Search Results (358)

The RasGAP SH3 domain binding protein (G3BP) is a highly conserved family of proteins in eukaryotic organisms that coordinates signal transduction and post-transcriptional gene regulation and functions in the formation of stress granules. G3BPs have important roles in abiotic/biotic stresses in mammals, and recent research suggests that they have similar functions in higher plants. Brassica contains many important oilseeds, vegetables, and ornamental plants, but there are no reports on the G3BP family in Brassica species. In this study, we identified G3BP family genes from six species of the U’s triangle (B. rapa, B. oleracea, B. nigra, B. napus, B. juncea, and B. carinata) at the genome-wide level. We then analyzed their gene structure, protein motifs, gene duplication type, phylogeny, subcellular localization, SSR loci, and upstream miRNAs. Based on transcriptome data, we analyzed the expression patterns of B. napus G3BP (BnaG3BP) genes in various tissues/organs in response to Sclerotinia disease, blackleg disease, powdery mildew, dehydration, drought, heat, cold, and ABA treatments, and its involvement in seed traits including germination, α-linolenic acid content, oil content, and yellow seed. Several BnaG3BP DEGs might be regulated by BnaTT1. The qRT-PCR assay validated the inducibility of two cold-responsive BnaG3BP DEGs. This study will enrich the systematic understanding of Brassica G3BP family genes and lay a molecular basis for the application of BnaG3BP genes in stress tolerance, disease resistance, and quality improvement in rapeseed. Full article

The rapid evolution of pathogens and the limited genetic diversity of hosts are two major factors contributing to the plant pathogenic phenomenon known as the loss of disease resistance in maize (Zea mays L.). It has emerged as a significant biological stressor threatening the global food supplies and security. Based on previous cross-species homologous gene screening assays conducted in the laboratory, this study identified the maize disease-resistance candidate gene ZmNLR-7 to investigate the maize immune regulation mechanism against Bipolaris maydis. Subcellular localization assays confirmed that the ZmNLR-7 protein is localized in the plasma membrane and nucleus, and phylogenetic analysis revealed that it contains a conserved NB-ARC domain. Analysis of tissue expression patterns revealed that ZmNLR-7 was expressed in all maize tissues, with the highest expression level (5.11 times) exhibited in the leaves, and that its transcription level peaked at 11.92 times 48 h post Bipolaris maydis infection. Upon inoculating the ZmNLR-7 EMS mutants with Bipolaris maydis, the disease index was increased to 33.89 and 43.33, respectively, and the lesion expansion rate was higher than that in the wild type, indicating enhanced susceptibility to southern corn leaf blight. Physiological index measurements revealed a disturbance of ROS metabolism in ZmNLR-7 EMS mutants, with SOD activity decreased by approximately 30% and 55%, and POD activity decreased by 18% and 22%. Moreover, H₂O₂ content decreased, while lipid peroxide MDA accumulation increased. Transcriptomic analysis revealed a significant inhibition of the expression of the key genes NPR1 and ACS6 in the SA/ET signaling pathway and a decrease in the expression of disease-related genes ERF1 and PR1. This study established a new paradigm for the study of NLR protein-mediated plant immune mechanisms and provided target genes for molecular breeding of disease resistance in maize. Overall, these findings provide the first evidence that ZmNLR-7 confers resistance to southern corn leaf blight in maize by synergistically regulating ROS homeostasis, SA/ET signal transduction, and downstream defense gene expression networks. Full article

Parkinson’s disease (PD) is the second most common neurodegenerative disease. It primarily affects the motor system but is also associated with a range of cognitive impairments that can manifest early in disease progression, indicating its multifaceted nature. In this paper, we performed a meta-analysis of transcriptomics and proteomics data using MultiOmicsIntegrator to gain insights into the post-transcriptional modifications and deregulated pathways associated with this disease. Our results reveal differential isoform usage between control and PD patient brain samples that result in enriched alternative splicing events, including an extended UTR length, domain loss, and the upregulation of non-coding isoforms. We found that Inositol-Requiring Enzyme 1 (IRE1) is active in PD samples and examined the role of its downstream signaling through X-box binding mRNA 1 (XBP1) and regulated IRE1-dependent decay (RIDD). We identified several RIDD candidates and showed that the enriched alternative splicing events observed are associated with RIDD. Moreover, in vitro mRNA cleavage assays demonstrated that OSBPL3, C16orf74, and SLC6A1 mRNAs are targets of IRE1 RNAse activity. Finally, a pathway enrichment analysis of both XBP1s and RIDD targets in the PD samples uncovered associations with processes such as immune response, oxidative stress, signal transduction, and cell–cell communication that have previously been linked to PD. These findings highlight a potential regulatory role of IRE in PD. Full article

Calcium-dependent protein kinases (CDPKs) are crucial regulators in calcium-mediated signal transduction pathways, playing a pivotal role in plant response to abiotic stresses. However, there is still limited knowledge regarding the genes of the Populus tomentosa CDPK family and their underlying functions in response to arsenic (As) stress and arbuscular mycorrhizal fungi (AMF) colonization. In our study, 20 PtCDPKs were identified in the P. tomentosa genome. Phylogenetic analysis categorized these PtCDPK genes into four subgroups based on sequence homology. Motif analysis revealed that PtCDPK genes within the same group share a similar exon–intron structure, conserved domains, and composition. The promoters of PtCDPK genes were found to contain a multitude of cis-acting elements, including light-response elements, phytohormone-response elements, and stress-response elements. The analysis of genes provided insights into the evolutionary dynamics and expansion of the PtCDPK gene family within P. tomentosa. The PtCDPK genes exhibited a strong collinear relationship with the CDPK genes of two model plants, namely, Arabidopsis thaliana and Oryza sativa L. Specifically, 10 gene pairs showed collinearity with Arabidopsis; in contrast, 14 gene pairs were collinear with rice. Transcriptome analysis of gene expression levels in P. tomentosa roots under both As stress and arbuscular mycorrhizal fungi (AMF) colonization conditions revealed that 20 PtCDPK genes had differential expression patterns. Under As stress, AMF inoculation led to the upregulation of 11 PtCDPK genes (PtCDPKSK5, X2, 1-3, 20-1, 24, 26-X1-1, 26-X1-2, 29-1, 29-2, 32, and 32-X1) and the downregulation of 8 PtCDPK genes, including PtCDPK1-1, 1-2, 8-X1, 10-X4, 13, 20-2, 26-X2, and 26-X3. The RT-qPCR results for 10 PtCDPK genes were consistent with the transcriptome data, indicating that AMF symbiosis plays a regulatory role in modulating the expression of PtCDPK genes in response to As stress. The principal findings of this study were that PtCDPK genes showed differential expression patterns under As stress and AMF colonization, with AMF regulating PtCDPK gene expression in response to As stress. Our study contributes to developing a deeper understanding of the function of PtCDPKs in the Ca²⁺ signaling pathway of P. tomentosa under As stress and AMF inoculation, which is pivotal for elucidating the molecular mechanisms underlying As tolerance in AMF-inoculated P. tomentosa. Full article

MIKC-type MADS-box transcription factors constitute one of the largest gene families in plants, playing pivotal roles in regulating plant growth and development, hormone signaling transduction, and responses to biotic and abiotic stresses. However, there have been no reports on the systematic identification and characterization of MIKC-type MADS-box proteins in walnuts. In this study, we identified 52 JrMADS genes in the walnut genome and transcriptome, and categorized them into 14 subfamilies through structural domain and phylogenetic tree analysis. It was found that these genes were unevenly distributed across 16 chromosomes. Within the MIKC-type MADS-box gene family, we identified three pairs of tandem-duplicated genes and 40 pairs of segmental duplicated genes, indicating that segmental duplication was the primary mechanism of gene amplification in walnut. Ka/Ks analysis showed that the family genes have undergone purifying selection during evolutionary processes. The promoter was predicted to contain cis-acting elements related to growth, development, plant hormones, and stress response. Expression profile analysis showed that JrMADS genes have different expression patterns in various tissues and developmental stages of male and female flower buds. Notably, an ancient clade of TM8 (JrMADS43) genes was found, which is absent in Arabidopsis but present in other flowering plants. Another gene, TM6 gene (JrMADS4), belongs to the AP3 subfamily and is a clade that has diverged from tomatoes. Through qPCR analysis, we verified the differential expression of JrMADS genes at different developmental stages (MB-1/2/3 and FB-1/2/3), with JrMADS5, JrMADS8, JrMADS14, JrMADS24, JrMADS40, JrMADS46, JrMADS47, JrGA3ox1, and JrGA3ox3 showing significantly higher expression in male than in female flower buds. In summary, our results provide valuable information for further biological functions research on MIKC-type MADS-box genes in walnut, such as flower organ development, and lays a solid foundation for future studies. Full article

Abscisic acid (ABA), a pivotal phytohormone regulating plant growth and stress adaptation, orchestrates abiotic stress responses through the ABA-responsive element-binding factors ABF/AREB/ABI5. Nevertheless, the functional characterization of ABF/AREB/ABI5 homologs in Z. jujuba cv. Dongzao remains unexplored. In this study, we identified seven ZjABF genes distributed across five chromosomes. Domain analyses revealed high structural conservation, particularly within the basic leucine zipper (bZIP) DNA-binding domain. Subcellular localization confirmed nuclear targeting of all seven ZjABF proteins. Phylogenetic classification resolved these factors into three clades (A–C). Cis-regulatory element profiling implicated the involvement of the ZjABFs in hormone signaling, abiotic stress transduction, and photoregulatory pathways. Synteny analyses identified three segmental duplication events within the gene family. Tissue-specific expression patterns indicated critical roles for ZjABF2 and ZjABF3 in fruit maturation, and most of the ABF/AREB/ABI5 genes were highly expressed in the root. Under drought stress, four ZjABF genes exhibited differential expression, with ZjABF2 demonstrating pronounced sensitivity. These findings establish a molecular framework for understanding ZjABF-mediated abiotic stress responses in non-model woody perennials. Full article

The 14-3-3 proteins play crucial roles in regulating plant growth, development, signal transduction and abiotic stress responses. However, there exists a scarcity of research on the role of 14-3-3 proteins in responding to abiotic stress in apples. In this study, we isolated the MdGRF22 gene from the apple 14-3-3 family. Through the screening of interacting proteins and genetic transformation of Arabidopsis thaliana and apple callus tissues, the function of the MdGRF22 gene under drought stress was verified. The coding sequence (CDS) of MdGRF22 consists of 786 bp and encodes for 261 amino acids. Through sequence alignment, the conserved 14-3-3 domain was identified in MdGRF22 and its homologous genes, which also share similar gene structures and conserved motifs. Subcellular localization revealed that the MdGRF22 protein was predominantly located in the cytoplasm and cell membrane. The yeast two-hybrid (Y2H) analysis demonstrated a possible interaction between MdGRF22 and MdSK. In addition, MdGRF22 transgenic plants generally exhibited lower superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) activities, higher malondialdehyde (MDA) levels and relative electrolyte leakage under drought conditions compared with wild-type (WT) plants. Our study suggests that MdGRF22 may reduce the drought resistance of transgenic A. thaliana and callus tissues by interacting with MdSK. This study provides a theoretical basis for further exploring the function of 14-3-3 family genes. Full article

Tubby-like proteins (TLPs) are essential multifunctional transcription factors in plants that significantly influence plant growth and development, signal transduction, and adaptation to environmental stress. Despite their importance, there is limited knowledge of the identification and functional roles of the TLP gene family in the common bean. In this study, we identified the PvTLP gene family, which consists of 10 PvTLP genes distributed unevenly across seven chromosomes. Phylogenetic analysis revealed that these genes could be classified into three subfamilies (A, B, and C). All PvTLP proteins contained both conserved tubby and F-box domains, with the exception of PvTLP7, which lacks the F-box domain. Conserved motif analysis revealed that 10 PvTLP genes contained motif 1 and motif 3. Cis-acting elements analysis indicated that PvTLP genes might be involved in light, hormone, and stress responses. Synteny analysis revealed a closer phylogenetic relationship between the common bean and dicotyledons than monocotyledons. qRT-PCR analysis confirmed the significant differences in the expression of most PvTLP genes in both leaves and roots under salt and drought stresses. These findings provide valuable insights for further exploration of the molecular functions of TLPs in plant responses to various stresses and offer key candidate genes for enhancing stress resistance in the common bean through molecular breeding. Full article

The Phosphoinositide Specific-Phospholipase C (PI-PLC) family of enzymes plays a crucial role in various cellular processes by catalyzing the hydrolysis of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P₂] into inositol 1,4,5-trisphosphate (IP₃) and diacylglycerol (DAG), which are essential messengers mediating critical intracellular signaling pathways. Herein, we carry out a comprehensive analysis of the structure, function, regulation, and implications of the PI-PLC family enzymes in both physiological and pathological contexts. More specifically, we discuss the structural features of PI-PLCs, elucidating their conserved domains and catalytic mechanisms. Furthermore, we explore the multifaceted roles of PI-PLCs in signal transduction, cellular homeostasis, and membrane dynamics, whilst highlighting the intricate regulatory mechanisms governing their activity such as protein–protein interactions, post-translational modifications, and lipid modulation. Lastly, we assess the involvement of PI-PLCs in various diseases, such as cancer, neurological disorders, immune dysregulation, and male infertility, emphasizing their potential as therapeutic targets. Full article

The Reverse Chimeric Antigen Receptor (RevCAR) system is an adapter CAR T cell technology that allows the precise tuning of T cell activity and, thus, improved safety management. RevCAR T cells recognize and eradicate tumor cells via a bispecific adapter molecule, termed the RevCAR Target Module (RevTM). To further reduce the risk of on-target off-tumor toxicities, Dual-RevCAR T cells can be employed. These cells harbor two different RevCAR constructs, with the signaling domain of either CD3zeta or CD28. Therefore, Dual-RevCAR T cells only exert their full function when both RevCAR constructs are triggered simultaneously upon recognition of two different tumor antigens via RevTMs, enabling a precise AND-gate targeting approach and rendering them highly interesting for clinical application. For this purpose, standardized and reproducible clinical-grade cell manufacturing is required, for which the CliniMACS Prodigy can be used. Here, we present that automated processing of RevCAR and Dual-RevCAR T cells via the CliniMACS Prodigy results in potent expansion, strong transduction, and a favorable phenotype for clinical application. Moreover, obtained cell products were highly functional in a strict RevTM-dependent manner for both monospecific and AND-gate targeting, clearly underlining their high potential for clinical application against various tumor entities. Full article

Bacterial chemoreceptors sense extracellular stimuli and drive bacteria toward a beneficial environment or away from harm. Their ligand-binding domains (LBDs) are highly diverse in terms of sequence and structure, and their ligands cover various chemical molecules that could serve as nitrogen, carbon, and energy sources. The mechanism of how this diverse range of LBDs senses different ligands is essential to signal transduction. Previously, we reported that the chemoreceptor MCP2201 from Comamonas testosteroni CNB-1 sensed citrate and L-malate, altered the ligand-free monomer–dimer equilibrium of LBD to citrate-bound monomer (with limited monomer) and L-malate-bound dimer, and triggered positive and negative chemotactic responses. Here, we present our findings, showing that D-malate binds to MCP2201, induces LBD dimerization, and triggers the chemorepellent response exactly as L-malate did. A single site mutation, T105A, can alter the D-malate-bound LBD dimer into a monomer–dimer equilibrium and switch the negative chemotactic response to D-malate to a positive one. Differences in attractant-bound LBD oligomerization, such as citrate-bound wildtype LBD monomer and D-malate-bound T105A dimer, indicated that LBD oligomerization is a consequence of signal transduction instead of a trigger. Our study expands our knowledge of chemoreceptor-sensing ligands and provides insight into the evolution of bacterial chemoreceptors. Full article

Leucine-rich repeat receptor-like kinases (LRR-RLKs) have evolved to perceive environmental changes. Among LRR-RLKs, PEPR1 perceives the pep1 peptide and triggers defense signal transduction in Arabidopsis thaliana. In the present study, we focused on PEPR1 and PEPR2, which are the receptors of pep1, to understand the role of tyrosine phosphorylation. PEPR1-CD (cytoplasmic domain) recombinant protein exhibited strong tyrosine autophosphorylation, including threonine autophosphorylation. We subjected all tyrosine residues in PEPR1-CD to site-directed mutagenesis. The recombinant proteins were purified along with PEPR1-CD, and Western blotting was performed using a tyrosine-specific antibody. Among the 13 tyrosine residues in PEPR1-CD, the PEPR1(Y995F)-CD recombinant protein showed significantly reduced tyrosine autophosphorylation intensity compared to PEPR1-CD and other tyrosine mutants, despite little change in threonine autophosphorylation. To confirm the autophosphorylation site, we generated a phospho-specific peptide Ab, pY995. As a result, Tyr-995 of PEPR1-CD was a major tyrosine autophosphorylation site in vitro. To understand the function of tyrosine phosphorylation in vivo, we generated transgenic plants, expressing PEPR1-Flag, PEPR1(Y995F)-Flag, and PEPR1(Y995D)-Flag in a pepr1/2 double mutant background. Interestingly, the root growths of PEPR1(Y995F)-Flag and PEPR1(Y995D)-Flag were not inhibited by pep1 peptide treatment, compared to Col-0 and PEPR1-Flag (pepr1/2) transgenic plants. Also, we analyzed downstream components, which included PROPEP1, MPK3, WRKY33, and RBOHD gene expressions in four different genotypes (Col-0, PEPR1-Flag, PEPR1(Y995F)-Flag, and PEPR1(Y995D)-Flag) of plants in the presence of the pep1 peptide. Interestingly, the expressions of PROPEP1, MPK3, WRKY33, and RBOHD were not regulated by pep1 peptide treatment in PEPR1(Y995F)-Flag and PEPR1(Y995D)-Flag transgenic plants, in contrast to Col-0 and PEPR1-Flag. These results suggest that specific tyrosine residues play an important role in vivo in the plant receptor function. Full article

In eukaryotes, the mitogen-activated protein kinase (MAPK) cascade pathway is a highly conserved cell signaling mechanism that is essential for stress response, growth, and development. MAPK cascade genes have currently been identified and characterized in a wide range of fungi, although they have not been fully understood in early divergent fungal lineages like the Mucoromycota, which contains Mucoromycotina, Glomeromycotina, and Mortierellomycotina. In this study, a genome-wide investigation of Blakeslea trispora (Mucorales, Choanephoraceae) revealed a total of 19 MAPK cascade genes, including 9 BtMAPKKKs, 4 BtMAPKKs, and 6 BtMAPKs genes. Using phylogenetic analysis, it was found that the kinase domain sequences and motif composition of the three MAPK, MAPKK, and MAPKKK lineages are substantially conserved in fungi. Whole genome duplication analysis indicated that B. trispora has four and nine duplication pairs in the MAPK and MAPKKK genes, respectively, which are expanded by segmental replication events. BtHog2, the orthologous protein of Hog1, exhibits a substantial rise in transcription levels under blue light irradiation, indicating its function in light signal response and transduction. Several sets of interacting protein pairs were found using molecular docking analysis and yeast two-hybrid assay, providing a comprehensive MAPK cascade signaling network in B. trispore. Furthermore, MAPK cascade proteins show varying transcription levels in response to blue light and sex hormone stimulation, as well as variable treatment duration. BtMAPKKK9 and BtBck1 are strongly induced during sexual interaction, indicating their involvement in the response to trisporic acid and the subsequent alterations in hyphal cell wall structure. These findings shed light on the evolution of MAPK cascade genes and the functional mechanisms underlying MAPK cascade genes in response to light and sex hormone signaling pathways in B. trispore. Full article

With the continuous change of climate, drought stress has emerged as the primary constraint on crop growth, posing a significant threat to the stability of global grain reserves. Arbuscular mycorrhizal fungi (AMF), as a kind of widely distributed root endophytes, enhance the drought tolerance of maize (Zea mays L.) through regulating the physiological and molecular responses. However, comprehensive transcriptome analysis to reveal the molecular mechanism of drought tolerance in the symbiotic process between AMF and maize is still limited. In the potted plant experiment, maizes inoculated with and without arbuscular mycorrhizal fungus Funneliformis mosseae were grown under well-watered (WW) or drought-stressed (DS) conditions. By using RNA-Seq and transcriptome analysis on maize roots and leaves, this work aimed to investigate the differential expressed genes (DEGs) related to the Ca²⁺ signaling pathway induced by AMF symbiosis under drought stress. Our findings indicated that F. mosseae inoculation resulted in a decrease in the net fluxes of Ca²⁺, while simultaneously elevating Ca²⁺ contents in the maize roots and leaves under well-watered or drought-stressed conditions. Notably, 189 DEGs were regulated not only by AMF symbiosis and drought stress, but also exhibited preferential expression in either leaves or roots. The annotation and enrichment of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that most of the DEGs were significantly enriched in Ca²⁺ signaling pathway genes, related to signal transduction, cellular process, and defense response. A high number of DEGs with this function (including calcineurin B-like protein (CBL), CBL-interacting protein kinase (CIPK), mitogen-activated protein kinase (MAPK), and calcium-dependent protein kinase (CDPK) receptor kinases) were upregulated-DEGs or downregulated-DEGs in F. mosseae-inoculated maizes under drought stress. Furthermore, some DEGs belong to transcription factor (TF) families, including bHLH ERF, and, MYB, were speculated to play key roles in improving the drought tolerance of maize. Based on the expression data and co-expression analysis between TF and Ca²⁺ signaling pathway genes, Whirly1 with CBL11, and BRI1-EMS-SUPPRESSOR 1 (BES1) with CBL10, CIPK24, CDPK1, CDPK14, CDPK19, and MAPK9 genes showed significant positive correlations, while B3 domain-containing transcription factors (B3 TFs) with MAPK1 and both CBL9 genes showed significant negative correlations in response to both F. mosseae inoculation and drought stress. The regulation of Ca²⁺ signaling pathways by AMF symbiosis was an important response mechanism of maize to improve their drought resistance. This study provides insightful perspectives on how AMF-induced modulation of gene expression within the Ca²⁺ signaling pathway can enhance the drought tolerance of mycorrhizal maize in the future. Full article

Bacterial communities in diverse environmental niches respond to various external stimuli for survival. A primary means of communication between bacterial cells involves one-component (OC) and two-component signal transduction systems (TCSs). These systems are key for sensing environmental changes and regulating bacterial physiology. TCSs, which are the more complex of the two, consist of a sensor histidine kinase for receiving an external input and a response regulator to convey changes in bacterial cell physiology. For numerous reasons, TCSs have emerged as significant targets for antibacterial drug design due to their role in regulating expression level, bacterial viability, growth, and virulence. Diverse studies have shown the molecular mechanisms by which TCSs regulate virulence and antibiotic resistance in pathogenic bacteria. In this study, we performed a thorough analysis of the data from multiple public databases to assemble a comprehensive catalog of the principal detection systems present in both the non-pathogenic Pseudomonas putida KT2440 and the pathogenic Pseudomonas aeruginosa PAO1 strains. Additionally, we conducted a sequence analysis of regulatory elements associated with transcriptional proteins. These were classified into regulatory families based on Helix-turn-Helix (HTH) protein domain information, a common structural motif for DNA-binding proteins. Moreover, we highlight the function of bacterial TCSs and their involvement in functions essential for bacterial survival and virulence. This comparison aims to identify novel targets that can be exploited for the development of advanced biotherapeutic strategies, potentially leading to new treatments for bacterial infections. Full article