Efficient templates for Qβ replicase are formed by recombination from heterologous sequences

Munishkin, Alexander; Voronin, L.A.; Ugarov, Victor I.; Bondareva, Larisa A.; Chetverina, Helena V.; Chetverin, Alexander B.

doi:10.1016/0022-2836(91)80067-5

Cited by 63 publications

(77 citation statements)

References 26 publications

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“…The two JS strains were isolated from wastewater samples from two geographically different regions (Massachusetts and South Carolina), confirming that JS viruses may form a stable lineage within the leviviruses. Further genomic sequence and serological data are needed to confirm that they belong to a novel subgroup or genotype or whether these strains are a result of recombination or rearrangement events (8,28). FDNA phages are primarily known from the widespread use of M13 as a platform for phage display technology (31).…”

Section: Discussionmentioning

confidence: 99%

Molecular Detection and Genotyping of Male-Specific Coliphages by Reverse Transcription-PCR and Reverse Line Blot Hybridization

Vinjé

Oudejans

Stewart

et al. 2004

Appl Environ Microbiol

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In recent years, there has been increased interest in the use of male-specific or F؉ coliphages as indicators of microbial inputs to source waters. Sero-or genotyping of these coliphages can also be used for microbial source tracking (MST). Among the male-specific coliphages, the F؉ RNA (FRNA) viruses are well studied, while little is known about the F؉ DNA (FDNA) viruses. We have developed a reverse line blot hybridization (RLB) assay which allows for the simultaneous detection and genotyping of both FRNA as well as FDNA coliphages. These assays included a novel generic duplex reverse transcription-PCR (RT-PCR) assay for FRNA viruses as well as a generic PCR for FDNA viruses. The RT-PCR assays were validated by using 190 field and prototype strains. Subsequent DNA sequencing and phylogenetic analyses of RT-PCR products revealed the classification of six different FRNA clusters, including the well-established subgroups I through IV, and three different FDNA clusters, including one (CH) not previously described. Within the leviviruses, a potentially new subgroup (called JS) including strains having more than 40% nucleotide sequence diversity with the known levivirus subgroups (MS2 and GA) was identified. We designed subgroup-specific oligonucleotides that were able to genotype all nine (six FRNA, three FDNA) different clusters. Application of the method to a panel of 351 enriched phage samples from animal feces and wastewater, including known prototype strains (MS2, GA, Q␤, M11, FI, and SP for FRNA and M13, f1, and fd for FDNA), resulted in successful genotyping of 348 (99%) of the samples. In summary, we developed a novel method for standardized genotyping of F؉ coliphages as a useful tool for large-scale MST studies.

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Section: Discussionmentioning

confidence: 99%

Molecular Detection and Genotyping of Male-Specific Coliphages by Reverse Transcription-PCR and Reverse Line Blot Hybridization

Vinjé

Oudejans

Stewart

et al. 2004

Appl Environ Microbiol

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“…The used variant of RQ135 RNA was prepared by transcription of SmaI-digested plasmid pT7RQ135 -1 (-) 42 modified by inserting CGAUCC between positions 52 and 53 of the original RQ135 -1 (-) sequence; the template properties of this variant were indistinguishable 35 from those of the authentic RQ135 RNA 22 . Qb( þ ) RNA was isolated from purified wild-type phage particles lysed with SDS, followed by centrifugation through a 15% sucrose cushion and phenol extraction 25 .…”

Section: Methodsmentioning

confidence: 99%

“…In the course of studies on functional properties of the core enzyme, we discovered that, in contrast to the common belief, the rate and yield of the exponential amplification of an RQ RNA, a 140-nucleotide (nt)-long variant of non-genomic RQ135 RNA 22 , dramatically increased upon the addition of equimolar amount of protein S1 (Fig. 1a,b).…”

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confidence: 99%

Ribosomal protein S1 functions as a termination factor in RNA synthesis by Qβ phage replicase

et al. 2013

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S1 is the largest ribosomal protein, and is vitally important for the cell. S1 is also a subunit of Qb replicase, the RNA-directed RNA polymerase of bacteriophage Qb. In both protein and RNA syntheses, S1 is commonly believed to bind to a template RNA at the initiation step, and not to be involved in later events. Here, we show that in Qb replicase-mediated RNA synthesis, S1 functions at the termination step by promoting release of the product strand in a single-stranded form. This function is fulfilled by the N-terminal fragment comprising the first two S1 domains. The results suggest that S1 might also have a role other than mRNA binding in the ribosome.

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“…Chetverin and co-workers have introduced and studied RNA colonies that grew and propagated on gels or other solid media provided that RNA replicases and ribonucleoside triphosphates were present [351,377,378]. It has been explicitly noted that such experimental systems might, in fact, model the amplification and propagation of the first replicators in primordial environmental settings [57,351,354].…”

Section: Colonization Wavesmentioning

confidence: 99%

Inorganic Polyphosphate Modulates TRPM8 Channels

Trimm¹

2011

Inorganic Chemistry

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Efficient templates for Qβ replicase are formed by recombination from heterologous sequences

Cited by 63 publications

References 26 publications

Molecular Detection and Genotyping of Male-Specific Coliphages by Reverse Transcription-PCR and Reverse Line Blot Hybridization

Molecular Detection and Genotyping of Male-Specific Coliphages by Reverse Transcription-PCR and Reverse Line Blot Hybridization

Ribosomal protein S1 functions as a termination factor in RNA synthesis by Qβ phage replicase

Inorganic Polyphosphate Modulates TRPM8 Channels

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