The tymobox, a sequence shared by most tymoviruses: its use in molecular studies of tymoviruses

Ding, Shou‐Wei; Howe, John Greg; Keese, Paul; Mackenzie, A. M.; Meek, David W.; Osorio-Keese, Maria E.; Skotnicki, M. L.; Srifah, Pattana; Torronen, M.; Gibbs, Adrian

doi:10.1093/nar/18.5.1181

Cited by 95 publications

(43 citation statements)

References 28 publications

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“…ORF 2 is the longest one, and encodes a protein of 206 kDa with various conserved domains found in RNA-dependent RNA-polymerases (RP). At the 3'end of this gene there is the so-called tymobox, a 16 nucleotides domain highly conserved among tymoviruses, which is thought to be the promoter for the transcription of the subgenomic mRNA for ORF 3 [13][14][15] that encodes the 20 kDa coat protein (CP). Tymoviral genomes have typical secondary structures at the 5' and 3' untranslated regions (UTR).…”

Section: Introductionmentioning

confidence: 99%

Genomic and biological characterization of chiltepín yellow mosaic virus, a new tymovirus infecting Capsicum annuum var. aviculare in Mexico

et al. 2010

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The characterization of viruses infecting wild plants is a key step towards understanding the ecology of plant viruses. In this work, the complete genomic nucleotide sequence of a new tymovirus species infecting chiltepin, the wild ancestor of Capsicum annuum pepper crops, in México was determined, and its host range has been explored. The genome of 6,517 nucleotides has the three open reading frames described for tymoviruses, putatively encoding an RNA-dependent RNA polymerase, a movement protein and a coat protein. The 5' and 3' untranslated regions have structures with typical signatures of the tymoviruses. Phylogenetic analyses revealed that this new virus is closely related to the other tymoviruses isolated from solanaceous plants. Its host range is mainly limited to solanaceous species, which notably include cultivated Capsicum species. In the latter, infection resulted in a severe reduction of growth, indicating the potential of this virus to be a significant crop pathogen. The ñame of chiltepin yellow mosaic virus (ChiYMV) is proposed for this new tymovirus.

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Section: Introductionmentioning

confidence: 99%

Genomic and biological characterization of chiltepín yellow mosaic virus, a new tymovirus infecting Capsicum annuum var. aviculare in Mexico

et al. 2010

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“…A close examination of the region surrounding the initiation site for sgRNA synthesis in TYMV RNA and in 14 other tymovirus genomes clearly demonstrated the presence of two highly conserved sequence blocks in a region of about 40 nt designated the tymobox region (8). The 5Ј-terminal block, the tymobox itself, is 16 nt long and is identical in 11 of the 15 tymovirus sequences compared.…”

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confidence: 96%

“…The sequence CAAU is common to 13 of the 15 tymovirus RNA sequences examined. It has thus been proposed that the two conserved sequence motifs may function as an sg promoter (8). This would imply that transcriptional control regions overlap coding regions.…”

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confidence: 99%

Identification and Functional Analysis of the Turnip Yellow Mosaic Tymovirus Subgenomic Promoter

Schirawski

Voyatzakis

Zaccomer

et al. 2000

J Virol

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Most plant viruses rely on the production of subgenomic RNAs (sgRNAs) for the expression of their genes and survival in the plant. Although this is a widely adopted strategy among viruses, the mechanism(s) whereby sgRNA production occurs remains poorly defined. Turnip yellow mosaic tymovirus (TYMV) is a positivestranded RNA virus that produces an sgRNA for the expression of its coat protein. Here we report that the subgenomic promoter sequence of TYMV is located on a 494-nucleotide fragment, containing previously identified highly conserved sequence elements, which are shown here to be essential for promoter function. After duplication, the subgenomic promoter can be inserted into the coat protein open reading frame, giving rise to the in vivo production of a second sgRNA. It is suggested that this promoter can function when contained on a different molecule than viral genomic RNA. This interesting trait may be of general use for plant and plant virus research.The genomes of the vast majority of positive-stranded RNA viruses contain more than one gene. Synthesis of internal genes is achieved by one or several strategies, including the formation of subgenomic RNAs (sgRNAs), internal translation initiation, leaky scanning, frameshift, and readthrough. Of these, the production of sgRNAs is by far the most common strategy used by viruses. Indeed, among positive-stranded RNA viruses of plants, only viruses of the Potyviridae and Comoviridae families and the sequiviruses of the Sequiviridae family do not resort to this strategy (reviewed in reference 29).Synthesis of sgRNA by internal initiation of transcription on promoters located on the complementary minus-strand RNA of genomic length is well documented for plant viruses such as brome mosaic bromovirus (BMV) (18), turnip yellow mosaic tymovirus (TYMV) (10), alfalfa mosaic ilarvirus (A1MV) (26), cucumber mosaic cucumovirus (CMV) (4), beet necrotic yellow vein benyvirus (BNYVV) (2), and turnip crinkle carmovirus (TCV) (27,28). For certain viruses such as potato potexvirus X (15) and tomato bushy stunt tombusvirus (31), internal initiation has been shown to also depend on interaction between distantly located cis regions and the promoter region in the genome. On the other hand, in red clover necrotic mosaic dianthovirus (24), sgRNA synthesis appears to occur by premature termination during minus-strand synthesis, with subsequent sgRNA production from the truncated nascent RNA. An interesting feature of this termination process is that it depends on trans activation between the two RNA components that make up the viral genome.The promoters for the synthesis of several sgRNAs (sg promoters) have been examined. Defining such regions has relied on several methods including site-specific mutations, duplication of the hypothetical promoter region followed by deletion mutations, RNA sequence and/or structure predictions, phylogenetic sequence comparisons, and the use of chemical and enzymatic probes. Frequently, sg promoters are composed of more than one region: a core promo...

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“…Initiation depends on the presence of a highly conserved sequence known as the tymobox (7,29). Unfortunately, the signals involved in the replication of the TYMV full-length plus-strand RNA are less clear.…”

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confidence: 99%

“…It was suggested that the 5Ј UTR is involved in a process of circularization, since complementary sequences were shown to be present in the 5Ј UTR and the 3Ј UTR (4,32). On the other hand, one can speculate that the conserved m 7 GpppGUAAU motif at the extreme 5Ј end of the tymovirus genomic RNA may have a function in viral plus-strand synthesis. The signals responsible for the initiation of synthesis of the full-length minus-strand RNA are located at the 3Ј end of the TYMV RNA genome, in which a crucial role is played by the ACCA sequence at the 3Ј end of the TLS (5,6,30).…”

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confidence: 99%

The 5′-Proximal Hairpin of Turnip Yellow Mosaic Virus RNA: Its Role in Translation and Encapsidation

Bink

Schirawski

Haenni

et al. 2003

J Virol

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The RNA genome of turnip yellow mosaic virus (TYMV) consists of more than 6,000 nucleotides. During a study of the roles of the two hairpins located in its 90-nucleotide 5 untranslated region, it was observed that stabilization of the 5-proximal hairpin leads to a delay in the development of symptoms on plants. This delay in symptom development for both locally and systemically infected leaves was found to be dependent on a change in the free energy of the hairpin caused by introduced mutations. A protoplast transfection assay revealed that the accumulation of plus-strand full-length RNA and subgenomic RNA, as well as protein expression levels, was affected by hairpin stability. Stabilization of this hairpin inhibited translation. A model is proposed in which a destabilized 5-proximal hairpin allows maximal translation of the viral proteins. It is suggested that this hairpin may exist in close proximity to the 5 cap as long as its stability is low enough to enable translation. However, at an acidic pH, the hairpin structure becomes more stable and is functionally transformed into the initiation signal for viral packaging. Slightly acidic conditions can be found in chloroplasts, where TYMV assembly is driven by a low pH generated by active photosynthesis.The 5Ј untranslated region (5Ј UTR) of single-stranded positive-sense RNA virus genomes often contains cis-acting elements involved in translation, replication, and/or encapsidation. Turnip yellow mosaic virus (TYMV) RNA has a 5Ј leader of 90 nucleotides which may regulate all three processes by means of signals embedded within this short stretch of RNA.Translation of TYMV RNA has been assumed to take place according to general principles for eukaryotic mRNAs, since the genomic RNA and the subgenomic RNA (sgRNA) for the coat protein (CP) are capped at the 5Ј end (10, 15). The cap would enable the binding of translation initiation factors, which subsequently would allow the docking of the 40S ribosomal subunit on the viral mRNA. By scanning the RNA, the ribosome reaches the start codons of the movement protein (MP) and the RNA-dependent RNA polymerase (RdRp). The AUG start codon of the latter open reading frame (ORF) overlaps that of the MP ORF and is situated only 4 nucleotides downstream of the first AUG (Fig. 1A). Translation of the RdRp gene was proposed to occur through leaky scanning (18, 34), although Weiland and Dreher reported that mutation of the first AUG did not affect translation starting at the downstream AUG (34), a finding which is at variance with leaky scanning. A number of exceptions to the eukaryotic scanning model of Kozak (18) exist, most of which come from the field of virology. Cap-independent initiation of translation was shown to occur through a strategy involving the use of an internal ribosomal entry site (IRES). The IRES-mediated translation initiation mechanism involves the binding of translation initiation factors and the ribosome to a complex RNA secondary structure, thereby placing the translation machinery in the start codon conte...

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The tymobox, a sequence shared by most tymoviruses: its use in molecular studies of tymoviruses

Cited by 95 publications

References 28 publications

Genomic and biological characterization of chiltepín yellow mosaic virus, a new tymovirus infecting Capsicum annuum var. aviculare in Mexico

Genomic and biological characterization of chiltepín yellow mosaic virus, a new tymovirus infecting Capsicum annuum var. aviculare in Mexico

Identification and Functional Analysis of the Turnip Yellow Mosaic Tymovirus Subgenomic Promoter

The 5′-Proximal Hairpin of Turnip Yellow Mosaic Virus RNA: Its Role in Translation and Encapsidation

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