Arabidopsis SMN2/HEN2, Encoding DEAD-box RNA Helicase, Governs Proper Expression of the Resistance GeneSMN1/RPS6and Is Involved in Dwarf, Autoimmune Phenotypes ofmekk1andmpk4Mutants

Abstract

In Arabidopsis thaliana, a mitogen-activated protein kinase pathway, MEKK1–MKK1/MKK2–MPK4, is important for basal resistance, and disruption of this pathway results in dwarf, autoimmune phenotypes. To elucidate the complex mechanisms activated by the disruption of this pathway, we have previously developed a mutant screening system based on a dwarf autoimmune line that overexpressed the N-terminal regulatory domain of MEKK1. Here, we report that the second group of mutants, smn2, had defects in the SMN2 gene, encoding a DEAD-box RNA helicase. SMN2 is identical to HEN2, whose function is vital for the nuclear RNA exosome because it provides non-ribosomal RNA specificity for RNA turnover, RNA quality control, and RNA processing. Aberrant SMN1/RPS6 transcripts were detected in smn2 and hen2 mutants. Disease resistance against Pseudomonas syringae pv. tomato DC3000 (hopA1), which is conferred by SMN1/RPS6, was decreased in smn2 mutants, suggesting a functional connection between SMN1/RPS6 and SMN2/HEN2. We produced double mutants mekk1smn2 and mpk4smn2 to determine whether the smn2 mutations suppress the dwarf, autoimmune phenotypes of the mekk1 and mpk4 mutants, as the smn1 mutations do. As expected, the mekk1 and mpk4 phenotypes were suppressed by the smn2 mutations. These results suggested that SMN2 is involved in proper function of SMN1/RPS6. The GO enrichment analysis using RNA-seq data showed that defense genes were downregulated in smn2, suggesting positive contribution of SMN2 to genome-wide expression of defense-related genes. In conclusion, this study provides novel insight into plant immunity via SMN2/HEN2, an essential component of the nuclear RNA exosome.

Widespread premature transcription termination ofArabidopsis thalianaNLR genes by the spen protein FPA

“…NLRs function in the immune response of plants and animals, where they sense the presence of pathogens or pathogen activity, for example by detecting pathogen effectors (Jones et al, 2016;Tamborski & Krasileva, 2020;Wu et al, 2017). (Gloggnitzer et al, 2014;Takagi et al, 2020). We found that RPS6 is transcribed through a previously unrecognised downstream gene that encodes an RPS6-like TIR domain.…”

“…Notably, we could also reannotate the chromosomal region around RPS6 (AT5G46470). The extreme autoimmunity phenotypes of NMD mutants and mitogen activated kinase pathway mutants are caused by the dysregulation of RPS6 but the mechanisms involved are not understood (Gloggnitzer et al, 2014;Takagi et al, 2020). Our nanopore DRS analysis reveals a long and complex RPS6 3'UTR, with multiple exons and alternative poly(A) sites ( Figure 5 -supplement 3).…”

“…We show that the expression of the downstream gene is dependent on the RNA exosome component HEN2. Mutations in HEN2 were recently identified as suppressors of RPS6-dependent autoimmune phenotypes (Takagi et al, 2020). Consequently, accurate annotation of complex NLR loci facilitates the interpretation of basic features of NLR function.…”

“…For example, null mutants defective in non-sense mediated RNA decay (NMD) are lethal in Arabidopsis because they trigger autoimmunity dependent on the NLR gene RPS6 (AT5G46470) (Gloggnitzer et al, 2014). Most recently, mutations in the RNA exosome, which degrades RNAs in a 3' to 5' direction, were reported to suppress autoimmunity by disrupting the function of RPS6 (Takagi et al, 2020). The signalling and activity of NLR proteins is controlled by intra and intermolecular protein interactions (Adachi et al, 2019).…”