The Role of MAPK Modules and ABA during Abiotic Stress Signaling

Investigation of wheat cold response pathway regulated by TaICE41 and TaCBFⅣd-B9 through Brachypodium distachyon transformation

Wheat (Triticum aestivum L.), a major global crop, is vulnerable to freezing stress, particularly during late spring frosts. Enhancing freezing tolerance through cold acclimation, primarily via the ICE-CBF-COR pathway, is crucial for improving wheat productivity. This study focuses on identifying genes regulated by the ICE-CBF pathway and those that function independently in response to freezing stress. TaICE41 and TaCBFⅣd-B9, two key genes associated with cold tolerance, were cloned and analyzed for their phylogenetic characteristics and subcellular localization. Transgenic Brachypodium distachyon overexpressing these genes demonstrated enhanced freezing tolerance, with increased survival rates and proline content, compared to wild-type plants. RNA-seq analysis revealed distinct gene expression profiles under cold stress, highlighting both shared and unique pathways regulated by ICE41 and CBF. Notably, the TaICE41-overexpressing lines exhibited upregulation of genes involved in phenylpropanoid biosynthesis and starch-sucrose metabolism, contributing to stress response. This study provides new insights into the ICE-CBF pathway and its role in cold tolerance, emphasizing the importance of understanding both ICE-CBF-regulated and independent cold-responsive genes for improving freezing tolerance in crops.

A review of the interaction mechanisms between jasmonic acid (JA) and various plant hormones, as well as the core regulatory role of MYC2

Jasmonic acid (JA), as a defensive plant hormone, can synergistically or antagonistically interact with common hormones such as gibberellin (GA), abscisic acid (ABA), indole-3-acetic hormone acid (IAA), and ethylene (ETH) during the plant growth process, as well as interact with hormones such as melatonin (MT), brassinolide (BR), and resveratrol to regulate plant growth and development processes such as metabolite synthesis, pest and disease defense, and organ growth. The core regulatory factor MYC2 of JA mainly mediates the signal transduction pathways of these hormone interactions by interacting with other genes or regulating transcription. This article reviews the mechanism of cross-talk between JA and hormones such as ABA, GA, and salicylic acid (SA), and discusses the role of MYC2 in hormone interactions.

The Good, the Bad, and the Epigenetic: Stress-Induced Metabolite Regulation and Transgenerational Effects

BACKGROUND

Plants face a wide range of environmental stresses that disrupt growth and productivity. To survive and adapt, they undergo complex metabolic reprogramming by redirecting carbon and nitrogen fluxes toward the biosynthesis of protective secondary metabolites such as phenylpropanoids, flavonoids, and lignin. Recent research has revealed that these stress-induced metabolic processes are tightly regulated by epigenetic mechanisms, including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNAs.

METHODS

This review synthesizes current findings from studies on both model and crop plants, examining the roles of key epigenetic regulators in controlling secondary metabolism under stress. Special focus is placed on dynamic changes in DNA methylation, histone acetylation, and the action of small RNAs such as siRNAs and miRNAs in transcriptional and post-transcriptional regulation.

RESULTS

Evidence indicates that stress triggers rapid and reversible epigenetic modifications that modulate gene expression linked to secondary metabolic pathways. These modifications not only facilitate immediate metabolic responses but can also contribute to stress memory. In some cases, this memory is retained and transmitted to the next generation, influencing progeny stress responses. However, critical knowledge gaps remain, particularly concerning the temporal dynamics, tissue specificity, and long-term stability of these epigenetic marks in crops.

CONCLUSIONS

Understanding how epigenetic regulation governs secondary metabolite production offers promising avenues to enhance crop resilience and productivity in the context of climate change. Future research should prioritize dissecting the stability and heritability of these modifications to support the development of epigenetically informed breeding strategies.

Research on the regulation mechanism of drought tolerance in wheat

Wheat (Triticum aestivum L.) is one of the most important crops in arid and semi-arid areas of the world, and its sustainable and efficient production is essential for ensuring food security in China and globally. However, with the global climate change, wheat production is increasingly endangered by abiotic stress, and drought stress has become the main abiotic stress factor restricting wheat production efficiently. Therefore, investigating drought resistance genes and elucidating the mechanisms underlying drought resistance regulation is crucial for the genetic enhancement of drought resistance and the development of new drought-resistant wheat varieties. This paper reviews the majority of research conducted on wheat drought resistance over the past five years, focusing on aspects, such as transcriptional regulation, protein post-translational modifications, and other regulatory mechanisms related to drought resistance in wheat. Additionally, this paper discusses future directions for the genetic improvement of drought resistance and the breeding of new drought-resistant wheat varieties.

Multiomics unraveled that gibberellin signaling underlies adaptation of rice to ciprofloxacin stress: Calling for concerns on the adverse effects of pharmaceutical residues in water during agricultural irrigations

Residual concentrations of antibiotics in water can reach ng mL-1 - µg mL-1 levels, which pose high risks to crops during irrigation; however, the interactions between rice and antibiotics, as well as the defense mechanisms of rice at their early growth phase remain unclear. In this study, we investigated the uptake dynamics of a ubiquitously found antibiotic, ciprofloxacin (CIP) at 0.1, 1, 6.5, and 20 µg mL-1 in rice seedlings. We found gradually bioaccumulated CIP induced significant physiological changes including inhibited growth of roots and leaves of rice seedlings, and decreased pigment contents, which can be caused by disrupted homeostasis of reactive oxygen species. Integrating roots transcriptomics, metabolomics, and validation experiments, we found that rice seedlings synthesized more gibberellins to trigger the expression of transcription factors such as group VII ethylene response factors, which induced metabolic reprogramming to yield more fatty acids derivates. These compounds including eicosanoids, isoprenoids, and fatty acids and conjugates can act as signaling molecules, as well as antioxidants and energy sources to achieve rice recovery. This conclusion is supported by the evidence showing that adding gibberellins in rice seedlings culture decreased the accumulated CIP and improved rice growth; whilst, disrupting gibberellin signaling pathway using paclobutrazol as an inhibitor increased uptaken CIP in both roots and leaves with augmenting the antibiotic stress on rice. This study has demonstrated a gibberellin-based defense mechanism in rice for defense of CIP stress, which might have significant environmental applications since we can add minor gibberellins to reduce bioaccumulated CIP with simultaneously promoting rice growth at their early phases.

Comprehensive transcriptome analysis reveals StMAPK7 regulate cold response in potato

Cultivated potato (Solanum tuberosum L.) is an important tuber crop in the world. Cold stress adversely affects productivity and quality of potato. However, the molecular mechanism underlying the cold stress responses remains unclear in potato. The chloroplast ultrastructure of S. cardiophyllum in non-acclimated and cold acclimation plants under -2 °C for 6 h contained fewer thylakoid membranes, more spherical than those in 0 h (control, non-acclimated). The chloroplast ultrastructure of S. commersonii in non-acclimated and cold acclimation plants under -2 °C 6 h were similar to the non-cold stress. RNA sequencing (RNA-seq) analysis showed that 3,623 DEGs (differentially expressed genes) were detected in the S. commersonii and S. cardiophyllum with or without cold acclimation. GO analysis revealed that the membrane protein complex, photosynthesis and molecular function regulator were enriched terms in three category of S. commersonii and S. cardiophyllum. KEGG analysis found that genes were enriched to photosynthesis and chlorophyll metabolism. A total of 27 distinct modules were identified by weighted gene co-expression network analysis, four regulatory networks contained cold related genes were constructed. The StMAPK7 were differently expressed in S. cardiophyllum. Subcellular location studies showed that the StMAPK7 protein is mainly localized to the nucleus in tobacco. Overexpression of StMAPK7 exhibited lower electrolyte leakage and less leaves injury area than that of wild type, indicating StMAPK7 positively regulates cold stress in potato. These findings would provide fundamental insight into the cold stress response regulatory networks and supply a theoretical basis for breeding cold-resistant potato cultivars.

Regulatory networks of bZIPs in drought, salt and cold stress response and signaling

Abiotic stresses adversely impact plants survival and growth, which in turn affect plants especially crop yields worldwide. To cope with these stresses, plant responses depend on the activation of molecular networks cascades, including stress perception, signal transduction, and the expression of specific stress-related genes. Plant bZIP (basic leucine zipper) transcription factors are important regulators that respond to diverse abiotic stresses.By binding to specific cis-elements, bZIPs can control the transcription of target genes, giving plants stress resistance. This review describes the structural characteristics of bZIPs and summarizes recent progress in analyzing the molecular mechanisms regulating plant responses to salinity, drought, and cold in different plant species. The main goal is to deepen the understanding of bZIPs and explore their value in genetic improvement of plants.

FtbHLH1, a transcription factor that interacts with FtATG8a, enhances the drought stress response in Tartary buckwheat

Tartary buckwheat (Fagopyrum tataricum) is a traditional cereal crop cultivated in hilly, arid, cool mountainous regions. The bHLH transcription factors play a pivotal role in regulating flavonoid metabolism and enhancing resistance to extreme environments in Tartary buckwheat. However, the functional characterization of bHLH genes in this species remains incomplete. Previous research identified FtbHLH1 as an interacting partner of the key autophagy protein FtATG8a through yeast library screening. Yeast two-hybrid, bimolecular fluorescence complementation, and luciferase complementation imaging assays confirmed that FtbHLH1 interacts with FtATG8a. This interaction depends on the AIM motifs (LEWYYL and QSWHFV) present in FtbHLH1, with both proteins co-localizing in the nucleus. The expression of FtbHLH1 was significantly induced by drought stress (P < 0.05), and its overexpression led to increased drought tolerance in transgenic Tartary buckwheat hairy roots. RNA sequencing revealed that FtbHLH1 up-regulated genes associated with stress response (e.g., FtCu/ZnSOD) as well as those involved in abscisic acid and methyl jasmonate biosynthesis and signaling pathways (e.g., FtCYP707As, FtRD29B, and FtJAZs). Further analysis indicated that the overexpression of FtbHLH1 enhances drought stress tolerance by altering the activities of antioxidant enzymes and promoting proline accumulation in both transgenic Arabidopsis and Tartary buckwheat hairy roots. This study provides theoretical support for selecting drought-resistant Tartary buckwheat varieties by elucidating the role of FtbHLH1 in the response to drought stress.

Synergistic Regulation at Physiological, Transcriptional, and Metabolic Levels in Dendrobium huoshanense Plants Under Combined Drought and High-Temperature Stress

Background: With global warming and climate change, the occurrence of abiotic stresses has become increasingly prevalent. Drought often occurs with high temperatures, especially in arid and semi-arid regions. However, the molecular mechanisms of plants responding to combined drought and high-temperature stress remains unclear. Results: Through integrative physiological, transcriptomic, and metabolomic analyses, we systematically investigated the adaptive mechanisms of Dendrobium huoshanense under combined drought and high-temperature stress. Our findings revealed that combined drought and high-temperature stress led to significant reductions in photosynthetic efficiency and increased oxidative damage in Dendrobium huoshanense, with high-temperature stress being the primary contributor to these adverse effects. The joint analysis shows that three core pathways-signal transduction, lipid metabolism, and secondary metabolite biosynthesis-were identified as critical for antioxidant defense and stress adaptation. Conclusions: These findings not only deepen our understanding of plant responses to combined drought and high-temperature stress but also provide new directions for future research on the cultivation and resistance improvement of Dendrobium huoshanense.

MPK3 mediated phosphorylation inhibits the dimerization of ABI5 to fine-tune the ABA signaling in Arabidopsis

Seed germination is, a critical physiological process, is tightly regulated by the phytohormone abscisic acid (ABA). However, the cross talk between multiple regulatory pathways involved in seed germination remains poorly understood. Here, we show that ABA activates two MAP kinases, AtMPK3/AtMPK6, which interact with and phosphorylate AtABI5, a master regulator of ABA signaling. MAP kinase-mediated AtABI5 phosphorylation at the serine-314 position regulates its nuclear localization and dimerization. Interestingly, AtABI5 provides feedback regulation by directly binding to the promoter of AtMPK3 to modulate its transcription. Further, functional analyses revealed that overexpression of a phospho-null AtABI5S314A variant in the abi5-8 mutant background conferred increased ABA sensitivity during seed germination, heightened drought sensitivity, and delayed flowering compared to wild-type plants. Conversely, overexpression of phospho-mimic AtABI5S314D in abi5-8 mutant showed ABA insensitivity during seed germination, drought tolerance, and early floral transition similar to abi5-8 mutant. Collectively, our findings highlight that MAP kinase-mediated phosphorylation of AtABI5 fine-tunes ABA signaling by regulating its dimerization, providing new insights into the dynamic regulation of plant responses to environmental and developmental cues.

Utilizing CRISPR-based genetic modification for precise control of seed dormancy: progress, obstacles, and potential directions

Seed dormancy, a complex trait that is influenced by both nuclear and cytoplasmic factors, poses a significant challenge to agricultural productivity. Conventional dormancy-breaking techniques, including mechanical, physiological, and chemical methods, often yield inconsistent results, impair seed quality, and lack precision. This has necessitated exploration of more targeted and efficient approaches. CRISPR-based gene editing has emerged as a promising tool for the precise regulation of seed dormancy without compromising seed viability or sustainability. Although CRISPR has been successfully applied to modify genes that govern physiological traits in various crops, its use in dormancy regulation remains in the early stages. This review examines recent advancements in CRISPR-based approaches for modulating seed dormancy and discusses key gene targets, modification techniques, and the resulting effects. We also consider the future potential of CRISPR to enhance dormancy control across diverse crop species.

Tomato mitogen-activated protein kinase: mechanisms of adaptation in response to biotic and abiotic stresses

Plants live under various biotic and abiotic stress conditions, and to cope with the adversity and severity of these conditions, they have developed well-established resistance mechanisms. These mechanisms begin with the perception of stimuli, followed by molecular, biochemical, and physiological adaptive measures. Tomato (Solanum lycopersicum) is a globally significant vegetable crop that experiences several biotic and abiotic stress events that can adversely impact its quality and production. Mitogen-activated protein kinases (MAPKs) in tomato plants have crucial functions of mediating responses to environmental cues, internal signals, defense mechanisms, cellular processes, and plant development and growth. MAPK cascades respond to various environmental stress factors by modulating associated gene expression, influencing plant hormone synthesis, and facilitating interactions with other environmental stressors. Here, we review the evolutionary relationships of 16 tomato SlMAPK family members and emphasize on recent studies describing the regulatory functions of tomato SlMAPKs in both abiotic and biotic stress conditions. This review could enhance our comprehension of the MAPK regulatory network in biotic and abiotic stress conditions and provide theoretical support for breeding tomatoes with agronomic traits of excellent stress resistance.

A Positive Role for CaMEKK17 in Response to Drought Stress, Modulated by Clade A PP2Cs

The abscisic acid (ABA) signaling pathway is essential for plant response to abiotic stresses and can be modulated positively or negatively by MAPKKK proteins. This study focuses on the functional characterization of CaMEKK17, a MAPKKK previously recognized for its rapid induction under drought stress. Functional analyses demonstrated that CaMEKK17 is an active serine/threonine kinase with a conserved catalytic domain that is crucial for its kinase activity. CaMEKK17 silencing in pepper plants resulted in reduced drought tolerance, characterized by increased transpirational water loss and impaired ABA-mediated stomatal closure. Conversely, CaMEKK17 overexpression in Arabidopsis increased kinase activity, enhancing ABA sensitivity and drought tolerance. Further investigation revealed that CaMEKK17 interacts with pepper group A type 2C protein phosphatases (PP2Cs), particularly CaAITP1 and CaAIPP1, which inhibit its kinase activity. Protein-protein interactions mediated inhibition by CaAITP1, whereas CaAIPP1 relied on its phosphatase activity. Double gene silencing of CaMEKK17 and CaAITP1 demonstrated that CaMEKK17 functions downstream of CaAITP1 in ABA-mediated drought tolerance. Taken together, our findings suggest that CaMEKK17 positively modulates drought tolerance in pepper plants but may be inhibited by PP2Cs.

Genome-Wide Analysis of the Phospholipase Ds in Perennial Ryegrass Highlights LpABFs-LpPLDδ3 Cascade Modulated Osmotic and Heat Stress Responses

The phospholipase Ds (PLDs) are crucial for cellular signalling and play roles in plant abiotic stress response. In this study, we identified 12 PLD genes from the genome data of perennial ryegrass (Lolium perenne), which is widely used as forage and turfgrass. Among them, LpPLDδ3 was significantly repressed by ABA treatment, and induced by drought stress and heat stress treatments. The ectopic overexpression (OE) of LpPLDδ3 in Arabidopsis enhanced plant tolerance to osmotic and heat stress as demonstrated by an increased survival rate and reduced malondialdehyde (MDA) accumulation and electrolyte leakage (EL). Arabidopsis endogenous ABA RESPONSIVE ELEMENT BINDING FACTORs (ABFs) and heat stress responsive genes were elevated in LpPLDδ3 OE lines under osmotic and heat stress treatments. Additionally, overexpression of LpPLDδ3 in perennial ryegrass protoplasts could increase heat stress tolerance and elevate expression level of heat stress responsive genes. Moreover, LpABF2 and LpABF4 depressed the LpPLDδ3 expression by directly binding to its ABRE core-binding motif of promoter region. In summary, LpPLDδ3 was repressed by LpABF2 and LpABF4 and positively involved in perennial ryegrass osmotic and heat stress responses.

Metal-organic framework-based dual function nanosystems for aluminum detoxification and plant growth in acidic soil

Plants encounter various abiotic stresses throughout growth and development, with aluminum stress emerging as a major global agricultural challenge that hinders plant growth and limits crop yields in acidic soils. In this study, nanomaterials with dual functions, controlled release and adsorption, were constructed to alleviate aluminum toxicity. Specifically, two metal-organic frameworks, UiO-66 and ZIF-8, were used to load naphthylacetic acid and tryptophan, respectively. These two controlled-release systems were then combined with a chitosan-based matrix (NT@CS@UZ) to enable the regulated release of both compounds at distinct rates. Concurrently, the porous structure of these materials facilitates the adsorption of soluble aluminum in the plant rhizosphere. Results show that the acidic environment accelerates ZIF-8 degradation, triggering an early release of tryptophan under aluminum stress conditions. This early release promotes plant growth and alleviates stress damage. Naphthylacetic acid is subsequently released at a slower, sustained rate to stimulate root growth and further mitigate aluminum toxicity in roots. Additionally, NT@CS@UZ effectively adsorbs aluminum ions, limiting Al3+ uptake by plants and creating a low-aluminum barrier to protect roots. These dual function nanomaterials significantly boost crop yield and enhance stress resilience, presenting new avenues for food security and sustainable agricultural practices.

Dehydration priming remodels protein abundance and phosphorylation level regulating tolerance to subsequent dehydration or salt stress in creeping bentgrass

Dehydration priming (DP) induces stress memory which plays a positive role in plant adaptability, but it is not well understood how DP differentially regulates subsequent dehydration (cis priming) or salt (trans priming) tolerance at the post-translational level. Purpose of this study was to identify proteins, phosphorylation levels and sites, and relevant metabolic pathways for DP-induced dehydration or salt tolerance in Agrostis stolonifera. DP-induced differentially regulated proteins (DRPs) were mostly located in the cytoplasm, chloroplast, and cell membrane, and differentially regulated phosphoproteins (DRPPs) were mostly nuclear proteins and cytoplasmic proteins. DP regulated common phosphorylation sites ([SP] and [RxxS]) under dehydration and salt conditions and also individually affected 8 or 11 phosphorylation sites under dehydration or salt stress. DP-regulated DRPPs were mainly rich in glycolysis and glutathione metabolism pathways, RNA splicing, and dynamin family proteins under dehydration stress, whereas DP-regulated salt tolerance was mainly related to chlorophyll metabolism, photosynthesis, MAPK signaling cascade, and ABC transporter I family at the phosphorylation level. In addition, the DP also significantly up-regulated phosphorylation of histones (ATXR3 and SETD1A) in response to subsequent dehydration and salt stress as well as abundances of antioxidant enzymes, dynamin family protein, and KCS6 under dehydration stress or abundances of PETE, HMGA, XTH, and ABCI6 under salt stress, respectively. Transcriptomics analysis further indicated that DP-regulated dehydration or salt tolerance was also related to transcriptional regulation in the early stage. Current results provided better understanding of the role of stress memory in plant adaptability to repeated or crossed stress via post-translational modifications (PTMs). SIGNIFICANCE: Recurrent moderate drought may buffer drought legacies in many plant species. When plants were exposed to repeated drought stress, their adaptability to subsequent stress could be enhanced, which is known as "stress memory". Dehydration priming has been found to be an important approach to induce stress memory. Current results provided better understanding of the role of stress memory in plant adaptability to repeated or crossed stress via post-translational modifications.

The FvABF3-FvALKBH10B-FvSEP3 cascade regulates fruit ripening in strawberry

Fruit ripening is a highly-orchestrated process that requires the fine-tuning and precise control of gene expression, which is mainly governed by phytohormones, epigenetic modifiers, and transcription factors. How these intrinsic regulators coordinately modulate the ripening remains elusive. Here we report the identification and characterization of FvALKBH10B as an N6-methyladenosine (m6A) RNA demethylase necessary for the normal ripening of strawberry (Fragaria vesca) fruit. FvALKBH10B is induced by phytohormone abscisic acid (ABA), and ABA-Responsive Element Binding Factor 3 (FvABF3), a master regulator in ABA signaling, is responsible for this activation. FvALKBH10B mutation leads to a delay in fruit ripening and causes global m6A hypermethylation of 1859 genes. Further analyses show that FvALKBH10B positively modulates the mRNA stability of SEPALLATA3 (FvSEP3) encoding a transcription factor via m6A demethylation. In turn, FvSEP3 targets numerous ripening-related genes including those associated with biosynthesis of ABA and anthocyanin and regulates their expression. Our findings uncover an FvABF3-FvALKBH10B-FvSEP3 cascade in controlling fruit ripening in strawberry and provide insights into the complex regulatory networks involved in this process.

ABA-regulated MAPK signaling pathway promotes hormesis in sugar beet under cadmium exposure

Sugar beet (Beta vulgaris L.) shows potential as an energy crop for cadmium (Cd) phytoremediation. To elucidate its in vivo response strategy to Cd exposure, seedlings were treated with 1, 3, and 5 mmol/L CdCl2 (Cd-1, Cd-3, and Cd-5) for 6 h, using 0 mmol/L CdCl2 (Cd-0) as the control. The results showed that Cd-3 promoted a unique "hormesis" effect, leading to superior growth performance, increased levels of chlorophyll, soluble protein, and SOD activity, and reduced MDA content in sugar beet, compared to Cd-1, Cd-5, and even Cd-0. GO and KEGG enrichments and PPI networks of transcriptomic analysis revealed that the differentially expressed genes (DEGs) were primarily involved in lipid metabolism, cellular protein catabolism, and photosynthesis. Notably, the MAPK signaling pathway was significantly enriched only under Cd-3, with the up-regulation of ABA-related core gene BvPYL9 and an increase in ABA content after 6 h of Cd exposure. Furthermore, overexpression of BvPYL9 in Arabidopsis thaliana (OE-1 and OE-2) resulted in enhanced growth (fresh weight, dry weight, and root length), as well as higher ABA and soluble protein contents under different Cd treatments. Cd-induced transcriptional responses of BvPYL9 were also evident in OE-1 and OE-2, especially at 10 µmol/L, indicated by qRT-PCR. These findings suggest that ABA-mediated MAPK signaling pathway is activated in response to Cd toxicity, with BvPYL9 being a key factor in the cascade effects for the Cd-induced hormesis in sugar beet.

MAPKKK28 functions upstream of the MKK1-MPK1 cascade to regulate abscisic acid responses in rice

The mitogen-activated protein kinase (MAPK) cascade (MAPKKK-MAPKK-MAPK) plays a critical role in biotic and abiotic stress responses and abscisic acid (ABA) signalling. A previous study has shown that the ABA-activated MKK1-MPK1 cascade is essential in regulating ABA response and stress tolerance in rice. However, the specific MAPKKK upstream of the MKK1-MPK1 cascade in ABA signalling remains unknown. Here, we identified that MAPKKK28, a previously uncharacterized member of the rice MEKK family, is involved in regulating ABA responses, including seed germination, root growth, stomatal closure, and the tolerance to oxidative stress and osmotic stress. We found that MAPKKK28 directly interacts with and phosphorylates MKK1. Further analysis indicated that the activation of both MKK1 and MPK1 depends on MAPKKK28 in ABA signalling. Genetic analysis revealed that MAPKKK28 functions upstream of the MKK1-MPK1 cascade to positively regulate ABA responses and enhance tolerance to oxidative and osmotic stress. These results not only reveal a new complete MAPK cascade in plants but also uncover its importance in ABA signalling.

The BpPP2C-BpMADS11-BpERF61 signaling confers drought tolerance in Betula platyphylla

Plant MADS-box proteins are vital for abiotic stress tolerance, yet their mechanisms for responding to drought remain poorly understood. Here, we investigated the drought tolerance mechanism of a MADS-box protein (BpMADS11) from birch (Betula platyphylla) using immunoprecipitation, Western blotting, yeast two-hybrid, yeast one-hybrid, ChIP, RNA-seq, and dual-luciferase assays to explore post-translational modifications, protein interactions, and gene regulation. Birch plants overexpressing BpMADS11 exhibited enhanced drought tolerance, while knockout lines displayed reduced tolerance. Under drought conditions, BpMADS11 interacts with protein phosphatase 2C22 (BpPP2C22), which dephosphorylates BpMADS11. Birch plants that overexpress BpMADS11 and lack BpPP2C22 show significantly reduced drought tolerance compared with those that only overexpress BpMADS11. BpMADS11 regulates the expression of BpERF61 by binding to CArG-box in its promoter. The dephosphorylated BpMADS11 exhibits increased DNA binding ability and increased expression of BpERF61. Like BpMADS11, birch plants overexpressing BpERF61 show improved drought tolerance, while those with BpERF61 knockout exhibit decreased tolerance. BpERF61 binds to specific DNA motifs including 'CACGTG' (G-box), 'GGGCCCC', and 'TTGGAT' to regulate the genes related to drought stress. Collectively, BpMADS11 undergoes dephosphorylation through its interaction with BpPP2C22, prompting the expression of BpERF61. Subsequently, BpERF61 regulates downstream genes by binding to specific DNA motifs, thereby enhancing drought tolerance.

Genome-Wide Identification of Freezing-Responsive Genes in a Rapeseed Line NTS57 Tolerant to Low-Temperature

Winter rapeseed is a high-oil crop that exhibits significant sensitivity to low temperatures, leading to a substantial reduction in production. Hence, it is of great significance to elucidate the genomic genetic mechanism of strong freezing-resistant winter rapeseed to improve their freezing-resistant traits. In this study, global transcriptome expression profiles of the freezing-resistant cultivar NTS57 (NS) under freezing stress were obtained for the years 2015, 2016, and 2017 by RNA sequencing (RNA-seq). Most differentially expressed genes (DEGs) were involved in the plant hormone signal transduction, alpha-linolenic acid metabolism, protein processing, glutathione metabolism, and plant-pathogen interaction pathways. Antioxidant enzyme activities and lipid peroxidation levels were significantly positively and negatively correlated with overwintering rate (OWR), respectively. After freezing treatment, the formation of freezing resistance of NS was attributed to the increase in antioxidant enzyme activities and content of osmotic regulation substances, as well as the decrease in lipid peroxidation level. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) and phenotypic verification indicated that heat stress transcription factor A2 (HSFA2) and 17.6 kDa class II heat shock protein (HSP17.6) participated in the response to freezing stress. This study will further refine the regulatory network of plants against freezing stress and help to screen candidate genes for improving plant freezing resistance.

Genome-wide identification, expression analysis of the R2R3-MYB gene family and their potential roles under cold stress in Prunus sibirica

BACKGROUND

The R2R3-MYB transcription factors in plants participate in various physiological and biochemical processes and responds to various external stimuli. Prunus sibirica (known as Siberian apricot) is a drupe tree species that produces extremely high nutritional value kernels. However, it is susceptiblility to frost damage during the flowering period, results in a marked reduction in kernel yield.

RESULTS

In this study, the MYB gene family of P. sibirica (PsMYB) was systematically analyzed, and 116 R2R3-MYB genes that were distributed unevenly over eight chromosomes were ultimately screened. Phylogenetic analysis divided these 116 genes into 30 subgroups. We discovered that 37 PsMYBs had cold stress-responsive promoters, and six PsMYBs were annotated to be associated with cold response. Intraspecific homology analysis identified segmental duplication as the primary gene amplification mechanism, and homology analysis of the PsMYB genes with those of five other species revealed phylogenetic relationships with Rosaceae species. Protein interaction studies revealed collaborative regulation of the PsMYB proteins with Arabidopsis protein, and transcriptome analysis identified PsMYB genes that were highly expressed at low temperatures. Additionally, the expression levels of 22 PsMYBs in different tissue parts of P. sibirica and under different low-temperature stress conditions were evaluated using quantitative real-time PCR, with the results verifying that PsMYBs are specifically expressed in different plant parts and may be involved in the growth and development of P. sibirica species. Genes upregulated after exposure to low-temperature stress and likely involved in cold response were identified.

CONCLUSION

This study lays a foundation for understanding the molecular biology of PsMYBs in P. sibirica and provides a theoretical basis for the future study of transgenic lines with cold resistance during the flowering period of this tree.

The U1 small nuclear RNA enhances drought tolerance in Arabidopsis

Alternative splicing (AS) is an important posttranscriptional regulatory mechanism that improves plant tolerance to drought stress by modulating gene expression and generating proteome diversity. The interaction between the 5' end of U1 small nuclear RNA (U1 snRNA) and the conserved 5' splice site of precursor messenger RNA (pre-mRNA) is pivotal for U1 snRNP involvement in AS. However, the roles of U1 snRNA in drought stress responses remain unclear. This study provides a comprehensive analysis of AtU1 snRNA in Arabidopsis (Arabidopsis thaliana), revealing its high conservation at the 5' end and a distinctive four-leaf clover structure. AtU1 snRNA is localized in the nucleus and expressed in various tissues, with prominent expression in young floral buds, flowers, and siliques. The overexpression of AtU1 snRNA confers enhanced abiotic stress tolerance, as evidenced in seedlings by longer seedling primary root length, increased fresh weight, and a higher greening rate compared with the wild-type. Mature AtU1 snRNA overexpressor plants exhibit higher survival rates and lower water loss rates under drought stress, accompanied by a significant decrease in H2O2 and an increase in proline. This study also provides evidence of altered expression levels of drought-related genes in AtU1 snRNA overexpressor or genome-edited lines, reinforcing the crucial role of AtU1 snRNA in drought stress responses. Furthermore, the overexpression of AtU1 snRNA influences the splicing of downstream target genes, with a notable impact on SPEECHLESS (SPCH), a gene associated with stomatal development, potentially explaining the observed decrease in stomatal aperture and density. These findings elucidate the critical role of U1 snRNA as an AS regulator in enhancing drought stress tolerance in plants, contributing to a deeper understanding of the AS pathway in drought tolerance and increasing awareness of the molecular network governing drought tolerance in plants.

Mechanisms of Cadmium stress response in watermelon: Insights from physiological, transcriptomic, and metabolic analyses

Cadmium (Cd) contamination of soil may lead to Cd stress for plants, which significantly hinders plant growth and development, posing a risk to human health through the consumption of Cd-contaminated foods. Watermelon (Citrullus lanatus), a widely consumed fruit, is particularly affected by Cd stress globally, yet the mechanisms underlying its response are not well understood. Here, we subjected watermelon seedlings to simulated Cd stress treatment and explored the physiological, transcriptomic, and metabolic response. Our findings revealed that Cd stress treatment led to increased accumulation of reactive oxygen species (ROS) in watermelon leaves. Transcriptome sequencing unveiled a multitude of osmotic and oxidative stress-responsive genes, including peroxidase (POD), MYB, voltage-dependent anion channel (SLAC1), and ABC transporter. KEGG enrichment analysis highlighted the predominant enrichment of Cd stress-responsive genes in pathways such as glutathione (GSH) metabolism, MAPK signaling, and biosynthesis of secondary metabolites. Within the GSH metabolism pathway, several glutathione S-transferase (GST) genes were up-regulated, alongside phytochelatin synthetase (PCS) genes involved in phytochelatin synthesis. In the MAPK signaling pathway, genes associated with ABA and ethylene signal transduction showed up-regulation following Cd stress. Metabolomic analysis demonstrated that Cd stress enhanced the production of amino acids, phenolamines, and esters. Overall, our study elucidates that watermelon responds to Cd stress by activating its antioxidant system, GSH metabolism pathway, MAPK signal pathway, and biosynthesis of key metabolites. These findings offer valuable insights for the remediation of heavy metal pollution in soil affecting plant life.

Bacterial N-Acyl Homoserine Lactone Priming Enhances Leaf-Rust Resistance in Winter Wheat and Some Genomic Regions Are Associated with Priming Efficiency

Leaf rust (Puccinia triticina) is a common disease that causes significant yield losses in wheat. The most frequently used methods to control leaf rust are the application of fungicides and the cultivation of resistant genotypes. However, high genetic diversity and associated adaptability of pathogen populations hamper achieving durable resistance in wheat. Emerging alternatives, such as microbial priming, may represent an effective measure to stimulate plant defense mechanisms and could serve as a means of controlling a broad range of pathogens. In this study, 175 wheat genotypes were inoculated with two bacterial strains: Ensifer meliloti strain expR+ch (producing N-acyl homoserine lactone (AHL)) or transformed E. meliloti carrying the lactonase gene attM (control). In total, 21 genotypes indicated higher resistance upon bacterial AHL priming. Subsequently, the phenotypic data of 175 genotypes combined with 9917 single-nucleotide polymorphisms (SNPs) in a genome-wide association study to identify quantitative trait loci (QTLs) and associated markers for relative infection under attM and expR+ch conditions and priming efficiency using the Genome Association and Prediction Integrated Tool (GAPIT). In total, 15 QTLs for relative infection under both conditions and priming efficiency were identified on chromosomes 1A, 1B, 2A, 3A, 3B, 3D, 6A, and 6B, which may represent targets for wheat breeding for priming and leaf-rust resistance.

A Mitogen-Activated Protein Kinase Pathway Is Required for Bacillus amyloliquefaciens PMB05 to Enhance Disease Resistance to Bacterial Soft Rot in Arabidopsis thaliana

When a plant is infected by a pathogen, endogenous immune responses are initiated. When the initiation of these defense responses is induced by a pathogen-associated molecular pattern (PAMP) of a pathogen, it is called PAMP-triggered immunity (PTI). Previous studies have shown that Bacillus amyloliquefaciens PMB05 can enhance PTI signals and improve disease control of bacterial soft rot and wilt in Arabidopsis thaliana. In the context of controlling bacterial wilt disease, the involvement of a mitogen-activated protein kinase (MAPK) signaling pathway has been established. Nevertheless, it remains unclear whether this pathway is also required for B. amyloliquefaciens PMB05 in controlling bacterial soft rot. In this study, A. thaliana ecotype Columbia (Col-0) and its mutants on a MAPK pathway-related pathway were used as a model and established that the ability of B. amyloliquefaciens PMB05 to control soft rot requires the participation of the MAPK pathway. Moreover, the enhancement of disease resistance by PMB05 is highly correlated with the activation of reactive oxygen species generation and stomata closure, rather than callose deposition. The spray inoculation method was used to illustrate that PMB05 can enhance stomatal closure, thereby restricting invasion by the soft rot bacterium. This control mechanism has also been demonstrated to require the activation of the MAPK pathway. This study demonstrates that B. amyloliquefaciens PMB05 can accelerate stomata closure via the activation of the MAPK pathway during PTI, thereby reducing pathogen invasion and achieving disease resistance against bacterial soft rot.

The Abscisic Acid Receptor Gene StPYL8-like from Solanum tuberosum Confers Tolerance to Drought Stress in Transgenic Plants

Pyrabactin resistance 1-like (PYL) proteins are abscisic acid (ABA) receptors that play a crucial role in the plant's response to adverse environmental conditions. However, as of yet, there is limited research on the role of PYL proteins in potato. In this study, a potato PYL gene, StPYL8-like, was identified through transcriptome analysis under drought stress. Molecular characterization revealed that the StPYL8-like protein possesses a highly conserved PYL family domain. Evolutionary analysis demonstrated that StPYL8-like protein clusters with various PYL proteins are involved in stress responses across different species. Functional assays showed that StPYL8-like robustly responds to different abiotic stresses, including drought and ABA treatment. Furthermore, the transient and stable expressions of StPYL8-like in tobacco enhanced their drought resistance, leading to increased plant height, leaf number, and fresh weight, as well as an improved root system. Transgenic tobacco carrying the StPYL8-like gene exhibited lower malondialdehyde (MDA) levels and higher proline accumulation and antioxidant enzyme activity compared to wild-type plants under drought conditions. Moreover, StPYL8-like upregulated the expression of stress-responsive genes (NtRD29A, NtLEA5, NtP5CS, NtPOD, NtSOD, and NtCAT) in transgenic plants subjected to drought stress. Collectively, these findings highlight the positive regulatory role of the StPYL8-like gene in enhancing potato plants' response to drought stress.

ABI5 binding proteins: key players in coordinating plant growth and development

During the course of terrestrial evolution, plants have developed complex networks that involve the coordination of phytohormone signalling pathways in order to adapt to an ever-changing environment. Transcription factors coordinate these responses by engaging in different protein complexes and exerting both positive and negative effects. ABA INSENSITIVE 5 (ABI5) binding proteins (AFPs), which are closely related to NOVEL INTERACTOR OF JAZ (NINJA)-like proteins, are known for their fundamental role in plants' morphological and physiological growth. Recent studies have shown that AFPs regulate several hormone-signalling pathways, including abscisic acid (ABA) and gibberellic acid (GA). Here, we review the genetic control of AFPs and their crosstalk with plant hormone signalling, and discuss the contributions of AFPs to plants' growth and development.

Biotechnological approaches for enhancement of heavy metal phytoremediation capacity of plants

Heavy metals are extremely hazardous for human health due to their toxic effects. They are non-biodegradable in nature, thus remain in the environment and enter and accumulate in the human body through biomagnification; hence, there is a serious need of their remediation. Phytoremediation has emerged as a green, sustainable, and effective solution for heavy metal removal and many plant species could be employed for this purpose. Plants are able to sequester substantial quantity of heavy metals, in some cases thousands of ppm, due to their robust physiology enabling high metal tolerance and anatomy supporting metal ion accumulation. Identification and modification of potential target genes involved in heavy metal accumulation have led to improved phytoremediation capacity of plants at the molecular level. The introduction of foreign genes through genetic engineering approaches has further enhanced phytoremediation capacity manifolds. This review gives an insight towards improving the phytoremediation efficiency through a better understanding of molecular mechanisms involved, expression of different proteins, genetic engineering approaches for transgenic production, and genetic modifications. It also comprehends novel omics tools such as genomics, metabolomics, proteomics, transcriptomics, and genome editing technologies for improvement of phytoremediation ability of plants.

CwJAZ4/9 negatively regulates jasmonate-mediated biosynthesis of terpenoids through interacting with CwMYC2 and confers salt tolerance in Curcuma wenyujin

Plant JASMONATE ZIM-DOMAIN (JAZ) genes play crucial roles in regulating the biosynthesis of specialized metabolites and stressful responses. However, understanding of JAZs controlling these biological processes lags due to numerous JAZ copies. Here, we found that two leaf-specific CwJAZ4/9 genes from Curcuma wenyujin are strongly induced by methyl-jasmonate (MeJA) and negatively correlated with terpenoid biosynthesis. Yeast two-hybrid, luciferase complementation imaging and in vitro pull-down assays confirmed that CwJAZ4/9 proteins interact with CwMYC2 to form the CwJAZ4/9-CwMYC2 regulatory cascade. Furthermore, transgenic hairy roots showed that CwJAZ4/9 acts as repressors of MeJA-induced terpenoid biosynthesis by inhibiting the terpenoid pathway and jasmonate response, thus reducing terpenoid accumulation. In addition, we revealed that CwJAZ4/9 decreases salt sensitivity and sustains the growth of hairy roots under salt stress by suppressing the salt-mediated jasmonate responses. Transcriptome analysis for MeJA-mediated transgenic hairy root lines further confirmed that CwJAZ4/9 negatively regulates the terpenoid pathway genes and massively alters the expression of genes related to salt stress signaling and responses, and crosstalks of multiple phytohormones. Altogether, our results establish a genetic framework to understand how CwJAZ4/9 inhibits terpenoid biosynthesis and confers salt tolerance, which provides a potential strategy for producing high-value pharmaceutical terpenoids and improving resistant C. wenyujin varieties by a genetic approach.

Post-Translational Modification of WRKY Transcription Factors

Post-translational modifications (PTMs) of proteins are involved in numerous biological processes, including signal transduction, cell cycle regulation, growth and development, and stress responses. WRKY transcription factors (TFs) play significant roles in plant growth, development, and responses to both biotic and abiotic stresses, making them one of the largest and most vital TF families in plants. Recent studies have increasingly highlighted the importance of PTMs of WRKY TFs in various life processes. This review focuses on the recent advancements in understanding the phosphorylation and ubiquitination of WRKY TFs, particularly their roles in resistance to biotic and abiotic stresses and in plant growth and development. Future research directions and prospects in this field are also discussed.

Comprehensive Review on Bimolecular Fluorescence Complementation and Its Application in Deciphering Protein-Protein Interactions in Cell Signaling Pathways

Signaling pathways are responsible for transmitting information between cells and regulating cell growth, differentiation, and death. Proteins in cells form complexes by interacting with each other through specific structural domains, playing a crucial role in various biological functions and cell signaling pathways. Protein-protein interactions (PPIs) within cell signaling pathways are essential for signal transmission and regulation. The spatiotemporal features of PPIs in signaling pathways are crucial for comprehending the regulatory mechanisms of signal transduction. Bimolecular fluorescence complementation (BiFC) is one kind of imaging tool for the direct visualization of PPIs in living cells and has been widely utilized to uncover novel PPIs in various organisms. BiFC demonstrates significant potential for application in various areas of biological research, drug development, disease diagnosis and treatment, and other related fields. This review systematically summarizes and analyzes the technical advancement of BiFC and its utilization in elucidating PPIs within established cell signaling pathways, including TOR, PI3K/Akt, Wnt/β-catenin, NF-κB, and MAPK. Additionally, it explores the application of this technology in revealing PPIs within the plant hormone signaling pathways of ethylene, auxin, Gibberellin, and abscisic acid. Using BiFC in conjunction with CRISPR-Cas9, live-cell imaging, and ultra-high-resolution microscopy will enhance our comprehension of PPIs in cell signaling pathways.

Perfluorobutanoic acid triggers metabolic and transcriptional reprogramming in wheat seedlings

The environmental risks of fluorinated alternatives are of great concern with the phasing out of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate. Here, multi-omics (i.e., metabolomics and transcriptomics) coupled with physiological and biochemical analyses were employed to investigate the stress responses of wheat seedings (Triticum aestivum L.) to perfluorobutanoic acid (PFBA), one of the short-chain per- and polyfluoroalkyl substances (PFAS) and PFOA alternatives, at environmentally relevant concentrations (0.1-100 ng/g). After 28 days of soil exposure, PFBA boosted the generation of OH and O2- in wheat seedlings, resulting in lipid peroxidation, protein perturbation and impaired photosynthesis. Non-enzymatic antioxidant defense systems (e.g., glutathione, phenolics, and vitamin C) and enzymatic antioxidant copper/zinc superoxide dismutase were strikingly activated (p < 0.05). PFBA-triggered oxidative stress induced metabolic and transcriptional reprogramming, including carbon and nitrogen metabolisms, lipid metabolisms, immune responses, signal transduction processes, and antioxidant defense-related pathways. Down-regulation of genes related to plant-pathogen interaction suggested suppression of the immune-response, offering a novel understanding on the production of reactive oxygen species in plants under the exposure to PFAS. The identified MAPK signaling pathway illuminated a novel signal transduction mechanism in plant cells in response to PFAS. These findings provide comprehensive understandings on the phytotoxicity of PFBA to wheat seedlings and new insights into the impacts of PFAS on plants.

Identification and Functional Analysis of KH Family Genes Associated with Salt Stress in Rice

Salinity stress has a great impact on crop growth and productivity and is one of the major factors responsible for crop yield losses. The K-homologous (KH) family proteins play vital roles in regulating plant development and responding to abiotic stress in plants. However, the systematic characterization of the KH family in rice is still lacking. In this study, we performed genome-wide identification and functional analysis of KH family genes and identified a total of 31 KH genes in rice. According to the homologs of KH genes in Arabidopsis thaliana, we constructed a phylogenetic tree with 61 KH genes containing 31 KH genes in Oryza sativa and 30 KH genes in Arabidopsis thaliana and separated them into three major groups. In silico tissue expression analysis showed that the OsKH genes are constitutively expressed. The qRT-PCR results revealed that eight OsKH genes responded strongly to salt stresses, and OsKH12 exhibited the strongest decrease in expression level, which was selected for further study. We generated the Oskh12-knockout mutant via the CRISPR/Cas9 genome-editing method. Further stress treatment and biochemical assays confirmed that Oskh12 mutant was more salt-sensitive than Nip and the expression of several key salt-tolerant genes in Oskh12 was significantly reduced. Taken together, our results shed light on the understanding of the KH family and provide a theoretical basis for future abiotic stress studies in rice.

Potential molecular mechanism of photosynthesis regulation by PeMPK7 in poplar under para-hydroxybenzoic acid stress

Due to continuous plantation of poplar, its growth and biomass accumulation may be negatively affected by the accumulation of allelochemicals such as para-hydroxybenzoic acid (pHBA) in soil. As photosynthesis is the most fundamental process in plants, it can be negatively impacted by pHBA stress. Therefore, it is crucial to improve photosynthetic capacity under pHBA stress to facilitate poplar plant growth. The mitogen-activated protein kinase (MAPK) cascade pathway is widely involved in environmental stress responses in plants. However, the regulation mechanisms of photosynthesis-related pathways by MAPK pathway genes under pHBA stress are still unclear. In this study, through transcriptome analysis and weighted gene co-expression network analysis, we observed that PeMPK7 overexpression in poplar can regulate the expression of photosynthesis-related genes and transcription factor genes, namely, WRKY1, WRKY33, and ERF3, during the early stage of pHBA stress. In addition, PeMPK7 can improve photosynthesis in poplar under long-term pHBA stress. Moreover, yeast two-hybrid and pull-down assays confirmed the interaction between PeMPK7 and PeMKK7/10. Based on these results, a schematic diagram of the pathways involved in the regulation of photosynthesis by PeMPK7 was constructed. This study provided novel insights into the molecular mechanisms of regulation of pHBA stress via MAPK cascade pathway.

Seasonal drought promotes citrate accumulation in citrus fruit through the CsABF3-activated CsAN1-CsPH8 pathway

Plenty of rainfall but unevenly seasonal distribution happens regularly in southern China. Seasonal drought from summer to early autumn leads to citrus fruit acidification, but how seasonal drought regulates citrate accumulation remains unknown. Herein, we employed a set of physiological, biochemical, and molecular approaches to reveal that CsABF3 responds to seasonal drought stress and modulates citrate accumulation in citrus fruits by directly regulating CsAN1 and CsPH8. Here, we demonstrated that irreversible acidification of citrus fruits is caused by drought lasting for > 30 d during the fruit enlargement stage. We investigated the transcriptome characteristics of fruits affected by drought and corroborated the pivotal roles of a bHLH transcription factor (CsAN1) and a P3A-ATPase gene (CsPH8) in regulating citrate accumulation in response to drought. Abscisic acid (ABA)-responsive element binding factor 3 (CsABF3) was upregulated by drought in an ABA-dependent manner. CsABF3 activated CsAN1 and CsPH8 expression by directly and specifically binding to the ABA-responsive elements (ABREs) in the promoters and positively regulated citrate accumulation. Taken together, this study sheds new light on the regulatory module ABA-CsABF3-CsAN1-CsPH8 responsible for citrate accumulation under drought stress, which advances our understanding of quality formation of citrus fruit.

An Escherichia coli-Based Phosphorylation System for Efficient Screening of Kinase Substrates

Posttranslational modifications (PTMs), particularly phosphorylation, play a pivotal role in expanding the complexity of the proteome and regulating diverse cellular processes. In this study, we present an efficient Escherichia coli phosphorylation system designed to streamline the evaluation of potential substrates for Arabidopsis thaliana plant kinases, although the technology is amenable to any. The methodology involves the use of IPTG-inducible vectors for co-expressing kinases and substrates, eliminating the need for radioactive isotopes and prior protein purification. We validated the system's efficacy by assessing the phosphorylation of well-established substrates of the plant kinase SnRK1, including the rat ACETYL-COA CARBOXYLASE 1 (ACC1) and FYVE1/FREE1 proteins. The results demonstrated the specificity and reliability of the system in studying kinase-substrate interactions. Furthermore, we applied the system to investigate the phosphorylation cascade involving the A. thaliana MKK3-MPK2 kinase module. The activation of MPK2 by MKK3 was demonstrated to phosphorylate the Myelin Basic Protein (MBP), confirming the system's ability to unravel sequential enzymatic steps in phosphorylation cascades. Overall, this E. coli phosphorylation system offers a rapid, cost-effective, and reliable approach for screening potential kinase substrates, presenting a valuable tool to complement the current portfolio of molecular techniques for advancing our understanding of kinase functions and their roles in cellular signaling pathways.

A B-box transcription factor OsBBX17 regulates saline-alkaline tolerance through the MAPK cascade pathway in rice

Rice OsBBX17 encodes a B-box zinc finger transcription factor in which the N-terminal B-box structural domain interacts with OsMPK1. In addition, it directly binds to the G-box of OsHAK2 and OsHAK7 promoters and represses their transcription. Under saline-alkaline conditions, the expression of OsBBX17 was inhibited. Meanwhile, activation of the OsMPK1-mediated mitogen-activated protein kinase cascade pathway caused OsMPK1 to interact with OsBBX17 and phosphorylate OsBBX17 at the Thr-95 site. It reduced OsBBX17 DNA-binding activity and enhanced saline-alkaline tolerance by deregulating transcriptional repression of OsHAK2 and OsHAK7. Genetic assays showed that the osbbx17-KO had an excellent saline-alkaline tolerance, whereas the opposite was in OsBBX17-OE. In addition, overexpression of OsMPK1 significantly improved saline-alkaline tolerance, but knockout of OsMPK1 caused an increased sensitivity. Further overexpression of OsBBX17 in the osmpk1-KO caused extreme saline-alkaline sensitivity, even a quick death. OsBBX17 was validated in saline-alkaline tolerance from two independent aspects, transcriptional level and post-translational protein modification, unveiling a mechanistic framework by which OsMPK1-mediated phosphorylation of OsBBX17 regulates the transcription of OsHAK2 and OsHAK7 to enhance the Na+ /K+ homeostasis, which partially explains light on the molecular mechanisms of rice responds to saline-alkaline stress via B-box transcription factors for the genetic engineering of saline-alkaline tolerant crops.

Membrane-associated NRPM proteins are novel suppressors of stomatal production in Arabidopsis

In Arabidopsis, stomatal development and patterning require tightly regulated cell division and cell-fate differentiation that are controlled by key transcription factors and signaling molecules. To identify new regulators of stomatal development, we assay the transcriptomes of plants bearing enriched stomatal lineage cells that undergo active division. A member of the novel regulators at the plasma membrane (NRPM) family annotated as hydroxyproline-rich glycoproteins was identified to highly express in stomatal lineage cells. Overexpressing each of the four NRPM genes suppressed stomata formation, while the loss-of-function nrpm triple mutants generated severely overproduced stomata and abnormal patterning, mirroring those of the erecta receptor family and MAPKKK yoda null mutants. Manipulation of the subcellular localization of NRPM1 surprisingly revealed its regulatory roles as a peripheral membrane protein instead of a predicted cell wall protein. Further functional characterization suggests that NRPMs function downstream of the EPF1/2 peptide ligands and upstream of the YODA MAPK pathway. Genetic and cell biological analyses reveal that NRPM may promote the localization and function of the ERECTA receptor proteins at the cell surface. Therefore, we identify NRPM as a new class of signaling molecules at the plasma membrane to regulate many aspects of plant growth and development.

Genome-wide identification of MAPK family in papaya (Carica papaya) and their involvement in fruit postharvest ripening

BACKGROUND

Papaya (Carica papaya) is an economically important fruit cultivated in the tropical and subtropical regions of China. However, the rapid softening rate after postharvest leads to a short shelf-life and considerable economic losses. Accordingly, understanding the mechanisms underlying fruit postharvest softening will be a reasonable way to maintain fruit quality and extend its shelf-life.

RESULTS

Mitogen-activated protein kinases (MAPKs) are conserved and play essential roles in response to biotic and abiotic stresses. However, the MAPK family remain poorly studied in papaya. Here, a total of nine putative CpMAPK members were identified within papaya genome, and a comprehensive genome-wide characterization of the CpMAPKs was performed, including evolutionary relationships, conserved domains, gene structures, chromosomal locations, cis-regulatory elements and expression profiles in response to phytohormone and antioxidant organic compound treatments during fruit postharvest ripening. Our findings showed that nearly all CpMAPKs harbored the conserved P-loop, C-loop and activation loop domains. Phylogenetic analysis showed that CpMAPK members could be categorized into four groups (A-D), with the members within the same groups displaying high similarity in protein domains and intron-exon organizations. Moreover, a number of cis-acting elements related to hormone signaling, circadian rhythm, or low-temperature stresses were identified in the promoters of CpMAPKs. Notably, gene expression profiles demonstrated that CpMAPKs exhibited various responses to 2-chloroethylphosphonic acid (ethephon), 1-methylcyclopropene (1-MCP) and the combined ascorbic acid (AsA) and chitosan (CTS) treatments during papaya postharvest ripening. Among them, both CpMAPK9 and CpMAPK20 displayed significant induction in papaya flesh by ethephon treatment, and were pronounced inhibition after AsA and CTS treatments at 16 d compared to those of natural ripening control, suggesting that they potentially involve in fruit postharvest ripening through ethylene signaling pathway or modulating cell wall metabolism.

CONCLUSION

This study will provide some valuable insights into future functional characterization of CpMAPKs, and hold great potential for further understanding the molecular mechanisms underlying papaya fruit postharvest ripening.

Comparative transcriptome analysis of two contrasting genotypes provides new insights into the drought response mechanism in pigeon pea (Cajanus cajan L. Millsp.)

BACKGROUND

Despite plant's ability to adapt and withstand challenging environments, drought poses a severe threat to their growth and development. Although pigeon pea is already quite resistant to drought, the prolonged dehydration induced by the aberrant climate poses a serious threat to their survival and productivity.

OBJECTIVE

Comparative physiological and transcriptome analyses of drought-tolerant (CO5) and drought-sensitive (CO1) pigeon pea genotypes subjected to drought stress were carried out in order to understand the molecular basis of drought tolerance in pigeon pea.

METHODS

The transcriptomic analysis allowed us to examine how drought affects the gene expression of C. cajan. Using bioinformatics tools, the unigenes were de novo assembled, annotated, and functionally evaluated. Additionally, a homology-based sequence search against the droughtDB database was performed to identify the orthologs of the DEGs.

RESULTS

1102 potential drought-responsive genes were found to be differentially expressed genes (DEGs) between drought-tolerant and drought-sensitive genotypes. These included Abscisic acid insensitive 5 (ABI5), Nuclear transcription factor Y subunit A-7 (NF-YA7), WD40 repeat-containing protein 55 (WDR55), Anthocyanidin reductase (ANR) and Zinc-finger homeodomain protein 6 (ZF-HD6) and were highly expressed in the tolerant genotype. Further, GO analysis revealed that the most enriched classes belonged to biosynthetic and metabolic processes in the biological process category, binding and catalytic activity in the molecular function category and nucleus and protein-containing complex in the cellular component category. Results of KEGG pathway analysis revealed that the DEGs were significantly abundant in signalling pathways such as plant hormone signal transduction and MAPK signalling pathways. Consequently, in our investigation, we have identified and validated by qPCR a group of genes involved in signal reception and propagation, stress-specific TFs, and basal regulatory genes associated with drought response.

CONCLUSION

In conclusion, our comprehensive transcriptome dataset enabled the discovery of candidate genes connected to pathways involved in pigeon pea drought response. Our research uncovered a number of unidentified genes and transcription factors that could be used to understand and improve susceptibility to drought.

Exploring cell aggregation as a defense strategy against perchlorate stress in Chlamydomonas reinhardtii through multi-omics analysis

Perchlorate (ClO4-) is a type of novel, widely distributed, and persistent inorganic pollutant. However, the impacts of perchlorate on freshwater algae remain unclear. In this study, the response and defense mechanisms of microalgae (Chlamydomonas reinhardtii) under perchlorate stress were investigated by integrating physiological and biochemical monitoring, transcriptomics, and metabolomics. Weighted gene co-expression network analysis (WGCNA) of transcriptome data was used to analyze the relationship between genes and phenotype and screen the key pathways. C. reinhardtii exhibited aggregate behavior when exposed to 100- and 200-mM perchlorate but was restored to its unicellular lifestyle when transferred to fresh medium. WGCNA results found that the "carbohydrate metabolism" and "lipid metabolism" pathways were closely related to cell aggregation phenotype. The differential expression genes (DEGs) and differentially accumulated metabolites (DAMs) of these pathways were upregulated, indicating that the lipid and carbohydrate metabolisms were enhanced in aggregated cells. Additionally, most genes and metabolites related to phytohormone abscisic acid (ABA) biosynthesis and the mitogen-activated protein kinase (MAPK) signaling pathway were significantly upregulated, indicating their crucial roles in the signal transmission of aggregated cells. Meanwhile, in aggregated cells, extracellular polymeric substances (EPS) and lipid contents increased, photosynthesis activity decreased, and the antioxidant system was activated. These characteristics contributed to C. reinhardtii's improved resistance to perchlorate stress. Above results demonstrated that cell aggregation behavior was the principal defense strategy of C. reinhardtii against perchlorate. Overall, this study sheds new light on the impact mechanisms of perchlorate to aquatic microalgae and provides multi-omics insights into the research of multicellular-like aggregation as an adaptation strategy to abiotic stress. These results are beneficial for assessing the risk of perchlorate in aquatic environments.

Multi-omics insights into the mechanism of the high-temperature tolerance in a thermotolerant Chlorella sorokiniana

Improving high-temperature tolerance of microalgae is crucial to enhance the robustness and economy of microalgae industrial production. Herein, a continuous adaptive laboratory evolution (ALE) system was developed to generate the thermotolerant strain of Chlorella sorokiniana. The resulting thermotolerant strain TR42 exhibited excellent cell growth and biomass production at 42 °C, the temperature that the original strain (OS) could not survive. The high-temperature resistant mechanism of TR42 was investigated by integrating the physiology, transcriptome, proteome and metabolome analyses, which involved enhancing antioxidant capacity, maintaining protein homeostasis, remodeling photosynthetic metabolism, and regulating the synthesis of heat-stress related metabolites. The proof-of-concept high-temperature outdoor cultivation demonstrated that TR42 exhibited 1.15- to 5.72-fold increases in biomass production and 1.62- to 7.04-fold increases in lipid productivity compared to those of OS, respectively, which provided a promising platform for microalgae industrial production. Thus, the multi-system thermotolerant mechanism of TR42 offered potential targets for enhancing high-temperature tolerance of microalgae.

Genome-wide identification and analysis of the MAPKK gene family in Chinese mitten crab (Eriocheir sinensis) and its response to bacterial challenge

Protein kinases of the MAPK cascade family (MAPKKK-MAPKK-MAPK) play an important role in the growth and development of organisms and their response to environmental stress. The MAPKK gene families in the Chinese mitten crab Eriocheir sinensis have never been systematically analyzed. We identified four MAPKK family genes, EsMEK, EsMAPKK4, EsMAPKK6, and EsMAPKK7, in E. sinensis and analyzed their molecular features and expression patterns. All four MAPKK genes are composed of multiple exons and introns, all have a conserved domain, and all have 10 conserved motifs (except EsMEK and EsMAPKK7 which are missing motif 10). The four MAPKK genes are on four different chromosomes and have no gene duplications, and the results of phylogenetic tree analysis indicate that the ESMAPKK gene family is highly conserved evolutionarily. The EsMAPKK genes were widely expressed in all the examined tissues with higher expression in hemocytes, hepatopancreas, and gills. Notably, EsMAPKK6 was also highly expressed in the ovary. Vibrio parahaemolyticus infection significantly increased the mRNA levels of the EsMAPKK genes in hemocytes. Further disruption of the EsMAPKK gene family expression affects the expression levels of multiple antimicrobial peptides in hemocytes. Our experimental results provide a starting point for a more in-depth study of the innate immunity functional roles of members of the MAPKK gene families in E. sinensis.

Co-Expression Network Analysis of the Transcriptome Identified Hub Genes and Pathways Responding to Saline-Alkaline Stress in Sorghum bicolor L

Soil salinization, an intractable problem, is becoming increasingly serious and threatening fragile natural ecosystems and even the security of human food supplies. Sorghum (Sorghum bicolor L.) is one of the main crops growing in salinized soil. However, the tolerance mechanisms of sorghum to saline-alkaline soil are still ambiguous. In this study, RNA sequencing was carried out to explore the gene expression profiles of sorghum treated with sodium bicarbonate (150 mM, pH = 8.0, treated for 0, 6, 12 and 24 h). The results show that 6045, 5122, 6804, 7978, 8080 and 12,899 differentially expressed genes (DEGs) were detected in shoots and roots after 6, 12 and 24 h treatments, respectively. GO, KEGG and weighted gene co-expression analyses indicate that the DEGs generated by saline-alkaline stress were primarily enriched in plant hormone signal transduction, the MAPK signaling pathway, starch and sucrose metabolism, glutathione metabolism and phenylpropanoid biosynthesis. Key pathway and hub genes (TPP1, WRKY61, YSL1 and NHX7) are mainly related to intracellular ion transport and lignin synthesis. The molecular and physiological regulation processes of saline-alkali-tolerant sorghum are shown by these results, which also provide useful knowledge for improving sorghum yield and quality under saline-alkaline conditions.

Comparative Physiological and Transcriptome Analysis of Crossostephium chinense Reveals Its Molecular Mechanisms of Salt Tolerance

Crossostephium chinense is a wild species with strong salt tolerance that has great potential to improve the salt tolerance of cultivated chrysanthemums. Conversely, the unique salt-tolerant molecular mechanisms of Cr. chinense are still unclear. This study performed a comparative physiological and transcriptome analysis of Cr. chinense, Chrysanthemum lavandulifolium, and three hybrids to investigate the salt-tolerant molecular mechanisms of Cr. chinense. The physiological results showed that Cr. chinense maintained higher superoxide dismutase (SOD) activity, alleviating oxidative damage to the membrane. KEGG enrichment analysis showed that plant hormone signaling transduction and the MAPK signaling pathway were mostly enriched in Cr. chinense and hybrids under salt stress. Further weighted gene co-expression network analysis (WGCNA) of DEGs suggested that abscisic acid (ABA) signaling transduction may play a significant role in the salt-tolerant mechanisms of Cr. chinense and hybrids. The tissue-specific expression patterns of the candidate genes related to ABA signaling transduction and the MAPK signaling pathway indicate that genes related to ABA signaling transduction demonstrated significant expression levels under salt stress. This study offers important insights into exploring the underlying salt-tolerant mechanisms of Cr. chinense mediated by ABA signaling transduction and broadens our understanding of the breeding strategies for developing salt-tolerant cultivars utilizing salt-tolerant chrysanthemum germplasms.

ABA signaling branches out: emerging ABA-related signaling functions in Solanum tuberosum

This article comments on:

Liu T, Dong L, Wang E, Liu S, Cheng Y, Zhao J, Xu S, Liang Z, Ma H, Nie B, Song B. 2023. StHAB1, a negative regulatory factor in abscisic acid signaling, plays crucial roles in potato drought tolerance and shoot branching. Journal of Experimental Botany 74, 6708–6721.

Zinc accumulation in Atriplex lentiformis is driven by plant genes and the soil microbiome

Successful phytoremediation of acidic metal-contaminated mine tailings requires amendments to condition tailings properties prior to plant establishment. This conditioning process is complex and includes multiple changes in tailings bio-physico-chemical properties. The objective of this project is to identify relationships between tailings properties, the soil microbiome, and plant stress response genes during growth of Atriplex lentiformis in compost-amended (10 %, 15 %, 20 % w/w) mine tailings. Analyses include RNA-Seq for plant root gene expression, 16S rRNA amplicon sequencing for bacterial/archaeal communities, metal concentrations in both tailings and plant organs, and phenotypic measures of plant stress. Zn accumulation in A. lentiformis leaves varied with compost levels and was the highest in the intermediate treatment (15 %, TC15). Microbial analysis identified Alicyclobacillus, Hydrotalea, and Pseudolabrys taxa with the highest relative abundance in TC15, and these taxa were strongly associated with Zn accumulation. Furthermore, we identified 190 root genes with significant gene expression changes. These root genes were associated with different pathways including, abscisic acid and auxin signaling, defense responses, ion channels, metal ion binding, oxidative stress, transcription regulation, and transmembrane transport. However, root gene expression changes were not driven by the increasing levels of compost. For example, there were 15 genes that were up-regulated in TC15, whereas 106 genes were down-regulated in TC15. The variables analyzed explained 86 % of the variance in Zn accumulation in A. lentiformis leaves. Importantly, Zn accumulation was driven by Zn shoot concentrations, leaf stress symptoms, plant root genes, and microbial taxa. Therefore, our results suggest there are strong plant-microbiome associations that drive Zn accumulation in A. lentiformis and different plant gene pathways are involved in alleviating varying levels of metal stress. Future work is needed to gain a mechanistic understanding of these plant-microbiome interactions to optimize phytoremediation strategies as they will govern the success or failure of the revegetation process.

OsSTS, a Novel Allele of Mitogen-Activated Protein Kinase Kinase 4 (OsMKK4), Controls Grain Size and Salt Tolerance in Rice

Soil salinization is one of the most common abiotic stresses of rice, which seriously affects the normal growth of rice. Breeding salt-tolerant varieties have become one of the important ways to ensure food security and sustainable agricultural development. However, the mechanisms underlying salt tolerance control still need to be clarified. In this study, we identified a mutant, termed salt-tolerant and small grains(sts), with salt tolerance and small grains. Gene cloning and physiological and biochemical experiments reveal that sts is a novel mutant allele of Mitogen-activated protein Kinase Kinase 4 (OsMKK4), which controls the grain size, and has recently been found to be related to salt tolerance in rice. Functional analysis showed that OsSTS is constitutively expressed throughout the tissue, and its proteins are localized to the nucleus, cell membrane, and cytoplasm. It was found that the loss of OsSTS function enhanced the salt tolerance of rice seedlings, and further studies showed that the loss of OsSTS function increased the ROS clearance rate of rice seedlings, independent of ionic toxicity. In order to explore the salt tolerance mechanism of sts, we found that the salt tolerance of sts is also regulated by ABA through high-throughput mRNA sequencing. Salt and ABA treatment showed that ABA might alleviate the inhibitory effect of salt stress on root length in sts. These results revealed new functions of grain size gene OsMKK4, expanded new research ideas related to salt tolerance mechanism and hormone regulation network, and provided a theoretical basis for salt-tolerant rice breeding.