A conserved RNA structure is essential for a satellite RNA-mediated inhibition of helper virus accumulation

Abstract

As a class of parasitic, non-coding RNAs, satellite RNAs (satRNAs) have to compete with their helper virus for limited amounts of viral and/or host resources for efficient replication, by which they usually reduce viral accumulation and symptom expression. Here, we report a cucumber mosaic virus (CMV)-associated satRNA (sat-T1) that ameliorated CMV-induced symptoms, accompanied with a significant reduction in the accumulation of viral genomic RNAs 1 and 2, which encode components of the viral replicase. Intrans replication assays suggest that the reduced accumulation is the outcome of replication competition. The structural basis of sat-T1 responsible for the inhibition of viral RNA accumulation was determined to be a three-way branched secondary structure that contains two biologically important hairpins. One is indispensable for the helper virus inhibition, and the other engages in formation of a tertiary pseudoknot structure that is essential for sat-T1 survival. The secondary structure containing the pseudoknot is the first RNA element with a biological phenotype experimentally identified in CMV satRNAs, and it is structurally conserved in most CMV satRNAs. Thus, this may be a generic method for CMV satRNAs to inhibit the accumulation of the helper virus via the newly-identified RNA structure.

The evolution of cheating in viruses

“…c, d In Vesicular Stomatitis Virus (VSV), when a defective interfering genome (labelled in green) is grown in a mixed infection with wild-type VSV (labelled in red), the defective interfering genome exploits replicase proteins encoded by the wild-type cooperator, resulting in a colony (c) that is dominated by the defective interfering genome, and grows less effectively than a colony consisting just of the cooperative wild-type (d) 144 . e, f In cucumber mosaic virus (CMV) infections, a satellite (satCMV) exploits gene products encoded by the wild-type, substantially reducing the overall viral load and leading to less severe infections in plants infected by both satellite and wild type (e) compared to plants infected by just the wild type (f) 145 . Panel a from Per Harald Olsen (CC BY-SA 3.0), no changes made, reference 146 .…”

High-Throughput Sequencing Discloses the Cucumber Mosaic Virus (CMV) Diversity in Slovakia and Reveals New Hosts of CMV from the Papaveraceae Family

“…The occurrence of CMV sat-RNA is considered generally low and the symptoms exacerbating CMV sat-RNA are rarest, while symptom attenuation is the most common effect of CMV sat-RNA observed [8]. Symptom attenuation can be expected, as the sat-RNA and helper virus compete for limited virus and host resources for replication [49]. It was also proven that cross-protection can be used using stand-alone non-necrogenic CMV sat-RNA [50], without its helper virus, to prevent severe symptom development after secondary infection by a necrogenic sat-RNA including a CMV strain.…”

“…In terms of genetic variability, sat-RNAs are much more diverse when compared with other RNA genomes, which could be accounted for by lower negative selection, as the sat-RNA itself is not vital for the virus [8]. Still, a partially conserved structure was reported for CMV sat-RNA-mediated inhibition of CMV accumulation, specifically inhibition of RNA1 and RNA2 accumulation by biologically relevant structures within the sat-RNA genome, predicted to be present in 70% of CMV sat-RNAs [49].…”

Transgenic approaches for plant disease control: Status and prospects 2021

“…the first example was with cucumber mosaic virus (CMV) in tobacco (Harrison et al, 1987). The satellite RNAs show low sequence homology with their helper virus, but a conserved RNA structure is needed that competes with the virus for replication (He et al, 2019).…”