Convergent Epigenetic Mechanisms Avoid Constitutive Expression of Immune Receptor Gene Subsets.

Damián Alejandro Cambiagno,José Roberto Torres,María Elena Alvarez

doi:10.3389/fpls.2021.703667

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.

Highlights

Plant genomes encode for large families of immune receptor proteins that perceive the presence of pathogens and activate defenses
Likewise, when we extended the analysis to Pattern recognition receptors (PRR)/nucleotidebinding leucine-rich repeat (LRR) proteins (NLR) genes from all available samples, met1 samples were grouped together (Figure 2D), mom1 and cmt3 were close to different mutants depending on the dataset, and suvh4/5/6 and ddm1 tended to cluster, consistently with previous results (Figure 2A)
We further evaluated the chromatin states of all induced PRR/NLR genes described in Figures 2B,C, to know whether epigenetic features of promoters or coding sequences correlate with their expression in the mutants

Summary

Introduction

Plant genomes encode for large families of immune receptor proteins that perceive the presence of pathogens and activate defenses. PRR/NLR receptors are master regulators of immune cascades that affect the expression of thousands of defense genes (Block and Alfano, 2011; Macho and Zipfel, 2014). Their activity is regulated at transcriptional and post-transcriptional levels by convergent mechanisms that maximize defenses with low fitness costs, since overstimulation of immune responses can lead to reduced growth or seed production, or cause cell death (Karasov et al, 2017). NLR/PRR genes can increase their expression (Dowen et al, 2012; Yu et al, 2013), or alter their alternative splicing or polyadenylation (Tsuchiya and Eulgem, 2013; Lai et al, 2020) in response to pathogens or elicitors, and both processes are affected by chromatin epigenetic marks. As well as DNA methylation, H3K9me controls the expression of pathogen defense genes (Dutta et al, 2017), and alternative polyadenylation of particular NLR genes (Lai and Eulgem, 2018)

Methods

Results

Conclusion