The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis

Integrated transcriptomic and metabolomic analyses of yellow horn (Xanthoceras sorbifolia) in response to cold stress

Xanthoceras sorbifolia, a medicinal and oil-rich woody plant, has great potential for biodiesel production. However, little study explores the link between gene expression level and metabolite accumulation of X. sorbifolia in response to cold stress. Herein, we performed both transcriptomic and metabolomic analyses of X. sorbifolia seedlings to investigate the regulatory mechanism of resistance to low temperature (4 °C) based on physiological profile analyses. Cold stress resulted in a significant increase in the malondialdehyde content, electrolyte leakage and activity of antioxidant enzymes. A total of 1,527 common differentially expressed genes (DEGs) were identified, of which 895 were upregulated and 632 were downregulated. Annotation of DEGs revealed that amino acid metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, galactose metabolism, fructose and mannose metabolism, and the citrate cycle (TCA) were strongly affected by cold stress. In addition, DEGs within the plant mitogen-activated protein kinase (MAPK) signaling pathway and TF families of ERF, WRKY, NAC, MYB, and bHLH were transcriptionally activated. Through metabolomic analysis, we found 51 significantly changed metabolites, particularly with the analysis of primary metabolites, such as sugars, amino acids, and organic acids. Moreover, there is an overlap between transcript and metabolite profiles. Association analysis between key genes and altered metabolites indicated that amino acid metabolism and sugar metabolism were enhanced. A large number of specific cold-responsive genes and metabolites highlight a comprehensive regulatory mechanism, which will contribute to a deeper understanding of the highly complex regulatory program under cold stress in X. sorbifolia.

Transcriptomic Profiling of Young Cotyledons Response to Chilling Stress in Two Contrasting Cotton (Gossypium hirsutum L.) Genotypes at the Seedling Stage

Young cotyledons of cotton seedlings are most susceptible to chilling stress. To gain insight into the potential mechanism of cold tolerance of young cotton cotyledons, we conducted physiological and comparative transcriptome analysis of two varieties with contrasting phenotypes. The evaluation of chilling injury of young cotyledons among 74 cotton varieties revealed that H559 was the most tolerant and YM21 was the most sensitive. The physiological analysis found that the ROS scavenging ability was lower, and cell membrane damage was more severe in the cotyledons of YM21 than that of H559 under chilling stress. RNA-seq analysis identified a total of 44,998 expressed genes and 19,982 differentially expressed genes (DEGs) in young cotyledons of the two varieties under chilling stress. Weighted gene coexpression network analysis (WGCNA) of all DEGs revealed four significant modules with close correlation with specific samples. The GO-term enrichment analysis found that lots of genes in H559-specific modules were involved in plant resistance to abiotic stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that pathways such as plant hormone signal transduction, MAPK signaling, and plant–pathogen interaction were related to chilling stress response. A total of 574 transcription factors and 936 hub genes in these modules were identified. Twenty hub genes were selected for qRT-PCR verification, revealing the reliability and accuracy of transcriptome data. These findings will lay a foundation for future research on the molecular mechanism of cold tolerance in cotyledons of cotton.

Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom®CicerSNP Array in Chickpea

Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom^®CicerSNP array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance.

E2 conjugases UBC1 and UBC2 regulate MYB42-mediated SOS pathway in response to salt stress in Arabidopsis

Histone H2B monoubiquitination (H2Bub1) is recognized as a crucial eukaryotic regulatory mechanism that controls a range of cellular processes during both development and adaptation to environmental changes. In Arabidopsis, the E2 conjugated enzymes UBIQUITIN CARRIER PROTEINs (UBCs) -1 and -2 mediate ubiquitination of H2B. Here, we elucidated the functions of UBC1 and -2 in salt-stress responses and revealed their downstream target genes. Real-time quantitative PCR assays showed that UBC1 and -2 positively regulated the salt-induced expression of MYB42 and Mitogen-Activated Protein Kinase 4 (MPK4). Chromatin immunoprecipitation assays revealed that H2Bub1 was enriched weakly on the chromatin of MYB42 and MPK4 in the ubc1,2 mutant. We further determined that UBC1/2-mediated H2Bub1 enhanced the level of histone H3 tri-methylated on K4 (H3K4me3) in the chromatin of MYB42 and MPK4 under salt-stress conditions. MPK4 interacted with and phosphorylated MYB42. The MPK4-mediated MYB42 phosphorylation enhanced the MYB42 protein stability and transcriptional activity under salt-stress conditions. We further showed that MYB42 directly bound to the SALT OVERLY SENSITIVE 2 (SOS2) promoter and mediated the rapid induction of its expression after a salt treatment. Our results indicate that UBC1 and -2 positively regulate salt-stress responses by modulating MYB42-mediated SOS2 expression.

A leucine-rich repeat receptor-like kinase, OsSTLK, modulates salt tolerance in rice

Leucine-rich repeat receptor-like kinases (LRR-RLKs) have been widely associated with plant abiotic stress responses. However, the functions of the majority of LRR-RLKs has not been well defined. Here, we identified a novel rice LRR-RLK member involved in salt tolerance and designated as OsSTLK (Oryza sativa L. Salt-Tolerance LRR-RLK). Transcript analysis showed that OsSTLK was significantly induced in response to salt stress in rice shoot and root in a time and dosage-dependent fashion. Phenotypic observations indicated that OsSTLK overexpression exhibited reduced salt sensitivity, and improved salt stress tolerance. Further physiological analysis showed that OsSTLK overexpression remarkably reduced electrolyte leakage, malondialdehyde (MDA) content, reactive oxygen species (ROS) accumulation under salt stress conditions by up-regulating ROS-scavenging activities and modifying stomatal patterning. Moreover, Na⁺/K⁺ ratio and MAPK phosphorylation level were also reduced in OsSTLK-overexpression transgenic rice plants compared with WT control. Taken together, our findings suggested that OsSTLK as an important positive regulator of salt stress tolerance perhaps through regulating ROS scavenging system, Na⁺/K⁺ ratio and MAPK signal pathway.

MEKK2 inhibits activation of MAP kinases in Arabidopsis

The Arabidopsis MEKK1-MKK1/MKK2-MPK4 kinase cascade is monitored by the nucleotide-binding leucine-rich-repeat immune receptor SUMM2. Disruption of this kinase cascade leads to activation of SUMM2-mediated immune responses. MEKK2, a close paralog of MEKK1, is required for defense responses mediated by SUMM2, the molecular mechanism of which is unclear. In this study, we showed that MEKK2 serves as a negative regulator of MPK4. It binds to MPK4 to directly inhibit its phosphorylation by upstream MKKs. Activation of SUMM2-mediated defense responses induces the expression of MEKK2, which in turn blocks MPK4 phosphorylation to further amplify immune responses mediated by SUMM2. Intriguingly, MEKK2 locates in a tandem repeat consisting of MEKK1, MEKK2 and MEKK3, which was generated from a recent gene duplication event, suggesting that MEKK2 evolved from a MAPKKK to become a negative regulator of MAP kinases.

Mechanisms of Plant Responses and Adaptation to Soil Salinity

Soil salinity is a major environmental stress that restricts the growth and yield of crops. Understanding the physiological, metabolic, and biochemical responses of plants to salt stress and mining the salt tolerance-associated genetic resource in nature will be extremely important for us to cultivate salt-tolerant crops. In this review, we provide a comprehensive summary of the mechanisms of salt stress responses in plants, including salt stress-triggered physiological responses, oxidative stress, salt stress sensing and signaling pathways, organellar stress, ion homeostasis, hormonal and gene expression regulation, metabolic changes, as well as salt tolerance mechanisms in halophytes. Important questions regarding salt tolerance that need to be addressed in the future are discussed.

Cloning, molecular and functional characterization by overexpression in Arabidopsis of MAPKK genes from grapevine (Vitis vinifera)

BACKGROUND

The mitogen-activated protein kinases (MAPKs), as a part of the MAPKKK-MAPKK-MAPK cascade, play crucial roles in plant development as an intracellular signal transduction pathway to respond various environmental signals. However, few MAPKK have been functionally characterized in grapevine.

RESULTS

In the study, five MAPKK (MKK) members were identified in grapevine (cultivar 'Pinot Noir'), cloned and designated as VvMKK1-VvMKK5. A phylogenetic analysis grouped them into four sub-families based on the similarity of their conserved motifs and gene structure to Arabidopsis MAPKK members. qRT-PCR results indicated that the expression of VvMKK1, VvMKK2, VvMKK4, and VvMKK5 were up-regulated in mature leaf and young blades, and roots, but exhibited low expression in leaf petioles. VvMKK2, VvMKK3, and VvMKK5 genes were differentially up-regulated when grapevine leaves were inoculated with spores of Erisyphe necator, or treated with salicylic acid (SA), ethylene (ETH), H2O2, or exposed to drought, indicating that these genes may be involved in a variety of signaling pathways. Over expression of VvMKK2 and VvMKK4 genes in transgenic Arabidopsis plants resulted in the production of seeds with a significantly higher germination and survival rate, and better seedling growth under stress conditions than wild-type plants. Overexpression of VvMKK2 in Arabidopsis improved salt and drought stress tolerance while overexpression of VvMKK4 only improved salt stress tolerance.

CONCLUSIONS

Results of the present investigation provide a better understanding of the interaction and function of MAPKKK-MAPKK-MAPK genes at the transcriptional level in grapevine and led to the identification of candidate genes for drought and salt stress in grapes.

Genome-wide identification of MAPK cascade genes reveals the GhMAP3K14-GhMKK11-GhMPK31 pathway is involved in the drought response in cotton

The mitogen-activated protein kinase (MAPK) cascade pathway, which has three components, MAP3Ks, MKKs and MPKs, is involved in diverse biological processes in plants. In the current study, MAPK cascade genes were identified in three cotton species, based on gene homology with Arabidopsis. Selection pressure analysis of MAPK cascade genes revealed that purifying selection occurred among the cotton species. Expression pattern analysis showed that some MAPK cascade genes differentially expressed under abiotic stresses and phytohormones treatments, and especially under drought stress. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) experiments showed extensive interactions between different MAPK cascade proteins. Virus-induced gene silencing (VIGS) assays showed that some MAPK cascade modules play important roles in the drought stress response, and the GhMAP3K14-GhMKK11-GhMPK31 signal pathway was demonstrated to regulate drought stress tolerance in cotton. This study provides new information on the function of MAPK cascade genes in the drought response, and will help direct molecular breeding for improved drought stress tolerance in cotton.

Transcriptome profiling reveals the crucial biological pathways involved in cold response in Moso bamboo (Phyllostachys edulis)

Most bamboo species including Moso bamboo (Phyllostachys edulis) are tropical or subtropical plants that greatly contribute to human well-being. Low temperature is one of the main environmental factors restricting bamboo growth and geographic distribution. Our knowledge of the molecular changes during bamboo adaption to cold stress remains limited. Here, we provided a general overview of the cold-responsive transcriptional profiles in Moso bamboo by systematically analyzing its transcriptomic response under cold stress. Our results showed that low temperature induced strong morphological and biochemical alternations in Moso bamboo. To examine the global gene expression changes in response to cold, 12 libraries (non-treated, cold-treated 0.5, 1 and 24 h at -2 °C) were sequenced using an Illumina sequencing platform. Only a few differentially expressed genes (DEGs) were identified at early stage, while a large number of DEGs were identified at late stage in this study, suggesting that the majority of cold response genes in bamboo are late-responsive genes. A total of 222 transcription factors from 24 different families were differentially expressed during 24-h cold treatment, and the expressions of several well-known C-repeat/dehydration responsive element-binding factor negative regulators were significantly upregulated in response to cold, indicating the existence of special cold response networks. Our data also revealed that the expression of genes related to cell wall and the biosynthesis of fatty acids were altered in response to cold stress, indicating their potential roles in the acquisition of bamboo cold tolerance. In summary, our studies showed that both plant kingdom-conserved and species-specific cold response pathways exist in Moso bamboo, which lays the foundation for studying the regulatory mechanisms underlying bamboo cold stress response and provides useful gene resources for the construction of cold-tolerant bamboo through genetic engineering in the future.

Salt-Induced Stability of SR1/CAMTA3 mRNA Is Mediated by Reactive Oxygen Species and Requires the 3' End of Its Open Reading Frame

Soil salinity, a prevalent abiotic stress, causes enormous losses in global crop yields annually. Previous studies have shown that salt stress-induced reprogramming of gene expression contributes to the survival of plants under this stress. However, mechanisms regulating gene expression in response to salt stress at the posttranscriptional level are not well understood. In this study, we show that salt stress increases the level of Signal Responsive 1 (SR1) mRNA, a member of signal-responsive Ca2+/calmodulin-regulated transcription factors, by enhancing its stability. We present multiple lines of evidence indicating that reactive oxygen species generated by NADPH oxidase activity mediate salt-induced SR1 transcript stability. Using mutants impaired in either nonsense-mediated decay, XRN4 or mRNA decapping pathways, we show that neither the nonsense-mediated mRNA decay pathway, XRN4 nor the decapping of SR1 mRNA is required for its decay. We analyzed the salt-induced accumulation of eight truncated versions of the SR1 coding region (∼3 kb) in the sr1 mutant background. This analysis identified a 500-nt region at the 3' end of the SR1 coding region to be required for the salt-induced stability of SR1 mRNA. Potential mechanisms by which this region confers SR1 transcript stability in response to salt are discussed.

The transcription factor ICE1 functions in cold stress response by binding to the promoters of CBF and COR genes

A recent paper by Kidokoro et al. (2020) in The Plant Cell reported a transgene-dependent transcriptional silencing phenomenon in the dominant ice1-1 Arabidopsis mutant containing the CBF3-LUC reporter, and questioned whether ICE1 may regulate CBF genes and may be involved in plant cold response. Here, we evaluate available evidence supporting the involvement of ICE1 in plant cold response, and provide ChIP-seq data showing ICE1 binding to the promoters of CBF genes and other regulatory genes known to be critical for cold response as well as to the promoters of some COR genes.

NADPH Oxidases: The Vital Performers and Center Hubs during Plant Growth and Signaling

NADPH oxidases (NOXs), mostly known as respiratory burst oxidase homologs (RBOHs), are the key producers of reactive oxygen species (ROS) in plants. A lot of literature has addressed ROS signaling in plant development regulation and stress responses as well as on the enzyme's structure, evolution, function, regulation and associated mechanisms, manifesting the role of NOXs/RBOHs as the vital performers and center hubs during plant growth and signaling. This review focuses on recent advances of NOXs/RBOHs on cell growth, hormone interaction, calcium signaling, abiotic stress responses, and immunity. Several primary particles, including Ca2+, CDPKs, BIK1, ROPs/RACs, CERK, FER, ANX, SnRK and SIK1-mediated regulatory mechanisms, are fully summarized to illustrate the signaling behavior of NOXs/RBOHs and their sophisticated and dexterous crosstalks. Diverse expression and activation regulation models endow NOXs/RBOHs powerful and versatile functions in plants to maintain innate immune homeostasis and development integrity. NOXs/RBOHs and their related regulatory items are the ideal targets for crop improvement in both yield and quality during agricultural practices.

Biological impacts of phosphomimic AtMYB75

The phosphorylation status of MYB75 at T-131 affects protein stability, flavonoid profiles, and patterns of gene expression. The Arabidopsis transcription factor Myeloblastosis protein 75 (MYB75, AT1G56650) is known to act as a positive transcriptional regulator of genes required for flavonoid and anthocyanin biosynthesis. MYB75 was also shown to negatively regulate lignin and other secondary cell wall biosynthetic genes (Bhargava et al. in Plant Physiol 154(3):1428-1438, 2010). While transcriptional regulation of MYB75 has been described in numerous publications, little is known about post-translational control of MYB75 protein function. In a recent publication, light-induced activation of a MAP kinase (MPK4, AT4G01370) in Arabidopsis was reported to lead to MYB75 phosphorylation at two canonical MPK target sites, threonines, T-126 and T-131. This double phosphorylation event positively influenced MYB75 protein stability (Li et al. in Plant Cell 28(11):2866-2883, 2016). We have examined this phenomenon through use of phosphomutant forms of MYB75 and found that MYB75 is phosphorylated primarily at T-131, and that the phosphorylation of MYB75 recombinant protein in vitro can be catalyzed by multiple MAP kinases, including MPK3 (AT3G45640), MPK6 (AT2G43790), MPK4 and MPK11 (AT1G01560). We also demonstrate that MYB75 can bind to a large number of Arabidopsis MPK's in vitro, suggesting it could be a target of multiple signalling pathways. The impact of MYB75 phosphorylation at T-131 on the function of this transcription factor, in terms of localization, stability, and protein-protein interactions with known binding partners was examined in transgenic lines expressing phosphomimic and phosphonull versions of MYB75, to capture the behaviour of permanently phosphorylated and unphosphorylated MYB75 protein, respectively. In addition, we describe how ectopic over-expression of different phosphovariant forms of MYB75 (MYB75^WT, MYB75^T131A, and MYB75^T131E) affects flavonoid biochemical profiles and global changes of gene expression in the corresponding transgenic Arabidopsis plants.

Salinity tolerance in barley during germination- homologs and potential genes

Salinity affects more than 6% of the world's total land area, causing massive losses in crop yield. Salinity inhibits plant growth and development through osmotic and ionic stresses; however, some plants exhibit adaptations through osmotic regulation, exclusion, and translocation of accumulated Na+ or Cl-. Currently, there are no practical, economically viable methods for managing salinity, so the best practice is to grow crops with improved tolerance. Germination is the stage in a plant's life cycle most adversely affected by salinity. Barley, the fourth most important cereal crop in the world, has outstanding salinity tolerance, relative to other cereal crops. Here, we review the genetics of salinity tolerance in barley during germination by summarizing reported quantitative trait loci (QTLs) and functional genes. The homologs of candidate genes for salinity tolerance in Arabidopsis, soybean, maize, wheat, and rice have been blasted and mapped on the barley reference genome. The genetic diversity of three reported functional gene families for salt tolerance during barley germination, namely dehydration-responsive element-binding (DREB) protein, somatic embryogenesis receptor-like kinase and aquaporin genes, is discussed. While all three gene families show great diversity in most plant species, the DREB gene family is more diverse in barley than in wheat and rice. Further to this review, a convenient method for screening for salinity tolerance at germination is needed, and the mechanisms of action of the genes involved in salt tolerance need to be identified, validated, and transferred to commercial cultivars for field production in saline soil.

Mapping proteome-wide targets of protein kinases in plant stress responses

Protein kinases are major regulatory components in almost all cellular processes in eukaryotic cells. By adding phosphate groups, protein kinases regulate the activity, localization, protein-protein interactions, and other features of their target proteins. It is known that protein kinases are central components in plant responses to environmental stresses such as drought, high salinity, cold, and pathogen attack. However, only a few targets of these protein kinases have been identified. Moreover, how these protein kinases regulate downstream biological processes and mediate stress responses is still largely unknown. In this study, we introduce a strategy based on isotope-labeled in vitro phosphorylation reactions using in vivo phosphorylated peptides as substrate pools and apply this strategy to identify putative substrates of nine protein kinases that function in plant abiotic and biotic stress responses. As a result, we identified more than 5,000 putative target sites of osmotic stress-activated SnRK2.4 and SnRK2.6, abscisic acid-activated protein kinases SnRK2.6 and casein kinase 1-like 2 (CKL2), elicitor-activated protein kinase CDPK11 and MPK6, cold-activated protein kinase MPK6, H₂O₂-activated protein kinase OXI1 and MPK6, and salt-induced protein kinase SOS1 and MPK6, as well as the low-potassium-activated protein kinase CIPK23. These results provide comprehensive information on the role of these protein kinases in the control of cellular activities and could be a valuable resource for further studies on the mechanisms underlying plant responses to environmental stresses.

Dynamic Phosphoproteome Profiling of Zebrafish Embryonic Fibroblasts during Cold Acclimation

Temperature affects almost all aspects of the fish life. To cope with low temperature, fish have evolved the ability of cold acclimation for survival. However, intracellular signaling events underlying cold acclimation in fish remain largely unknown. Here, the formation of cold acclimation in zebrafish embryonic fibroblasts (ZF4) is monitored and the phosphorylation events during the process are investigated through a large-scale quantitative phosphoproteomic approach. In total, 11 474 phosphorylation sites are identified on 4066 proteins and quantified 5772 phosphosites on 2519 proteins. Serine, threonine, and tyrosine (Ser/Thr/Tyr) phosphorylation accounted for 85.5%, 13.3%, and 1.2% of total phosphosites, respectively. Among all phosphosites, 702 phosphosites on 510 proteins show differential regulation during cold acclimation of ZF4 cells. These phosphosites are divided into six clusters according to their dynamic changes during cold exposure. Kinase-substrate prediction reveals that mitogen-activated protein kinase (MAPK) among the kinase groups is predominantly responsible for phosphorylation of these phosphosites. The differentially regulated phosphoproteins are functionally associated with various cellular processes such as regulation of actin cytoskeleton and MAPK signaling pathway. These data enrich the database of protein phosphorylation sites in zebrafish and provide key clues for the elucidation of intracellular signaling networks during cold acclimation of fish.

In-depth proteome analysis reveals multiple pathways involved in tomato SlMPK1-mediated high-temperature responses

High temperature (HT) is one of the major environmental factors which limits plant growth and yield. The mitogen-activated protein kinase (MAPK) plays vital roles in environmental stress responses. However, the mechanisms triggered by MAPKs in plants in response to HT are still extremely limited. In this study, the proteomic data of differences between SlMPK1 RNA-interference mutant (SlMPK1i) and wild type and of tomato (Solanum lycopersicum) plants under HT stress using isobaric tags for relative and absolute quantitation (iTRAQ) was re-analyzed in depth. In total, 168 differently expressed proteins (DEPs) were identified in response to HT stress, including 38 DEPs only found in wild type, and 84 DEPs specifically observed in SlMPK1i after HT treatment. The majority of higher expression of 84 DEPs were annotated into photosynthesis, oxidation-reduction process, protein folding, translation, proteolysis, stress response, and amino acid biosynthetic process. More importantly, SlMPK1-mediated photosynthesis was confirmed by the physiological characterization of SlMPK1i with a higher level of photosynthetic capacity under HT stress. Overall, the results reveal a set of potential candidate proteins helping to further understand the intricate regulatory network regulated by SlMPK1 in response to HT.

Dormant but Active: Chilling Accumulation Modulates the Epigenome and Transcriptome of Prunus avium During Bud Dormancy

Temperate deciduous fruit tree species like sweet cherry (Prunus avium) require long periods of low temperatures to trigger dormancy release and flowering. In addition to sequence-based genetic diversity, epigenetic variation may contribute to different chilling requirements among varieties. For the low chill variety 'Royal Dawn' and high chill variety 'Kordia', we studied the methylome of floral buds during chilling accumulation using MethylC-seq to identify differentially methylated regions (DMRs) during chilling hours (CH) accumulation, followed by transcriptome analysis to correlate changes in gene expression with DNA methylation. We found that during chilling accumulation, DNA methylation increased from 173 CH in 'Royal Dawn' and 443 CH in 'Kordia' and was mostly associated with the CHH context. In addition, transcriptional changes were observed from 443 CH in 'Kordia' with 1,210 differentially expressed genes, increasing to 4,292 genes at 1,295 CH. While 'Royal Dawn' showed approximately 5,000 genes differentially expressed at 348 CH and 516 CH, showing a reprogramming that was specific for each genotype. From conserved upregulated genes that overlapped with hypomethylated regions and downregulated genes that overlapped with hypermethylated regions in both varieties, we identified genes related to cold-sensing, cold-signaling, oxidation-reduction process, metabolism of phenylpropanoids and lipids, and a MADS-box SVP-like gene. As a complementary analysis, we used conserved and non-conserved DEGs that presented a negative correlation between DNA methylations and mRNA levels across all chilling conditions, obtaining Gene Ontology (GO) categories related to abiotic stress, metabolism, and oxidative stress. Altogether, this data indicates that changes in DNA methylation precedes transcript changes and may occur as an early response to low temperatures to increase the cold tolerance in the endodormancy period, contributing with the first methylome information about the effect of environmental cues over two different genotypes of sweet cherry.

A bHLH transcription factor, MYC2, imparts salt intolerance by regulating proline biosynthesis in Arabidopsis

MYC2, a bHLH TF, acts as regulatory hub within several signaling pathways by integration of various endogenous and exogenous signals which shape plant growth and development. However, its involvement in salt stress regulation is still elusive. This study has deciphered a novel role of MYC2 in imparting salt stress intolerance by regulating delta1 -pyrroline-5-carboxylate synthase1 (P5CS1) gene and hence proline synthesis. P5CS1 is a rate-limiting enzyme in the biosynthesis of proline. Y-1-H and EMSA studies confirmed the binding of MYC2 with the 5'UTR region of P5CS1. Transcript and biochemical studies have revealed MYC2 as a negative regulator of proline biosynthesis. Proline is necessary for imparting tolerance toward abiotic stress; however, its overaccumulation is toxic for the plants. Hence, studying the regulation of proline biosynthesis is requisite to understand the mechanism of stress tolerance. We have also studied that MYC2 is regulated by mitogen-activated protein kinase (MAPK) cascade mitogen-activated protein kinase kinase 3-MPK6 and vice versa. Altogether, this study demonstrates salt stress-mediated activation of MYC2 by MAPK cascade, regulating proline biosynthesis and thus salt stress.

HTRgene: a computational method to perform the integrated analysis of multiple heterogeneous time-series data: case analysis of cold and heat stress response signaling genes in Arabidopsis

Background

Integrated analysis that uses multiple sample gene expression data measured under the same stress can detect stress response genes more accurately than analysis of individual sample data. However, the integrated analysis is challenging since experimental conditions (strength of stress and the number of time points) are heterogeneous across multiple samples.

Results

HTRgene is a computational method to perform the integrated analysis of multiple heterogeneous time-series data measured under the same stress condition. The goal of HTRgene is to identify “response order preserving DEGs” that are defined as genes not only which are differentially expressed but also whose response order is preserved across multiple samples. The utility of HTRgene was demonstrated using 28 and 24 time-series sample gene expression data measured under cold and heat stress in Arabidopsis. HTRgene analysis successfully reproduced known biological mechanisms of cold and heat stress in Arabidopsis. Also, HTRgene showed higher accuracy in detecting the documented stress response genes than existing tools.

Conclusions

HTRgene, a method to find the ordering of response time of genes that are commonly observed among multiple time-series samples, successfully integrated multiple heterogeneous time-series gene expression datasets. It can be applied to many research problems related to the integration of time series data analysis.

Phosphatidic acid promotes the activation and plasma membrane localization of MKK7 and MKK9 in response to salt stress

Phosphatidic acid (PA) is a lipid secondary messenger involved in intracellular signaling in eukaryotes. It has been confirmed that PA mediates salt stress signaling by promoting activation of Mitogen-activated Protein Kinase 6 (MPK6) which phosphorylates Na⁺/H⁺ antiporter SOS1. However, the MPK6-upstream kinases and their relationship to PA remain unclear. Here, we found that, among the six tested Arabidopsis Mitogen-activated Protein Kinase Kinases (MKKs), PA specifically bound to MKK7 and MKK9 which phosphorylate MPK6, and promoted the activation of MKK7/MKK9. Based on phenotypic and physiological analyses, we found that MKK7 and MKK9 positively regulate Arabidopsis salt tolerance and are functionally redundant. NaCl treatment can induce significant increase in MKK7/MKK9 activities, and this depends, in part, on the Phospholipase Dα1 (PLDα1). MKK7 and MKK9 also mediate the NaCl-induced activation of MPK6. Furthermore, PA or NaCl treatment could induce translocation of MKK7/MKK9 to the plasma membrane, whereas this translocation disappeared in pldα1. These results indicate that PA binds to MKK7 and MKK9, increases their kinase activity and plasma membrane localization during Arabidopsis response to salt stress. Together with the PA-MPK6-SOS1 pathway identified previously, this mechanism may maximize the signal transduction efficiency, providing novel insights into the link between lipid signaling and MAPK cascade.

Identifying S-nitrosylated proteins and unraveling S-nitrosoglutathione reductase-modulated sodic alkaline stress tolerance in Solanum lycopersicum L

S-nitrosylation, regulated by S-nitrosoglutathione reductase (GSNOR), is considered as an important route for nitric oxide (NO)-modulated stress tolerance in plants. However, genetic evidence for the GSNOR-mediated integrated regulation of S-nitrosylation and plant stress response remains elusive until now. In the present study, we used a site-specific nitrosoproteomic approach to identify 334 endogenously S-nitrosylated proteins with 425 S-nitrosylated sites from the wild type (WT) and GSNOR-knockdown (G) tomato plants under both control (C) and sodic alkaline stress (S) conditions. In detail, the results revealed 68, 92, 54 and 56 up-regulated, as well as 10, 36, 14 and 10 down-regulated S-nitrosylated proteins in G-C/WT-C, G-S/WT-S, WT-S/WT-C, and G-S/G-C, which is the first dataset for S-nitrosylated proteins in Solanaceae. These S-nitrosylated proteins are involved in a wide range of various metabolic, cellular and catalytic processes. Based on this data, proteins involving in NO homeostasis control, signaling of Ca²⁺, ethylene and MAPK, reactive oxygen species (ROS) scavenging, osmotic regulation, as well as energy support pathway have been identified and selected as the key and sensitive targets that were regulated by GSNOR-modulated S-nitrosylation in response to sodic alkaline stress. Taken together, GSNOR is actively involved in the regulation of sodic alkaline stress tolerance by S-nitrosylation. And the present study provided valuable resources and new clues for the study of S-nitrosylation-regulated metabolism in tomato plants.

Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis

BACKGROUND

Low temperature restricts the planting range of all crops, but cold acclimation induces adaption to cold stress in many plants. Camellia sinensis, a perennial evergreen tree that is the source of tea, is mainly grown in warm areas. Camellia sinensis var. sinensis (CSS) has greater cold tolerance than Camellia sinensis var. assamica (CSA). To gain deep insight into the molecular mechanisms underlying cold adaptation, we investigated the physiological responses and transcriptome profiles by RNA-Seq in two tea varieties, cold resistant SCZ (classified as CSS) and cold susceptible YH9 (classified as CSA), during cold acclimation.

RESULTS

Under freezing stress, lower relative electrical conductivity and higher chlorophyll fluorescence (Fv/Fm) values were detected in SCZ than in YH9 when subjected to freezing acclimation. During cold treatment, 6072 and 7749 DEGs were observed for SCZ and YH9, respectively. A total of 978 DEGs were common for both SCZ and YH9 during the entire cold acclimation process. DEGs were enriched in pathways of photosynthesis, hormone signal transduction, and transcriptional regulation of plant-pathogen interactions. Further analyses indicated that decreased expression of Lhca2 and higher expression of SnRK2.8 are correlated with cold tolerance in SCZ.

CONCLUSIONS

Compared with CSA, CSS was significantly more resistant to freezing after cold acclimation, and this increased resistance was associated with an earlier expression of cold-induced genes. Because the greater transcriptional differentiation during cold acclimation in SCZ may contribute to its greater cold tolerance, our studies identify specific genes involved in photoinhibition, ABA signal conduction, and plant immunity that should be studied for understanding the processes involved in cold tolerance. Marker-assisted breeding focused on the allelic variation at these loci provides an avenue for the possible generation of CSA cultivars that have CSS-level cold tolerance.

Role of calreticulin in biotic and abiotic stress signalling and tolerance mechanisms in plants

Calreticulin (CRT) is calcium binding protein of endoplasmic reticulum (ER) which performs plethora of functions besides it's role as molecular chaperone. Among the three different isoforms of this protein, CRT3 is most closely related to primitive CRT gene of higher plants. Based on their distinct structural and functional organisation, the plant CRTs have been known to contain three different domains: N, P and the C domain. The domain organisation and various biochemical characterstics of plant and animal CRTs are common with the exception of some differences. In plant calreticulin, the important N-glycosylation site(s) are replaced by the glycan chain(s) and several consensus sequences for in vitro phosphorylation by protein kinase CK2 (casein kinase-2), are also present unlike the animal calreticulin. Biotic and abiotic stresses play a significant role in bringing down the crop production. The role of various phytohormones in defense against fungal pathogens is well documented. CRT3 has been reported to play important role in protecting the plants against fungal and bacterial pathogens and in maintaining plant innate immunity. There is remarkable crosstalk between CRT mediated signalling and biotic, abiotic stress, and phytohormone mediated signalling pathways The role of CRT mediated pathway in mitigating biotic and abiotic stress can be further explored in plants so as to strategically modify it for development of stress tolerant plants.

Development of efficient protocol for rice transformation overexpressing MAP kinase and their effect on root phenotypic traits

Exhaustive studies on mitogen-activated protein kinase (MAPK) have reported the importance in regulating a variety of responses during plant growth and development. In particular, the potential MAPK genes, MPK3 and MPK6, seem to regulate a plethora of responses, conferring tolerance to varied abiotic, biotic, and developmental stimuli. This makes both MPK3 and MPK6 potential targets for further studies. It would be an important concern to overexpress and knock out these pivotal proteins and then, in turn, to monitor the plant response which is expected to correlate action of a gene to a trait in cellular and organismal contexts. However, overexpression of MAPK genes has remained a puzzle in plants. In the present study, we report the generation of stable transgenic lines overexpressing OsMPK3 in indica and japonica cultivars and OsMPK6 in japonica cultivar under the control of an inducible promoter. We also establish the crucial steps and troubleshooting for each of the indicated rice transformation medium components. Later, we study the potential role of these MAPKs in high-throughput analysis of root system architectural (RSA) traits. It was observed that OsMPK6 overexpression lines had a more robust and spread out root architectural system while OsMPK3 overexpression lines had a typical bushy phenotype.

Effects of early cold stress on gene expression in Chlamydomonas reinhardtii

Cold stress imposes a great impact on the growth of nearly all photosynthetic organisms, including Chlamydomonas reinhardtii (C. reinhardtii). Despite prior studies on the mechanism of stress acclimation in plants, little has been done on the early events of cold sensing in C. reinhardtii. Here, we used C. reinhardtii as a model to study early events of cold signal transduction. By analyzing transcriptomic changes of C. reinhardtii exposed to cold, we found that 3471 genes were differentially expressed after 1 h of cold exposure. These genes were associated with a wide range of biological events and processes such as protein synthesis, cell cycle and protein kinase-based phosphorylation. Besides, the promoter of one gene (named as crAP2) which belongs to AP2/EREBP family and was significantly induced by cold was cloned, and functional analysis was conducted using GUS activity analysis through Agrobacterium-mediated transient assay in tobacco leaves.

Salicylic Acid Alleviated Salt Damage of Populus euphratica: A Physiological and Transcriptomic Analysis

Populus euphratica Oliv. is a model tree for studying abiotic stress, especially salt stress response. Salt stress is one of the most extensive abiotic stresses, which has an adverse effect on plant growth and development. Salicylic acid (SA) is an important signaling molecule that plays an important role in modulating the plant responses to abiotic stresses. To answer whether the endogenous SA can be induced by salt stress, and whether SA effectively alleviates the negative effects of salt on poplar growth is the main purpose of the study. To elucidate the effects of SA and salt stress on the growth of P. euphratica, we examined the morphological and physiological changes of P. euphratica under 300 mM NaCl after treatment with different concentrations of SA. A pretreatment of P. euphratica with 0.4 mM SA for 3 days effectively improved the growth status of plants under subsequent salt stress. These results indicate that appropriate concentrations of exogenous SA can effectively counteract the negative effect of salt stress on growth and development. Subsequently, transcripts involved in salt stress response via SA signaling were captured by RNA sequencing. The results indicated that numerous specific genes encoding mitogen-activated protein kinase, calcium-dependent protein kinase, and antioxidant enzymes were upregulated. Potassium transporters and Na+/H+ antiporters, which maintain K+/Na+ balance, were also upregulated after SA pretreatment. The transcriptome changes show that the ion transport and antioxidant enzymes were the early enhanced systems in response of P. euphratica to salt via SA, expanding our knowledge about SA function in salt stress defense in P. euphratica. This provides a solid foundation for future study of functional genes controlling effective components in metabolic pathways of trees.

Ethylene signaling involves in seeds germination upon submergence and antioxidant response elicited confers submergence tolerance to rice seedlings

BACKGROUND

Flooding has negative impact on agriculture. The plant hormone ethylene is involved in plant growth and stress responses, which are important role in tolerance and adaptation regulatory mechanisms during submergence stress. Ethylene signaling crosstalk with gibberellin signaling enhances tolerance in lowland rice (Flood Resistant 13A) through a quiescence strategy or in deepwater rice through an escape strategy when rice is submerged. Information regarding ethylene-mediated priming in submergence stress tolerance in rice is scant. Here, we used 1-aminocyclopropane-1-carboxylic acid, an ethylene precursor, to evaluate the response in submerged rice seedlings.

RESULTS

The germination rate and mean germination times of rice seeds was higher in seedlings under submergence only when ethylene signaling was inhibited by supplemented with silver nitrate (AgNO₃). Reduced leaf chlorophyll contents and induced senescence-associated genes in rice seedlings under submergence were relieved by pretreatment with an ethylene precursor. The ethylene-mediated priming by pretreatment with an ethylene precursor enhanced the survival rate and hydrogen peroxide (H₂O₂) and superoxide (O₂^-) anion accumulation and affected antioxidant response in rice seedlings.

CONCLUSIONS

Pretreatment with an ethylene precursor leads to reactive oxygen species generation, which in turn triggered the antioxidant response system, thus improving the tolerance of rice seedlings to complete submergence stress. Thus, H₂O₂ signaling may contribute to ethylene-mediated priming to submergence stress tolerance in rice seedlings.

A CIPK protein kinase targets sucrose transporter MdSUT2.2 at Ser254 for phosphorylation to enhance salt tolerance

Soil salinity is one of the major abiotic stressors that negatively affect crop growth and yield. Salt stress can regulate antioxidants and the accumulation of osmoprotectants. In the study, a sucrose transporter MdSUT2.2 was identified in apple. Overexpression of MdSUT2.2 gene increased salt tolerance in the transgenic apple, compared with the WT control "Gala." In addition, it was found that protein MdSUT2.2 was phosphorylated at Ser²⁵⁴ site in response to salt. A DUAL membrane yeast hybridization system through an apple cDNA library demonstrated that a protein kinase MdCIPK13 interacted with MdSUT2.2. A series of transgenic analysis in apple calli showed that MdCIPK13 was required for the salt-induced phosphorylation of MdSUT2.2 protein and enhanced its stability and transport activity. Finally, it was found that MdCIPK13 improved salt resistance in an MdSUT2.2-dependent manner. These findings had enriched our understanding of the molecular mechanisms underlying abiotic stress.

TaZFP1, a C2H2 type-ZFP gene of T. aestivum, mediates salt stress tolerance of plants by modulating diverse stress-defensive physiological processes

Salt stress suppresses plant growth, development, and crop productivity. In this study, we characterized the role of TaZFP1, a C2H2 type-zinc finger protein family member of T. aestivum, in salt stress tolerance. TaZFP1 possesses a conserved C2H2 motif (CX2-4CX12HX3-5H) shared by plant ZFP proteins, translocates to the nucleus after endoplasmic reticulum (ER) assortment, and displays a ZF 3-D structure similar to its eukaryote homologs. The transcripts of TaZFP1 were upregulated during salt stress condition and this effect was restored under normal conditions. Compared to wild type (WT), the transgenic lines of TaZFP1 overexpression or knockdown displayed improved phenotypes, biomass, photosynthesis parameters (Pn, ΨPSII, and NPQ), osmolytes contents (i.e. proline and soluble sugar), and enhanced antioxidant enzyme (AE) activity following salt stress treatment. A set of genes associated with proline synthesis (i.e., NtP5CS1 and NtP5CS2) and encoding AEs (i.e., NtSOD2, NtCAT1, and NtPOD4) were upregulated in the salt-challenged transgenic lines of TaZFP1 expression. Additionally, the transgenic lines exhibited similar stomata movement patterns and leaf water retention properties under salinity conditions compared to those induced by exogenous abscisic acid (ABA) treatment, suggesting that the TaZFP1-mediated salt response is dependent on the ABA signaling. High throughput RNAseq analysis revealed significant alteration of gene transcription in transgenic lines upon salt stress. Among them, the differentially expressed genes (DEGs) represented by the gene ontology (GO) terms were associated with organic acid, carboxylic acid, carbohydrate, and coenzyme as well as organonitrogen compounds, translation, peptide metabolism, and peptide biosynthesis. A set of upregulated DEGs were found to be thylakoid- and photosystem-associated, which is consistent with the TaZFP1-mediated improvement in photosynthesis in salt-stressed transgenic lines. Our investigation indicated that the TaZFP1-mediated salt tolerance is ascribed to the regulation of gene functions related to photosynthesis, osmolytes metabolism and ROS homeostasis mediated by ABA signaling.

Analysis of wheat gene expression related to the oxidative stress response and signal transduction under short-term osmotic stress

Water shortage is a major environmental stress that causes the generation of reactive oxygen species (ROS). The increase in ROS production induces molecular responses, which are key factors in determining the level of plant tolerance to stresses, including drought. The aim of this study was to determine the expression levels of genes encoding MAPKs (MAPK3 and MAPK6), antioxidant enzymes (CAT, APX and GPX) and enzymes involved in proline biosynthesis (P5CS and P5CR) in Triticum aestivum L. seedlings in response to short-term drought conditions. A series of wheat intervarietal substitution lines (ISCSLs) obtained by the substitution of single chromosomes from a drought-sensitive cultivar into the genetic background of a drought-tolerant cultivar was used. This source material allowed the chromosomal localization of the genetic elements involved in the response to the analyzed stress factor (drought). The results indicated that the initial plant response to drought stress resulted notably in changes in the expression of MAPK6 and CAT and both the P5CS and P5CR genes. Our results showed that the substitution of chromosomes 3B, 5A, 7B and 7D had the greatest impact on the expression level of all tested genes, which indicates that they contain genetic elements that have a significant function in controlling tolerance to water deficits in the wheat genome.

Overexpression of a Mitogen-Activated Protein Kinase SlMAPK3 Positively Regulates Tomato Tolerance to Cadmium and Drought Stress

Mitogen-activated protein kinases (MAPKs) activation is a common defense response of plants to a range of abiotic stressors. SlMPK3, a serine-threonine protein kinase, has been reported as an important member of protein kinase cascade that also functions on plant stress tolerance. In this study, we cloned SlMPK3 from tomato and studied its role in cadmium (Cd²⁺) and drought tolerance. The results showed that transcripts of SlMAPK3 differentially accumulated in various plant tissues and were remarkably induced by different abiotic stressors and exogenous hormone treatments. Overexpression of SlMAPK3 increased tolerance to Cd²⁺ and drought as reflected by an increased germination rate and improved seedling growth. Furthermore, transgenic plants overexpressing SlMAPK3 showed an increased leaf chlorophyll content, root biomass accumulation and root activity under Cd²⁺ stress. Chlorophyll fluorescence analysis revealed that transgenic plants demonstrated an increased photosynthetic activity as well as contents of chlorophyll, proline, and sugar under drought stress. Notably, cadmium- and drought-induced oxidative stress was substantially attenuated in SlMAPK3 overexpressing plants as evidenced by lower malondialdehyde and hydrogen peroxide accumulation, and increased activity and transcript abundance of enzymatic antioxidants under stress conditions compared to that of wild-type. Our findings provide solid evidence that overexpression of SlMAPK3 gene in tomato positively regulates tolerance to Cd²⁺ and drought stress, which may have strengthen the molecular understanding of SlMAPK3 gene to improve abiotic stress tolerance.

A member of the CONSTANS-Like protein family is a putative regulator of reactive oxygen species homeostasis and spaceflight physiological adaptation

A feature of the physiological adaptation to spaceflight in Arabidopsis thaliana (Arabidopsis) is the induction of reactive oxygen species (ROS)-associated gene expression. The patterns of ROS-associated gene expression vary among Arabidopsis ecotypes, and the role of ROS signalling in spaceflight acclimation is unknown. What could differences in ROS gene regulation between ecotypes on orbit reveal about physiological adaptation to novel environments? Analyses of ecotype-dependent responses to spaceflight resulted in the elucidation of a previously uncharacterized gene (OMG1) as being ROS-associated. The OMG1 5' flanking region is an active promoter in cells where ROS activity is commonly observed, such as in pollen tubes, root hairs, and in other tissues upon wounding. qRT-PCR analyses revealed that upon wounding on Earth, OMG1 is an apparent transcriptional regulator of MYB77 and GRX480, which are associated with the ROS pathway. Fluorescence-based ROS assays show that OMG1 affects ROS production. Phylogenetic analysis of OMG1 and closely related homologs suggests that OMG1 is a distant, unrecognized member of the CONSTANS-Like protein family, a member that arose via gene duplication early in the angiosperm lineage and subsequently lost its first DNA-binding B-box1 domain. These data illustrate that members of the rapidly evolving COL protein family play a role in regulating ROS pathway functions, and their differential regulation on orbit suggests a role for ROS signalling in spaceflight physiological adaptation.

Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower (Helianthus annuus L.)

Mitogen-Activated Protein Kinase (MAPK) genes encode proteins that regulate biotic and abiotic stresses in plants through signaling cascades comprised of three major subfamilies: MAP Kinase (MPK), MAPK Kinase (MKK), and MAPKK Kinase (MKKK). The main objectives of this research were to conduct genome-wide identification of MAPK genes in Helianthus annuus and examine functional divergence of these genes in relation to those in nine other plant species (Amborella trichopoda, Aquilegia coerulea, Arabidopsis thaliana, Daucus carota, Glycine max, Oryza sativa, Solanum lycopersicum, Sphagnum fallax, and Vitis vinifera), representing diverse taxonomic groups of the Plant Kingdom. A Hidden Markov Model (HMM) profile of the MAPK genes utilized reference sequences from A. thaliana and G. max, yielding a total of 96 MPKs and 37 MKKs in the genomes of A. trichopoda, A. coerulea, C. reinhardtii, D. carota, H. annuus, S. lycopersicum, and S. fallax. Among them, 28 MPKs and eight MKKs were confirmed in H. annuus. Phylogenetic analyses revealed four clades within each subfamily. Transcriptomic analyses showed that at least 19 HaMPK and seven HaMKK genes were induced in response to salicylic acid (SA), sodium chloride (NaCl), and polyethylene glycol (Peg) in leaves and roots. Of the seven published sunflower microRNAs, five microRNA families are involved in targeting eight MPKs. Additionally, we discussed the need for using MAP Kinase nomenclature guidelines across plant species. Our identification and characterization of MAP Kinase genes would have implications in sunflower crop improvement, and in advancing our knowledge of the diversity and evolution of MAPK genes in the Plant Kingdom.

The MKKK62-MKK3-MAPK7/14 module negatively regulates seed dormancy in rice

BACKGROUND

Seed dormancy directly affects the phenotype of pre-harvest sprouting, and ultimately affects the quality and yield of rice seeds. Although many genes controlling seed dormancy have been cloned from cereals, the regulatory mechanisms controlling this process are complex, and much remains unknown. The MAPK cascade is involved in many signal transduction pathways. Recently, MKK3 has been reported to be involved in the regulation of seed dormancy, but its mechanism of action is unclear.

RESULTS

We found that MKKK62-overexpressing rice lines (OE) lost seed dormancy. Further analyses showed that the abscisic acid (ABA) sensitivity of OE lines was decreased. In yeast two-hybrid experiments, MKKK62 interacted with MKK3, and MKK3 interacted with MAPK7 and MAPK14. Knock-out experiments confirmed that MKK3, MAPK7, and MAPK14 were involved in the regulation of seed dormancy. The OE lines showed decreased transcript levels of OsMFT, a homolog of a gene that controls seed dormancy in wheat. The up-regulation of OsMFT in MKK3-knockout lines (OE/mkk3) and MAPK7/14-knockout lines (OE/mapk7/mapk14) indicated that the MKKK62-MKK3-MAPK7/MAPK14 system controlled seed dormancy by regulating the transcription of OsMFT.

CONCLUSION

Our results showed that MKKK62 negatively controls seed dormancy in rice, and that during the germination stage and the late stage of seed maturation, ABA sensitivity and OsMFT transcription are negatively controlled by MKKK62. Our results have clarified the entire MAPK cascade controlling seed dormancy in rice. Together, these results indicate that protein modification by phosphorylation plays a key role in controlling seed dormancy.

Diversity among Pomegranate Varieties in Chilling Tolerance and Transcriptome Responses to Cold Storage

We found great variability in chilling tolerance among 84 pomegranate varieties from the Newe Ya'ar collection; among them, 'Ganesh' was chilling-sensitive, whereas 'Wonderful' was relatively chilling-tolerant. To evaluate the different molecular responses of these varieties to cold storage, we analyzed the transcriptomic changes in the inner membrane tissues of 'Ganesh' and 'Wonderful' fruit after 2 weeks of cold storage at 1 °C. By functional categorization of the differentially expressed transcripts using MapMan, we found that many transcripts related to various pathways, such as jasmonic acid biosynthesis and signaling, galactinol, raffinose, phenol, and phenylpropanoid biosynthesis, calcium and mitogen-activated protein kinase signaling, lipid metabolism, and various transcription factors and heat-shock proteins, have been massively upregulated in 'Wonderful' but not in 'Ganesh' fruit. Thus, it is suggested that these pathways most likely participate in imparting chilling tolerance in pomegranate fruit.

Biochemical and Genetic Interactions of Phospholipase D Alpha 1 and Mitogen-Activated Protein Kinase 3 Affect Arabidopsis Stress Response

Phospholipase D alpha 1 (PLDα1, AT3G15730) and mitogen-activated protein kinases (MAPKs) participate on signaling-dependent events in plants. MAPKs are able to phosphorylate a wide range of substrates putatively including PLDs. Here we have focused on functional regulations of PLDα1 by interactions with MAPKs, their co-localization and impact on salt stress and abscisic acid (ABA) tolerance in Arabidopsis. Yeast two-hybrid and bimolecular fluorescent assays showed that PLDα1 interacts with MPK3. Immunoblotting analyses likewise confirmed connection between both these enzymes. Subcellularly we co-localized PLDα1 with MPK3 in the cortical cytoplasm close to the plasma membrane and in cytoplasmic strands. Moreover, genetic interaction studies revealed that pldα1mpk3 double mutant was resistant to a higher salinity and showed a higher tolerance to ABA during germination in comparison to single mutants and wild type. Thus, this study revealed importance of new biochemical and genetic interactions between PLDα1 and MPK3 for Arabidopsis stress (salt and ABA) response.

Cold Influences Male Reproductive Development in Plants: A Hazard to Fertility, but a Window for Evolution

Being sessile organisms, plants suffer from various abiotic stresses including low temperature. In particular, male reproductive development of plants is extremely sensitive to cold which may dramatically reduce viable pollen shed and plant fertility. Cold stress disrupts stamen development and prominently interferes with the tapetum, with the stress-responsive hormones ABA and gibberellic acid being greatly involved. In particular, low temperature stress delays and/or inhibits programmed cell death of the tapetal cells which consequently damages pollen development and causes male sterility. On the other hand, studies in Arabidopsis and crops have revealed that ectopically decreased temperature has an impact on recombination and cytokinesis during meiotic cell division, implying a putative role for temperature in manipulating plant genomic diversity and architecture during the evolution of plants. Here, we review the current understanding of the physiological impact of cold stress on the main male reproductive development processes including tapetum development, male meiosis and gametogenesis. Moreover, we provide insights into the genetic factors and signaling pathways that are involved, with putative mechanisms being discussed.

Patterns of Drought Response of 38 WRKY Transcription Factors of Zanthoxylum bungeanum Maxim

The WRKY family of transcription factors (TFs) includes a number of transcription-specific groupings that play important roles in plant growth and development and in plant responses to various stresses. To screen for WRKY transcription factors associated with drought stress in Zanthoxylum bungeanum, a total of 38 ZbWRKY were identified and these were then classified and identified with Arabidopsis WRKY. Using bioinformatics analyses based on the structural characteristics of the conservative domain, 38 WRKY transcription factors were identified and categorized into three groups: Groups I, II, and III. Of these, Group II can be divided into four subgroups: subgroups IIb, IIc, IId, and IIe. No ZbWRKY members of subgroup IIa were found in the sequencing data. In addition, 38 ZbWRKY were identified by real-time PCR to determine the behavior of this family of genes under drought stress. Twelve ZbWRKY transcription factors were found to be significantly upregulated under drought stress and these were identified by relative quantification. As predicted by the STRING website, the results show that the WRKYs are involved in four signaling pathways—the jasmonic acid (JA), the salicylic acid (SA), the mitogen-activated protein kinase (MAPK), and the ethylene signaling pathways. ZbWRKY33 is the most intense transcription factor in response to drought stress. We predict that WRKY33 binds directly to the ethylene synthesis precursor gene ACS6, to promote ethylene synthesis. Ethylene then binds to the ethylene activator release signal to activate a series of downstream genes for cold stress and osmotic responses. The roles of ZbWRKY transcription factors in drought stress rely on a regulatory network center on the JA signaling pathway.

Brassinosteroid Signaling in Plant⁻Microbe Interactions

As sessile organisms, plants are frequently exposed to different stress conditions caused by either biotic or abiotic factors. Understanding the mechanisms that underlie plant interaction with the biotic and abiotic environments is fundamental to both plant biotechnology and sustainable agriculture. Brassinosteroids (BRs) are a group of plant-specific steroidal compounds essential for normal growth and development. Recent research evidence indicates that BRs are also actively involved in plant–environment interactions and play important roles in shaping plant fitness and the growth–defense trade-offs. In this minireview, we focus our attention on recent advances in the understanding of BR functions in modulating plant interactions with different pathogenic microbes, with particular focus on how BR signaling primes the plant innate immunity pathways and achieves a trade-off between growth and immunity.

Mitogen-activated protein kinases MPK4 and MPK12 are key components mediating CO2 -induced stomatal movements

Respiration in leaves and the continued elevation in the atmospheric CO2 concentration cause CO2 -mediated reduction in stomatal pore apertures. Several mutants have been isolated for which stomatal responses to both abscisic acid (ABA) and CO2 are simultaneously defective. However, there are only few mutations that impair the stomatal response to elevated CO2 , but not to ABA. Such mutants are invaluable in unraveling the molecular mechanisms of early CO2 signal transduction in guard cells. Recently, mutations in the mitogen-activated protein (MAP) kinase, MPK12, have been shown to partially impair CO2 -induced stomatal closure. Here, we show that mpk12 plants, in which MPK4 is stably silenced specifically in guard cells (mpk12 mpk4GC homozygous double-mutants), completely lack CO2 -induced stomatal responses and have impaired activation of guard cell S-type anion channels in response to elevated CO2 /bicarbonate. However, ABA-induced stomatal closure, S-type anion channel activation and ABA-induced marker gene expression remain intact in the mpk12 mpk4GC double-mutants. These findings suggest that MPK12 and MPK4 act very early in CO2 signaling, upstream of, or parallel to the convergence of CO2 and ABA signal transduction. The activities of MPK4 and MPK12 protein kinases were not directly modulated by CO2 /bicarbonate in vitro, suggesting that they are not direct CO2 /bicarbonate sensors. Further data indicate that MPK4 and MPK12 have distinguishable roles in Arabidopsis and that the previously suggested role of RHC1 in stomatal CO2 signaling is minor, whereas MPK4 and MPK12 act as key components of early stomatal CO2 signal transduction.

Quantitative and functional posttranslational modification proteomics reveals that TREPH1 plays a role in plant touch-delayed bolting

Environmental mechanical forces, such as wind and touch, trigger gene-expression regulation and developmental changes, called "thigmomorphogenesis," in plants, demonstrating the ability of plants to perceive such stimuli. In Arabidopsis, a major thigmomorphogenetic response is delayed bolting, i.e., emergence of the flowering stem. The signaling components responsible for mechanotransduction of the touch response are largely unknown. Here, we performed a high-throughput SILIA (stable isotope labeling in Arabidopsis)-based quantitative phosphoproteomics analysis to profile changes in protein phosphorylation resulting from 40 seconds of force stimulation in Arabidopsis thaliana Of the 24 touch-responsive phosphopeptides identified, many were derived from kinases, phosphatases, cytoskeleton proteins, membrane proteins, and ion transporters. In addition, the previously uncharacterized protein TOUCH-REGULATED PHOSPHOPROTEIN1 (TREPH1) became rapidly phosphorylated in touch-stimulated plants, as confirmed by immunoblots. TREPH1 fractionates as a soluble protein and is shown to be required for the touch-induced delay of bolting and gene-expression changes. Furthermore, a nonphosphorylatable site-specific isoform of TREPH1 (S625A) failed to restore touch-induced flowering delay of treph1-1, indicating the necessity of S625 for TREPH1 function and providing evidence consistent with the possible functional relevance of the touch-regulated TREPH1 phosphorylation. Taken together, these findings identify a phosphoprotein player in Arabidopsis thigmomorphogenesis regulation and provide evidence that TREPH1 and its touch-induced phosphorylation may play a role in touch-induced bolting delay, a major component of thigmomorphogenesis.

Identification of tyrosine autophosphorylation sites of Arabidopsis MEKK1 and their involvement in the regulation of kinase activity

The MEKK1 kinase is a key regulator of stress signaling in Arabidopsis; however, little is known about the regulation of its kinase activity. Here, we found that recombinant MEKK1, expressed in both mammalian HEK293 cells and Escherichia coli, shows a mobility shift in SDS-PAGE, and immunoblotting detected phosphorylation of serine, threonine, and tyrosine residues. N-terminal deletions, site-directed mutagenesis, and protein phosphatase treatment revealed that the mobility shift results from autophosphorylation of the kinase domain. We identified the tyrosine autophosphorylation sites in the N-terminal region of MEKK1. Tyrosine to phenylalanine mutations decrease phosphorylation of the substrate MKK1, suggesting the important role of this residue in the regulation of MEKK1 kinase activity. The present study is the first to show that plant MAPKKKs are regulated by tyrosine phosphorylation.

Unraveling salt stress signaling in plants

Salt stress is a major environmental factor limiting plant growth and productivity. A better understanding of the mechanisms mediating salt resistance will help researchers design ways to improve crop performance under adverse environmental conditions. Salt stress can lead to ionic stress, osmotic stress and secondary stresses, particularly oxidative stress, in plants. Therefore, to adapt to salt stress, plants rely on signals and pathways that re-establish cellular ionic, osmotic, and reactive oxygen species (ROS) homeostasis. Over the past two decades, genetic and biochemical analyses have revealed several core stress signaling pathways that participate in salt resistance. The Salt Overly Sensitive signaling pathway plays a key role in maintaining ionic homeostasis, via extruding sodium ions into the apoplast. Mitogen-activated protein kinase cascades mediate ionic, osmotic, and ROS homeostasis. SnRK2 (sucrose nonfermenting 1-related protein kinase 2) proteins are involved in maintaining osmotic homeostasis. In this review, we discuss recent progress in identifying the components and pathways involved in the plant's response to salt stress and their regulatory mechanisms. We also review progress in identifying sensors involved in salt-induced stress signaling in plants.

Cold signaling in plants: Insights into mechanisms and regulation

To survive under cold temperatures plants must be able to perceive a cold signal and transduce it into downstream components that induce appropriate defense mechanisms. In addition to inducing adaptive defenses, such as the production of osmotic factors to prevent freezing and the reprogramming of transcriptional pathways, cold temperatures induce changes in plant growth and development which can affect the plant life cycle. In this review, we summarize recent progress in characterizing cold-related genes and the pathways that allow transduction of the cold signal in plants, focusing primarily on studies in Arabidopsis thaliana and rice (Oryza sativa). We summarize cold perception and signal transduction from the plasma membrane to the nucleus, which involves cold sensors, calcium signals, calcium-binding proteins, mitogen-activated protein kinase cascades, and the C-repeat binding factor/dehydration-responsive element binding pathways, as well as trehalose metabolism. Finally, we describe the balance between plant organogenesis and cold tolerance mechanisms in rice. This review encapsulates the known cold signaling factors in plants and provides perspectives for ongoing cold signaling research.

Comparative transcriptome analysis reveals an early gene expression profile that contributes to cold resistance in Hevea brasiliensis (the Para rubber tree)

The rubber tree (Hevea brasiliensis Muell. Arg) is a tropical, perennial, woody plant that is susceptible to cold stress. In China, cold stress has been found to severely damage rubber plants in plantations in past decades. Although several Hevea clones that are resistant to cold have been developed, their cold hardiness mechanism has yet to be elucidated. For the study reported herein, we subjected the cold-resistant clone CATAS93-114 and the cold-sensitive clone Reken501 to chilling stress, and characterized their transcriptomes at 0, 2, 8 and 24 h after the start of chilling. We found that 7870 genes were differentially expressed in the transcriptomes of the two clones. In CATAS93-114, a greater number of genes were found to be up- or downregulated between 2 h and 8 h than in Reken501, which indicated a more rapid and intensive response by CATAS93-114 than by Reken501. The differentially expressed genes were grouped into seven major clusters, according to their Gene Ontology terms. The expression profiles for genes involved in abscisic acid metabolism and signaling, in an abscisic acid-independent pathway, and in early signal perception were found to have distinct expression patterns for the transcriptomes of the two clones. The differential expression of 22 genes that appeared to have central roles in response to chilling was confirmed by quantitative real-time PCR.