Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology

Abstract

The major components of RNA silencing include both transitive and systemic small RNAs, which are technically called secondary sRNAs. Double-stranded RNAs trigger systemic silencing pathways to negatively regulate gene expression. The secondary siRNAs generated as a result of transitive silencing also play a substantial role in gene silencing especially in antiviral defense. In this review, we first describe the discovery and pathways of transitivity with emphasis on RNA-dependent RNA polymerases followed by description on the short range and systemic spread of silencing. We also provide an in-depth view on the various size classes of secondary siRNAs and their different roles in RNA silencing including their categorization based on their biogenesis. The other regulatory roles of secondary siRNAs in transgene silencing, virus-induced gene silencing, transitivity, and trans-species transfer have also been detailed. The possible implications and applications of systemic silencing and the different gene silencing tools developed are also described. The details on mobility and roles of secondary siRNAs derived from viral genome in plant defense against the respective viruses are presented. This entails the description of other compatible plant–virus interactions and the corresponding small RNAs that determine recovery from disease symptoms, exclusion of viruses from shoot meristems, and natural resistance. The last section presents an overview on the usefulness of RNA silencing for management of viral infections in crop plants.

Viral suppressors from members of the family Closteroviridae combating antiviral RNA silencing: a tale of a sophisticated arms race in host-pathogen interactions

“…The mechanism of antiviral RNA silencing in plants reveals a related process, termed as post-transcriptional gene silencing (PTGS). Recently, biological evidences have indicated that PTGS and transcriptional gene silencing (TGS), induced by endogenic small RNAs (sRNAs), are evolving as significantly crucial drivers of ETI and PTI signaling pathways, as well as R gene expression (Zhai et al 2011;Baltusnikas et al 2018;Tan et al 2020;Sanan-Mishra et al 2021). Furthermore, several classes of microorganisms, such as plant viruses, bacteria, and oomycetes, have been discovered to produce suppressor proteins as part of their virulence effectors, to suppress RNA silencing in host plants and cause disease (Navarro et al 2008;He et al 2019).…”

Non-Coding RNAs in Response to Drought Stress

“…The lncRNAs can also guide gene silencing through siRNA-dependent DNA methylation [47]. The role of small RNA-directed DNA methylation (RdDM) and heterochromatinization has been well studied in plants [138][139][140]. The plant-specific RNA polymerases, RNA Pol IV and V play a crucial role in this process [24,51,[141][142][143][144].…”

“…Briefly, Pol IV, along with the CLASSY chromatin remodeling factors (CCRFs) and homeodomain transcription factors, such as DTF1/ SHH1, transcribes transposons and repetitive sequences. The transcripts are converted to double-stranded RNAs (dsRNAs) by the action of RNA-dependent RNA polymerase-2 (RDR2) and the dsRNAs are processed into small ncRNAs, specifically siRNA duplexes by Dicer-like 3 (DCL3) enzyme [138,139]. These siRNAs are loaded in Argonaute 4 (AGO4)-containing complex to guide RdDM.…”

“…The small ncRNAs comprise a number of categories among which the miRNAs and siRNAs constitute the major groups. They function as key regulators of transcriptional and post-transcriptional gene expression [139,[150][151][152] and are therefore implicated in the control of various physiological and developmental processes in plants, such as growth, organ formation, phase transition, nutrient balance and stress response [10,22,[153][154][155][156]. Several online tools and databases have been developed that have enabled the prediction, documentation and analysis of the small ncRNAs and their targets [48,57,124].…”

“…Overall, siRNAs are generally 21-24 nt in length and are produced by the sequential processing of long dsRNAs in a phased or non-overlapping manner. They may arise either from endogenous sources, such as TEs, repetitive elements and centromere, or exogenous sources, such as invading viruses or aberrant inverted repeats [139,160]. The siRNAs can target endogenous as well as exogenous sequences serving as the first line of host defense [161].…”