Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato

Abstract

Nucleotide binding site leucine-rich repeat (NLR) proteins of the plant innate immune system are negatively regulated by the miR482/2118 family microRNAs (miRNAs) that are in a distinct 22nt class of miRNAs with a double mode of action. First they cleave the target RNA, as with the canonical 21nt miR-NAs, and second they trigger secondary siRNA production using the target RNA as a template. Here we address the extent to which the miR482/2118 family affects expression of NLR mR-NAs and disease resistance. First we show that structural differences of miR482/2118 family members in tomato (Solanum lycopersicum) are functionally significant. The predicted target of the miR482 subfamily is conserved motif in multiple NLR mRNAs whereas, for miR2118b, it is a novel non-coding RNA target formed by rearrangement of several different NLR genes. From RNA sequencing and degradome data in lines expressing short tandem target mimic (STTM) RNAs of miR482/2118 we confirm the different targets of these miRNAs. The effect on NLR mRNA accumulation is slight but, nevertheless, the tomato STTM lines display enhanced resistance to infection with the oomycete and bacterial pathogens. These data implicate an RNA cascade of miRNAs and secondary siRNAs in the regulation of NLR RNAs and show that the encoded NLR proteins have a role in quantitative disease resistance in addition to dominant gene resistance that has been well characterized elsewhere. We also illustrate the use of STTM RNA in a biotechnological approach for enhancing quantitative disease resistance in highly bred cultivars. microRNA | NLR | siRNA | Solanum lycopersicum | Phytophthora infestans | Pseudomonas syringaeCorrespondence: dcb40@cam.ac.uk

The roles of rice microRNAs in rice-Magnaporthe oryzae interaction

“…In such cases, blocking or overexpressing a single miRNA can achieve up-or down-regulation of multiple genes, facilitating gene manipulation when these target genes have functional redundancy. For example, in tomato, blocking miR482 and miR2118 via STTM resulted in increased resistance to at least two different pathogens (Canto-Pastor et al 2019). Therefore, it would be worthwhile investigating the roles of miRNAs in rice-M. oryzae interaction and applying them to breeding programs to improve agronomic traits such as disease resistance.…”

Identification of potential genes for resistance to tomato spotted wilt and leaf spots in peanut (Arachis hypogaea L.) through GWAS analysis

“…RPPL1 (Putative disease resistance RPP13-like protein 1) and 205D04_12 (TIR-NBS-LRR disease resistance protein) are known to be related to plant defense responses. Canto-Pastor et al [46] reported that disease resistance protein (TIR-NBS-LRR class), retrovirus-related Pol polyprotein from transposon TNT 1-94 (KK1_048795), and transposon Ty3-I Gag-Pol polyprotein (KK1_043666) were targets of miR482/2118 members and they could affect expression of nucleotide binding site leucinerich repeat (NLR) mRNAs and disease resistance. NLR proteins of the plant innate immune system had a role in quantitative disease resistance in addition to dominant gene resistance that has been well characterized [46,47].…”

“…Canto-Pastor et al [46] reported that disease resistance protein (TIR-NBS-LRR class), retrovirus-related Pol polyprotein from transposon TNT 1-94 (KK1_048795), and transposon Ty3-I Gag-Pol polyprotein (KK1_043666) were targets of miR482/2118 members and they could affect expression of nucleotide binding site leucinerich repeat (NLR) mRNAs and disease resistance. NLR proteins of the plant innate immune system had a role in quantitative disease resistance in addition to dominant gene resistance that has been well characterized [46,47]. Signal transducer and activator of transcription A (LOC107484292) was identified with gene expression regulation related functions within the genome-wide significant association regions on LGB08, which had similar function with STAT1 in mammals (Additional file 8: Table S6).…”

“…Several reports have indicated that activation of the PKA/cAMP pathway could cause down-regulation of STAT1 activation [51][52][53]. KK1_048795 and KK1_043666 were reported to involve DNA integration and reverse transcriptase activity [46,54]. It seems possible that resistance to ELS and LLS were at least partially controlled by the same genes.…”

Expansion of MIR482/2118 by a class‐II transposable element in cotton

“…In dicots and gymnosperms, miR482/2118 members co-ordinately regulate many nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance genes by targeting their conserved P-loop domains (Zhai et al, 2011;Li et al, 2012;Shivaprasad et al, 2012;Zhu et al, 2013;Xia et al, 2015;Canto-Pastor et al, 2019), and are thought to be continually co-evolving with their resistance gene targets (Gonzalez et al, 2015;Zhang et al, 2016). miR482/2118 post-transcriptionally represses the transcript levels of NBS-LRR genes, but upon infection with viral, bacterial and fungal pathogens, miR482/2118 levels are themselves repressed to relieve the suppression of their target disease resistance genes (Shivaprasad et al, 2012;Zhu et al, 2013;Canto-Pastor et al, 2019), suggesting a critical role for the miR482/ 2118-NBS-LRR regulatory module in the balance of disease resistance and fitness of plants. Like most other plants, cotton contains hundreds of NBS-LRR genes with approximately 12% of them being targets of miR482/2118 (Zhu et al, 2013).…”