JASMONATE-ZIM DOMAIN proteins engage Polycomb chromatin modifiers to modulate Jasmonate signaling in Arabidopsis

Transcription-metabolism analysis of various signal transduction pathways in Brassica chinensis L. exposed to PLA-MPs

Biodegradable plastics, regarded as an ideal substitute for traditional plastics, are increasingly utilized across various industries. However, due to their unique degradation properties, they can generate microplastics (MPs) at a faster rate, potentially posing a threat to plant development. This study employed transcriptomics and metabolomics to investigate the effects of polylactic acid microplastics (PLA-MPs) on the physiological and biochemical characteristics of Brassica chinensis L. over different periods. The findings indicated that exposure to varying concentrations of PLA-MPs had distinct influences on the growth and development of Brassica chinensis L. Transcriptomic analysis showed different concentrations of PLA-MPs directly influenced the expression of genes associated with plant hormones, such as SnRK2 and BnaA01g27170D. In addition, it was observed that these PLA-MPs also impacted plant growth and development by modulating the expression of other genes, eg. related to sulfur metabolism and glycerophosphate metabolism. Metabolomic analysis demonstrated alterations levels of metabolites such as L-glutamine, and arginine in response to PLA-MPs, which influenced pathways related to vitamin B6 metabolism, the one-carbon folate pool, glycerophospholipid metabolism, and cysteine. This study offers new insights into the potential impacts of biodegradable microplastics (BMPs) on plants and underscores the need for further investigation into the potentially more significant effects of BMPs on terrestrial ecosystems.

EMBRYONIC FLOWER 1 regulates male reproduction by repressing the jasmonate pathway downstream transcription factor MYB26

The evolutionarily conserved Polycomb repressive complexes (PRCs) mediate genome-wide transcriptional silencing and regulate a plethora of development, as well as environmental responses in multicellular organisms. The PRC2-catalyzed trimethylation of lysine 27 on histone H3 (H3K27me3) is recognized by reader-effector modules of Polycomb repressive complex 1 (PRC1) to implement gene repression. Here, we report that the Arabidopsis (Arabidopsis thaliana) H3K27me3 effector EMBRYONIC FLOWER 1 (EMF1) interacts with and constrains the R2R3 DNA binding transcription factor MYB26 by a eudicot-conserved motif in the stamen. MYB26 activates the transcription of two NAC domain genes, NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) and NST2, whose encoded proteins mediate anther secondary cell thickening in jasmonate (JA)-regulated stamen maturation. In this process, the transcriptional activity of MYB26 is negatively modulated by the JAZ-PRC repressive complex to precisely regulate the expression of NST1 and NST2. Disruption of EMF1 repression stimulates MYB26, leading to the excessive transcription of the two NAC genes and male sterility. Our results reveal a novel mechanism in Polycomb-mediated gene silencing and illustrate that the plant Polycomb complex regulates stamen development by preventing the hypersensitivity of JA responses in male reproduction.

Jasmonic acid mediates Ca2+ dependent signal transduction and plant immunity

Pathogen attacks can cause significant damage to plants, posing a threaten to global food production. Plants have developed exquisite methods to rapidly store a key defensive hormone jasmonate (JA), which stimulates their entire evolutionary adaptive response to pathogen attack. However, understanding how plants initiate JA biosynthesis in response to pathogen attacks has remained elusive. In this review, we discuss the newly discovered JAV1-JAZ8-WRKY51 (JJW) complex, which plays a crucial role in regulating JA production to deter insect attacks. The JJW complex inhibits JA production in plants, maintaining a low baseline level of JA that promotes optimal plant development. However, when plants are attacked by insects, a rapid influx of calcium stimulates the JAV1 calcium-dependent protein phosphate, leading to the breakdown of the JJW complex and the activation of JA production. This surge in JA levels, initiates plant defense mechanisms against the invading insects. These findings shed light on the intricate defense system that plants have evolved to combat diseases.

Genome-wide investigation of the TIFY transcription factors in alfalfa (Medicago sativa L.): identification, analysis, and expression

BACKGROUND

Alfalfa (Medicago sativa L.) is an essential leguminous forage with high nutrition and strong adaptability. The TIFY family is a plant-specific transcription factor identified in many plants. However, few reports have been reported on the phylogenetic analysis and gene expression profiling of TIFY family genes in alfalfa.

RESULT

A total of 84 TIFY genes belonging to 4 categories were identified in alfalfa, including 58 MsJAZs, 18 MsZMLs, 4 MsTIFYs and 4 MsPPDs, respectively. qRT-PCR data from 8 genes in different tissues revealed that most MsTIFY genes were highly expressed in roots. The expression of MsTIFY14 was up-regulated after different times in both thrips-resistant and susceptible alfalfa after thrips feeding, and the expression of the remaining MsTIFYs had a strong correlation with the time of thrips feeding. Different abiotic stresses, including drought, salt, and cold, could induce or inhibit the expression of MsTIFY genes to varying degrees. In addition, the eight genes were all significantly up-regulated by JA and/or SA. Interestingly, MsTIFY77 was induced considerably by all the biotic, abiotic, or plant hormones (JA or SA) except ABA.

CONCLUSION

Our study identified members of the TIFY gene family in alfalfa and analyzed their structures and possible functions. It laid the foundation for further research on the molecular functions of TIFYs in alfalfa.

An epigenetically mediated double negative cascade from EFD to HB21 regulates anther development

Epigenetic modifications are crucial for plant development. EFD (Exine Formation Defect) encodes a SAM-dependent methyltransferase that is essential for the pollen wall pattern formation and male fertility in Arabidopsis. In this study, we find that the expression of DRM2, a de novo DNA methyltransferase in plants, complements for the defects in efd, suggesting its potential de novo DNA methyltransferase activity. Genetic analysis indicates that EFD functions through HB21, as the knockout of HB21 fully restores fertility in efd mutants. DNA methylation and histone modification analyses reveal that EFD represses the transcription of HB21 through epigenetic mechanisms. Additionally, we demonstrate that HB21 directly represses the expression of genes crucial for pollen formation and anther dehiscence, including CalS5, RPG1/SWEET8, CYP703A2 and NST2. Collectively, our findings unveil a double negative regulatory cascade mediated by epigenetic modifications that coordinates anther development, offering insights into the epigenetic regulation of this process.

Biocontrol agents modulate phyllosphere microbiota interactions against pathogen Pseudomonas syringae

The pathogen Pseudomonas syringae, responsible for a variety of diseases, poses a considerable threat to global crop yields. Emerging biocontrol strategies employ antagonistic microorganisms, utilizing phyllosphere microecology and systemic resistance to combat this disease. However, the interactions between phyllosphere microbial dynamics and the activation of the plant defense system remain poorly understood. Here we show significant alterations in phyllosphere microbiota structure and plant gene expression following the application of biocontrol agents. We reveal enhanced collaboration and integration of Sphingomonas and Methylobacterium within the microbial co-occurrence network. Notably, Sphingomonas inhibits P. syringae by disrupting pathogen chemotaxis and virulence. Additionally, both Sphingomonas and Methylobacterium activate plant defenses by upregulating pathogenesis-related gene expression through abscisic acid, ethylene, jasmonate acid, and salicylic acid signaling pathways. Our results highlighted that biocontrol agents promote plant health, from reconstructing beneficial microbial consortia to enhancing plant immunity. The findings enrich our comprehension of the synergistic interplays between phyllosphere microbiota and plant immunity, offering potential enhancements in biocontrol efficacy for crop protection.

A pair of nuclear factor Y transcription factors act as positive regulators in jasmonate signaling and disease resistance in Arabidopsis

The plant hormone jasmonate (JA) regulates plant growth and immunity by orchestrating a genome-wide transcriptional reprogramming. In the resting stage, JASMONATE-ZIM DOMAIN (JAZ) proteins act as main repressors to regulate the expression of JA-responsive genes in the JA signaling pathway. However, the mechanisms underlying de-repression of JA-responsive genes in response to JA treatment remain elusive. Here, we report two nuclear factor Y transcription factors NF-YB2 and NF-YB3 (thereafter YB2 and YB3) play key roles in such de-repression in Arabidopsis. YB2 and YB3 function redundantly and positively regulate plant resistance against the necrotrophic pathogen Botrytis cinerea, which are specially required for transcriptional activation of a set of JA-responsive genes following inoculation. Furthermore, YB2 and YB3 modulated their expression through direct occupancy and interaction with histone demethylase Ref6 to remove repressive histone modifications. Moreover, YB2 and YB3 physically interacted with JAZ repressors and negatively modulated their abundance, which in turn attenuated the inhibition of JAZ proteins on the transcription of JA-responsive genes, thereby activating JA response and promoting disease resistance. Overall, our study reveals the positive regulators of YB2 and YB3 in JA signaling by positively regulating transcription of JA-responsive genes and negatively modulating the abundance of JAZ proteins.

PagJAZ5 regulates cambium activity through coordinately modulating cytokinin concentration and signaling in poplar

Wood is resulted from the radial growth paced by the division and differentiation of vascular cambium cells in woody plants, and phytohormones play important roles in cambium activity. Here, we identified that PagJAZ5, a key negative regulator of jasmonate (JA) signaling, plays important roles in enhancing cambium cell division and differentiation by mediating cytokinin signaling in poplar 84K (Populus alba × Populus glandulosa). PagJAZ5 is preferentially expressed in developing phloem and cambium, weakly in developing xylem cells. Overexpression (OE) of PagJAZ5m (insensitive to JA) increased cambium activity and xylem differentiation, while jaz mutants showed opposite results. Transcriptome analyses revealed that cytokinin oxidase/dehydrogenase (CKXs) and type-A response regulators (RRs) were downregulated in PagJAZ5m OE plants. The bioactive cytokinins were significantly increased in PagJAZ5m overexpressing plants and decreased in jaz5 mutants, compared with that in 84K plants. The PagJAZ5 directly interact with PagMYC2a/b and PagWOX4b. Further, we found that the PagRR5 is regulated by PagMYC2a and PagWOX4b and involved in the regulation of xylem development. Our results showed that PagJAZ5 can increase cambium activity and promote xylem differentiation through modulating cytokinin level and type-A RR during wood formation in poplar.

iJAZ-based approach to engineer lepidopteran pest resistance in multiple crop species

The fall armyworm (FAW) poses a significant threat to global crop production. Here we showed that overexpression of jasmonate ZIM-domain (JAZ) protein GhJAZ24 confers resistance to cotton bollworm and FAW, while also causing sterility in transgenic cotton by recruiting TOPLESS and histone deacetylase 6. We identified the NGR motif of GhJAZ24 that recognizes and binds the aminopeptidase N receptor, enabling GhJAZ24 to enter cells and disrupt histone deacetylase 3, leading to cell death. To overcome plant sterility associated with GhJAZ24 overexpression, we developed iJAZ (i, induced), an approach involving damage-induced expression and a switch from intracellular to extracellular localization of GhJAZ24. iJAZ transgenic cotton maintained fertility and showed insecticidal activity against cotton bollworm and FAW. In addition, iJAZ transgenic rice, maize and tobacco plants showed insecticidal activity against their lepidopteran pests, resulting in an iJAZ-based approach for generating alternative insecticidal proteins with distinctive mechanisms of action, thus holding immense potential for future crop engineering.

The Histone Variant H3.3 Is Required for Plant Growth and Fertility in Arabidopsis

Histones are the core components of the eukaryote chromosome, and have been implicated in transcriptional gene regulation. There are three major isoforms of histone H3 in Arabidopsis. Studies have shown that the H3.3 variant is pivotal in modulating nucleosome structure and gene transcription. However, the function of H3.3 during development remains to be further investigated in plants. In this study, we disrupted all three H3.3 genes in Arabidopsis. Two triple mutants, h3.3cr-4 and h3.3cr-5, were created by the CRISPR/Cas9 system. The mutant plants displayed smaller rosettes and decreased fertility. The stunted growth of h3.3cr-4 may result from reduced expression of cell cycle regulators. The shorter stamen filaments, but not the fertile ability of the gametophytes, resulted in reduced fertility of h3.3cr-4. The transcriptome analysis suggested that the reduced filament elongation of h3.3cr-4 was probably caused by the ectopic expression of several JASMONATE-ZIM DOMAIN (JAZ) genes, which are the key repressors of the signaling pathway of the phytohormone jasmonic acid (JA). These observations suggest that the histone variant H3.3 promotes plant growth, including rosette growth and filament elongation.

Xylobiose treatment triggers a defense-related response and alters cell wall composition

Plant cell wall-derived oligosaccharides, i.e., damage-associated molecular patterns (DAMPs), could be generated after pathogen attack or during normal plant development, perceived by cell wall receptors, and can alter immunity and cell wall composition. Therefore, we hypothesised that xylo-oligosaccharides (XOS) could act as an elicitor and trigger immune responses. To test this, we treated Arabidopsis with xylobiose (XB) and investigated different parameters. XB-treatment significantly triggered the generation of reactive oxygen species (ROS), activated MAPK protein phosphorylation, and induced callose deposition. The combination of XB (DAMP) and flg22 a microbe-associated molecular pattern (MAMP) further enhanced ROS response and gene expression of PTI marker genes. RNA sequencing analysis revealed that more genes were differentially regulated after 30 min compared to 24 h XB-treated leaves, which correlated with ROS response. Increased xylosidase activity and soluble xylose level after 30 min and 3 h of XB-treatment were observed which might have weakened the DAMP response. However, an increase in total cell wall sugar and a decrease in uronic acid level was observed at both 30 min and 24 h. Additionally, arabinose, rhamnose, and xylose levels were increased in 30 min, and glucose was increased in 24 h compared to mock-treated leaves. The level of jasmonic acid, abscisic acid, auxin, and cytokinin were also affected after XB treatment. Overall, our data revealed that the shortest XOS can act as a DAMP, which triggers the PTI response and alters cell wall composition and hormone level.

Assembly of JAZ-JAZ and JAZ-NINJA complexes in jasmonate signaling

Jasmonates (JAs) are plant hormones with crucial roles in development and stress resilience. They activate MYC transcription factors by mediating the proteolysis of MYC inhibitors called JAZ proteins. In the absence of JA, JAZ proteins bind and inhibit MYC through the assembly of MYC-JAZ-Novel Interactor of JAZ (NINJA)-TPL repressor complexes. However, JAZ and NINJA are predicted to be largely intrinsically unstructured, which has precluded their experimental structure determination. Through a combination of biochemical, mutational, and biophysical analyses and AlphaFold-derived ColabFold modeling, we characterized JAZ-JAZ and JAZ-NINJA interactions and generated models with detailed, high-confidence domain interfaces. We demonstrate that JAZ, NINJA, and MYC interface domains are dynamic in isolation and become stabilized in a stepwise order upon complex assembly. By contrast, most JAZ and NINJA regions outside of the interfaces remain highly dynamic and cannot be modeled in a single conformation. Our data indicate that the small JAZ Zinc finger expressed in Inflorescence Meristem (ZIM) motif mediates JAZ-JAZ and JAZ-NINJA interactions through separate surfaces, and our data further suggest that NINJA modulates JAZ dimerization. This study advances our understanding of JA signaling by providing insights into the dynamics, interactions, and structure of the JAZ-NINJA core of the JA repressor complex.

Histone H3 lysine 27 trimethylation suppresses jasmonate biosynthesis and signaling to affect male fertility under high temperature in cotton

High-temperature (HT) stress causes male sterility in crops, thus decreasing yields. To explore the possible contribution of histone modifications to male fertility under HT conditions, we defined the histone methylation landscape for the marks histone H3 lysine 27 trimethylation (H3K27me3) and histone H3 lysine 4 trimethylation (H3K4me3) by chromatin immunoprecipitation sequencing (ChIP-seq) in two differing upland cotton (Gossypium hirsutum) varieties. We observed a global disruption in H3K4me3 and H3K27me3 modifications, especially H3K27me3, in cotton anthers subjected to HT. HT affected the bivalent H3K4me3-H3K27me3 modification more than either monovalent modification. We determined that removal of H3K27me3 at the promoters of jasmonate-related genes increased their expression, maintaining male fertility under HT in the HT-tolerant variety at the anther dehiscence stage. Modulating jasmonate homeostasis or signaling resulted in an anther indehiscence phenotype under HT. Chemical suppression of H3K27me3 deposition increased jasmonic acid contents and maintained male fertility under HT. In summary, our study provides new insights into the regulation of male fertility by histone modifications under HT and suggests a potential strategy for improving cotton HT tolerance.

Control of histone demethylation by nuclear-localized α-ketoglutarate dehydrogenase

Methylations on nucleosomal histones play fundamental roles in regulating eukaryotic transcription. Jumonji C domain-containing histone demethylases (JMJs) dynamically control the level of histone methylations. However, how JMJ activity is generally regulated is unknown. We found that the tricarboxylic acid cycle-associated enzyme α-ketoglutarate (α-KG) dehydrogenase (KGDH) entered the nucleus, where it interacted with various JMJs to regulate α-KG-dependent histone demethylations by JMJs, and thus controlled genome-wide gene expression in plants. We show that nuclear targeting is regulated by environmental signals and that KGDH is enriched at thousands of loci in Arabidopsis thaliana. Chromatin-bound KGDH catalyzes α-KG decarboxylation and thus may limit its local availability to KGDH-coupled JMJs, inhibiting histone demethylation. Thus, our results uncover a regulatory mechanism for histone demethylations by JMJs.

Jasmonate perception: Ligand-receptor interaction, regulation, and evolution

Phytohormones integrate external environmental and developmental signals with internal cellular responses for plant survival and multiplication in changing surroundings. Jasmonate (JA), which might originate from prokaryotes and benefit plant terrestrial adaptation, is a vital phytohormone that regulates diverse developmental processes and defense responses against various environmental stresses. In this review, we first provide an overview of ligand-receptor binding techniques used for the characterization of phytohormone-receptor interactions, then introduce the identification of the receptor COI1 and active JA molecules, and finally summarize recent advances on the regulation of JA perception and its evolution.

SlMYC2 interacted with the SlTOR promoter and mediated JA signaling to regulate growth and fruit quality in tomato

Tomato (Solanum lycopersicum) is a major vegetable crop cultivated worldwide. The regulation of tomato growth and fruit quality has long been a popular research topic. MYC2 is a key regulator of the interaction between jasmonic acid (JA) signaling and other signaling pathways, and MYC2 can integrate the interaction between JA signaling and other hormone signals to regulate plant growth and development. TOR signaling is also an essential regulator of plant growth and development. However, it is unclear whether MYC2 can integrate JA signaling and TOR signaling during growth and development in tomato. Here, MeJA treatment and SlMYC2 overexpression inhibited the growth and development of tomato seedlings and photosynthesis, but increased the sugar-acid ratio and the contents of lycopene, carotenoid, soluble sugar, total phenol and flavonoids, indicating that JA signaling inhibited the growth of tomato seedlings and altered fruit quality. When TOR signaling was inhibited by RAP, the JA content increased, and the growth and photosynthesis of tomato seedlings decreased, indicating that TOR signaling positively regulated the growth and development of tomato seedlings. Further yeast one-hybrid assays showed that SlMYC2 could bind directly to the SlTOR promoter. Based on GUS staining analysis, SlMYC2 regulated the transcription of SlTOR, indicating that SlMYC2 mediated the interaction between JA and TOR signaling by acting on the promoter of SlTOR. This study provides a new strategy and some theoretical basis for tomato breeding.

Integration of mRNA and microRNA analysis reveals the molecular mechanisms underlying drought stress tolerance in maize (Zea mays L.)

Drought is among the most serious environmental issue globally, and seriously affects the development, growth, and yield of crops. Maize (Zea mays L.), an important crop and industrial raw material, is planted on a large scale worldwide and drought can lead to large-scale reductions in maize corn production; however, few studies have focused on the maize root system mechanisms underlying drought resistance. In this study, miRNA-mRNA analysis was performed to deeply analyze the molecular mechanisms involved in drought response in the maize root system under drought stress. Furthermore, preliminary investigation of the biological function of miR408a in the maize root system was also conducted. The morphological, physiological, and transcriptomic changes in the maize variety "M8186" at the seedling stage under 12% PEG 6000 drought treatment (0, 7, and 24 h) were analyzed. With prolonged drought stress, seedlings gradually withered, the root system grew significantly, and abscisic acid, brassinolide, lignin, glutathione, and trehalose content in the root system gradually increased. Furthermore, peroxidase activity increased, while gibberellic acid and jasmonic acid gradually decreased. Moreover, 32 differentially expressed miRNAs (DEMIRs), namely, 25 known miRNAs and 7 new miRNAs, and 3,765 differentially expressed mRNAs (DEMRs), were identified in maize root under drought stress by miRNA-seq and mRNA-seq analysis, respectively. Through combined miRNA-mRNA analysis, 16 miRNA-target gene pairs, comprising 9 DEMIRs and 15 DEMRs, were obtained. In addition, four metabolic pathways, namely, "plant hormone signal transduction", "phenylpropane biosynthesis", "glutathione metabolism", and "starch and sucrose metabolism", were predicted to have important roles in the response of the maize root system to drought. MiRNA and mRNA expression results were verified by real-time quantitative PCR. Finally, miR408a was selected for functional analysis and demonstrated to be a negative regulator of drought response, mainly through regulation of reactive oxygen species accumulation in the maize root system. This study helps to elaborate the regulatory response mechanisms of the maize root system under drought stress and predicts the biological functions of candidate miRNAs and mRNAs, providing strategies for subsequent mining for, and biological breeding to select for, drought-responsive genes in the maize root system.

Regulation of jasmonate signaling by reversible acetylation of TOPLESS in Arabidopsis

The plant hormone jasmonate (JA) regulates plant immunity and adaptive growth by orchestrating a genome-wide transcriptional program. Key regulators of JA-responsive gene expression include the master transcription factor MYC2, which is repressed by the conserved Groucho/Tup1-like corepressor TOPLESS (TPL) in the resting state. However, the mechanisms underlying TPL-mediated transcriptional repression of MYC2 activity and hormone-dependent switching between repression and de-repression remain enigmatic. Here, we report the regulation of TPL activity and JA signaling by reversible acetylation of TPL. We found that the histone acetyltransferase GCN5 could mediate TPL acetylation, which enhances its interaction with the NOVEL-INTERACTOR-OF-JAZ (NINJA) adaptor and promotes its recruitment to MYC2 target promoters, facilitating transcriptional repression. Conversely, TPL deacetylation by the histone deacetylase HDA6 weakens TPL-NINJA interaction and inhibits TPL recruitment to MYC2 target promoters, facilitating transcriptional activation. In the resting state, the opposing activities of GCN5 and HDA6 maintain TPL acetylation homeostasis, promoting transcriptional repression activity of TPL. In response to JA elicitation, HDA6 expression is transiently induced, resulted in decreased TPL acetylation and repressor activity, thereby transcriptional activation of MYC2 target genes. Thus, the GCN5-TPL-HDA6 module maintains the homeostasis of acetylated TPL, thereby determining the transcriptional state of JA-responsive genes. Our findings uncovered a mechanism by which the TPL corepressor activity in JA signaling is actively tuned in a rapid and reversible manner.

Jasmonate: A hormone of primary importance for plant metabolism

Over the years, jasmonates (JAs) have become recognized as one of the main plant hormones that regulate stress responses by activating defense programs and the production of specialized metabolites. High JA levels have been associated with reduced plant growth, supposedly as a result of the reallocation of carbon sources from primary growth to the biosynthesis of defense compounds. Recent advances suggest however that tight regulatory networks integrate several sensing pathways to steer plant metabolism, and thereby drive the trade-off between growth and defense. In this review, we discuss how JA influences primary metabolism and how it is connected to light-regulated processes, nutrient sensing and energy metabolism. Finally, we speculate that JA, in a conceptual parallelism with adrenaline for humans, overall boosts cellular processes to keep up with an increased metabolic demand during harsh times.

The Importance of Networking: Plant Polycomb Repressive Complex 2 and Its Interactors

Polycomb Repressive Complex 2 (PRC2) is arguably the best-known plant complex of the Polycomb Group (PcG) pathway, formed by a group of proteins that epigenetically represses gene expression. PRC2-mediated deposition of H3K27me3 has amply been studied in Arabidopsis and, more recently, data from other plant model species has also been published, allowing for an increasing knowledge of PRC2 activities and target genes. How PRC2 molecular functions are regulated and how PRC2 is recruited to discrete chromatin regions are questions that have brought more attention in recent years. A mechanism to modulate PRC2-mediated activity is through its interaction with other protein partners or accessory proteins. Current evidence for PRC2 interactors has demonstrated the complexity of its protein network and how far we are from fully understanding the impact of these interactions on the activities of PRC2 core subunits and on the formation of new PRC2 versions. This review presents a list of PRC2 interactors, emphasizing their mechanistic action upon PRC2 functions and their effects on transcriptional regulation.

Genome-Wide Analysis of the Gene Structure, Expression and Protein Interactions of the Peach (Prunus persica) TIFY Gene Family

The TIFY family is a plant-specific gene family involved in regulating many plant processes, such as development and growth, defense and stress responses, fertility and reproduction, and the biosynthesis of secondary metabolites. The v2.0 peach (Prunus persica) genome, which has an improved chromosome-scale assembly and contiguity, has recently been released, but a genome-wide investigation of the peach TIFY family is lacking. In this study, 16 TIFY family genes from the peach genome were identified according to the peach reference genome sequence information and further validated by cloning sequencing. The synteny, phylogenetics, location, structure, and conserved domains and motifs of these genes were analyzed, and finally, the peach TIFY family was characterized into 9 JAZ, 1 TIFY, 1 PPD and 5 ZML subfamily members. Expression profiles of peach JAZ, PPD, and ZML genes in various organs and fruit developmental stages were analyzed, and they showed limited effects with fruit ripening cues. Four TIFY members were significantly affected at the mRNA level by exogenous treatment with MeJA in the peach epicarp, and among them, PpJAZ1, PpJAZ4 and PpJAZ5 were significantly correlated with fruit epicarp pigmentation. In addition, the TIFY family member protein interaction networks established by the yeast two-hybrid (Y2H) assay not only showed similar JAZ-MYC2 and JAZ homo- and heterodimer patterns as those found in Arabidopsis but also extended the JAZ dimer network to ZML-ZML and JAZ-ZML interactions. The PpJAZ3-PpZML4 interaction found in this study suggests the potential formation of the ZML-JAZ-MYC complex in the JA-signaling pathway, which may extend our knowledge of this gene family's functions in diverse biological processes.

Resistance to Powdery Mildew in Qingke Involves the Accumulation of Aromatic Phenolamides Through Jasmonate-Mediated Activation of Defense-Related Genes

Powdery mildew (PM) leads to severe yield reduction in qingke (Hordeum vulgare L. var. nudum). Although studies have focused on identifying PM-related resistance genes, mechanistic insights into the metabolic regulation networks of resistance against PM have rarely been explored in qingke. Here, we integrated transcriptomic, proteomic and metabolomic data using PM-susceptible (G72) and PM-resistant (K69) accessions to systemically explore the mechanisms of PM resistance. The integrated results show that a rapidly transduction of jasmonic acid (JA) and (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile), and importantly, a inducing accumulation of aromatic PAs conferred qingke-specific resistance for PM stress. Functional analysis revealed that the four BAHD N-acyltransferase genes were responsible for the synthesis of aliphatic and aromatic PAs. The expression of the four genes are induced by methyl jasmonate (MeJA) and PM treatment. Co-expression network analysis shows that a histone lysine demethylase, JMJ705 gene, also induced by MeJA and PM treatment, had highly correlation with PAs biosynthesis. Chromatin immunoprecipitation (ChIP)-seq assays revealed that the level of trimethylated histone H3 lysine 27 (H3K27me3) of the four genes in MeJA and PM-treated plants was significantly reduced. Overall, our results suggest that a novel strategy for jasmonic acid signal-mediated demethylation controlling the accumulation of aromatic PAs to enhance plant immune resistance through removal of H3K27me3 and activating defense-related gene expression.

Interaction between Rag genes results in a unique synergistic transcriptional response that enhances soybean resistance to soybean aphids

BACKGROUND

Pyramiding different resistance genes into one plant genotype confers enhanced resistance at the phenotypic level, but the molecular mechanisms underlying this effect are not well-understood. In soybean, aphid resistance is conferred by Rag genes. We compared the transcriptional response of four soybean genotypes to aphid feeding to assess how the combination of Rag genes enhanced the soybean resistance to aphid infestation.

RESULTS

A strong synergistic interaction between Rag1 and Rag2, defined as genes differentially expressed only in the pyramid genotype, was identified. This synergistic effect in the Rag1/2 phenotype was very evident early (6 h after infestation) and involved unique biological processes. However, the response of susceptible and resistant genotypes had a large overlap 12 h after aphid infestation. Transcription factor (TF) analyses identified a network of interacting TF that potentially integrates signaling from Rag1 and Rag2 to produce the unique Rag1/2 response. Pyramiding resulted in rapid induction of phytochemicals production and deposition of lignin to strengthen the secondary cell wall, while repressing photosynthesis. We also identified Glyma.07G063700 as a novel, strong candidate for the Rag1 gene.

CONCLUSIONS

The synergistic interaction between Rag1 and Rag2 in the Rag1/2 genotype can explain its enhanced resistance phenotype. Understanding molecular mechanisms that support enhanced resistance in pyramid genotypes could facilitate more directed approaches for crop improvement.

Chromatin enrichment for proteomics in plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling

Background

Covalent modifications of core histones govern downstream DNA-templated processes such as transcription by altering chromatin structure and function. Previously, we reported that the plant homeodomain protein ALFIN-LIKE 6 (AL6), a bona fide histone reader that preferentially binds trimethylated lysin 4 on histone 3 (H3K4me3), is critical for recalibration of cellular phosphate (Pi) homeostasis and root hair elongation under Pi-deficient conditions.

Results

Here, we demonstrate that AL6 is also involved in the response of Arabidopsis seedlings to jasmonic acid (JA) during skotomorphogenesis, possibly by modulating chromatin dynamics that affect the transcriptional regulation of JA-responsive genes. Dark-grown al6 seedlings showed a compromised reduction in hypocotyl elongation upon exogenously supplied JA, a response that was calibrated by the availability of Pi in the growth medium. A comparison of protein profiles between wild-type and al6 mutant seedlings using a quantitative Chromatin Enrichment for Proteomics (ChEP) approach, that we modified for plant tissue and designated ChEP-P (ChEP in Plants), yielded a comprehensive suite of chromatin-associated proteins and candidates that may be causative for the mutant phenotype.

Conclusions

Altered abundance of proteins involved in chromatin organization in al6 seedlings suggests a role of AL6 in coordinating the deposition of histone variants upon perception of internal or environmental stimuli. Our study shows that ChEP-P is well suited to gain holistic insights into chromatin-related processes in plants. Data are available via ProteomeXchange with identifier PXD026541.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08160-6.

Dynamics of H3K27me3 Modification on Plant Adaptation to Environmental Cues

Given their sessile nature, plants have evolved sophisticated regulatory networks to confer developmental plasticity for adaptation to fluctuating environments. Epigenetic codes, like tri-methylation of histone H3 on Lys27 (H3K27me3), are evidenced to account for this evolutionary benefit. Polycomb repressive complex 2 (PRC2) and PRC1 implement and maintain the H3K27me3-mediated gene repression in most eukaryotic cells. Plants take advantage of this epigenetic machinery to reprogram gene expression in development and environmental adaption. Recent studies have uncovered a number of new players involved in the establishment, erasure, and regulation of H3K27me3 mark in plants, particularly highlighting new roles in plants’ responses to environmental cues. Here, we review current knowledge on PRC2-H3K27me3 dynamics occurring during plant growth and development, including its writers, erasers, and readers, as well as targeting mechanisms, and summarize the emerging roles of H3K27me3 mark in plant adaptation to environmental stresses.