The OsICS1 is directly regulated by OsWRKY6 and increases resistance against Xanthomonas oryzae pv. oryzae.

KEY MESSAGE: OsICS1 but not OsICS1-L mediates the rice response to Xoo inoculation, with its overexpression increasing resistance against this pathogen. OsICS1 but not OsICS-L is directly upregulated by OsWRKY6. Rice (Oryza sativa) is a staple crop for about half of the global population and is particularly important in the diets of people living in Asia, Latin America, and Africa. This crop is continually threatened by bacterial leaf blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo), which drastically reduces yields; therefore, it is needed to elucidate the plant's resistance mechanisms against Xoo. Isochorismate synthase (ICS1) generates salicylic acid (SA) and increases resistance against bacterial disease. The OsICS1 is differently annotated in rice genome databases and has not yet been functionally characterized in the context of Xoo infection. Here, we report that the expression of the OsICS1 is directly regulated by OsWRKY6 and increases plant resistance against Xoo. Inoculation with Xoo increased the expression of OsICS1 but not that of the long variant of OsICS1 (OsICS1-L). OsWRKY6 directly activated the OsICS1 promoter but not the OsICS1-L promoter. OsICS1 overexpression in rice increased resistance against Xoo through the induction of SA-dependent bacterial defense genes. These data show that OsICS1 promotes resistance against Xoo infection.

The rice SnRK family: biological roles and cell signaling modules.

Stimulus-activated signaling pathways orchestrate cellular responses to control plant growth and development and mitigate the effects of adverse environmental conditions. During this process, signaling components are modulated by central regulators of various signal transduction pathways. Protein phosphorylation by kinases is one of the most important events transmitting signals downstream, via the posttranslational modification of signaling components. The plant serine and threonine kinase SNF1-related protein kinase (SnRK) family, which is classified into three subgroups, is highly conserved in plants. SnRKs participate in a wide range of signaling pathways and control cellular processes including plant growth and development and responses to abiotic and biotic stress. Recent notable discoveries have increased our understanding of how SnRKs control these various processes in rice (Oryza sativa). In this review, we summarize current knowledge of the roles of OsSnRK signaling pathways in plant growth, development, and stress responses and discuss recent insights. This review lays the foundation for further studies on SnRK signal transduction and for developing strategies to enhance stress tolerance in plants.

Heat shock factor binding protein BrHSBP1 regulates seed and pod development in Brassica rapa.

Plant heat shock factor binding proteins (HSBPs) are well known for their implication in the negative regulation of heat stress response (HSR) pathways. Herein, we report on the hitherto unknown functions of HSBP1 in Brassica rapa (BrHSBP1). BrHBSP1 was found to be predominant in flower buds and young leaves, while its segmental duplicate, BrHSBP1-like, was abundant in green siliques. Exposure to abiotic stress conditions, such as heat, drought, cold, and H2O2, and to phytohormones was found to differentially regulate BrHSBP1. The activity of BrHSBP1-GFP fusion proteins revealed their cellular localization in nuclei and cytosols. Transgenic overexpression of BrHSBP1 (BrHSBP1OX) improved pod and seed sizes, while CRISPR-Cas BrHSBP1 knock-out mutants (Brhsbp1_KO) were associated with aborted seed and pod development. The transcriptomic signatures of BrHSBP1OX and Brhsbp1_KO lines revealed that 360 and 2381 genes, respectively, were differentially expressed (Log2FC≥2, padj<0.05) expressed relative to control lines. In particular, developmental processes, including plant reproductive structure development (RSD)-related genes, were relatively downregulated in Brhsbp1_KO. Furthermore, yeast two-hybrid assays confirmed that BrHSBP1 can physically bind to RSD and other genes. Taking the findings together, it is clear that BrHSBP1 is involved in seed development via the modulation of RSD genes. Our findings represent the addition of a new regulatory player in seed and pod development in B. rapa.

OsWRKY114 Is a Player in Rice Immunity against Fusarium fujikuroi.

Every year, invasive pathogens cause significant damage to crops. Thus, identifying genes conferring broad-spectrum resistance to invading pathogens is critical for plant breeding. We previously demonstrated that OsWRKY114 contributes to rice (Oryza sativa L.) immunity against the bacterial pathovar Xanthomonas oryzae pv. oryzae (Xoo). However, it is not known whether OsWRKY114 is involved in defense responses to other pathogens. In this study, we revealed that OsWRKY114 enhances innate immunity in rice against the fungal pathogen Fusarium fujikuroi, which is the causal agent of bakanae disease. Transcript levels of various gibberellin-related genes that are required for plant susceptibility to F. fujikuroi were reduced in rice plants overexpressing OsWRKY114. Analysis of disease symptoms revealed increased innate immunity against F. fujikuroi in OsWRKY114-overexpressing rice plants. Moreover, the expression levels of OsJAZ genes, which encode negative regulators of jasmonic acid signaling that confer immunity against F. fujikuroi, were reduced in OsWRKY114-overexpressing rice plants. These results indicate that OsWRKY114 confers broad-spectrum resistance not only to Xoo but also to F. fujikuroi. Our findings provide a basis for developing strategies to mitigate pathogen attack and improve crop resilience to biotic stress.

Plant translational reprogramming for stress resilience.

Organisms regulate gene expression to produce essential proteins for numerous biological processes, from growth and development to stress responses. Transcription and translation are the major processes of gene expression. Plants evolved various transcription factors and transcriptome reprogramming mechanisms to dramatically modulate transcription in response to environmental cues. However, even the genome-wide modulation of a gene's transcripts will not have a meaningful effect if the transcripts are not properly biosynthesized into proteins. Therefore, protein translation must also be carefully controlled. Biotic and abiotic stresses threaten global crop production, and these stresses are seriously deteriorating due to climate change. Several studies have demonstrated improved plant resistance to various stresses through modulation of protein translation regulation, which requires a deep understanding of translational control in response to environmental stresses. Here, we highlight the translation mechanisms modulated by biotic, hypoxia, heat, and drought stresses, which are becoming more serious due to climate change. This review provides a strategy to improve stress tolerance in crops by modulating translational regulation.

Climate change impedes plant immunity mechanisms.

Rapid climate change caused by human activity is threatening global crop production and food security worldwide. In particular, the emergence of new infectious plant pathogens and the geographical expansion of plant disease incidence result in serious yield losses of major crops annually. Since climate change has accelerated recently and is expected to worsen in the future, we have reached an inflection point where comprehensive preparations to cope with the upcoming crisis can no longer be delayed. Development of new plant breeding technologies including site-directed nucleases offers the opportunity to mitigate the effects of the changing climate. Therefore, understanding the effects of climate change on plant innate immunity and identification of elite genes conferring disease resistance are crucial for the engineering of new crop cultivars and plant improvement strategies. Here, we summarize and discuss the effects of major environmental factors such as temperature, humidity, and carbon dioxide concentration on plant immunity systems. This review provides a strategy for securing crop-based nutrition against severe pathogen attacks in the era of climate change.

OsDWD1 E3 ligase-mediated OsNPR1 degradation suppresses basal defense in rice.

Many ubiquitin E3 ligases function in plant immunity. Here, we show that Oryza sativa (rice) DDB1 binding WD (OsDWD1) suppresses immune responses by targeting O. sativa non-expresser of pathogenesis-related gene 1 (OsNPR1) for degradation. Knock-down and overexpression experiments in rice plants showed that OsDWD1 is a negative regulator of the immune response and that OsNPR1 is a substrate of OsDWD1 and a substrate receptor of OsCRL4. After constructing the loss-of-function mutant OsDWD1R239A , we showed that the downregulation of OsNPR1 seen in rice lines overexpressing wild-type (WT) OsDWD1 (OsDWD1WT -ox) was compromised in OsDWD1R239A -ox lines, and that OsNPR1 upregulation enhanced resistance to pathogen infection, confirming that OsCRL4OsDWD1 regulates OsNPR1 protein levels. The enhanced disease resistance seen in OsDWD1 knock-down (OsDWD1-kd) lines contrasted with the reduced disease resistance in double knock-down (OsDWD1/OsNPR1-kd) lines, indicating that the enhanced disease resistance of OsDWD1-kd resulted from the accumulation of OsNPR1. Moreover, an in vivo heterologous protein degradation assay in Arabidopsis thaliana ddb1 mutants confirmed that the CUL4-based E3 ligase system can also influence OsNPR1 protein levels in Arabidopsis. Although OsNPR1 was degraded by the OsCRL4OsDWD1 -mediated ubiquitination system, the phosphodegron-motif-mutated NPR1 was partially degraded in the DWD1-ox protoplasts. This suggests that there might be another degradation process for OsNPR1. Taken together, these results indicate that OsDWD1 regulates OsNPR1 protein levels in rice to suppress the untimely activation of immune responses.

TMT-based quantitative membrane proteomics identified PRRs potentially involved in the perception of MSP1 in rice leaves.

Pathogen-associated molecular patterns (PAMPs) play a key role in triggering PAMPs triggered immunity (PTI) in plants. In the case of the rice-Magnaporthe oryzae pathosystem, fewer PAMPs and their pattern recognition receptors (PRRs) have been characterized. Recently, a M. oryzae snodprot1 homolog protein (MSP1) has been identified that functions as PAMP and triggering the PTI responses in rice. However, the molecular mechanism underlying MSP1-induced PTI is currently elusive. Therefore, we generated MSP1 overexpressed transgenic lines of rice, and a tandem mass tag (TMT)-based quantitative membrane proteomic analysis was employed to decipher the potential MSP1-induced signaling in rice using total cytosolic as well as membrane protein fractions. This approach led to the identification of 8033 proteins of which 1826 were differentially modulated in response to overexpression of MSP1 and/or exogenous jasmonic acid treatment. Of these, 20 plasma membrane-localized receptor-like kinases (RLKs) showed increased abundance in MSP1 overexpression lines. Moreover, activation of proteins related to the protein degradation and modification, calcium signaling, redox, and MAPK signaling was observed in transgenic lines expressing MSP1 in the apoplast. Taken together, our results identified potential PRR candidates involved in MSP1 recognition and suggested the overview mechanism of the MSP1-induced PTI signaling in rice leaves. SIGNIFICANCE: In plants, recognition of pathogen pathogen-derived molecules, such as PAMPs, by plant plant-derived PRRs has an essential role for in the activation of PTI against pathogen invasion. Typically, PAMPs are recognized by plasma membrane (PM) localized PRRs, however, identifying the PM-localized PRR proteins is challenging due to their low abundance. In this study, we performed an integrated membrane protein enrichment by microsomal membrane extraction (MME) method and subsequent TMT-labeling-based quantitative proteomic analysis using MSP1 overexpressed rice. Based on these results, we successfully identified various intracellular and membrane membrane-localized proteins that participated in the MSP1-induced immune response and characterized the potential PM-localized PRR candidates in rice.

OsWRKY114 Inhibits ABA-Induced Susceptibility to Xanthomonas oryzae pv. oryzae in Rice.

The phytohormone abscisic acid (ABA) regulates various aspects of plant growth, development, and stress responses. ABA suppresses innate immunity to Xanthomonas oryzae pv. oryzae (Xoo) in rice (Oryza sativa), but the identity of the underlying regulator is unknown. In this study, we revealed that OsWRKY114 is involved in the ABA response during Xoo infection. ABA-induced susceptibility to Xoo was reduced in OsWRKY114-overexpressing rice plants. OsWRKY114 attenuated the negative effect of ABA on salicylic acid-dependent immunity. Furthermore, OsWRKY114 decreased the transcript levels of ABA-associated genes involved in ABA response and biosynthesis. Moreover, the endogenous ABA level was lower in OsWRKY114-overexpressing plants than in the wild-type plants after Xoo inoculation. Taken together, our results suggest that OsWRKY114 is a negative regulator of ABA that confers susceptibility to Xoo in rice.

OsWRKY114 Negatively Regulates Drought Tolerance by Restricting Stomatal Closure in Rice.

The WRKY family of transcription factors plays a pivotal role in plant responses to biotic and abiotic stress. The WRKY Group III transcription factor OsWRKY114 is a positive regulator of innate immunity against Xanthomonas oryzae pv. oryzae; however, its role in abiotic stress responses is largely unknown. In this study, we showed that the abundant OsWRKY114 transcripts present in transgenic rice plants are reduced under drought conditions. The overexpression of OsWRKY114 significantly increased drought sensitivity in rice, which resulted in a lower survival rate after drought stress. Moreover, we showed that stomatal closure, which is a strategy to save water under drought, is restricted in OsWRKY114-overexpressing plants compared with wild-type plants. The expression levels of PYR/PYL/RCAR genes, such as OsPYL2 and OsPYL10 that confer drought tolerance through stomatal closure, were also markedly lower in the OsWRKY114-overexpressing plants. Taken together, these results suggest that OsWRKY114 negatively regulates plant tolerance to drought stress via inhibition of stomatal closure, which would otherwise prevent water loss in rice.

Challenges Facing CRISPR/Cas9-Based Genome Editing in Plants.

The development of plant varieties with desired traits is imperative to ensure future food security. The revolution of genome editing technologies based on the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system has ushered in a new era in plant breeding. Cas9 and the single-guide RNA (sgRNA) form an effective targeting complex on a locus or loci of interest, enabling genome editing in all plants with high accuracy and efficiency. Therefore, CRISPR/Cas9 can save both time and labor relative to what is typically associated with traditional breeding methods. However, despite improvements in gene editing, several challenges remain that limit the application of CRISPR/Cas9-based genome editing in plants. Here, we focus on four issues relevant to plant genome editing: (1) plant organelle genome editing; (2) transgene-free genome editing; (3) virus-induced genome editing; and (4) editing of recalcitrant elite crop inbred lines. This review provides an up-to-date summary on the state of CRISPR/Cas9-mediated genome editing in plants that will push this technique forward.

SNF1-Related Protein Kinase 1 Activity Represses the Canonical Translational Machinery.

Protein biosynthesis is achieved through translation, which consumes enormous energy. Therefore, under conditions of limited energy supply, translation progress should be strictly coordinated. Sucrose non-fermenting kinase1 (SNF1)-related protein kinase 1 (SnRK1) is an evolutionarily conserved master regulator of cellular energy stress signaling in plants. Rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) SnRK1 enhance hypoxia tolerance and induce the expression of stress-related genes. However, whether SnRK1 modulates protein synthesis in plants is unknown. In this study, using translational reporter constructs transfected in Arabidopsis protoplasts we showed that the expression of OsSnRK1A and AtSnRK1.1 decreases the abundance of canonical proteins without affecting their encoding transcript levels and protein stability. Moreover, the loading of total mRNAs and GFP mRNAs into the heavy polysome fraction which is normally translated was attenuated in transgenic Arabidopsis lines constitutively expressing OsSnRK1A or AtSnRK1.1. Taken together, these results suggest that OsSnRK1A and AtSnRK1.1 suppress protein translation to maintain energy homeostasis.

Label-free proteome data of susceptible and resistant rice cultivars in response to Xanthomonas oryzae pv. oryzae inoculation.

Here we report the data associated with the article: "Comparative proteome profiling of susceptible and resistant rice cultivars identified an arginase involved in rice defense against Xanthomonas oryzae pv. oryzae" [1]. Bacterial blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating diseases of rice across the globe; however, the underlying molecular mechanism of rice-Xoo interaction is currently not well understood. In this manuscript, we report the proteome profiles of rice leaves generated using a label-free quantitative proteomic analysis using QExactive™ Orbitrap High-Resolution Mass Spectrometer, MapMan, and rice interactome viewer [1].

Comparative proteome profiling of susceptible and resistant rice cultivars identified an arginase involved in rice defense against Xanthomonas oryzae pv. oryzae.

Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight, is one of the major threats to rice productivity. Yet, the molecular mechanism of rice-Xoo interaction is elusive. Here, we report comparative proteome profiles of Xoo susceptible (Dongjin) and resistant (Hwayeong) cultivars of rice in response to two-time points (3 and 6 days) of Xoo infection. Low-abundance proteins were enriched using a protamine sulfate (PS) precipitation method and isolated proteins were quantified by a label-free quantitative analysis, leading to the identification of 3846 proteins. Of these, 1128 proteins were significantly changed between mock and Xoo infected plants of Dongjin and Hwayeong cultivars. Based on the abundance pattern and functions of the identified proteins, a total of 23 candidate proteins were shortlisted that potentially participate in plant defense against Xoo in the resistant cultivar. Of these candidate proteins, a mitochondrial arginase-1 showed Hwayeong specific abundance and was significantly accumulated following Xoo inoculation. Overexpression of arginase 1 (OsArg 1) in susceptible rice cultivar (Dongjin) resulted in enhanced tolerance against Xoo as compared to the wild-type. In addition, expression analysis of defense-related genes encoding PR1, glucanase I, and chitinase II by qRT-PCR showed their enhanced expression in the overexpression lines as compared to wild-type. Taken together, our results uncover the proteome changes in the rice cultivars and highlight the functions of OsARG1 in plant defense against Xoo.

The OsWRKY6 transcriptional cascade functions in basal defense and Xa1-mediated defense of rice against Xanthomonas oryzae pv. oryzae.

MAIN CONCLUSION: The rice protein OsWRKY6 directly activates OsWRKY45 and OsWRKY47 expression, and also activates OsPR1a and OsPR1b through the two OsWRKYs, and this transcriptional module participates in Xa1-mediated defense against the pathogen Xanthomonas oryzae pv. oryzae. Biotic stress, the pathogen Xanthomonas oryzae pv. oryzae (Xoo) in particular, negatively impacts worldwide productivity and yield in the staple crop rice (Oryza sativa). OsWRKY transcription factors are involved in various biotic stress responses in rice, and OsWRKY6 specifically acts as an important defense regulator against Xoo. However, the relationship between OsWRKY6 and other OsWRKYs, as well as its role in resistance (R) gene-mediated defense, have yet to be studied in depth. Here, we characterized a transcriptional cascade triggered by OsWRKY6 that regulated defense against Xoo infection mediated by the NBS-LRR protein Xa1. OsWRKY45 and OsWRKY47 were identified as direct transcriptional targets of OsWRKY6, and their two gene products reciprocally activated their two genes. Furthermore, OsWRKY6 activated OsPR1a and OsPR1b via the OsWRKY45 and OsWRKY47. Two OsWRKY6 RNAi knockdown lines showed significantly reduced defense even against an incompatible Xoo infection, and the expression of OsWRKY6 was not regulated by OsWRKY51 and OsWRKY88. This study reveals that a novel downstream transcriptional pathway activated by OsWRKY6 is involved in Xa1-mediated defense against Xoo.

Identification of the Capsicum baccatum NLR Protein CbAR9 Conferring Disease Resistance to Anthracnose.

Anthracnose is caused by Colletotrichum species and is one of the most virulent fungal diseases affecting chili pepper (Capsicum) yield globally. However, the noble genes conferring resistance to Colletotrichum species remain largely elusive. In this study, we identified CbAR9 as the causal locus underlying the large effect quantitative trait locus CcR9 from the anthracnose-resistant chili pepper variety PBC80. CbAR9 encodes a nucleotide-binding and leucine-rich repeat (NLR) protein related to defense-associated NLRs in several other plant species. CbAR9 transcript levels were induced dramatically after Colletotrichum capsici infection. To explore the biological function, we generated transgenic Nicotiana benthamiana lines overexpressing CbAR9, which showed enhanced resistance to C. capsici relative to wild-type plants. Transcript levels of pathogenesis-related (PR) genes increased markedly in CbAR9-overexpressing N. benthamiana plants. Moreover, resistance to anthracnose and transcript levels of PR1 and PR2 were markedly reduced in CbAR9-silenced chili pepper fruits after C. capsici infection. Our results revealed that CbAR9 contributes to innate immunity against C. capsici.

The Capsicum baccatum-Specific Truncated NLR Protein CbCN Enhances the Innate Immunity against Colletotrichum acutatum.

Chili pepper (Capsicumannuum) is an important fruit and spice used globally, but its yield is seriously threatened by anthracnose. Capsicum baccatum is particularly valuable as it carries advantageous disease resistance genes. However, most of the genes remain to be identified. In this study, we identified the C. baccatum-specific gene CbCN, which encodes a truncated nucleotide-binding and leucine-rich repeat protein in the anthracnose resistant chili pepper variety PBC80. The transcription of CbCN was greater in PBC80 than it was in the susceptible variety An-S after Colletotrichum acutatum inoculation. In order to investigate the biological function of CbCN, we generated transgenic tobacco lines constitutively expressing CbCN. Notably, CbCN-overexpressing transgenic plants exhibited enhanced resistance to C. acutatum compared to wild-type plants. Moreover, the expression of pathogenesis-related (PR) genes was remarkably increased in a CbCN-overexpressing tobacco plants. In order to confirm these results in chili pepper, we silenced the CbCN gene using the virus-induced gene silencing system. The anthracnose resistance and expressions of PR1, PR2, and NPR1 were significantly reduced in CbCN-silenced chili peppers after C. acutatum inoculations. These results indicate that CbCN enhances the innate immunity against anthracnose caused by C. acutatum by regulating defense response genes.

Identification of a novel NPR1 homolog gene, OsNH5N16, which contributes to broad-spectrum resistance in rice.

Over half of the earth's population consumes rice as the primary food crop for dietary calories. However, severe loss of rice yield occurs due to bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) and bakanae disease caused by Fusarium fujikuroi (F. fujikuroi). Therefore, broad-spectrum resistance (BSR) to these pathogens is essential for rice cultivation. The Nonexpressor of Pathogenesis-Related Genes1 (NPR1), which is related to the signal molecule salicylic acid (SA) and the expression of pathogenesis-related (PR) genes, is a key regulator of systemic acquired resistance (SAR). Although five NPR1 homologs (NHs) have been identified in rice thus far, their cellular and biological functions remain largely unexplored. In this study, we identified a novel rice NH gene from Oryza sativa L. cv. Dongjin. The genetic variation of single nucleotide polymorphisms in OsNH5 caused a single amino acid substitution of asparagine for serine at residue 16. OsNH5N16 was mainly located in the nucleus, and its transcription was induced by Xoo. We generated transgenic rice lines constitutively expressing OsNH5N16 to investigate its function. Plants that overexpressed OsNH5N16 displayed enhanced BSR to Xoo and F. fujikuroi compared with wild varieties, and the transcription of PR genes such as OsPR1, GLUC, and CHIT2 was considerably upregulated. Moreover, we revealed that SA increases the transcription of OsNH5N16 and the promoter activity of OsPR1 regulated by OsNH5N16. These results showed that OsNH5N16 enhances BSR by regulating the expression of PR genes related to SAR and it is controlled by SA at the transcriptional and post-translational levels. This is the first report on the innate immune response conferring BSR associated with NH5.

Rice glutaredoxin GRXS15 confers broad-spectrum resistance to Xanthomonas oryzae pv. oryzae and Fusarium fujikuroi.

Rice is a particularly widely consumed food crop globally, but its yield is seriously damaged by bacterial blight due to Xanthomonas oryzae pv. oryzae (Xoo) and bakanae disease due to Fusarium fujikuroi (F. fujikuroi). However, broad-spectrum resistance (BSR) to both Xoo and F. fujikuroi remains largely elusive. In this study, we showed that rice monothiol glutaredoxin GRXS15 localizes in mitochondria and the nucleus, and its transcription is induced by Xoo. Transgenic rice lines constitutively expressing OsGRXS15 showed enhanced disease resistance to Xoo and F. fujikuroi, while CRISPR/Cas9-based knockout mutants showed reduced resistance compared with the wild-type plants. The transcription of pathogenesis-related (PR) genes was significantly induced in OsGRXS15-expressing plants. The rice transcription factor OsWRKY65 was identified as a binding partner, and it directly interacted with OsGRXS15 in the nucleus. Moreover, we revealed that the interaction of OsGRXS15 and OsWRKY65 results in the upregulation of OsPR1. These results suggested that OsGRXS15 interacts with transcription factors, and it confers BSR through regulating the expression of genes related to pathogen response. This is the first report on the nuclear function associated with the monothiol glutaredoxin GRXS15.