Molecular characterization, expression and interaction of MAPK, MAPKK and MAPKKK genes in upland cotton

Identification of the MAP4K gene family reveals GhMAP4K13 regulates drought and salt stress tolerance in cotton

Mitogen-activated protein kinase kinase kinase kinases (MAP4Ks) are a class of highly conserved serine/threonine-protein kinases in eukaryotes. They participate in the typical MAPK cascade system and various signal transduction pathways regulating biological processes in plants, during stressful conditions. To date, genome-wide identification of MAP4Ks in cotton has not been reported. In this study, 77 MAP4K genes were identified in four Gossypium species. Protein characteristics, gene structures, conserved motifs and gene expression analysis were carried out. Genome-wide or fragment duplication has played an important role in the expansion of the GhMAP4K. Promoter cis-acting elements and expression patterns indicated that GhMAP4Ks are related to plant hormones (ABA, MeJA, GA, IAA, SA) and various stresses (drought, hypothermia and wound). Overexpressing GhMAP4K13 in Arabidopsis showed higher stem length in response to drought and salt stress. The wilting degree in virus-induced GhMAP4K13 gene silenced plants was substantially greater than wild type plants under drought and salt stress. Transcriptomic analysis showed that most differentially expressed genes were involved in the MAPK signaling pathway, carbon metabolism and porphyrin metabolism. Additionally, transgenic Arabidopsis and VIGS cotton showed that GhMAP4K13 was positively responsive to drought and salt stresses. This study will play an important role in understanding the function of the MAP4K gene family in response to abiotic stress in cotton.

Molecular traits of MAPK kinases and the regulatory mechanism of GhMAPKK5 alleviating drought/salt stress in cotton

Mitogen-activated protein kinase kinases (MAPKKs) play a critical role in the mitogen-activated protein kinase (MAPK) signaling pathway, transducing external stimuli into intracellular responses and enabling plant adaptation to environmental challenges. Most research has focused on the model plant Arabidopsis (Arabidopsis thaliana). The systematic analysis and characterization of MAPKK genes across different plant species, particularly in cotton (Gossypium hirsutum), are somewhat limited. Here, we identified MAPKK family members from 66 different species, which clustered into five different sub-groups, and MAPKKs from four cotton species clustered together. Through further bioinformatic and expression analyses, GhMAPKK5 was identified as the most responsive MAPKK member to salt and drought stress among the 23 MAPKKs identified in Gossypium hirsutum. Silencing GhMAPKK5 in cotton through virus-induced gene silencing (VIGS) led to quicker wilting under salt and drought conditions, while overexpressing GhMAPKK5 in Arabidopsis enhanced root growth and seed germination under these stresses, demonstrating GhMAPKK5's positive role in stress tolerance. Transcriptomics and Yeast-Two-Hybrid assays revealed a MAPK cascade signal module comprising GhMEKK (mitogen-activated protein kinase kinase kinases)3/8/31-GhMAPKK5-GhMAPK11/23. This signaling cascade may play a role in managing drought and salt stress by regulating transcription factor genes, such as WRKYs, which are involved in the biosynthesis and transport pathways of ABA, proline, and RALF. This study is highly important for further understanding the regulatory mechanism of MAPKK in cotton, contributing to its stress tolerance and offering potential in targets for genetic enhancement.

Single-cell transcriptome landscape elucidates the cellular and developmental responses to tomato chlorosis virus infection in tomato leaf

Plant viral diseases compromise the growth and yield of the crop globally, and they tend to be more serious under extreme temperatures and drought climate changes. Currently, regulatory dynamics during plant development and in response to virus infection at the plant cell level remain largely unknown. In this study, single-cell RNA sequencing on 23 226 individual cells from healthy and tomato chlorosis virus-infected leaves was established. The specific expression and epigenetic landscape of each cell type during the viral infection stage were depicted. Notably, the mesophyll cells showed a rapid function transition in virus-infected leaves, which is consistent with the pathological changes such as thinner leaves and decreased chloroplast lamella in virus-infected samples. Interestingly, the F-box protein SKIP2 was identified to play a pivotal role in chlorophyll maintenance during virus infection in tomato plants. Knockout of the SlSKIP2 showed a greener leaf state before and after virus infection. Moreover, we further demonstrated that SlSKIP2 was located in the cytomembrane and nucleus and directly regulated by ERF4. In conclusion, with detailed insights into the plant responses to viral infections at the cellular level, our study provides a genetic framework and gene reference in plant-virus interaction and breeding in the future research.

StMAPKK5 responds to heat stress by regulating potato growth, photosynthesis, and antioxidant defenses

Backgrounds

As a conserved signaling pathway, mitogen-activated protein kinase (MAPK) cascade regulates cellular signaling in response to abiotic stress. High temperature may contribute to a significant decrease in economic yield. However, research into the expression patterns of StMAPKK family genes under high temperature is limited and lacks experimental validation regarding their role in supporting potato plant growth.

Methods

To trigger heat stress responses, potato plants were grown at 35°C. qRT-PCR was conducted to analyze the expression pattern of StMAPKK family genes in potato plants. Plant with StMAPKK5 loss-of-function and gain-of-function were developed. Potato growth and morphological features were assessed through measures of plant height, dry weight, and fresh weight. The antioxidant ability of StMAPKK5 was indicated by antioxidant enzyme activity and H2O2 content. Cell membrane integrity and permeability were suggested by relative electrical conductivity (REC), and contents of MDA and proline. Photosynthetic capacity was next determined. Further, mRNA expression of heat stress-responsive genes and antioxidant enzyme genes was examined.

Results

In reaction to heat stress, the expression profiles of StMAPKK family genes were changed. The StMAPKK5 protein is located to the nucleus, cytoplasm and cytomembrane, playing a role in controlling the height and weight of potato plants under heat stress conditions. StMAPKK5 over-expression promoted photosynthesis and maintained cell membrane integrity, while inhibited transpiration and stomatal conductance under heat stress. Overexpression of StMAPKK5 triggered biochemical defenses in potato plant against heat stress, modulating the levels of H2O2, MDA and proline, as well as the antioxidant activities of CAT, SOD and POD. Overexpression of StMAPKK5 elicited genetic responses in potato plants to heat stress, affecting heat stress-responsive genes and genes encoding antioxidant enzymes.

Conclusion

StMAPKK5 can improve the resilience of potato plants to heat stress-induced damage, offering a promising approach for engineering potatoes with enhanced adaptability to challenging heat stress conditions.

StMAPKK5 Positively Regulates Response to Drought and Salt Stress in Potato

MAPKKs, as one of the main members of the mitogen-activated protein kinase (MAPK) cascade pathway, are located in the middle of the cascade and are involved in many physiological processes of plant growth and development, as well as stress tolerance. Previous studies have found that StMAPKK5 is responsive to drought and salt stress. To further investigate the function and regulatory mechanism of StMAPKK5 in potato stress response, potato variety 'Atlantic' was subjected to drought and NaCl treatments, and the expression of the StMAPKK5 gene was detected by qRT-PCR. StMAPKK5 overexpression and RNA interference-mediated StMAPKK5 knockdown potato plants were constructed. The relative water content, superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities, as well as proline (Pro) and malondialdehyde (MDA) contents of plant leaves, were also assayed under drought and NaCl stress. The StMAPKK5 interacting proteins were identified and validated by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC). The results showed that the expression of StMAPKK5 was significantly up-regulated under drought and NaCl stress conditions. The StMAPKK5 protein was localized in the nucleus, cytoplasm, and cell membrane. The expression of StMAPKK5 affected the relative water content, the enzymatic activities of SOD, CAT, and POD, and the proline and MDA contents of potatoes under drought and salt stress conditions. These results suggest that StMAPKK5 plays a significant role in regulating drought and salt tolerance in potato crop. Yeast two-hybrid (Y2H) screening identified four interacting proteins: StMYB19, StZFP8, StPUB-like, and StSKIP19. BiFC confirmed the authenticity of the interactions. These findings suggest that StMAPKK5 is crucial for potato growth, development, and response to adversity.

Identification and expression analysis of MAPK cascade gene family in foxtail millet (Setaria italica)

The mitogen-activated protein kinase (MAPK) cascade pathway is a highly conserved plant cell signaling pathway that plays an important role in plant growth and development and stress response. Currently, MAPK cascade genes have been identified and reported in a variety of plants including Arabidopsis thaliana, Oryza sativa, and Triticum aestivum, but have not been identified in foxtail millet (Setaria italica). In this study, a total of 93 MAPK cascade genes, including 15 SiMAPKs, 10 SiMAPKKs and 68 SiMAPKKKs genes, were identified by genome-wide analysis of foxtail millet, and these genes were distributed on nine chromosomes of foxtail millet. Using phylogenetic analysis, we divided the SiMAPKs and SiMAPKKs into four subgroups, respectively, and the SiMAPKKKs into three subgroups (Raf, ZIK, and MEKK). Whole-genome duplication analysis revealed that there are 14 duplication pairs in the MAPK cascade family in foxtail millet, and they are expanded by segmental replication events. Results from quantitative real-time PCR (qRT-PCR) revealed that the expression levels of most SiMAPKs and SiMAPKKs were changed under both exogenous hormone and abiotic stress treatments, with SiMAPK3 and SiMAPKK4-2 being induced under almost all treatments, while the expression of SiMAPKK5 was repressed. In a nutshell, this study will shed some light on the evolution of MAPK cascade genes and the functional mechanisms underlying MAPK cascade genes in response to hormonal and abiotic stress signaling pathways in foxtail millet (Setaria italica).

A comprehensive overview of cotton genomics, biotechnology and molecular biological studies

Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.

The resilient cotton plant: uncovering the effects of stresses on secondary metabolomics and its underlying molecular mechanisms

Cotton is an important fiber crop cultivated around the world under diverse climate conditions and generates billions of dollars in annual revenue globally. Biotic and abiotic stresses have caused reduction in yield and productivity of cotton crops. In this review, we comprehensively analyzed and summarized the effect of biotic and abiotic stress on secondary metabolite production in cotton. The development of cotton varieties with improved tolerance against abiotic and biotic stress can play an important role in sustainable cotton production. Under stress conditions, plants develop a variety of defense mechanisms such as initiating signaling functions to upregulate defense responsive genes and accumulation of secondary metabolites. Understanding the impact of stress on secondary metabolite production in cotton is crucial for developing strategies to alleviate the negative effects of stress on crop yield and quality. Further, the potential industrial applications of these secondary metabolites in cotton, such as gossypol, could provide new opportunities for sustainable cotton production and the development of value-added products. Additionally, transgenic and genome-edited cotton cultivars can be developed to provide tolerance to both abiotic and biotic stress in cotton production.

Insights into the Genomic Regions and Candidate Genes of Senescence-Related Traits in Upland Cotton via GWAS

Senescence is the last stage of plant development and is controlled by both internal and external factors. Premature senescence significantly affects the yield and quality of cotton. However, the genetic architecture underlying cotton senescence remains unclear. In this study, genome-wide association studies (GWAS) were performed based on 3,015,002 high-quality SNP markers from the resequencing data of 355 upland cotton accessions to detect genomic regions for cotton senescence. A total of 977 candidate genes within 55 senescence-related genomic regions (SGRs), SGR1-SGR55, were predicted. Gene ontology (GO) analysis of candidate genes revealed that a set of biological processes was enriched, such as salt stress, ethylene processes, and leaf senescence. Furthermore, in the leaf senescence GO term, one candidate gene was focused on: Gohir.A12G270900 (GhMKK9), located in SGR36, which encodes a protein of the MAP kinase kinase family. Quantitative real-time PCR (qRT-PCR) analysis showed that GhMKK9 was up-regulated in old cotton leaves. Overexpression of GhMKK9 in Arabidopsis accelerated natural leaf senescence. Virus-induced gene silencing (VIGS) of GhMKK9 in cotton increased drought tolerance. These results suggest that GhMKK9 is a positive regulator and might be involved in drought-induced senescence in cotton. The results provide new insights into the genetic basis of cotton senescence and will be useful for improving cotton breeding in the future.

Genome-wide identification and expression profiling of thes MAPK, MAPKK, and MAPKKK gene families in Ophiocordyceps sinensis

Mitogen-activated protein kinase (MAPK) cascades have a universal cell signaling mechanism in eukaryotes. A typical MAPK signal transduction module comprises three kinds of sequentially phosphorylated protein kinases: MAPK, Mitogen-activated protein kinase kinase (MAPKK), and Mitogen-activated protein kinase kinase kinase (MAPKKK). However, little is known regarding the genes involved in MAPK cascades in Ophiocordyceps sinensis. Nine genes (three MAPK, three MAPKK, and three MAPKKK) were identified in this study. The MAPK, MAPKK, and MAPKKK genes were divided into three subfamilies, according to the phylogenetic analysis. TEY and TGY represented the activation domains of the MAPKs; the corresponding domains in MAPKKs were SDIWS and SDVWS, and those in the MAPKKs were GSVFYWMAPEV and GTPMYMSPEV. Transcription data analysis and quantitative real-time polymerase chain reaction showed that the MAPK cascade was related to the growth of the fruiting body. This is the first study to report a genome-wide identification of the MAPK, MAPKK, and MAPKK gene families in O. sinensis.

Molecular Traits and Functional Analysis of the CLAVATA3/Endosperm Surrounding Region-Related Small Signaling Peptides in Three Species of Gossypium Genus

The CLAVATA3/endosperm surrounding region-related (CLE) small peptides are a group of C-terminally encoded and post-translationally modified signal molecules involved in regulating the growth and development of various plants. However, the function and evolution of these peptides have so far remained elusive in cotton. In this study, 55, 56, and 86 CLE genes were identified in the Gossypium raimondii, Gossypium arboreum, and Gossypium hirsutum genomes, respectively, and all members were divided into seven groups. These groups were distinctly different in their protein characteristics, gene structures, conserved motifs, and multiple sequence alignment. Whole genome or segmental duplications played a significant role in the expansion of the CLE family in cotton, and experienced purifying selection during the long evolutionary process in cotton. Cis-acting regulatory elements and transcript profiling revealed that the CLE genes of cotton exist in different tissues, developmental stages, and respond to abiotic stresses. Protein properties, structure prediction, protein interaction network prediction of GhCLE2, GhCLE33.2, and GhCLE28.1 peptides were, respectively, analyzed. In addition, the overexpression of GhCLE2, GhCLE33.2, or GhCLE28.1 in Arabidopsis, respectively, resulted in a distinctive shrub-like dwarf plant, slightly purple leaves, large rosettes with large malformed leaves, and lack of reproductive growth. This study provides important insights into the evolution of cotton CLEs and delineates the functional conservatism and divergence of CLE genes in the growth and development of cotton.

Regulatory Network of Cotton Genes in Response to Salt, Drought and Wilt Diseases (Verticillium and Fusarium): Progress and Perspective

In environmental conditions, crop plants are extremely affected by multiple abiotic stresses including salinity, drought, heat, and cold, as well as several biotic stresses such as pests and pathogens. However, salinity, drought, and wilt diseases (e.g., Fusarium and Verticillium) are considered the most destructive environmental stresses to cotton plants. These cause severe growth interruption and yield loss of cotton. Since cotton crops are central contributors to total worldwide fiber production, and also important for oilseed crops, it is essential to improve stress tolerant cultivars to secure future sustainable crop production under adverse environments. Plants have evolved complex mechanisms to respond and acclimate to adverse stress conditions at both physiological and molecular levels. Recent progresses in molecular genetics have delivered new insights into the regulatory network system of plant genes, which generally includes defense of cell membranes and proteins, signaling cascades and transcriptional control, and ion uptake and transport and their relevant biochemical pathways and signal factors. In this review, we mainly summarize recent progress concerning several resistance-related genes of cotton plants in response to abiotic (salt and drought) and biotic (Fusarium and Verticillium wilt) stresses and classify them according to their molecular functions to better understand the genetic network. Moreover, this review proposes that studies of stress related genes will advance the security of cotton yield and production under a changing climate and that these genes should be incorporated in the development of cotton tolerant to salt, drought, and fungal wilt diseases (Verticillium and Fusarium).