A negative regulator encoded by a rice WRKY gene represses both abscisic acid and gibberellins signaling in aleurone cells

Functional analysis of TkWRKY33: A key regulator in drought-induced natural rubber synthesis in Taraxacum kok-saghyz

WRKY proteins, which form a transcription factor superfamily that responds to jasmonic acid (JA) signals, regulate various developmental processes and stress responses in plants, including Taraxacum kok-saghyz (TKS). TKS serves as an ideal model plant for studying rubber production and lays the foundation for a comprehensive understanding of JA-mediated regulation of natural rubber synthesis. In the present study, we screened and identified a valuable transcription factor, TkWRKY33, based on transcriptome data from TKS in response to JA. We investigated its role in the regulation of natural rubber synthesis within the JA signaling pathway and its function in response to drought stress. Through protein-protein interactions and transcriptional regulation analysis, we found that TkWRKY33 may regulate natural rubber synthesis through the JA-TkMPK3-TkWRKY33-(TkGGPS5/TkACAT8) cascade pathway, possibly by participating in JA-activated mitogen-activated protein kinase (MAPK) signaling. Overexpression of TkWRKY33 in tobacco, along with functional analysis of drought resistance and comparative analysis of natural rubber content after drought stress, revealed that TkWRKY33 not only enhances plant drought resistance by regulating the expression of genes related to reactive oxygen species (ROS) scavenging through the JA signaling pathway, but also has a close relationship with the signal transduction pathway mediated by the JA hormone in regulating natural rubber synthesis. The TkWRKY33 is recognized as a valuable transcription factor, which likely plays a role in regulating natural rubber biosynthesis through the JA-activated MAPK cascade signaling pathway JA-TkMPK3-TkWRKY33-(TkGGPS5/TkACAT8).

Beyond green and red: unlocking the genetic orchestration of tomato fruit color and pigmentation

Fruit color is a genetic trait and a key factor for consumer acceptability and is therefore receiving increasing importance in several breeding programs. Plant pigments offer plants with a variety of colored organs that attract animals for pollination, favoring seed dispersers and conservation of species. The pigments inside plant cells not only play a light-harvesting role but also provide protection against light damage and exhibit nutritional and ecological value for health and visual pleasure in humans. Tomato (Solanum lycopersicum) is a leading vegetable crop; its fruit color formation is associated with the accumulation of several natural pigments, which include carotenoids in the pericarp, flavonoids in the peel, as well as the breakdown of chlorophyll during fruit ripening. To improve tomato fruit quality, several techniques, such as genetic engineering and genome editing, have been used to alter fruit color and regulate the accumulation of secondary metabolites in related pathways. Recently, clustered regularly interspaced short palindromic repeat (CRISPR)-based systems have been extensively used for genome editing in many crops, including tomatoes, and promising results have been achieved using modified CRISPR systems, including CAS9 (CRISPR/CRISPR-associated-protein) and CRISPR/Cas12a systems. These advanced tools in biotechnology and whole genome sequencing of various tomato species will certainly advance the breeding of tomato fruit color with a high degree of precision. Here, we attempt to summarize the current advancement and effective application of genetic engineering techniques that provide further flexibility for fruit color formation. Furthermore, we have also discussed the challenges and opportunities of genetic engineering and genome editing to improve tomato fruit color.

Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa)

Modeling biological processes and genetic-regulatory networks using in silico approaches provides a valuable framework for understanding how genes and associated allelic and genotypic differences result in specific traits. Submergence tolerance is a significant agronomic trait in rice; however, the gene-gene interactions linked with this polygenic trait remain largely unknown. In this study, we constructed a network of 57 transcription factors involved in seed germination and coleoptile elongation under submergence. The gene-gene interactions were based on the co-expression profiles of genes and the presence of transcription factor binding sites in the promoter region of target genes. We also incorporated published experimental evidence, wherever available, to support gene-gene, gene-protein, and protein-protein interactions. The co-expression data were obtained by re-analyzing publicly available transcriptome data from rice. Notably, this network includes OSH1, OSH15, OSH71, Sub1B, ERFs, WRKYs, NACs, ZFP36, TCPs, etc., which play key regulatory roles in seed germination, coleoptile elongation and submergence response, and mediate gravitropic signaling by regulating OsLAZY1 and/or IL2. The network of transcription factors was manually biocurated and submitted to the Plant Reactome Knowledgebase to make it publicly accessible. We expect this work will facilitate the re-analysis/re-use of OMICs data and aid genomics research to accelerate crop improvement.

Characterization of ZmPMP3g function in drought tolerance of maize

The genes enconding proteins containing plasma membrane proteolipid 3 (PMP3) domain are responsive to abiotic stresses, but their functions in maize drought tolerance remain largely unknown. In this study, the transgenic maize lines overexpressing maize ZmPMP3g gene were featured by enhanced drought tolerance; increases in total root length, activities of superoxide dismutase and catalase, and leaf water content; and decreases in leaf water potential, levels of O₂^-·and H₂O₂, and malondialdehyde content under drought. Under treatments with foliar spraying with abscisic acid (ABA), drought tolerance of both transgenic line Y7-1 overexpressing ZmPMP3g and wild type Ye478 was enhanced, of which Y7-1 showed an increased endogenous ABA and decreased endogenous gibberellin (GA) 1 (significantly) and GA3 (very slightly but not significantly) and Ye478 had a relatively lower ABA and no changes in GA1 and GA3. ZmPMP3g overexpression in Y7-1 affected the expression of multiple key transcription factor genes in ABA-dependent and -independent drought signaling pathways. These results indicate that ZmPMP3g overexpression plays a role in maize drought tolerance by harmonizing ABA-GA1-GA3 homeostasis/balance, improving root growth, enhancing antioxidant capacity, maintaining membrane lipid integrity, and regulating intracellular osmotic pressure. A working model on ABA-GA-ZmPMP3g was proposed and discussed.

Comprehensive analysis of the WRKY gene family in Cucumis metuliferus and their expression profile in response to an early stage of root knot nematode infection

Root-knot nematode (RKN) is a major factor that limits the growth and productivity of important Cucumis crops, such as cucumber and melon, which lack RKN-resistance genes in their genome. Cucumis metuliferus is a wild Cucumis species that displays a high degree of RKN-resistance. WRKY transcription factors were involved in plant response to biotic stresses. However, little is known on the function of WRKY genes in response to RKN infection in Cucumis crops. In this study, Cucumis metuliferus 60 WRKY genes (CmWRKY) were identified in the C. metuliferus genome, and their conserved domains were classified into three main groups based on multiple sequence alignment and phylogenetic analysis. Synteny analysis indicated that the WRKY genes were highly conserved in Cucumis crops. Transcriptome data from of C. metuliferus roots inoculated with RKN revealed that 16 CmWRKY genes showed differential expression, of which 13 genes were upregulated and three genes were downregulated, indicating that these CmWRKY genes are important to C. metuliferus response to RKN infection. Two differentially expression CmWRKY genes (CmWRKY10 and CmWRKY28) were selected for further functional analysis. Both CmWRKY genes were localized in nucleus, indicating they may play roles in transcriptional regulation. This study provides a foundation for further research on the function of CmWRKY genes in RKN stress resistance and elucidation of the regulatory mechanism.

Transcriptome Analysis Revealed the Dynamic and Rapid Transcriptional Reprogramming Involved in Cold Stress and Related Core Genes in the Rice Seedling Stage

Cold damage is one of the most important environmental factors influencing crop growth, development, and production. In this study, we generated a pair of near-isogenic lines (NILs), Towada and ZL31, and Towada showed more cold sensitivity than ZL31 in the rice seedling stage. To explore the transcriptional regulation mechanism and the reason for phenotypic divergence of the two lines in response to cold stress, an in-depth comparative transcriptome study under cold stress was carried out. Our analysis uncovered that rapid and high-amplitude transcriptional reprogramming occurred in the early stage of cold treatment. GO enrichment and KEGG pathway analysis indicated that genes of the response to stress, environmental adaptation, signal transduction, metabolism, photosynthesis, and the MAPK signaling pathway might form the main part of the engine for transcriptional reprogramming in response to cold stress. Furthermore, we identified four core genes, OsWRKY24, OsCAT2, OsJAZ9, and OsRR6, that were potential candidates affecting the cold sensitivity of Towada and ZL31. Genome re-sequencing analysis between the two lines revealed that only OsWRKY24 contained sequence variations which may change its transcript abundance. Our study not only provides novel insights into the cold-related transcriptional reprogramming process, but also highlights the potential candidates involved in cold stress.

Cytological observation and transcriptome analysis reveal dynamic changes of Rhizoctonia solani colonization on leaf sheath and different genes recruited between the resistant and susceptible genotypes in rice

Sheath blight, caused by Rhizoctonia solani, is a big threat to the global rice production. To characterize the early development of R. solani on rice leaf and leaf sheath, two genotypes, GD66 (a resistant genotype) and Lemont (a susceptible genotype), were observed using four cytological techniques: the whole-mount eosin B-staining confocal laser scanning microscopy (WE-CLSM), stereoscopy, fluorescence microscopy, and plastic semi-thin sectioning after in vitro inoculation. WE-CLSM observation showed that, at 12 h post-inoculation (hpi), the amount of hyphae increased dramatically on leaf and sheath surface, the infection cushions occurred and maintained at a huge number from about 18 to 36 hpi, and then the infection cushions disappeared gradually from about 42 to 72 hpi. Interestingly, R. solani could not only colonize on the abaxial surfaces of leaf sheath but also invade the paraxial side of the leaf sheath, which shows a different behavior from that of leaf. RNA sequencing detected 6,234 differentially expressed genes (DEGs) for Lemont and 7,784 DEGs for GD66 at 24 hpi, and 2,523 DEGs for Lemont and 2,719 DEGs for GD66 at 48 hpi, suggesting that GD66 is recruiting more genes in fighting against the pathogen. Among DEGs, resistant genes, such as OsRLCK5, Xa21, and Pid2, displayed higher expression in the resistant genotype than the susceptible genotype at both 24 and 48 hpi, which were validated by quantitative reverse transcription-PCR. Our results indicated that the resistance phenotype of GD66 was the consequence of recruiting a series of resistance genes involved in different regulatory pathways. WE-CLSM is a powerful technique for uncovering the mechanism of R. solani invading rice and for detecting rice sheath blight-resistant germplasm.

Rice CIRCADIAN CLOCK ASSOCIATED 1 transcriptionally regulates ABA signaling to confer multiple abiotic stress tolerance

The circadian clock facilitates the survival and reproduction of crop plants under harsh environmental conditions such as drought and osmotic and salinity stresses, mainly by reprogramming the endogenous transcriptional landscape. Nevertheless, the genome-wide roles of core clock components in rice (Oryza sativa L.) abiotic stress tolerance are largely uncharacterized. Here, we report that CIRCADIAN CLOCK ASSOCIATED1 (OsCCA1), a vital clock component in rice, is required for tolerance to salinity, osmotic, and drought stresses. DNA affinity purification sequencing coupled with transcriptome analysis identified 692 direct transcriptional target genes of OsCCA1. Among them, the genes involved in abscisic acid (ABA) signaling, including group A protein phosphatase 2C genes and basic region and leucine zipper 46 (OsbZIP46), were substantially enriched. Moreover, OsCCA1 could directly bind the promoters of OsPP108 and OsbZIP46 to activate their expression. Consistently, oscca1 null mutants generated via genome editing displayed enhanced sensitivities to ABA signaling. Together, our findings illustrate that OsCCA1 confers multiple abiotic stress tolerance likely by orchestrating ABA signaling, which links the circadian clock with ABA signaling in rice.

Increasing SnRK1 activity with the AMPK activator A-769662 accelerates seed germination in rice

Sucrose non-fermenting-1-related protein kinase 1 (SnRK1) plays a key role in rice germination. The small molecule drug, A-769662, activates AMP-activated protein kinase, a mammalian homolog of SnRK1. However, it is unknown whether A-769662 activates SnRK1, thereby affecting germination. SnRK1 in desalted extracts from germinating rice seeds was strongly activated by adding A-769662 in vitro. Applying 50 or 100 μM A-769662 accelerated germination and increased the root length, shoot length, and seedling fresh weight. 50 μM A-769662 treatment increased the catalytic activity and phosphorylation of SnRK1 during germination. Transcriptome analysis and biochemical validation were performed to investigate the mechanism whereby A-769662 treatment promoted rice germination. A-769662 treatment promoted starch hydrolysis by increasing the expression and activity of amylase and inhibited starch biosynthesis by decreasing the expression of OsAGPL2, OsAGPS2a, Wx, and SSIIa. The abscisic acid (ABA) level and gene expression of ABA-induced transcription factors, including OsNF-YC9, OsNF-YC12, OsWRKY24, OsPYL8, OsMKKK62, and OsMKKK63, which reduced the inhibition of germination by ABA were decreased under 50 μM A-769662 treatment. The increased expression of the OsACO3 and OsACO5 genes and increased ethylene levels under A-769662 treatment, which counteracted the inhibition of ABA on germination and, thus, promoted germination. These results demonstrate the activation of A-769662 on SnRK1 and further reveal the regulatory mechanism of A-769662 in rice seed germination and nutrient remobilization.

Genome-wide analysis and transcriptional reprogrammings of MYB superfamily revealed positive insights into abiotic stress responses and anthocyanin accumulation in Carthamus tinctorius L

The MYB transcription factors comprise one of the largest superfamilies in plants that have been implicated in the regulation of plant-specific metabolites and responses to biotic and abiotic stresses. Here, we present the first comprehensive genome-wide analysis and functional characterization of the CtMYB family in Carthamus tinctorius. A total of 272 CtMYBs were identified and classified into 12 subgroups using comparative phylogenetic analysis with Arabidopsis and rice orthologs. The overview of conserved motifs, gene structures, and cis elements as well as the expression pattern of CtMYB genes indicated the diverse roles of these transcription factors during plant growth, regulation of secondary metabolites, and various abiotic stress responses. The subcellular localization and transactivation analysis of four CtMYB proteins indicated predominant localization in the nuclei with enhanced transcriptional activation in yeast. The expression of CtMYB63 induced with various abiotic stress conditions showed upregulation in its transcription level. In addition, the expression analysis of the core structural genes of anthocyanin biosynthetic pathway under drought and cold stress in CtMYB63 overexpressed transgenic lines also supports the notion of CtMYB63 transcriptional reprogramming in response to abiotic stress by upregulating the anthocyanin biosynthesis. Together, our findings revealed the underlying regulatory mechanism of CtMYB TF network involving enhanced cold and drought stress tolerance through activating the rapid biosynthesis of anthocyanin in C. tinctorius. This study also presents useful insights towards the establishment of new strategies for crop improvements.

Alterations in the Transcriptome of Rye Plants following the Microdochium nivale Infection: Identification of Resistance/Susceptibility-Related Reactions Based on RNA-Seq Analysis

Microdochium nivale is a progressive and devastating phytopathogen that causes different types of cereal crop and grass diseases that are poorly characterized at the molecular level. Although rye (Secale cereale L.) is one of the most resistant crops to most of the phytopathogens, it is severely damaged by M. nivale. The recent high-quality chromosome-scale assembly of rye genome has improved whole-genome studies of this crop. In the present work, the first transcriptome study of the M. nivale-infected crop plant (rye) with the detailed functional gene classification was carried out, along with the physiological verification of the RNA-Seq data. The results revealed plant reactions that contributed to their resistance or susceptibility to M. nivale. Phytohormone abscisic acid was shown to promote plant tolerance to M. nivale. Flavonoids were proposed to contribute to plant resistance to this pathogen. The upregulation of plant lipase encoding genes and the induction of lipase activity in M. nivale-infected plants revealed in our study were presumed to play an important role in plant susceptibility to the studied phytopathogen. Our work disclosed important aspects of plant-M. nivale interactions, outlined the directions for future studies on poorly characterized plant diseases caused by this phytopathogen, and provided new opportunities to improve cereals breeding and food security strategies.

Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice

WRKY transcription factors play key roles in stress responses, growth, and development. We previously reported on the evolution of WRKYs from unicellular green algae to land plants. To address recent evolution events, we studied three domesticated and eight wild species in the genus Oryza, an ideal model due to its long history of domestication, economic importance, and central role as a model system. We have identified prevalence of Group III WRKYs despite differences in breeding of cultivated and wild species. Same groups of WRKY genes tend to cluster together, suggesting recent, multiple duplication events. Duplications followed by divergence may result in neofunctionalizations of co-expressed WRKY genes that finely tune the regulation of target genes in a same metabolic or response pathway. WRKY genes have undergone recent rearrangements to form novel genes. Group Ib WRKYs, unique to AA genome type Oryza species, are derived from Group III genes dated back to 6.76 million years ago. Gene tree reconciliation analysis with the species tree revealed details of duplication and loss events in the 11 genomes. Selection analysis on single copy orthologs reveals the highly conserved nature of the WRKY domain and clusters of fast evolving sites under strong positive selection pressure. Also, the numbers of single copy orthologs under positive or negative selection almost evenly split. Our results provide valuable insights into the preservation and diversification of an important gene family under strong selective pressure for biotechnological improvements of the world's most valued food crop.

WRKY transcription factors and plant defense responses: latest discoveries and future prospects

WRKY transcription factors are among the largest families of transcriptional regulators. In this review, their pivotal role in modulating various signal transduction pathways during biotic and abiotic stresses is discussed. Transcription factors (TFs) are important constituents of plant signaling pathways that define plant responses against biotic and abiotic stimuli besides playing a role in response to internal signals which coordinate different interacting partners during developmental processes. WRKY TFs, deriving their nomenclature from their signature DNA-binding sequence, represent one of the largest families of transcriptional regulators found exclusively in plants. By modulating different signal transduction pathways, these TFs contribute to various plant processes including nutrient deprivation, embryogenesis, seed and trichome development, senescence as well as other developmental and hormone-regulated processes. A growing body of research suggests transcriptional regulation of WRKY TFs in adapting plant to a variety of stressed environments. WRKY TFs can regulate diverse biological functions from receptors for pathogen triggered immunity, modulator of chromatin for specific interaction and signal transfer through a complicated network of genes. Latest discoveries illustrate the interaction of WRKY proteins with other TFs to form an integral part of signaling webs that regulate several seemingly disparate processes and defense-related genes, thus establishing their significant contributions to plant immune response. The present review starts with a brief description on the structural characteristics of WRKY TFs followed by the sections that present recent evidence on their roles in diverse biological processes in plants. We provide a comprehensive overview on regulatory crosstalks involving WRKY TFs during multiple stress responses in plants and future prospects of WRKY TFs as promising molecular diagnostics for enhancing crop improvement.

IPA1 Negatively Regulates Early Rice Seedling Development by Interfering with Starch Metabolism via the GA and WRKY Pathways

Ideal Plant Architecture 1 (IPA1) encodes SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 14 (SPL14) with a pleiotropic effect on regulating rice development and biotic stress responses. To investigate the role of IPA1 in early seedling development, we developed a pair of IPA1/ipal-NILs and found that seed germination and early seedling growth were retarded in the ipa1-NIL. Analysis of the soluble sugar content, activity of amylase, and expression of the α-amylase genes revealed that the starch metabolism was weakened in the ipa1-NIL germinating seeds. Additionally, the content of bioactive gibberellin (GA) was significantly lower than that in the IPA1-NIL seeds at 48 h of imbibition. Meanwhile, the expression of GA synthesis-related gene OsGA20ox1 was downregulated, whereas the expression of GA inactivation-related genes was upregulated in ipa1-NIL seeds. In addition, the expression of OsWRKY51 and OsWRKY71 was significantly upregulated in ipa1-NIL seeds. Using transient dual-luciferase and yeast one-hybrid assays, IPA1 was found to directly activate the expression of OsWRKY51 and OsWRKY71, which would interfere with the binding affinity of GA-induced transcription factor OsGAMYB to inhibit the expression of α-amylase genes. In summary, our results suggest that IPA1 negatively regulates seed germination and early seedling growth by interfering with starch metabolism via the GA and WRKY pathways.

When rice gets the chills: comparative transcriptome profiling at germination shows WRKY transcription factor responses

Rice is vital for food security. Due to its tropical origin, rice suffers from cold temperatures that affect its entire life cycle. Key genes have been identified involved in cold tolerance. WRKYs are generally downstream of the MAPK cascade and can act together with VQ proteins to regulate stress-responsive genes. Chilling treatment was applied at germination to two rice genotypes (tolerant and sensitive). Shoots at S3 stage were collected for RNA-seq to identify OsWRKY, OsMAPKs and OsVQs expression. Relationships among MAPKs, WRKYs and VQs were predicted through correlation analysis. OsWRKY transcriptional regulation was predicted by in silico analysis of cis-regulatory elements. A total of 39 OsWRKYs were differentially expressed. OsWRKY21, OsWRK24 and OsWRKY69 are potential positive regulators, while OsWRKY10, OsWRK47, OsWRKY62, OsWRKY72 and OsWRKY77 are potential negative regulators, of chilling tolerance. 12 OsMAPKs were differentially expressed. OsMAPKs were downregulated and negatively correlated with the upregulated OsWRKYs in the tolerant genotype. 19 OsVQs were differentially expressed, three and six OsVQs were positively correlated with OsWRKYs in the tolerant and sensitive genotypes, respectively. Seven differentially expressed OsWRKYs have cold-responsive elements in their promoters and five upregulated OsWRKYs in the tolerant genotype contained the W-box motif. Chilling causes changes in OsWRKY, OsMAPK and OsVQ gene expression at germination. OsWRKYs may not act downstream of the MAPK cascade to coordinate chilling tolerance, but OsWRKYs may act with VQs to regulate chilling tolerance. Candidate OsWRKYs are correlated and have a W-box in the promoter, suggesting an auto-regulation mechanism.

Involvement of CsWRKY70 in salicylic acid-induced citrus fruit resistance against Penicillium digitatum

Penicillium digitatum causes serious losses in postharvest citrus fruit. Exogenous salicylic acid (SA) can induce fruit resistance against various pathogens, but the mechanism remains unclear. Herein, a transcriptome-based approach was used to investigate the underlying mechanism of SA-induced citrus fruit resistance against P. digitatum. We found that CsWRKY70 and genes related to methyl salicylate (MeSA) biosynthesis (salicylate carboxymethyltransferase, SAMT) were induced by exogenous SA. Moreover, significant MeSA accumulation was detected in the SA-treated citrus fruit. The potential involvement of CsWRKY70 in regulating CsSAMT expression in citrus fruit was studied. Subcellular localization, dual luciferase, and electrophoretic mobility shift assays and an analysis of transient expression in fruit peel revealed that the nucleus-localized transcriptional activator CsWRKY70 can activate the CsSAMT promoter by recognizing the W-box element. Taken together, the findings from this study offer new insights into the transcriptional regulatory mechanism of exogenous SA-induced disease resistance in Citrus sinensis fruit.

Transcriptome Analysis of Early Defenses in Rice against Fusarium fujikuroi

BACKGROUND

Bakanae is a seedborne disease caused by Fusarium fujikuroi. Rice seedlings emerging from infected seeds can show diverse symptoms such as elongated and slender stem and leaves, pale coloring, a large leaf angle, stunted growth and even death. Little is known about rice defense mechanisms at early stages of disease development.

RESULTS

This study focused on investigating early defenses against F. fujikuroi in a susceptible cultivar, Zerawchanica karatals (ZK), and a resistant cultivar, Tainung 67 (TNG67). Quantitative PCR revealed that F. fujikuroi colonizes the root and stem but not leaf tissues. Illumina sequencing was conducted to analyze the stem transcriptomes of F. fujikuroi-inoculated and mock-inoculated ZK and TNG67 plants collected at 7 days post inoculation (dpi). More differentially expressed genes (DEGs) were identified in ZK (n = 169) than TNG67 (n = 118), and gene ontology terms related to transcription factor activity and phosphorylation were specifically enriched in ZK DEGs. Among the complex phytohormone biosynthesis and signaling pathways, only DEGs involved in the jasmonic acid (JA) signaling pathway were identified. Fourteen DEGs encoding pattern-recognition receptors, transcription factors, and JA signaling pathway components were validated by performing quantitative reverse transcription PCR analysis of individual plants. Significant repression of jasmonate ZIM-domain (JAZ) genes (OsJAZ9, OsJAZ10, and OsJAZ13) at 3 dpi and 7 dpi in both cultivars, indicated the activation of JA signaling during early interactions between rice and F. fujikuroi. Differential expression was not detected for salicylic acid marker genes encoding phenylalanine ammonia-lyase 1 and non-expressor of pathogenesis-related genes 1. Moreover, while MeJA did not affect the viability of F. fujikuroi, MeJA treatment of rice seeds (prior to or after inoculation) alleviated and delayed bakanae disease development in susceptible ZK.

CONCLUSIONS

Different from previous transcriptome studies, which analyzed the leaves of infected plants, this study provides insights into defense-related gene expression patterns in F. fujikuroi-colonized rice stem tissues. Twelve out of the 14 selected DEGs were for the first time shown to be associated with disease resistance, and JA-mediated resistance was identified as a crucial component of rice defense against F. fujikuroi. Detailed mechanisms underlying the JA-mediated bakanae resistance and the novel defense-related DEGs are worthy of further investigation.

Two light responsive WRKY genes exhibit positive and negative correlation with picroside content in Picrorhiza kurrooa Royle ex Benth, an endangered medicinal herb

Picrorhiza kurrooa is an endangered herb known to produce the medicinally important picrosides through isoprenoid pathway. The present work showed the functionality of WRKY motifs (TGAC cis-acting elements) present in the promoters of regulatory genes 3-hydroxy-3-methylglutaryl coenzyme A reductase (Pkhmgr) and 1-deoxy-d-xylulose-5-phosphate synthase (Pkdxs) of the picrosides biosynthetic pathway by electrophoretic mobility shift assay. Also, the two WRKY genes, PkdWRKY and PksWRKY, were characterized and found to contain double and single characteristic WRKY domains, respectively along with a zinc-finger motif in each domain. Expression analysis revealed that PkdWRKY and PksWRKY exhibited a positive and negative correlation, respectively, with picrosides content under the environment of light and in different tissues. Functional evaluation in yeast showed DNA binding ability of both PksWRKY and PkdWRKY; however, only PkdWRKY exhibited transcriptional activation ability. Transient overexpression of PkdWRKY and PksWRKY in tobacco modulated the expression of selected native genes of tobacco involved in MVA and MEP pathway suggesting functionality of PkdWRKY and PksWRKY in planta. Collectively, data suggested that PkdWRKY and PksWRKY might be positive and negative regulators, respectively in the picrosides biosynthetic pathway.

A Meta-Analysis of Comparative Transcriptomic Data Reveals a Set of Key Genes Involved in the Tolerance to Abiotic Stresses in Rice

Several environmental factors, such as drought, salinity, and extreme temperatures, negatively affect plant growth and development, which leads to yield losses. The tolerance or sensitivity to abiotic stressors are the expression of a complex machinery involving molecular, biochemical, and physiological mechanisms. Here, a meta-analysis on previously published RNA-Seq data was performed to identify the genes conferring tolerance to chilling, osmotic, and salt stresses, by comparing the transcriptomic changes between tolerant and susceptible rice genotypes. Several genes encoding transcription factors (TFs) were identified, suggesting that abiotic stress tolerance involves upstream regulatory pathways. A gene co-expression network defined the metabolic and signalling pathways with a prominent role in the differentiation between tolerance and susceptibility: (i) the regulation of endogenous abscisic acid (ABA) levels, through the modulation of genes that are related to its biosynthesis/catabolism, (ii) the signalling pathways mediated by ABA and jasmonic acid, (iii) the activity of the "Drought and Salt Tolerance" TF, involved in the negative regulation of stomatal closure, and (iv) the regulation of flavonoid biosynthesis by specific MYB TFs. The identified genes represent putative key players for conferring tolerance to a broad range of abiotic stresses in rice; a fine-tuning of their expression seems to be crucial for rice plants to cope with environmental cues.

TaWRKY51 promotes lateral root formation through negative regulation of ethylene biosynthesis in wheat (Triticum aestivum L.)

Common wheat (Triticum aestivum L.) is an important staple food crop worldwide. Lateral roots (LRs), as the major component of root architecture, affect water and nutrient uptake in wheat. The phytohormone ethylene is known to affect LR formation; however, the factor(s) modulating ethylene during this process have not yet been elucidated in wheat. Here we identified wheat TaWRKY51 as a key factor that functions in LR formation by modulating ethylene biosynthesis. Wheat TaWRKY51RNA interference lines (TaWRKY51-RNAi) and the homozygous mutants tawrky51-2a and tawrky51-2b all produced fewer LRs than the wild type and negative transgenic plants, whereas the TaWRKY51 overexpression lines (TaWRKY51-OE) had the opposite phenotype. Transcription analysis revealed that 1-aminocyclopropane-1-carboxylic acid synthase (ACS) genes (TaACS2, TaACS7 and TaACS8) involved in ethylene biosynthesis were downregulated in TaWRKY51-OE lines but upregulated in TaWRKY51-RNAi lines. The rate of ethylene production also decreased in TaWRKY51-OE lines but increased in TaWRKY51-RNAi lines compared with their respective negative transgenic controls. Electrophoretic mobility shift and transient expression assays revealed that TaWRKY51 inhibits the expression of ACS genes by binding to the W-box cis-element present in their promoter region. Moreover, overexpression of ACS2 or exogenous application of 1-aminocyclopropane-1-carboxylic acid reversed the phenotype of enhanced LR number in TaWRKY51-OE Arabidopsis lines, and overexpression of TaWRKY51 in the ethylene-overproducing mutant eto1-1 rescued its LR defect phenotype. In addition, genetic evidence demonstrates that TaWRKY51-regulated LR formation is also dependent on ethylene and auxin signaling pathways. Our findings reveal a molecular genetic mechanism by which a WRKY gene coordinates ethylene production and LR formation in wheat.

Overexpression of OsAP2 and OsWRKY24 in Arabidopsis results in reduction of plant size

Recently, two rice genes, OsAPETALA2 (OsAP2) and OsWRKY24 have been reported to be positive regulators involved in increased lamina inclination and grain size through cell elongation. Here, we found that the two genes have tightly linked expression patterns and functional convergence in rice, and are also likely to play an opposite role in Arabidopsis. Overexpression of the two rice transcription factors in Arabidopsis caused smaller plant size with reduced cell size, and the expression of a series of genes encoding expansins and xyloglucan endotransglucosylase/hydrolases (XTHs) involved in cell elongation was reduced. However, transgenic Arabidopsis expressing OsWRKY24-SRDX as a synthetic chimeric repressor displayed indistinguishable phenotypes from wild-type plants. Moreover, the subcellular localization pattern of OsWRKY24 in Arabidopsis was different from that in rice. Thus, we demonstrate an example of transcription factors from one species playing distinct roles in different plant species.

The R2R3MYB Gene Family in Phyllostachys edulis: Genome-Wide Analysis and Identification of Stress or Development-Related R2R3MYBs

The MYB transcription factor (TF) is one of the largest gene families in plants and involved to multiple biological processes. However, little is known about the MYB family and its functional role in the genome of moso bamboo. In the present study, a total of 114 R2R3MYB genes were first identified from moso bamboo genome and full-length non-chimeric (FLNC) reads. Phylogenetic analysis coupled with gene structure analysis and motif determination resulted in the division of these PheR2R3MYBs into 17 subgroups. The position of eight proteins along an external branch in the phylogenetic tree suggested their relatively ancient origin. The genes in this group were all substituted by (Met, M)/(Arg, R) at conservative W residues in both R2 and R3 repeats, and half were found to possess no transcriptional activation activity. The analysis of evolutionary patterns and divergence suggests that the expansion of PheMYBs was mainly attributable to whole genome duplication (WGD) under different selection pressures. Expressional analysis based on microarray and qRT-PCR data performed diverse expression patterns of R2R3MYBs in response to both various abiotic stimuli and flower development. Furthermore, the co-expression analysis of R2R3MYBs suggested an intricate interplay of growth- and stress-related responses. Finally, we found a hub gene, PheMYB4, was involved in a complex proteins interaction network. Further functional analysis indicated that ectopic overexpression of its homologous gene, PheMYB4-1, could increase tolerance to cold treatment and sensitivity to drought and salt treatment of transgenic Arabidopsis seedlings. These findings provide comprehensive insights into the MYB family members in moso bamboo and offer candidate MYB genes for further studies on their roles in stress resistance.

Regulation of ethylene-responsive SlWRKYs involved in color change during tomato fruit ripening

WRKY transcription factors (TFs) play important roles in stress responses in planta. However, the function of WRKY TFs in the regulation of fruit ripening is unclear. Here, 23 tomato SlWRKYs that are similar to ethylene-responsive WRKY genes from other plant species, or show up-regulation during fruit ripening in previous genome-wide study, were selected, and their function in fruit ripening was investigated. Twelve SlWRKYs were found to be responsive to ethylene (SlER-WRKYs), showing expression patterns similar to those of genes related to fruit ripening. Eight SlER-WRKYs—SlWRKY16, 17, 22, 25, 31, 33, 53, and 54, detected in the nuclei—interacted with and activated the promoters of 4 genes related to color change: Pheophytin Pheophorbide Hydrolase (SlPPH), Pheophorbide a Oxygenase (SlPAO), Phytoene Synthase 1 (SlPSY1) and Phytoene Desaturase (SlPDS). Yeast two-hybrid and bimolecular fluorescence complement (BiFC) assays in Arabidopsis protoplasts indicated that protein interactions occurred between SlWRKY17 and SlRIN, SlERF2b or SlERF7; SlWRKY33 and SlERF7; SlWRKY54 and SlERF2b; and SlWRKY16 and SlWRKY17. Suppression of SlWRKY 16, 17, 53 or 54 by virus-induced gene silencing (VIGS) retarded the red coloration of the fruit. Our study provides comprehensive molecular evidence that WRKY TFs function in fruit ripening, particularly in color change, and are linked to the intricate regulatory network of other ripening regulators.

Differential transcriptome profiling of chilling stress response between shoots and rhizomes of Oryza longistaminata using RNA sequencing

Rice (Oryza sativa) is very sensitive to chilling stress at seedling and reproductive stages, whereas wild rice, O. longistaminata, tolerates non-freezing cold temperatures and has overwintering ability. Elucidating the molecular mechanisms of chilling tolerance (CT) in O. longistaminata should thus provide a basis for rice CT improvement through molecular breeding. In this study, high-throughput RNA sequencing was performed to profile global transcriptome alterations and crucial genes involved in response to long-term low temperature in O. longistaminata shoots and rhizomes subjected to 7 days of chilling stress. A total of 605 and 403 genes were respectively identified as up- and down-regulated in O. longistaminata under 7 days of chilling stress, with 354 and 371 differentially expressed genes (DEGs) found exclusively in shoots and rhizomes, respectively. GO enrichment and KEGG pathway analyses revealed that multiple transcriptional regulatory pathways were enriched in commonly induced genes in both tissues; in contrast, only the photosynthesis pathway was prevalent in genes uniquely induced in shoots, whereas several key metabolic pathways and the programmed cell death process were enriched in genes induced only in rhizomes. Further analysis of these tissue-specific DEGs showed that the CBF/DREB1 regulon and other transcription factors (TFs), including AP2/EREBPs, MYBs, and WRKYs, were synergistically involved in transcriptional regulation of chilling stress response in shoots. Different sets of TFs, such as OsERF922, OsNAC9, OsWRKY25, and WRKY74, and eight genes encoding antioxidant enzymes were exclusively activated in rhizomes under long-term low-temperature treatment. Furthermore, several cis-regulatory elements, including the ICE1-binding site, the GATA element for phytochrome regulation, and the W-box for WRKY binding, were highly abundant in both tissues, confirming the involvement of multiple regulatory genes and complex networks in the transcriptional regulation of CT in O. longistaminata. Finally, most chilling-induced genes with alternative splicing exclusive to shoots were associated with photosynthesis and regulation of gene expression, while those enriched in rhizomes were primarily related to stress signal transduction; this indicates that tissue-specific transcriptional and post-transcriptional regulation mechanisms synergistically contribute to O. longistaminata long-term CT. Our findings provide an overview of the complex regulatory networks of CT in O. longistaminata.

Silencing OsSLR1 enhances the resistance of rice to the brown planthopper Nilaparvata lugens

DELLA proteins, negative regulators of the gibberellin (GA) pathway, play important roles in plant growth, development and pathogen resistance by regulating multiple phytohormone signals. Yet, whether and how they regulate plant herbivore resistance remain unknown. We found that the expression of the rice DELLA gene OsSLR1 was down-regulated by an infestation of female adults of the brown planthopper (BPH) Nilaparvata lugens. On one hand, OsSLR1 positively regulated BPH-induced levels of two mitogen-activated protein kinase and four WRKY transcripts, and of jasmonic acid, ethylene and H₂ O₂ . On the other hand, silencing OsSLR1 enhanced constitutive levels of defence-related compounds, phenolic acids, lignin and cellulose, as well as the resistance of rice to BPH in the laboratory and in the field. The increased resistance in rice with silencing of OsSLR1 is probably due to impaired JA and ethylene pathways, and, at least in part, to the increased lignin level and mechanical hardness of rice leaf sheaths. Our findings illustrate that OsSLR1, acting as an early negative regulator, plays an important role in regulating the resistance of rice to BPH by activating appropriate defence-related signalling pathways and compounds. Moreover, our data also provide new insights into relationships between plant growth and defence.

OsWRKY51, a rice transcription factor, functions as a positive regulator in defense response against Xanthomonas oryzae pv. oryzae

OsWRKY51 functions as a positive transcriptional regulator in defense signaling against Xanthomonas oryzae pv. oryzae by direct DNA binding to the promoter of defense related gene, OsPR10a. OsWRKY51 in rice (Oryza sativa L.) is induced by exogenous salicylic acid (SA) and inoculation with Xanthomonas oryzae pv. oryzae (Xoo). To examine the role of OsWRKY51 in the defense response of rice, we generated OsWRKY51 overexpressing and underexpressing transgenic rice plants. OsWRKY51-overexpressing transgenic rice lines were more resistant to Xoo and showed greater expression of defense-related genes than wild-type (WT) plants, while OsWRKY51-underexpressing lines were more susceptible to Xoo and showed less expression of defense-associated genes than WT plants. Transgenic lines overexpressing OsWRKY51 showed growth retardation compared to WT plants. In contrast, transgenic lines underexpressing OsWRKY51 by RNA interference showed similar plant height with WT plants. Transient expression of OsWRKY51-green fluorescent protein fusion protein in rice protoplasts revealed that OsWRKY51 was localized in the nucleus. OsWRKY51 bound to the W-box and WLE1 elements of the OsPR10a promoter. Based on these results, we suggest that OsWRKY51 is a positive transcriptional regulator of defense signaling and has direct DNA binding ability to the promoter of OsPR10a, although it is reported to be a negative regulator in GA signaling.

WRKY transcription factor genes in wild rice Oryza nivara

The WRKY transcription factor family is one of the largest gene families involved in plant development and stress response. Although many WRKY genes have been studied in cultivated rice (Oryza sativa), the WRKY genes in the wild rice species Oryza nivara, the direct progenitor of O. sativa, have not been studied. O. nivara shows abundant genetic diversity and elite drought and disease resistance features. Herein, a total of 97 O. nivara WRKY (OnWRKY) genes were identified. RNA-sequencing demonstrates that OnWRKY genes were generally expressed at higher levels in the roots of 30-day-old plants. Bioinformatic analyses suggest that most of OnWRKY genes could be induced by salicylic acid, abscisic acid, and drought. Abundant potential MAPK phosphorylation sites in OnWRKYs suggest that activities of most OnWRKYs can be regulated by phosphorylation. Phylogenetic analyses of OnWRKYs support a novel hypothesis that ancient group IIc OnWRKYs were the original ancestors of only some group IIc and group III WRKYs. The analyses also offer strong support that group IIc OnWRKYs containing the HVE sequence in their zinc finger motifs were derived from group Ia WRKYs. This study provides a solid foundation for the study of the evolution and functions of WRKY genes in O. nivara.

WRKY Transcription Factors: Molecular Regulation and Stress Responses in Plants

Plants in their natural habitat have to face multiple stresses simultaneously. Evolutionary adaptation of developmental, physiological, and biochemical parameters give advantage over a single window of stress but not multiple. On the other hand transcription factors like WRKY can regulate diverse responses through a complicated network of genes. So molecular orchestration of WRKYs in plant may provide the most anticipated outcome of simultaneous multiple responses. Activation or repression through W-box and W-box like sequences is regulated at transcriptional, translational, and domain level. Because of the tight regulation involved in specific recognition and binding of WRKYs to downstream promoters, they have become promising candidate for crop improvement. Epigenetic, retrograde and proteasome mediated regulation enable WRKYs to attain the dynamic cellular homeostatic reprograming. Overexpression of several WRKYs face the paradox of having several beneficial affects but with some unwanted traits. These overexpression-associated undesirable phenotypes need to be identified and removed for proper growth, development and yeild. Taken together, we have highlighted the diverse regulation and multiple stress response of WRKYs in plants along with the future prospects in this field of research.

Three WRKY transcription factors additively repress abscisic acid and gibberellin signaling in aleurone cells

Members of the WRKY transcription factor superfamily are essential for the regulation of many plant pathways. Functional redundancy due to duplications of WRKY transcription factors, however, complicates genetic analysis by allowing single-mutant plants to maintain wild-type phenotypes. Our analyses indicate that three group I WRKY genes, OsWRKY24, -53, and -70, act in a partially redundant manner. All three showed characteristics of typical WRKY transcription factors: each localized to nuclei and yeast one-hybrid assays indicated that they all bind to W-boxes, including those present in their own promoters. Quantitative real time-PCR (qRT-PCR) analyses indicated that the expression levels of the three WRKY genes varied in the different tissues tested. Particle bombardment-mediated transient expression analyses indicated that all three genes repress the GA and ABA signaling in a dosage-dependent manner. Combination of all three WRKY genes showed additive antagonism of ABA and GA signaling. These results suggest that these WRKY proteins function as negative transcriptional regulators of GA and ABA signaling. However, different combinations of these WRKY genes can lead to varied strengths in suppression of their targets.

Prioritizing plant defence over growth through WRKY regulation facilitates infestation by non-target herbivores

Plants generally respond to herbivore attack by increasing resistance and decreasing growth. This prioritization is achieved through the regulation of phytohormonal signaling networks. However, it remains unknown how this prioritization affects resistance against non-target herbivores. In this study, we identify WRKY70 as a specific herbivore-induced, mitogen-activated protein kinase-regulated rice transcription factor that physically interacts with W-box motifs and prioritizes defence over growth by positively regulating jasmonic acid (JA) and negatively regulating gibberellin (GA) biosynthesis upon attack by the chewing herbivore Chilo suppressalis. WRKY70-dependent JA biosynthesis is required for proteinase inhibitor activation and resistance against C. suppressalis. In contrast, WRKY70 induction increases plant susceptibility against the rice brown planthopper Nilaparvata lugens. Experiments with GA-deficient rice lines identify WRKY70-dependent GA signaling as the causal factor in N. lugens susceptibility. Our study shows that prioritizing defence over growth leads to a significant resistance trade-off with important implications for the evolution and agricultural exploitation of plant immunity.

DOI:http://dx.doi.org/10.7554/eLife.04805.001

Many different animals feed on plants, including almost half of all known insect species. Some herbivores—like caterpillars for example—feed by chewing. Others, such as aphids and planthoppers, use syringe-like mouthparts to pierce plants and then feed on the fluids within.

To minimize the damage caused by these herbivores, plants activate specific defenses upon attack, including proteins that can inhibit the insect's digestive enzymes. The inhibitors are effective against chewing herbivores but seem to have little or no effect on some insects that feed by the ‘pierce-and-suck’ method.

Investing in defense requires energy, and so plants attacked by herbivores actively slow their growth to meet this demand. Plants achieve this trade-off by changing the levels of different plant hormones. These hormones can control the expression of thousands of genes and have widespread effects throughout the plant. However, little is known about how prioritizing defense overgrowth in response to an attack by one herbivore affects the plant's ability to defend itself against other herbivores.

Transcription factors are proteins that control which genes inside a cell are active or inactive. Li et al. searched for a transcription factor in rice plants that was specifically triggered in response to an attack by the caterpillars of a moth called the rice striped stem borer. This search identified a protein called WRKY70 as a transcription factor that prioritizes defense overgrowth. WRKY70 achieves this by increasing the levels of a defensive plant hormone (called jasmonic acid) while reducing the levels of a growth hormone (called gibberellin). Further experiments show that the increase in jasmonic acid production is required to activate the enzyme inhibitors and for resistance against these caterpillars.

Li et al. then found that increased WRKY70 activity makes rice plants more susceptible to attack by a second herbivore, a piercing-sucking insect called the rice brown planthopper. Further experiments revealed that this is due to the reduced levels of gibberillin. These findings show that while prioritizing defense overgrowth is effective against some insect herbivores, it comes with a cost as it makes the plants more susceptible to attack by other herbivores. This trade-off has important implications for both the evolution of plant immunity, and efforts to exploit plant immunity to help protect crops from herbivore attack.

DOI:http://dx.doi.org/10.7554/eLife.04805.002

Activation of Endogenous Phytase and Degradation of Phytate in Wheat Bran

Wheat bran contains a significant amount of the anti-nutritional factor phytate. This study is the first to explore the effectiveness of activating endogenous phytase and further reducing phytate content through resulting programmed cell death (PCD). Effects of solid-liquid ratio (1:1, 1:2, 1:3, and 1:6), incubation temperature (4, 20, 38, 55, and 70 °C), metal ions (Na⁺, K⁺, Ca²⁺, and Mg²⁺), gibberellin concentration (0, 5, 50, 500, 2000, and 5000 mg/L), hydrogen peroxide concentration (0, 0.2, 0.4, 0.6, 0.8, and 1.0%), and incubation time (30, 80, 180, and 360 min) on activation of endogenous phytase activity and phytate degradation in wheat bran samples are discussed in this study. It was found that when the wheat bran was incubated with distilled water at 55 °C for 80 min, its endogenous phytase activity was dramatically increased 4-fold from 12.96 to 53.54 FTU/g, whereas the phytate content was reduced by about 70% from 45.20 to 13.52 mg/g. By comparison of photomicrographs of raw wheat bran sample and sample incubated with distilled water for 360 min at 55 °C, a conclusion could be drawn that PCD in aleurone cells had occurred.

RNA-sequencing reveals previously unannotated protein- and microRNA-coding genes expressed in aleurone cells of rice seeds

The rice genome annotation has been greatly improved in recent years, largely due to the availability of full length cDNA sequences derived from many tissues. Among those yet to be studied is the aleurone layer, which produces hydrolases for mobilization of seed storage reserves during seed germination and post germination growth. Herein, we report transcriptomes of aleurone cells treated with the hormones abscisic acid, gibberellic acid, or both. Using a comprehensive approach, we identified hundreds of novel genes. To minimize the number of false positives, only transcripts that did not overlap with existing annotations, had a high level of expression, and showed a high level of uniqueness within the rice genome were considered to be novel genes. This approach led to the identification of 553 novel genes that encode proteins and/or microRNAs. The transcriptome data reported here will help to further improve the annotation of the rice genome.

Characterization of HbWRKY1, a WRKY transcription factor from Hevea brasiliensis that negatively regulates HbSRPP

Small rubber particle protein (SRPP) is a major component of Hevea brasiliensis (H. brasiliensis) latex, which is involved in natural rubber (NR) biosynthesis. However, little information is available on the regulation of SRPP gene (HbSRPP) expression. To study the transcriptional regulation of HbSRPP, the yeast one-hybrid experiment was performed to screen the latex cDNA library using the HbSRPP promoter as bait. One cDNA that encodes the WRKY transcription factor, designated as HbWRKY1, was isolated from H. brasiliensis. HbWRKY1 contains a 1437 bp open reading frame that encodes 478 amino acids. The deduced HbWRKY1 protein was predicted to possess two conserved WRKY domains and a C2H2 zinc-finger motif. HbWRKY1 was expressed at different levels, with the highest transcription in the flower, followed by the bark, latex, and leaf. Furthermore, the co-expression of pHbSRP::GUS with CaMV35S::HbWRKY1 significantly decreased the GUS activity in transgenic tobacco, indicating that HbWRKY1 significantly suppressed the HbSRPP promoter. These results suggested that HbWRKY1 maybe a negative transcription regulator of HbSRPP involved in NR biosynthesis in H. brasiliensis.

Transcriptome profile reveals heat response mechanism at molecular and metabolic levels in rice flag leaf

Flag leaf is one of the key photosynthesis organs during rice reproductive stage. A time course microarray analysis of rice flag leaf was done after 40°C treatment for 0 min, 20 min, 60 min, 2h, 4h, and 8h. The identified significant heat responsive genes were mainly involved in transcriptional regulation, transport, protein binding, antioxidant, and stress response. KMC analysis discovered the time-dependent gene expression pattern under heat. MapMan analysis demonstrated that, under heat treatment, Hsp genes and genes involved in glycolysis and ubiquitin-proteasome were enhanced, and genes involved in TCA, carotenoid, dihydroflavonol and anthocyanin metabolisms and light-reaction in the photosynthesis were widely repressed. Meanwhile, some rate-limiting enzyme genes in shikimate, lignin, and mevalonic acid metabolisms were up-regulated, revealing the importance of maintaining specific secondary metabolites under heat stress. The present study increased our understanding of heat response in rice flag leaf and provided good candidate genes for crop improvement.

Abscisic Acid Promotes Susceptibility to the Rice Leaf Blight Pathogen Xanthomonas oryzae pv oryzae by Suppressing Salicylic Acid-Mediated Defenses

The plant hormone abscisic acid (ABA) is involved in a wide variety of plant processes, including the initiation of stress-adaptive responses to various environmental cues. Recently, ABA also emerged as a central factor in the regulation and integration of plant immune responses, although little is known about the underlying mechanisms. Aiming to advance our understanding of ABA-modulated disease resistance, we have analyzed the impact, dynamics and interrelationship of ABA and the classic defense hormone salicylic acid (SA) during progression of rice infection by the leaf blight pathogen Xanthomonas oryzae pv. oryzae (Xoo). Consistent with ABA negatively regulating resistance to Xoo, we found that exogenously administered ABA renders rice hypersusceptible to infection, whereas chemical and genetic disruption of ABA biosynthesis and signaling, respectively, led to enhanced Xoo resistance. In addition, we found successful Xoo infection to be associated with extensive reprogramming of ABA biosynthesis and response genes, suggesting that ABA functions as a virulence factor for Xoo. Interestingly, several lines of evidence indicate that this immune-suppressive effect of ABA is due at least in part to suppression of SA-mediated defenses that normally serve to limit pathogen growth. Resistance induced by the ABA biosynthesis inhibitor fluridone, however, appears to operate in a SA-independent manner and is likely due to induction of non-specific physiological stress. Collectively, our findings favor a scenario whereby virulent Xoo hijacks the rice ABA machinery to cause disease and highlight the importance of ABA and its crosstalk with SA in shaping the outcome of rice-Xoo interactions.

Functional analysis of TaABF1 during abscisic acid and gibberellin signalling in aleurone cells of cereal grains

The wheat transcription factor TaABF1 physically interacts with the protein kinase PKABA1 and mediates both abscisic acid (ABA)-induced and ABA-suppressed gene expression. In bombarded aleurone cells of imbibing grains, the effect of TaABF1 in down-regulating the gibberellin (GA)-induced Amy32b promoter was stronger in the presence of exogenous ABA. As these grains contained low levels of endogenous ABA, the effect of TaABF1 may also be mediated by ABA-induced activation even in the absence of exogenous ABA. Levels of TaABF1 protein decreased slightly during imbibition of afterripened grains. However, TaABF1 levels (especially in aleurone layers) were not substantially affected by exogenous ABA or GA, indicating that changes in TaABF1 protein level are not an important part of regulating its role in hormone signalling. We found that TaABF1 was phosphorylated in vivo in aleurone cells, suggesting a role for post-translational modification in regulating TaABF1 activity. Induction of Amy32b by overexpression of the transcription factor GAMyb could not be prevented by TaABF1, indicating that TaABF1 acts upstream of GAMyb transcription in the signalling pathway. Supporting this view, knockdown of TaABF1 by RNA interference resulted in increased expression from the GAMyb promoter. These results are consistent with a model in which TaABF1 is constitutively present in aleurone cells, while its ability to down-regulate GAMyb is regulated in response to ABA.

Expression profile in rice panicle: insights into heat response mechanism at reproductive stage

Rice at reproductive stage is more sensitive to environmental changes, and little is known about the mechanism of heat response in rice panicle. Here, using rice microarray, we provided a time course gene expression profile of rice panicle at anther developmental stage 8 after 40°C treatment for 0 min, 20 min, 60 min, 2 h, 4 h, and 8 h. The identified differentially expressed genes were mainly involved in transcriptional regulation, transport, cellular homeostasis, and stress response. The predominant transcription factor gene families responsive to heat stress were Hsf, NAC, AP2/ERF, WRKY, MYB, and C₂H₂. KMC analysis discovered the time-dependent gene expression pattern under heat stress. The motif co-occurrence analysis on the promoters of genes from an early up-regulated cluster showed the important roles of GCC box, HSE, ABRE, and CE3 in response to heat stress. The regulation model central to ROS combined with transcriptome and ROS quantification data in rice panicle indicated the great importance to maintain ROS balance and the existence of wide cross-talk in heat response. The present study increased our understanding of the heat response in rice panicle and provided good candidate genes for crop improvement.

WRKY transcription factors: key components in abscisic acid signalling

WRKY transcription factors (TFs) are key regulators of many plant processes, including the responses to biotic and abiotic stresses, senescence, seed dormancy and seed germination. For over 15 years, limited evidence has been available suggesting that WRKY TFs may play roles in regulating plant responses to the phytohormone abscisic acid (ABA), notably some WRKY TFs are ABA-inducible repressors of seed germination. However, the roles of WRKY TFs in other aspects of ABA signalling, and the mechanisms involved, have remained unclear. Recent significant progress in ABA research has now placed specific WRKY TFs firmly in ABA-responsive signalling pathways, where they act at multiple levels. In Arabidopsis, WRKY TFs appear to act downstream of at least two ABA receptors: the cytoplasmic PYR/PYL/RCAR-protein phosphatase 2C-ABA complex and the chloroplast envelope-located ABAR-ABA complex. In vivo and in vitro promoter-binding studies show that the target genes for WRKY TFs that are involved in ABA signalling include well-known ABA-responsive genes such as ABF2, ABF4, ABI4, ABI5, MYB2, DREB1a, DREB2a and RAB18. Additional well-characterized stress-inducible genes such as RD29A and COR47 are also found in signalling pathways downstream of WRKY TFs. These new insights also reveal that some WRKY TFs are positive regulators of ABA-mediated stomatal closure and hence drought responses. Conversely, many WRKY TFs are negative regulators of seed germination, and controlling seed germination appears a common function of a subset of WRKY TFs in flowering plants. Taken together, these new data demonstrate that WRKY TFs are key nodes in ABA-responsive signalling networks.

ABO3, a WRKY transcription factor, mediates plant responses to abscisic acid and drought tolerance in Arabidopsis

The biological functions of WRKY transcription factors in plants have been widely studied, but their roles in abiotic stress are still not well understood. We isolated an ABA overly sensitive mutant, abo3, which is disrupted by a T-DNA insertion in At1g66600 encoding a WRKY transcription factor AtWRKY63. The mutant was hypersensitive to ABA in both seedling establishment and seedling growth. However, stomatal closure was less sensitive to ABA, and the abo3 mutant was less drought tolerant than the wild type. Northern blot analysis indicated that the expression of the ABA-responsive transcription factor ABF2/AREB1 was markedly lower in the abo3 mutant than in the wild type. The abo3 mutation also reduced the expression of stress-inducible genes RD29A and COR47, especially early during ABA treatment. ABO3 is able to bind the W-box in the promoter of ABF2in vitro. These results uncover an important role for a WRKY transcription factor in plant responses to ABA and drought stress.

GhWRKY3, a novel cotton (Gossypium hirsutum L.) WRKY gene, is involved in diverse stress responses

WRKY proteins play important roles in plant defense responses. In the present study, a novel WRKY gene, nominated as GhWRKY3, was isolated from cotton (Gossypium hirsutum L.). The full-length cDNA of GhWRKY3 is 1,705 bp in length and encodes a protein with 507 amino acids containing two typical WRKY domains and two zinc finger motifs. Amino acid sequence alignment revealed that GhWRKY3 shares a high degree of identity with other higher plant WRKY proteins. The subcellular localization assay indicated that GhWRKY3 is localized to the nucleus. Analysis of 5'-flanking region of GhWRKY3 revealed a group of putative cis-acting elements. The results of expression analysis indicated that GhWRKY3 is constitutively expressed in roots, stems and leaves. Semi-quantitative RT-PCR showed that GhWRKY3 is up-regulated by application of various phytohormones including salicylic acid (SA), methyl jasmonate (MeJA), abscisic acid (ABA), gibberellins (GAs) and ethylene (ET). Furthermore, the transcripts of GhWRKY3 are enhanced after infection with Rhizoctonia solani, Colletotrichum gossypii and Fusarium oxysporum f. sp. vasinfectum, respectively. Also, GhWRKY3 can be induced by wounding treatment, but not by cytokinin (6-benzylaminopurine, 6-BA), auxin analogue, drought, NaCl, and cold (4°C). These data suggested that GhWRKY3 might play an important role in plant defense responses and fulfill a pivotal role in plant development.