Induced Genome-Wide Binding of Three Arabidopsis WRKY Transcription Factors during Early MAMP-Triggered Immunity

NMD-mediated posttranscriptional regulation fine-tunes the NLR-WRKY regulatory module to modulate bacterial defense response

Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic surveillance system that maintains transcriptome integrity by degrading aberrant RNA transcripts. NMD ensures proper growth and development by preventing autoimmunity through the direct regulation of nucleotide-binding, leucine-rich repeat (NLR) genes. Whether NMD directly regulates WRKY genes remains unclear, despite their upregulation in NMD-deficient plants, and potential feedback between NLRs and WRKYs is also poorly understood. In this study, we showed that NMD also directly regulates a subset of WRKY (WRKY15, 18, 25, 33, 46, 60, and 70) genes, particularly at lower temperatures (16°C). NMD signature-containing transcripts of WRKY46 and WRKY70, selected as representative NMD-regulated WRKY genes, showed increased half-lives in NMD-deficient mutants. Transcriptome analyses showed that these seven NMD-regulated WRKY genes are induced in response to bacterial infection. Potential homologues of these seven NMD-regulated WRKY genes in maize and rice showed similar induction in response to bacterial pathogen infection. Furthermore, these NMD-regulated WRKY genes are induced in plants overexpressing RESISTANT TO P. SYRINGAE 4 (RPS4) in a temperature-dependent manner. By using ChIP-seq and DAP-seq data of WRKY transcription factors, we showed that WRKYs potentially regulate a significant number of NLR genes by directly binding to the W-box in their promoter regions. Taken together, our findings revealed that in addition to the NLRs, the NMD machinery also regulates WRKY genes to keep the basal defense levels in check and the WRKY transcription factors directly regulate NLR genes to constitutes a positive feedback regulatory loop to optimize the plant response to invading pathogens.

Development of a Matrix-Assisted Laser Desorption Ionization High Resolution Mass Spectrometry Method for the Quantification of Camalexin and Scopoletin in Arabidopsis thaliana

RATIONALE

Understanding plant defense mechanisms against pathogens is essential for enhancing agricultural productivity and crop protection. This study focuses on the quantification of camalexin and scopoletin, two critical phytoalexins in Arabidopsis thaliana, using mass spectrometry techniques. Precise measurement of these compounds provides insights into plant resistance and supports agricultural research.

METHODS

Camalexin and scopoletin were quantified using matrix-assisted laser desorption ionization high-resolution mass spectrometry (MALDI-HRMS). The matrix and solvent conditions were optimized to maximize sensitivity and accuracy. MS/MS experiments confirmed compound identification with high mass accuracy (mass error < 5 ppm). The method was validated through comparative analysis of wild-type (WT) and mutant Arabidopsis lines, using internal standards and multiple replicates to ensure precision and reliability.

RESULTS

The method exhibited high linearity for scopoletin (R2 = 0.9992) and camalexin (R2 = 0.9987) across concentration ranges of 0.16-5 and 0.31-5 μM, respectively. Limits of detection (LOD) were 0.16 μM for camalexin and 0.04 μM for scopoletin, with limits of quantification (LOQ) at 0.2 μM and 0.08 μM, respectively. Samples analysis demonstrated reliable quantification in WT and mutant lines, with significant reductions in camalexin and scopoletin levels observed in the atwrky33-2 and atmyb15-1 mutants, respectively. Additionally, the method detected sub-physiological concentrations, confirming its sensitivity and robustness for low-level detection.

CONCLUSIONS

This study presents a validated, precise, and accurate MALDI-HRMS method for the quantification of camalexin and scopoletin in Arabidopsis thaliana. The approach not only enhances understanding of plant defense mechanisms but also offers potential applications for biotechnological and agricultural research, especially for investigating genetic variations and stress-induced phytoalexin production.

The physiological and molecular mechanisms of WRKY transcription factors regulating drought tolerance: A review

WRKY transcription factors (TFs) play crucial roles in responses to abiotic and biotic stresses that significantly impact plant growth and development. Advancements in molecular biology and sequencing technologies have elevated WRKY TF studies from merely determining expression patterns and functional characterization to uncovering molecular regulatory networks. Numerous WRKY TFs regulate drought tolerance in plants through various regulatory networks. This review details the physiological and molecular mechanisms of WRKY TFs regulating drought tolerance. The review focuses on the WRKY TFs involved in the phytohormone and metabolic pathways associated with the drought stress response and the multiple functions of these WRKY TFs, including biotic and abiotic stress responses and their participation in plant growth and development.

Infiltration-RNAseq Reveals Enhanced Defense Responses in Nicothiana benthamiana Leaves Overexpressing the Banana Gene MaWRKY45

The banana gene MaWRKY45 gene encodes a WRKY transcription factor (TF) that is closely related to OsWRKY45, which is a master regulator of defense responses in rice. MaWRKY45 is a transcription factor with proven transactivation activity and nuclear localization. Its expression is upregulated by the defense phytohormones salicylic acid (SA) and jasmonic acid (JA). Despite these findings, its transcriptome-wide impact during overexpression remains unexplored. Accordingly, the present study employed the Infiltration-RNAseq method to identify differentially expressed genes (DEGs) resulting from the overexpression of MaWRKY45 in the leaves of the model plant Nicotiana benthamiana. A total of 2473 DEGs were identified in N. benthamiana leaves overexpressing the banana gene MaWRKY45. Of these, 1092 were up-regulated and 1381 were down-regulated. Among the genes that were found to be up-regulated, those encoding proteins that are involved in plant immunity were identified. These included disease resistance receptors, proteins that are involved in cell wall reinforcement, proteins that possess antimicrobial and insecticidal activities, and defense-related TFs. It was thus concluded that the function of the banana gene MaWRKY45 is associated with the plant immune system, and that its overexpression can lead to enhance defense responses.

Lattice light-sheet microscopy allows for super-resolution imaging of receptors in leaf tissue

Plant leaf tissues are difficult to image via fluorescence microscopy due to the presence of chlorophyll and other pigments, which provide large background fluorescence. Lattice light-sheet microscopy offers the advantage of using Bessel beams to illuminate a thin focal region of interest for microscopy, allowing for the excitation of fluorescent molecules within this region without surrounding chlorophyll-like objects outside of the region of interest. Here, we apply STORM super-resolution techniques to observe receptor-like kinases in Arabidopsis thaliana leaf cells. By applying this technique with lattice light-sheet microscopy, we can localize immune-response proteins at sub-100-nm length scales and reconstruct three-dimensional locations of proteins within individual leaf cells. Using this technique, we observed the effect of the ATP and flg22 elicitors, where we observed a significant degree of internalization of cognate receptors P2K1 and FLS2. We were also able to similarly observe differences in colocalization due to stimulation with these elicitors, whereby we observe proteins on the membrane becoming less colocalized as a result of stimulation, suggesting an immune-response mechanism involving receptor internalization via distinct pathways. These data show lattice light-sheet microscopy's capabilities for imaging tissue with problematic background fluorescence that otherwise makes super-resolution fluorescence microscopy difficult.

NbNAC1 enhances plant immunity against TMV by regulating isochorismate synthase 1 expression and the SA pathway

Salicylic acid (SA) plays important roles in plant local and systemic resistance. Isochorismate synthase 1 (ICS1) is a key enzyme in SA synthesis. Pathogens infection triggered the ICS1 expression and induced SA production. However, the molecular regulation mechanism of ICS1 against virus infection remains unclear. Here, we employed molecular genetics and physiobiochemical approaches to confirm a transcription factor NbNAC1 from Nicotiana benthamiana is a positive regulator of resistance against tobacco mosaic virus (TMV). The pathways NbNAC1 and NbICS1 can be triggered by TMV infection. Silencing NbNAC1 accelerated TMV-induced oxidative damage and increased reactive oxygen species (ROS) production. It also weakened both local and systemic resistance against TMV and decreased the expression of NbICS1, SA signaling gene NbNPR1, and SA defense-related genes. The effects of NbNAC1-silencing were restored by overexpression of NbICS1 or foliar SA applications. Overexpressing NbNAC1 prevented oxidative damage and reduced the production of ROS, enhanced plant resistance against viral pathogen, and activated NbICS1 expression, and SA downstream signaling and defense-related genes. NbNAC1 localized in nuclear and emerged the ability of transcriptional regulation. ChIP and EMSA results indicated that NbNAC1 directly binds to a fragment containing GAAATT motif of NbICS1 promoter. Luciferase reporter assays confirmed that NbNAC1 activates NbICS1 expression. Taken together, our results demonstrate that NbNAC1 plays a critical role in plant immunity through activation of SA production.

Genome-wide identification of the bHLH gene family in Scutellaria baicalensis and their relationship with baicalin biosynthesis under drought stress

The bHLH gene family plays a critical role in regulating internal responses in plants. Although the pharmacological properties of Scutellaria baicalensis have been extensively studied, its bHLH gene family remains poorly investigated. In this study, 142 SbbHLH genes were identified using the complete genome data of S. baicalensis. Phylogenetic and conserved motif analyses were performed. Gene duplication events were analyzed, and cis-element analysis was conducted to explore regulatory factors. The expression patterns of these genes in different tissues and under drought stress were investigated using transcriptome data and qRT-PCR analysis. Phylogenetic and conserved motif analyses revealed that the gene structures within each SbbHLH clade are relatively conserved. Gene duplication analysis identified 29 duplication events in the SbbHLH gene family, most of which involved gene pairs under purifying selection. Cis-element analysis revealed that these genes are regulated by various environmental and hormonal factors. Transcriptomic data and qRT-PCR results demonstrated tissue-specific expression patterns for the 142 SbbHLH genes. Additionally, bHLH genes potentially involved in baicalin biosynthesis were identified under drought stress. The findings suggest that under drought stress, SbbHLH74, SbbHLH98, and SbbHLH142 are regulated by a network centered on SbbHLH53, which enhances baicalin biosynthesis. In conclusion, this study provides a comprehensive analysis of the bHLH gene family in S. baicalensis and identifies 4 potential SbbHLH genes involved in regulating baicalin biosynthesis under drought stress.

The coordinated responses of host plants to diverse N-acyl homoserine lactones

In nature, co-evolution shaped balanced entities of host plants and their associated microorganism. Plants maintain this balance by detecting their associated microorganism and coordinating responses to them. Quorum sensing (QS) is a widespread bacterial cell-to-cell communication mechanism to modulate the collective behavior of bacteria. As a well-characterized QS signal, N-acyl homoserine lactones (AHL) also influence plant fitness. Plants need to coordinate their responses to diverse AHL molecules since they might host bacteria producing various AHL. This opinion paper discusses plants response to a mixture of multiple AHL molecules. The function of various phytohormones and WRKY transcription factors seems to be characteristic for plants' response to multiple AHL. Additionally, the perspectives and possible approaches to facilitate further research and the application of AHL-producing bacteria are discussed.

Multiple functions and regulatory networks of WRKY33 and its orthologs

Arabidopsis thaliana WRKY33 is currently one of the most studied members of the Group I WRKY transcription factor family. Research has confirmed that WRKY33 is involved in the regulation of various biological and abiotic stresses and occupies a central position in the regulatory network. The functional studies of orthologous genes of WRKY33 from other species are also receiving increasing attention. In this article, we summarized thirty-eight orthologous genes of AtWKRY33 from twenty-five different species. Their phylogenetic relationship and conserved WRKY domain were analyzed and compared. Similar to AtWKRY33, the well-studied orthologous gene members from rice and tomato also have multiple functions. In addition to playing important regulatory roles in responding to their specific pathogens, they are also involved in regulating various abiotic stresses and development. AtWKRY33 exerts its multiple functions through a complex regulatory network. Upstream transcription factors or other regulatory factors activate or inhibit the expression of AtWKRY33 at the chromatin and transcriptional levels. Interacting proteins affect the transcriptional activity of AtWKRY33 through phosphorylation, ubiquitination, SUMOylation, competition, or cooperation. The downstream genes are diverse and include three major categories: transcription factors, synthesis, metabolism, and signal transduction of various hormones, and disease resistance genes. In the regulatory network of AtWRKY33 orthologs, many conserved regulatory characteristics have been discovered, such as self-activation and phosphorylation by MAP kinases. This can provide a comparative reference for further studying the functions of other orthologous genes of AtWKRY33.

Transcription factor PagWRKY33 regulates gibberellin signaling and immune receptor pathways in Populus

Enhanced autoimmunity often leads to impaired plant growth and development, and the coordination of immunity and growth in Populus remains elusive. In this study, we have identified the transcription factors PagWRKY33a/b as key regulators of immune response and growth maintenance in Populus. The disruption of PagWRKY33a/b causes growth issues and autoimmunity while conferring resistance to anthracnose caused by Colletotrichum gloeosporioides. PagWRKY33a/b binds to the promoters of N requirement gene 1.1 (NRG1.1) and Gibberellic Acid-Stimulated in Arabidopsis (GASA14) during infection, activating their transcription. This process maintains disease resistance and engages in GA signaling to reduce growth costs from immune activation. The oxPagWRKY33a/nrg1.1 mutant results in reduced resistance to C. gloeosporioides. Further, PagWRKY33a/b is phosphorylated and activated by mitogen-activated protein kinase kinase 1, which inhibits respiratory burst oxidase homolog D (RBOHD) and respiratory burst oxidase homolog I (RBOHI) transcription, causing reactive oxygen species bursts in wrky33a/b double mutants. This leads to an upregulation of PagNRG1.1 in the absence of pathogens. However, the wrky33a/b/nrg1.1 and wrky33a/b/rbohd triple mutants show compromised defense responses, underscoring the complexity of WRKY33 regulation. Additionally, the stability of PagWRKY33 is modulated by Ring Finger Protein 5 (PagRNF5)-mediated ubiquitination, balancing plant immunity and growth. Together, our results provide key insights into the complex function of WRKY33 in Populus autoimmunity and its impact on growth and development.

Phytosulfokine downregulates defense-related WRKY transcription factors and attenuates pathogen-associated molecular pattern-triggered immunity

Phytosulfokine (PSK) is a plant growth-promoting peptide hormone that is perceived by its cell surface receptors PSKR1 and PSKR2 in Arabidopsis. Plants lacking the PSK receptors show phenotypes consistent with PSK signaling repressing some plant defenses. To gain further insight into the PSK signaling mechanism, comprehensive transcriptional profiling of Arabidopsis treated with PSK was performed, and the effects of PSK treatment on plant defense readouts were monitored. Our study indicates that PSK's major effect is to downregulate defense-related genes; it has a more modest effect on the induction of growth-related genes. WRKY transcription factors (TFs) emerged as key regulators of PSK-responsive genes, sharing commonality with a pathogen-associated molecular pattern (PAMP) responses, flagellin 22 (flg22), but exhibiting opposite regulatory directions. These PSK-induced transcriptional changes were accompanied by biochemical and physiological changes that reduced PAMP responses, notably mitogen-activated protein kinase (MPK) phosphorylation (previously implicated in WRKY activation) and the cell wall modification of callose deposition. Comparison with previous studies using other growth stimuli (the sulfated plant peptide containing sulfated tyrosine [PSY] and Pseudomonas simiae strain WCS417) also reveals WRKY TFs' overrepresentations in these pathways, suggesting a possible shared mechanism involving WRKY TFs for plant growth-defense trade-off.

PpWRKY33 positively regulates PpPGIP1 to enhance defense against Monilinia fructicola in peach fruit

In plant-pathogen interactions, numerous pathogens secrete polygalacturonase (PG) to degrade plants cell walls, whereas plants produce PG-inhibiting protein (PGIP) that specifically binds to pathogen-derived PG to inhibit its activity and resist pathogen infection. In the present study, we dshowed that PpPGIP1 was significantly upregulated in peaches after Monilinia fructicola infection, and the prokaryotic expression of the PpPGIP1 protein inhibited M. fructicola by mitigating its PG activity. Transient overexpression of PpPGIP1 in peaches significantly enhanced their resistance to M. fructicola. PpPGIP1 promoter had several W-box the defense elements that can bind to WRKY transcription factors. Transcriptome analysis identified 20 differentially expressed WRKY genes, including the classic disease resistance gene WRKY33. PpWRKY33 is significantly upregulated in M. fructicola infected peaches. PpWRKY33 is localized in the nucleus and can bind to the W-box in the PpPGIP1 promoter to transcriptional activate the expression of PpPGIP1. Transient overexpression PpWRKY33 upregulated PpPGIP1 expression in peaches, and silencing PpWRKY33 decreased the PpPGIP1 expression. These results indicated that PpPGIP1 positively regulates fungal disease resistance in peaches and is transcriptionally activated by PpWRKY33. These findings reveal the disease resistant role of PpPGIP1 in peaches, and provide new insights into its transcriptional regulation.

EjWRKY6 Is Involved in the ABA-Induced Carotenoid Biosynthesis in Loquat Fruit during Ripening

The yellow-fleshed loquat is abundant in carotenoids, which determine the fruit's color, provide vitamin A, and offer anti-inflammatory and anti-cancer health benefits. In this research, the impact of abscisic acid (ABA), a plant hormone, on carotenoid metabolism and flesh pigmentation in ripening loquat fruits was determined. Results revealed that ABA treatment enhanced the overall content of carotenoids in loquat fruit, including major components like β-cryptoxanthin, lutein, and β-carotene, linked to the upregulation of most genes in the carotenoid biosynthesis pathway. Furthermore, a transcription factor, EjWRKY6, whose expression was induced by ABA, was identified and was thought to play a role in ABA-induced carotenoid acceleration. Transient overexpression of EjWRKY6 in Nicotiana benthamiana and stable genetic transformation in Nicotiana tabacum with EjWRKY6 indicated that both carotenoid production and genes related to carotenoid biosynthesis could be upregulated in transgenic plants. A dual-luciferase assay proposed a probable transcriptional control between EjWRKY6 and promoters of genes associated with carotenoid production. To sum up, pre-harvest ABA application could lead to carotenoid biosynthesis in loquat fruit through the EjWRKY6-induced carotenoid biosynthesis pathway.

Unlocking nature's secrets: The pivotal role of WRKY transcription factors in plant flowering and fruit development

The WRKY transcription factor family is a key player in the regulatory mechanisms of flowering plants, significantly influencing both their biotic and abiotic response systems as well as being vital to numerous physiological and biological functions. Over the past two decades, the functionality of WRKY proteins has been the subject of extensive research in over 50 plant species, with a strong focus on their roles in responding to various stresses. Despite this extensive research, there remains a notable gap in comprehensive studies aimed at understanding how specific WRKY genes directly influence the timing of flowering and fruit development. This review offers an up-to-date look at WRKY family genes and provides insights into the key genes of WRKY to control flowering, enhance fruit ripening and secondary metabolism synthesis, and maintain fruit quality of various plants, including annuals, perennials, medicinal, and crop plants. The WRKY transcription factors serve as critical regulators within the transcriptional regulatory network, playing a crucial role in the precise enhancement of flowering processes. It is also involved in the up-regulation of fruit ripening was strongly demonstrated by combined transcriptomics and metabolomic investigation. Therefore, we speculated that the WRKY family is known to be a key regulator of flowering and fruiting in plants. This detailed insight will enable the identification of the series of molecular occurrences featuring WRKY proteins throughout the stages of flowering and fruiting.

New Insights into the Connections between Flooding/Hypoxia Response and Plant Defenses against Pathogens

The impact of global climate change has highlighted the need for a better understanding of how plants respond to multiple simultaneous or sequential stresses, not only to gain fundamental knowledge of how plants integrate signals and mount a coordinated response to stresses but also for applications to improve crop resilience to environmental stresses. In recent years, there has been a stronger emphasis on understanding how plants integrate stresses and the molecular mechanisms underlying the crosstalk between the signaling pathways and transcriptional programs that underpin plant responses to multiple stresses. The combination of flooding (or resulting hypoxic stress) with pathogen infection is particularly relevant due to the frequent co-occurrence of both stresses in nature. This review focuses on (i) experimental approaches and challenges associated with the study of combined and sequential flooding/hypoxia and pathogen infection, (ii) how flooding (or resulting hypoxic stress) influences plant immunity and defense responses to pathogens, and (iii) how flooding contributes to shaping the soil microbiome and is linked to plants' ability to fight pathogen infection.

Up-regulation of growth-related gene expression in tobacco by volatile compounds released by Bacillus velezensis WSW007

In order to investigate the mechanism of plant growth promoting (PGP) effects of strain Bacillus velezensis WSW007, its PGP traits and production of volatile organic compounds (VOCs) were tested. The effects of VOCs produced by strain WSW007 on plant growth were observed by co-culturing this strain with tobacco seedlings in I-plates. Meanwhile, the effects of VOCs on tobacco gene expression were analysed by a transcriptome analysis and VOCs were identified by solid phase micro extraction coupled with gas chromatography-mass spectrometry (SPME-GC-MS) analysis. As results, strains WSW007 produced acetic acid and siderophore, and could solubilize phosphate; while it also significantly increased the fresh weight of tobacco seedlings via production of VOCs. In transcriptome analysis, plants co-cultured with strain WSW007 presented the highest up-regulated expression for the genes involved in plant growth and development processes, implying that the bacterial VOCs played a role as regulator of plant gene expression. Conclusively, the up-regulation in expression of growth- and development-related genes via VOCs production is an important PGP mechanism in strain B. velezensis WSW007.

Stress responsive ZmWRKY53 gene increases cold tolerance in rice

Plant WRKY transcription factors are responsible for biotic and abiotic stresses and play an important role in enhancing their adaptability. The AtWRKY33 is a gene that functions in response to abiotic stresses such as low temperature, drought, salinity, etc. In this study, a recombinant vector YG8198-ZmWRKY53 carrying the ZmWRKY53, an interspecific homolog of the dicotyledonous AtWRKY33, was transferred to rice plants by Agrobacterium mediated transformation. The ectopic expression of the ZmWRKY53 in transgenic rice plants conferred cold tolerance with a higher accumulation of free proline and water-soluble sugars, an increase in chlorophyll content, a decrease in electrolyte leakage rate and MDA levels compared to control plants. This result suggests that ZmWRKY53 may confer cold tolerance in rice.

Enhancing cowpea wilt resistance: insights from gene coexpression network analysis with exogenous melatonin treatment

BACKGROUND

Cowpea wilt is a harmful disease caused by Fusarium oxysporum, leading to substantial losses in cowpea production. Melatonin reportedly regulates plant immunity to pathogens; however the specific regulatory mechanism underlying the protective effect of melatonin pretreated of cowpea against Fusarium oxysporum remains known. Accordingly, the study sought to evaluate changes in the physiological and biochemical indices of cowpea following melatonin treated to facilitate Fusarium oxysporum resistance and elucidate the associated molecular mechanism using a weighted gene coexpression network.

RESULTS

Treatment with 100 µM melatonin was effective in increasing cowpea resistance to Fusarium oxysporum. Glutathione peroxidase (GSH-PX), catalase (CAT), and salicylic acid (SA) levels were significantly upregulated, and hydrogen peroxide (H2O2) levels were significantly downregulated in melatonin treated samples in roots. Weighted gene coexpression network analysis of melatonin- and Fusarium oxysporum-treated samples identified six expression modules comprising 2266 genes; the number of genes per module ranged from 9 to 895. In particular, 17 redox genes and 32 transcription factors within the blue module formed a complex interconnected expression network. KEGG analysis revealed that the associated pathways were enriched in secondary metabolism, peroxisomes, phenylalanine metabolism, flavonoids, and flavonol biosynthesis. More specifically, genes involved in lignin synthesis, catalase, superoxide dismutase, and peroxidase were upregulated. Additionally, exogenous melatonin induced activation of transcription factors, such as WRKY and MYB.

CONCLUSIONS

The study elucidated changes in the expression of genes associated with the response of cowpea to Fusarium oxysporum under melatonin treated. Specifically, multiple defence mechanisms were initiated to improve cowpea resistance to Fusarium oxysporum.

A dual function of the IDA peptide in regulating cell separation and modulating plant immunity at the molecular level

The abscission of floral organs and emergence of lateral roots in Arabidopsis is regulated by the peptide ligand inflorescence deficient in abscission (IDA) and the receptor protein kinases HAESA (HAE) and HAESA-like 2 (HSL2). During these cell separation processes, the plant induces defense-associated genes to protect against pathogen invasion. However, the molecular coordination between abscission and immunity has not been thoroughly explored. Here, we show that IDA induces a release of cytosolic calcium ions (Ca2+) and apoplastic production of reactive oxygen species, which are signatures of early defense responses. In addition, we find that IDA promotes late defense responses by the transcriptional upregulation of genes known to be involved in immunity. When comparing the IDA induced early immune responses to known immune responses, such as those elicited by flagellin22 treatment, we observe both similarities and differences. We propose a molecular mechanism by which IDA promotes signatures of an immune response in cells destined for separation to guard them from pathogen attack.

CaSTH2 disables CaWRKY40 from activating pepper thermotolerance and immunity against Ralstonia solanacearum via physical interaction

CaWRKY40 coordinately activates pepper immunity against Ralstonia solanacearum infection (RSI) and high temperature stress (HTS), forms positive feedback loops with other positive regulators and is promoted by CaWRKY27b/CaWRKY28 through physical interactions; however, whether and how it is regulated by negative regulators to function appropriately remain unclear. Herein, we provide evidence that CaWRKY40 is repressed by a SALT TOLERANCE HOMOLOG2 in pepper (CaSTH2). Our data from gene silencing and transient overexpression in pepper and epoptic overexpression in Nicotiana benthamiana plants showed that CaSTH2 acted as negative regulator in immunity against RSI and thermotolerance. Our data from BiFC, CoIP, pull down, and MST indicate that CaSTH2 interacted with CaWRKY40, by which CaWRKY40 was prevented from activating immunity or thermotolerance-related genes. It was also found that CaSTH2 repressed CaWRKY40 at least partially through blocking interaction of CaWRKY40 with CaWRKY27b/CaWRKY28, but not through directly repressing binding of CaWRKY40 to its target genes. The results of study provide new insight into the mechanisms underlying the coordination of pepper immunity and thermotolerance.

Transcription factors VviWRKY10 and VviWRKY30 co-regulate powdery mildew resistance in grapevine

Grapevine (Vitis vinifera) is an economically important fruit crop worldwide. The widely cultivated grapevine is susceptible to powdery mildew caused by Erysiphe necator. In this study, we used CRISPR-Cas9 to simultaneously knock out VviWRKY10 and VviWRKY30 encoding two transcription factors reported to be implicated in defense regulation. We generated 53 wrky10 single mutant transgenic plants and 15 wrky10 wrky30 double mutant transgenic plants. In a 2-yr field evaluation of powdery mildew resistance, the wrky10 mutants showed strong resistance, while the wrky10 wrky30 double mutants showed moderate resistance. Further analyses revealed that salicylic acid (SA) and reactive oxygen species contents in the leaves of wrky10 and wrky10 wrky30 were substantially increased, as was the ethylene (ET) content in the leaves of wrky10. The results from dual luciferase reporter assays, electrophoretic mobility shift assays and chromatin immunoprecipitation (ChIP) assays demonstrated that VviWRKY10 could directly bind to the W-boxes in the promoter of SA-related defense genes and inhibit their transcription, supporting its role as a negative regulator of SA-dependent defense. By contrast, VviWRKY30 could directly bind to the W-boxes in the promoter of ET-related defense genes and promote their transcription, playing a positive role in ET production and ET-dependent defense. Moreover, VviWRKY10 and VviWRKY30 can bind to each other's promoters and mutually inhibit each other's transcription. Taken together, our results reveal a complex mechanism of regulation by VviWRKY10 and VviWRKY30 for activation of measured and balanced defense responses against powdery mildew in grapevine.

Bacillus cereus NJ01 induces SA- and ABA-mediated immunity against bacterial pathogens through the EDS1-WRKY18 module

Emerging evidence suggests a beneficial role of rhizobacteria in ameliorating plant disease resistance in an environment-friendly way. In this study, we characterize a rhizobacterium, Bacillus cereus NJ01, that enhances bacterial pathogen resistance in rice and Arabidopsis. Transcriptome analyses show that root inoculation of NJ01 induces the expression of salicylic acid (SA)- and abscisic acid (ABA)-related genes in Arabidopsis leaves. Genetic evidence showed that EDS1, PAD4, and WRKY18 are required for B. cereus NJ01-induced bacterial resistance. An EDS1-PAD4 complex interacts with WRKY18 and enhances its DNA binding activity. WRKY18 directly binds to the W box in the promoter region of the SA biosynthesis gene ICS1 and ABA biosynthesis genes NCED3 and NCED5 and contributes to the NJ01-induced bacterial resistance. Taken together, our findings indicate a role of the EDS1/PAD4-WRKY18 complex in rhizobacteria-induced disease resistance.

Dissection of the IDA promoter identifies WRKY transcription factors as abscission regulators in Arabidopsis

Plants shed organs such as leaves, petals, or fruits through the process of abscission. Monitoring cues such as age, resource availability, and biotic and abiotic stresses allow plants to abscise organs in a timely manner. How these signals are integrated into the molecular pathways that drive abscission is largely unknown. The INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) gene is one of the main drivers of floral organ abscission in Arabidopsis and is known to transcriptionally respond to most abscission-regulating cues. By interrogating the IDA promoter in silico and in vitro, we identified transcription factors that could potentially modulate IDA expression. We probed the importance of ERF- and WRKY-binding sites for IDA expression during floral organ abscission, with WRKYs being of special relevance to mediate IDA up-regulation in response to biotic stress in tissues destined for separation. We further characterized WRKY57 as a positive regulator of IDA and IDA-like gene expression in abscission zones. Our findings highlight the promise of promoter element-targeted approaches to modulate the responsiveness of the IDA signaling pathway to harness controlled abscission timing for improved crop productivity.

DNA methylation regulates the secondary metabolism of saponins to improve the adaptability of Eleutherococcus senticosus during drought stress

Plant growth and development can be significantly impacted by drought stress. Plants will adjust the synthesis and accumulation of secondary metabolites to improve survival in times of water constraint. Simultaneously, drought stress can lead to modifications in the DNA methylation status of plants, and these modifications can directly impact gene expression and product synthesis by changing the DNA methylation status of functional genes involved in secondary metabolite synthesis. However, further research is needed to fully understand the extent to which DNA methylation modifies the content of secondary metabolites to mediate plants' responses to drought stress, as well as the underlying mechanisms involved. Our study found that in Eleutherococcus senticosus (E. senticosus), moderate water deprivation significantly decreased DNA methylation levels throughout the genome and at the promoters of EsFPS, EsSS, and EsSE. Transcription factors like EsMYB-r1, previously inhibited by DNA methylation, can re-bind to the EsFPS promotor region following DNA demethylation. This process promotes gene expression and, ultimately, saponin synthesis and accumulation. The increased saponin levels in E. senticosus acted as antioxidants, enhancing the plant's adaptability to drought stress.

Mining Heat-Resistant Key Genes of Peony Based on Weighted Gene Co-Expression Network Analysis

The RNA-Seq and gene expression data of mature leaves under high temperature stress of Paeonia suffruticosa 'Hu Hong' were used to explore the key genes of heat tolerance of peony. The weighted gene co-expression network analysis (WGCNA) method was used to construct the network, and the main modules and core genes of co-expression were screened according to the results of gene expression and module function enrichment analysis. According to the correlation of gene expression, the network was divided into 19 modules. By analyzing the expression patterns of each module gene, Blue, Salmon and Yellow were identified as the key modules of peony heat response related functions. GO and KEGG functional enrichment analysis was performed on the genes in the three modules and a network diagram was constructed. Based on this, two key genes PsWRKY53 (TRINITY_DN60998_c1_g2, TRINITY_DN71537_c0_g1) and PsHsfB2b (TRINITY_DN56794_c0_g1) were excavated, which may play a key role in the heat shock response of peony. The three co-expression modules and two key genes were helpful to further elucidate the heat resistance mechanism of P. suffruticosa 'Hu Hong'.

Alternaria TeA toxin activates a chloroplast retrograde signaling pathway to facilitate JA-dependent pathogenicity

The chloroplast is a critical battleground in the arms race between plants and pathogens. Among microbe-secreted mycotoxins, tenuazonic acid (TeA), produced by the genus Alternaria and other phytopathogenic fungi, inhibits photosynthesis, leading to a burst of photosynthetic singlet oxygen (1O2) that is implicated in damage and chloroplast-to-nucleus retrograde signaling. Despite the significant crop damage caused by Alternaria pathogens, our understanding of the molecular mechanism by which TeA promotes pathogenicity and cognate plant defense responses remains fragmentary. We now reveal that A. alternata induces necrotrophic foliar lesions by harnessing EXECUTER1 (EX1)/EX2-mediated chloroplast-to-nucleus retrograde signaling activated by TeA toxin-derived photosynthetic 1O2 in Arabidopsis thaliana. Mutation of the 1O2-sensitive EX1-W643 residue or complete deletion of the EX1 singlet oxygen sensor domain compromises expression of 1O2-responsive nuclear genes and foliar lesions. We also found that TeA toxin rapidly induces nuclear genes implicated in jasmonic acid (JA) synthesis and signaling, and EX1-mediated retrograde signaling appears to be critical for establishing a signaling cascade from 1O2 to JA. The present study sheds new light on the foliar pathogenicity of A. alternata, during which EX1-dependent 1O2 signaling induces JA-dependent foliar cell death.

Genome and Transcriptome Analysis of the Torreya grandis WRKY Gene Family during Seed Development

Torreya grandis, an economically significant evergreen tree species exclusive to subtropical China, is highly valued for its seeds. However, the seed development process of T. grandis remains relatively unexplored. Given the pivotal role WRKY transcription factors (TFs) play in coordinating diverse cellular and biological activities, as well as crucial signaling pathways essential for plant growth and development, and the lack of comprehensive investigation into their specific functions in T. grandis, our study investigated its genome and successfully isolated 78 WRKY genes and categorized them into three distinct clades. A conserved motif analysis unveiled the presence of the characteristic WRKY domain in each identified TgWRKY protein. The examination of gene structures revealed variable numbers of introns (ranging from zero to eight) and exons (ranging from one to nine) among TgWRKY genes. A chromosomal distribution analysis demonstrated the presence of TgWRKY across eight chromosomes in T. grandis. Tissue-specific expression profiling unveiled distinctive patterns of these 78 TgWRKY genes across various tissues. Remarkably, a co-expression analysis integrating RNA-seq data and morphological assessments pinpointed the pronounced expression of TgWRKY25 during the developmental stages of T. grandis seeds. Moreover, a KEGG enrichment analysis, focusing on genes correlated with TgWRKY25 expression, suggested its potential involvement in processes such as protein processing in the endoplasmic reticulum, starch, and sucrose metabolism, thereby modulating seed development in T. grandis. These findings not only underscore the pivotal role of WRKY genes in T. grandis seed development but also pave the way for innovative breeding strategies.

Whitefly-Plant Interactions: An Integrated Molecular Perspective

The rapid advances in available transcriptomic and genomic data and our understanding of the physiology and biochemistry of whitefly-plant interactions have allowed us to gain new and significant insights into the biology of whiteflies and their successful adaptation to host plants. In this review, we provide a comprehensive overview of the mechanisms that whiteflies have evolved to overcome the challenges of feeding on phloem sap. We also highlight the evolution and functions of gene families involved in host perception, evaluation, and manipulation; primary metabolism; and metabolite detoxification. We discuss the emerging themes in plant immunity to whiteflies, focusing on whitefly effectors and their sites of action in plant defense-signaling pathways. We conclude with a discussion of advances in the genetic manipulation of whiteflies and the potential that they hold for exploring the interactions between whiteflies and their host plants, as well as the development of novel strategies for the genetic control of whiteflies.

Plant growth-promoting rhizobacterium Bacillus cereus AR156 induced systemic resistance against multiple pathogens by priming of camalexin synthesis

Phytoalexins play a crucial role in plant immunity. However, the mechanism of how phytoalexin is primed by beneficial microorganisms against broad-spectrum pathogens remains elusive. This study showed that Bacillus cereus AR156 could trigger ISR against broad-spectrum disease. RNA-sequencing and camalexin content assays showed that AR156-triggered ISR can prime the accumulation of camalexin synthesis and secretion-related genes. Moreover, it was found that AR156-triggered ISR elevates camalexin accumulation by increasing the expression of camalexin synthesis genes upon pathogen infection. We observed that the priming of camalexin accumulation by AR156 was abolished in cyp71a13 and pad3 mutants. Further investigations reveal that in the wrky33 mutant, the ability of AR156 to prime camalexin accumulation is abolished, and the mediated ISR against the three pathogens is significantly compromised. Furthermore, PEN3 and PDR12, acting as camalexin transporters, participate in AR156-induced ISR against broad-spectrum pathogens differently. In addition, salicylic acid and JA/ET signalling pathways participate in AR156-primed camalexin synthesis to resist pathogens in different forms depending on the pathogen. In summary, B. cereus AR156 triggers ISR against Botrytis cinerea, Pst DC3000 and Phytophthora capsici by priming camalexin synthesis. Our study provides deeper insights into the significant role of camalexin for AR156-induced ISR against broad-spectrum pathogens.

The bHLH transcription factor AhbHLH121 improves salt tolerance in peanut

Plants have developed a number of protective mechanisms to respond to salt and other stresses. Previous studies have shown that the basic helix-loop-helix (bHLH) transcription factor AhbHLH121 plays a crucial role in the response to abiotic stresses in peanut, but the mechanisms and functions related to AhbHLH121 remain unclear. In the current research, AhbHLH121 was induced by salt treatment. Overexpression of AhbHLH121 improved salt resistance, whereas silencing AhbHLH121 resulted in the inverse correlation. Our results also demonstrated that overexpression of AhbHLH121 results in greater activity of antioxidant enzymes under stress condition by promoting the expression of the genes for peroxidase, catalase and superoxide dismutase (AhPOD, AhCAT and AhSOD), indicating enhanced scavenging of reactive oxygen species. Further analysis including Yeast one-hybrid (Y1H) assays and electrophoretic mobility shift assays (EMSAs), suggested that AhbHLH121 can bind directly to the G/E-box regions of the AhPOD, AhCAT and AhSOD promoters, thereby promoting their expression and leading to improved antioxidant enzyme activity. Our research improves the understanding of the mechanisms that allow this peanut bHLH transcription factor to improve abiotic tolerance, and provides valuable gene resources for breeding programs to promote salt stress resistance.

Multifaceted roles of WRKY transcription factors in abiotic stress and flavonoid biosynthesis

Increasing biotic and abiotic stresses are seriously impeding the growth and yield of staple crops and threatening global food security. As one of the largest classes of regulators in vascular plants, WRKY transcription factors play critical roles governing flavonoid biosynthesis during stress responses. By binding major W-box cis-elements (TGACCA/T) in target promoters, WRKYs modulate diverse signaling pathways. In this review, we optimized existing WRKY phylogenetic trees by incorporating additional plant species with WRKY proteins implicated in stress tolerance and flavonoid regulation. Based on the improved frameworks and documented results, we aim to deduce unifying themes of distinct WRKY subfamilies governing specific stress responses and flavonoid metabolism. These analyses will generate experimentally testable hypotheses regarding the putative functions of uncharacterized WRKY homologs in tuning flavonoid accumulation to enhance stress resilience.

RNA-Sequencing Analysis Revealed Genes Associated with Sweet Potato (Ipomoea batatas (L.) Lam.) Responses to Stem Rot during Different Infection Stages

The sweet potato, which is an important tuber crop in China, is susceptible to a variety of pathogens and insect pests during cultivation and production. Stem rot is a common sweet potato disease that seriously affects tuber yield and quality. Unfortunately, there have been relatively few studies on the mechanism mediating the stem rot resistance of sweet potatoes. In this study, a transcriptome sequencing analysis was completed using Xushu 48 samples at different stages (T1, T2, and T3) of the stem rot infection. The T1 vs. T2, T1 vs. T3, and T2 vs. T3 comparisons detected 44,839, 81,436, and 61,932 differentially expressed genes (DEGs), respectively. The DEGs encoded proteins primarily involved in alanine, aspartate, and glutamate metabolism (ko00250), carbon fixation in photosynthetic organisms (ko00710), and amino sugar and nucleotide sugar metabolism (ko00520). Furthermore, some candidate genes induced by phytopathogen infections were identified, including gene-encoding receptor-like protein kinases (RLK5 and RLK7), an LRR receptor-like serine/threonine protein kinase (SERK1), and transcription factors (bHLH137, ERF9, MYB73, and NAC053). The results of this study provide genetic insights that are relevant to future explorations of sweet potato stem rot resistance, while also providing the theoretical basis for breeding sweet potato varieties that are resistant to stem rot and other diseases.

WRKY transcription factors in Arachis hypogaea and its donors: From identification to function prediction

WRKY transcription factors (TFs) play important roles in plant growth and development and responses to abiotic and biotic stresses. Since the initial isolation of a WRKY TF in Ipomoea batatas in 1994, WRKY TFs have been identified in plants, protozoa, and fungi. Peanut (Arachis hypogaea) is a key oil and protein crop for humans and a forage source for animal consumption. Several Arachis genomes have been sequenced and genome-wide WRKY TFs have been identified. In this review, we summarized WRKY TFs and their functions in A. hypogaea and its donors. We also standardized the nomenclature for Arachis WRKY TFs to ensure uniformity. We determined the evolutionary relationships between Arachis and Arabidopsis thaliana WRKY (AtWRKY) TFs using a phylogenetic analysis. Biological functions and regulatory networks of Arachis WRKY TFs were predicted using AtWRKY TFs. Thus, this review paves the way for studies of Arachis WRKY TFs.

The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes

The mobility of transposable elements (TEs) contributes to evolution of genomes. Their uncontrolled activity causes genomic instability; therefore, expression of TEs is silenced by host genomes. TEs are marked with DNA and H3K9 methylation, which are associated with silencing in flowering plants, animals, and fungi. However, in distantly related groups of eukaryotes, TEs are marked by H3K27me3 deposited by the Polycomb repressive complex 2 (PRC2), an epigenetic mark associated with gene silencing in flowering plants and animals. The direct silencing of TEs by PRC2 has so far only been shown in one species of ciliates. To test if PRC2 silences TEs in a broader range of eukaryotes, we generated mutants with reduced PRC2 activity and analyzed the role of PRC2 in extant species along the lineage of Archaeplastida and in the diatom P. tricornutum. In this diatom and the red alga C. merolae, a greater proportion of TEs than genes were repressed by PRC2, whereas a greater proportion of genes than TEs were repressed by PRC2 in bryophytes. In flowering plants, TEs contained potential cis-elements recognized by transcription factors and associated with neighbor genes as transcriptional units repressed by PRC2. Thus, silencing of TEs by PRC2 is observed not only in Archaeplastida but also in diatoms and ciliates, suggesting that PRC2 deposited H3K27me3 to silence TEs in the last common ancestor of eukaryotes. We hypothesize that during the evolution of Archaeplastida, TE fragments marked with H3K27me3 were selected to shape transcriptional regulation, controlling networks of genes regulated by PRC2.

Review: WRKY transcription factors: Understanding the functional divergence

WRKY transcription factors (TFs) play crucial roles in the growth and development of plants and their response to environmental changes. WRKY TFs have been detected in sequenced plant genomes. The functions and regulatory networks of many WRKY TFs, especially from Arabidopsis thaliana (AtWRKY TFs), have been revealed, and the origin of WRKY TFs in plants is clear. Nonetheless, the relationship between WRKY TFs function and classification is unclear. Furthermore, the functional divergence of homologous WRKY TFs in plants is unclear. In this review, WRKY TFs were explored based on WRKY-related literature published from 1994 to 2022. WRKY TFs were identified in 234 species at the genome and transcriptome levels. The biological functions of ∼ 71 % of AtWRKY TFs were uncovered. Although functional divergence occurred in homologous WRKY TFs, different WRKY TF groups had no preferential function.

Cell-specific RNA profiling reveals host genes expressed in Arabidopsis cells haustoriated by downy mildew

The downy mildew oomycete Hyaloperonospora arabidopsidis, an obligate filamentous pathogen, infects Arabidopsis (Arabidopsis thaliana) by forming structures called haustoria inside host cells. Previous transcriptome analyses have revealed that host genes are specifically induced during infection; however, RNA profiling from whole-infected tissues may fail to capture key transcriptional events occurring exclusively in haustoriated host cells, where the pathogen injects virulence effectors to modulate host immunity. To determine interactions between Arabidopsis and H. arabidopsidis at the cellular level, we devised a translating ribosome affinity purification system using 2 high-affinity binding proteins, colicin E9 and Im9 (immunity protein of colicin E9), applicable to pathogen-responsive promoters, thus enabling haustoriated cell-specific RNA profiling. Among the host genes specifically expressed in H. arabidopsidis-haustoriated cells, we found genes that promote either susceptibility or resistance to the pathogen, providing insights into the Arabidopsis-downy mildew interaction. We propose that our protocol for profiling cell-specific transcripts will apply to several stimulus-specific contexts and other plant-pathogen interactions.

SnRK2.10 kinase differentially modulates expression of hub WRKY transcription factors genes under salinity and oxidative stress in Arabidopsis thaliana

In nature, all living organisms must continuously sense their surroundings and react to the occurring changes. In the cell, the information about these changes is transmitted to all cellular compartments, including the nucleus, by multiple phosphorylation cascades. Sucrose Non-Fermenting 1 Related Protein Kinases (SnRK2s) are plant-specific enzymes widely distributed across the plant kingdom and key players controlling abscisic acid (ABA)-dependent and ABA-independent signaling pathways in the plant response to osmotic stress and salinity. The main deleterious effects of salinity comprise water deficiency stress, disturbances in ion balance, and the accompanying appearance of oxidative stress. The reactive oxygen species (ROS) generated at the early stages of salt stress are involved in triggering intracellular signaling required for the fast stress response and modulation of gene expression. Here we established in Arabidopsis thaliana that salt stress or induction of ROS accumulation by treatment of plants with H2O2 or methyl viologen (MV) induces the expression of several genes encoding transcription factors (TFs) from the WRKY DNA-Binding Protein (WRKY) family. Their induction by salinity was dependent on SnRK2.10, an ABA non-activated kinase, as it was strongly reduced in snrk2.10 mutants. The effect of ROS was clearly dependent on their source. Following the H2O2 treatment, SnRK2.10 was activated in wild-type (wt) plants and the induction of the WRKY TFs expression was only moderate and was enhanced in snrk2.10 lines. In contrast, MV did not activate SnRK2.10 and the WRKY induction was very strong and was similar in wt and snrk2.10 plants. A bioinformatic analysis indicated that the WRKY33, WRKY40, WRKY46, and WRKY75 transcription factors have a similar target range comprising numerous stress-responsive protein kinases. Our results indicate that the stress-related functioning of SnRK2.10 is fine-tuned by the source and intracellular distribution of ROS and the co-occurrence of other stress factors.

Differential CaKAN3-CaHSF8 associations underlie distinct immune and heat responses under high temperature and high humidity conditions

High temperature and high humidity (HTHH) conditions increase plant susceptibility to a variety of diseases, including bacterial wilt in solanaceous plants. Some solanaceous plant cultivars have evolved mechanisms to activate HTHH-specific immunity to cope with bacterial wilt disease. However, the underlying mechanisms remain poorly understood. Here we find that CaKAN3 and CaHSF8 upregulate and physically interact with each other in nuclei under HTHH conditions without inoculation or early after inoculation with R. solanacearum in pepper. Consequently, CaKAN3 and CaHSF8 synergistically confer immunity against R. solanacearum via activating a subset of NLRs which initiates immune signaling upon perception of unidentified pathogen effectors. Intriguingly, when HTHH conditions are prolonged without pathogen attack or the temperature goes higher, CaHSF8 no longer interacts with CaKAN3. Instead, it directly upregulates a subset of HSP genes thus activating thermotolerance. Our findings highlight mechanisms controlling context-specific activation of high-temperature-specific pepper immunity and thermotolerance mediated by differential CaKAN3-CaHSF8 associations.

Antifungal mechanisms of the antagonistic bacterium Bacillus mojavensis UTF-33 and its potential as a new biopesticide

Biological control has gradually become the dominant means of controlling fungal disease over recent years. In this study, an endophytic strain of UTF-33 was isolated from acid mold (Rumex acetosa L.) leaves. Based on 16S rDNA gene sequence comparison, and biochemical and physiological characteristics, this strain was formally identified as Bacillus mojavensis. Bacillus mojavensis UTF-33 was sensitive to most of the antibiotics tested except neomycin. Moreover, the filtrate fermentation solution of Bacillus mojavensis UTF-33 had a significant inhibitory effect on the growth of rice blast and was used in field evaluation tests, which reduced the infestation of rice blast effectively. Rice treated with filtrate fermentation broth exhibited multiple defense mechanisms in response, including the enhanced expression of disease process-related genes and transcription factor genes, and significantly upregulated the gene expression of titin, salicylic acid pathway-related genes, and H₂O₂ accumulation, in plants; this may directly or indirectly act as an antagonist to pathogenic infestation. Further analysis revealed that the n-butanol crude extract of Bacillus mojavensis UTF-33 could retard or even inhibit conidial germination and prevent the formation of adherent cells both in vitro and in vivo. In addition, the amplification of functional genes for biocontrol using specific primers showed that Bacillus mojavensis UTF-33 expresses genes that can direct the synthesis of bioA, bmyB, fenB, ituD, srfAA and other substances; this information can help us to determine the extraction direction and purification method for inhibitory substances at a later stage. In conclusion, this is the first study to identify Bacillus mojavensis as a potential agent for the control of rice diseases; this strain, and its bioactive substances, have the potential to be developed as biopesticides.

Single-cytosine methylation at W-boxes repels binding of WRKY transcription factors through steric hindrance

DNA methylation is an epigenetic mark that fine-tunes gene expression, notably by negatively or positively regulating transcription factor (TF)-DNA binding. In plants, DNA methylation has primarily been shown to inhibit TF-DNA binding. However, little is known about the underlying mechanisms. Here, we show that DNA methylation decreases the binding of several Arabidopsis (Arabidopsis thaliana) WRKY TFs to their genomic regions and their binding sites in vitro. We also provide evidence that DNA methylation at a single cytosine located in a functional core W-box motif repels DNA binding of AtWRKY40 in vitro. Using structural modelling, we further demonstrate that this cytosine interacts through van der Waals contacts with the conserved tyrosine of WRKY-DNA binding domains. Importantly, our model predicts steric hindrance when a 5-methyl group is present on this specific cytosine, thereby likely preventing tight binding of WRKY-DNA binding domains. Finally, because the WRKY motif and the residues involved in DNA contacts are conserved across Arabidopsis and rice (Oryza sativa) WRKY TFs, we propose that this methylation-dependent WRKY-DNA binding inhibitory mechanism could be widespread across plant species.

Suppression of ETI by PTI priming to balance plant growth and defense through an MPK3/MPK6-WRKYs-PP2Cs module

Pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) are required for host defense against pathogens. Although PTI and ETI are intimately connected, the underlying molecular mechanisms remain elusive. In this study, we demonstrate that flg22 priming attenuates Pseudomonas syringae pv. tomato DC3000 (Pst) AvrRpt2-induced hypersensitive cell death, resistance, and biomass reduction in Arabidopsis. Mitogen-activated protein kinases (MAPKs) are key signaling regulators of PTI and ETI. The absence of MPK3 and MPK6 significantly reduces pre-PTI-mediated ETI suppression (PES). We found that MPK3/MPK6 interact with and phosphorylate the downstream transcription factor WRKY18, which regulates the expression of AP2C1 and PP2C5, two genes encoding protein phosphatases. Furthermore, we observed that the PTI-suppressed ETI-triggered cell death, MAPK activation, and growth retardation are significantly attenuated in wrky18/40/60 and ap2c1 pp2c5 mutants. Taken together, our results suggest that the MPK3/MPK6-WRKYs-PP2Cs module underlies PES and is essential for the maintenance of plant fitness during ETI.

Progress in the understanding of WRKY transcription factors in woody plants

The WRKY transcription factor (TF) family, named for its iconic WRKY domain, is among the largest and most functionally diverse TF families in higher plants. WRKY TFs typically interact with the W-box of the target gene promoter to activate or inhibit the expression of downstream genes; these TFs are involved in the regulation of various physiological responses. Analyses of WRKY TFs in numerous woody plant species have revealed that WRKY family members are broadly involved in plant growth and development, as well as responses to biotic and abiotic stresses. Here, we review the origin, distribution, structure, and classification of WRKY TFs, along with their mechanisms of action, the regulatory networks in which they are involved, and their biological functions in woody plants. We consider methods currently used to investigate WRKY TFs in woody plants, discuss outstanding problems, and propose several new research directions. Our objective is to understand the current progress in this field and provide new perspectives to accelerate the pace of research that enable greater exploration of the biological functions of WRKY TFs.

Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis

BACKGROUND

Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs to the transcriptome, is critical for determining the traits that influence wheat growth and development. Asymmetric transcription of homoeologs has been so far investigated in a tissue or organ-specific manner, which could be misleading due to a mixture of cell types.

RESULTS

Here, we perform single nuclei RNA sequencing and ATAC sequencing of wheat root to study the asymmetric gene transcription, reconstruct cell differentiation trajectories and cell-type-specific gene regulatory networks. We identify 22 cell types. We then reconstruct cell differentiation trajectories that suggest different origins between epidermis/cortex and endodermis, distinguishing bread wheat from Arabidopsis. We show that the ratio of asymmetrically transcribed triads varies greatly when analyzing at the single-cell level. Hub transcription factors determining cell type identity are also identified. In particular, we demonstrate that TaSPL14 participates in vasculature development by regulating the expression of BAM1. Combining single-cell transcription and chromatin accessibility data, we construct the pseudo-time regulatory network driving root hair differentiation. We find MYB3R4, REF6, HDG1, and GATAs as key regulators in this process.

CONCLUSIONS

Our findings reveal the transcriptional landscape of root organization and asymmetric gene transcription at single-cell resolution in polyploid wheat.

RAV1 family members function as transcriptional regulators and play a positive role in plant disease resistance

Phytopathogens pose a severe threat to agriculture and strengthening the plant defense response is an important strategy for disease control. Here, we report that AtRAV1, an AP2 and B3 domain-containing transcription factor, is required for basal plant defense in Arabidopsis thaliana. The atrav1 mutant lines demonstrate hyper-susceptibility against fungal pathogens (Rhizoctonia solani and Botrytis cinerea), whereas AtRAV1 overexpressing lines exhibit disease resistance against them. Enhanced expression of various defense genes and activation of mitogen-activated protein kinases (AtMPK3 and AtMPK6) are observed in the R. solani infected overexpressing lines, but not in the atrav1 mutant plants. An in vitro phosphorylation assay suggests AtRAV1 to be a novel phosphorylation target of AtMPK3. Bimolecular fluorescence complementation and yeast two-hybrid assays support physical interactions between AtRAV1 and AtMPK3. Overexpression of the native as well as phospho-mimic but not the phospho-defective variant of AtRAV1 imparts disease resistance in the atrav1 mutant A. thaliana lines. On the other hand, overexpression of AtRAV1 fails to impart disease resistance in the atmpk3 mutant. These analyses emphasize that AtMPK3-mediated phosphorylation of AtRAV1 is important for the elaboration of the defense response in A. thaliana. Considering that RAV1 homologs are conserved in diverse plant species, we propose that they can be gainfully deployed to impart disease resistance in agriculturally important crop plants. Indeed, overexpression of SlRAV1 (a member of the RAV1 family) imparts disease tolerance against not only fungal (R. solani and B. cinerea), but also against bacterial (Ralstonia solanacearum) pathogens in tomato, whereas silencing of the gene enhances disease susceptibility.

WRKY transcription factors: evolution, regulation, and functional diversity in plants

The recent advancements in sequencing technologies and informatic tools promoted a paradigm shift to decipher the hidden biological mysteries and transformed the biological issues into digital data to express both qualitative and quantitative forms. The transcriptomic approach, in particular, has added new dimensions to the versatile essence of plant genomics through the large and deep transcripts generated in the process. This has enabled the mining of super families from the sequenced plants, both model and non-model, understanding their ancestry, diversity, and evolution. The elucidation of the crystal structure of the WRKY proteins and recent advancement in computational prediction through homology modeling and molecular dynamic simulation has provided an insight into the DNA-protein complex formation, stability, and interaction, thereby giving a new dimension in understanding the WRKY regulation. The present review summarizes the functional aspects of the high volume of sequence data of WRKY transcription factors studied from different species, till date. The review focuses on the dynamics of structural classification and lineage in light of the recent information. Additionally, a comparative analysis approach was incorporated to understand the functions of the identified WRKY transcription factors subjected to abiotic (heat, cold, salinity, senescence, dark, wounding, UV, and carbon starvation) stresses as revealed through various sets of studies on different plant species. The review will be instrumental in understanding the events of evolution and the importance of WRKY TFs under the threat of climate change, considering the new scientific evidences to propose a fresh perspective.

Elevated CO2 mitigates the impact of drought stress by upregulating glucosinolate metabolism in Arabidopsis thaliana

Elevated CO₂ (eCO₂ ) reduces the impact of drought, but the mechanisms underlying this effect remain unclear. Therefore, we used a multidisciplinary approach to investigate the interaction of drought and eCO₂ in Arabidopsis thaliana leaves. Transcriptome and subsequent metabolite analyses identified a strong induction of the aliphatic glucosinolate (GL) biosynthesis as a main effect of eCO₂ in drought-stressed leaves. Transcriptome results highlighted the upregulation of ABI5 and downregulation of WRKY63 transcription factors (TF), known to enhance and inhibit the expression of genes regulating aliphatic GL biosynthesis (e.g., MYB28 and 29 TFs), respectively. In addition, eCO₂ positively regulated aliphatic GL biosynthesis by MYB28/29 and increasing the accumulation of GL precursors. To test the role of GLs in the stress-mitigating effect of eCO₂ , we investigated the effect of genetic perturbations of the GL biosynthesis. Overexpression of MYB28, 29 and 76 improved drought tolerance by inducing stomatal closure and maintaining plant turgor, whereas loss of cyp79f genes reduced the stress-mitigating effect of eCO₂ and decreased drought tolerance. Overall, the crucial role of GL metabolism in drought stress mitigation by eCO₂ could be a beneficial trait to overcome future climate challenges.

Arabidopsis EXECUTER1 interacts with WRKY transcription factors to mediate plastid-to-nucleus singlet oxygen signaling

Chloroplasts produce singlet oxygen (1O2), which causes changes in nuclear gene expression through plastid-to-nucleus retrograde signaling to increase plant fitness. However, the identity of this 1O2-triggered pathway remains unclear. Here, we identify mutations in GENOMES UNCOUPLED4 (GUN4) and GUN5 as suppressors of phytochrome-interacting factor1 (pif1) pif3 in regulating the photo-oxidative response in Arabidopsis thaliana. GUN4 and GUN5 specifically interact with EXECUTER1 (EX1) and EX2 in plastids, and this interaction is alleviated by treatment with Rose Bengal (RB) or white light. Impaired expression of GUN4, GUN5, EX1, or EX2 leads to insensitivity to excess light and overexpression of EX1 triggers photo-oxidative responses. Strikingly, upon light irradiation or RB treatment, EX1 transiently accumulates in the nucleus and the nuclear fraction of EX1 shows a similar molecular weight as the plastid-located protein. Point mutagenesis analysis indicated that nuclear localization of EX1 is required for its function. EX1 acts as a transcriptional co-activator and interacts with the transcription factors WRKY18 and WRKY40 to promote the expression of 1O2-responsive genes. This study suggests that EX1 may act in plastid-to-nucleus signaling and establishes a 1O2-triggered retrograde signaling pathway that allows plants adapt to changing light environments during chloroplast development.

RING-Type E3 Ubiquitin Ligases AtRDUF1 and AtRDUF2 Positively Regulate the Expression of PR1 Gene and Pattern-Triggered Immunity

The importance of E3 ubiquitin ligases from different families for plant immune signaling has been confirmed. Plant RING-type E3 ubiquitin ligases are members of the E3 ligase superfamily and have been shown to play positive or negative roles during the regulation of various steps of plant immunity. Here, we present Arabidopsis RING-type E3 ubiquitin ligases AtRDUF1 and AtRDUF2 which act as positive regulators of flg22- and SA-mediated defense signaling. Expression of AtRDUF1 and AtRDUF2 is induced by pathogen-associated molecular patterns (PAMPs) and pathogens. The atrduf1 and atrduf2 mutants displayed weakened responses when triggered by PAMPs. Immune responses, including oxidative burst, mitogen-activated protein kinase (MAPK) activity, and transcriptional activation of marker genes, were attenuated in the atrduf1 and atrduf2 mutants. The suppressed activation of PTI responses also resulted in enhanced susceptibility to bacterial pathogens. Interestingly, atrduf1 and atrduf2 mutants showed defects in SA-mediated or pathogen-mediated PR1 expression; however, avirulent Pseudomonas syringae pv. tomato DC3000-induced cell death was unaffected. Our findings suggest that AtRDUF1 and AtRDUF2 are not just PTI-positive regulators but are also involved in SA-mediated PR1 gene expression, which is important for resistance to P. syringae.

HISTONE DEACETYLASE 9 transduces heat signal in plant cells

Heat stress limits plant growth, development, and crop yield, but how plant cells precisely sense and transduce heat stress signals remains elusive. Here, we identified a conserved heat stress response mechanism to elucidate how heat stress signal is transmitted from the cytoplasm into the nucleus for epigenetic modifiers. We demonstrate that HISTONE DEACETYLASE 9 (HDA9) transduces heat signals from the cytoplasm to the nucleus to play a positive regulatory role in heat responses in Arabidopsis. Heat specifically induces HDA9 accumulation in the nucleus. Under heat stress, the phosphatase PP2AB'β directly interacts with and dephosphorylates HDA9 to protect HDA9 from 26S proteasome-mediated degradation, leading to the translocation of nonphosphorylated HDA9 to the nucleus. This heat-induced enrichment of HDA9 in the nucleus depends on the nucleoporin HOS1. In the nucleus, HDA9 binds and deacetylates the target genes related to signaling transduction and plant development to repress gene expression in a transcription factor YIN YANG 1-dependent and -independent manner, resulting in rebalance of plant development and heat response. Therefore, we uncover an HDA9-mediated positive regulatory module in the heat shock signal transduction pathway. More important, this cytoplasm-to-nucleus translocation of HDA9 in response to heat stress is conserved in wheat and rice, which confers the mechanism significant implication potential for crop breeding to cope with global climate warming.