Innate Immunity Activation and RNAi Interplay in Citrus Exocortis Viroid—Tomato Pathosystem

Abstract

Although viroids are the smallest and simplest plant pathogens known, the molecular mechanisms underlying their pathogenesis remain unclear. To unravel these mechanisms, a dual approach was implemented consisting of in silico identification of potential tomato silencing targets of pospiviroids, and the experimental validation of these targets through the sequencing of small RNAs and RNA ends extracted from tomatoes infected with a severe isolate of Citrus exocortis viroid (CEVd). The generated RNA ends were also used to monitor the differentially-expressed genes. These analyses showed that when CEVd symptoms are well established: (i) CEVd are degraded by at least three Dicer-like (DCL) proteins and possibly by RNA-induced silencing complex (RISC), (ii) five different mRNAs are partially degraded through post-transcriptional gene silencing (PTGS), including argonaute 2a, which is further degraded in phasiRNAs, (iii) Dicer-like 2b and 2d are both upregulated and degraded in phasiRNAs, and (iv) CEVd infection induced a significant shift in gene expression allowing to explain the usual symptoms of pospiviroids on tomato and to demonstrate the constant activation of host innate immunity and systemic acquired resistance (SAR) by these pathogenic RNAs. Finally, based on in silico analysis, potential immunity receptor candidates of viroid-derived RNAs are suggested.

Transcriptomic analysis reveals insights into the response to Hop stunt viroid (HSVd) in sweet cherry (Prunus avium L.) fruits

“…However, changes in the expression of genes that were associated with brassinosteroid (BA) and gibberellin (GA) metabolism or response were not observed in the present study. Similarly, genes involved in SA, JA, ET and ABA biosynthesis and responses were observed in CBCVd-infected hops and CEVd-infected tomato ( Mishra et al, 2018 ), and no significantly different genes were associated with BA-or GA-dependent pathways in CEVd-infected tomato ( Thibaut & Claude, 2018 ).…”

Current overview on viroid–host interactions

“…Using computer‐based target prediction algorithms coupled with molecular biology experiments, it was shown that a single vd‐sRNA is capable of inducing the RNA silencing of more than one host defense gene in a PSTVd‐tomato combination (Adkar‐Purushothama & Perreault, ). Several research groups have demonstrated the involvement of vd‐sRNAs in the down regulation of host genes using different approaches (summarized in Table ) (Adkar‐Purushothama et al, , ; Aviña‐Padilla et al, ; Aviña‐Padilla, Rivera‐Bustamante, Kovalskaya, & Hammond, ; Thibaut & Claude, ; Wang et al, ).…”

Impact of Nucleic Acid Sequencing on Viroid Biology

“…The direct interaction between vd-sRNA and the predicted host target sequence was demonstrated by expressing the PSTVd-sRNA that was predicted to target the callose synthase gene in an artificial miRNA experiment in a transient expression system [ 144 ]. Based on both in silico and in vivo studies, several research groups have demonstrated the involvement of vd-sRNAs in the down regulation of host genes [ 145 , 146 , 147 , 148 , 149 , 150 , 151 ]. This was recently reviewed elsewhere [ 114 ].…”

“…This is done by comparing the transcription data obtained from a control plant at a given moment, such as at a specific developmental stage or under a specific physiological condition, with that from an infected plant, as well as by comparing the data from normal and diseased tissues. Prior to RNA-seq, differential gene expression studies in viroid infected plants were performed using both macro- and microarrays [ 138 , 150 , 156 , 157 , 158 , 159 , 160 ]. Although these technologies required a priori knowledge of the sequence, as well as presenting technical concerns over issues such as cross-hybridization, poor quantification of both lower and highly expressed RNAs [ 161 ], the data obtained suggested that global transcriptomic alterations were triggered by viroid infection.…”