Hot new virus, deep connections

Hendrix, Roger W.

doi:10.1073/pnas.0402151101

Cited by 10 publications

(3 citation statements)

References 10 publications

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“…Phages are the most abundant organisms in the biosphere; the entire population turns over every few days ( Brüssow and Hendrix, 2002 ; Comeau et al, 2008 ; Hatfull, 2015 ). Diversity of the bacteriophage population at the genetic level is highly dynamic due to horizontal exchange of segments between genomes ( Wommack and Colwell, 2000 ; Hendrix, 2004 ; Suttle, 2007 ). Furthermore, virion structures suggest that bacteriophages are extremely old ( Krupovič and Bamford, 2010 ).…”

Section: Introductionmentioning

confidence: 99%

Microsatellite Diversity, Complexity, and Host Range of Mycobacteriophage Genomes of the Siphoviridae Family

Alam

Iqbal²,

Sharma

et al. 2019

Front. Genet.

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The incidence, distribution, and variation of simple sequence repeats (SSRs) in viruses is instrumental in understanding the functional and evolutionary aspects of repeat sequences. Full-length genome sequences retrieved from NCBI were used for extraction and analysis of repeat sequences using IMEx software. We have also developed two MATLAB-based tools for extraction of gene locations from GenBank in tabular format and simulation of this data with SSR incidence data. Present study encompassing 147 Mycobacteriophage genomes revealed 25,284 SSRs and 1,127 compound SSRs (cSSRs) through IMEx. Mono- to hexa-nucleotide motifs were present. The SSR count per genome ranged from 78 (M100) to 342 (M58) while cSSRs incidence ranged from 1 (M138) to 17 (M28, M73). Though cSSRs were present in all the genomes, their frequency and SSR to cSSR conversion percentage varied from 1.08 (M138 with 93 SSRs) to 8.33 (M116 with 96 SSRs). In terms of localization, the SSRs were predominantly localized to coding regions (∼78%). Interestingly, genomes of around 50 kb contained a similar number of SSRs/cSSRs to that in a 110 kb genome, suggesting functional relevance for SSRs which was substantiated by variation in motif constitution between species with different host range. The three species with broad host range (M97, M100, M116) have around 90% of their mono-nucleotide repeat motifs composed of G or C and only M16 has both A and T mononucleotide motifs. Around 20% of the di-nucleotide repeat motifs in the genomes exhibiting a broad host range were CT/TC, which were either absent or represented to a much lesser extent in the other genomes.

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Section: Introductionmentioning

confidence: 99%

Microsatellite Diversity, Complexity, and Host Range of Mycobacteriophage Genomes of the Siphoviridae Family

Alam

Iqbal²,

Sharma

et al. 2019

Front. Genet.

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“…Strong support for such a proposal would come from data that viruses with such architecture also infect archaeal hosts. The first such proposal has been made based on structural studies of STIV (31,60). However, rigorous evidence of a lipid component in the STIV virion has yet to be provided.…”

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confidence: 99%

Constituents of SH1, a Novel Lipid-Containing Virus Infecting the Halophilic Euryarchaeon Haloarcula hispanica

Bamford

Ravantti²,

Rönnholm

et al. 2005

J Virol

129

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Recent studies have indicated that a number of bacterial and eukaryotic viruses that share a common architectural principle are related, leading to the proposal of an early common ancestor. A prediction of this model would be the discovery of similar viruses that infect archaeal hosts. Our main interest lies in icosahedral double-stranded DNA (dsDNA) viruses with an internal membrane, and we now extend our studies to include viruses infecting archaeal hosts. While the number of sequenced archaeal viruses is increasing, very little sequence similarity has been detected between bacterial and eukaryotic viruses. In this investigation we rigorously show that SH1, an icosahedral dsDNA virus infecting Haloarcula hispanica, possesses lipid structural components that are selectively acquired from the host pool. We also determined the sequence of the 31-kb SH1 genome and positively identified genes for 11 structural proteins, with putative identification of three additional proteins. The SH1 genome is unique and, except for a few open reading frames, shows no detectable similarity to other published sequences, but the overall structure of the SH1 virion and its linear genome with inverted terminal repeats is reminiscent of lipid-containing dsDNA bacteriophages like PRD1.

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“…T he bacteriophage population is large (9), dynamic (8), and old (3). The genetic diversity of the population is sufficiently great that phages of different bacterial hosts typically share little recognizable sequence similarity (2).…”

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confidence: 99%

Complete Genome Sequences of 138 Mycobacteriophages

Hatfull

Students²,

Program³

2012

J Virol

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Bacteriophages are the most numerous biological entities in the biosphere, and although their genetic diversity is high, it remains ill defined. Mycobacteriophages-the viruses of mycobacterial hosts-provide insights into this diversity as well as tools for manipulating Mycobacterium tuberculosis. We report here the complete genome sequences of 138 new mycobacteriophages, which-together with the 83 mycobacteriophages previously reported-represent the largest collection of phages known to infect a single common host, Mycobacterium smegmatis mc 2 155.T he bacteriophage population is large (9), dynamic (8), and old (3). The genetic diversity of the population is sufficiently great that phages of different bacterial hosts typically share little recognizable sequence similarity (2). Comparing the genomes of phages that infect a single common bacterial host-and are therefore likely to be in genetic contact with one another-provides insights into both viral diversity and the mechanisms giving rise to new viruses (4). An emerging central theme is that phage genomes are pervasively mosaic, with segments being readily exchanged between genomes by horizontal exchange and thus present in numerous genomic contexts with different genetic neighbors (2). Eighty-three complete mycobacteriophage genome sequences have been previously reported (5, 6) and are grouped into 22 clusters or subclusters except for 5 singletons that have no close relatives (5, 6).The isolation, purification, and genomic analysis of new bacteriophages offer an effective platform for providing authentic research experiences to novice scientists (1). Of the 138 phages whose genomes are reported here, 80 were isolated by participants in the Howard Hughes Medical Institute Science Education Alliance's Phage Hunters Advancing Genomics and Evolutionary Science Program (SEA-PHAGES), 10 were isolated in a mycobacterial genetics course at the University of KwaZulu-Natal, and 47 were isolated by teachers, undergraduates, and high school students in the Phage Hunters Integrating Research and Education Program (PHIRE) at the University of Pittsburgh. Each of the new phages was plaque purified, named, sequenced, and annotated by participating students and faculty. In addition, the previously isolated phage DS6A-the only one of the 138 phages that does not infect M. smegmatis (7)-was sequenced and annotated.Genomic DNA isolated from each phage was shotgun sequenced using either Sanger sequencing, 454 pyrosequencing (6), or Illumina sequencing. The qualities of the sequence assemblies were evaluated, and targeted Sanger sequencing was used to resolve weak areas and to determine genome ends. All studentannotated genomes were reviewed and revised as necessary at the University of Pittsburgh prior to GenBank submission.Of the 138 new genomes, 19 do not belong within an existing cluster and form five new clusters (J, L, M, N, and O), incorporating 3 prior singletons to form new clusters J, L, and O. Six new singletons were identified. Representatives of all existing clusters ...

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Hot new virus, deep connections

Cited by 10 publications

References 10 publications

Microsatellite Diversity, Complexity, and Host Range of Mycobacteriophage Genomes of the Siphoviridae Family

Microsatellite Diversity, Complexity, and Host Range of Mycobacteriophage Genomes of the Siphoviridae Family

Constituents of SH1, a Novel Lipid-Containing Virus Infecting the Halophilic Euryarchaeon Haloarcula hispanica

Complete Genome Sequences of 138 Mycobacteriophages

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