The heterologous overexpression of VrCIPK5 in tobacco conferred enhanced drought tolerance by promoting proline accumulation, increasing antioxidant enzyme activities, accelerating stomatal closure, and upregulating downstream stress-responsive genes, thus alleviating reactive oxygen species overaccumulation and membrane lipid peroxidation.
Abstract
Calcineurin B-like protein-interacting protein kinases (CIPKs) act as core regulators in plant calcium (Ca2+) signaling pathways and mediate abiotic stress adaptation. Mung bean (Vigna radiata L.) is an economically important legume that is widely grown in arid and semi-arid regions; however, drought stress significantly reduces its yield and quality. Despite this, genome-wide identification and functional analysis of the CIPK gene family have not been reported in mung bean, limiting our understanding of drought-resistance mechanisms and stress-tolerant variety breeding. In this study, 23 VrCIPK genes were identified from the mung bean genome, which were unevenly distributed across 6 chromosomes, with the remaining genes located on scaffolds. Phylogenetic analysis classified the VrCIPK family into five groups (A–E), characterized by high structural conservation of the N-terminal kinase and the C-terminal NAF/FISL regulatory domains. Gene Ontology annotation further indicated their conserved involvement in protein phosphorylation and calcium signal transduction. Collinearity analysis revealed that CIPK genes in mung bean and other species have relatively conserved evolutionary patterns. Segmental duplication contributed to VrCIPK gene family expansion, and most duplicated gene pairs underwent purifying selection during evolution. Gene structure and motif analyses showed that VrCIPK genes within the same group shared conserved structural features. Cis-acting element profiling revealed abundant hormone- and stress-responsive elements in VrCIPK promoters, indicating diverse transcriptional regulatory potential. Transcriptomics analysis and quantitative real-time PCR demonstrated that VrCIPK5 was significantly induced under drought stress. The heterologous overexpression of VrCIPK5 in tobacco conferred enhanced drought tolerance by promoting proline accumulation, increasing antioxidant enzyme (superoxide dismutase, peroxidase, and catalase) activities, accelerating stomatal closure, and upregulating downstream stress-responsive genes (NtSOD, NtCAT, NtP5CS1, NtLEA5, and NtRD29A), thus alleviating reactive oxygen species overaccumulation and membrane lipid peroxidation. Collectively, these findings fill the research gap in the genome-wide identification and functional analysis of the CIPK gene family in mung bean and provide key genetic resources and theoretical support for breeding drought-resistant mung bean varieties.
Introduction Drought is a major abiotic stress limiting the growth and ecological adaptation of tropical and subtropical trees. The SnRK2 gene family is a core regulator in ABA signaling and drought response pathways. However, genome-wide identification and functional characterization of the SnRK2 family remain unclear in Bombax ceiba, a typical drought-tolerant tropical pioneer tree species with important ecological and economic value. Methods We performed genome-wide identification of the BcSnRK2 gene family using bioinformatics approaches. Phylogenetic relationships, gene structures, conserved motifs, cis-acting elements, chromosomal localization, and protein structures were systematically analyzed. Subcellular localization was verified by transient expression in Nicotiana benthamiana. Tissue-specific expression and drought-responsive patterns were detected by qRT-PCR under 10% PEG6000 treatment. Protein–protein interaction networks were predicted using the STRING database. Results A total of nine BcSnRK2 genes were identified and unevenly distributed across eight chromosomes. All BcSnRK2 proteins contained conserved kinase domains and shared a highly conserved exon–intron structure. Promoter regions harbored abundant ABA-responsive and stress-related cis-elements. BcSnRK2 genes exhibited distinct tissue-specific expression profiles. All genes were significantly induced by drought stress in a tissue- and time-dependent manner, with BcSnRK2.9 and BcSnRK2.7 showing strong and sustained activation in shoots and BcSnRK2.7 and BcSnRK2.3 responding prominently in roots. BcSnRK2 proteins were localized in the cytoplasm, plasma membrane, and nucleus, and were predicted to interact with core components of the ABA signaling pathway. Discussion The BcSnRK2 family exhibits evolutionary conservation and functional divergence in Bombax ceiba. The compact size of the SnRK2 family, conserved structural features, and distinct tissue-specific drought response patterns are consistent with a streamlined stress signaling system that may contribute to the ecological adaptation of Bombax ceiba in seasonally dry tropical environments, although formal evolutionary analyses are required to establish adaptive significance. This study provides valuable gene resources for drought resistance breeding of woody plants and advances the understanding of stress signaling mechanisms in tropical trees.
Yumei Shi, Zhifang Zhang, Ruoxin He et al.· Frontiers in Plant Science· 0 citations
The TCP (Teosinte branched 1/Cycloidea/Proliferating) gene family comprises plant-specific transcription factors essential for regulating growth, development, and environmental adaptation. Utilizing the high-quality ‘Rui Youpan 1’ (‘RYP1’) reference genome, we conducted a comprehensive genome-wide identification and characterization of the TCP family in peach (Prunus persica). We identified 20 PpTCP genes and systematically evaluated their physicochemical properties, chromosomal distribution, phylogeny, gene architecture, and promoter cis-regulatory elements. Notably, the enrichment of abscisic acid-responsive elements (ABREs) in their promoters suggests a significant role in abiotic stress signaling. Integrated RNA-seq and RT-qPCR analyses identified six putative candidates (PpTCP3, 5, 6, 11, 14, and 15) with pronounced differential expression under drought conditions. Subcellular localization confirmed that all tested PpTCPs function within the nucleus. Moreover, the results of STRING-based computer simulations predicting protein–protein interactions indicate that PpTCP3 and PpTCP5 interact with key hormone pathways and stress-related transcription factors (TFs), including auxin signaling and strigolactone signaling.
Yanfu Jing, Yang Yu, Zimin Xiao et al.· International Journal of Mol...· 0 citations
First comprehensive characterization of the RLCK gene family in sugarcane is presented, elucidating its evolutionary features, expression dynamics and functional roles, and providing compelling evidence that ScRLCK53 modulates salt tolerance through activation of the JA signaling pathway.
Shichao Wang, Pingping Lin, Deng Wu et al.· Plant physiology and biochem...· 0 citations
Brassinosteroid signaling kinases (BSKs) act as core signal transducers downstream of Brassinosteroid (BR) perception and integrate plant growth regulation with broad-spectrum biotic and abiotic stress tolerance. Despite well-established functional characterizations of BSK gene families in Arabidopsis thaliana and rice, comprehensive genome-wide profiling and salt response analysis of BSK homologs remain lacking in wheat. In this study, we systematically identified 18 TaBSK family members. Phylogenetic analysis separated wheat TaBSKs into three distinct evolutionary subgroups. The 18 TaBSK loci were unevenly distributed across 14 chromosomes derived from the A, B, and D subgenomes. Motif scanning uncovered 10 universal conserved amino acid motifs, including two signature functional domains: the tetratricopeptide repeat (TPR) and protein kinase catalytic domain (PKc). Intra-genomic collinearity analysis confirmed that segmental duplication constituted the primary evolutionary driver underlying TaBSK family expansion. Extensive cis-regulatory element profiling identified abundant hormone- and stress-responsive cis-motifs. Transcriptome profiling RNA-seq datasets revealed five TaBSK genes exhibiting significant differential transcription under salt stress. Specifically, TaBSK16, TaBSK17, and TaBSK18 were markedly upregulated following salt exposure. Collectively, this study delivers an evolutionary and transcriptional atlas of the wheat TaBSK family and provides candidate genes for functional validation and molecular breeding toward salt-tolerant wheat varieties. Collectively, this study explores the evolution and transcriptional patterns of the wheat TaBSK gene family and provides candidate genes for subsequent functional validation and molecular breeding of salt-tolerant wheat varieties.
Yongtao Zhao, Jun-Sen Wang, Zhong-Zhou Zhang et al.· Current Issues in Molecular...· 0 citations
The TIFY gene family comprises plant-specific transcriptional regulators central to jasmonic acid (JA) signaling and responses to biotic and abiotic stresses. Despite the economic importance of the banana (Musa spp.), the TIFY family remains largely uncharacterized in this crop. Here, we conducted a genome-wide identification and comprehensive analysis of the MaTIFY gene family in Musa acuminata. A total of 47 MaTIFY genes were identified, distributed across all 11 chromosomes. Phylogenetic analysis classified these into four subfamilies (TIFY, ZIZ/ZML, PPD, and JAZ), and conserved motif and domain analyses revealed a core TIFY domain architecture with subfamily-specific structural features. Gene Ontology (GO) enrichment and cis-acting regulatory element analyses suggested potential involvement in JA-mediated signaling, defense response, and hormone cross-talk. Expression profiling under drought, Fusarium oxysporum f. sp. cubense race 4 (Foc 4), and cold stress revealed distinct transcriptional responses, with MaTIFY5, MaTIFY16, MaTIFY20, MaTIFY26, and MaTIFY30 exhibiting enhanced induction in resistant cultivars compared to their susceptible counterparts. Functional characterization of MaTIFY20 confirmed its significant upregulation under drought stress and its ability to confer enhanced osmotic tolerance when heterologously expressed in yeast. These findings provide novel insights into the evolutionary dynamics and stress-responsive functions of banana TIFY genes and identify candidate targets for molecular breeding to improve abiotic and biotic stress resilience in banana.
Sheraz Ahmad, Huimin Song, Hangbo Cao et al.· International Journal of Mol...· 0 citations
Abiotic stress severely limits plant growth and productivity. Taraxacum kok-saghyz Rodin (TKS), known for its environmental resilience, represents a valuable resource for identifying stress-tolerant genes to improve stress-adaptive crops. Plant AT-rich protein and zinc-binding protein (PLATZ) transcription factors serve as core regulators of plant growth, developmental processes, and adaptive responses to various stress conditions; however, they remain uncharacterized in TKS. Here, we identified 10 TksPLATZ genes through a whole-genome analysis. Phylogenetically, these genes were grouped into five distinct evolutionary branches. Promoter sequence analysis revealed multiple types of cis-acting regulatory elements that are connected with hormonal signal responses and environmental stress adaptation. Integrated analysis of transcriptome datasets and RT-qPCR validation demonstrated that TksPLATZ genes display tissue-specific expression profiles and show distinct responsive patterns to drought and salt stress treatments. Among them, TksPLATZ1, TksPLATZ2 and TksPLATZ7 were markedly induced under both stressors and were selected for further functional study. We demonstrated that TksPLATZ1, TksPLATZ2 and TksPLATZ7 localize to the cell nucleus and act as transcriptional activators and repressors, respectively. Phenotypic data from overexpression experiments in plants confirm that heterologous expression of TksPLATZ1, TksPLATZ2, and TksPLATZ7 enhances the tolerance of Arabidopsis to salt and osmotic stress. These findings provide valuable genetic resources for improving plant tolerance to environmental stresses.
Jinxian Chen, Wenhao Wu, Ming-Hua Luo et al.· Phytochemistry· 0 citations