Kluyvera bacteriophage Kvp1: a new member of the Podoviridae family phylogenetically related to the coliphage T7

Gadaleta, Patricia; Zorzopulos, Jorge

doi:10.1016/s0168-1702(97)00078-6

Cited by 8 publications

(8 citation statements)

References 19 publications

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“…By scanning the available pieces of genome of the phages Kvp1, K1E and K5 with the 76-site model, several promoters of 19–24 bits were found ( Figure 6C ). One site of 20.3 bits was picked up by the 76-site model from one piece of phage Kvp1 sequence (X96817 at 112) ( 28 ). One site of 23.4 bits was picked up by the 76-site model from one piece of phage K1E sequence (X78310 at 692) ( 75 ), this site was also picked up by the SP6 model (29 bits) and the K1-5 model (37.2 bits, data not shown).…”

Section: Resultsmentioning

confidence: 99%

“…The Vibrio parahaemolyticus phage VpV262 ( 24 ) and rosephage SIO1 ( 25 ) lack an RNAP gene in their genome, but contain a T7-like head structure module; thus, they have been thought to be members of the T7 supergroup ( 24 ). The Klebsiella phage K11 ( 26 , 27 ), Kluyveraphage Kvp1 ( 28 ), coliphage BA14 ( 29 , 30 ) and several others ( 3 , 31 , 32 ) were clearly shown to be closely related to phage T7, though no complete genome sequences are available for them.…”

Section: Introductionmentioning

confidence: 99%

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Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases

Chen

Schneider

2005

Nucleic Acids Research

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Molecular information theory was used to create sequence logos and promoter models for eight phages of the T7 group: T7, φA1122, T3, φYeO3-12, SP6, K1-5, gh-1 and K11. When these models were used to scan the corresponding genomes, a significant gap in the individual information distribution was observed between functional promoter sites and other sequences, suggesting that the models can be used to identify new T7-like promoters. When a combined 76-site model was used to scan the eight phages, 108 of the total 109 promoters were found, while none were found for other T7-like phages, φKMV, P60, VpV262, SIO1, PaP3, Xp10, P-SSP7 and Ppu40, indicating that these phages do not belong to the T7 group. We propose that the T7-like transcription system, which consists of a phage-specific RNA polymerase and a set of conserved T7-like promoters, is a hallmark feature of the T7 group and can be used to classify T7-like phages. Phylogenetic trees of the T7-like promoter models and their corresponding RNA polymerases are similar, suggesting that the eight phages of the T7 group can be classified into five subgroups. However the SP6-like polymerases have apparently diverged from other polymerases more than their promoters have diverged from other promoters.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases

Chen

Schneider

2005

Nucleic Acids Research

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“…As a result of a reanalysis, at the protein level, of relationships within the "T7-like viruses" this group of bacteriophages have been classified into the subfamily Autographivirinae which currently possesses three genera: T7-like, Sp6-like and φKMV-like viruses [ 5 ]. Kvp1, the first Kluyvera cryocrescens -specific bacteriophage, was isolated from the Matanza River in Buenos Aires (Argentina) by Gadaleta and Zorzopulos [ 6 ]. Morphologically this phage is a member of the Podoviridae .…”

Section: Introductionmentioning

confidence: 99%

The genome and proteome of the Kluyvera bacteriophage Kvp1 – another member of the T7-like Autographivirinae

Lingohr

Villegas

She

et al. 2008

Virol J

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At 39,472 bp, the annotated genome revealed a closer relationship to coliphage T3 than T7 with Kvp1 containing homologs to T3 early proteins S-adenosyl-L-methionine hydrolase (0.3) and protein kinase (0.7). The quantitative nature of the relationships between Kvp1 and the other members of the T7-like virus genus (T7, T3, phiA1122, phiYeO3-12, Berlin, K1F, VP4 and gh-1) was confirmed using CoreGenes.

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“…Gp0.7 homologues have been found in T7-like phages infecting Yersinia pestis (Savalia, Molineux, and Severinov, unpublished), Yersinia enterocolitica (32), Caulobacter crescentus (44), and Kluyvera cryocrescens (15). In the case of Caulobacter crescentus, a threonine residue(s) in the RNAP ␤Ј subunit is phosphorylated during phage Cd1 infection (20).…”

Section: Resultsmentioning

confidence: 99%

“…First, even though the 0.7 gene is dispensable for T7 growth under standard laboratory conditions, it is essential at elevated temperatures or in nutrient-poor media (19), as well as in the presence of certain extrachromosomal genetic elements (16). Second, the protein kinase activity appears to be conserved: it is present in T7-like coliphages (25,41), as well as in phages that infect Yersinia enterocolitica (32), Kluyvera cryocrescens (15), Klebsiella pneumoniae (D. Savalia, I. J. Molineux, and K. Severinov, unpublished observation), and Caulobacter crescentus (20).…”

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confidence: 99%

Localization of theEscherichia coliRNA Polymerase β′ Subunit Residue Phosphorylated by Bacteriophage T7 Kinase Gp0.7

Severinova

Severinov

2006

J Bacteriol

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During bacteriophage T7 infection, the Escherichia coli RNA polymerase ␤ subunit is phosphorylated by the phage-encoded kinase Gp0.7. Here, we used proteolytic degradation and mutational analysis to localize the phosphorylation site to a single amino acid, Thr 1068 , in the evolutionarily hypervariable segment of ␤. Using a phosphomimetic substitution of Thr 1068 , we show that phosphorylation of ␤ leads to increased -dependent transcription termination, which may help to switch from host to viral RNA polymerase transcription during phage development.Bacteriophage T7 is a prototypic member of a large family of phages that use host RNA polymerase (RNAP) for expression of their early genes but rely on their own, single-subunit RNAP for middle and late viral gene expression. The early T7 genes include, in addition to gene 1 coding for T7 RNAP, several genes whose products participate in host transcription shutoff. The shutoff occurs concurrently with the beginning of transcription of viral genes by T7 RNAP.The products of two viral genes, Gp0.7 and Gp2, are implicated in host transcription shutoff (33)(34)(35)39). Gp0.7 is a serine/threonine protein kinase (31,36). Among the identified targets are components of translation (IF1, IF2, IF3, elongation factor G, and ribosomal proteins S1 and S6 [37,38]) and transcription (RNAP ␤Ј subunit [47]) machineries; RNase III (24), the enzyme responsible for mRNA processing; and RNase E (23), which controls mRNA decay. Several lines of evidence suggest that Gp0.7 plays an important role in bacteriophage development. First, even though the 0.7 gene is dispensable for T7 growth under standard laboratory conditions, it is essential at elevated temperatures or in nutrient-poor media (19), as well as in the presence of certain extrachromosomal genetic elements (16). Second, the protein kinase activity appears to be conserved: it is present in T7-like coliphages (25, 41), as well as in phages that infect Yersinia enterocolitica (32), Kluyvera cryocrescens (15), Klebsiella pneumoniae (D. Savalia, I. J. Molineux, and K. Severinov, unpublished observation), and Caulobacter crescentus (20).Gp2 is a 64-amino-acid-long protein that binds to and abolishes promoter recognition by host RNAP (28). Gene 0.7 becomes essential when Gp2 function is attenuated by a mutation in its binding site in a functionally dispensable domain of RNAP ␤Ј (18), supporting the idea that phosphorylation of ␤Ј by Gp0.7 is functionally relevant and suggesting that Gp2 and Gp0.7 may cooperate with each other during bacteriophage development.Phosphorylation is a common covalent modification of proteins. In eukaryotes, core components of all three nuclear RNAPs are phosphorylated (4, 7). Phosphorylation of the largest subunit, A190, which is homologous to ␤Ј, may regulate the function of yeast (Saccharomyces cerevisiae) RNAP I (14). However, with the exception of the largest RNAP II subunit C-terminal domain phosphorylation, RNAP phosphorylation sites have not been mapped and functional consequences of RNAP phosphorylat...

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Kluyvera bacteriophage Kvp1: a new member of the Podoviridae family phylogenetically related to the coliphage T7

Cited by 8 publications

References 19 publications

Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases

Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases

The genome and proteome of the Kluyvera bacteriophage Kvp1 – another member of the T7-like Autographivirinae

Localization of theEscherichia coliRNA Polymerase β′ Subunit Residue Phosphorylated by Bacteriophage T7 Kinase Gp0.7

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