Functional characterization of Arabidopsis thaliana WRKY39 in heat stress

MfWRKY7.2 of woody resurrection plant Myrothamnus flabellifolia is involved in tolerance to drought and salt stress

Myrothamnus flabellifolia, the only known woody resurrection plant, can survive in extremely long-term drought environments, representing a valuable resource for exploring drought tolerance genes. However, few genes functioning in drought tolerance have been identified from M. flabellifolia. WRKY7, belonging to subgroup IId of the WRKY transcription factor family, is known to regulate plant responses to pathogens. However, its involvement in response to plant abiotic stress has been rarely reported. Here we reported cloning and functional characterization of a dehydration-induced gene MfWRKY7.2 of M. flabellifolia. MfWRKY7.2 is localized in the nucleus, but no transactivation ability of the complete or partial MfWRKY7.2 was detected by yeast two hybrid. Arabidopsis plants overexpressing MfWRKY7.2 exhibited longer root length and better growth performance under drought and salt stress compared to the wild type. Measurements of physiological indicators related to stress response showed that overexpression of MfWRKY7.2 significantly increased contents of leaf water and chlorophyll, osmolyte accumulation, as well as reactive oxygen species (ROS) scavenging ability under both drought and salt stress. Interestingly, the enhanced sensitivity of stomatal closure to abscisic acid (ABA) and expression levels of ABA-responsive marker genes in transgenic lines suggested that MfWRKY7.2 may contribute to drought tolerance through promoting ABA biosynthesis or (and) signaling.

A naturally occurring SNP modulates thermotolerance divergence among grapevines

With the increasing challenges posed by global warming and climate change, heat stress has become a significant threat to the sustainable production of grapevines. However, the genetic basis of grapevine thermotolerance remains poorly understood. Here, we combine genome-wide association study with transcriptomic profiling to identify TTC4 (thermotolerance on chromosome 4), a gene encoding a WRKY transcription factor, as a key determinant of thermotolerance in grapevine. TTC4 directly activates two thermotolerance-related genes, HSP18.1 and APX3. We also identify a heat-suppressed repressor SPL13 (SQUAMOSA-promoter binding protein-like 13) that cannot bind to the GTAT element (TTC4T(7631)) in intron 2 of TTC4, but can bind to the natural variant, GTAC (TTC4C(7631)). Grapevine accessions with TTC4C/C(7631) genotype exhibit significantly lower thermotolerance compared to those with the TTC4T/T(7631) and TTC4C/T(7631) genotypes. This fine-tuned regulation contributes to thermotolerance divergence among grapevine populations. The TTC4T(7631) haplotype holds significant potential as a genetic resource for breeding thermotolerant grapevine varieties.

Magnesium-dependent phosphatase 1 (MDP1) interacts with WRKY 53 and protein phosphatase 2C 80 (PP2C80) to improve salt stress tolerance by scavenging reactive oxygen species in Salix psammophila

The roles of haloacid dehalogenase-like hydrolase (HAD) proteins in plants under salt stress remain largely unexplored. In the present study, we identified and functionally characterized SpsMDP1, a member of the HAD family, from Salix psammophila, which is a shrub adapted to desert environments. SpsMDP1 was strongly upregulated by salt stress. Ectopic expression of SpsMDP1 in Arabidopsis and poplar enhanced salt tolerance, with increased peroxidase activity and less ROS accumulation. Enhanced xylem development was in transgenic poplar plants overexpressing SpsMDP1. Moreover, Y2H, Co-IP, BiFC, and luciferase complementation analyses demonstrated that SpsPP2C80 can interact with SpsMDP1 both in vitro and in vivo. In addition, Y1H, EMSA, and transient expression analysis revealed that SpsWRKY53 is an upstream regulator of SpsMDP1 and can directly bind to the W-box in the promoter region and activate its expression. Both SpsWRKY53 and SpsPP2C80 can increase salt stress tolerance by increasing the activity of antioxidant enzymes. Taken together, in our study we propose a model for the SpsWRKY53-SpsMDP1-SpsPP2C80 module to defend against salt stress by scavenging reactive oxygen species. Our results provide a foundation for better understanding the function of SpsMDP1 in response to salt in S. psammophila and identifying candidate genes for transgenic salt resistance breeding.

Roles of WRKY Transcription Factors in Response to Sri Lankan Cassava Mosaic Virus Infection in Susceptible and Tolerant Cassava Cultivars

Cassava mosaic disease (CMD) is caused by viruses such as Sri Lankan cassava mosaic virus (SLCMV). It poses a significant threat to the cassava (Manihot esculenta) yield in Southeast Asia. Here, we investigated the expression of WRKY transcription factors (TFs) in SLCMV-infected cassava cultivars KU 50 (tolerant) and R 11 (susceptible) at 21, 32, and 67 days post-inoculation (dpi), representing the early, middle/recovery, and late infection stages, respectively. The 34 identified WRKYs were classified into the following six groups based on the functions of their homologs in the model plant Arabidopsis thaliana (AtWRKYs): plant defense; plant development; hormone signaling (abscisic, salicylic, and jasmonic acid); reactive oxygen species production; basal immune mechanisms; and other related hormones, metabolites, and abiotic stress responses. Regarding the protein interactions of the identified WRKYs, based on the interactions of their homologs (AtWRKYs), WRKYs increased reactive oxygen species production, leading to salicylic acid accumulation and systemic acquired resistance (SAR) against SLCMV. Additionally, some WRKYs were involved in defense-related mitogen-activated protein kinase signaling and abiotic stress responses. Furthermore, crosstalk among WRKYs reflected the robustly restricted viral multiplication in the tolerant cultivar, contributing to CMD recovery. This study highlights the crucial roles of WRKYs in transcriptional reprogramming, innate immunity, and responses to geminivirus infections in cassava, providing valuable insights to enhance disease resistance in cassava and, potentially, other crops.

Heat stress in plants: sensing, signalling, and ferroptosis

In the current context of global warming, high temperature events are becoming more frequent and intense in many places around the world. In this context, understanding how plants sense and respond to heat is essential to develop new tools to prevent plant damage and address global food security, as high temperature events are threatening agricultural sustainability. This review summarizes and integrates our current understanding underlying the cellular, physiological, biochemical, and molecular regulatory pathways triggered in plants under moderately high and extremely high temperature conditions. Given that extremely high temperatures can also trigger ferroptosis, the study of this cell death mechanism constitutes a strategic approach to understand how plants might overcome otherwise lethal temperature events.

Transcriptomic analysis reveals role of lncRNA LOC100257036 to regulate AGAMOUS during cluster compactness of Vitis vinifera cv. sistan yaghooti

Yaghooti grape, as the earliest grape variety in Iran, is considered as more resistant to heat, drought, and salinity than other cultivars. Cluster compactness is regarded as an inappropriate feature for the productivity of Yaghooti grape as a critical commercial and nutritional product. In plants, lncRNAs play a critical role in regulating biological processes related to growth and development. However, the potential role of lncRNAs was not assessed in cluster compactness. Totally, 1549 lncRNAs were identified by RNA-Seq data analysis in three steps of cluster formation, berry formation, and final cluster size after a thorough screening process. In addition, 229 lncRNAs were differentially expressed in the cluster development steps. Based on the functional analysis, lncRNAs are related to AG and MYB, bHLH, LBD, NAC, and WRKY TFs. Further, the target genes enrichment analysis revealed a relationship between lncRNAs with grape growth and development, as well as resistance to abiotic stresses such as heat and drought, plant defense against pathogens, and early grapes ripening. The study identified four lncRNAs as precursors of miRNAs, predicting that 112 other lncRNAs could potentially be targeted by 166 miRNAs. The results provide new insights into the regulatory functions of lncRNAs in Yaghooti grape to improve overall understanding of the molecular mechanisms related to grape compactness.

Comprehensive analysis of transcription factor binding sites and expression profiling of rice pathogenesis related genes (OsPR1)

Pathogenesis-related (PR) proteins, found in plants, play a crucial role in responding to both biotic and abiotic stresses and are categorized into 17 distinct families based on their properties and functions. We have conducted a phylogenetic analysis of OsPR1 genes (rice PR1 genes) in conjunction with 58 putative PR1 genes identified in Brachypodium distachyon, Hordeum vulgare, Brassica rapa, and Zea mays through BLASTP predictions. We extensively investigated the responses of the remaining 11 rice PR1 genes, using OsPR1a as a reference, under various stress conditions, including phytohormone treatments (salicylic acid and brassinosteroid [BR]), wounding, and heat stress (HS). In rice, of the 32 predicted OsPR1 genes, 12 have been well-characterized for their roles in disease resistance, while the functions of the remaining genes have not been studied extensively. In our study, we selected an additional 11 OsPR1 genes for further analysis and constructed a phylogenetic tree based on the presence of a 10-amino-acid-long conserved motif within these proteins. The phylogenetic analysis revealed that both OsPR1a from earlier studies and OsPR1-74 from our current study belong to the same clade. These genes consistently exhibit upregulation in response to diverse stress treatments such as biotic stress and abiotic stresses such as heat, drought, and salinity, indicating their potential roles in enhancing stress tolerance in rice. Significantly, this study delves into the previously unexplored role of OsPR1 genes in responding to Brassinosteroid (BR) and heat stress (HS) treatments, confirming their involvement in stress responses through qRT-PCR analysis. We found that seven genes were upregulated by EBR treatment. During heat stress (HS), six and seven genes were upregulated at 1hand 4h HS, respectively. The remaining genes OsPR1-22 and OsPR1-75 were upregulated at 1h but downregulated at 4h HS and under EBR treatment. In contrast, OsPR1-76 was upregulated at both 1h and 4h HS, but downregulated under EBR treatment. Promoters of PR1 genes in rice and other crops are rich in transcription factor binding sites (TFBSs) and feature a conserved Cysteine-rich secretory protein (SCP or CAP) motif. This study advances our understanding of PR1 gene regulation and its potential to enhance stress tolerance in rice.

Genome-wide association study and genotypic variation for the major tocopherol content in rice grain

Rice tocopherols, vitamin E compounds with antioxidant activity, play essential roles in human health. Even though the key genes involved in vitamin E biosynthetic pathways have been identified in plants, the genetic architecture of vitamin E content in rice grain remains unclear. A genome-wide association study (GWAS) on 179 genotypically diverse rice accessions with 34,323 SNP markers was conducted to detect QTLs that define total and α- tocopherol contents in rice grains. Total and α-tocopherol contents had a strong positive correlation and varied greatly across the accessions, ranging from 0.230-31.76 and 0.011-30.83 (μg/g), respectively. A total of 13 QTLs were identified, which were spread across five of the rice chromosomes. Among the 13 QTLs, 11 were considered major with phenotypic variation explained (PVE) greater than 10%. Twelve transcription factor (TF) genes, one microprotein (miP), and a transposon were found to be associated with the QTLs with putative roles in controlling tocopherol contents. Moreover, intracellular transport proteins, ABC transporters, nonaspanins, and SNARE, were identified as associated genes on chromosomes 1 and 8. In the vicinity of seven QTLs, protein kinases were identified as key signaling factors. Haplotype analysis revealed the QTLs qAlph1.1, qTot1.1, qAlph2.1, qAlph6.1, qTot6.1, and qTot8.3 to have significant haplogroups. Quantitative RT-PCR validated the expression direction and magnitude of WRKY39 (Os02g0265200), PIP5Ks (Os08g0450800), and MADS59 (Os06g0347700) in defining the major tocopherol contents. This study provides insights for ongoing biofortification efforts to breed and/or engineer vitamin E and antioxidant levels in rice and other cereals.

Transcriptomics and metabolomics analyses of Rosa hybrida to identify heat stress response genes and metabolite pathways

BACKGROUND

Global warming has greatly increased the impact of high temperatures on crops, resulting in reduced yields and increased mortality. This phenomenon is of significant importance to the rose flower industry because high-temperature stress leads to bud dormancy or even death, reducing ornamental value and incurring economic losses. Understanding the molecular mechanisms underlying the response and resistance of roses to high-temperature stress can serve as an important reference for cultivating high-temperature-stress-resistant roses.

RESULTS

To evaluate the impact of high temperatures on rose plants, we measured physiological indices in rose leaves following heat stress. Protein and chlorophyll contents were significantly decreased, whereas proline and malondialdehyde (MDA) contents, and peroxidase (POD) activity were increased. Subsequently, transcriptomics and metabolomics analyses identified 4,652 common differentially expressed genes (DEGs) and 57 common differentially abundant metabolites (DAMs) in rose plants from four groups. Enrichment analysis showed that DEGs and DAMs were primarily involved in the mitogen-activated protein kinases (MAPK) signaling pathway, plant hormone signal transduction, alpha-linolenic acid metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis. The combined analysis of the DEGs and DAMs revealed that flavonoid biosynthesis pathway-related genes, such as chalcone isomerase (CHI), shikimate O-hydroxycinnamoyl transferase (HCT), flavonol synthase (FLS), and bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase (DFR), were downregulated after heat stress. Moreover, in the MAPK signaling pathway, the expression of genes related to jasmonic acid exhibited a decrease, but ethylene receptor (ETR/ERS), P-type Cu + transporter (RAN1), ethylene-insensitive protein 2/3 (EIN2), ethylene-responsive transcription factor 1 (ERF1), and basic endochitinase B (ChiB), which are associated with the ethylene pathway, were mostly upregulated. Furthermore, heterologous overexpression of the heat stress-responsive gene RcHSP70 increased resistance to heat stress in Arabidopsis thaliana.

CONCLUSION

The results of this study indicated that the flavonoid biosynthesis pathway, MAPK signaling pathway, and plant hormones may be involved in high-temperature resistance in roses. Constitutive expression of RcHSP70 may contribute to increasing high-temperature tolerance. This study provides new insights into the genes and metabolites induced in roses in response to high temperature, and the results provide a reference for analyzing the molecular mechanisms underlying resistance to heat stress in roses.

PlWRKY47 Coordinates With Cytosolic Glyceraldehyde-3-Phosphate Dehydrogenase 2 Gene to Improve Thermotolerance Through Inhibiting Reactive Oxygen Species Generation in Herbaceous Peony

Although WRKY transcription factors play crucial roles in plant responses to high-temperature stress, little is known about Group IIb WRKY family members. Here, we identified the WRKY-IIb protein PlWRKY47 from herbaceous peony (Paeonia lactiflora Pall.), which functioned as a nuclear-localized transcriptional activator. The expression level of PlWRKY47 was positively correlated with high-temperature tolerance. Silencing of PlWRKY47 in P. lactiflora resulted in the decreased tolerance to high-temperature stress by accumulating reactive oxygen species (ROS). Overexpression of PlWRKY47 improved plant high-temperature tolerance through decreasing ROS accumulation. Moreover, PlWRKY47 directly bound to the promoter of cytosolic glyceraldehyde-3-phosphate dehydrogenase 2 (PlGAPC2) gene and activated its transcription. PlGAPC2 was also positively regulated high-temperature tolerance in P. lactiflora by increasing NAD+ content to inhibit ROS generation. Additionally, PlWRKY47 physically interacted with itself to form a homodimer, and PlWRKY47 could also interact with one Group IIb WRKY family member PlWRKY72 to form a heterodimer, they all promoted PlWRKY47 to bind to and activate PlGAPC2. These data support that the PlWRKY47-PlWRKY47 homodimer and PlWRKY72-PlWRKY47 heterodimer can directly activate PlGAPC2 expression to improve high-temperature tolerance by inhibiting ROS generation in P. lactiflora. These results will provide important insights into the plant high-temperature stress response by WRKY-IIb transcription factors.

SlWRKY55 coordinately acts with SlVQ11 to enhance tomato thermotolerance by activating SlHsfA2

High temperature (HT) severely restricts plant growth, development, and productivity. Plants have evolved a set of mechanisms to cope with HT, including the regulation of heat stress transcription factors (Hsfs) and heat shock proteins (Hsps). However, it is not clear how the transcriptional and translational levels of Hsfs and Hsps are controlled in tomato. Here, we reported that the HT-induced transcription factor SlWRKY55 recruited SlVQ11 to coordinately regulate defense against HT. SlWRKY55 directly bound to the promoter of SlHsfA2 and promoted its expression, which was increased by SlVQ11. Moreover, both SlWRKY55 and SlVQ11 physically interacted with SlHsfA2 to enhance the transcriptional activity of SlHsfA2. Thus, our results revealed a molecular mechanism that the SlWRKY55/SlVQ11-SlHsfA2 cascade enhanced thermotolerance and provided potential target genes for improving the adaptability of crops to HT.

PtWRKY2, a WRKY transcription factor from Pinellia ternata confers heat tolerance in Arabidopsis

High temperatures are a major stress factor that limit the growth of Pinellia ternata. WRKY proteins widely distribute in plants with the important roles in plant growth and stress responses. However, WRKY genes have not been identified in P. ternata thus far. In this study, five PtWRKYs with four functional subgroups were identified in P. ternata. One group III WRKY transcription factor, PtWRKY2, was strongly induced by high temperatures, whereas the other four PtWRKYs were suppressed. Analysis of transcription factor characteristics revealed that PtWRKY2 localized to the nucleus and specifically bound to W-box elements without transcriptional activation activity. Overexpression of PtWRKY2 increased the heat tolerance of Arabidopsis, as shown by the higher percentage of seed germination and survival rate, and the longer root length of transgenic lines under high temperatures compared to the wild-type. Moreover, PtWRKY2 overexpression significantly decreased reactive oxygen species accumulation by increasing the catalase, superoxide dismutase, and peroxidase activities. Furthermore, the selected heat shock-associated genes, including five transcription factors (HSFA1A, HSFA7A, bZIP28, DREB2A, and DREB2B), two heat shock proteins (HSP70 and HSP17.4), and three antioxidant enzymes (POD34, CAT1, and SOD1), were all upregulated in transgenic Arabidopsis. The study identifies that PtWRKY2 functions as a key transcriptional regulator in the heat tolerance of P. ternata, which might provide new insights into the genetic improvement of P. ternata.

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

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

Transcription factor CaHDZ15 promotes pepper basal thermotolerance by activating HEAT SHOCK FACTORA6a

High temperature stress (HTS) is a serious threat to plant growth and development and to crop production in the context of global warming, and plant response to HTS is largely regulated at the transcriptional level by the actions of various transcription factors (TFs). However, whether and how homeodomain-leucine zipper (HD-Zip) TFs are involved in thermotolerance are unclear. Herein, we functionally characterized a pepper (Capsicum annuum) HD-Zip I TF CaHDZ15. CaHDZ15 expression was upregulated by HTS and abscisic acid in basal thermotolerance via loss- and gain-of-function assays by virus-induced gene silencing in pepper and overexpression in Nicotiana benthamiana plants. CaHDZ15 acted positively in pepper basal thermotolerance by directly targeting and activating HEAT SHOCK FACTORA6a (HSFA6a), which further activated CaHSFA2. In addition, CaHDZ15 interacted with HEAT SHOCK PROTEIN 70-2 (CaHsp70-2) and glyceraldehyde-3-phosphate dehydrogenase1 (CaGAPC1), both of which positively affected pepper thermotolerance. CaHsp70-2 and CaGAPC1 promoted CaHDZ15 binding to the promoter of CaHSFA6a, thus enhancing its transcription. Furthermore, CaHDZ15 and CaGAPC1 were protected from 26S proteasome-mediated degradation by CaHsp70-2 via physical interaction. These results collectively indicate that CaHDZ15, modulated by the interacting partners CaGAPC1 and CaHsp70-2, promotes basal thermotolerance by directly activating the transcript of CaHSFA6a. Thus, a molecular linkage is established among CaHsp70-2, CaGAPC1, and CaHDZ15 to transcriptionally modulate CaHSFA6a in pepper thermotolerance.

How the Ethylene Biosynthesis Pathway of Semi-Halophytes Is Modified with Prolonged Salinity Stress Occurrence?

The mechanism of ethylene (ET)-regulated salinity stress response remains largely unexplained, especially for semi-halophytes and halophytes. Here, we present the results of the multifaceted analysis of the model semi-halophyte Mesembryanthemum crystallinum L. (common ice plant) ET biosynthesis pathway key components' response to prolonged (14 days) salinity stress. Transcriptomic analysis revealed that the expression of 3280 ice plant genes was altered during 14-day long salinity (0.4 M NaCl) stress. A thorough analysis of differentially expressed genes (DEGs) showed that the expression of genes involved in ET biosynthesis and perception (ET receptors), the abscisic acid (ABA) catabolic process, and photosynthetic apparatus was significantly modified with prolonged stressor presence. To some point this result was supported with the expression analysis of the transcript amount (qPCR) of key ET biosynthesis pathway genes, namely ACS6 (1-aminocyclopropane-1-carboxylate synthase) and ACO1 (1-aminocyclopropane-1-carboxylate oxidase) orthologs. However, the pronounced circadian rhythm observed in the expression of both genes in unaffected (control) plants was distorted and an evident downregulation of both orthologs' was induced with prolonged salinity stress. The UPLC-MS analysis of the ET biosynthesis pathway rate-limiting semi-product, namely of 1-aminocyclopropane-1-carboxylic acid (ACC) content, confirmed the results assessed with molecular tools. The circadian rhythm of the ACC production of NaCl-treated semi-halophytes remained largely unaffected by the prolonged salinity stress episode. We speculate that the obtained results represent an image of the steady state established over the past 14 days, while during the first hours of the salinity stress response, the view could be completely different.

WRKY48 negatively regulates plant acclimation to a combination of high light and heat stress

Plants growing under natural conditions experience high light (HL) intensities that are often accompanied by elevated temperatures. These conditions could affect photosynthesis, reduce yield, and negatively impact agricultural productivity. The combination of different abiotic challenges creates a new type of stress for plants by generating complex environmental conditions that often exceed the impact of their individual parts. Transcription factors (TFs) play a key role in integrating the different molecular signals generated by multiple stress conditions, orchestrating the acclimation response of plants to stress. In this study, we show that the TF WRKY48 negatively controls the acclimation of Arabidopsis thaliana plants to a combination of HL and heat stress (HL + HS), and its expression is attenuated by jasmonic acid under HL + HS conditions. Using comparative physiological and transcriptomic analyses between wild-type and wrky48 mutants, we further demonstrate that under control conditions, WRKY48 represses the expression of a set of transcripts that are specifically required for the acclimation of plants to HL + HS, hence its suppression during the HL + HS stress combination contributes to plant survival under these conditions. Accordingly, mutants that lack WRKY48 are more resistant to HL + HS, and transgenic plants that overexpress WRKY48 are more sensitive to it. Taken together, our findings reveal that WRKY48 is a negative regulator of the transcriptomic response of Arabidopsis to HL + HS and provide new insights into the complex regulatory networks of plant acclimation to stress combination.

Differential heat-response characteristics of two plastid isoforms of triose phosphate isomerase in tomato

Heat stress causes dysfunction of the carbon-assimilation metabolism. As a member of Calvin-Benson-Bassham (CBB) cycle, the chloroplast triose phosphate isomerases (TPI) catalyse the interconversion of glyceraldehyde 3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP). The tomato (Solanum lycopersicum) genome contains two individual SlTPI genes, Solyc10g054870 and Solyc01g111120, which encode the chloroplast-located proteins SlTPI1 and SlTPI2, respectively. The tpi1 and tpi2 single mutants had no visible phenotypes, but the leaves of their double mutant lines tpi1tpi2 had obviously reduced TPI activity and displayed chlorotic variegation, dysplasic chloroplasts and lower carbon-assimilation efficiency. In addition to altering carbon metabolism, proteomic data showed that the loss of both SlTPI1 and SlTPI2 severely affected photosystem proteins, reducing photosynthetic capacity. None of these phenotypes was evident in the tpi1 or tpi2 single mutants, suggesting that SlTPI1 and SlTPI2 are functionally redundant. However, the two proteins differed in their responses to heat stress; the protein encoded by the heat-induced SlTPI2 showed a higher level of thermotolerance than that encoded by the heat-suppressed SlTPI1. Notably, heat-induced transcription factors, SlWRKY21 and SlHSFA2/7, which negatively regulated SlTPI1 expression and positively regulated SlTPI2 expression, respectively. Our findings thus reveal that SlTPI1 and SlTPI2 have different thermostabilities and expression patterns in response to heat stress, which have the potential to be applied in thermotolerance strategies in crops.

Genome-wide identification, structural characterization and gene expression analysis of the WRKY transcription factor family in pea (Pisum sativum L.)

BACKGROUND

The WRKY gene family is one of the largest families of transcription factors in higher plants, and WRKY transcription factors play important roles in plant growth and development as well as in response to abiotic stresses; however, the WRKY gene family in pea has not been systematically reported.

RESULTS

In this study, 89 pea WRKY genes were identified and named according to the random distribution of PsWRKY genes on seven chromosomes. The gene family was found to have nine pairs of tandem duplicates and 19 pairs of segment duplicates. Phylogenetic analyses of the PsWRKY and 60 Arabidopsis WRKY proteins were performed to determine their homology, and the PsWRKYs were classified into seven subfamilies. Analysis of the physicochemical properties, motif composition, and gene structure of pea WRKYs revealed significant differences in the physicochemical properties within the PsWRKY family; however, their gene structure and protein-conserved motifs were highly conserved among the subfamilies. To further investigate the evolutionary relationships of the PsWRKY family, we constructed comparative syntenic maps of pea with representative monocotyledonous and dicotyledonous plants and found that it was most recently homologous to the dicotyledonous WRKY gene families. Cis-acting element analysis of PsWRKY genes revealed that this gene family can respond to hormones, such as abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin (GA), methyl jasmonate (MeJA), and salicylic acid (SA). Further analysis of the expression of 14 PsWRKY genes from different subfamilies in different tissues and fruit developmental stages, as well as under five different hormone treatments, revealed differences in their expression patterns in the different tissues and fruit developmental stages, as well as under hormone treatments, suggesting that PsWRKY genes may have different physiological functions and respond to hormones.

CONCLUSIONS

In this study, we systematically identified WRKY genes in pea for the first time and further investigated their physicochemical properties, evolution, and expression patterns, providing a theoretical basis for future studies on the functional characterization of pea WRKY genes during plant growth and development.

A review of changes at the phenotypic, physiological, biochemical, and molecular levels of plants due to high temperatures

MAIN CONCLUSION

This review summarizes the physiological, biochemical, and molecular regulatory network changes in plants in response to high temperature. With the continuous rise in temperature, high temperature has become an important issue limiting global plant growth and development, affecting the phenotype and physiological and biochemical processes of plants and seriously restricting crop yield and tree growth speed. As sessile organisms, plants inevitably encounter high temperatures and improve their heat tolerance by activating molecular networks related to heat stress, such as signal transduction, synthesis of metabolites, and gene expression. Heat tolerance is a polygenic trait regulated by a variety of genes, transcription factors, proteins, and metabolites. Therefore, this review summarizes the changes in physiological, biochemical and molecular regulatory networks in plants under high-temperature conditions to lay a foundation for an in-depth understanding of the mechanisms involved in plant heat tolerance responses.

Review: Structural-functional relationship of WRKY transcription factors: Unfolding the role of WRKY in plants

WRKY as the name suggests, are the transcription factors (TFs) that contain the signature WRKY domains, hence named after it. Since their discovery in 1994, they have been well studied in plants with exploration of approximately 74 WRKY genes in the model plant, Arabidopsis alone. However, the study of these transcription factors (TFs) is not just limited to model plant now. They have been studied widely in crop plants as well, because of their tremendous contribution in stress as well as in growth and development. Here, in this review, we describe the story of WRKY TFs from their identification to their origin, the binding mechanisms, structure and their contribution in regulating plant development and stress physiology. High throughput transcriptomics-based data also opened a doorway to understand the comprehensive and detailed functioning of WRKY TFs in plants. Indeed, the detailed functional role of each and every WRKY member in regulating the gene expression is required to pave the path to develop holistic understanding of their role in stress physiology and developmental processes in plants.

Molecular switches in plant stress adaptation

Climate change poses a significant threat to the global ecosystem, prompting plants to use various adaptive mechanisms via molecular switches to combat biotic and abiotic stress factors. These switches activate stress-induced pathways by altering their configuration between stable states. In this review, we investigated the regulation of molecular switches in different plant species in response to stress, including the stress-regulated response of multiple switches in Arabidopsis thaliana. We also discussed techniques for developing stress-resilient crops using molecular switches through advanced biotechnological tools. The literature search, conducted using databases such as PubMed, Google Scholar, Web of Science, and SCOPUS, utilized keywords such as molecular switch, plant adaptation, biotic and abiotic stresses, transcription factors, Arabidopsis thaliana, and crop improvement. Recent studies have shown that a single molecular switch can regulate multiple stress networks, and multiple switches can regulate a single stress condition. This multifactorial understanding provides clarity to the switch regulatory network and highlights the interrelationships of different molecular switches. Advanced breeding techniques, along with genomic and biotechnological tools, have paved the way for further research on molecular switches in crop improvement. The use of synthetic biology in molecular switches will lead to a better understanding of plant stress biology and potentially bring forth a new era of stress-resilient, climate-smart crops worldwide.

Jasmonate: A Hormone of Primary Importance for Temperature Stress Response in Plants

Temperature is a critical environmental factor that plays a vital role in plant growth and development. Temperatures below or above the optimum ranges lead to cold or heat stress, respectively. Temperature stress retards plant growth and development, and it reduces crop yields. Jasmonates (JAs) are a class of oxylipin phytohormones that play various roles in growth, development, and stress response. In recent years, studies have demonstrated that cold and heat stress affect JA biosynthesis and signaling, and JA plays an important role in the response to temperature stress. Recent studies have provided a large body of information elucidating the mechanisms underlying JA-mediated temperature stress response. In the present review, we present recent advances in understanding the role of JA in the response to cold and heat stress, and how JA interacts with other phytohormones during this process.

SlMYB41 positively regulates tomato thermotolerance by activating the expression of SlHSP90.3

High-temperature stress has become a major abiotic factor that dramatically limits plant growth and crop yield. Plants have evolved complex mechanisms to cope with high-temperature stress, but the factors that regulate plant thermotolerance remain to be discovered. Here, a high temperature-induced MYB transcription factor SlMYB41 was cloned from tomato (Solanum lycopersicum). Two individual SlMYB41-RNA interference (RNAi) lines (MR) and one CRISPR/Cas9 mediated myb41 mutant (MC) were obtained to investigate the function of SlMYB41 in tomato thermotolerance. Under high-temperature stress, we found that the MR and MC lines showed more wilting than the wild type (WT), with more ion leakage, more MDA accumulation, lower contents of osmotic adjustment substances, and more accumulation of reactive oxygen species (ROS) which was resulted from lower antioxidative enzyme activities. In addition, the photosynthetic capacity and complex of MR and MC lines were damaged more seriously than WT plants under high-temperature stress, mainly manifested in lower photosynthetic rate and Fv/Fm. Moreover, heat stress-related genes, such as SlHSP17.6, SlHSP17.7, and SlHSP90.3 were downregulated in MR and MC lines. Importantly, Y1H and LUC analysis indicated that SlMYB41 can directly activate the transcription of SlHSP90.3. Together, our study suggest that SlMYB41 positively regulates tomato thermotolerance by activating the expression of SlHSP90.3.

A detailed study on genetic diversity, antioxidant machinery, and expression profile of drought-responsive genes in rice genotypes exposed to artificial osmotic stress

Seasonal variations in rainfall patterns, particularly during sowing, early growing season, and flowering, drastically affect rice production in northeastern India. However, sensitivity to drought stress is genotype-specific. Since 80% of the land in this region is used for rice production, it is crucial to understand how they have adapted to water stress. This study evaluated 112 rice genotypes grown in NE India for seed germination percentage and seedling development under PEG-mediated drought stress. Among the rice genotype, Sahbhagi dhan, RCPL-1-82, Bhalum-3 and RCPL-1-128 showed drought-tolerant traits, while Ketaki Joha, Chakhao, Chandan, RCPL-1-185 and IR-64 were the most drought-sensitive rice genotypes. Drought-tolerant rice also showed significantly higher seed germination potential, proline content, antioxidant activity and expression of drought-responsive genes than drought-sensitive rice genotypes. A similar expression pattern of genes was also observed in the rice genotype treated with a 50% water deficit in pot culture. In addition, drought stress reduced the pollen fertility and yield per plant in sensitive rice genotypes. Molecular markers associated with drought stress were also used to characterize genetic diversity among the rice genotypes studied.

BcWRKY22 Activates BcCAT2 to Enhance Catalase (CAT) Activity and Reduce Hydrogen Peroxide (H2O2) Accumulation, Promoting Thermotolerance in Non-Heading Chinese Cabbage (Brassica campestris ssp. chinensis)

WRKY transcription factors (TFs) participate in plant defense mechanisms against biological and abiotic stresses. However, their regulatory role in heat resistance is still unclear in non-heading Chinese cabbage. Here, we identified the WRKY-IIe gene BcWRKY22(BraC09g001080.1), which is activated under high temperatures and plays an active role in regulating thermal stability, through transcriptome analysis. We further discovered that the BcWRKY22 protein is located in the nucleus and demonstrates transactivation activity in both the yeast and plant. Additionally, our studies showed that the transient overexpression of BcWRKY22 in non-heading Chinese cabbage activates the expression of catalase 2 (BcCAT2), enhances CAT enzyme activity, and reduces Hydrogen Peroxide (H2O2) accumulation under heat stress conditions. In addition, compared to its wild-type (WT) counterparts, Arabidopsis thaliana heterologously overexpresses BcWRKY22, improving thermotolerance. When the BcWRKY22 transgenic root was obtained, under heat stress, the accumulation of H2O2 was reduced, while the expression of catalase 2 (BcCAT2) was upregulated, thereby enhancing CAT enzyme activity. Further analysis revealed that BcWRKY22 directly activates the expression of BcCAT2 (BraC08g016240.1) by binding to the W-box element distributed within the promoter region of BcCAT2. Collectively, our findings suggest that BcWRKY22 may serve as a novel regulator of the heat stress response in non-heading Chinese cabbage, actively contributing to the establishment of thermal tolerance by upregulating catalase (CAT) activity and downregulating H2O2 accumulation via BcCAT2 expression.

Insights into morphological and physio-biochemical adaptive responses in mungbean (Vigna radiata L.) under heat stress

Mungbean (Vigna radiata L. Wilczek) is an important food legume crop which contributes significantly to nutritional and food security of South and Southeast Asia. The crop thrives in hot and humid weather conditions, with an optimal temperature range of 28°-35°C, and is mainly cultivated under rainfed environments. However, the rising global temperature has posed a serious threat to mungbean cultivation. Optimal temperature is a vital factor in cellular processes, and every crop species has evolved with its specific temperature tolerance ability. Moreover, variation within a crop species is inevitable, given the diverse environmental conditions under which it has evolved. For instance, various mungbean germplasm can grow and produce seeds in extreme ambient temperatures as low as 20°C or as high as 45°C. This range of variation in mungbean germplasm for heat tolerance plays a crucial role in developing heat tolerant and high yielding mungbean cultivars. However, heat tolerance is a complex mechanism which is extensively discussed in this manuscript; and at the same time individual genotypes have evolved with various ways of heat stress tolerance. Therefore, to enhance understanding towards such variability in mungbean germplasm, we studied morphological, anatomical, physiological, and biochemical traits which are responsive to heat stress in plants with more relevance to mungbean. Understanding heat stress tolerance attributing traits will help in identification of corresponding regulatory networks and associated genes, which will further help in devising suitable strategies to enhance heat tolerance in mungbean. The major pathways responsible for heat stress tolerance in plants are also discussed.

Genome-Wide Identification and Expression Analysis of WRKY Gene Family in Neolamarckia cadamba

The WRKY transcription factor family plays important regulatory roles in multiple biological processes in higher plants. They have been identified and functionally characterized in a number of plant species, but very little is known in Neolamarckia cadamba, a 'miracle tree' for its fast growth and potential medicinal resource in Southeast Asia. In this study, a total of 85 WRKY genes were identified in the genome of N. cadamba. They were divided into three groups according to their phylogenetic features, with the support of the characteristics of gene structures and conserved motifs of protein. The NcWRKY genes were unevenly distributed on 22 chromosomes, and there were two pairs of segmentally duplicated events. In addition, a number of putative cis-elements were identified in the promoter regions, of which hormone- and stress-related elements were shared in many NcWRKYs. The transcript levels of NcWRKY were analyzed using the RNA-seq data, revealing distinct expression patterns in various tissues and at different stages of vascular development. Furthermore, 16 and 12 NcWRKY genes were confirmed to respond to various hormone treatments and two different abiotic stress treatments, respectively. Moreover, the content of cadambine, the active metabolite used for the various pharmacological activities found in N. cadamba, significantly increased after Methyl jasmonate treatment. In addition, expression of NcWRKY64/74 was obviously upregulated, suggesting that they may have a potential function of regulating the biosynthesis of cadambine in response to MeJA. Taken together, this study provides clues into the regulatory roles of the WRKY gene family in N. cadamba.

Progress in the understanding of WRKY transcription factors in woody plants

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

Comprehensive metabolomic and lipidomic alterations in response to heat stress during seed germination and seedling growth of Arabidopsis

Temperature affects seed germination and seedling growth, which is a critical and complex stage in plant life cycle. However, comprehensive metabolic basis on temperature implicating seed germination and seedling growth remains less known. Here, we applied the high-throughput untargeted metabolomic and advanced shotgun lipidomic approaches to profile the Arabidopsis 182 metabolites and 149 lipids under moderate (22°C, 28°C) and extreme high (34°C, 40°C) temperatures. Our results showed that a typical feature of the metabolism related to organic acids/derivates and amines was obviously enriched at the moderate temperature, which was implicated in many cellular responses towards tricarboxylic acid cycle (TCA), carbohydrates and amino acids metabolism, peptide biosynthesis, phenylpropanoid biosynthesis and indole 3-acetate (IAA) biosynthetic pathway. Whereas, under extreme high temperatures, there was no seed germination, but 148 out of total 182 metabolites were highly enriched, involving in the galactose metabolism, fatty acid degradation, tryptophan/phenylalanine metabolism, and shikimic acid-mediated pathways especially including alkaloids metabolism and glucosinolate/flavone/flavonol biosynthesis. Phosphatidylcholine (PC) and phosphatidylethanolamine (PE) also exhibited the gradually increased tendency from moderate temperatures to extreme high temperatures; whereas phosphatidylserine (PS), phosphatidic acid (PA), phosphatidylglycerol (PG), monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG) and sulfoquinovosyldiacylglycerol (SQDG) were contrary to decrease. Another typical feature of the distinguished metabolites between 22°C and 28°C, the TCA, disaccharides, nucleotides, polypeptides, SQDG and the biosynthesis of fatty acids and glucobrassicin-mediated IAA were obviously decreased at 28°C, while amino acids, trisaccharides, PE, PC, PA, PS, MGDG, DGDG and diacylglycerol (DAG) preferred to enrich at 28°C, which characterized the alteration of metabolites and lipids during fast seedling growth. Taking together, our results provided the comprehensive metabolites phenotyping, revealed the characteristics of metabolites necessary for seed germination and/or seedling growth under different temperatures, and provided insights into the different metabolic regulation of metabolites and lipid homeostasis for seed germination and seedling growth.

Global Analysis of Dark- and Heat-Regulated Alternative Splicing in Arabidopsis

Alternative splicing (AS) is one of the major post-transcriptional regulation mechanisms that contributes to plant responses to various environmental perturbations. Darkness and heat are two common abiotic factors affecting plant growth, yet the involvement and regulation of AS in the plant responses to these signals remain insufficiently examined. In this study, we subjected Arabidopsis seedlings to 6 h of darkness or heat stress and analyzed their transcriptome through short-read RNA sequencing. We revealed that both treatments altered the transcription and AS of a subset of genes yet with different mechanisms. Dark-regulated AS events were found enriched in photosynthesis and light signaling pathways, while heat-regulated AS events were enriched in responses to abiotic stresses but not in heat-responsive genes, which responded primarily through transcriptional regulation. The AS of splicing-related genes (SRGs) was susceptible to both treatments; while dark treatment mostly regulated the AS of these genes, heat had a strong effect on both their transcription and AS. PCR analysis showed that the AS of the Serine/Arginine-rich family gene SR30 was reversely regulated by dark and heat, and heat induced the upregulation of multiple minor SR30 isoforms with intron retention. Our results suggest that AS participates in plant responses to these two abiotic signals and reveal the regulation of splicing regulators during these processes.

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

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

Ocean warming and acidification affect the transitional C:N:P ratio and macromolecular accumulation in the harmful raphidophyte Heterosigma akashiwo

Despite an increase in ocean warming and acidification that is expected to increase the number of harmful algal species worldwide, the population of the raphidophyte Heterosigma akashiwo has been reported to be reduced. However, how this species physically and metabolically modifies transitional C:N:P ratio and macromolecule accumulation is unknown. Considering 1st, 10th, and 20th culture generations under present (low-temperature; low-carbon-dioxide [LTLC] 21 °C; pCO2 400 ppm) and future (high-temperature; high-carbon-dioxide [HTHC] 25 °C; pCO2 1000 ppm) ocean conditions, we examined transitional C:N:P ratio and macromolecule level changes and performed transcriptome sequencing. The results showed that compared to 1st generation cells, 20th generation cells under HTHC conditions showed a large decrease in carbon quota (QC: 34%), nitrogen quota (QN: 36%), and phosphorus quota (QP: 32%), which were reflected in an overall reduction in DNA and RNA quantity. Decreased activation of photosynthetic, carbon fixation and lipid metabolic pathways coincided with changes in photosynthetic efficiency, carbon concentration, and lipid accumulation after long-term (20th generation) exposure to HTHC conditions. We observed that these variations in internal metabolic pathways were caused by external changes in temperature, which activated the (Ca+) signaling pathway, and external changes in pCO2, which altered proton exchange pathways. Our results suggest that H. akashiwo in a temperate environment will undergo profound changes in C:N:P ratio and macromolecular properties, leading to programmed cell death, in the future.

The wheat WRKY transcription factor TaWRKY1-2D confers drought resistance in transgenic Arabidopsis and wheat (Triticum aestivum L.)

The WRKY transcription factor family has been associated with a variety of plant biological processes, such as biotic and abiotic stress responses. In this study, 13 wheat TaWRKY DEGs in transcriptome data before and after drought stress, namely TaWRKY1 to TaWRKY8, including various copies, were identified and classified as Group I, II, or III. TaWRKY1-2D overexpression enhanced drought tolerance in transgenic Arabidopsis. Moreover, the AtRD29A, AtP5CS1, AtPOD1, AtCAT1, and AtSOD (Cu/Zn) genes, which are related to the stress response and antioxidant system, were significantly upregulated in TaWRKY1-2D transgenic Arabidopsis under drought stress. TaWRKY1-2 silencing in wheat increases the MDA content, reduces the contents of proline and chlorophyll and the activities of antioxidant enzymes, and inhibits the expression levels of antioxidant (TaPOD, TaCAT, and TaSOD (Fe))- and stress-related genes (TaP5CS) under drought stress. Yeast two-hybrid screening revealed TaDHN3 as an interaction partner of TaWRKY1-2D; their interaction was further confirmed using yeast two-hybrid and bimolecular fluorescence complementation. Furthermore, TaWRKY1-2D may play essential roles in wheat drought tolerance through posttranslational regulation of TaDHN3. Overall, these findings contribute to our knowledge of the WRKY family in wheat and identify TaWRKY1-2D as a promising candidate gene for improving wheat breeding to generate drought-tolerant wheat.

Transitional traits determine the acclimation characteristics of the coccolithophore Chrysotila dentata to ocean warming and acidification

Ocean warming and acidification interactively affect the coccolithophore physiology and drives major biogeochemical changes. While numerous studies investigated coccolithophore under short-term conditions, knowledge on how different transitional periods over long-exposure could influence the element, macromolecular and metabolic changes for its acclimation are largely unknown. We cultured the coccolithophore Chrysotila dentata, (culture generations of 1st, 10th, and 20th) under present (low-temperature low-carbon-dioxide [LTLC]) and projected (high-temperature high-carbon-dioxide [HTHC]) ocean conditions. We examined elemental and macromolecular component changes and sequenced a transcriptome. We found that with long-exposure, most physiological responses in HTHC cells decreased when compared with those in LTLC, however, HTHC cell physiology showed constant elevation between each generation. Specifically, compared to 1st generation, the 20th generation HTHC cells showed increases in quota carbon (Qc:29%), nitrogen (Q_N :101%), and subsequent changes in C:N-ratio (68%). We observed higher lipid accumulation than carbohydrates within HTHC cells under long-exposure, suggesting that lipids were used as an alternative energy source for cellular acclimation. Protein biosynthesis pathways increased their efficiency during long-term HTHC condition, indicating that cells produced more proteins than required to initiate acclimation. Our findings suggest that the coccolithophore resilience increased between the 1st-10th generation to initiate the acclimation process under ocean warming and acidifying conditions.

Integrating GWAS and transcriptomics to identify candidate genes conferring heat tolerance in rice

INTRODUCTION

Rice (Oryza sativa L.) production is being challenged by global warming. Identifying new loci and favorable alleles associated with heat tolerance is crucial to developing rice heat-tolerant varieties.

METHODS

We evaluated the heat tolerance at the seedling stage using 620 diverse rice accessions. A total of six loci associated with heat tolerance were identified by a genome-wide association study (GWAS) with ~2.8 million single nucleotide polymorphisms (SNPs).

RESULTS

Among the six detected loci, qHT7 harbored the strongest association signal and the most associated SNPs. By comparing the transcriptomes of two representative accessions with contrasting heat tolerance, LOC_Os07g48710 (OsVQ30) was selected as a promising candidate gene in qHT7 due to the significant difference in its expression level between the two accessions. Haplotype 4 (Hap4) of LOC_Os07g48710 was determined as the favorable haplotype for heat tolerance via the gene-based haplotype analysis. The heat-tolerant haplotype LOC_Os07g48710Hap4 is highly enriched in the tropical Geng/Japonica accessions, and its frequency has decreased significantly during the improvement process of rice varieties.

DISCUSSION

Based on the GWAS and transcriptomics integrated results, a hypothetical model modulated by qHT7 in response to heat stress was proposed. Our results provide valuable candidate genes for improving rice heat tolerance through molecular breeding.

Maize cytolines as models to study the impact of different cytoplasms on gene expression under heat stress conditions

BACKGROUND

Crops are under constant pressure due to global warming, which unfolds at a much faster pace than their ability to adapt through evolution. Agronomic traits are linked to cytoplasmic-nuclear genome interactions. It thus becomes important to understand the influence exerted by the organelles on gene expression under heat stress conditions and profit from the available genetic diversity. Maize (Zea mays) cytolines allow us to investigate how the gene expression changes under heat stress conditions in three different cytoplasmic environments, but each having the same nucleus. Analyzing retrograde signaling in such an experimental set-up has never been done before. Here, we quantified the response of three cytolines to heat stress as differentially expressed genes (DEGs), and studied gene expression patterns in the context of existing polymorphism in their organellar genomes.

RESULTS

Our study unveils a plethora of new genes and GO terms that are differentially expressed or enriched, respectively, in response to heat stress. We report 19,600 DEGs as responding to heat stress (out of 30,331 analyzed), which significantly enrich 164 GO biological processes, 30 GO molecular functions, and 83 GO cell components. Our approach allowed for the discovery of a significant number of DEGs and GO terms that are not common in the three cytolines and could therefore be linked to retrograde signaling. Filtering for DEGs with a fold regulation > 2 (absolute values) that are exclusive to just one of the cytolines, we find a total of 391 up- and down-DEGs. Similarly, there are 19 GO terms with a fold enrichment > 2 that are cytoline-specific. Using GBS data we report contrasting differences in the number of DEGs and GO terms in each cytoline, which correlate with the genetic distances between the mitochondrial genomes (but not chloroplast) and the original nuclei of the cytolines, respectively.

CONCLUSIONS

The experimental design used here adds a new facet to the paradigm used to explain how gene expression changes in response to heat stress, capturing the influence exerted by different organelles upon one nucleus rather than investigating the response of several nuclei in their innate cytoplasmic environments.

Transcriptome-wide identification of WRKY transcription factors and their expression profiles in response to methyl jasmonate in Platycodon grandiflorus

Platycodon grandiflorus, a perennial flowering plant widely distributed in China and South Korea, is an excellent resource for both food and medicine. The main active compounds of P. grandiflorus are triterpenoid saponins. WRKY transcription factors (TFs) are among the largest gene families in plants and play an important role in regulating plant terpenoid accumulation, physiological metabolism, and stress response. Numerous studies have been reported on other medicinal plants; however, little is known about WRKY genes in P. grandiflorus. In this study, 27 PgWRKYs were identified in the P. grandiflorus transcriptome. Phylogenetic analysis showed that PgWRKY genes were clustered into three main groups and five subgroups. Transcriptome analysis showed that the PgWRKY gene expression patterns in different tissues differed between those in Tongcheng City (Southern Anhui) and Taihe County (Northern Anhui). Gene expression analysis based on RNA sequencing and qRT-PCR analysis showed that most PgWRKY genes were expressed after induction with methyl jasmonate (MeJA). Co-expressing PgWRKY genes with triterpenoid biosynthesis pathway genes revealed four PgWRKY genes that may have functions in triterpenoid biosynthesis. Additionally, functional annotation and protein-protein interaction analysis of PgWRKY proteins were performed to predict their roles in potential regulatory networks. Thus, we systematically analyzed the structure, evolution, and expression patterns of PgWRKY genes to provide an important theoretical basis for further exploring the molecular basis and regulatory mechanism of WRKY TFs in triterpenoid biosynthesis.

A systematical genome-wide analysis and screening of WRKY transcription factor family engaged in abiotic stress response in sweetpotato

BACKGROUND

WRKY transcription factors play pivotal roles in regulating plant multiple abiotic stress tolerance, however, a genome-wide systematical analysis of WRKY genes in sweetpotato is still missing.

RESULTS

Herein, 84 putative IbWRKYs with WRKY element sequence variants were identified in sweetpotato reference genomes. Fragment duplications, rather than tandem duplications, were shown to play prominent roles in IbWRKY gene expansion. The collinearity analysis between IbWRKYs and the related orthologs from other plants further depicted evolutionary insights into IbWRKYs. Phylogenetic relationships displayed that IbWRKYs were divided into three main groups (I, II and III), with the support of the characteristics of exon-intron structures and conserved protein motifs. The IbWRKY genes, mainly from the group Ib, displayed remarkable and diverse expression profiles under multiple abiotic stress (NaCl, PEG6000, cold and heat) and hormone (ABA, ACC, JA and SA) treatments, which were determined by RNA-seq and qRT-PCR assays, suggesting their potential roles in mediating particular stress responses. Moreover, IbWRKY58L could interact with IbWRKY82 as revealed by yeast two-hybrid based on the protein interaction network screening. And abiotic stress-remarkably induced IbWRKY21L and IbWRKY51 were shown to be localized in the nucleus and had no transactivation activities.

CONCLUSION

These results provide valuable insights into sweetpotato IbWRKYs and will lay a foundation for further exploring functions and possible regulatory mechanisms of IbWRKYs in abiotic stress tolerance.

The LEA gene family in tomato and its wild relatives: genome-wide identification, structural characterization, expression profiling, and role of SlLEA6 in drought stress

BACKGROUND

Late embryogenesis abundant (LEA) proteins are widely distributed in higher plants and play crucial roles in regulating plant growth and development processes and resisting abiotic stress. Cultivated tomato (Solanum lycopersicum) is an important vegetable crop worldwide; however, its growth, development, yield, and quality are currently severely constrained by abiotic stressors. In contrast, wild tomato species are more tolerant to abiotic stress and can grow normally in extreme environments. The main objective of this study was to identify, characterize, and perform gene expression analysis of LEA protein families from cultivated and wild tomato species to mine candidate genes and determine their potential role in abiotic stress tolerance in tomatoes.

RESULTS

Total 60, 69, 65, and 60 LEA genes were identified in S. lycopersicum, Solanum pimpinellifolium, Solanum pennellii, and Solanum lycopersicoides, respectively. Characterization results showed that these genes could be divided into eight clusters, with the LEA_2 cluster having the most members. Most LEA genes had few introns and were non-randomly distributed on chromosomes; the promoter regions contained numerous cis-acting regulatory elements related to abiotic stress tolerance and phytohormone responses. Evolutionary analysis showed that LEA genes were highly conserved and that the segmental duplication event played an important role in evolution of the LEA gene family. Transcription and expression pattern analyses revealed different regulatory patterns of LEA genes between cultivated and wild tomato species under normal conditions. Certain S. lycopersicum LEA (SlLEA) genes showed similar expression patterns and played specific roles under different abiotic stress and phytohormone treatments. Gene ontology and protein interaction analyses showed that most LEA genes acted in response to abiotic stimuli and water deficit. Five SlLEA proteins were found to interact with 11 S. lycopersicum WRKY proteins involved in development or resistance to stress. Virus-induced gene silencing of SlLEA6 affected the antioxidant and reactive oxygen species defense systems, increased the degree of cellular damage, and reduced drought resistance in S. lycopersicum.

CONCLUSION

These findings provide comprehensive information on LEA proteins in cultivated and wild tomato species and their possible functions under different abiotic and phytohormone stresses. The study systematically broadens our current understanding of LEA proteins and candidate genes and provides a theoretical basis for future functional studies aimed at improving stress resistance in tomato.

WRKY transcription factors (TFs): Molecular switches to regulate drought, temperature, and salinity stresses in plants

The WRKY transcription factor (TF) belongs to one of the major plant protein superfamilies. The WRKY TF gene family plays an important role in the regulation of transcriptional reprogramming associated with plant stress responses. Change in the expression patterns of WRKY genes or the modifications in their action; participate in the elaboration of numerous signaling pathways and regulatory networks. WRKY proteins contribute to plant growth, for example, gamete formation, seed germination, post-germination growth, stem elongation, root hair growth, leaf senescence, flowering time, and plant height. Moreover, they play a key role in many types of environmental signals, including drought, temperature, salinity, cold, and biotic stresses. This review summarizes the current progress made in unraveling the functions of numerous WRKY TFs under drought, salinity, temperature, and cold stresses as well as their role in plant growth and development.

Activation tagging identifies WRKY14 as a repressor of plant thermomorphogenesis in Arabidopsis

Increases in recorded high temperatures around the world are causing plant thermomorphogenesis and decreasing crop productivity. PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is a central positive regulator of plant thermomorphogenesis. However, the molecular mechanisms underlying PIF4-regulated thermomorphogenesis remain largely unclear. In this study, we identified ABNORMAL THERMOMORPHOGENESIS 1 (ABT1) as an important negative regulator of PIF4 and plant thermomorphogenesis. Overexpression of ABT1 in the activation tagging mutant abt1-D caused shorter hypocotyls and petioles under moderately high temperature (HT). ABT1 encodes WRKY14, which belongs to subgroup II of the WRKY transcription factors. Overexpression of ABT1/WRKY14 or its close homologs, including ABT2/WRKY35, ABT3/WRKY65, and ABT4/WRKY69in transgenic plants caused insensitivity to HT, whereas the quadruple mutant abt1 abt2 abt3 abt4 exhibited greater sensitivity to HT. ABTs were expressed in hypocotyls, cotyledons, shoot apical meristems, and leaves, but their expression were suppressed by HT. Biochemical assays showed that ABT1 can interact with TCP5, a known positive regulator of PIF4, and interrupt the formation of the TCP5-PIF4 complex and repress its transcriptional activation activity. Genetic analysis showed that ABT1 functioned antagonistically with TCP5, BZR1, and PIF4 in plant thermomorphogenesis. Taken together, our results identify ABT1/WRKY14 as a critical repressor of plant thermomorphogenesis and suggest that ABT1/WRKY14, TCP5, and PIF4 may form a sophisticated regulatory module to fine-tune PIF4 activity and temperature-dependent plant growth.

Comprehensive Genomic Survey, Structural Classification, and Expression Analysis of WRKY Transcription Factor Family in Rhododendron simsii

(1) Rhododendron is one of the top ten traditional flowers in China, with both high ornamental and economic values. However, with the change of the environment, Rhododendron suffers from various biological stresses. The WRKY transcription factor is a member of the most crucial transcription factor families, which plays an essential regulatory role in a variety of physiological processes and developmental stresses. (2) In this study, 57 RsWRKYs were identified using genome data and found to be randomly distributed on 13 chromosomes. Based on gene structure and phylogenetic relationships, 57 proteins were divided into three groups: I, II, and III. Multiple alignments of RsWRKYs with Arabidopsis thaliana homologous genes revealed that WRKY domains in different groups had different conserved sites. RsWRKYs have a highly conserved domain, WRKYGQK, with three variants, WRKYGKK, WRKYGEK, and WRKYGRK. Furthermore, cis-acting elements analysis revealed that all of the RsWRKYs had stress and plant hormone cis-elements, with figures varying by group. Finally, the expression patterns of nine WRKY genes treated with gibberellin acid (GA), methyl jasmonate (MeJA), heat, and drought in Rhododendron were also measured using quantitative real-time PCR (qRT-PCR). The results showed that the expression levels of the majority of RsWRKY genes changed in response to multiple phytohormones and abiotic stressors. (3) This current study establishes a theoretical basis for future studies on the response of RsWRKY transcription factors to various hormone and abiotic stresses as well as a significant foundation for the breeding of new stress-tolerant Rhododendron varieties.

WRKY transcription factor family in lettuce plant (Lactuca sativa): Genome-wide characterization, chromosome location, phylogeny structures, and expression patterns

WRKY transcription factors (TF) have been identified in many plant species and play critical roles in multiple stages of growth and development and under various stress conditions. As one of the most popular vegetable crops, asparagus lettuce has important medicinal and nutritional value. However, study of WRKY TFs family in asparagus lettuce is limited. With the lettuce (Lactuca sativa L.) genome publication, we identified 76 WRKY TFs and analyzed structural characteristics, phylogenetic relationships, chromosomal distribution, interaction network, and expression profiles. The 76 LsWRKY TFs were phylogenetically classified as Groups I, II (IIa-IIe), and III. Cis element analysis revealed complex regulatory relationships of LsWRKY genes in response to different biological progresses. Interaction network analysis indicated that LsWRKY TFs could interact with other proteins, such as SIB (sigma factor binding protein), WRKY TFs, and MPK. The WRKYIII subfamily genes showed different expression patterns during the progress of asparagus lettuce stem enlargement. According to qRT-PCR analysis, abiotic stresses (drought, salt, low temperature, and high temperature) and phytohormone treatment could induce specific LsWRKYIII gene expression. These results will provide systematic and comprehensive information on LsWRKY TFs and lay the foundation for further clarification of the regulatory mechanism of LsWRKY, especially LsWRKYIII TFs, involved in stress response and the progress of plant growth and development.

Gene Networks Involved in Plant Heat Stress Response and Tolerance

Global warming is an environmental problem that cannot be ignored. High temperatures seriously affect the normal growth and development of plants, and threaten the development of agriculture and the distribution and survival of species at risk. Plants have evolved complex but efficient mechanisms for sensing and responding to high temperatures, which involve the activation of numerous functional proteins, regulatory proteins, and non-coding RNAs. These mechanisms consist of large regulatory networks that regulate protein and RNA structure and stability, induce Ca²⁺ and hormone signal transduction, mediate sucrose and water transport, activate antioxidant defense, and maintain other normal metabolic pathways. This article reviews recent research results on the molecular mechanisms of plant response to high temperatures, highlighting future directions or strategies for promoting plant heat tolerance, thereby helping to identify the regulatory mechanisms of heat stress responses in plants.

Identification of WRKY transcription factor family genes in Pinus massoniana Lamb. and their expression patterns and functions in response to drought stress

BACKGROUND

Pinus massoniana Lamb. is the timber species with the widest distribution and the largest afforestation area in China, providing a large amount of timber, turpentine and ecological products. Seasonal drought caused by climate warming severely constrains the quality and growth of P. massoniana forests. WRKY transcription factors play an important role in plant responses to abiotic stress. In this study, the molecular mechanisms by which P. massoniana responds to drought stress were analysed based on the P. massoniana WRKY (PmWRKY) family of genes.

RESULTS

Forty-three PmWRKYs are divided into three major families, 7 sub-families, and the conserved motifs are essentially the same. Among these 43 PmWRKYs express under drought stress but with different expression patterns in response to stress. PmWRKYs respond to drought stress induced by exogenous hormones of SA, ABA, and MeJA. The expression of PmWRKY6, PmWRKY10, and PmWRKY30 up-regulate in different families and tissues under drought stress, while PmWRKY22 down-regulate. Transgenetic tobaccos of PmWRKY31 are with lower malondialdehyde (MDA) content and higher proline (Pro) content than wild type (WT) tobaccos. In transgenic tobaccos of PmWRKY31, expression levels of related genes significantly improve, and drought tolerance enhance.

CONCLUSIONS

This study analysed the molecular biological characteristics of PmWRKYs and investigated the expression patterns and functions of PmWRKYs in response to drought stress in P. massoniana. The results of this study provide a basis for in-depth research of the molecular functions of PmWRKYs in response to drought stress.

Lily WRKY factor LlWRKY22 promotes thermotolerance through autoactivation and activation of LlDREB2B

Most of WRKY transcription factors play important roles in plant development, protection against disease, and response to abiotic stress; however, their roles in lily are largely unknown. Transcriptome analysis in lily (Lilium longiflorum) led to the identification and isolation of a WRKY-IIe gene, LlWRKY22, which was found to be activated at high temperature and play a positive role in thermotolerance regulation. LlWRKY22 expression was continuously activated by heat stress. We further found that LlWRKY22 protein localized to the nucleus and exhibited transactivation activity in both yeast and plant cells, and that its C terminus contributed to its transactivation activity. Meanwhile, overexpression of LlWRKY22 in lily improved thermotolerance and activated the expression of heat-related LlDREB2B gene; however, silencing of LlWRKY22 exerted the opposite effects. Further analysis revealed that LlWRKY22 directly activated the expression of LlDREB2B by binding to two tandem W-box elements on its promoter. Simultaneously, we also found that LlWRKY22 can directly bind its own promoter, thereby activating its own expression and forming a positive regulatory loop. Combined, our findings demonstrated that LlWRKY22 may be a new regulator of heat stress response and positively participates in the establishment of thermotolerance by activating itself and LlDREB2B.

Overexpression of NDR1 leads to pathogen resistance at elevated temperatures

Abiotic and biotic environments influence a myriad of plant-related processes, including growth, development, and the establishment and maintenance of interaction(s) with microbes. In the case of the latter, elevated temperature has been shown to be a key factor that underpins host resistance and pathogen virulence. In this study, we elucidate a role for Arabidopsis NON-RACE-SPECIFIC DISEASE RESISTANCE1 (NDR1) by exploiting effector-triggered immunity to define the regulation of plant host immunity in response to both pathogen infection and elevated temperature. We generated time-series RNA sequencing data of WT Col-0, an NDR1 overexpression line, and ndr1 and ics1-2 mutant plants under elevated temperature. Not surprisingly, the NDR1-overexpression line showed genotype-specific gene expression changes related to defense response and immune system function. The results described herein support a role for NDR1 in maintaining cell signaling during simultaneous exposure to elevated temperature and avirulent pathogen stressors.

Heterologous Expression of MfWRKY7 of Resurrection Plant Myrothamnus flabellifolia Enhances Salt and Drought Tolerance in Arabidopsis

Drought and salinity have become major environmental problems that affect the production of agriculture, forestry and horticulture. The identification of stress-tolerant genes from plants adaptive to harsh environments might be a feasible strategy for plant genetic improvement to address the challenges brought by global climate changes. In this study, a dehydration-upregulated gene MfWRKY7 of resurrection Plant Myrothamnusflabellifolia, encoding a group IId WRKY transcription factor, was cloned and characterized. The overexpression of MfWRKY7 in Arabidopsis increased root length and tolerance to drought and NaCl at both seedling and adult stages. Further investigation indicated that MfWRKY7 transgenic plants had higher contents of chlorophyll, proline, soluble protein, and soluble sugar but a lower water loss rate and malondialdehyde content compared with wild-type plants under both drought and salinity stresses. Moreover, the higher activities of antioxidant enzymes and lower accumulation of O₂⁻ and H₂O₂ in MfWRKY7 transgenic plants were also found, indicating enhanced antioxidation capacity by MfWRKY7. These findings showed that MfWRKY7 may function in positive regulation of responses to drought and salinity stresses, and therefore, it has potential application value in genetic improvement of plant tolerance to abiotic stress.

The WRKY10-VQ8 module safely and effectively regulates rice thermotolerance

WRKY transcription factors (TFs) play crucial roles in biotic and abiotic stress responses. However, their roles in thermal response are still largely elusive, especially in rice. In this study, we revealed the functions of WRKY10 TF and VQ8 protein containing VQ motif in rice thermotolerance. Overexpression of WRKY10 or loss of VQ8 function increases thermosensitivity, whereas conversely, overexpression of VQ8 or loss of WRKY10 function enhances thermotolerance. Overexpression of WRKY10 accelerates reactive oxygen species (ROS) accumulation in chloroplasts and apoplasts, and it also induces the expression of heat shock TF and protein genes. We also found that WRKY10 regulates nuclear DNA fragmentation and hypersensitive response by modulating NAC4 TF expression. The balance between destructive and protective responses in WRKY10-overexpression plant is more fragile and more easily broken by heat stress compared with wild type. In vitro and in vivo assays revealed that VQ8 interacts with WRKY10 and inhibits the transcription activity via repressing its DNA-binding activity. Our study demonstrates that WRKY10 negatively regulates thermotolerance by modulating the ROS balance and the hypersensitive response and that VQ8 functions antagonistically to positively regulate thermotolerance. The functional module of WRKY10-VQ8 provides safe and effective regulatory mechanisms in the heat stress response.

Transcriptome Analysis Reveals the Response Mechanism of Frl-Mediated Resistance to Fusarium oxysporum f. sp. radicis-lycopersici (FORL) Infection in Tomato

Tomato Fusarium crown and root rot (FCRR) is an extremely destructive soil-borne disease. To date, studies have shown that only plants with tomato mosaic virus (TMV) resistance exhibit similar resistance to tomato Fusarium oxysporum f. sp. radicis-lycopersici (FORL) and have identified a single relevant gene, Frl, in Peruvian tomato. Due to the relative lack of research on FCRR disease-resistance genes in China and elsewhere, transcriptome data for FORL-resistant (cv. ‘19912’) and FORL-susceptible (cv. ‘Moneymaker’) tomato cultivars were analysed for the first time in this study. The number of differentially expressed genes (DEGs) was higher in Moneymaker than in 19912, and 189 DEGs in the ‘plant–pathogen interaction’ pathway were subjected to GO and KEGG enrichment analyses. MAPK and WRKY genes were enriched in major metabolic pathways related to plant disease resistance; thus, we focused on these two gene families. In the early stage of tomato infection, the content of JA and SA increased, but the change in JA was more obvious. Fourteen genes were selected for confirmation of their differential expression levels by qRT-PCR. This study provides a series of novel disease resistance resources for tomato breeding and genetic resources for screening and cloning FORL resistance genes.