Valine-Specific tRNA-like Structure in Turnip Yellow Mosaic Virus RNA
01 Nov 1970-Proceedings of the National Academy of Sciences of the United States of America (National Academy of Sciences)-Vol. 67, Iss: 3, pp 1345-1352
TL;DR: The 3' terminal nucleotide of turnip yellow mosaic virus (TYMV) RNA may be esterified with valine in the presence of ATP and an enzyme preparation from Escherichia coli, and the nucleotide composition near the valine-binding site is different for TYMV RNA and tRNA(Val) from cabbage.
Abstract: The 3′ terminal nucleotide of turnip yellow mosaic virus (TYMV) RNA (23-25 S) may be esterified with valine in the presence of ATP and an enzyme preparation from Escherichia coli. The nucleotide composition near the valine-binding site is different for TYMV RNA and tRNAVal from cabbage, as shown by comparison of the valine adducts of nucleotides labeled with radioactive valine in T1 RNase digests. Consequently, host tRNAVal is not involved in the observed charging of TYMV RNA with valine. The TYMV RNA appears to have a tRNA-like structure, at or near its 3′ end, that is recognized by three different enzymes which specifically catalyze reactions involving tRNA.
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TL;DR: In this paper, the role of tRNA structure in the recognition process with synthetases and on the implications for aminoacylation efficiency is discussed, and a comparison of recent results with previous observations is made.
Abstract: Publisher Summary This chapter discusses the role of tRNA structure in the recognition process with synthetases and on the implications for aminoacylation efficiency. Many examples are taken from our own research on several specific aminoacylation systems, for example aspartate, histidine, valine, but concepts are presented more globally with reference to the complete set of aminoacylation systems. It emphasizes on the importance of tRNA-like structures for understanding the interaction of canonical tRNAs with synthetase. Although tRNA-like molecules found in some plant viral RNAs do not participate in protein synthesis, they represent interesting natural mutants to be compared to canonical tRNAs. This is also the case of tRNAlike structures found in some messenger RNAs as well as of bizarre tRNAs from mitochondria . In addition, competition and kinetic effects may also contribute to the overall specificity of the various aminoacylation systems; the balance between the concentration of tRNAs and synthetases would be essential for ensuring optimal specificity. According to this view, individual aminoacylation systems do not work at their optimal chemical efficiency, but work instead to assure optimal discrimination among the different aminoacylation systems. Such a balance may be perturbed under certain physiological or pathological conditions. Finally, this chapter discusses a comparison of recent results with previous observations, and show how old concepts established phenomenologically can now be tested more explicitly.
188 citations
TL;DR: The solution structure of the pseudoknotted T arm and acceptor arm of the transfer RNA-like structure of turnip yellow mosaic virus (TYMV) was determined by nuclear magnetic resonance (NMR) spectroscopy.
Abstract: Pseudoknot formation folds the 3' ends of many plant viral genomic RNAs into structures that resemble transfer RNA in global folding and in their reactivity to transfer RNA-specific proteins. The solution structure of the pseudoknotted T arm and acceptor arm of the transfer RNA-like structure of turnip yellow mosaic virus (TYMV) was determined by nuclear magnetic resonance (NMR) spectroscopy. The molecule is stabilized by the hairpin formed by the 5' end of the RNA, and by the intricate interactions related to the loops of the pseudoknot. Loop 1 spans the major groove of the helix with only two of its four nucleotides. Loop 2, which crosses the minor groove, interacts closely with its opposing helix, in particular through hydrogen bonds with a highly conserved adenine. The structure resulting from this interaction between the minor groove and single-stranded RNA at helical junctions displays internal mobility, which may be a general feature of RNA pseudoknots that regulates their interaction with proteins or other RNA molecules.
149 citations
TL;DR: A fragment representing the 3'-terminal 'tRNA-like' region of turnip yellow mosaic (TYM) virus RNA has been purified following incubation of intact TYM virus RNA with Escherichia coli 'RNase P' and the nucleotide sequence at the 5' end indicates that this fragment includes the end of theTYM virus coat protein gene.
Abstract: A fragment representing the 3′-terminal ‘tRNA-like’ region of turnip yellow mosaic (TYM) virus RNA has been purified following incubation of intact TYM virus RNA with Escherichia coli‘RNase P’. This fragment, which is 112 ± 3-nucleotides long has been completely digested with T1 RNase and pancreatic RNase and all the oligonucleotides present in such digests have been sequenced using 32P-end labelling techniques in vitro. The TYM virus RNA fragment is free of modified nucleosides and does not contain a G-U-U-C-R sequence. Using nuclease P1 from Penicillium citrinum, the sequence of 26 nucleotides from the 5′ end and 16 nucleotides from the 3′ end of this fragment has been deduced. The nucleotide sequence at the 5′ end of the TYM virus RNA fragment indicates that this fragment includes the end of the TYM virus coat protein gene.
148 citations
TL;DR: It is demonstrated 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.
Abstract: 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.
144 citations
TL;DR: This chapter summarizes the results obtained with different viral RNAs that accept an amino acid and are recognized by various tRNA-specific enzymes, indicating that different primary and secondary structures of two nucleic acid molecules, such as tRNAs and certain viralRNAs, can be recognized efficiently by the same enzyme systems that play a central role in the transfer of genetic information.
Abstract: Publisher Summary All structural studies of ribonucleic acids (RNAs) from various origins—be they cellular messenger RNAs or viral RNAs—show that these molecules contain nucleotide sequences that are not translated into polypeptides. At the 5' end, besides the “cap” structure generally found in eukaryotic mRNAs and viral RNAs, the untranslated sequence is heteropolymeric and of variable length—from a few nucleotides to a few hundred nucleotides. The physiological role of these untranslated heteropolymeric regions is not well understood. This chapter summarizes the results obtained with different viral RNAs that accept an amino acid and are recognized by various tRNA-specific enzymes. For a number of these viral RNAs, the nucleotide sequence of the amino-acid-acceptor regions has been determined and the structures have been compared. Results indicated that different primary and secondary structures of two nucleic acid molecules, such as tRNAs and certain viral RNAs, can be recognized efficiently by the same enzyme systems that play a central role in the transfer of genetic information. The nucleotide sequence of virtually all tRNA molecules can be drawn in a hydrogen-bonded “cloverleaf” structure. The existence of this structure, further folded into a tertiary structure, has been proved by X-ray diffraction analyses. The chapter concludes with a discussion on the possible role of tRNA-like structures in viral RNA genomes.
135 citations