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Viral tRNAs and tRNA‐like structures

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Abstract Viruses commonly exploit or modify some aspect of tRNA biology. Large DNA viruses, especially bacteriophages, phycodnaviruses, and mimiviruses, produce their own tRNAs, apparently to adjust translational capacity during infection. Retroviruses recruit specific host tRNAs for use in priming the reverse transcription of their genome. Certain positive‐strand RNA plant viral genomes possess 3′‐tRNA‐like structures (TLSs) that are built quite differently from authentic tRNAs, and yet efficiently recapitulate several properties of tRNAs. The structures and roles of these TLSs are discussed, emphasizing the variety in both structure and function. © 2010 John Wiley & Sons, Ltd. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications Translation > Translation Regulation RNA Processing > tRNA Processing

Valylatable tRNA‐like structures (TLSs). (a) Secondary structure of the turnip yellow mosaic virus TLS, the prototypical TLS aminoacylatable with valine. The T, D and anticodon (A/C) stems are labeled, and the numbers of base pairs (4/3/5) in the three stacked segments of the acceptor‐T arm are indicated. The T and anticodon loop sequences and the 3′‐CCA resemble sequences in tRNAVal. Nucleotides are numbered from the 3′‐end. The relative importance of valine identity elements at nucleotides 56, 55, 53 and 4 is indicated by arrow size (red arrows). (b) Acceptor‐T arm of the eggplant mosaic tymovirus TLS, which is built of 3‐bp, 3‐bp and 6‐bp segments. (c) Proposed secondary structure of nucleotides inserted between the two halves (shown in cartoon form) of the PCV TLS.

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Brome mosaic virus tRNA‐like structure (TLS). Secondary structure of the tyrosine‐specific brome mosaic virus (BMV) TLS as proposed.29 The major tyrosine identity elements are located at the end of the acceptor‐T arm, with minor identity in the loop of stem B2, indicated by red arrows. Conserved T‐loop nucleotides are indicated by underlining. Stems B3 and E are outside the core TLS but support fully efficient tyrosylation.29,31 Stem C (shaded) serves as the polymerase binding site directing the minus strand synthesis phase of viral RNA replication.33

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Tobacco mosaic virus (TMV) tRNA‐like structures (TLS). Proposed secondary structure of the histidine‐specific TMV TLS. Nucleotide A18, which is positioned as a non‐base‐paired extension of the acceptor‐T arm, is the major histidine identity element, supported by C4.

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RNA Processing > tRNA Processing
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
Translation > Translation Regulation
RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems

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