An expanded class of histidine-accepting viral tRNA-like structures

Langeberg, Conner J.; Sherlock, Madeline E.; MacFadden, Andrea; Kieft, Jeffrey

doi:10.1261/rna.078550.120

Cited by 4 publications

(7 citation statements)

References 86 publications

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“…TLSs are located at the 3′ end of viral genomic RNAs. They are found in several genera of plant viral RNAs and are recognized and aminoacylated ( 222 ) by either ValRSs ( 247 ), HisRSs ( 248 ) or TyrRSs ( 249 ). TLSs do not participate in protein synthesis but act in amplification of viral genomes.…”

Section: Identities In Atypical Trna Folds and Organellar Trnasmentioning

confidence: 99%

“…The recent search for sequence covariations in viral genomic RNAs, complemented by biochemical studies, has expanded the world of viral TLSs ( 247 , 248 ). As for TLSs Val , 108 examples of in vitro valylatable TLSs were found in plant-infecting viruses and in some insect-infecting tetraviruses.…”

Section: Expanding the World Of Trna Identitymentioning

confidence: 99%

“…Similarly, many new examples of histidinylatable TLSs His have been added to the previously described TLSs His ( 222 ). Like other viral TLSs, their sequences are organized in a consensus secondary structure in a pseudoknotted secondary structure (Figure 4C ) that contains the identity elements previously characterized in tobamoviral TLS His , including the atypical pair N −1 –N 73 and G 34 , U 35 of the His anticodon ( 248 ).…”

Section: Expanding the World Of Trna Identitymentioning

confidence: 99%

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The tRNA identity landscape for aminoacylation and beyond

Giegé

Eriani

2023

Nucleic Acids Research

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tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.

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Section: Identities In Atypical Trna Folds and Organellar Trnasmentioning

confidence: 99%

Section: Expanding the World Of Trna Identitymentioning

confidence: 99%

Section: Expanding the World Of Trna Identitymentioning

confidence: 99%

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The tRNA identity landscape for aminoacylation and beyond

Giegé

Eriani

2023

Nucleic Acids Research

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“…These authors studied the minimal sequence necessary to form TLS, as well as the implication of Mg 2+ ions into aminoacylation. Up to now, the exact function of the 3 TLS remains unclear [82]. Yet, numerous insights on 3 TLS were acquired.…”

Section: -Terminal Region Of Plant Viruses: Trna Mimicry For Replicationmentioning

confidence: 99%

Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond

Gilmer

Quignon

Jousset

et al. 2021

Viruses

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RNA molecules are key players in a variety of biological events, and this is particularly true for viral RNAs. To better understand the replication of those pathogens and try to block them, special attention has been paid to the structure of their RNAs. Methods to probe RNA structures have been developed since the 1960s; even if they have evolved over the years, they are still in use today and provide useful information on the folding of RNA molecules, including viral RNAs. The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) methodology and to show how they have influenced the current probing techniques. Actually, these technological breakthroughs, which involved advanced detection methods, were made possible thanks to the development of next-generation sequencing (NGS) but also to the previous works accumulated in the field of structural RNA biology. Finally, we will also discuss how high-throughput SHAPE (hSHAPE) paved the way for the development of sophisticated RNA structural techniques.

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“…Notably, viruses that contain an authentic TLS have a canonical tRNA 'CCA' tail appended to the 3' end of a pseudoknot that mimics the acceptor stem, and they undergo aminoacylation by a host amino-acyl tRNA synthetase (AARS) (Rietveld et al 1984;Pleij et al 1985;Dreher and Hall 1988;Bonilla et al 2021;Langeberg et al 2021;Sherlock et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Diversity and modularity of tyrosine-accepting tRNA-like structures

Sherlock,

Langeberg,

Kieft

2023

RNA

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Certain positive-sense single-stranded RNA viruses contain elements at their 3’ termini that structurally mimic tRNAs. These tRNA-like structures (TLSs) are classified based on which amino acid is covalently added to the 3' end by host aminoacyl-tRNA synthetase. Recently, a cryoEM reconstruction of a representative tyrosine-accepting tRNA-like structure (TLSTyr) from brome mosaic virus (BMV) revealed a unique mode of recognition of the viral anticodon-mimicking domain by tyrosyl-tRNA synthetase. Some viruses in the hordeivirus genus of Virgaviridae are also selectively aminoacylated with tyrosine, yet these TLS RNAs have a different architecture in the 5' domain that comprises the atypical anticodon loop mimic. Herein, we present bioinformatic and biochemical data supporting a distinct secondary structure for the 5′ domain of the hordeivirus TLSTyr compared to those in Bromoviridae. Despite forming a different secondary structure, the 5′ domain is necessary to achieve robust in vitro aminoacylation. Furthermore, a chimeric RNA containing the 5′ domain from the BMV TLSTyr and the 3′ domain from a hordeivirus TLSTyr are aminoacylated, illustrating modularity in these structured RNA elements. We propose that the structurally distinct 5′ domain of the hordeivirus TLSTyrs performs the same role in mimicking the anticodon loop as its counterpart in the BMV TLSTyr. Finally, these structurally and phylogenetically divergent types of TLSTyr provide insight into the evolutionary connections between all classes of viral tRNA-like structures.

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An expanded class of histidine-accepting viral tRNA-like structures

Cited by 4 publications

References 86 publications

The tRNA identity landscape for aminoacylation and beyond

The tRNA identity landscape for aminoacylation and beyond

Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond

Diversity and modularity of tyrosine-accepting tRNA-like structures

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