The tRNA-like structure of turnip yellow mosaic virus RNA: structural organization of the last 159 nucleotides from the 3′ OH terminus

Florentz, Catherine; Briand, Jean‐Paul; Romby, Pascale; Hirth, L.; Ebel, Jean‐Pierre; Glegé, R.

doi:10.1002/j.1460-2075.1982.tb01158.x

Cited by 82 publications

(33 citation statements)

References 39 publications

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“…The 3'-terminal sequence of the KYMV-JB genome can be folded into a five-stem secondary structure (Fig. 4) similar to those proposed for TYMV (Florentz et al, 1982), EMV (Osorio-Keese et al, 1989) and OYMV . However, the 3'-terminal non-coding region of the KYMV-JB genome is clearly different from those of other tymoviruses in that the stop codon (UGA, underlined in Fig.…”

Section: Organization Of the Kymv-jb Genomementioning

confidence: 59%

“…The free energy was calculated by the method of Freier et al (1986) to be AG = -13.4 kJ/mol. (Florentz et al, 1982;Rietveld et al, 1982). The nucleotide sequences that potentially basepair the folds into a tertiary structure are boxed and the stop codon of the VP gene is underlined.…”

Section: Sequence Similarities To Other Viruses Containing Rna Genomesmentioning

confidence: 99%

“…The sequence of 83 nucleotides at the 3' terminus of KYMV genomic RNA was determined by van Belkum et al (1987) using the direct RNA enzymic sequencing method. It was shown that the 3' terminus of KYMV RNA could form a tRNA-like structure and could be acylated with valine, thus the structure and behaviour is similar to that of the 3' terminus of TYMV RNA (Florentz et al, 1982).…”

Section: Introductionmentioning

confidence: 95%

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The nucleotide sequence of the genomic RNA of kennedya yellow mosaic tymovirus-Jervis Bay isolate: relationships with potex- and carlaviruses

Ding

Keese

Gibbs

1990

Journal of General Virology

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The nucleotide sequence of the genomic RNA of kennedya yellow mosaic tymovirus-Jervis Bay isolate (KYMV-JB) has been determined. The genome of KYMV-JB is 6362 nucleotide residues long and encodes three major open reading frames. The genomic organization and the encoded proteins of KYMV-JB are very similar to those of three other tymoviruses that have recently been reported. Sequence comparisons revealed that the possible replicase proteins of tymoviruses are closely related to those of potexviruses and carlaviruses, suggesting a close evolutionary relationship among these viruses, despite differences in their genome organization and particle morphology.

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Section: Organization Of the Kymv-jb Genomementioning

confidence: 59%

Section: Sequence Similarities To Other Viruses Containing Rna Genomesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 95%

See 1 more Smart Citation

The nucleotide sequence of the genomic RNA of kennedya yellow mosaic tymovirus-Jervis Bay isolate: relationships with potex- and carlaviruses

Ding

Keese

Gibbs

1990

Journal of General Virology

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“…The genomes of many RNA viruses are not polyadenylated but terminate with a tRNA-like structure (Hall 1979;Haenni et al 1982), which, although deviating from the cloverleaf model of tRNA (Florentz et a!. 1982;Rietveld et al 1983), can be strikingly similar to the Lshaped tertiary conformation proposed for tRNAs (Rietveld et al 1983;Joshi et al 1983).…”

mentioning

confidence: 88%

RNA pseudoknot domain of tobacco mosaic virus can functionally substitute for a poly(A) tail in plant and animal cells.

Gallie¹,

Walbot²

1990

Genes Dev.

144

119

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The genomes of many RNA viruses terminate in a tertiary structure similar to the L-conformation of tRNAs and this structure is recognized by many tRNA-specific enzymes such as aminoacyl-tRNA synthetase. Virtually the entire 3'-untranslated region (UTR) of tobacco mosaic virus (TMV) RNA is involved in an extended tertiary structure containing, in addition to a tRNA-like structure, a pseudoknot domain that lies immediately upstream. Although the functions of these structures are not well understood, they are essential to the virus. We demonstrate that the addition of the 204-base TMV 3'-untranslated region to foreign mRNA constructs can increase gene expression up to 100-fold compared to nonadenylated mRNA. The 3'-UTR of TMV was equal to or greater than a polyadenylated tail in enhancing gene expression in electroporated dicot and monocot protoplasts. The TMV 3'-UTR is functionally similar to a polyadenylated tail in that it increases mRNA stability and translation and must be positioned at the 3' terminus to function efficiently. Similar effects on expression were observed in Chinese hamster ovary cells, demonstrating that the sequence functions in a wide range of eukaryotes. When the extended tertiary structure was dissected, the upstream pseudoknot domain was found to be largely responsible for increasing expression. The inclusion of the tRNA-like structure, however, was important for full regulation.

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“…It is clear that pseudoknots are important elements in RNA structure and functioning. The pseudoknot that has been investigated most thoroughly using both biochemical [3,4,14,15] and computer graphics [16] methods, is the one present in the aminoacyl acceptor arm of the tRNA-like structure of turnip yellow mosaic virus RNA. However, the current model, which accomodates most of the data available, needs biophysical verification.…”

mentioning

confidence: 99%

Biochemical and biophysical analysis of pseudoknot‐containing RNA fragments

Belkum¹,

Wiersema²,

Joordens³

et al. 1989

European Journal of Biochemistry

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Three overlapping RNA fragments containing the pseudoknot, as found in the tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA, have been isolated and purified. Site-directed cleavage of TYMV RNA by RNase H, followed by ammonium sulphate precipitation and ion-exchange HPLC, yielded a pure preparation of a 3'-terminal, 112-nucleotide TYMV RNA fragment. Transcription of TYMV cDNA by T7 RNA polymerase, resulted in the isolation of an 88-nucleotide fragment. Finally, a 44-nucleotide fragment containing the TY MV RNA pseudoknot and strongly resembling the aminoacyl acceptor arm of the viral RNA was also synthesised using T7 RNA polymerase. The three fragments were isolated in milligram amounts and used for biochemical structure mapping, ultraviolet melting studies and NMR spectroscopy.Chemical modification with diethyl pyrocarbonate and sodium bisulphite and enzymatic digestion with RNase TI confirmed the presence of the pseudoknot in the 44-nucleotide fragment. Also the analogue of the T-stem and T-loop of the tRNA-like structure of TYMV RNA was found. The results of modification at various temperatures in Mg2+-containing buffers were in general agreement with optical melting studies. Ultraviolet melting analysis of the longer fragments revealed their greater complexity and the results appear similar to those obtained for some tRNA species.To obtain direct biophysical evidence for base-pairing and stacking interactions in the pseudoknot, NMR studies were initiated. The first proton-NMR spectra ever obtained for plant viral RNA fragments are presented. NMR spectra were recorded at various buffer conditions and at various temperatures. The spectra for the 112-nucleotide and 88-nucleotide fragment are too complicated to be solved at present. In the case of the 44-nucleotide fragment, however, the imino proton resonances are well separated and this system turns out to be most promising for structural studies.tRNA-like structures are found at the 3' termini of a number of plant viral RNAs [l, 21. These structures are recognised not only by the viral replicase, but also by tRNA-specific enzymes. In recent years these tRNA-like structures were investigated in detail by biochemical methods. Structural models demonstrating the resemblance between canonical tRNA and the tRNA-like moieties were proposed [3 -61.A striking feature of these models is the presence of a new structural element called an RNA pseudoknot. Pseudoknots of the type found in the tRNA-like structures involve base pairing between nucleotides in a hairpin loop with nucleotides in a single-stranded region of the molecule. This type of interaction gives rise to quasi-continuous helical domains and has been discussed in detail by Pleij et al. [7]. Beside the pseudoknots found in the tRNA-like structures, tandemly arranged pseudoknots appear to be common elements in the 3' non-coding region of several non-polyadenylated plant viral RNAs [8, 91. Pseudoknots were also found in ribosomal RNAs and in a center of autocatalytic RNA splicing [7]. Recently, pseu...

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The tRNA-like structure of turnip yellow mosaic virus RNA: structural organization of the last 159 nucleotides from the 3′ OH terminus

Cited by 82 publications

References 39 publications

The nucleotide sequence of the genomic RNA of kennedya yellow mosaic tymovirus-Jervis Bay isolate: relationships with potex- and carlaviruses

The nucleotide sequence of the genomic RNA of kennedya yellow mosaic tymovirus-Jervis Bay isolate: relationships with potex- and carlaviruses

RNA pseudoknot domain of tobacco mosaic virus can functionally substitute for a poly(A) tail in plant and animal cells.

Biochemical and biophysical analysis of pseudoknot‐containing RNA fragments

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