RNA-Mediated Trans-Activation of Transcription from a Viral RNA

Abstract

The red clover necrotic mosaic virus genome is composed of two single-stranded RNA components, RNA-1 and RNA-2. The viral capsid protein is translated from a subgenomic RNA (sgRNA) that is transcribed from genomic RNA-1. Here, a 34-nucleotide sequence in RNA-2 is shown to be required for transcription of sgRNA. Mutations that prevent base-pairing between the RNA-1 subgenomic promoter and the 34-nucleotide trans-activator prevent expression of a reporter gene. A model is proposed in which direct binding of RNA-2 to RNA-1 trans-activates sgRNA synthesis. This RNA-mediated regulation of transcription is unusual among RNA viruses, which typically rely on protein regulators.

Subgenomic mRNA transcription in Tombusviridae

“…4A). 25 A similar configuration is also observed for the AS equivalent in RCNMV RNA2, termed the trans-activator (TA), 17 (Fig. 4B), and in both cases this positioning is predicted to facilitate local single strandedness and long-range pairing with partner sequences.…”

“…In RCNMV the activator element also acts as a cis-acting RNA element that is necessary for RNA2 replication 26 and essential for genome packaging. 27 These findings, combined with the fact that ASs (and RSs) can reside in essential coding regions, 13,17,25 underscore the multifunctional nature of these elements.…”

“…Based on this requirement, it was proposed that the base paired region acted as an attenuation signal for the RdRp while copying RNA1, leading to generation of a 3'-truncated minus-strand RNA1 that served as the template for sg mRNA transcription, i.e., a PT mechanism. 17 Subsequent studies with TBSV found that a comparable long-range RNA-RNA base pairing interaction (spanning ~1 kb) that occurred in cis (i.e., intra-molecularly) in the viral genome was required for sg mRNA1 transcription (Fig. 3B).…”

“…24 However, a report on sg mRNA transcription in the dianthovirus RCNMV provided evidence that a different mechanism, namely the PT model, likely operated in this member of Tombusviridae. 17 of Tombusviridae, a small non-coding sg RNA corresponding roughly to the genomic 3'UTR is observed in infections. [8][9][10] In Red clover necrotic mosaic virus (RCNMV), this RNA has been shown to be generated by host ribonucleolytic cleavage, rather than by viral RdRp-mediated transcription, and it functions to help regulate the translation of viral mRNAs.…”

“…1). 13,[17][18][19] Like all plus-strand RNA viruses, members of Tombusviridae replicate their genomes via synthesis of a fulllength minus-strand RNA copy of the genome or antigenome, which is then used repeatedly as a template to produce progeny genomes (Fig. 2).…”