Improved pathogen and stress tolerance in tomato mutants of SET domain histone 3 lysine methyltransferases

Abstract

Histone lysine methylations (HLMs) are implicated in control of gene expression in different eukaryotes. However, the role of HLMs in regulating desirable crop traits and the enzymes involved in these modifications are poorly understood.We studied the functions of tomato histone H3 lysine methyltransferases SET Domain Group 33 (SDG33) and SDG34 in biotic and abiotic stress responses. SDG33 and SDG34 gene edited mutants were altered in H3K36 and H3K4 methylations, and expression of genes involved in diverse processes and responses to biotic and abiotic stimuli.The double but not the single mutants show resistance to the fungal pathogen Botrytis cinerea. Interestingly, single mutants were tolerant to drought and the double mutant showed superior tolerance and plant growth consistent with independent and additive functions. Mutants maintained higher water status during drought and improved recovery and survival after lapse of drought.Notably, diminution of H3K4 and H3K36 trimethylation and expression of negative regulators in challenged plants contributes to stress tolerance of the mutants. Mutations in SDG33 and SDG34 are likely to remove predisposition to biotic and abiotic stress by disrupting permissive transcriptional context promoting expression of negative regulatory factors. These allows improvement of stress and pathogen tolerance, without growth trade-offs, through modification of histone epigenetic marks.

Histone methyltransferases SDG33 and SDG34 regulate organ-specific nitrogen responses in tomato

“…To investigate the roles of tomato SDG33 and SDG34 in regulating N responses, we compared transcriptomes of CRISPR mutants sdg33 or sdg34 ( Bvindi et al., 2022 ) and wild type plants (WT) grown under N-supplied (+N) or N-starved (-N) conditions ( Figure 1A ). In detail, sdg33 and sdg34 mutants, as well as WT, were grown hydroponically in N-rich media for two weeks, followed by N starvation for 48 hours, and then transferred to media supplemented with N (+N) or control media without N (-N).…”

“…The cluster 3 genes are significantly enriched with biological processes “transport” and “response to auxin” ( Supplemental Table S14 ). Given that SDG33 and SDG34 are required for depositing permissive marks H3K36me3 and H3K4me3 ( Bvindi et al., 2022 ), it is likely that cluster 2 and 3 are enriched with the direct targets of SDG33/34.…”

“…CRISPR mutants sdg33 and sdg34 created previously in our labs ( Bvindi et al., 2022 ) and the corresponding wild type (WT) tomato ( Solanum lycopersicum ) cultivar CastlemartII, a widely grown cultivated tomato cultivar, was used in this study. Specifically, sdg33.1 (referred to as sdg33-64B in Bvindi et al., 2022 ), sdg33.2 (a.k.a sdg33-64S ), sdg34.1 ( sdg34-76 ), and sdg34.2 ( sdg34-27 ) were used, while sdg33.1 and sdg34.1 were used for transcriptome specifically. Seeds were surface sterilized with 20% sodium hypochlorite for 20 minutes and rinsed with distilled water.…”

“…In Arabidopsis, SDG8 functions as H3K36 methyltransferase to regulate multiple metabolic processes and environmental responses, including nitrogen response ( Zhao et al., 2005 ; Xu et al., 2008 ; Berr et al., 2010 ; Li et al., 2015 ; Lee et al., 2016 ; Jiang et al., 2018 ; Li et al., 2020 ), and is highly conserved among eukaryotes, with homologs in human ( Li et al., 2007 ), yeast ( Krogan et al., 2003 ), rice ( Liu et al., 2016 ), and tomato ( Aiese Cigliano et al., 2013 ). The tomato homologs of SDG8, SDG33 and SDG34, are also shown to affect H3K4 and H3K36 methylation ( Bvindi et al., 2022 ). We test the hypothesis that the function of SDG8 in mediating N responses is conserved across species and that the tomato SDG33 and/or SDG34 also regulate N response.…”

Histone modification and chromatin remodeling in plant response to pathogens

“…Lastly, SDG8 was also reported to regulate CAROTENOID ISOMERASE 2 ( CCR2 ) and ECERIFERUM 3 ( CER3 ), which encode proteins to catalyze the biosynthesis of carotenoids and be involved in the biosynthesis of cuticular wax, respectively, and loss of SDG8 resulted in the reduction of lipid accumulation and loss of cuticle integrity leading to impeded plant immunity ( Lee et al, 2016 ). In tomato ( Solanum lycopersicum , Sl ), the SDG8-orthologues SlSDG33 and SlSDG34 were required for pathogen- and stress-induced enrichment of H3K36me3 and H3K4me3 at target genes, but their loss increased plant resistance to Botrytis cinerea ( Bvindi et al, 2022 ). It was proposed that mutations in Sl SDG33 and Sl SDG34 may disrupt permissive transcriptional context promoting expression of negative regulatory factors to allow improvement of plant tolerance without growth trade-offs.…”