Cooperative regulation of PBI1 and MAPKs controls WRKY45 transcription factor in rice immunity

Identification of host specificity determinants in brome mosaic virus for rice infection

Brome mosaic virus (BMV) is a tripartite positive-stranded RNA plant virus. The genomic RNA2 encodes the 2a protein, which has conserved RNA-dependent RNA polymerase motifs and is required for viral RNA replication. In this study, we have used two BMV strains, F and KU5, and identified two key amino acid residues, 776R and 784T, in the C-terminal non-conserved region of the 2a protein that are critical for systemic infection of BMV-F in rice. While KU5 strain was not able to systemically infect rice, the KU5 mutant strain with two codon changes for 776R and 784T in the 2a gene gained the ability to establish systemic infection in rice, which affects long-distance movement, but not replication or cell-to-cell movement. Through infection assays of KU5 synonymous mutant strains, we demonstrated that amino acids, rather than RNA sequences or secondary structures, are responsible for viral infectivity in rice. Computer predictions and yeast two-hybrid screening revealed that the C-terminal region of 2a functions as an intrinsically disordered region, capable of interacting with host proteins. These results provide molecular insights into the host specificity of BMV and advance our understanding of RNA virus evolution and host-pathogen interactions.

Role of the beneficial phyllosphere microbiome in the defense against red clover anthracnose caused by Colletotrichum americae-borealis

Red clover (Trifolium pratense), a high-quality forage plant, faces significant threats from anthracnose in northeastern China, but the pathogen responsible remains unidentified. The phyllosphere microbiota is crucial in plantpathogen interactions, yet its role in the resistance of red clover to anthracnose is poorly understood. Using morphological, molecular, and multigene phylogenetic analyses, we identified Colletotrichum americae-borealis (Cab) as the pathogen that causes anthracnose in red clover in China. We also investigated changes in the phyllosphere microbiomes of highly resistant (XJ) and susceptible (SC) red clover materials after Cab infection, via 16S rRNA gene sequencing. The results revealed significant differences in bacterial α- and β-diversity, with novel microbial taxa and a complex microbial network emerging postinfection. Notably, after Cab inoculation, the Shannon diversity index in XJ exhibited more pronounced changes, manifested as an increase in the abundance of beneficial microorganisms such as Bacillus, Pantoea, and Pseudomonas. Network analysis revealed that the XJ microbiome was more complex and stable than the SC microbiome was, regardless of infection status. Bacillus J2, the dominant bacterium, significantly inhibited Cab growth in vitro and reduced the disease index by 33.4-47.7 % when it was reapplied to the leaf surface, suggesting its role in enhancing disease resistance. This study is the first to report that C. americae-borealis causes anthracnose in red clover in China, and demonstrates the potential of the beneficial bacterium J2 in enhancing disease resistance, providing insights into disease resistance mechanisms and the role of the phyllosphere microbiome in pathogen challenge.

The E3 ubiquitin ligase BRG3 and the protein kinase MPK7 antagonistically regulate LBD36 turnover, a key node for integrating nitrate and gibberellin signaling in apple

Nitrate is the main source of nitrogen in plants. Nitrate stimulation causes changes in plant secondary metabolites, including anthocyanins. However, the molecular mechanism underlying how nitrate regulates anthocyanin biosynthesis remains unclear. In this study, we identified a nitrate response factor MdLBD36 in apple. This factor positively regulated nitrate deficiency-induced anthocyanin biosynthesis by promoting the transcriptional activity of MdABI5, an important regulator of anthocyanins, and directly activated MdABI5 expression. The E3 ubiquitin ligase MdBRG3 promoted the ubiquitinated degradation of MdLBD36 to reduce anthocyanin biosynthesis under nitrate-sufficient conditions. Nitrate deficiency-activated MdMPK7 maintained the stimulating effect of MdLBD36 on anthocyanin biosynthesis by counteracting the MdBRG3-mediated degradation of MdLBD36. Nitrate coordinated gibberellin (GA) signaling to regulate anthocyanin biosynthesis. The GA signaling repressor MdRGL2a contributed to MdLBD36-promoted anthocyanin biosynthesis by enhancing the MdLBD36-MdABI5 interaction and increasing the MdLBD36 transcriptional activation of MdABI5. In summary, our results elucidate the molecular framework of the coordinated regulation of the nitrate signaling response and anthocyanin biosynthesis by ubiquitination and phosphorylation. This study revealed the cross talk between nitrate and GA signaling in the regulation of anthocyanin biosynthesis and provides references for an in-depth exploration of the nitrate signal transduction pathway and its interactions with hormones.

A close-up of regulatory networks and signaling pathways of MKK5 in biotic and abiotic stresses

Mitogen-activated protein Kinase Kinase 5 (MKK5) is a central hub in the complex phosphorylation chain reaction of the Mitogen-activated protein kinases (MAPK) cascade, regulating plant responses to biotic and abiotic stresses. This review manuscript aims to provide a comprehensive analysis of the regulatory mechanism of the MKK5 involved in stress adaptation. This review will delve into the intricate post-transcriptional and post-translational modifications of the MKK5, discussing how they affect its expression, activity, and subcellular localization in response to stress signals. We also discuss the integration of the MKK5 into complex signaling pathways, orchestrating plant immunity against pathogens and its modulating role in regulating abiotic stresses, such as: drought, cold, heat, and salinity, through the phytohormonal signaling pathways. Furthermore, we highlight potential applications of the MKK5 for engineering stress-resilient crops and provide future perspectives that may pave the way for future studies. This review manuscript aims to provide valuable insights into the mechanisms underlying MKK5 regulation, bridge the gap from numerous previous findings, and offer a firm base in the knowledge of MKK5, its regulating roles, and its involvement in environmental stress regulation.

Control of H2S synthesis by the monomer-oligomer transition of OsCBSX3 for modulating rice growth-immunity balance

Hydrogen sulfide (H2S) is recognized as an important gaseous signaling molecule, similar to nitric oxide and carbon monoxide. However, less is known about the biosynthetic mechanism of H2S in plants and its role in plant-pathogen interactions. Here, we show that H2S induces the bursts of reactive oxygen species and upregulates the expression of defense-related genes in rice. However, excessive H2S concentrations inhibit rice growth. We found that the cystathionine β-synthase OsCBSX3 regulates rice growth and resistance to bacteria pathogens, Xanthomonas oryzae pv. oryzicola (Xoc) and X. oryzae pv. oryzae (Xoo), by modulating H2S biosynthesis. OsCBSX3 exists in both oligomeric and monomeric forms in rice. Compared with wild-type OsCBSX3, an oligomerization-disrupted mutant exhibits the reduced capacity for H2S synthesis, diminished resistance to X. oryzae, and inability to localize to the chloroplast. Upon pathogen infection, rice triggers PsbO-dependent oligomerization of OsCBSX3, leading to increased H2S production and enhanced defense responses. However, excessive concentrations of H2S reduce the oligomerized form of OsCBSX3, facilitating its dissociation from PsbO, an important subunit of photosystem II, and its binding to OsTrxZ, a member of the thioredoxin family. We further demonstrated that OsTrxZ can directly convert OsCBSX3 into monomers, thereby mitigating the excessive H2S synthesis and its negative effects on rice growth and development. Overexpression of PsbO enhances rice resistance to both Xoc and Xoo, whereas overexpression of OsTrxZ exerts the opposite effect. Taken together, these findings suggest that PsbO and OsTrxZ antagonistically modulate the interconversion between oligomeric and monomeric forms of OsCBSX3, thereby balancing rice resistance and developmental processes.

Rice E3 ubiquitin ligases balance immunity and yield through non-proteolytic ubiquitination

The rice E3 ubiquitin ligases OsCIE1 and IPI7 mediate the non-proteolytic polyubiquitination of the pattern-recognition receptor kinase OsCERK1 and the transcription factor IPA1, respectively, in response to Magnaporthe oryzae infection, thereby fine-tuning rice growth-immunity trade-offs.

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

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

Nei 6 You 7075, a hybrid rice cultivar, exhibits enhanced disease resistance and drought tolerance traits

BACKGROUND

Rice is the main food crop for much of the population in China. Therefore, selecting and breeding new disease resistance and drought tolerance in rice is essential to ensure national food security. The utilization of heterosis has significantly enhanced rice productivity, yet many of the molecular mechanisms underlying this phenomenon remain largely unexplored. 'Nei 6 You 7075' ('N6Y7075') is a novel hybrid rice cultivar with exceptional quality, developed through the crossbreeding of 'Fuhui 7075' ('FH7075') and 'Neixiang 6 A' ('NX6A'). However, the precise mechanisms underlying the disease resistance and drought tolerance in 'N6Y7075' are poorly understood. In this study, we investigated the resistance of hybrid rice 'N6Y7075' to bacterial blight (Xanthomonas oryzae pv. oryzae), rice blast (Magnaporthe oryzae), and drought and identified differentially expressed genes between hybrid rice 'N6Y7075' and its parents through RNA-seq analysis.

RESULTS

Our research found that the hybrid 'N6Y7075' and its female parent 'NX6A' were less susceptible to bacterial blight and rice blast than the male parent 'FH7075', while 'FH7075' showed better drought tolerance than 'NX6A'. The hybrid 'N6Y7075' exhibited heterosis. Clustering results revealed that the expression profiles of the F1 hybrid closely resembled those of its parental lines rather than exhibiting an intermediate profile between the two parental lines. The disease resistance of hybrid rice 'N6Y7075' may be attributed to the plant-pathogen interaction pathways involving Xa21, CDPK, and RPM1-mediated hypersensitive response and WRKY1-induced defense-related gene expression and programmed cell death. The MAPK signaling pathway PR1 could also be associated with plant defense responses. Hybrid rice 'N6Y7075' may enhance drought tolerance by regulating MAPKKK17 and WAK60 in the MAPK signaling pathway. These proteins affect ABA stress adaptation and stomatal development in plants, respectively.

CONCLUSIONS

Our results provide a preliminary exploration of 'N6Y7075' disease resistance and drought tolerance and provide a relevant theoretical basis for its further study and use. This study provides insights into the molecular mechanisms of heterosis in hybrid rice and identifies potential associated genes.

Rice E3 ubiquitin ligases: From key modulators of host immunity to potential breeding applications

To combat pathogen attacks, plants have developed a highly advanced immune system, which requires tight regulation to initiate robust defense responses while simultaneously preventing autoimmunity. The ubiquitin-proteasome system (UPS), which is responsible for degrading excess or misfolded proteins, has vital roles in ensuring strong and effective immune responses. E3 ligases, as key UPS components, play extensively documented roles in rice immunity by modulating the ubiquitination and degradation of downstream substrates involved in various immune signaling pathways. Here, we summarize the crucial roles of rice E3 ligases in both pathogen/microbe/damage-associated molecular pattern-triggered immunity and effector-triggered immunity, highlight the molecular mechanisms by which E3 ligases function in rice immune signaling, and emphasize the functions of E3 ligases as targets of pathogen effectors for pathogenesis. We also discuss potential strategies for application of immunity-associated E3 ligases in breeding of disease-resistant rice varieties without growth penalty. This review provides a comprehensive and updated understanding of the sophisticated and interconnected regulatory functions of E3 ligases in rice immunity and in balancing immunity with growth and development.

A pair of E3 ubiquitin ligases control immunity and flowering by targeting different ELF3 proteins in rice

The ubiquitin-proteasome system (UPS) plays crucial roles in cellular processes including plant growth, development, and stress responses. In this study, we report that a pair of E3 ubiquitin ligases, AvrPiz-t-interaction protein 6 (APIP6) and IPA1-interaction protein 1 (IPI1), intricately target early flowering3 (ELF3) paralogous proteins to control rice immunity and flowering. APIP6 forms homo-oligomers or hetero-oligomers with IPI1. Both proteins interact with OsELF3-2, promoting its degradation to positively control resistance against the rice blast fungus (Magnaporthe oryzae). Intriguingly, overexpression of IPI1 in Nipponbare caused significantly late-flowering phenotypes similar to the oself3-1 mutant. Except for late flowering, oself3-1 enhances resistance against M. oryzae. IPI1 also interacts with and promotes the degradation of OsELF3-1, a paralog of OsELF3-2. Notably, IPI1 and APIP6 synergistically modulate OsELF3s degradation, finely tuning blast disease resistance by targeting OsELF3-2, while IPI1 controls both disease resistance and flowering by targeting OsELF3-1. This study unravels multiple functions for a pair of E3 ligases in rice.

Use of CRISPR Technology in Gene Editing for Tolerance to Biotic Factors in Plants: A Systematic Review

The objective of this systematic review (SR) was to select studies on the use of gene editing by CRISPR technology related to plant resistance to biotic stresses. We sought to evaluate articles deposited in six electronic databases, using pre-defined inclusion and exclusion criteria. This SR demonstrates that countries such as China and the United States of America stand out in studies with CRISPR/Cas. Among the most studied crops are rice, tomatoes and the model plant Arabidopsis thaliana. The most cited biotic agents include the genera, Xanthomonas, Manaporthe, Pseudomonas and Phytophthora. This SR also identifies several CRISPR/Cas-edited genes and demonstrates that plant responses to stressors are mediated by many complex signaling pathways. The Cas9 enzyme is used in most articles and Cas12 and 13 are used as additional editing tools. Furthermore, the quality of the articles included in this SR was validated by a risk of bias analysis. The information collected in this SR helps to understand the state of the art of CRISPR/Cas aimed at improving resistance to diseases and pests to understand the mechanisms involved in most host-pathogen relationships. This SR shows that the CRISPR/Cas system provides a straightforward method for rapid gene targeting, providing useful information for plant breeding programs.

Deciphering the mechanism of E3 ubiquitin ligases in plant responses to abiotic and biotic stresses and perspectives on PROTACs for crop resistance

With global climate change, it is essential to find strategies to make crops more resistant to different stresses and guarantee food security worldwide. E3 ubiquitin ligases are critical regulatory elements that are gaining importance due to their role in selecting proteins for degradation in the ubiquitin-proteasome proteolysis pathway. The role of E3 Ub ligases has been demonstrated in numerous cellular processes in plants responding to biotic and abiotic stresses. E3 Ub ligases are considered a class of proteins that are difficult to control by conventional inhibitors, as they lack a standard active site with pocket, and their biological activity is mainly due to protein-protein interactions with transient conformational changes. Proteolysis-targeted chimeras (PROTACs) are a new class of heterobifunctional molecules that have emerged in recent years as relevant alternatives for incurable human diseases like cancer because they can target recalcitrant proteins for destruction. PROTACs interact with the ubiquitin-proteasome system, principally the E3 Ub ligase in the cell, and facilitate proteasome turnover of the proteins of interest. PROTAC strategies harness the essential functions of E3 Ub ligases for proteasomal degradation of proteins involved in dysfunction. This review examines critical advances in E3 Ub ligase research in plant responses to biotic and abiotic stresses. It highlights how PROTACs can be applied to target proteins involved in plant stress response to mitigate pathogenic agents and environmental adversities.

Effectors and environment modulating rice blast disease: from understanding to effective control

Rice blast is a highly destructive crop disease that requires the interplay of three essential factors: the virulent blast fungus, the susceptible rice plant, and favorable environmental conditions. Although previous studies have focused mainly on the pathogen and rice, recent research has shed light on the molecular mechanisms by which the blast fungus and environmental conditions regulate host resistance and contribute to blast disease outbreaks. This review summarizes significant achievements in understanding the sophisticated modulation of blast resistance by Magnaporthe oryzae effectors and the dual regulatory mechanisms by which environmental conditions influence rice resistance and virulence of the blast fungus. Furthermore, it emphasizes potential strategies for developing blast-resistant rice varieties to effectively control blast disease.

KIN10-mediated HB16 protein phosphorylation and self-association improve cassava disease resistance by transcriptional activation of lignin biosynthesis genes

Cassava bacterial blight significantly affects cassava yield worldwide, while major cassava cultivars are susceptible to this disease. Therefore, it is crucial to identify cassava disease resistance gene networks and defence molecules for the genetic improvement of cassava cultivars. In this study, we found that MeHB16 transcription factor as a differentially expressed gene in cassava cultivars with contrasting disease resistance, positively modulated disease resistance by modulating defence molecule lignin accumulation. Further investigation showed that MeHB16 physically interacted with itself via the leucine-Zippe domain (L-Zip), which was necessary for the transcriptional activation of downstream lignin biosynthesis genes. In addition, protein kinase MeKIN10 directly interacted with MeHB16 to promote its phosphorylation at Ser6, which in turn enhanced MeHB16 self-association and downstream lignin biosynthesis. In summary, this study revealed the molecular network of MeKIN10-mediated MeHB16 protein phosphorylation improved cassava bacterial blight resistance by fine-tuning lignin biosynthesis and provides candidate genes and the defence molecule for improving cassava disease resistance.

Rice SRO1a Contributes to Xanthomonas TAL Effector-mediated Expression of Host Susceptible Genes

Xanthomonas species infect many important crops and cause huge yield loss. These pathogens deliver transcription activator-like (TAL) effectors into the cytoplasm of plant cells. TAL effectors move to host nuclei, directly bind to the promoters of host susceptible genes, and activate their transcription. However, the molecular mechanisms by which TAL effectors induce host transcription remain unclear. We herein demonstrated that TAL effectors interacted with the SIMILAR TO RCD ONE (SRO) family proteins OsSRO1a and OsSRO1b in nuclei. A transactivation assay using rice protoplasts indicated that OsSRO1a and OsSRO1b enhanced the activation of the OsSWEET14 promoter by the TAL effector AvrXa7. The AvrXa7-mediated expression of OsSWEET14 was significantly reduced in ossro1a mutants. However, the overexpression of OsSRO1a increased disease resistance by up-regulating the expression of defense-related genes, such as WRKY62 and PBZ1. This was attributed to OsSRO1a and OsSRO1b also enhancing the transcriptional activity of WRKY45, a direct regulator of WRKY62 expression. Therefore, OsSRO1a and OsSRO1b appear to positively contribute to transcription mediated by bacterial TAL effectors and rice transcription factors.

Proteolysis in plant immunity

Compared with transcription and translation, protein degradation machineries can act faster and be targeted to different subcellular compartments, enabling immediate regulation of signaling events. It is therefore not surprising that proteolysis has been used extensively to control homeostasis of key regulators in different biological processes and pathways. Over the past decades, numerous studies have shown that proteolysis, where proteins are broken down to peptides or amino acids through ubiquitin-mediated degradation systems and proteases, is a key regulatory mechanism to control plant immunity output. Here, we briefly summarize the roles various proteases play during defence activation, focusing on recent findings. We also update the latest progress of ubiquitin-mediated degradation systems in modulating immunity by targeting plant membrane-localized pattern recognition receptors, intracellular nucleotide-binding domain leucine-rich repeat receptors, and downstream signaling components. Additionally, we highlight recent studies showcasing the importance of proteolysis in maintaining broad-spectrum resistance without obvious yield reduction, opening new directions for engineering elite crops that are resistant to a wide range of pathogens with high yield.

Carbohydrate elicitor-induced plant immunity: Advances and prospects

The perceived negative impacts of synthetic agrochemicals gave way to alternative, biological plant protection strategies. The deployment of induced resistance, comprising boosting the natural defense responses of plants, is one of those. Plants developed multi-component defense mechanisms to defend themselves against biotic and abiotic stresses. These are activated upon recognition of stress signatures via membrane-localized receptors. The induced immune responses enable plants to tolerate and limit the impact of stresses. A systemic cascade of signals enables plants to prime un-damaged tissues, which is crucial during secondary encounters with stress. Comparable stress tolerance mechanisms can be induced in plants by the application of carbohydrate elicitors such as chitin/chitosan, β-1,3-glucans, oligogalacturonides, cellodextrins, xyloglucans, alginates, ulvans, and carrageenans. Treating plants with carbohydrate-derived elicitors enable the plants to develop resistance appliances against diverse stresses. Some carbohydrates are also known to have been involved in promoting symbiotic signaling. Here, we review recent progresses on plant resistance elicitation effect of various carbohydrate elicitors and the molecular mechanisms of plant cell perception, cascade signals, and responses to cascaded cues. Besides, the molecular mechanisms used by plants to distinguish carbohydrate-induced immunity signals from symbiotic signals are discussed. The structure-activity relationships of the carbohydrate elicitors are also described. Furthermore, we forwarded future research outlooks that might increase the utilization of carbohydrate elicitors in agriculture in order to improve the efficacy of plant protection strategies.

Quantitative phosphoproteomics reveals molecular pathway network in wheat resistance to stripe rust

Protein phosphorylation plays an important role in immune signaling transduction in plant resistance to pathogens. Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), severely devastates wheat production. Nonetheless, the molecular mechanism of wheat resistance to stripe rust remains limited. In this study, quantitative phosphoproteomics was employed to investigate the protein phosphorylation changes in wheat challenged by Pst. A total of 1537 and 2470 differentially accumulated phosphoproteins (DAPs) were identified from four early infection stage (6, 12, 18 and 24 h post-inoculation) in incompatible and compatible wheat-Pst interactions respectively. KEGG analysis revealed that Oxidative Phosphorylation, Phosphatidylinositol Signaling, and MAPK signaling processes are distinctively enriched in incompatible interaction, while Biosynthesis of secondary metabolites and RNA degradation process were significantly enriched in compatible interactions. In particular, abundant changes in phosphorylation levels of chloroplast proteins were identified, suggesting the regulatory role of photosynthesis in wheat-Pst interaction, which is further emphasized by protein-protein interaction (PPI) network analysis. Motif-x analysis identified [xxxxSPxxxx] motif, likely phosphorylation sites for defensive response-related kinases, and a new [xxxxSSxxxx] motif significantly enriched in incompatible interaction. The results shed light on the early phosphorylation events contributing to wheat resistance against Pst. Moreover, our study demonstrated that the phosphorylation levels of Nucleoside diphosphate kinase TaNAPK1 are upregulated at 12 hpi with CYR23 and at 24 hpi with CYR31. Transient silencing of TaNAPK1 was able to attenuate wheat resistance to CYR23 and CYR31. Our study provides new insights into the mechanisms underlying Pst-wheat interactions and may provide database to find potential targets for the development of new resistant varieties.

JrPHL8-JrWRKY4-JrSTH2L module regulates resistance to Colletotrichum gloeosporioides in walnut

Walnut anthracnose (Colletotrichum gloeosporioides) reduces walnut yield and quality and seriously threatens the healthy development of the walnut industry. WRKY transcription factors (TFs) are crucial regulatory factors involved in plant-pathogen interactions. Our previous transcriptome analysis results indicate that JrWRKY4 responds to infection by C. gloeosporioides, but its specific regulatory network and disease resistance mechanism are still unclear. Herein, the characteristics of JrWRKY4 as a transcription activator located in the nucleus were first identified. Gain-of-function and loss-of-function analyses showed that JrWRKY4 could enhance walnut resistance against C. gloeosporioides. A series of molecular experiments showed that JrWRKY4 directly interacted with the promoter region of JrSTH2L and positively regulated its expression. In addition, JrWRKY4 interacted with JrVQ4 to form the protein complex, which inhibited JrWRKY4 for the activation of JrSTH2L. Notably, a MYB TF JrPHL8 interacting with the JrWRKY4 promoter has also been identified, which directly bound to the MBS element in the promoter of JrWRKY4 and induced its activity. Our study elucidated a novel mechanism of the JrPHL8-JrWRKY4-JrSTH2L in regulating walnut resistance to anthracnose. This mechanism improves our understanding of the molecular mechanism of WRKY TF mediated resistance to anthracnose in walnut, which provides new insights for molecular breeding of disease-resistant walnuts in the future.

Effect of Bacterial Extracellular Polymeric Substances from Enterobacter spp. on Rice Growth under Abiotic Stress and Transcriptomic Analysis

Plant biostimulants have received attention as sustainable alternatives to chemical fertilizers. Extracellular polymeric substances (EPSs), among the compounds secreted by plant growth-promoting rhizobacteria (PGPRs), are assumed to alleviate abiotic stress. This study aims to investigate the effect of purified EPSs on rice under abiotic stress and analyze their mechanisms. A pot experiment was conducted to elucidate the effects of inoculating EPSs purified from PGPRs that increase biofilm production in the presence of sugar on rice growth in heat-stress conditions. Since all EPSs showed improvement in SPAD after the stress, Enterobacter ludwigii, which was not characterized as showing higher PGP bioactivities such as phytohormone production, nitrogen fixation, and phosphorus solubilization, was selected for further analysis. RNA extracted from the embryos of germinating seeds at 24 h post-treatment with EPSs or water was used for transcriptome analysis. The RNA-seq analysis revealed 215 differentially expressed genes (DEGs) identified in rice seeds, including 139 up-regulated and 76 down-regulated genes. A gene ontology (GO) enrichment analysis showed that the enriched GO terms are mainly associated with the ROS scavenging processes, detoxification pathways, and response to oxidative stress. For example, the expression of the gene encoding OsAAO5, which is known to function in detoxifying oxidative stress, was two times increased by EPS treatment. Moreover, EPS application improved SPAD and dry weights of shoot and root by 90%, 14%, and 27%, respectively, under drought stress and increased SPAD by 59% under salt stress. It indicates that bacterial EPSs improved plant growth under abiotic stresses. Based on our results, we consider that EPSs purified from Enterobacter ludwigii can be used to develop biostimulants for rice.

Zinc-finger (ZiF) fold secreted effectors form a functionally diverse family across lineages of the blast fungus Magnaporthe oryzae

Filamentous plant pathogens deliver effector proteins into host cells to suppress host defence responses and manipulate metabolic processes to support colonization. Understanding the evolution and molecular function of these effectors provides knowledge about pathogenesis and can suggest novel strategies to reduce damage caused by pathogens. However, effector proteins are highly variable, share weak sequence similarity and, although they can be grouped according to their structure, only a few structurally conserved effector families have been functionally characterized to date. Here, we demonstrate that Zinc-finger fold (ZiF) secreted proteins form a functionally diverse effector family in the blast fungus Magnaporthe oryzae. This family relies on the Zinc-finger motif for protein stability and is ubiquitously present in blast fungus lineages infecting 13 different host species, forming different effector tribes. Homologs of the canonical ZiF effector, AVR-Pii, from rice infecting isolates are present in multiple M. oryzae lineages. Wheat infecting strains of the fungus also possess an AVR-Pii like allele that binds host Exo70 proteins and activates the immune receptor Pii. Furthermore, ZiF tribes may vary in the proteins they bind to, indicating functional diversification and an intricate effector/host interactome. Altogether, we uncovered a new effector family with a common protein fold that has functionally diversified in lineages of M. oryzae. This work expands our understanding of the diversity of M. oryzae effectors, the molecular basis of plant pathogenesis and may ultimately facilitate the development of new sources for pathogen resistance.

Arabidopsis transcription factor WRKY45 confers cadmium tolerance via activating PCS1 and PCS2 expression

Cadmium (Cd) has long been recognized as toxic pollutant to crops worldwide. The biosynthesis of glutathione-dependent phytochelatin (PC) plays crucial roles in the detoxification of Cd in plants. However, its regulatory mechanism remains elusive. Here, we revealed that Arabidopsis transcription factor WRKY45 confers Cd tolerance via promoting the expression of PC synthesis-related genes PCS1 and PCS2, respectively. Firstly, we found that Cd stress induces the transcript levels of WRKY45 and its protein abundance. Accordingly, in contrast to wild type Col-0, the increased sensitivity to Cd is observed in wrky45 mutant, while overexpressing WRKY45 plants are more tolerant to Cd. Secondly, quantitative real-time PCR revealed that the expression of AtPCS1 and AtPCS2 is stimulated in overexpressing WRKY45 plants, but decreased in wrky45 mutant. Thirdly, WRKY45 promotes the expression of PCS1 and PCS2, electrophoresis mobility shift assay analysis uncovered that WRKY45 directly binds to the W-box cis-element of PCS2 promoter. Lastly, the overexpression of WRKY45 in Col-0 leads to more accumulation of PCs in Arabidopsis, and the overexpression of PCS1 or PCS2 in wrky45 mutant plants rescues the phenotypes induced by Cd stress. In conclusion, our results show that AtWRKY45 positively regulates Cd tolerance in Arabidopsis via activating PCS1 and PCS2 expression.

The E3 ubiquitin ligase OsRGLG5 targeted by the Magnaporthe oryzae effector AvrPi9 confers basal resistance against rice blast

Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases of rice. During infection, M. oryzae secretes effectors to facilitate blast development. Among these effectors, the avirulence factor AvrPi9 is recognized by Pi9, a broad-spectrum blast resistance protein that triggers Pi9-mediated resistance in rice. However, little is known about the interaction between AvrPi9 and Pi9 and how AvrPi9 exerts virulence to promote infection. In this study, we found that ectopic expression of AvrPi9 in the Pi9-lacking cultivar TP309 suppressed basal resistance against M. oryzae. Furthermore, we identified an AvrPi9-interacting protein in rice, which we named OsRGLG5, encoding a functional RING-type E3 ubiquitin ligase. During infection, AvrPi9 was ubiquitinated and degraded by OsRGLG5. Meanwhile, AvrPi9 affected the stability of OsRGLG5. Infection assays revealed that OsRGLG5 is a positive regulator of basal resistance against M. oryzae, but it is not essential for Pi9-mediated blast resistance in rice. In conclusion, our results revealed that OsRGLG5 is targeted by the M. oryzae effector AvrPi9 and positively regulates basal resistance against rice blast.

The E3 ubiquitin ligase SINA1 and the protein kinase BIN2 cooperatively regulate PHR1 in apple anthocyanin biosynthesis

PHR1 (PHOSPHATE STARVATION RESPONSE1) plays key roles in the inorganic phosphate (Pi) starvation response and in Pi deficiency-induced anthocyanin biosynthesis in plants. However, the post-translational regulation of PHR1 is unclear, and the molecular basis of PHR1-mediated anthocyanin biosynthesis remains elusive. In this study, we determined that MdPHR1 was essential for Pi deficiency-induced anthocyanin accumulation in apple (Malus × domestica). MdPHR1 interacted with MdWRKY75, a positive regulator of anthocyanin biosynthesis, to enhance the MdWRKY75-activated transcription of MdMYB1, leading to anthocyanin accumulation. In addition, the E3 ubiquitin ligase SEVEN IN ABSENTIA1 (MdSINA1) negatively regulated MdPHR1-promoted anthocyanin biosynthesis via the ubiquitination-mediated degradation of MdPHR1. Moreover, the protein kinase apple BRASSINOSTEROID INSENSITIVE2 (MdBIN2) phosphorylated MdPHR1 and positively regulated MdPHR1-mediated anthocyanin accumulation by attenuating the MdSINA1-mediated ubiquitination degradation of MdPHR1. Taken together, these findings not only demonstrate the regulatory role of MdPHR1 in Pi starvation induced anthocyanin accumulation, but also provide an insight into the post-translational regulation of PHR1.

Engineering Climate-Resilient Rice Using a Nanobiostimulant-Based "Stress Training" Strategy

Under a changing climate, cultivating climate-resilient crops will be critical to maintaining food security. Here, we propose the application of reactive oxygen species (ROS)-generating nanoparticles as nanobiostimulants to trigger stress/immune responses and subsequently increase the stress resilience of plants. We established three regimens of silver nanoparticles (AgNPs)-based "stress training": seed training (ST), leaf training (LT), and combined seed and leaf training (SLT). Trained rice seedlings were then exposed to either rice blast fungus (Magnaporthe oryzae) or chilling stress (10 °C). The results show that all "stress training" regimes, particularly SLT, significantly enhanced the resistance of rice against the fungal pathogen (lesion size reduced by 82% relative to untrained control). SLT also significantly enhanced rice tolerance to cold stress. The mechanisms for the enhanced resilience were investigated with metabolomics and transcriptomics, which show that "stress training" induced considerable metabolic and transcriptional reprogramming in rice leaves. AgNPs boosted ROS-activated stress signaling pathways by oxidative post-translational modifications of stress-related kinases, hormones, and transcriptional factors (TFs). These signaling pathways subsequently modulated the expression of defense genes, including specialized metabolites (SMs) biosynthesis genes, cell membrane lipid metabolism genes, and pathogen-plant interaction genes. Importantly, results showed that the "stress memory" can be transferred transgenerationally, conferring offspring seeds with improved seed germination and seedling vigor. This may provide an epigenetic breeding strategy to fortify stress resilience of crops. This nanobiostimulant-based stress training strategy will increase yield vigor against a changing climate and will contribute to sustainable agriculture by reducing agrochemical use.

The E3 ubiquitin ligases SINA1 and SINA2 integrate with the protein kinase CIPK20 to regulate the stability of RGL2a, a positive regulator of anthocyanin biosynthesis

Although DELLA protein destabilization mediated by post-translational modifications is essential for gibberellin (GA) signal transduction and GA-regulated anthocyanin biosynthesis, the related mechanisms remain largely unknown. In this study, we report the ubiquitination and phosphorylation of an apple DELLA protein MdRGL2a in response to GA signaling and its regulatory role in anthocyanin biosynthesis. MdRGL2a could interact with MdWRKY75 to enhance the MdWRKY75-activated transcription of anthocyanin activator MdMYB1 and interfere with the interaction between anthocyanin repressor MdMYB308 and MdbHLH3 or MdbHLH33, thereby promoting anthocyanin accumulation. A protein kinase MdCIPK20 was found to phosphorylate and protect MdRGL2a from degradation, and it was essential for MdRGL2a-promoting anthocyanin accumulation. However, MdRGL2a and MdCIPK20 were ubiquitinated and degraded by E3 ubiquitin ligases MdSINA1 and MdSINA2, respectively, both of which were activated in the presence of GA. Our results display the integration of SINA1/2 with CIPK20 to dynamically regulate GA signaling and will be helpful toward understanding the mechanism of GA signal transduction and GA-inhibited anthocyanin biosynthesis. The discovery of extensive interactions between DELLA and SINA and CIPK proteins in apple will provide reference for the study of ubiquitination and phosphorylation of DELLA proteins in other species.

Genome-Wide Association Study Identifies Resistance Loci for Bacterial Blight in a Collection of Asian Temperate Japonica Rice Germplasm

Growing resistant rice cultivars is the most effective strategy to control bacterial blight (BB), a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo). Screening resistant germplasm and identifying resistance (R) genes are prerequisites for breeding resistant rice cultivars. We conducted a genome-wide association study (GWAS) to detect quantitative trait loci (QTL) associated with BB resistance using 359 East Asian temperate Japonica accessions inoculated with two Chinese Xoo strains (KS6-6 and GV) and one Philippine Xoo strain (PXO99^A). Based on the 55K SNPs Array dataset of the 359 Japonica accessions, eight QTL were identified on rice chromosomes 1, 2, 4, 10, and 11. Four of the QTL coincided with previously reported QTL, and four were novel loci. Six R genes were localized in the qBBV-11.1, qBBV-11.2, and qBBV-11.3 loci on chromosome 11 in this Japonica collection. Haplotype analysis revealed candidate genes associated with BB resistance in each QTL. Notably, LOC_Os11g47290 in qBBV-11.3, encoding a leucine-rich repeat receptor-like kinase, was a candidate gene associated with resistance to the virulent strain GV. Knockout mutants of Nipponbare with the susceptible haplotype of LOC_Os11g47290 exhibited significantly improved BB resistance. These results will be useful for cloning BB resistance genes and breeding resistant rice cultivars.

Transcriptomic analysis of pea plant responses to chitooligosaccharides' treatment revealed stimulation of mitogen-activated protein kinase cascade

Since chitooligosaccharides (COs) are water-soluble, biodegradable and nontoxic compounds, their application may be considered as a promising plant-protecting agent. However, the molecular and cellular modes of action of COs are not yet understood. In this study, transcriptional changes in pea roots treated with COs were investigated via RNA sequencing. Pea roots treated with the deacetylated CO8-DA at low concentration (10^-5 М) were harvested 24 h after treatment and their expression profiles were compared against medium-treated control plants. We observed 886 differentially expressed genes (fold change ≥ 1; p-value < 0.05) 24 h after treatment with CO8-DA. Gene Ontology term over-representation analysis allowed us to identify the molecular functions of the genes activated in response to CO8-DA treatment and their relation to biological processes. Our findings suggest that calcium signaling regulators and MAPK cascade play a key role in pea plant responses to treatment. Here we found two MAPKKKs, the PsMAPKKK5 and PsMAPKKK20, which might function redundantly in the CO8-DA-activated signaling pathway. In accordance with this suggestion, we showed that PsMAPKKK knockdown decreases resistance to pathogenic Fusarium culmorum fungi. Therefore, analysis showed that typical regulators of intracellular signal transduction pathways involved in triggering of plant responses via CERK1 receptors to chitin/COs in Arabidopsis and rice may also be recruited in legume pea plants.

Genome-wide survey and expression analysis of Dof transcription factor family in sweetpotato shed light on their promising functions in stress tolerance

DNA-binding with one finger (Dof) transcription factors play a crucial role in plant abiotic stress regulatory networks, although massive Dofs have been systematically characterized in plants, they have not been identified in the hexaploid crop sweetpotato. Herein, 43 IbDof genes were detected to be disproportionally dispersed across 14 of the 15 chromosomes of sweetpotato, and segmental duplications were discovered to be the major driving force for the expansion of IbDofs. The collinearity analysis of IbDofs with their related orthologs from eight plants revealed the potential evolutionary history of Dof gene family. Phylogenetic analysis displayed that IbDof proteins were assigned into nine subfamilies, and the regularity of gene structures and conserved motifs was consistent with the subgroup classification. Additionally, five chosen IbDof genes were shown to be substantially and variably induced under various abiotic conditions (salt, drought, heat, and cold), as well as hormone treatments (ABA and SA), according to their transcriptome data and qRT-PCR experiments. Consistently, the promoters of IbDofs contained a number of cis-acting elements associated with hormone and stress responses. Besides, it was noted that IbDof2 had transactivation activity in yeasts, while IbDof-11/-16/-36 did not, and protein interaction network analysis and yeast two-hybrid experiments revealed a complicated interaction connection amongst IbDofs. Collectively, these data lay a foundation for further functional explorations of IbDof genes, especially with regards to the possible application of multiple IbDof members in breeding the tolerant plants.

Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by Penicillium digitatum

WRKY transcription factors (TFs) play a vital role in plant stress signal transduction and regulate the expression of various stress resistance genes. Sweet orange (Citrus sinensis) accounts for a large proportion of the world's citrus industry, which has high economic value, while Penicillium digitatum is a prime pathogenic causing postharvest rot of oranges. There are few reports on how CsWRKY TFs play their regulatory roles after P. digitatum infects the fruit. In this study, we performed genome-wide identification, classification, phylogenetic and conserved domain analysis of CsWRKY TFs, visualized the structure and chromosomal localization of the encoded genes, explored the expression pattern of each CsWRKY gene under P. digitatum stress by transcriptome data, and made the functional prediction of the related genes. This study provided insight into the characteristics of 47 CsWRKY TFs, which were divided into three subfamilies and eight subgroups. TFs coding genes were unevenly distributed on nine chromosomes. The visualized results of the intron-exon structure and domain are closely related to phylogeny, and widely distributed cis-regulatory elements on each gene played a global regulatory role in gene expression. The expansion of the CSWRKY TFs family was probably facilitated by twenty-one pairs of duplicated genes, and the results of Ka/Ks calculations indicated that this gene family was primarily subjected to purifying selection during evolution. Our transcriptome data showed that 95.7% of WRKY genes were involved in the transcriptional regulation of sweet orange in response to P. digitatum infection. We obtained 15 differentially expressed genes and used the reported function of AtWRKY genes as references. They may be involved in defense against P. digitatum and other pathogens, closely related to the stress responses during plant growth and development. Two interesting genes, CsWRKY2 and CsWRKY14, were expressed more than 60 times and could be used as excellent candidate genes in sweet orange genetic improvement. This study offers a theoretical basis for the response of CSWRKY TFs to P. digitatum infection and provides a vital reference for molecular breeding.

The MAPK-Alfin-like 7 module negatively regulates ROS scavenging genes to promote NLR-mediated immunity

Nucleotide-binding leucine-rich repeat (NLR) receptor-mediated immunity includes rapid production of reactive oxygen species (ROS) and transcriptional reprogramming, which is controlled by transcription factors (TFs). Although some TFs have been reported to participate in NLR-mediated immune response, most TFs are transcriptional activators, and whether and how transcriptional repressors regulate NLR-mediated plant defenses remains largely unknown. Here, we show that the Alfin-like 7 (AL7) interacts with N NLR and functions as a transcriptional repressor. Knockdown and knockout of AL7 compromise N NLR-mediated resistance against tobacco mosaic virus, whereas AL7 overexpression enhances defense, indicating a positive regulatory role for AL7 in immunity. AL7 binds to the promoters of ROS scavenging genes to inhibit their transcription during immune responses. Mitogen-activated protein kinases (MAPKs), salicylic acid-induced protein kinase (SIPK), and wound-induced protein kinase (WIPK) directly interact with and phosphorylate AL7, which impairs the AL7-N interaction and enhances its DNA binding activity, which promotes ROS accumulation and enables immune activation. In addition to N, AL7 is also required for the function of other Toll interleukin 1 receptor/nucleotide-binding/leucine-rich repeats (TNLs) including Roq1 and RRS1-R/RPS4. Our findings reveal a hitherto unknown MAPK-AL7 module that negatively regulates ROS scavenging genes to promote NLR-mediated immunity.

Plant Chitinase Mutants as the Catalysts for Chitooligosaccharide Synthesis Using the Sugar Oxazoline Derivatives

Sugar oxazolines, (GlcNAc)_n-oxa (n = 2, 3, 4, and 5), were synthesized from a mixture of chitooligosaccharides, (GlcNAc)_n (n = 2, 3, 4, and 5), and utilized for synthesis of (GlcNAc)₇ with higher elicitor activity using plant chitinase mutants as the catalysts. From isothermal titration calorimetry, the binding affinity of (GlcNAc)₂-oxa toward an inactive mutant obtained from Arabidopsis thaliana GH18 chitinase was found to be higher than those of the other (GlcNAc)_n-oxa (n = 3, 4, and 5). To synthesize (GlcNAc)₇, the donor/acceptor substrates with different size combinations, (GlcNAc)₂-oxa/(GlcNAc)₅ (1), (GlcNAc)₃-oxa/(GlcNAc)₄ (2), (GlcNAc)₄-oxa/(GlcNAc)₃ (3), and (GlcNAc)₅-oxa/(GlcNAc)₂ (4), were incubated with hypertransglycosylating mutants of GH18 chitinases from A. thaliana and Cycas revoluta. The synthetic activities of these plant chitinase mutants were lower than that of a mutant of Bacillus circulans chitinase A1. Nevertheless, in the plant chitinase mutants, the synthetic efficiency of combination (1) was higher than those of the other combinations (2), (3), and (4), suggesting that the synthetic reaction is mostly dominated by the binding affinities of (GlcNAc)_n-oxa. In contrast, the Bacillus enzyme mutant with a different subsite arrangement synthesized (GlcNAc)₇ from combination (1) in the lowest efficiency. Donor/acceptor-size dependency of the enzymatic synthesis appeared to be strongly related to the subsite arrangement of the enzyme used as the catalyst. The A. thaliana chitinase mutant was found to be useful when combination (1) is employed for the substrates.

The host exocyst complex is targeted by a conserved bacterial type-III effector that promotes virulence

For most Gram-negative bacteria, pathogenicity largely depends on the type-III secretion system that delivers virulence effectors into eukaryotic host cells. The subcellular targets for the majority of these effectors remain unknown. Xanthomonas campestris, the causal agent of black rot disease of crucifers such as Brassica spp., radish, and turnip, delivers XopP, a highly conserved core-effector protein produced by X. campestris, which is essential for virulence. Here, we show that XopP inhibits the function of the host-plant exocyst complex by direct targeting of Exo70B, a subunit of the exocyst complex, which plays a significant role in plant immunity. XopP interferes with exocyst-dependent exocytosis and can do this without activating a plant NOD-like receptor that guards Exo70B in Arabidopsis. In this way, Xanthomonas efficiently inhibits the host's pathogen-associated molecular pattern (PAMP)-triggered immunity by blocking exocytosis of pathogenesis-related protein-1A, callose deposition, and localization of the FLAGELLIN SENSITIVE2 (FLS2) immune receptor to the plasma membrane, thus promoting successful infection. Inhibition of exocyst function without activating the related defenses represents an effective virulence strategy, indicating the ability of pathogens to adapt to host defenses by avoiding host immunity responses.