Genome Sequences of
            <i>Gordonia</i>
            Bacteriophages Obliviate, UmaThurman, and Guacamole

Pope, Welkin H.; Akbar, Armaan F.; Ayers, Taylor N.; Belohoubek, Selena G.; Chung, Connie F.; Hartman, Allison C.; Kayiti, Tejus; Kessler, Cecilia M.; Koman, Philipp I.; Kotovskiy, Grigoriy A.; Morgan, Taylor M.; Rohac, Rebecca; Silva, Gabriela M.; Willis, Charles E.; Milliken, Katherine A.; Shedlock, Kathleen A.; Stanton, Ann-Catherine J.; Toner, Chelsea L.; Furbee, Emily C.; Grubb, Sarah R.; Warner, Marcie H.; Montgomery, Matthew T.; Garlena, Rebecca A.; Russell, Daniel A.; Jacobs-Sera, Deborah; Hatfull, Graham F.

doi:10.1128/genomea.00595-16

Cited by 2 publications

(3 citation statements)

References 13 publications

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“…Sixty phages isolated on Gordonia spp. through enrichment culture or direct plating as part of the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) and the Phage Hunters Integrating Research and Education (PHIRE) programs ( 15 , 18 – 28 ) were used for comparative analysis ( Table 1 ), together with 19 Gordonia phages described previously ( 13 , 16 , 17 ). All but two of the SEA-PHAGES/PHIRE phages were isolated on G. terrae 3612; the other two were isolated on Gordonia neofelifaecis ( 34 ); the 19 previously described phages were isolated on Gordonia spp., including G. terrae , G. rubripertincta , G. malaquae , G. sputi , or G. alkanivorans ( Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

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Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships

Pope

Mavrich

Garlena

et al. 2017

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The global bacteriophage population is large, dynamic, old, and highly diverse genetically. Many phages are tailed and contain double-stranded DNA, but these remain poorly characterized genomically. A collection of over 1,000 phages infecting Mycobacterium smegmatis reveals the diversity of phages of a common bacterial host, but their relationships to phages of phylogenetically proximal hosts are not known. Comparative sequence analysis of 79 phages isolated on Gordonia shows these also to be diverse and that the phages can be grouped into 14 clusters of related genomes, with an additional 14 phages that are “singletons” with no closely related genomes. One group of six phages is closely related to Cluster A mycobacteriophages, but the other Gordonia phages are distant relatives and share only 10% of their genes with the mycobacteriophages. The Gordonia phage genomes vary in genome length (17.1 to 103.4 kb), percentage of GC content (47 to 68.8%), and genome architecture and contain a variety of features not seen in other phage genomes. Like the mycobacteriophages, the highly mosaic Gordonia phages demonstrate a spectrum of genetic relationships. We show this is a general property of bacteriophages and suggest that any barriers to genetic exchange are soft and readily violable.

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Section: Resultsmentioning

confidence: 99%

“…Sixty phages were isolated on Gordonia spp. through enrichment culture or direct plating as part of the SEA-PHAGES and PHIRE programs, and dsDNA was extracted ( 15 , 18 – 28 ). Double-stranded DNA genomes were sequenced using Illumina Mi-Seq and assembled using Newbler and Consed.…”

Section: Methodsmentioning

confidence: 99%

Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships

Pope

Mavrich

Garlena

et al. 2017

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“…As for the majority of temperate Siphoviridae mycobacteriophages, the genes playing a role in their integration are located at the middle of the genome; in the case of Weirdo19ES ORFs 43-45 encode a tyrosine integrase, an immunity repressor and an excisionase. ORF43 has homology to members of the pham 43705 and it is related to integrases present in mycobacteriophages of cluster G1 (such as BPs, Halo, Annihilator and Avrafan); it is also closely related to the integrase of phage UmaThurman (pham 41717, having 3 members), a Gordonia infecting phage belonging to cluster CV, and a few members of cluster Y [36] (Fig 3A). A representative set of amino acid sequences of repressors (Rep) of temperate phages was used to build a Maximum Likelihood phylogenetic tree, showing that ORF44 of Weirdo19ES is more related to its homologues present in mycobacteriophages of the cluster Y.…”

Section: Plos Onementioning

confidence: 99%

Weirdo19ES is a novel singleton mycobacteriophage that selects for glycolipid deficient phage-resistant M. smegmatis mutants

et al. 2020

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The sequencing and bioinformatics analysis of bacteriophages infecting mycobacteria has yielded a large amount of information on their evolution, including that on their environmental propagation on other genera such as Gordonia, closely related to Mycobacterium. However, little is known on mycobacteriophages cell biology such as the nature of their receptor (s) or their replication cycle. As part of our ongoing screening for novel mycobacteriophages, we herein report the isolation and genome bioinformatics analysis of Weirdo19ES, a singleton Siphoviridae temperate mycobacteriophage with a 70.19% GC content. Nucleotide and protein sequence comparison to actinobacteriophage databases revealed that Weirdo19ES shows low homology to Gordonia phage Ruthy and mycobacteriophages falling in clusters Q and G and to singleton DS6A.Weirdo19ES also displays uncommon features such as a very short Lysin A gene (with only one enzymatic domain) and two putative HNH endonucleases. Mycobacterium smegmatis mutants resistant to Weirdo19ES are cross-resistant to I3. In agreement with that phenotype, analysis of cell envelope of those mutants showed that Weirdo19ES shares receptors with the transducing mycobacteriophage I3.This singleton mycobacteriophage adds up to the uncommonness of local mycobacteriophages previously isolated by our group and helps understanding the nature of mycobacteriophage receptors.

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Genome Sequences of Gordonia Bacteriophages Obliviate, UmaThurman, and Guacamole

Cited by 2 publications

References 13 publications

Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships

Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships

Weirdo19ES is a novel singleton mycobacteriophage that selects for glycolipid deficient phage-resistant M. smegmatis mutants

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