Small RNA derived from Tobacco mosaic virus targets a host C2-domain abscisic acid-related (CAR) 7-like protein gene

Tobacco mosaic virus (TMV) is a positive-sense single-stranded RNA virus. The 3′ end of TMV genome is consisted of an upstream pseudoknot domain (UPD) and a tRNA-like structure (TLS), both of which are important RNA elements to enhance TMV replication and translation. Deep-sequencing analysis revealed that TMV-specific viral small interfering RNAs (vsiRNAs) were generated in TMV-infected Nicotiana benthamiana plants. A vsiRNA derived from the juxtaposition between UPD and TLS, named TMV-vsiRNA 22 nt (6285–6306), possessed high sequence complementarity to a host gene which encodes a C2-domain abscisic acid (ABA)-related (CAR) 7-like protein. CAR proteins play a critical role in ABA signaling pathway. The CAR protein-encoding gene was amplified from N. benthamiana leaves and termed as Nb-CAR7. In TMV-infected plants, accumulation of Nb-CAR7 transcripts was significantly decreased, as compared with that of mock-inoculated and TMV-43A-infected plants. TMV-43A is a mutant without the UPD sequence in its genome. Overexpression of Nb-CAR7 led to decreased TMV RNA accumulation in the TMV-inoculated leaves. Silencing of Nb-CAR7 enhanced TMV replication and resulted in a higher viral RNA accumulation. In addition, the expression level of Nb-CAR7 was positively correlated to that of a low-temperature-induced ABA responsive gene (LTI65). The effect of Nb-CAR7 on TMV RNA accumulation in host plants was linked to ABA signaling pathway. In conclusion, a vsiRNA derived from the juxtaposition between UPD and TLS at the 3′UTR of TMV targets a host CAR7 gene.