteomics to identify 83% of the structural proteins. The presence of uncommon nucleotide metabolism genes in four genera likely underscores the importance of scavenging nutrient-rich molecules as previously seen for phages in marine environments. Metagenomic recruitment analyses suggest that these particular Cellulophaga phages are rare and may represent a first glimpse into the phage side of the rare biosphere. However, these analyses also revealed that these phage genera are widespread, occurring in 94% of 137 investigated metagenomes. Together, this diverse and novel collection of phages identifies a small but ubiquitous fraction of unknown marine viral diversity and provides numerous environmentally relevant phage-host systems for experimental hypothesis testing. model systems | phage genomics | phage taxonomy | queuosine biosynthesis | prophage

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Section: Resultsmentioning

confidence: 99%

Twelve previously unknown phage genera are ubiquitous in global oceans

Holmfeldt

Solonenko

Shah

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

168

173

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“…The first gene in the late gene cluster encodes a putative virion-encapsidated RNA polymerase (vRNAP). This genome organization resembles those of E. coli phage N4 (19,29) and other N4-like phages infecting marine roseobacters (DSS3⌽2, EE36⌽1) (61) and Pseudomonas aeruginosa (LUZ7, LIT1, PEV2) (12). A major hallmark of N4-like phages is the use of three different DNA-dependent RNA polymerases during their growth cycles (29).…”

Section: Novel E Amylovora Phages Feature Unique Characteristicsmentioning

confidence: 99%

Novel Virulent and Broad-Host-Range Erwinia amylovora Bacteriophages Reveal a High Degree of Mosaicism and a Relationship to Enterobacteriaceae Phages

Born

Fieseler

Marazzi

et al. 2011

Appl Environ Microbiol

115

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A diverse set of 24 novel phages infecting the fire blight pathogen Erwinia amylovora was isolated from fruit production environments in Switzerland. Based on initial screening, four phages (L1, M7, S6, and Y2) with broad host ranges were selected for detailed characterization and genome sequencing. Phage L1 is a member of the Podoviridae, with a 39.3-kbp genome featuring invariable genome ends with direct terminal repeats. Phage S6, another podovirus, was also found to possess direct terminal repeats but has a larger genome (74.7 kbp), and the virus particle exhibits a complex tail fiber structure. Phages M7 and Y2 both belong to the Myoviridae family and feature long, contractile tails and genomes of 84.7 kbp (M7) and 56.6 kbp (Y2), respectively, with direct terminal repeats. The architecture of all four phage genomes is typical for tailed phages, i.e., organized into function-specific gene clusters. All four phages completely lack genes or functions associated with lysogeny control, which correlates well with their broad host ranges and indicates strictly lytic (virulent) lifestyles without the possibility for host lysogenization. Comparative genomics revealed that M7 is similar to E. amylovora virus ⌽Ea21-4, whereas L1, S6, and Y2 are unrelated to any other E. amylovora phage. Instead, they feature similarities to enterobacterial viruses T7, N4, and ⌽EcoM-GJ1. In a series of laboratory experiments, we provide proof of concept that specific two-phage cocktails offer the potential for biocontrol of the pathogen.

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“…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 distributed and abundant group of marine bacteria (16).…”

mentioning

confidence: 99%

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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Genome sequences of two novel phages infecting marine roseobacters

Cited by 63 publications

References 40 publications

Twelve previously unknown phage genera are ubiquitous in global oceans

Twelve previously unknown phage genera are ubiquitous in global oceans

Novel Virulent and Broad-Host-Range Erwinia amylovora Bacteriophages Reveal a High Degree of Mosaicism and a Relationship to Enterobacteriaceae Phages

Novel N4 Bacteriophages Prevail in the Cold Biosphere

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