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A genome-wide DNA methylation survey reveals salicylic acid-induced distinct hypomethylation linked to defense responses against biotrophic pathogens

ABSTRACT: DNA methylation is a conserved regulatory mechanism of gene expression, genome stability, and development, and highly associated with effective induction of defense responses for plant priming. In the Green Deal era, the use of plant defense inducers (PDIs), compounds that activate defense and prime plants against imminent pathogen attacks, is a safe and environmentally sustainable approach to support plants against pathogens. Even though efforts have deciphered part of PDIs mode of action, more information is needed to understand the underlying pathways of their effectiveness. Here, salicylic acid (SA) loaded in chitosan nanoparticles, increased hypomethylation more than 25% on 56 genomic regions that corresponded to defense-related genes, such as pectin lyases, defensins and leucine-rich repeat transmembrane protein kinases against the biotrophic fungal pathogen Podosphaera xanthii. A genomic region of the promoter of SKP1A, a core member of the SCF E3 ubiquitin ligase complex, was found to be a Differentially Methylated region (DMR) with 60% hypomethylation, both after PDI application and pathogen inoculation, possibly indicating a similar activation mechanism. Examination of this DMR revealed the presence of SA-, auxin-, and defense-related cis-elements. Investigation of proteins associated with the above cis-elements showed significant upregulation in expression after PDI. Moreover, association of the identified DMR with transcriptomics showed enrichment of the SA pathway. Overall, these findings shed light on the epigenetic mechanisms that underlie SA- related defense priming in plants

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE319280 | GEO | 2026/02/12

REPOSITORIES: GEO

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An immune-inducible trihelix transcription factor suppresses bacterial resistance in Arabidopsis thaliana

Project description:The plant innate immunity consists of the two interconnected mechanisms, pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Although much is known about how plants trigger immune responses upon pathogen recognition, the genetic program by which plants avoid an overshoot in pathogen-triggered immune responses remains largely unknown. Here, we discovered a trihelix transcription factor, GT-3a, as an immune-inducible negative regulator of bacterial resistance in Arabidopsis thaliana. Analysis of public RNA-seq data revealed that GT-3a is specifically induced by ETI activation not by PTI activation. Overexpression of GT-3a suppressed resistance against the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto) and Pto-elicited expression of salicylic acid (SA)-responsive genes. Our results suggest that transcriptional induction of GT-3a circumvents the overshooting of SA-mediated defense responses during ETI.

2024-02-18 | GSE248054 | GEO

The sulfated laminarin triggers a stress transcriptome before priming the SA- and ROSdependent defenses during grapevine's induced resistance against Plasmopara viticola

Project description:Cultivated grapevine (Vitis vinifera) is susceptible to many pathogens which cause significant losses to viticulture worldwide. Chemical control is available, but agro-ecological concerns have raised interest in alternative methods, especially in elicitation of plant immunity by bio-molecules such as Pathogen Associated Molecular Patterns (PAMPs). We have demonstrated that the beta-glucan laminarin (Lam) and its sulfated derivative (PS3) induce a PAMP-triggered immunity in grapevine against downy mildew (Plasmopara viticola). However, if Lam elicits classical grapevine defenses, PS3 triggered grapevine resistance via a poorly understood priming phenomenon. The aim of this study was to discover the mechanism of the PS3-induced resistance. On uninfected grapevine, we first investigated defense signaling and performed microarray experiments to identify early events and genes directly triggered by PS3. Our results showed that PS3 i) was unable to elicit ROS and NO production, cytosolic Ca2+ variations, MAPK activation but triggered a long lasting plasma membrane depolarization in grapevine cells ii) up-regulated a stress-responsive transcriptome close to the one induced by Lam but only partly overlapping the ones triggered by salicylate (SA) or jasmonate (JA). Finally, in response to P. viticola infection, PS3 specifically primed the SA- and ROS-dependent defense pathways leading to grapevine triggered immunity against this biotroph. Keywords: cell death, induced resistance, oomycete, priming, reactive oxygen species, salicylate, sulfated laminarin, transcriptomics, Vitis vinifera. 6 samples (Adj, PS3, Lam, ctrl, SA, JA) were analized with 3 biological replicates each, Adj and ctrl samples are reference samples

2013-12-16 | E-GEOD-42972 | biostudies-arrayexpress

DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis [DNA methylation]

Project description:Background: Plants memorize previous pathogen attacks and are ‘primed’ to produce a faster and stronger defense response, which is critical for defense against pathogens. In plants, cytosines in transposons and gene bodies are reported to be frequently methylated. Demethylation of transposons can affect disease resistance by regulating the transcription of nearby genes during defense response, but the role of gene body methylation (GBM) in defense responses remains unclear. Results: Here, we find that loss of the chromatin remodeler decrease in DNA methylation 1 (ddm1) synergistically enhances resistance to a biotrophic pathogen under mild chemical priming. DDM1 mediates gene body methylation at a subset of stress-responsive genes with distinct chromatin properties from conventional gene body methylated genes. Decreased gene body methylation in loss of ddm1 mutant is associated with hyperactivation of these gene body methylated genes. Knockout of glyoxysomal protein kinase 1 (gpk1), a hypomethylated gene in ddm1 loss of function mutant, impairs priming of defense response to pathogen infection in Arabidopsis. We also find that DDM1-mediated gene body methylation is prone to epigenetic variation among natural Arabidopsis populations, and GPK1 expression is hyperactivated in natural variants with demethylated GPK1. Conclusions: Based on our collective results, we propose that DDM1-mediated GBM provides a possible regulatory axis for plants to modulate the inducibility of the immune response.

2023-04-14 | GSE98162 | GEO

DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis [expression]

2023-04-14 | GSE59914 | GEO

A Conserved Salicylic Acid Signaling Pathway Controls Plant Immunity against Pseudomonas thought the unique TGA transcription factor in Marchantia polymorpha

Project description:Land plants have co-evolved with microorganisms since its transition to a terrestrial habitat around 500 million years ago. In angiosperms, salicylic acid (SA) activates plant immunity against hemibiotrophic pathogens thought TGA transcription factors, which bind to the promoter of SA-responsive loci, such as pathogenesis-related (PR) genes, to enforce plants immunity. While those mechanisms are well-known in flowering plants, our understanding in bryophytes remains limited, as genetic evidences for the role of SA in plant immunity are still largely missing. Here, we explore the interaction between Marchantia polymorpha and the bacterium Pseudomonas syringae to gain insights into the evolutionary immune function of SA during bryophyte-pathogen interactions. We combined transcriptomic profiling of P. syringae-infected M. polymorpha with the generation of SA-deficient plants in this liverwort by overexpressing the bacterial NahG gene, a SA-degrading enzyme. Our results indicate that P. syringae induced transcriptional footprint is enriched in SA-responsive genes and that Marchantia NahG plants are compromised in immune responses against P. syringae. We found that MpTGA is modulated by SA and essential for controlling resistance against Pseudomonas. Further transcriptional analysis to identify the coregulatory network controlled by SA and MpTGA, indicate that a SA/MpTGA module might execute the boost of plants' defence responses thought a variety of MpPRs, highlighting a notable control of class III secretory peroxidases belonging to the MpPR9 subfamily. Altogether, our data demonstrate the functional conservation of SA as an immune hormone and underpin the existence of a SA-controlled MpTGA transcriptional cluster driving resistance against Pseudomonas in M. polymorpha

2026-01-16 | GSE300298 | GEO

CBP60g and CBP60h play partially redundant and critical roles in salicylic acid signaling

Project description:Our previous study on CBP60g, a calmodulin binding protein that is important for disease resistance and microbe-associated molecular pattern (MAMP)-induced SA accumulation, led to our discovery of a closely related family member CBP60h. CBP60h is also important for defense against P. syringae but is induced differently by pathogen and MAMP stimulus. Transcriptome profiling of cbp60h mutants suggested that CBP60h might be primarily functioning in response against P. syringae. We constructed a double mutant of cbp60g and cbp60h, which demonstrated severely defective defense against P. syringae and SA accumulation. Profiling of the cbp60g/h showed that its expression pattern is very similar to that of pad4. Transient expression in Tobacco showed that both CBP60g and CBP60h localized to nucleus. Our observation suggest that CBP60g and CBP60h share partially redundant but critical role in defense response and SA signaling.

2009-11-04 | GSE18865 | GEO

CBP60g and CBP60h play partially redundant and critical roles in salicylic acid signaling

2009-11-03 | E-GEOD-18865 | biostudies-arrayexpress

The sulfated laminarin triggers a stress transcriptome before priming the SA- and ROSdependent defenses during grapevine's induced resistance against Plasmopara viticola

2013-12-16 | GSE42972 | GEO

Comparative proteomic analysis of susceptible and resistance maize lines to southern corn rust

Project description:Southern corn rust (SCR) is one of destructive diseases in maize caused by Puccinia polysora Undrew. (P. polysara), widely occurring in warm-temperate and tropical regions globally. To identify candidate SCR resistance-related proteins and understand the molecular mechanism underlaying the maize and P. polysara interaction, comparative proteomic analysis of susceptible and resistance maize lines was performed. A total of 6,612 proteins were successfully identified using an iTRAQ-based proteomic approach. Fold changes and statistical analysis demonstrated that 687 proteins increased and 802 proteins decreased in the resistant line, while 571 increased and 464 decreased in the susceptible line. One remorin protein, namely ZmREM1.3 (B4G1B0), was significantly induced by SCR in the resistant genotype, while decreased in susceptible genotype after P. polysara infection. Plant-specific remorin proteins have been shown to play important roles during microbial infection and plant signaling processes. Transgenic analysis showed that overexpression of ZmREM1.3 in maize confers enhanced resistance to the biotrophic fungal pathogen SCR. Upon pathogen challenge, the ZmREM1.3-overexpressing plants accumulated higher levels of defense hormones, SA and JA. Moreover, stronger induction of defense gene expression was also observed in ZmREM1.3-overexpressing maize plants in response to SCR infection. Taken together, our results support that ZmREM1.3 plays a positive role in regulating the maize defense against SCR likely through SA/JA-mediated defense signaling pathways. This is the first attempt for large scale analysis of the molecular mechanisms underlaying the maize and P. polysara interaction at the proteomic level, and the first evidence for remorin protein family in resistant to fungal disease.

2019-04-18 | PXD008904 | Pride

Elicitor specific mechanisms of defense priming in oak seedlings against powdery mildew

Project description:Defense priming sensitises plant defenses to enable a faster and stronger response to subsequent stress. Various chemicals can trigger priming, however the response remains unexplored in oak. Following treatment with salicylic acid (SA), jasmonic acid (JA), or β-aminobutyric acid (BABA), oak (Quercus robur) seedlings were infected with oak powdery mildew (Erysiphe alphitoides, PM). Whilst JA increased susceptibility to PM, BABA and SA enhanced resistance by priming callose deposition and SA-dependent gene expression, respectively. All three treatments had no impact on growth. To characterise molecular markers of priming, untargeted transcriptome and metabolome analyses were performed using RNAseq and LC-MS/MS. Differential gene expression analysis revealed around 2900, 1600, and 900 genes uniquely primed by each treatment BABA, SA, and JA, respectively. A limited number of enriched GO terms differentiated the three treatments. Meanwhile, metabolome analysis found roughly 340, 220, and 40 accumulated masses uniquely primed by BABA, SA, and JA, respectively. Pathway enrichment analysis linked BABA priming to alkaloids biosynthesis, whereas no specific pathways were identified for SA and JA priming. Our results confirm the existence of chemical-induced priming in oak and putatively identify associated molecular markers.

2025-02-28 | GSE277279 | GEO

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