Isolation and Characterization of vB_ArS-ArV2 – First Arthrobacter sp. Infecting Bacteriophage with Completely Sequenced Genome

Šimoliūnas, Eugenijus; Kalinienė, Laura; Stasilo, Miroslav; Truncaitė, Lidija; Zajančkauskaitė, Aurelija; Staniulis, J.; Nainys, Juozas; Kaupinis, Algirdas; Valius, Mindaugas; Meškys, Rolandas

doi:10.1371/journal.pone.0111230

Cited by 17 publications

(22 citation statements)

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“…Phage isolation and propagation were carried out as described previously (17). The determination of the efficiency of plating (EOP) was performed as described by Kaliniene and colleagues (75).…”

Section: Methodsmentioning

confidence: 99%

“…Analysis of ArV1 virion structural proteins was performed as described previously (17). Accession number(s).…”

Section: Methodsmentioning

confidence: 99%

“…As mentioned above, bacteria of the genus Arthrobacter are ubiquitous in soil environments (19). However, the first Arthrobacter phage genome, that of siphovirus vB_ArtM-ArV2 (ArV2), became available in the GenBank nucleotide sequence database and was published only in 2014 (17). Bacteriophages ArV2 and vB_ArtM-ArV1, a myovirus described in this study, were isolated from soil in Lithuania.…”

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confidence: 88%

“…As summarized in reference 17, the majority of reports about this particular group of bacterial viruses (podoviruses and siphoviruses exclusively) were published more than 30 years ago and focused mostly on the isolation and/or partial characterization of bacteriophages active on laboratory strains or soil isolates of Arthrobacter. With the exception of two podoviruses, AN25S-1 and AN29-R-2 (18), all Arthrobacter phages described to date belong to the family Siphoviridae (17). As mentioned above, bacteria of the genus Arthrobacter are ubiquitous in soil environments (19).…”

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confidence: 99%

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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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Section: Methodsmentioning

confidence: 99%

“…Analysis of ArV1 virion structural proteins was performed as described previously (17). Accession number(s).…”

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 88%

mentioning

confidence: 99%

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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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“…A group of eleven oral phages (1, 5, 6, 7, 8, 9, 12, 13, 18, 19, and 23) were well-connected to a large and interconnected group of the RefSeq phages. Phage 16 was only connected to Oral Phage 18 and a single other phage, Arthrobacter phage vB_ArS-ArV2 (42). This phage is part of a group of related phages that mainly infect Actinobacteria, including many infecting Mycobacterium and Propionibacterium .…”

Section: Resultsmentioning

confidence: 99%

Oral bacteriophages are maintained at high levels for months in individuals but infrequently transmitted between mothers and infants

Beall

et al. 2019

Preprint

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14In this work, we exploit recent advances in metagenomic assembly and bacteriophage 15 identification to describe the phage content of saliva from 5 mother-baby pairs sampled 16 twice 7 -11 months apart during the first year of the babies' lives. We identify 25 phage 17 genomes that are comprised of one to 71 contigs, with 16 having a single contig. At the 18 detectable level, phage were sparsely distributed with the most common one being 19 present in 4 of the 20 samples, derived from two mothers and one baby. However, if 20 they were present in the early time point sample from an individual, they were also 21 present in the later sample from the same person more frequently than expected by 22 DNA and library preparation 74 DNA was isolated with QIAamp DNA mini kits (QIAgen, www.qiagen.com) using the included 75 protocol augmented by the inclusion of a bead-beating step to increase bacterial cell lysis. 100 76 ng of DNA in a volume of 50 µl was subjected to fragmentation in a Covaris S2 instrument with 77Intensity 5, Duty cycle 10%, Cycles per burst 200 and Treatment time 50s. 40 ng of the 78 fragmented DNA was used to make Illumina sequencing libraries with the NEB Next DNA library 79 kit for Illumina (New England Biolabs, www.neb.com). For 3 samples (family 1 mother 10 month, 80 family 2 baby 3 month, and family 2 baby 10 month) we performed enrichment with the NEB 81 Next Microbiome Enrichment Kit (New England Biolabs, www.neb.com) and sequenced both 82 the pre-enrichment and post-enrichment samples. For one sample (family 1 mother 2 month), 83 we sequenced only an enriched sample. Comparisons of the pre-and post-enrichment samples 84 with Metaphlan2 (17) showed only minor differences in the bacterial content of the two samples 85 so we pooled sequence data from the three repeated samples and used only the enriched data 86 for the one sample. 87 We sequenced the pooled libraries in one lane of the HiSeq 4000 (Illumina, www.illumina.com) 88 with 150 PE chemistry. 89 90 Sequence filtering and assembly 91 The sequencing reads were trimmed to remove adapter sequences and low quality regions with 92 Trimmomatic v. 0.32 (18), using the parameters ILLUMINACLIP::2:30:10:1:true and MINLEN:70. Human reads were removed by mapping against the 94 human genome (human_g1k_v37.fasta from 95 ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/reference/) with BWA-MEM 0.7.8 (19), and 96 processing with FilterSamReads and SamToFastq from Picard tools 1.112 97 6 (github.com/broadinstitute/picard). The reads from all samples were co-assembled using 98 MEGAHIT v1.0.6-3-gfb1e59b (20). The assembly was examined with metaquast (21). The 99 human-depleted sequences are deposited in the NCBI SRA associated with BioProject 100 accession PRJNA448135. 101 102 Clustering of contigs and identification of phage-encoding contigs 103We processed the contigs through the CONCOCT clustering pipeline (16), which incorporates 104 the following steps: (1) Co-assembly of all samples using MEGAHIT (20); (2) Discarding contigs ...

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Molecular analysis of the low-temperature Escherichia coli phage vB_EcoS_NBD2

et al. 2017

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A novel low-temperature Escherichia coli phage vB_EcoS_NBD2 was isolated in Lithuania from agricultural soil. With an optimum temperature for plating around 20 °C, vB_EcoS_NBD2 efficiently produced plaques on Escherichia coli NovaBlue (DE3) at a temperature range of 10-30 °C, yet failed to plate at temperatures above 35 °C. Phage vB_EcoS_NBD2 virions have a siphoviral morphology with an isometric head (65 nm in diameter), and a non-contractile flexible tail (170 nm). The 51,802-bp genome of vB_EcoS_NBD2 has a G + C content of 49.8%, and contains 87 probable protein-encoding genes as well as 1 gene for tRNA. Comparative sequence analysis revealed that 22 vB_EcoS_NBD2 ORFs encode unique proteins that have no reliable identity to database entries. Based on homology to biologically defined proteins and/or proteomics analysis, 36 vB_EcoS_NBD2 ORFs were given a putative functional annotation, including 20 genes coding for morphogenesis-related proteins and 13 associated with DNA metabolism. Phylogenetic analysis revealed that vB_EcoS_NBD2 belongs to the subfamily Tunavirinae, but cannot be assigned to any genus currently recognized by ICTV.

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Isolation and Characterization of vB_ArS-ArV2 – First Arthrobacter sp. Infecting Bacteriophage with Completely Sequenced Genome

Cited by 17 publications

References 77 publications

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

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

Oral bacteriophages are maintained at high levels for months in individuals but infrequently transmitted between mothers and infants

Molecular analysis of the low-temperature Escherichia coli phage vB_EcoS_NBD2

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