Genome Sequence and Characterization of the
            <i>Tsukamurella</i>
            Bacteriophage TPA2

Petrovski, Steve; Seviour, Robert J.; Tillett, Daniel

doi:10.1128/aem.01938-10

Cited by 66 publications

(88 citation statements)

References 49 publications

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“…nase genes. Twenty-two of these genes are orphams and have no close relatives in other mycobacteriophages; most also have no database matches, although protein gp2 (gene product 2=) has weak similarity (31% identity) to gp59 of Tsukamurella phage TPA2 (44). We note though that they are all small, and none is longer than 600 bp.…”

Section: Resultsmentioning

confidence: 87%

Mycobacteriophage Marvin: a New Singleton Phage with an Unusual Genome Organization

Mageeney

Pope

Harrison

et al. 2012

J Virol

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bMycobacteriophages represent a genetically diverse group of viruses that infect mycobacterial hosts. Although more than 80 genomes have been sequenced, these still poorly represent the likely diversity of the broader population of phages that can infect the host, Mycobacterium smegmatis mc 2 155. We describe here a newly discovered phage, Marvin, which is a singleton phage, having no previously identified close relatives. The 65,100-bp genome contains 107 predicted protein-coding genes arranged in a noncanonical genomic architecture in which a subset of the minor tail protein genes are displaced about 20 kbp from their typical location, situated among nonstructural genes anticipated to be expressed early in lytic growth. Marvin is not temperate, and stable lysogens cannot be recovered from infections, although the presence of a putative xis gene suggests that Marvin could be a relatively recent derivative of a temperate parent. The Marvin genome is replete with novel genes not present in other mycobacteriophage genomes, and although most are of unknown function, the presence of amidoligase and glutamine amidotransferase genes suggests intriguing possibilities for the interactions of Marvin with its mycobacterial hosts.

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Section: Resultsmentioning

confidence: 87%

Mycobacteriophage Marvin: a New Singleton Phage with an Unusual Genome Organization

Mageeney

Pope

Harrison

et al. 2012

J Virol

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“…The bacterial strains used in this study are listed in a study by Petrovski et al (31). All were grown in peptone yeast extract calcium (PYCa) broth or agar (31).…”

Section: Methodsmentioning

confidence: 99%

“…After purification, host range studies were performed using a drop dilution series of RRH1 phage (ϳ10 10 PFU/ml) spotted onto swabbed lawn plates of 65 bacterial strains (31). Plates were incubated for 2 days at 30°C before inspection for the presence of plaques.…”

Section: Methodsmentioning

confidence: 99%

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Small but Sufficient: the Rhodococcus Phage RRH1 Has the Smallest Known Siphoviridae Genome at 14.2 Kilobases

Petrovski

Dyson

Seviour

et al. 2012

J Virol

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Bacteriophages are considered to be the most abundant biological entities on the planet. The Siphoviridae are the most commonly encountered tailed phages and contain double-stranded DNA with an average genome size of ϳ50 kb. This paper describes the isolation from four different activated sludge plants of the phage RRH1, which is polyvalent, lysing five Rhodococcus species. It has a capsid diameter of only ϳ43 nm. Whole-genome sequencing of RRH1 revealed a novel circularly permuted DNA sequence (14,270 bp) carrying 20 putative open reading frames. The genome has a modular arrangement, as reported for those of most Siphoviridae phages, but appears to encode only structural proteins and carry a single lysis gene. All genes are transcribed in the same direction. RRH1 has the smallest genome yet of any described functional Siphoviridae phage. We demonstrate that lytic phage can be recovered from transforming naked DNA into its host bacterium, thus making it a potentially useful model for studying gene function in phages. There are thought to be at least 10 31 phage particles on the planet (22), making them the most abundant of biological entities. Our understanding of their genetic variety is scant, and we have only just begun to explore this enormous phage diversity (35). Phages are classified on the basis of their morphology into 13 families and one named order (Caudovirales) that embraces more than 95% of all described phages (3). The Caudovirales are divided into three families differing in their tail morphology and function: the Myoviridae (contractile tails), the Podoviridae (short noncontractile tails), and the Siphoviridae (long noncontractile tails) (2). The most commonly observed phages (ϳ60%) are members of the Siphoviridae (1).Siphoviridae phages contain typically 35 to 70 kb of DNA in either an icosahedral capsid ranging in size from 55 to 60 nm or a prolate capsid (2,20). Despite phage lambda, a member of this family, being one of the most studied model organisms, what constitutes the core genome of this family is still unknown. Complicating any attempt to determine the minimal functional Siphoviridae genome is that the known genomes cover a wide size range (16.9 kb to more than 121 kb), a lack of gene conservation between phages (8), and DNA packing constraints limit the ability to create deletion mutants (10). Identification of new phages with inherently small genomes and gene sets should provide useful models for unraveling the complexities of phage reproduction and ecology (39).One group of phages that has received little attention is the group of phages that target Rhodococcus species, organisms found in a wide range of habitats, especially soil (16). Most species are nonpathogenic, although R. equi causes serious infections in foals (28), while other strains are responsible for operational problems in wastewater treatment systems (30). Summers et al. (41) and Petrovski et al. (32) have characterized five phages able to propagate on Rhodococcus species. These phages all have novel genome sequence...

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“…The ORFs with an attributed function (a total of 24) encode proteins involved in replication, such as DNA polymerase III, and recombination/integration and also those involved in phage morphogenesis. Despite the abundance of viruses in the biosphere (3), only two viruses have been isolated from Tsukamurella species: TPA1 and TPA2 (10). Further studies will be performed to determine the nature of TPA4 (provirus or virus), from which only 2 proteins share a high identity to TPA2 proteins.…”

mentioning

confidence: 99%

Draft Genome Sequence of Tsukamurella sp. Strain 1534

et al. 2012

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A draft genome sequence of Tsukamurella sp., an aerobic bacterium isolated from a human sputum specimen, is described here. A new virus or provirus, TPA4, was characterized.T he genus Tsukamurella includes Gram-positive rods isolated from sludge foams, arthropods, soil, and in opportunistic clinical infections. Tsukamurella sp. strain 1534 was isolated from a human sputum specimen. Recently, the whole genome of Tsukamurella paurometabola was published (9).Both a shotgun sequencing and 3-kb paired-end sequencing were performed. The shotgun library was constructed with the GS Rapid library Prep kit (Roche). The library was constructed according to the 454 GS FLX Titanium paired-end protocol. The run was analyzed on the cluster through the GS RunBrowser and Newbler assembler 2.5.3. A total of 482,748 passed filter wells were obtained from the both strategies and generated 168.2 Mb with an average length of 348.5 bp. The draft genome of Tsukamurella sp. strain 1534 (about 4.5 Mb) contains 4 scaffolds and 42 large contigs (Ͼ1,500 bp). One other contig had a size of 935 bp.The GϩC content was 71.1%. The genome contains 54 tRNA genes and encodes 4,400 putative proteins. Of the coding sequences, 89.4% could be assigned to Cluster of Orthologous Groups (COG) families. The sequences of the rRNAs were found in one contig, but its average coverage was 55ϫ, compared with 37ϫ for the average coverage of the whole genome. It was therefore possible to conclude that probably 2 ribosomal operons were present. Open reading frames (ORFs) were predicted using Prodigal (http://prodigal.ornl.gov/) with default parameters but the predicted ORFs were excluded if they were spanning a sequencing gap region. The predicted bacterial protein sequences were searched against the National Center for Biotechnology Information (NCBI) Nonredundant (NR), UNIPROT (7), and CharProtDB (6) databases using BLASTP and the Clusters of Orthologous Groups (COG) (11) database using RPSBLAST (1). The ARAGORN tool (5) was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer (4) and BLASTn against the NR database.Reciprocal best BLAST analysis with the available genome of Tsukamurella paurometabola indicated that they shared 3,037 orthologs.Bacteriophages were described in other Tsukamurella spp., and the PHAST server (12) and Prophage Finder (2) were used to identify potential proviruses in Tsukamurella sp. strain 1534 genome. The bacterium contains one genetic element of around 49.4 kb (with a GϩC content of 70.1%) related to a virus named TPA4.

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Genome Sequence and Characterization of the Tsukamurella Bacteriophage TPA2

Cited by 66 publications

References 49 publications

Mycobacteriophage Marvin: a New Singleton Phage with an Unusual Genome Organization

Mycobacteriophage Marvin: a New Singleton Phage with an Unusual Genome Organization

Small but Sufficient: the Rhodococcus Phage RRH1 Has the Smallest Known Siphoviridae Genome at 14.2 Kilobases

Draft Genome Sequence of Tsukamurella sp. Strain 1534

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