Arabidopsis SMN2/HEN2, Encoding DEAD-Box RNA Helicase, Governs Proper Expression of the Resistance Gene SMN1/RPS6 and Is Involved in Dwarf, Autoimmune Phenotypes of mekk1 and mpk4 Mutants

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 the proper function of SMN1/RPS6. The Gene Ontology enrichment analysis using RNA-seq data showed that defense genes were downregulated in smn2, suggesting a positive contribution of SMN2 to the genome-wide expression of defense 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 of Arabidopsis thaliana NLR genes by the spen protein FPA

“…Notably, we could also reannotate the chromosomal region around RPS6 itself. The extreme autoimmunity phenotypes of NMD mutants and mitogen-activated kinase pathway mutants require RPS6 but the mechanisms involved are not understood (Gloggnitzer et al, 2014;Takagi et al, 2020).…”

“…For example, null mutants defective in nonsense mediated RNA decay (NMD) are lethal in Arabidopsis because they trigger NLR RPS6-dependent autoimmunity (Gloggnitzer et al, 2014). Conversely, mutations in the RNA exosome, which degrades RNAs in a 3′ to 5′ direction, suppress RPS6-dependent autoimmune phenotypes (Takagi et al, 2020). Fine tuning of different levels of NLR control may be integrated to produce quantitative patterns of disease resistance (Corwin and Kliebenstein, 2017), but our understanding of how this occurs globally is fragmentary and incomplete (Adachi et al, 2019).…”

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

“…For example, our reannotation of the RPS6 locus is essential to understand the recurring role of RPS6 in autoimmunity. The autoimmune phenotypes of mutants defective in NMD or the mitogen-activated kinase pathway are RPS6 dependent, but the mechanisms involved are unclear (Gloggnitzer et al, 2014;Takagi et al, 2020). We found that RPS6 is transcribed through a previously unrecognised downstream gene that encodes an RPS6like TIR domain.…”

“…Notably, we could also reannotate the chromosomal region around RPS6 itself. The extreme autoimmunity phenotypes of NMD mutants and mitogen-activated kinase pathway mutants require RPS6 but the mechanisms involved are not understood (Gloggnitzer et al, 2014;Takagi et al, 2020). Nanopore DRS indicates that the 3′UTR of RPS6 is complex, with multiple splicing events and poly(A) sites (Figure 3C).…”

PAMP-triggered Genetic Reprogramming Involves Widespread Alternative Transcription Initiation and an Immediate Transcription Factor Wave

“…Incidentally, in addition to facilitation of eRNA detection, an assessment of the relevance of nuclear exosomal RNA decay for PTI activation has merit on its own. In yeast, there is evidence that mechanisms of alternative transcription termination coupled to exosome-mediated nuclear pre-mRNA decay contribute to shape rapid reprogramming of gene expression in response to stress (Bresson et al 2017), and a recent study in Arabidopsis provided an example of requirement of HEN2 for expression of a specific intracellular immune receptor (RPS6) (Takagi et al 2020), belonging to the Nucleotide Binding-Leucine Rich Repeat (NB-LRR)-class well known to be induced in PTI (Navarro et al 2004).…”