Plant viruses are often accompanied by small parasitic RNAs termed satellite RNAs. Satellite RNAs range in size from ~220 to 1400 nucleotides (nt) in length and depend on their associated viruses (known as the helper virus) for replication, encapsidation, movement and transmission, but share little or no sequence homology to the helper virus itself. Most satellite RNAs do not encode functional proteins, yet can induce disease symptoms which range from chlorosis and necrosis, to total death of the infected plant. How such non-protein-coding RNA pathogens induce disease symptoms has been a longstanding question.
Early studies showed that the pathogenicity of a satellite RNA is determined at the nucleotide level, with one to several nucleotide changes dramatically altering both the virulence and host specificity of disease induction. Subsequent studies demonstrated that satellite RNA replication is associated with the accumulation of high levels of satellite RNA-derived small interfering RNAs (siRNA). These findings led to the suggestion that pathogenic satellite-derived siRNAs might have sequence complementarity to a physiologically important host gene, and that the observed disease symptoms are in fact due to satellite siRNA-directed silencing of the targeted host gene. However, to date, no such host gene has been identified, leaving the satellite RNA-induced disease mechanism unsolved.
This paper explores the sRNA-mediated disease mechanism using the Y-satellite of Cucumber mosaic virus (CMV Y-Sat). The CMV Y-Sat consists of a 369-nt single-stranded RNA genome and induces distinct yellowing symptoms in a number of Nicotiana species including N. tabacum (tobacco). Y-Sat-induced yellowing symptoms result from Y-Sat siRNA-directed silencing of the host chlorophyll biosynthetic gene, CHLI, and Y-Sat-induced symptoms can be prevented by transforming tobacco with a silencing-resistant version of CHLI. The observed species specificity of Y-Sat-induced disease symptoms is due to natural sequence variation within the targeted region of the CHLI transcript.
Viral Small Interfering RNAs Target Host Genes to Mediate Disease Symptoms in Plants. (2011) PLoS Pathog 7(5): e1002022. doi:10.1371/journal.ppat.1002022
The Cucumber mosaic virus (CMV) Y-satellite RNA (Y-Sat) has a small non-protein-coding RNA genome that induces yellowing symptoms in infected Nicotiana tabacum (tobacco). How this RNA pathogen induces such symptoms has been a longstanding question. We show that the yellowing symptoms are a result of small interfering RNA (siRNA)-directed RNA silencing of the chlorophyll biosynthetic gene, CHLI. The CHLI mRNA contains a 22-nucleotide (nt) complementary sequence to the Y-Sat genome, and in Y-Sat-infected plants, CHLI expression is dramatically down-regulated. Small RNA sequencing and 5′ RACE analyses confirmed that this 22-nt sequence was targeted for mRNA cleavage by Y-Sat-derived siRNAs. Transformation of tobacco with a RNA interference (RNAi) vector targeting CHLI induced Y-Sat-like symptoms. In addition, the symptoms of Y-Sat infection can be completely prevented by transforming tobacco with a silencing-resistant variant of the CHLI gene. These results suggest that siRNA-directed silencing of CHLI is solely responsible for the Y-Sat-induced symptoms. Furthermore, we demonstrate that two Nicotiana species, which do not develop yellowing symptoms upon Y-Sat infection, contain a single nucleotide polymorphism within the siRNA-targeted CHLI sequence. This suggests that the previously observed species specificity of Y-Sat-induced symptoms is due to natural sequence variation in the CHLI gene, preventing CHLI silencing in species with a mismatch to the Y-Sat siRNA. Taken together, these findings provide the first demonstration of small RNA-mediated viral disease symptom production and offer an explanation of the species specificity of the viral disease.