Biogenesis, Function, and Applications of Virus-Derived Small RNAs in Plants

Abstract

RNA silencing, an evolutionarily conserved and sequence-specific gene-inactivation system, has a pivotal role in antiviral defense in most eukaryotic organisms. In plants, a class of exogenous small RNAs (sRNAs) originating from the infecting virus called virus-derived small interfering RNAs (vsiRNAs) are predominantly responsible for RNA silencing-mediated antiviral immunity. Nowadays, the process of vsiRNA formation and the role of vsiRNAs in plant viral defense have been revealed through deep sequencing of sRNAs and diverse genetic analysis. The biogenesis of vsiRNAs is analogous to that of endogenous sRNAs, which require diverse essential components including dicer-like (DCL), argonaute (AGO), and RNA-dependent RNA polymerase (RDR) proteins. vsiRNAs trigger antiviral defense through post-transcriptional gene silencing (PTGS) or transcriptional gene silencing (TGS) of viral RNA, and they hijack the host RNA silencing system to target complementary host transcripts. Additionally, several applications that take advantage of the current knowledge of vsiRNAs research are being used, such as breeding antiviral plants through genetic engineering technology, reconstructing of viral genomes, and surveying viral ecology and populations. Here, we will provide an overview of vsiRNA pathways, with a primary focus on the advances in vsiRNA biogenesis and function, and discuss their potential applications as well as the future challenges in vsiRNAs research.

Different Virus-Derived siRNAs Profiles between Leaves and Fruits in Cucumber Green Mottle Mosaic Virus-Infected Lagenaria siceraria Plants

“…Through the process, virus-infected plants produce virus-derived small interfering RNAs (vsiRNAs) which play important roles in host antiviral defense (Zhu et al, 2011; Szittya and Burgyán, 2013; Zhang et al, 2015). The endoribonuclease activity of the dicer-like proteins (DCLs) 2 and 4 is essential for the production of these vsiRNAs (Deleris et al, 2006).…”

“…In general, 21-nt vsiRNAs usually predominate in the population, there is a strong A/U bias at the first nucleotide of vsiRNAs, and vsiRNA-producing hotspots can be identified within the viral genome (Miozzi et al, 2013; Visser et al, 2014; Xia et al, 2014; Yang et al, 2014; Kutnjak et al, 2015; Li et al, 2016). Previous studies indicated that vsiRNAs are predominantly responsible for RNA silencing-mediated antiviral immunity and the main function of vsiRNAs is to target and degrade viral mRNA through post-transcriptional gene silencing in plants (Zhu et al, 2011; Zhang et al, 2015). Moreover, recent studies have shown that vsiRNAs may also occasionally regulate host mRNAs with near perfect complementarity.…”

Plant immunity against viruses: antiviral immune receptors in focus

“…2). For more detailed information, a collection of excellent, updated reviews describing antiviral RNA silencing mechanisms and suppressors is available (Carbonell and Carrington, 2015;Csorba et al, 2015;Zhang et al, 2015). The diversity in RNAi mechanisms relies mainly on the existence of multiple copies of AGO (Argonaute), RNAdependent RNA polymerase (RDR), DRB (double-stranded RNA binding) and DCL (Dicer-like) genes, which probably result from gene duplication followed by specialization (Parent et al, 2015;Zhang et al, 2015).…”

“…LNYV P impairs RNA silencing through inhibition of micro RNA (miRNA)-guided AGO1 cleavage and translational repression and also compromises RDR6/SGS3-dependent amplification of silencing (Mann et al, 2016). One of the best-characterized suppressors of antiviral RNA silencing is the potyviral helper component proteinase (HCPro), which plays multiple roles in the suppression of vsiRNA biogenesis, such as ds-siRNA binding, HEN1 binding, blocking HEN1 methyltransferase activity, blocking primary siRNA biogenesis by RAV2 interaction and downregulating RDR6 (Zhang et al, 2015). A recent study suggested two mechanisms by which HCPro exerts its RNA silencing suppressor functions (Ivanov et al, 2016).…”

Small RNA Based Genetic Engineering for Plant Viral Resistance: Application in Crop Protection

“…In Arabidopsis many studies have shown that DCL2, DCL4, AGO1, AGO2, RDR1, and RDR6 are the major components in antiviral RNA silencing (Carbonell and Carrington, 2015; Zhang et al, 2015). It is suggested that the double stranded replicative intermediates of RNA viruses or structured single stranded viral RNA can be processed by plant DCL4 or DCL2 into primary viral siRNAs (Voinnet, 2005; Bouche et al, 2006; Deleris et al, 2006; Ding and Voinnet, 2007).…”