scholarly journals The subgenomic promoter of brome mosaic virus folds into a stem-loop structure capped by a pseudo-triloop that is structurally similar to the triloop of the genomic promoter

RNA ◽  
2012 ◽  
Vol 18 (5) ◽  
pp. 992-1000 ◽  
Author(s):  
J. Skov ◽  
M. Gaudin ◽  
P. Podbevsek ◽  
R. C. L. Olsthoorn ◽  
M. Petersen
Keyword(s):  
Mosaic Virus ◽  
Brome Mosaic Virus ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure ◽  
Subgenomic Promoter

scholarly journals The 5′ Untranslated Region of Alfalfa Mosaic Virus RNA 1 Is Involved in Negative-Strand RNA Synthesis

2003 ◽  
Vol 77 (20) ◽  
pp. 11284-11289 ◽  
Author(s):  
A. Corina Vlot ◽  
John F. Bol
Keyword(s):  
Mosaic Virus ◽  
Untranslated Region ◽  
Rna Synthesis ◽  
Alfalfa Mosaic Virus ◽  
Loop Structure ◽  
Stem Loop ◽  
Genomic Rnas ◽  
Negative Strand ◽  
Stem Loop Structure ◽  
Virus Rna

ABSTRACT The three genomic RNAs of alfalfa mosaic virus each contain a unique 5′ untranslated region (5′ UTR). Replacement of the 5′ UTR of RNA 1 by that of RNA 2 or 3 yielded infectious replicons. The sequence of a putative 5′ stem-loop structure in RNA 1 was found to be required for negative-strand RNA synthesis. A similar putative 5′ stem-loop structure is present in RNA 2 but not in RNA 3.

scholarly journals In Vitro Synthesis of Minus-Strand RNA by an Isolated Cereal Yellow Dwarf Virus RNA-Dependent RNA Polymerase Requires VPg and a Stem-Loop Structure at the 3′ End of the Virus RNA

2006 ◽  
Vol 80 (21) ◽  
pp. 10743-10751 ◽  
Author(s):  
Toba A. M. Osman ◽  
Robert H. A. Coutts ◽  
Kenneth W. Buck
Keyword(s):  
Rna Polymerase ◽  
Mosaic Virus ◽  
Rna Synthesis ◽  
Loop Structure ◽  
Minus Strand ◽  
Stem Loop ◽  
Stem Loop Structure ◽  
Virus Rna ◽  
Yellow Dwarf Virus

ABSTRACT Cereal yellow dwarf virus (CYDV) RNA has a 5′-terminal genome-linked protein (VPg). We have expressed the VPg region of the CYDV genome in bacteria and used the purified protein (bVPg) to raise an antiserum which was able to detect free VPg in extracts of CYDV-infected oat plants. A template-dependent RNA-dependent RNA polymerase (RdRp) has been produced from a CYDV membrane-bound RNA polymerase by treatment with BAL 31 nuclease. The RdRp was template specific, being able to utilize templates from CYDV plus- and minus-strand RNAs but not those of three unrelated viruses, Red clover necrotic mosaic virus, Cucumber mosaic virus, and Tobacco mosaic virus. RNA synthesis catalyzed by the RdRp required a 3′-terminal GU sequence and the presence of bVPg. Additionally, synthesis of minus-strand RNA on a plus-strand RNA template required the presence of a putative stem-loop structure near the 3′ terminus of CYDV RNA. The base-paired stem, a single-nucleotide (A) bulge in the stem, and the sequence of a tetraloop were all required for the template activity. Evidence was produced showing that minus-strand synthesis in vitro was initiated by priming by bVPg at the 3′ end of the template. The data are consistent with a model in which the RdRp binds to the stem-loop structure which positions the active site to recognize the 3′-terminal GU sequence for initiation of RNA synthesis by the addition of an A residue to VPg.

A predicted stem-loop in coat protein-coding sequencing of tobacco vein banding mosaic virus is required for efficient replication

2021 ◽  
Author(s):  
Zhi-Yong Yan ◽  
Le Fang ◽  
Xiao-Jie Xu ◽  
De-Jie Cheng ◽  
Cheng-Ming Yu ◽  
...  
Keyword(s):  
Coat Protein ◽  
Mosaic Virus ◽  
Spontaneous Mutant ◽  
Loop Structure ◽  
Base Pairs ◽  
Stem Loop ◽  
Synonymous Substitutions ◽  
Coding Sequence ◽  
Stem Loop Structure ◽  
Viral Accumulation

Potyviral Coat protein (CP) is involved in the replication and movement of potyviruses. However, little information is available on the roles of CP-coding sequence in potyviral infection. Here, we introduced synonymous substitutions to the codon c574g575c576 coding conserved residue arginine at position 192 (R192) of tobacco vein banding mosaic virus (TVBMV) CP. Substitution of the codon c574g575c576 to a574g575a576 or a574g575g576, but not c574g575a576, c574g575t576, or c574g575g576, reduced the replication, cell-to-cell movement, and accumulation of TVBMV in Nicotiana benthamiana plants, suggesting that c574 was critical for replication of TVBMV. Nucleotides 531 to 576 of the TVBMV CP-coding sequence were predicted to form a stem-loop structure, in which four consecutive c-g base pairs (C576-G531, c532-g575, c574-g533, and C534-G573) were located at the stem. Synonymous substitutions of R178-codon c532g533c534 to A532G533A534 and A532G533G534, but not c532g533a534, c532g533t534, or c532g533g534, reduced the replication levels, cell-to-cell, and systemic movement of TVBMV, suggesting that c532 was critical for TVBMV replication. Synonymous substitutions disrupting base pairs C576-G531 and C534-G573 did not affect viral accumulation. After three serial passage inoculation, the accumulation of spontaneous mutant viruses was restored and codons A532G533A534, A532G533G534, a574g575a576, or a574g575g576 of mutants was separately changed to C532G533A534, C532G533G534, C574g575a576, or C574g575g576. Synonymous mutation of R178 and R192 also reduced viral accumulation in N. tabacum plants. Therefore, we concluded that the two consecutive c532-g575 and c574-g533 base pairs played critical roles in TVBMV replication via maintaining the stability of stem-loop structure formed by nucleotides 531 to 576 of CP-coding sequence.

scholarly journals The Ribosomal Shunt Translation Strategy of Cauliflower Mosaic Virus Has Evolved from Ancient Long Terminal Repeats

2006 ◽  
Vol 80 (8) ◽  
pp. 3811-3822 ◽  
Author(s):  
Monir Shababi ◽  
June Bourque ◽  
Karuppaiah Palanichelvam ◽  
Anthony Cole ◽  
Dong Xu ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Promoter Activity ◽  
Sequence Similarity ◽  
Cauliflower Mosaic Virus ◽  
Yeast Genome ◽  
Loop Structure ◽  
Long Terminal Repeats ◽  
Stem Loop ◽  
Stem Loop Structure ◽  
The Right

ABSTRACT We have screened portions of the large intergenic region of the Cauliflower mosaic virus (CaMV) genome for promoter activity in baker's yeast (Saccharomyces cerevisiae) and have identified an element that contributes to promoter activity in yeast but has negligible activity in plant cells when expressed in an agroinfiltration assay. A search of the yeast genome sequence revealed that the CaMV element had sequence similarity with the R region of the long terminal repeat (LTR) of the yeast Ty1 retrotransposon, with significant statistical confidence. In plants, the same CaMV sequence has been shown to have an essential role in the ribosomal shunt mechanism of translation, as it forms the base of the right arm of the stem-loop structure that is required for the ribosomal shunt. Since the left arm of the stem-loop structure must represent an imperfect reverse copy of the right arm, we propose that the ribosomal shunt has evolved from a pair of LTRs that have become incorporated end to end into the CaMV genome.

scholarly journals Dissecting the Requirement for Subgenomic Promoter Sequences by RNA Recombination of Brome Mosaic Virus In Vivo: Evidence for Functional Separation of Transcription and Recombination

2004 ◽  
Vol 78 (16) ◽  
pp. 8552-8564 ◽  
Author(s):  
Rafal Wierzchoslawski ◽  
Aleksandra Dzianott ◽  
Jozef Bujarski
Keyword(s):  
Mosaic Virus ◽  
Transcription Initiation ◽  
De Novo ◽  
Brome Mosaic Virus ◽  
Rna Recombination ◽  
Recombination Activity ◽  
Nucleotide Substitutions ◽  
Stem Loop ◽  
Subgenomic Promoter

ABSTRACT Previously, we and others mapped an increased homologous recombination activity within the subgenomic promoter (sgp) region in brome mosaic virus (BMV) RNA3 (A. Bruyere et al., J. Virol. 74:4214-4219, 2000; R. Wierzchoslawski et al., J. Virol. 77:6769-6776, 2003). In order to correlate sgp-mediated recombination and transcription, in the present work we used BMV RNA3 constructs that carried altered sgp repeats. We observed that the removal or extension of the poly(U) tract reduced or increased recombination, respectively. Deletion of the sgp core hairpin or its replacement by a different stem-loop structure inhibited recombination activity. Nucleotide substitutions at the +1 or +2 transcription initiation position reduced recombination. The sgp core alone supported only basal recombination activity. The sites of crossovers mapped to the poly(U) region and to the core hairpin. The observed effects on recombination did not parallel those observed for transcription. To explain how both activities operate within the sgp sequence, we propose a dual mechanism whereby recombination is primed at the poly(U) tract by the predetached nascent plus strand, whereas transcription is initiated de novo at the sgp core.

Malvaviscus yellow mosaic virus, a divergent begomovirus carrying a nanovirus‐like nonanucleotide and a modified stem‐loop structure

2021 ◽  
Author(s):  
Alison T. M. Lima ◽  
Anelise F. Orílio ◽  
Mariana M. S. Almeida ◽  
Carolina S. Rocha ◽  
Danielle R. Barros ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Yellow Mosaic Virus ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure
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