Subgenomic mRNA transcription in an aureusvirus: Down-regulation of transcription and evolution of regulatory RNA elements

Abstract

The genus Aureusvirus is composed of a group of positive-strand RNA plant viruses that belong to the family Tombusviridae. Expression of certain aureusvirus genes requires the transcription of two subgenomic (sg) mRNAs. Interestingly, the level of sg mRNA2 accumulation in aureusvirus infections is considerably lower than that of sg mRNA1. The nature of this difference was investigated using the aureusvirus Cucumber leaf spot virus (CLSV). Analysis of sg mRNA2 transcription indicated that it is synthesized by a premature termination mechanism. The results also implicated the transcriptional promoter, the attenuation signal, and global RNA folding of the viral genome as mediators of sg mRNA2 suppression. Additionally, evaluation of the transcriptional regulatory RNA elements in aureusviruses and related tombusviruses revealed alternative strategies for building functionally-equivalent stem-loop structures and showed that sequences encoding a critical and invariant amino acid can be successfully incorporated into essential long-distance tertiary RNA-RNA interactions.

Subgenomic mRNA transcription in Tombusviridae

“…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.…”

“…Additionally, the levels of sg mRNA accumulation can vary significantly. For instance, in the aureusvirus Cucumber leafspot virus (CLSV), sg mRNA1 is produced at significantly higher levels than sg mRNA2, 13 while the two corresponding sg mRNAs produced by TBSV accumulate to similar levels. 14 For carmoviruses, the smaller sg mRNA2 is expressed at higher levels than sg mRNA1.…”

“…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).…”

“…1). 13,[17][18][19] repositioning an internally-located genomic-like promoter to a 3'-terminal position (analogous to its position in genome replication), which is the greatly preferred location for efficient initiation of the RdRp. 32…”

“…3C). 13,36 Such diverse intervening distances both between and within viruses are probably consequences of "random" spatial proximity of RS elements to potential AS elements during genesis of the attenuator structures. That is, for an AS-RS element to originate, the RS element would have to encounter a compatible upstream partner sequence (i.e., pre-AS element) to base pair with and form an effective attenuation structure.…”