Convergent Epigenetic Mechanisms Avoid Constitutive Expression of Immune Receptor Gene Subsets

Abstract

The gene pool encoding PRR and NLR immune receptors determines the ability of a plant to resist microbial infections. Basal expression of these genes is prevented by diverse mechanisms since their hyperactivity can be harmful. To approach the study of epigenetic control of PRR/NLR genes we here analyzed their expression in mutants carrying abnormal repressive 5-methyl cytosine (5-mC) and histone 3 lysine 9 dimethylation (H3K9me2) marks, due to lack of MET1, CMT3, MOM1, SUVH4/5/6, or DDM1. At optimal growth conditions, none of the mutants showed basal expression of the defense gene marker PR1, but all of them had greater resistance to Pseudomonas syringae pv. tomato than wild type plants, suggesting they are primed to stimulate immune cascades. Consistently, analysis of available transcriptomes indicated that all mutants showed activation of particular PRR/NLR genes under some growth conditions. Under low defense activation, 37 PRR/NLR genes were expressed in these plants, but 29 of them were exclusively activated in specific mutants, indicating that MET1, CMT3, MOM1, SUVH4/5/6, and DDM1 mediate basal repression of different subsets of genes. Some epigenetic marks present at promoters, but not gene bodies, could explain the activation of these genes in the mutants. As expected, suvh4/5/6 and ddm1 activated genes carrying 5-mC and H3K9me2 marks in wild type plants. Surprisingly, all mutants expressed genes harboring promoter H2A.Z/H3K27me3 marks likely affected by the chromatin remodeler PIE1 and the histone demethylase REF6, respectively. Therefore, MET1, CMT3, MOM1, SUVH4/5/6, and DDM1, together with REF6, seemingly contribute to the establishment of chromatin states that prevent constitutive PRR/NLR gene activation, but facilitate their priming by modulating epigenetic marks at their promoters.

Coordinated Epigenetic Regulation in Plants: A Potent Managerial Tool to Conquer Biotic Stress

“…In general, Arabidopsis mutant plants with DNA hypomethylation are more resistant to disease and exhibit an elevated SA-dependent response. For example, met1 , drm1/drm2 and drm1/drm2/cmt3 ( ddc ), nrpd1 (PolIV mutant), nrpe1 (PolV mutant), nrpd1/nrpe1 , nrpd2 (subunit shared by PolIV and PolV), drd1 ( defective in RNA-directed DNA methylation ), rdr2 , and dcl2/3/4 are more resistant to the bacterial pathogen Pst ; cmt3 , drd1 , and nrpe1 are more resistant to the obligate biotrophic oomycete pathogen Hyaloperonospora arabidopsidis ( Hpa ; Lopez et al, 2011 ; Dowen et al, 2012 ; Yu et al, 2013 ; Lopez Sanchez et al, 2016 ; Cambiagno et al, 2021 ; Table 1 and Figure 1A ).…”

“…In addition to DNA methylation on TEs regulating the transcription of neighboring NLR genes ( Dowen et al, 2012 ), some NLR loci or clusters associated with TEs are also controlled by histone marks, such as H3K9me2 ( Lai and Eulgem, 2018 ). Through Arabidopsis mutant screening, the methylation of DNA and H3K9 was observed to regulate resistance against Pst infection ( Cambiagno et al, 2021 ) and infestation by the pest, green peach aphid Myzus persicae ( Annacondia et al, 2021 ). The study revealed that nrpd1 and kyp mutant plants are more resistant to aphids ( Annacondia et al, 2021 ).…”

“…Whether and how does the crosstalk between DNA and H3K9 methylation contribute to aphid resistance is still largely unknown. The drm1/drm2 , ddc , and suvh4/5/6 mutant plants do not exhibit constitutive expression of the defense gene marker PR1 (PATHOGENESIS-RELATED GENE 1) but are more resistant to Pst due to a faster and stronger PR1 induction after Pst infection compared to wild-type plants ( Cambiagno et al, 2021 ). This suggest that drm1/drm2 , ddc , and suvh4/5/6 mutant plants acquired a primed state of defense against Pst , which is regulated by both DNA and H3K9 methylation levels.…”

“…For instance, Swi2/Snf2-related 1 (SWR1) complex replaces the histone H2A with the histone variant H2A.Z to maintain the suppression of several SA-dependent defense genes ( March-Diaz et al, 2008 ). These genes include CLASSY1 (CLSY1), which is implicated in the RdDM pathway, is required for accumulation of hc-siRNA, and interacts with H3K9 methylation ( Luna and Ton, 2012 ; Zhang et al, 2013 ; Zhou et al, 2018 ), as well as DDM1, which is required for DNA methylation and regulates expression of NLRs ( Jeddeloh et al, 1998 , 1999 ; Stokes et al, 2002 ; Li et al, 2010 ; Cambiagno et al, 2021 ). In addition, the expression of NLR SNC1 is suppressed by SPLAYED (SYD), another SWI2/SNF2-like ATPase, which is confirmed by the elevated transcription in the syd mutant.…”

Genome-Wide Characterization of the Methyl CpG Binding Domain-Containing Proteins in Watermelon and Functional Analysis of Their Roles in Disease Resistance Through Ectopic Overexpression in Arabidopsis thaliana

“…Importantly, DNA methylation, as one of the epigenetic regulation mechanisms, plays crucial roles in plant immunity ( Huang and Jin, 2022 ); for example, Arabidopsis mutants with DNA hypomethylation are more resistant to Pseudomonas syringae pv. tomato ( Pst ) DC3000 and exhibit an elevated salicylic acid (SA)-dependent response ( Dowen et al, 2012 ; Yu et al, 2013 ; Cambiagno et al, 2021 ).…”