Complete Genome Sequence of the Broad Host Range Single-Stranded RNA Phage PRR1 Places It in the
            <i>Levivirus</i>
            Genus with Characteristics Shared with Alloleviviruses

Ruokoranta, Tanja; Grahn, Ammi; Ravantti, Janne J.; Poranen, Minna M.; Bamford, Dennis H.

doi:10.1128/jvi.01005-06

Cited by 29 publications

(32 citation statements)

References 35 publications

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“…Pseudomonas aeruginosa ssRNA phage PP7 shares secondary regulatory RNA structures with FRNA viruses and has been classified into the genus Levivirus (39) despite the lack of sequence similarity (27,39) and amino acid clustering (29). The Pfam protein domain profile supports the observation that the lysis and capsid proteins of phage PP7 do not cluster to these proteins in leviviruses or the capsid and read-through proteins of alloleviviruses.…”

Section: Discussionsupporting

confidence: 54%

Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae )

Friedman

Genthner

Gentry

et al. 2009

J Virol

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Male-specific single-stranded RNA (FRNA) coliphages belong to the family Leviviridae. They are classified into two genera (Levivirus and Allolevivirus), which can be subdivided into four genogroups (genogroups I and II in Levivirus and genogroups III and IV in Allolevivirus). Relatively few strains have been completely characterized, and hence, a detailed knowledge of this virus family is lacking. In this study, we sequenced and characterized the complete genomes of 19 FRNA strains (10 Levivirus strains and 9 Allolevivirus strains) and compared them to the 11 complete genome sequences available in GenBank. Nucleotide similarities among strains of Levivirus genogroups I and II were 75% to 99% and 83 to 94%, respectively, whereas similarities among strains of Allolevivirus genogroups III and IV ranged from 70 to 96% and 75 to 95%, respectively. Although genogroup I strain fr and genogroup III strains MX1 and M11 share only 70 to 78% sequence identity with strains in their respective genogroups, phylogenetic analyses of the complete genome and the individual genes suggest that strain fr should be grouped in Levivirus genogroup I and that the MX1 and M11 strains belong in Allolevivirus genogroup III. Strains within each genus share >50% sequence identity, whereas between the two genera, strains have <40% nucleotide sequence identity. Overall, amino acid composition, nucleotide similarities, and replicase catalytic domain location contributed to phylogenetic assignments. A conserved eight-nucleotide signature at the 3 end of the genome distinguishes leviviruses (5 ACCACCCA 3) from alloleviviruses (5 TCCTCCCA 3).

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Section: Discussionsupporting

confidence: 54%

Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae )

Friedman

Genthner

Gentry

et al. 2009

J Virol

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“…Indeed, genome sequences of more distantly related ssRNA viruses infecting hosts other than E. coli display more divergence. For example, PRR1, infecting diverse Gramnegative bacteria carrying the broad-host-range incompatibility group P plasmid, was found to possess a levivirus-like genome organization, with all proteins but one being more similar at the sequence level to those of alloleviviruses (240). The complete genome sequence of virus AP205, infecting Acinetobacter species, revealed a genomic organization different from the two layouts consistently found for the ssRNA coliphages (137).…”

Section: Leviviridaementioning

confidence: 99%

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Krupovìč

Prangishvili

Hendrix

et al. 2011

Microbiol Mol Biol Rev

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216

176

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SUMMARY Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.

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“…Upon ORF cloning and expression, the optical density (OD) decreased ( Fig. 2A) in a manner similar to that described for AP205 and PRR1 LPs (10,14). The cell growth was not affected by a similar expression plasmid with an identical sequence except for a termination codon that was placed after the second codon of the putative LP gene (Fig.…”

mentioning

confidence: 74%

“…Capsids of alloleviviruses contain about 5% of A1 protein, which is a prolonged read-through variant of CP that has been shown to be necessary for infection (8). The genome organizations of the Pseudomonas phage PP7 (12) and broad-host-range phage PRR1 (14) are similar to that of leviviruses, while the Acinetobacter AP205 phage (10) has a slightly different genome organization (Fig. 1A).…”

mentioning

confidence: 79%

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Genome Structure of Caulobacter Phage phiCb5

Kazāks

Voronkova

Rumnieks

et al. 2011

J Virol

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The complete genome sequence of caulobacter phage phiCb5 has been determined, and four open reading frames (ORFs) have been identified and characterized. As for related phages, the ORFs code for maturation, coat, replicase, and lysis proteins, but unlike other Leviviridae members, the lysis protein gene of phiCb5 entirely overlaps with the replicase in a different reading frame. The lysis protein of phiCb5 is about two times longer than that of the distantly related MS2 phage and presumably contains two transmembrane helices. Analysis of the proposed genome secondary structure revealed a stable 5 stem-loop, similar to other phages, and a substantially shorter 3 untranslated region (UTR) structure with only three stem-loops.

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Complete Genome Sequence of the Broad Host Range Single-Stranded RNA Phage PRR1 Places It in the Levivirus Genus with Characteristics Shared with Alloleviviruses

Cited by 29 publications

References 35 publications

Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae )

Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae )

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

Genome Structure of Caulobacter Phage phiCb5

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