Integration of genomic and proteomic analyses in the classification of the Siphoviridae family

Adriaenssens, Evelien M.; Edwards, Robert A.; Nash, John H. E.; Mahadevan, Padmanabhan; Seto, Donald; Ackermann, Hans-Wolfgang; Lavigne, Rob; Kropinski, Andrew M.

doi:10.1016/j.virol.2014.10.016

Cited by 57 publications

(54 citation statements)

References 164 publications

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“…The Bacterial and Archaeal Viruses Subcommittee has previously used overall proteome similarity to define genera and subfamilies, with 40 % homologous proteins indicating membership in the same genus [9][10][11]. This has resulted in spurious taxonomic lumping [12][13][14].…”

Section: Further Considerationsmentioning

confidence: 99%

Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee

et al. 2016

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Section: Further Considerationsmentioning

confidence: 99%

Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee

et al. 2016

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“…Journal of Virology valuable in phage taxonomic analysis (55,56), was used to compare the phage proteomes using ArV1 as a reference phage. In total, 32 core genes (32% of the ArV1 coding capacity) belonging to different functional groups (see Table S1 in the supplemental material) were identified by CoreGenes3.5.…”

Section: Arthrobacter Myovirus Vb_artm-arv1mentioning

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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“…Since the 8th Report of ICTV, both genome and proteome-based methods have been used by the BAVS to classify phages into species, genera, and subfamilies, resulting in 14 subfamilies, 204 genera, and 873 species in the 2015 taxonomy release [15,16,17,18,19,20]. …”

Section: Introductionmentioning

confidence: 99%

How to Name and Classify Your Phage: An Informal Guide

Adriaenssens

Brister

2017

Viruses

366

246

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With this informal guide, we try to assist both new and experienced phage researchers through two important stages that follow phage discovery; that is, naming and classification. Providing an appropriate name for a bacteriophage is not as trivial as it sounds, and the effects might be long-lasting in databases and in official taxon names. Phage classification is the responsibility of the Bacterial and Archaeal Viruses Subcommittee (BAVS) of the International Committee on the Taxonomy of Viruses (ICTV). While the BAVS aims at providing a holistic approach to phage taxonomy, for individual researchers who have isolated and sequenced a new phage, this can be a little overwhelming. We are now providing these researchers with an informal guide to phage naming and classification, taking a “bottom-up” approach from the phage isolate level.

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Integration of genomic and proteomic analyses in the classification of the Siphoviridae family

Cited by 57 publications

References 164 publications

Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee

Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee

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

How to Name and Classify Your Phage: An Informal Guide

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