Aminoacylation of 3′ terminal tRNA-like fragments of turnip yellow mosaic virus RNA: The influence of 5′ nonviral sequences

Mans, R. M. W.; Verlaan, P. W. G.; Pleij, C.W.A.; Bosch, L.

doi:10.1016/0167-4781(90)90164-w

Cited by 14 publications

(18 citation statements)

References 14 publications

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“…A previous study reported that nonviral 5′ upstream nucleotides can affect the secondary structure of the TYMV TLS, creating multiple conformations upon the addition of divalent magnesium ions 30. To determine if the reduction of aminoacylation efficiency of TYMV0G and TYMVUUAG TLSs is due to formation of a polydisperse sample, we used native gel electrophoresis, where the RNA’s migration rate is based on a combination of molecular weight and global conformation.…”

Section: Resultsmentioning

confidence: 99%

“…Previous experiments using in vitro transcribed TYMV TLS species that contained 5′ nonviral nucleotides showed that this RNA was not an optimal substrate for aminoacylation, likely because these nonviral nucleotides promote an alternative secondary structure 30,34. For technical reasons that study did not test a construct containing exactly 82 nts.…”

Section: Introductionmentioning

confidence: 99%

“…The idea that the TYMV TLS is a physical switch that controls multiple viral processes presents a hypothesis that the three-dimensional folded structure, and alterations to the stability of this structure, are critical components of regulation 9,11,28–30. However, in most cases direct interrogation of changes to the folded TYMV TLS structure has not been conducted and hence key aspects of this hypothesis remain largely untested.…”

Section: Introductionmentioning

confidence: 99%

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Multi-domain Packing in the Aminoacylatable 3′ End of a Plant Viral RNA

Hammond

Rambo

Kieft

2010

Journal of Molecular Biology

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Turnip yellow mosaic virus (TYMV) contains a tRNA-like structure (TLS) in its 3′ untranslated region (3′ UTR). This highly structured element induces valylation of the viral RNA by host cell enzymes and is important for virus proliferation. Directly upstream of the TYMV TLS is an upstream pseudoknot domain (UPD) that has been considered to be structurally distinct from the TLS. However, using a combination of functional, biochemical, and biophysical assays, we show that the entire 3′ UTR of the viral genome is a single structured element in the absence of cellular protein. This packing architecture stabilizes RNA structure and creates a better substrate for aminoacylation, and thus the UPD and TLS are functionally and structurally coupled. It has been proposed that the TYMV TLS acts as a molecular switch between translation and replication. Our results suggest that this putative switch could be based on structural changes within the global architecture the UTR induced by interactions with the ribosome. The TYMV·TLS UPD may demonstrate how RNA structural plasticity can play a role in regulation of biological processes.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Multi-domain Packing in the Aminoacylatable 3′ End of a Plant Viral RNA

Hammond

Rambo

Kieft

2010

Journal of Molecular Biology

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“…The TYMV TLS sequences used in the above probing study contains 85 nt (initially, we used a 59 GGG sequence to promote efficient in vitro transcription followed by 82 viral nucleotides and no upstream ribozyme), as previous aminoacylation assays identified 82 nt as comprising the functional TLS. However, there is some ambiguity regarding this boundary and the effects of 59 sequences on the TLS structure (Joshi et al 1982;Dreher et al 1988;Mans et al 1990). To systematically explore the structural role of the 59 end, we d OH probed four RNAs with systematic variation of the number of G's on this terminus.…”

Section: Tymv Tls: Determinants Of the Fold Include 59 Nucleotidesmentioning

confidence: 99%

“…The minimal length of the TYMV TLS for aminoacylation has been reported as 82 nucleotides (nt) (Mans et al 1990), the BMV TLS has been reported to require 134 nt for aminoacylation (although more efficient aminoacylation requires 169 nt) (Fechter et al 2001a), and the TMV TLS needs 106 nt (Rietveld et al 1984). While the 39 and 59 ends base pair in the acceptor stem in canonical tRNAs (Fig.…”

Section: Introductionmentioning

confidence: 99%

Comparison and functional implications of the 3D architectures of viral tRNA-like structures

Hammond

Rambo²,

Filbin³

et al. 2009

RNA

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RNA viruses co-opt the host cell's biological machinery, and their infection strategies often depend on specific structures in the viral genomic RNA. Examples are tRNA-like structures (TLSs), found at the 39 end of certain plant viral RNAs, which can use the cell's aminoacyl tRNA-synthetases (AARSs) to drive addition of an amino acid to the 39 end of the viral RNA. TLSs are multifunctional RNAs involved in processes such as viral replication, translation, and viral RNA stability; these functions depend on their fold. Experimental result-based structural models of TLSs have been published. In this study, we further examine these structures using a combination of biophysical and biochemical approaches to explore the three-dimensional (3D) architectures of TLSs from the turnip yellow mosaic virus (TYMV), tobacco mosaic virus (TMV), and brome mosaic virus (BMV). We find that despite similar function, these RNAs are biophysically diverse: the TYMV TLS adopts a characteristic tRNA-like L shape, the BMV TLS has a large compact globular domain with several helical extensions, and the TMV TLS aggregates in solution. Both the TYMV and BMV TLS RNAs adopt structures with tight backbone packing and also with dynamic structural elements, suggesting complexities and subtleties that cannot be explained by simple tRNA mimicry. These results confirm some aspects of existing models and also indicate how these models can be improved. The biophysical characteristics of these TLSs show how these multifunctional RNAs might regulate various viral processes, including negative strand synthesis, and also allow comparison with other structured RNAs.

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Transfer RNA Mimicry in a New Group of Positive-Strand RNA Plant Viruses, the Furoviruses: Differential Aminoacylation between the RNA Components of One Genome

Goodwin

Dreher

1998

Virology

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Aminoacylation of 3′ terminal tRNA-like fragments of turnip yellow mosaic virus RNA: The influence of 5′ nonviral sequences

Cited by 14 publications

References 14 publications

Multi-domain Packing in the Aminoacylatable 3′ End of a Plant Viral RNA

Multi-domain Packing in the Aminoacylatable 3′ End of a Plant Viral RNA

Comparison and functional implications of the 3D architectures of viral tRNA-like structures

Transfer RNA Mimicry in a New Group of Positive-Strand RNA Plant Viruses, the Furoviruses: Differential Aminoacylation between the RNA Components of One Genome

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