Global Regulation of Plant Immunity by Histone Lysine Methyl Transferases

Plant immune resilience to a changing climate: molecular insights and biotechnological roadmaps

Successful resistance to disease-causing pathogens is underpinned by properly regulated immune signalling and defence responses in plants. The plant immune system is controlled at multiple levels of gene and protein regulation-from chromatin-associated epigenetic processes to protein post-translational modifications. Optimal fine-tuning of plant immune signalling and responses is important to prevent plant disease development, which is being exacerbated by a globally changing climate. In this review, we focus on how changing climatic factors mechanistically intercept plant immunity at different levels of regulation (chromatin, transcriptional, post-transcriptional, translational, and post-translational). We specifically highlight recent studies that have provided molecular insights into critically important climate-sensitive nodes and mechanisms of the plant immune system. We then propose several potential future directions to build climate-resilient plant disease resistance using cutting-edge biotechnology. Overall, this conceptual understanding and promising biotechnological advances provide a foundational platform towards novel approaches to engineer plant immune resilience.

Identification of grape H3K27 methyltransferase genes and their expression profiles during grape fruit ripening

BACKGROUND

H2O2 treatment can accelerate grape ripening and mediate changes in histone methylation levels. Histone methylation, as an epigenetic modification, is involved in regulating the expression of genes related to fruit ripening, including H3K27ac, H3K4me1, H3K27me3 and H3K4me3. Among them, H3K27me3 methylation is generally negatively regulated in development, and H3K27 methyltransferase can participate in the development process of fruit by regulate the level of H3K27me3. The H3K27 methyltransferase members in grapes are not yet clear, and a better understanding of their functions contributes to regulating fruit development.

METHODS AND RESULTS

By analyzing the conserved domains of the grape genome, three H3K27 methyltransferases were identified and named as VvH3K27-1, VvH3K27-2 and VvH3K27-3, respectively. Further analysis included their conserved domains, gene structure, phylogenetic relationship, protein physicochemical properties, chromosome localization, subcellular localization, and cis-acting elements in the promoter region. It is worth noting that all H3K27 methyltransferase genes have a highly conserved SET domain. VvH3K27-2 was localized in the nucleus and H2O2 treatment resulted in a decrease in the expression of these genes.

CONCLUSION

Three H3K27 methyltransferase genes were identified in grape, which are down-regulated during berry development, and their expression is inhibited by H2O2 treatment. Thus, H3K27 methyltransferase genes are involved in the regulation of fruit development.

The SET-Domain-Containing Protein MdSDG26 Negatively Regulates Alternaria alternata Resistance in Apple

Apple leaf spot is one of the most devastating diseases in the apple industry, caused by Alternaria alternata f. sp mali (A. alternata). SET-domain group (SDG) proteins function as the histone methyltransferases and participate in plant development and stress responses. However, whether SDG proteins are associated with A. alternata resistance is largely unclear. Here, we describe the pathogen-inducible MdSDG26 gene in apple (Malus × domestica). MdSDG26 has two transcript variants that function similarly in catalyzing histone methylation and A. alternata resistance. Transient overexpression of MdSDG26 increased the global levels of H3K4me3 and H3K36me3, whereas knockdown of MdSDG26 only reduced the H3K36me3 level. Transcriptome analysis revealed that MdSDG26 affected the genome-wide transcriptome changes in response to A. alternata infection. ChIP-qPCR analysis demonstrated that MdSDG26 modulates the levels of H3K36me3 and H3K4me3 at both the promoter and exon regions of MdNTL9. As a negative regulator of A. alternata resistance in apples, MdNTL9 plays a pivotal role in MdSDG26-mediated resistance to A. alternata. Therefore, our findings provide compelling evidence for the regulatory function of MdSDG26 in histone methylation and its molecular role in conferring resistance to A. alternata.

H3K36 methyltransferase GhKMT3;1a and GhKMT3;2a promote flowering in upland cotton

BACKGROUND

The SET domain group (SDG) genes encode histone lysine methyltransferases, which regulate gene transcription by altering chromatin structure and play pivotal roles in plant flowering determination. However, few studies have investigated their role in the regulation of flowering in upland cotton.

RESULTS

A total of 86 SDG genes were identified through genome-wide analysis in upland cotton (Gossypium hirsutum). These genes were unevenly distributed across 25 chromosomes. Cluster analysis revealed that the 86 GhSDGs were divided into seven main branches. RNA-seq data and qRT‒PCR analysis revealed that lysine methyltransferase 3 (KMT3) genes were expressed at high levels in stamens, pistils and other floral organs. Using virus-induced gene silencing (VIGS), functional characterization of GhKMT3;1a and GhKMT3;2a revealed that, compared with those of the controls, the GhKMT3;1a- and GhKMT3;2a-silenced plants exhibited later budding and flowering and lower plant heightwere shorter. In addition, the expression of flowering-related genes (GhAP1, GhSOC1 and GhFT) significantly decreased and the expression level of GhSVP significantly increased in the GhKMT3;1a- and GhKMT3;2a-silenced plants compared with the control plants.

CONCLUSION

A total of 86 SDG genes were identified in upland cotton, among which GhKMT3;1a and GhKMT3;2a might regulate flowering by affecting the expression of GhAP1, GhSOC1, GhFT and GhSVP. These findings will provide genetic resources for advanced molecular breeding in the future.

Epigenetic weapons of plants against fungal pathogens

In the natural environment, plants face constant exposure to biotic stress caused by fungal attacks. The plant's response to various biotic stresses relies heavily on its ability to rapidly adjust the transcriptome. External signals are transmitted to the nucleus, leading to activation of transcription factors that subsequently enhance the expression of specific defense-related genes. Epigenetic mechanisms, including histone modifications and DNA methylation, which are closely linked to chromatin states, regulate gene expression associated with defense against biotic stress. Additionally, chromatin remodelers and non-coding RNA play a significant role in plant defense against stressors. These molecular modifications enable plants to exhibit enhanced resistance and productivity under diverse environmental conditions. Epigenetic mechanisms also contribute to stress-induced environmental epigenetic memory and priming in plants, enabling them to recall past molecular experiences and utilize this stored information for adaptation to new conditions. In the arms race between fungi and plants, a significant aspect is the cross-kingdom RNAi mechanism, whereby sRNAs can traverse organismal boundaries. Fungi utilize sRNA as an effector molecule to silence plant resistance genes, while plants transport sRNA, primarily through extracellular vesicles, to pathogens in order to suppress virulence-related genes. In this review, we summarize contemporary knowledge on epigenetic mechanisms of plant defense against attack by pathogenic fungi. The role of epigenetic mechanisms during plant-fungus symbiotic interactions is also considered.

Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato

Environmental stimuli trigger rapid transcriptional reprogramming of gene networks. These responses occur in the context of the local chromatin landscape, but the contribution of organ-specific dynamic chromatin modifications in responses to external signals remains largely unexplored. We treated tomato seedlings with a supply of nitrate and measured the genome-wide changes of four histone marks, the permissive marks H3K27ac, H3K4me3, and H3K36me3 and repressive mark H3K27me3, in shoots and roots separately, as well as H3K9me2 in shoots. Dynamic and organ-specific histone acetylation and methylation were observed at functionally relevant gene loci. Integration of transcriptomic and epigenomic datasets generated from the same organ revealed largely syngenetic relations between changes in transcript levels and histone modifications, with the exception of H3K27me3 in shoots, where an increased level of this repressive mark is observed at genes activated by nitrate. Application of a machine learning approach revealed organ-specific rules regarding the importance of individual histone marks, as H3K36me3 is the most successful mark in predicting gene regulation events in shoots, while H3K4me3 is the strongest individual predictor in roots. Our integrated study substantiates a view that during plant environmental responses, the relationships between histone code dynamics and gene regulation are highly dependent on organ-specific contexts.

Epigenetic regulation of plant immunity: from chromatin codes to plant disease resistance

Facing a deteriorating natural environment and an increasing serious food crisis, bioengineering-based breeding is increasing in importance. To defend against pathogen infection, plants have evolved multiple defense mechanisms, including pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). A complex regulatory network acts downstream of these PTI and ETI pathways, including hormone signal transduction and transcriptional reprogramming. In recent years, increasing lines of evidence show that epigenetic factors act, as key regulators involved in the transcriptional reprogramming, to modulate plant immune responses. Here, we summarize current progress on the regulatory mechanism of DNA methylation and histone modifications in plant defense responses. In addition, we also discuss the application of epigenetic mechanism-based resistance strategies in plant disease breeding.

The role of corepressor HOS15-mediated epigenetic regulation of flowering

Regulation of gene expression underpins gene function and is essential for regulation of physiological roles. Epigenetic modifications regulate gene transcription by physically facilitating relaxation or condensation of target loci in chromatin. Transcriptional corepressors are involved in chromatin remodeling and regulate gene expression by establishing repressive complexes. Genetic and biochemical studies reveal that a member of the Groucho/Thymidine uptake 1 (Gro/Tup1) corepressor family, HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15), is recruited via the evening complex (EC) to the GIGANTEA (GI) promoter to repress gene expression, and modulating flowering time. Therefore, HOS15 connects photoperiodic pathway and epigenetic mechanism to control flowering time in plants. In addition, growing body of evidence support a diverse roles of the epigenetic regulator HOS15 in fine-tuning plant development and growth by integrating intrinsic genetic components and various environmental signals.

Histone variants and modifications during abiotic stress response

Plants have developed multiple mechanisms as an adaptive response to abiotic stresses, such as salinity, drought, heat, cold, and oxidative stress. Understanding these regulatory networks is critical for coping with the negative impact of abiotic stress on crop productivity worldwide and, eventually, for the rational design of strategies to improve plant performance. Plant alterations upon stress are driven by changes in transcriptional regulation, which rely on locus-specific changes in chromatin accessibility. This process encompasses post-translational modifications of histone proteins that alter the DNA-histones binding, the exchange of canonical histones by variants that modify chromatin conformation, and DNA methylation, which has an implication in the silencing and activation of hypervariable genes. Here, we review the current understanding of the role of the major epigenetic modifications during the abiotic stress response and discuss the intricate relationship among them.

Exploring and exploiting cuticle biosynthesis for abiotic and biotic stress tolerance in wheat and barley

Wheat and barley are widely distributed cereal crops whose yields are adversely affected by environmental stresses such as drought, salinity, extreme temperatures, and attacks of pathogens and pests. As the interphase between aerial plant organs and their environments, hydrophobic cuticle largely consists of a cutin matrix impregnated and sealed with cuticular waxes. Increasing evidence supports that the cuticle plays a key role in plant adaptation to abiotic and biotic stresses, which could be harnessed for wheat and barley improvement. In this review, we highlighted recent advances in cuticle biosynthesis and its multifaceted roles in abiotic and biotic stress tolerance of wheat and barley. Current strategies, challenges, and future perspectives on manipulating cuticle biosynthesis for abiotic and biotic stress tolerance in wheat and barley are discussed.

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

Histone posttranslational modifications shape the chromatin landscape of the plant genome and affect gene expression in response to developmental and environmental cues. To date, the role of histone modifications in regulating plant responses to environmental nutrient availability, especially in agriculturally important species, remains largely unknown. We describe the functions of two histone lysine methyltransferases, SET Domain Group 33 (SDG33) and SDG34, in mediating nitrogen (N) responses of shoots and roots in tomato. By comparing the transcriptomes of CRISPR edited tomato lines sdg33 and sdg34 with wild-type plants under N-supplied and N-starved conditions, we uncovered that SDG33 and SDG34 regulate overlapping yet distinct downstream gene targets. In response to N level changes, both SDG33 and SDG34 mediate gene regulation in an organ-specific manner: in roots, SDG33 and SDG34 regulate a gene network including Nitrate Transporter 1.1 (NRT1.1) and Small Auxin Up-regulated RNA (SAUR) genes. In agreement with this, mutations in sdg33 or sdg34 abolish the root growth response triggered by an N-supply; In shoots, SDG33 and SDG34 affect the expression of photosynthesis genes and photosynthetic parameters in response to N. Our analysis thus revealed that SDG33 and SDG34 regulate N-responsive gene expression and physiological changes in an organ-specific manner, thus presenting previously unknown candidate genes as targets for selection and engineering to improve N uptake and usage in crop plants.

Histone modification and chromatin remodeling in plant response to pathogens

As sessile organisms, plants are constantly exposed to changing environments frequently under diverse stresses. Invasion by pathogens, including virus, bacterial and fungal infections, can severely impede plant growth and development, causing important yield loss and thus challenging food/feed security worldwide. During evolution, plants have adapted complex systems, including coordinated global gene expression networks, to defend against pathogen attacks. In recent years, growing evidences indicate that pathogen infections can trigger local and global epigenetic changes that reprogram the transcription of plant defense genes, which in turn helps plants to fight against pathogens. Here, we summarize up plant defense pathways and epigenetic mechanisms and we review in depth current knowledge's about histone modifications and chromatin-remodeling factors found in the epigenetic regulation of plant response to biotic stresses. It is anticipated that epigenetic mechanisms may be explorable in the design of tools to generate stress-resistant plant varieties.

N-Methyltransferase CaASHH3 Acts as a Positive Regulator of Immunity against Bacterial Pathogens in Pepper

Proteins with conserved SET domain play a critical role in plant immunity. However, the means of organization and functions of these proteins are unclear, particularly in non-model plants such as pepper (Capsicum annum L.). Herein, we functionally characterized CaASHH3, a member of class II (the ASH1 homologs H3K36) proteins in pepper immunity against Ralstonia solanacearum and Pseudomonas syringae pv tomato DC3000 (Pst DC3000). The CaASHH3 was localized in the nucleus, and its transcript levels were significantly enhanced by R. solanacearum inoculation (RSI) and exogenous application of salicylic acid (SA), methyl jasmonate (MeJA), ethephon (ETH), and abscisic acid (ABA). Knockdown of CaASHH3 by virus-induced gene silencing (VIGS) compromised peppers’ resistance to RSI. Furthermore, silencing of CaASHH3 impaired hypersensitive-response (HR)-like cell death response due to RSI and downregulated defense-associated marker genes, including CaPR1, CaNPR1, and CaABR1. The CaASHH3 protein was revealed to affect the promoters of CaNPR1, CaPR1, and CaHSP24. Transiently over-expression of CaASHH3 in pepper leaves elicited HR-like cell death and upregulated immunity-related marker genes. To further study the role of CaASHH3 in plant defense in vivo, CaASHH3 transgenic plants were generated in Arabidopsis. Overexpression of CaASHH3 in transgenic Arabidopsis thaliana enhanced innate immunity against Pst DC3000. Furthermore, CaASHH3 over-expressing transgenic A. thaliana plants exhibited upregulated transcriptional levels of immunity-associated marker genes, such as AtNPR1, AtPR1, and AtPR2. These results collectively confirm the role of CaASHH3 as a positive regulator of plant cell death and pepper immunity against bacterial pathogens, which is regulated by signaling synergistically mediated by SA, JA, ET, and ABA.

Genomic Variations and Mutational Events Associated with Plant-Pathogen Interactions

Phytopathologists are actively researching the molecular basis of plant-pathogen interactions. The mechanisms of responses to pathogens have been studied extensively in model crop plant species and natural populations. Today, with the rapid expansion of genomic technologies such as DNA sequencing, transcriptomics, proteomics, and metabolomics, as well as the development of new methods and protocols, data analysis, and bioinformatics, it is now possible to assess the role of genetic variation in plant-microbe interactions and to understand the underlying molecular mechanisms of plant defense and microbe pathogenicity with ever-greater resolution and accuracy. Genetic variation is an important force in evolution that enables organisms to survive in stressful environments. Moreover, understanding the role of genetic variation and mutational events is essential for crop breeders to produce improved cultivars. This review focuses on genetic variations and mutational events associated with plant-pathogen interactions and discusses how these genome compartments enhance plants' and pathogens' evolutionary processes.

A nuclear-targeted effector of Rhizophagus irregularis interferes with histone 2B mono-ubiquitination to promote arbuscular mycorrhisation

Arguably, symbiotic arbuscular mycorrhizal (AM) fungi have the broadest host range of all fungi, being able to intracellularly colonise root cells in the vast majority of all land plants. This raises the question how AM fungi effectively deal with the immune systems of such a widely diverse range of plants. Here, we studied the role of a nuclear-localisation signal-containing effector from Rhizophagus irregularis, called Nuclear Localised Effector1 (RiNLE1), that is highly and specifically expressed in arbuscules. We showed that RiNLE1 is able to translocate to the host nucleus where it interacts with the plant core nucleosome protein histone 2B (H2B). RiNLE1 is able to impair the mono-ubiquitination of H2B, which results in the suppression of defence-related gene expression and enhanced colonisation levels. This study highlights a novel mechanism by which AM fungi can effectively control plant epigenetic modifications through direct interaction with a core nucleosome component. Homologues of RiNLE1 are found in a range of fungi that establish intimate interactions with plants, suggesting that this type of effector may be more widely recruited to manipulate host defence responses.

Transcriptome dynamics underlying elicitor-induced defense responses against Septoria leaf spot disease of tomato (Solanum lycopersicum L.)

Elicitor-induced defense response against potential plant pathogens has been widely reported in several crop plants; however, transcriptome dynamics underlying such defense response remains elusive. Our previous study identified and characterized a novel elicitor, κ-carrageenan, from Kappaphycus alvarezii, a marine red seaweed. Our preliminary studies have shown that the elicitor-treatment enhances the tolerance of a susceptible tomato cultivar to Septoria lycopersici (causative agent of leaf spot disease). To gain further insights into the genes regulated during elicitor treatment followed by pathogen infection, we have performed RNA-Seq experiments under different treatments, namely, control (untreated and uninfected), elicitor treatment, pathogen infection alone, and elicitor treatment followed by pathogen infection. To validate the results, forty-three genes belonging to five different classes, namely, ROS activating and detoxifying enzyme encoding genes, DEAD-box RNA helicase genes, autophagy-related genes, cysteine proteases, and pathogenesis-related genes, were chosen. Expression profiling of each gene was performed using qRT-PCR, and the data was correlated with the RNA-seq data. Altogether, the study has pinpointed a repertoire of genes that could be potential candidates for further functional characterization to provide insights into novel elicitor-induced fungal defense and develop transgenic lines resistant to foliar diseases.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00970-y.

Multifaceted Chromatin Structure and Transcription Changes in Plant Stress Response

Sessile plants are exposed throughout their existence to environmental abiotic and biotic stress factors, such as cold, heat, salinity, drought, dehydration, submergence, waterlogging, and pathogen infection. Chromatin organization affects genome stability, and its dynamics are crucial in plant stress responses. Chromatin dynamics are epigenetically regulated and are required for stress-induced transcriptional regulation or reprogramming. Epigenetic regulators facilitate the phenotypic plasticity of development and the survival and reproduction of plants in unfavorable environments, and they are highly diversified, including histone and DNA modifiers, histone variants, chromatin remodelers, and regulatory non-coding RNAs. They contribute to chromatin modifications, remodeling and dynamics, and constitute a multilayered and multifaceted circuitry for sophisticated and robust epigenetic regulation of plant stress responses. However, this complicated epigenetic regulatory circuitry creates challenges for elucidating the common or differential roles of chromatin modifications for transcriptional regulation or reprogramming in different plant stress responses. Particularly, interacting chromatin modifications and heritable stress memories are difficult to identify in the aspect of chromatin-based epigenetic regulation of transcriptional reprogramming and memory. Therefore, this review discusses the recent updates from the three perspectives—stress specificity or dependence of transcriptional reprogramming, the interplay of chromatin modifications, and transcriptional stress memory in plants. This helps solidify our knowledge on chromatin-based transcriptional reprogramming for plant stress response and memory.

A Systems Biology Approach to Identify Essential Epigenetic Regulators for Specific Biological Processes in Plants

Upon sensing developmental or environmental cues, epigenetic regulators transform the chromatin landscape of a network of genes to modulate their expression and dictate adequate cellular and organismal responses. Knowledge of the specific biological processes and genomic loci controlled by each epigenetic regulator will greatly advance our understanding of epigenetic regulation in plants. To facilitate hypothesis generation and testing in this domain, we present EpiNet, an extensive gene regulatory network (GRN) featuring epigenetic regulators. EpiNet was enabled by (i) curated knowledge of epigenetic regulators involved in DNA methylation, histone modification, chromatin remodeling, and siRNA pathways; and (ii) a machine-learning network inference approach powered by a wealth of public transcriptome datasets. We applied GENIE3, a machine-learning network inference approach, to mine public Arabidopsis transcriptomes and construct tissue-specific GRNs with both epigenetic regulators and transcription factors as predictors. The resultant GRNs, named EpiNet, can now be intersected with individual transcriptomic studies on biological processes of interest to identify the most influential epigenetic regulators, as well as predicted gene targets of the epigenetic regulators. We demonstrate the validity of this approach using case studies of shoot and root apical meristem development.

Arabidopsis thaliana Cuticle Composition Contributes to Differential Defense Response to Botrytis cinerea

The chemical composition of a plant cuticle can change in response to various abiotic or biotic stresses and plays essential functions in disease resistance responses. Arabidopsis thaliana mutants altered in cutin content are resistant to Botrytis cinerea, presumably because of increased cuticular water and solute permeability, allowing for faster induction of defense responses. Within this context, our knowledge of wax mutants is limited against this pathogen. We tested the contribution of cuticular components to immunity to B. cinerea using mutants altered in either cutin or wax alone, or in both cutin and wax contents. We found that even all the tested mutants showed increased permeability and reactive oxygen species (ROS) accumulation in comparison with wild-type plants and that only cutin mutants showed resistance. To elucidate the early molecular mechanisms underlying cuticle-related immunity, we performed a transcriptomic analysis. A set of upregulated genes involved in cell wall integrity and accumulation of ROS were shared by the cutin mutants bdg, lacs2-3, and eca2, but not by the wax mutants cer1-4 and cer3-6. Interestingly, these genes have recently been shown to be required in B. cinerea resistance. In contrast, we found the induction of genes involved in abiotic stress shared by the two wax mutants. Our study reveals new insight that the faster recognition of a pathogen by changes in cuticular permeability is not enough to induce resistance to B. cinerea, as has previously been hypothesized. In addition, our data suggest that mutants with resistant phenotype can activate other defense pathways, different from those canonical immune ones.

Exploiting Epigenetic Variations for Crop Disease Resistance Improvement

Pathogen infections seriously threaten plant health and global crop production. Epigenetic processes such as DNA methylation, histone post-translational modifications, chromatin assembly and remodeling play important roles in transcriptional regulation of plant defense responses and could provide a new direction to drive breeding strategies for crop disease resistance improvement. Although past decades have seen unprecedented proceedings in understanding the epigenetic mechanism of plant defense response, most of these advances were derived from studies in model plants like Arabidopsis. In this review, we highlighted the recent epigenetic studies on crop-pathogen interactions and discussed the potentials, challenges, and strategies in exploiting epigenetic variations for crop disease resistance improvement.

Two Arabidopsis Homologs of Human Lysine-Specific Demethylase Function in Epigenetic Regulation of Plant Defense Responses

Epigenetic marks such as covalent histone modification and DNA methylation are crucial for mitotically and meiotically inherited cellular memory-based plant immunity. However, the roles of individual players in the epigenetic regulation of plant immunity are not fully understood. Here we reveal the functions of two Arabidopsis thaliana homologs of human lysine-specific demethylase1-like1, LDL1 and LDL2, in the maintenance of methyl groups at lysine 4 of histone H3 and in plant immunity to Pseudomonas syringae infection. The growth of virulent P. syringae strains was reduced in ldl1 and ldl2 single mutants compared to wild-type plants. Local and systemic disease resistance responses, which coincided with the rapid, robust transcription of defense-related genes, were more stably expressed in ldl1 ldl2 double mutants than in the single mutants. At the nucleosome level, mono-methylated histone H3K4 accumulated in ldl1 ldl2 plants genome-wide and in the mainly promoter regions of the defense-related genes examined in this study. Furthermore, in silico comparative analysis of RNA-sequencing and chromatin immunoprecipitation data suggested that several WRKY transcription factors, e.g., WRKY22/40/70, might be partly responsible for the enhanced immunity of ldl1 ldl2. These findings suggest that LDL1 and LDL2 control the transcriptional sensitivity of a group of defense-related genes to establish a primed defense response in Arabidopsis.

Regulation of chlorogenic acid, flavonoid, and iridoid biosynthesis by histone H3K4 and H3K9 methylation in Lonicera japonica

Lonicera japonica is used in Chinese herbal medicines with a wide spectrum of pharmacological properties associated with chlorogenic acid, flavonoid and iridoid. The biosynthesis of these compounds could be affected by genetic inheritance and epigenetic modification. However, the mechanisms that regulate the expression of genes involved in the biosynthesis of these compounds are rarely known. The results of qRT-PCR showed that the biosynthesis gene expression of these compounds was related to histone H3K4 and H3K9 methylation levels. These active compounds content of L. japonica were measured by UPLC-MS/MS. H3K4me3 showed a positive correlation with chlorogenic acid and loganic acid content, and H3K9me positively correlated with luteolin content. The correlation between histone methylation levels and the levels of luteolin and loganic acid in L. japonica from different producing areas validate the regulatory role of histone methylation in biosynthesis of bioactive compounds. Our study demonstrated a potential regulatory network of H3K9/H3K4 methylation to gene expression and content of secondary metabolites, and provided a basis for understanding the mechanism underlying the variation of major bioactive compounds in L. japonica.

Epigenetic Mechanisms of Plant Adaptation to Biotic and Abiotic Stresses

Unlike animals, plants are immobile and could not actively escape the effects of aggressive environmental factors, such as pathogenic microorganisms, insect pests, parasitic plants, extreme temperatures, drought, and many others. To counteract these unfavorable encounters, plants have evolved very high phenotypic plasticity. In a rapidly changing environment, adaptive phenotypic changes often occur in time frames that are too short for the natural selection of adaptive mutations. Probably, some kind of epigenetic variability underlines environmental adaptation in these cases. Indeed, isogenic plants often have quite variable phenotypes in different habitats. There are examples of successful “invasions” of relatively small and genetically homogenous plant populations into entirely new habitats. The unique capability of quick environmental adaptation appears to be due to a high tendency to transmit epigenetic changes between plant generations. Multiple studies show that epigenetic memory serves as a mechanism of plant adaptation to a rapidly changing environment and, in particular, to aggressive biotic and abiotic stresses. In wild nature, this mechanism underlies, to a very significant extent, plant capability to live in different habitats and endure drastic environmental changes. In agriculture, a deep understanding of this mechanism could serve to elaborate more effective and safe approaches to plant protection.

Arabidopsis SDG8 Potentiates the Sustainable Transcriptional Induction of the Pathogenesis-Related Genes PR1 and PR2 During Plant Defense Response

Post-translational covalent modifications of histones play important roles in modulating chromatin structure and are involved in the control of multiple developmental processes in plants. Here we provide insight into the contribution of the histone lysine methyltransferase SET DOMAIN GROUP 8 (SDG8), implicated in histone H3 lysine 36 trimethylation (H3K36me3), in connection with RNA polymerase II (RNAPII) to enhance Arabidopsis immunity. We showed that even if the sdg8-1 loss-of-function mutant, defective in H3K36 methylation, displayed a higher sensitivity to different strains of the bacterial pathogen Pseudomonas syringae, effector-triggered immunity (ETI) still operated, but less efficiently than in the wild-type (WT) plants. In sdg8-1, the level of the plant defense hormone salicylic acid (SA) was abnormally high under resting conditions and was accumulated similarly to WT at the early stage of pathogen infection but quickly dropped down at later stages. Concomitantly, the transcription of several defense-related genes along the SA signaling pathway was inefficiently induced in the mutant. Remarkably, albeit the defense genes PATHOGENESIS-RELATED1 (PR1) and PR2 have retained responsiveness to exogenous SA, their inductions fade more rapidly in sdg8-1 than in WT. At chromatin, while global levels of histone methylations were found to be stable, local increases of H3K4 and H3K36 methylations as well as RNAPII loading were observed at some defense genes following SA-treatments in WT. In sdg8-1, the H3K36me3 increase was largely attenuated and also the increases of H3K4me3 and RNAPII were frequently compromised. Lastly, we demonstrated that SDG8 could physically interact with the RNAPII C-terminal Domain, providing a possible link between RNAPII loading and H3K36me3 deposition. Collectively, our results indicate that SDG8, through its histone methyltransferase activity and its physical coupling with RNAPII, participates in the strong transcriptional induction of some defense-related genes, in particular PR1 and PR2, to potentiate sustainable immunity during plant defense response to bacterial pathogen.

CER16 Inhibits Post-Transcriptional Gene Silencing of CER3 to Regulate Alkane Biosynthesis

The aerial surfaces of land plants have a protective layer of cuticular wax. Alkanes are common components of these waxes, and their abundance is affected by a range of stresses. The CER16 protein has been implicated in alkane biosynthesis in the cuticular wax of Arabidopsis (Arabidopsis thaliana). Here, we identified two new mutant alleles of CER16 in Arabidopsis resulting in production of less wax with dramatically fewer alkanes than the wild type. Map-based cloning with genetic analysis revealed that the cer16 phenotype was caused by complete loss of AT5G44150, encoding a protein with no known domains or motifs. Comparative transcriptomic analysis revealed that transcripts of CER3, previously shown to play a principal role in alkane production, were markedly reduced in the cer16 mutants. To define the relationship between CER3 and CER16, we transformed the full CER3 gene into a cer16 mutant. Transgenic CER3 expression was silenced, and levels of small interfering RNAs targeting CER3 were significantly increased. Mutating two major components of the RNA-silencing machinery in a cer16 genetic background restored CER3 transcript levels to wild-type levels, with the stems restored to wild-type glaucousness. We suggest that CER16 deficiency induces post-transcriptional gene silencing of both endogenous and exogenous expression of CER3.

The Histone Marks Signature in Exonic and Intronic Regions Is Relevant in Early Response of Tomato Genes to Botrytis cinerea and in miRNA Regulation

Research into the relationship between epigenetic regulation and resistance to biotic stresses provides alternatives for plant protection and crop improvement. To unravel the mechanisms underlying tomato responses to Botrytis cinerea, we performed a chromatin immunoprecipitation (ChIP) analysis showing the increase in H3K9ac mark along the early induced genes SlyDES, SlyDOX1, and SlyLoxD encoding oxylipin-pathway enzymes, and SlyWRKY75 coding for a transcriptional regulator of hormonal signaling. This histone mark showed a more distinct distribution than the previously studied H3K4me3. The RNAPol-ChIP analysis reflected the actual gene transcription associated with increased histone modifications. A different pattern of marks in the oxylipin-related genes against P. syringae supported a pathogen-specific profile, while no significant differences occurred in SlyWRKY75. The epigenetic regulation of SlyWRKY75 by the intron-binding miR1127-3p was supported by the presence of SlyWRKY75 pre-mRNA in control plants. Interestingly, mRNA was found to be accumulated in response to B. cinerea and P. syringae, while reduction in miRNA only occurred against B. cinerea. The intronic region presented a similar pattern of marks than the rest of the gene in both pathosystems, except for H3K4me3 in the miRNA binding site upon B. cinerea. We located the gene encoding Sly-miR1127-3p, which presented reduced H3K4me3 on its promoter against B. cinerea.

Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum

BACKGROUND

Dendrobium catenatum, as a precious Chinese herbal medicine, is an epiphytic orchid plant, which grows on the trunks and cliffs and often faces up to diverse environmental stresses. SET DOMAIN GROUP (SDG) proteins act as histone lysine methyltransferases, which are involved in pleiotropic developmental events and stress responses through modifying chromatin structure and regulating gene transcription, but their roles in D. catenatum are unknown.

RESULTS

In this study, we identified 44 SDG proteins from D. catenatum genome. Subsequently, comprehensive analyses related to gene structure, protein domain organization, and phylogenetic relationship were performed to evaluate these D. catenatum SDG (DcSDG) proteins, along with the well-investigated homologs from the model plants Arabidopsis thaliana and Oryza sativa as well as the newly characterized 42 SDG proteins from a closely related orchid plant Phalaenopsis equestris. We showed DcSDG proteins can be grouped into eight distinct classes (I~VII and M), mostly consistent with the previous description. Based on the catalytic substrates of the reported SDG members mainly in Arabidopsis, Class I (E(z)-Like) is predicted to account for the deposition of H3K27me2/3, Class II (Ash-like) for H3K36me, Class III (Trx/ATX-like) for H3K4me2/3, Class M (ATXR3/7) for H3K4me, Class IV (Su (var)-like) for H3K27me1, Class V (Suv-like) for H3K9me, as well as class VI (S-ET) and class VII (RBCMT) for methylation of both histone and non-histone proteins. RNA-seq derived expression profiling showed that DcSDG proteins usually displayed wide but distinguished expressions in different tissues and organs. Finally, environmental stresses examination showed the expressions of DcASHR3, DcSUVR3, DcATXR4, DcATXR5b, and DcSDG49 are closely associated with drought-recovery treatment, the expression of DcSUVH5a, DcATXR5a and DcSUVR14a are significantly influenced by low temperature, and even 61% DcSDG genes are in response to heat shock.

CONCLUSIONS

This study systematically identifies and classifies SDG genes in orchid plant D. catenatum, indicates their functional divergence during the evolution, and discovers their broad roles in the developmental programs and stress responses. These results provide constructive clues for further functional investigation and epigenetic mechanism dissection of SET-containing proteins in orchids.

H2Bub1 Regulates RbohD-Dependent Hydrogen Peroxide Signal Pathway in the Defense Responses to Verticillium dahliae Toxins

Histone H2B monoubiquitination (H2Bub1) plays critical roles in regulating growth and development as well as stress responses in Arabidopsis (Arabidopsis thaliana). In this study, we used wild-type and HUB1 and HUB2 loss-of-function Arabidopsis plants to elucidate the mechanisms involved in the regulation of the plant's defense responses to Verticillium dahliae toxins (Vd-toxins). We demonstrated that HUB-mediated H2Bub1 regulates the expression of the NADPH oxidase RbohD by enhancing the enrichment of histone H3 trimethylated on Lys-4 in response to Vd-toxins. RbohD-dependent hydrogen peroxide (H₂O₂) signaling is a critical modulator in the defense response against Vd-toxins. Moreover, H2Bub1 also affects posttranscriptional mitogen-activated protein kinase (or MPK) signaling. H2Bub1 was required for the activation of MPK3 and MPK6. MPK3 and MPK6 are involved in regulating RbohD-mediated H₂O₂ production. MPK3 and MPK6 are associated with protein tyrosine phosphatases (PTPs), such as Tyr-specific phosphatase1 and mitogen-activated protein kinases phosphatase1, which negatively regulated H₂O₂ production. In addition, H2Bub1 is involved in regulating the expression of WRKY33 WRKY33 directly binds to RbohD promoter and functions as a transcription factor to regulate the expression of RbohD Collectively, our results indicate that H2Bub1 regulates the NADPH oxidase RbohD-dependent H₂O₂ production and that the PTP-MPK3/6-WRKY pathway plays an important role in the regulation of RbohD-dependent H₂O₂ signaling in defense responses to Vd-toxins in Arabidopsis.

SDG8-Mediated Histone Methylation and RNA Processing Function in the Response to Nitrate Signaling

Chromatin modification has gained increased attention for its role in the regulation of plant responses to environmental changes, but the specific mechanisms and molecular players remain elusive. Here, we show that the Arabidopsis (Arabidopsis thaliana) histone methyltransferase SET DOMAIN GROUP8 (SDG8) mediates genome-wide changes in H3K36 methylation at specific genomic loci functionally relevant to nitrate treatments. Moreover, we show that the specific H3K36 methyltransferase encoded by SDG8 is required for canonical RNA processing, and that RNA isoform switching is more prominent in the sdg8-5 deletion mutant than in the wild type. To demonstrate that SDG8-mediated regulation of RNA isoform expression is functionally relevant, we examined a putative regulatory gene, CONSTANS, CO-like, and TOC1 101 (CCT101), whose nitrogen-responsive isoform-specific RNA expression is mediated by SDG8. We show by functional expression in shoot cells that the different RNA isoforms of CCT101 encode distinct regulatory proteins with different effects on genome-wide transcription. We conclude that SDG8 is involved in plant responses to environmental nitrogen supply, affecting multiple gene regulatory processes including genome-wide histone modification, transcriptional regulation, and RNA processing, and thereby mediating developmental and metabolic processes related to nitrogen use.

Metatranscriptomic Analysis of Multiple Environmental Stresses Identifies RAP2.4 Gene Associated with Arabidopsis Immunity to Botrytis cinerea

In this study, we aimed to identify common genetic components during stress response responsible for crosstalk among stresses, and to determine the role of differentially expressed genes in Arabidopsis-Botrytis cinerea interaction. Of 1,554 B. cinerea up-regulated genes, 24%, 1.4% and 14% were induced by biotic, abiotic and hormonal treatments, respectively. About 18%, 2.5% and 22% of B. cinerea down-regulated genes were also repressed by the same stress groups. Our transcriptomic analysis indicates that plant responses to all tested stresses can be mediated by commonly regulated genes; and protein-protein interaction network confirms the cross-interaction between proteins regulated by these genes. Upon challenges to individual or multiple stress(es), accumulation of signaling molecules (e.g. hormones) plays a major role in the activation of downstream defense responses. In silico gene analyses enabled us to assess the involvement of RAP2.4 (related to AP2.4) in plant immunity. Arabidopsis RAP2.4 was repressed by B. cinerea, and its mutants enhanced resistance to the same pathogen. To the best of our knowledge, this is the first report demonstrating the role of RAP2.4 in plant defense against B. cinerea. This research can provide a basis for breeding programs to increase tolerance and improve yield performance in crops.

Proteomics of PTI and Two ETI Immune Reactions in Potato Leaves

Plants have a variety of ways to defend themselves against pathogens. A commonly used model of the plant immune system is divided into a general response triggered by pathogen-associated molecular patterns (PAMPs), and a specific response triggered by effectors. The first type of response is known as PAMP triggered immunity (PTI), and the second is known as effector-triggered immunity (ETI). To obtain better insight into changes of protein abundance in immunity reactions, we performed a comparative proteomic analysis of a PTI and two different ETI models (relating to Phytophthora infestans) in potato. Several proteins showed higher abundance in all immune reactions, such as a protein annotated as sterol carrier protein 2 that could be interesting since Phytophthora species are sterol auxotrophs. RNA binding proteins also showed altered abundance in the different immune reactions. Furthermore, we identified some PTI-specific changes of protein abundance, such as for example, a glyoxysomal fatty acid beta-oxidation multifunctional protein and a MAR-binding protein. Interestingly, a lysine histone demethylase was decreased in PTI, and that prompted us to also analyze protein methylation in our datasets. The proteins upregulated explicitly in ETI included several catalases. Few proteins were regulated in only one of the ETI interactions. For example, histones were only downregulated in the ETI-Avr2 interaction, and a putative multiprotein bridging factor was only upregulated in the ETI-IpiO interaction. One example of a methylated protein that increased in the ETI interactions was a serine hydroxymethyltransferase.

A Phytophthora effector recruits a host cytoplasmic transacetylase into nuclear speckles to enhance plant susceptibility

Oomycete pathogens secrete host cell-entering effector proteins to manipulate host immunity during infection. We previously showed that PsAvh52, an early-induced RxLR effector secreted from the soybean root rot pathogen, Phytophthora sojae, could suppress plant immunity. Here, we found that PsAvh52 is required for full virulence on soybean and binds to a novel soybean transacetylase, GmTAP1, in vivo and in vitro. PsAvh52 could cause GmTAP1 to relocate into the nucleus where GmTAP1 could acetylate histones H2A and H3 during early infection, thereby promoting susceptibility to P. sojae. In the absence of PsAvh52, GmTAP1 remained confined to the cytoplasm and did not modify plant susceptibility. These results demonstrate that GmTAP1 is a susceptibility factor that is hijacked by PsAvh52 in order to promote epigenetic modifications that enhance the susceptibility of soybean to P. sojae infection.

GCN5 contributes to stem cuticular wax biosynthesis by histone acetylation of CER3 in Arabidopsis

Cuticular wax is a major component of the surface cuticle of plants, which performs crucial functions in optimizing plant growth. Histone acetylation regulates gene expression in diverse biological processes, but its role in cuticular wax synthesis is not well understood. In this study, we observed that mutations of the Arabidopsis thaliana histone acetyltransferase GENERAL CONTROL NON-REPRESSED PROTEIN5 (GCN5) impaired the accumulation of stem cuticular wax. Three target genes of GCN5, ECERIFERUM3 (CER3), CER26, and CER1-LIKE1 (CER1-L1), were identified by RNA-seq and ChIP assays. H3K9/14 acetylation levels at the promoter regions of CER3, CER26, and CER1-L1 were consistently and significantly decreased in the gcn5-2 mutant as compared to the wild-type. Notably, overexpression of CER3 in the gcn5-2 mutant rescued the defect in stem cuticular wax biosynthesis. Collectively, these data demonstrate that GCN5 is involved in stem cuticular wax accumulation by modulating CER3 expression via H3K9/14 acetylation, which underlines the important role of histone acetylation in cuticular wax biosynthesis.

Determination of histone epigenetic marks in Arabidopsis and tomato genes in the early response to Botrytis cinerea

Determination of histone epigenetic marks in Arabidopsis and tomato genes in the early response to Botrytis cinerea may contribute to find biomarkers of the early detection of this devastating pathogen. Recent studies have linked epigenetic modifications with plant responses to biotic stresses. Information about specific histone marks upon necrotrophic pathogens is scarce. Here we wondered whether the altered responsiveness of specific genes in plants infected with Botrytis cinerea was associated with changes in chromatin structure. We performed a chromatin immunoprecipitation analysis that obtained differential epigenetic signature of activating marks H3K4me3, H3K9ac, and the repressor one H3K27me3 on both the promoter and the body of the highly induced PR1 in Arabidopsis plants infected with B. cinerea at 24 and 33 h after inoculation. We also determined the histone marks' profile in two differentially expressed genes in response to B. cinerea, as well as to oxidative stress, given its relevance in this infection. These are both the induced CYP71A13, which encodes a cytochrome P450 involved in camalexin synthesis, and is essential against this necrotroph and the repressed EXL7 (Exordium-like 1). We also adapted our protocol in tomato plants infected with B. cinerea. At 24 hpi, H3K4me3 level increased on the promoter and at different locations of the body of the genes induced upon B. cinerea, including DES (divinyl ethyl synthase), LoxD (lipoxygenase D), DOX1 (α-dioxygenase 1), PR2 (pathogenesis-related protein2), WRKY53 and WRKY33. The histone modifications determined herein will allow future studies on epigenetic marks and their transgenerational inheritance in plants infected with B. cinerea. In addition, the analyzed genes are potential biomarkers of B. cinerea infection that could contribute to its early detection in tomato and related crops.

Modify the Histone to Win the Battle: Chromatin Dynamics in Plant-Pathogen Interactions

Relying on an immune system comes with a high energetic cost for plants. Defense responses in these organisms are therefore highly regulated and fine-tuned, permitting them to respond pertinently to the attack of a microbial pathogen. In recent years, the importance of the physical modification of chromatin, a highly organized structure composed of genomic DNA and its interacting proteins, has become evident in the research field of plant-pathogen interactions. Several processes, including DNA methylation, changes in histone density and variants, and various histone modifications, have been described as regulators of various developmental and defense responses. Herein, we review the state of the art in the epigenomic aspects of plant immunity, focusing on chromatin modifications, chromatin modifiers, and their physiological consequences. In addition, we explore the exciting field of understanding how plant pathogens have adapted to manipulate the plant epigenomic regulation in order to weaken their immune system and thrive in their host, as well as how histone modifications in eukaryotic pathogens are involved in the regulation of their virulence.

Computational characterization of substrate and product specificities, and functionality of S-adenosylmethionine binding pocket in histone lysine methyltransferases from Arabidopsis, rice and maize

Histone lysine methylation by histone lysine methyltransferases (HKMTs) has been implicated in regulation of gene expression. While significant progress has been made to understand the roles and mechanisms of animal HKMT functions, only a few plant HKMTs are functionally characterized. To unravel histone substrate specificity, degree of methylation and catalytic activity, we analyzed Arabidopsis Trithorax-like protein (ATX), Su(var)3-9 homologs protein (SUVH), Su(var)3-9 related protein (SUVR), ATXR5, ATXR6, and E(Z) HKMTs of Arabidopsis, maize and rice through sequence and structure comparison. We show that ATXs may exhibit methyltransferase specificity toward histone 3 lysine 4 (H3K4) and might catalyse the trimethylation. Our analyses also indicate that most SUVH proteins of Arabidopsis may bind histone H3 lysine 9 (H3K9). We also predict that SUVH7, SUVH8, SUVR1, SUVR3, ZmSET20 and ZmSET22 catalyse monomethylation or dimethylation of H3K9. Except for SDG728, which may trimethylate H3K9, all SUVH paralogs in rice may catalyse monomethylation or dimethylation. ZmSET11, ZmSET31, SDG713, SDG715, and SDG726 proteins are predicted to be catalytically inactive because of an incomplete S-adenosylmethionine (SAM) binding pocket and a post-SET domain. E(Z) homologs can trimethylate H3K27 substrate, which is similar to the Enhancer of Zeste homolog 2 of humans. Our comparative sequence analyses reveal that ATXR5 and ATXR6 lack motifs/domains required for protein-protein interaction and polycomb repressive complex 2 complex formation. We propose that subtle variations of key residues at substrate or SAM binding pocket, around the catalytic pocket, or presence of pre-SET and post-SET domains in HKMTs of the aforementioned plant species lead to variations in class-specific HKMT functions and further determine their substrate specificity, the degree of methylation and catalytic activity.

Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants

Plants frequently have to weather both biotic and abiotic stressors, and have evolved sophisticated adaptation and defense mechanisms. In recent years, chromatin modifications, nucleosome positioning, and DNA methylation have been recognized as important components in these adaptations. Given their potential epigenetic nature, such modifications may provide a mechanistic basis for a stress memory, enabling plants to respond more efficiently to recurring stress or even to prepare their offspring for potential future assaults. In this review, we discuss both the involvement of chromatin in stress responses and the current evidence on somatic, intergenerational, and transgenerational stress memory.