Minimal Template Requirements for Initiation of Minus-Strand Synthesis In Vitro by the RNA-Dependent RNA Polymerase of Turnip Yellow Mosaic Virus

Deiman, Birgit; Koenen, A. K.; Verlaan, P. W. G.; Pleij, C.W.A.

doi:10.1128/jvi.72.5.3965-3972.1998

Cited by 70 publications

(48 citation statements)

References 28 publications

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“…Thus, following an initial burst of translation, the viral mRNA must be cleared of ribosomes to allow replication from the 3′ end. Negativestrand synthesis in TYMV is initiated from the second C of the 3′ CCA triplet following pseudoknot-dependent binding of the replicase to the TLS 103,104 . It has been demonstrated recently that this reaction is inhibited by the binding of eEF1A to the valylated TLS 105 .…”

Section: Stop Codon Readthroughmentioning

confidence: 99%

Viral RNA pseudoknots: versatile motifs in gene expression and replication

Pennell²,

2007

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RNA pseudoknots are structural elements found in almost all classes of RNA. First recognized in the genomes of plant viruses, they are now established as a widespread motif with diverse functions in various biological processes. This Review focuses on viral pseudoknots and their role in virus gene expression and genome replication. Although emphasis is placed on those well defined pseudoknots that are involved in unusual mechanisms of viral translational initiation and elongation, the broader roles of pseudoknots are also discussed, including comparisons with relevant cellular counterparts. The relationship between RNA pseudoknot structure and function is also addressed.

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Section: Stop Codon Readthroughmentioning

confidence: 99%

Viral RNA pseudoknots: versatile motifs in gene expression and replication

Pennell²,

2007

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“…In vitro RNA-dependent RNA polymerase (RdRp) systems are commonly used to analyze the components of host and viral proteins associated with RdRp complexes, as well as for identifying the putative cis-acting elements of the RNA templates (3,24). Such systems have been established for several plus-strand RNA plant viruses (4,5,10,18,34,35,36,40,44,47), as well as satellite RNAs (satRNAs) (16,19,22,33,41,52,53).…”

mentioning

confidence: 99%

Glyceraldehyde 3-Phosphate Dehydrogenase Negatively Regulates the Replication of Bamboo Mosaic Virus and Its Associated Satellite RNA

Prasanth

Huang

Liou

et al. 2011

J Virol

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The identification of cellular proteins associated with virus replicase complexes is crucial to our understanding of virus-host interactions, influencing the host range, replication, and virulence of viruses. A previous in vitro study has demonstrated that partially purified Bamboo mosaic virus (BaMV) replicase complexes can be employed for the replication of both BaMV genomic and satellite BaMV (satBaMV) RNAs. In this study, we investigated the BaMV and satBaMV 3 untranslated region (UTR) binding proteins associated with these replicase complexes. Two cellular proteins with molecular masses of ϳ35 and ϳ55 kDa were specifically cross-linked with RNA elements, whereupon the ϳ35-kDa protein was identified as the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Gel mobility shift assays confirmed the direct interaction of GAPDH with the 3 UTR sequences, and competition gel shift analysis revealed that GAPDH binds preferentially to the positive-strand BaMV and satBaMV RNAs over the negative-strand RNAs. It was observed that the GAPDH protein binds to the pseudoknot poly(A) tail of BaMV and stem-loop-C poly(A) tail of satBaMV 3 UTR RNAs. It is important to note that knockdown of GAPDH in Nicotiana benthamiana enhances the accumulation of BaMV and satBaMV RNA; conversely, transient overexpression of GAPDH reduces the accumulation of BaMV and satBaMV RNA. The recombinant GAPDH principally inhibits the synthesis of negative-strand RNA in exogenous RdRp assays. These observations support the contention that cytosolic GAPDH participates in the negative regulation of BaMV and satBaMV RNA replication.The replication of plus-strand RNA viruses is arbitrated by virus-specific replicase complexes (RC) (3), which are membrane-associated replication complexes derived from cell organelles. These membrane structures recruit several host proteins, providing a suitable environment for the synthesis of viral RNA. Unraveling the interactions between viruses and their host cells as a function of time could make considerable contributions to our understanding of the dynamics of viral infections. In vitro RNA-dependent RNA polymerase (RdRp) systems are commonly used to analyze the components of host and viral proteins associated with RdRp complexes, as well as for identifying the putative cis-acting elements of the RNA templates (3, 24). Such systems have been established for several plus-strand RNA plant viruses (4,5,10,18,34,35,36,40,44,47), as well as satellite RNAs (satRNAs) (16,19,22,33,41,52,53).Bamboo mosaic virus (BaMV) is a member of the Potexvirus genus containing a single-stranded, positive-sense RNA genome with flexuous rod-shaped morphology. The BaMV genome consists of a 6,366-nucleotide (nt)-long RNA molecule [excluding the 3Ј poly(A) tail] with a 5Ј cap and a 3Ј poly (A) tail. This single-stranded RNA genome encodes five conserved open reading frames (ORFs) coding for polypeptides of 155 kDa (ORF1), 28 kDa (ORF2), 13 kDa (ORF3), 6 kDa (ORF4), and 25 kDa (ORF5), flanked by 5Ј 94-nt and 3Ј 142-nt untr...

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“…The 3Ј UTRs of positive-sense viral RNA genomes have been thought to be involved in regulating minus-sense RNA synthesis. The 3Ј-end tRNA-like structures of the genomic RNAs of brome mosaic virus (BMV) and turnip yellow mosaic virus (TYMV) were demonstrated to contain the signal for initiating minus-strand RNA synthesis in vitro (5,11,18,22). A hairpin structure in the 3Ј-terminal region of turnip crinkle virus satellite RNA C was demonstrated to be involved in minus-sense RNA synthesis (23).…”

mentioning

confidence: 99%

“…The initiation of BMV and TYMV minus-strand RNA synthesis has been mapped to the guanylate residue opposite the penultimate residue of the 3Ј-terminal -CCA (2,5,18,22). No empirical experiment has been done to identify the initiation site of minus-strand RNA synthesis of RNA viruses possessing poly(A)-tailed genomes.…”

mentioning

confidence: 99%

The Synthesis of Minus-Strand RNA of Bamboo Mosaic Potexvirus Initiates from Multiple Sites within the Poly(A) Tail

Cheng

Peng

Hsu

et al. 2002

J Virol

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. 75: [2818][2819][2820][2821][2822][2823][2824] 2001). Approximately 20 nucleotides of the poly(A) tail adjacent to the 3 untranslated region (UTR) are protected from diethylpyrocarbonate modification, suggesting that this region may be used to initiate minus-strand RNA synthesis. The 5 terminus of the minus-strand RNA synthesized by the RdRp in vitro was examined using 5 rapid amplification of cDNA ends (RACE) and DNA sequencing. Minus-strand RNA synthesis was found to initiate from several positions within the poly(A) tail, with the highest frequency of initiation being from the 7th to the 10th adenylates counted from the 5-most adenylate of the poly(A) tail. Sequence analyses of BaMV progeny RNAs recovered from Nicotiana benthamiana protoplasts which were inoculated with mutants containing a mutation at the 1st, 4th, 7th, or 16th position of the poly(A) tail suggested the existence of variable initiation sites, similar to those found in 5 RACE experiments. We deduce that the initiation site for minus-strand RNA synthesis is not fixed at one position but resides opposite one of the 15 adenylates of the poly(A) tail immediately downstream of the 3 UTR of BaMV genomic RNA.Bamboo mosaic potexvirus (BaMV) consists of a 6,366-nucleotide-long single-stranded positive-sense RNA genome with a 5Ј m 7 GpppG cap structure and a 3Ј poly(A) tail (15,30). Five major open reading frames (1 to 5) encode polypeptides of 155, 28, 13, 6, and 25 kDa. Besides the two major 2.0-and 1.0-kb-long subgenomic RNAs detected in infected cells (14), a satellite RNA could also be found in association with some strains of BaMV (16). The tertiary structure of the 3Ј untranslated region (UTR) of BaMV RNA was determined by enzymatic and chemical structural probing and was determined to be involved in viral RNA replication (3, 27). The advantages of using BaMV as a model for studying the mechanism of viral RNA replication are as follows. (i) The full-length infectious cDNA clone has been constructed successfully (27) and can be used as a good tool for studying viral RNA replication in vivo.(ii) The Escherichia coli-overexpressed BaMV recombinant RNA-dependent RNA polymerase (RdRp) has been purified and demonstrated to be capable of transcribing the viral RNA in vitro (13). (iii) The functional RdRp extract from BaMVinfected plants was shown to specifically use short transcript templates for both minus-and plus-strand RNA syntheses in vitro (4).In order to faithfully complete the replication cycle of positive-sense RNA viruses, it is important to initiate minus-sense RNA synthesis at the correct position to ensure the generation of full-length positive-sense progeny (12). The 3Ј UTRs of positive-sense viral RNA genomes have been thought to be involved in regulating minus-sense RNA synthesis. The 3Ј-end tRNA-like structures of the genomic RNAs of brome mosaic virus (BMV) and turnip yellow mosaic virus (TYMV) were demonstrated to contain the signal for initiating minus-strand RNA synthesis in vitro (5,11,18,22). A hairpin structure in the 3Ј-termi...

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Minimal Template Requirements for Initiation of Minus-Strand Synthesis In Vitro by the RNA-Dependent RNA Polymerase of Turnip Yellow Mosaic Virus

Cited by 70 publications

References 28 publications

Viral RNA pseudoknots: versatile motifs in gene expression and replication

Viral RNA pseudoknots: versatile motifs in gene expression and replication

Glyceraldehyde 3-Phosphate Dehydrogenase Negatively Regulates the Replication of Bamboo Mosaic Virus and Its Associated Satellite RNA

The Synthesis of Minus-Strand RNA of Bamboo Mosaic Potexvirus Initiates from Multiple Sites within the Poly(A) Tail

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