Differential expression of cucumber RNA‐dependent RNA polymerase 1 genes during antiviral defence and resistance

Abstract

RNA-dependent RNA polymerase 1 (RDR1) plays a crucial role in plant defence against viruses. In this study, it was observed that cucumber, Cucumis sativus, uniquely encodes a small gene family of four RDR1 genes. The cucumber RDR1 genes (CsRDR1a, CsRDR1b and duplicated CsRDR1c1/c2) shared 55%-60% homology in their encoded amino acid sequences. In healthy cucumber plants, RDR1a and RDR1b transcripts were expressed at higher levels than transcripts of RDR1c1/c2, which were barely detectable. The expression of all four CsRDR1 genes was induced by virus infection, after which the expression level of CsRDR1b increased 10-20-fold in several virus-resistant cucumber cultivars and in a broad virus-resistant transgenic cucumber line expressing a high level of transgene small RNAs, all without alteration in salicylic acid (SA) levels. By comparison, CsRDR1c1/c2 genes were highly induced (25-1300-fold) in susceptible cucumber cultivars infected with RNA or DNA viruses. Inhibition of RDR1c1/c2 expression led to increased virus accumulation. Ectopic application of SA induced the expression of cucumber RDR1a, RDR1b and RDRc1/c2 genes. A constitutive high level of RDR1b gene expression independent of SA was found to be associated with broad virus resistance. These findings show that multiple RDR1 genes are involved in virus resistance in cucumber and are regulated in a coordinated fashion with different expression profiles.

In silico prediction and segregation analysis of putative virus defense genes based on SSR markers in sweet potato F1 progenies of cultivars New Kawogo and Resisto

“…Plant gene products, such as the RNA dependent RNA polymerases (RDRs), are part of the gene silencing machinery that independently synthesizes viral dsRNA in an amplification step for viral small RNA (21 to 24 nts) production. The dsRNAs are processed by Dicer-like (DCL) proteins to small RNAs, which are subsequently incorporated into the RNA-induced silencing complex with an Argonaute (AGO) protein that uses complementary small RNAs to target viral RNA (Baulcombe, 2004;Peragine et al, 2004;Hunter et al, 2016;Leibman et al, 2017). Thus, identification of putative defense genes involved in gene silencing is important in plant breeding for the management of virus diseases.…”

“…Defense genes have been studied and identified/ predicted in silico in species such as Nicotiana benthamiana (Baulcombe, 2004), cucumber (Leibman et al, 2017), potato (Hunter et al, 2016), and cassava (Chellappan et al, 2004); however, the identity and nature of segregation and inheritance of defense genes in sweet potato require investigation. Different methods (webservers) of gene prediction and alignment have been developed.…”

Analysis of RDR1/RDR2/RDR6‐independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals unexplained types of short interfering RNA loci

“…RNA‐dependent RNA polymerases (RDRs) are a family of proteins that produce double‐stranded small RNA (sRNA) precursors by synthesizing the complementary strand of a single‐stranded RNA molecule (Baulcombe, ; Wassenegger and Krczal, ; Willmann et al ., ). Six RDR s, divided into the RDR α (consisting of RDR1 , RDR2 and RDR6 ) (Leibman et al ., ) and RDR γ (consisting of RDR3 , RDR4 and RDR5 ) subclades (Willmann et al ., ), are encoded by the Arabidopsis thaliana genome. RDR6 in concert with the RNase‐III like enzyme DICER‐LIKE 4 (DCL4) is necessary for the production of phased short interfering RNAs (siRNAs) (Bouché et al ., ; Howell et al ., ).…”

“…RDR2 and DCL3 are involved in the biogenesis of repeat‐associated siRNAs (Matzke et al ., ). RDR1 is involved with defense responses by converting viral‐derived single‐stranded RNAs into double‐stranded RNAs (Leibman et al ., ), which are then metabolized by DCL4 (or DCL2 when DCL4 function is ablated) (Bouché et al ., ; Diaz‐Pendon et al ., ). At least one study suggests that RDR1 is also involved in endogenous gene regulation (Lam et al ., ).…”

Analysis of RDR1/RDR2/RDR6-independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals novel siRNA loci

“…RNA DEPENDENT RNA POLYMERASES (RDRs) are a family of proteins that produce double-stranded small RNA (sRNA) precursors by synthesizing the complementary strand of a single-stranded RNA molecule (Baulcombe., 2004;Wassenegger and Krczal., 2006;Willmann et al, 2011). Six RDRs, divided into the RDRα (consisting of RDR1, RDR2, and RDR6) (Leibman et al 2017) and RDRγ sub-clades (consisting of RDR3, RDR4, and RDR5) (Willmann et al, 2011), are encoded by the Arabidopsis thaliana genome. RDR6 in concert with the RNAse-III like enzyme DICER-LIKE 4 (DCL4) is necessary for the production of phased short interfering RNAs (siRNAs) (Bouché et al,2006;Howell et al, 2007).…”