Phage Taxonomy: We Agree To Disagree

Nelson, Daniel

doi:10.1128/jb.186.21.7029-7031.2004

Cited by 60 publications

(53 citation statements)

References 27 publications

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“…Host-range studies have revealed that some cyanophages have broad host ranges and are able to infect strains that are distantly related (Suttle and Chan, 1993;Waterbury and Valois, 1993) or that even belong to different genera (Sullivan et al, 2003). Nonetheless, the mosaic architecture of phage genomes, including structural genes that result in similar morphology but that appear to have a different evolutionary origin (Sabehi et al, 2012), increasingly call into question the use of a Linnaeanbased hierarchical classification, including morphology, as a basis for classifying phage (Lawrence et al, 2002;Nelson, 2004).…”

Section: Introductionmentioning

confidence: 99%

“…can be in excess of 10 5 ml À 1 , and vary with temperature, salinity and host abundance (Waterbury and Valois, 1993;Suttle and Chan, 1993;1994), and are estimated to remove up to a few percent of the Synechococcus population each day (Suttle and Chan, 1993;Suttle, 1994). Historically, cyanophages have been classified into the families Myoviridae, Siphoviridae and Podoviridae based largely on tail morphologies that are either contractile, non-contractile and flexible, or short and non-contractile, respectively (Suttle, 2000;Nelson, 2004;Lavigne et al, 2012). Representatives of all three families have been isolated from seawater (Wilson et al, 1993;Suttle and Chan, 1993;Waterbury and Valois, 1993;Sullivan et al, 2003) and freshwater Morris, 1963, 1964;Adolph and Haselkorn, 1971;Yoshida et al, 2006;Liu et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

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Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages

et al. 2015

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Cyanobacteria are often the dominant phototrophs in polar freshwater communities; yet, the phages that infect them remain unknown. Here, we present a genomic and morphological characterization of cyanophage S-EIV1 that was isolated from freshwaters on Ellesmere Island (Nunavut, High Arctic Canada), and which infects the polar Synechococcus sp., strain PCCC-A2c. S-EIV1 represents a newly discovered evolutionary lineage of bacteriophages whose representatives are widespread in aquatic systems. Among the 130 predicted open reading frames (ORFs) there is no recognizable similarity to genes that encode structural proteins other than the large terminase subunit and a distant viral morphogenesis protein, indicating that the genes encoding the structural proteins of S-EIV1 are distinct from other viruses. As well, only 19 predicted coding sequences on the 79 178 bp circularly permuted genome have homology with genes encoding proteins of known function. Although S-EIV1 is divergent from other sequenced phage isolates, it shares synteny with phage genes captured on a fosmid from the deep-chlorophyll maximum in the Mediterranean Sea, as well as with an incision element in the genome of Anabaena variabilis (ATCC 29413). Sequence recruitment of metagenomic data indicates that S-EIV1-like viruses are cosmopolitan and abundant in a wide range of aquatic systems, suggesting they have an important ecological role.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages

et al. 2015

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“…On the basis of tail morphology, members of the Caudovirales are further subdivided into three families: Podoviridae (with short noncontractile tails), Siphoviridae (with long noncontractile tails), and Myoviridae (with long contractile tails) (14). With the advent of next-generation sequencing and molecular biology, it has become increasingly evident that the current phage classification system, which does not reflect genomic and proteomic data, is in need of revision, since some phages (e.g., podovirus P22 and siphovirus lambda), while having closely related genomes, are separated into different families based on the tail morphology alone (15). Since it is thought that tailed phages originated in the early Precambrian Era and very likely evolved from a common ancestor (16), more and more such "unrelated and yet related" bacterial viruses will likely be sequenced and/or isolated in the future.…”

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confidence: 99%

Molecular Analysis of Arthrobacter Myovirus vB_ArtM-ArV1: We Blame It on the Tail

Kalinienė

Šimoliūnas

Truncaitė

et al. 2017

J Virol

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This is the first report on a myophage that infects Arthrobacter. A novel virus, vB_ArtM-ArV1 (ArV1), was isolated from soil using Arthrobacter sp. strain 68b for phage propagation. Transmission electron microscopy showed its resemblance to members of the family Myoviridae: ArV1 has an isometric head (ϳ74 nm in diameter) and a contractile, nonflexible tail (ϳ192 nm). Phylogenetic and comparative sequence analyses, however, revealed that ArV1 has more genes in common with phages from the family Siphoviridae than it does with any myovirus characterized to date. The genome of ArV1 is a linear, circularly permuted, double-stranded DNA molecule (71,200 bp) with a GC content of 61.6%. The genome includes 101 open reading frames (ORFs) yet contains no tRNA genes. More than 50% of ArV1 genes encode unique proteins that either have no reliable identity to database entries or have homologues only in Arthrobacter phages, both sipho-and myoviruses. Using bioinformatics approaches, 13 ArV1 structural genes were identified, including those coding for head, tail, tail fiber, and baseplate proteins. A further 6 ArV1 ORFs were annotated as encoding putative structural proteins based on the results of proteomic analysis. Phylogenetic analysis based on the alignment of four conserved virion proteins revealed that Arthrobacter myophages form a discrete clade that seems to occupy a position somewhat intermediate between myo-and siphoviruses. Thus, the data presented here will help to advance our understanding of genetic diversity and evolution of phages that constitute the order Caudovirales. IMPORTANCE Bacteriophages, which likely originated in the early Precambrian Era, represent the most numerous population on the planet. Approximately 95% of known phages are tailed viruses that comprise three families: Podoviridae (with short tails), Siphoviridae (with long noncontractile tails), and Myoviridae (with contractile tails). Based on the current hypothesis, myophages, which may have evolved from siphophages, are thought to have first emerged among Gram-negative bacteria, whereas they emerged only later among Gram-positive bacteria. The results of the molecular characterization of myophage vB_ArtM-ArV1 presented here conform to the aforementioned hypothesis, since, at a glance, bacteriophage vB_ArtM-ArV1 appears to be a siphovirus that possesses a seemingly functional contractile tail. Our work demonstrates that such "chimeric" myophages are of cosmopolitan nature and are likely characteristic of the ecologically important soil bacterial genus Arthrobacter.KEYWORDS Arthrobacter, Myoviridae, Siphoviridae, bacterial viruses, bacteriophage evolution, tailed viruses, vB_ArtM-ArV1

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“…Many bacteriophages exist, and are classified based on their morphology. Like other viruses, the genome can consist of either single-or double-stranded DNA or single-or double-stranded RNA (Nelson, 2004).…”

Section: Methods To Study Bioaerosol Transportmentioning

confidence: 99%