Search Results (1,758)

The LHCB gene family plays a crucial role in light harvesting and photoprotection in plants by encoding key components of the photosystem II antenna complex. The LHCB genes are also involved in salt stress. In this study, we systematically identified and characterized 16 LbaLHCB genes in the economically important medicinal plant Lycium barbarum. Comprehensive bioinformatics analyses revealed that these genes are unevenly distributed across seven chromosomes, with notable gene clustering on chromosome 11. Phylogenetic analysis classified them into seven distinct subfamilies, with the LbaLHCB1 subfamily showing significant expansion through gene duplication events. qRT-PCR and transcriptome analyses revealed tissue-specific expression patterns, with LbaLHCB1.6 exhibiting preferential expression in developing fruits, suggesting its potential involvement in fruit development and quality formation. Under salt stress conditions, the LbaLHCB genes displayed dynamic temporal responses: LbaLHCB1.5 was rapidly induced during early stress (1–3 h), LbaLHCB7 reached peak expression at mid-phase (6–12 h), while LbaLHCB1.2 showed significant downregulation during late stress response (24 h). Promoter analysis identified multiple stress-responsive cis-elements, providing molecular insights into their regulation under abiotic stress. These findings significantly advance our understanding of the LbaLHCB gene family’s structural characteristics and functional diversification in L. barbarum, particularly in relation to photosynthesis regulation and stress adaptation. The study provides valuable genetic resources for future molecular breeding aimed at improving stress tolerance and fruit quality in this important medicinal crop. Full article

CCCH zinc finger proteins play critical roles in plant growth, development and stress responses. Here, 56 CCCH genes were identified in Morus alba. These genes displayed wide variation in coding sequence (456–6318 bp) and protein length (151–2105 aa), with most proteins predicted to localize in the nucleus and a few in chloroplasts, the endoplasmic reticulum or cytoplasm. Chromosomal mapping showed uneven distribution across 14 chromosomes, with tandem clusters on chromosomes 1, 6 and 13. Phylogenetic analysis classified 53 MaC3Hs into 13 subfamilies, while three genes remained ungrouped. Synteny analysis revealed four segmental duplication events, suggesting segmental duplication as the major expansion mechanism, under purifying selection. Comparative collinearity showed higher conservation with Arabidopsis thaliana than with rice or maize. Promoter analysis identified 22 cis-acting elements, mainly related to phytohormones, followed by abiotic stress and developmental regulation. Expression profiling under drought stress revealed differential expression across tissues, with MaC3H33 showing strong induction (>200-fold in stems on day 6). Subcellular localization confirmed MaC3H33 is nuclear, and yeast assays indicated no self-activation. These findings provide comprehensive insights into the MaC3H gene family and lay a foundation for functional studies related to drought tolerance in mulberry. Full article

Waterlogging poses a grave abiotic stress that hampers crop productivity and survival due to reduced oxygen availability in the impacted tissues. To adapt to this hypoxic environment, the hypocotyls of melon (Cucumis melo L.) seedlings can produce a profusion of adventitious roots when exposed to waterlogging stress. However, research on the significance of these adventitious roots under waterlogging stress has been limited. The present study aimed to elucidate the critical role of adventitious roots by investigating the physiological, biochemical, and metabolic changes that occur following their removal during waterlogging stress. The removal of adventitious roots compromised the normal growth of melon seedlings, resulting in phenotypic abnormalities such as chlorotic and withered leaves. Our results indicated that the removal of adventitious roots led to significant reductions in total chlorophyll levels by 62.89% and 43.60% compared to the normal control condition and waterlogging stress alone, respectively. Additionally, in the adventitious root removal treatment, higher malondialdehyde (MDA) content, O₂^•− production rate, monodehydroascorbate reductase (MDHAR) activity, alcohol dehydrogenase (ADH) activity, the AsA/DHA ratio, proline content, jasmonic acid (JA) content, and 1-aminocyclopropane-1-carboxylic acid (ACC) content were observed. Specifically, JA levels were significantly enhanced by 180.54% and 52.05%, and ACC levels were significantly increased by 519.23% and 125.16% compared to the control and waterlogging stress conditions, respectively. Through untargeted metabolomic analysis, a total of 447 differentially accumulated metabolites (DAMs) were identified. Notably, jasmonic acid and brassinolide, which are involved in plant hormone signal transduction, along with cyanidin 3-(2G-xylosylrutinoside) classified as flavonoids, (2S,3′S)-α-amino-2-carboxy-5-oxo-1-pyrrolidinebutanoic acid categorized as proline and derivatives, and ligstroside-aglycone and foeniculoside VII annotated as terpenoids, exhibited key roles in the waterlogging response. This research enhances our understanding of the mechanisms underlying the removal of adventitious roots during waterlogging stress, as well as the associated physiological, biochemical, and metabolic changes. These findings provide valuable insights into the crucial role of adventitious roots in melon seedlings subjected to waterlogging stress and may inform strategies for enhancing waterlogging tolerance in breeding practices. Full article

Glutamine synthetase plays an essential role in regulating plant growth and development. However, few studies have analyzed the roles of TaGS in wheat under abiotic stress conditions. In this study, we identified and analyzed the members of the TaGS gene family in Triticum aestivum L., focusing on their gene characteristics, phylogenetic evolution, cis-elements, transcriptional and post-translational modifications, and expression profiling in response to abiotic stress. Twelve TaGS genes were divided into four subfamilies. The synteny analysis revealed that wheat and the five other species share GS homologs. Several potential transcription factors were identified as regulators of TaGS genes. TaGS contains 19 microRNA binding sites, phosphorylation sites, and ubiquitination sites. TaGS genes exhibited tissue-specific expression across various developmental stages and were differentially expressed in response to abiotic stress. For instance, TaGS1-3-4A/4B/4D were upregulated in the leaves and roots of wheat seedlings under abiotic stress conditions. Furthermore, gene ontology annotation was performed on the TaGS-interacting proteins screened by immunoprecipitation–mass spectrometry to elucidate the regulatory network associated with TaGS. This study lays a foundation for further functional research of TaGS genes in response to abiotic stress and provides potential information for enhancing stress tolerance in wheat. Full article

Abiotic stressors such as drought, salinity, waterlogging, and high and low temperatures significantly reduce the growth and productivity of rice (Oryza sativa) and soybean (Glycine max), which are vital for global food and nutritional security. These stressors disrupt physiological, biochemical, and molecular processes, resulting in decreased yield and quality. Biostimulants represent promising sustainable solutions to alleviate stress-induced damage and improve crop performance under stressful conditions. This review provides a comprehensive analysis of the role of biostimulants in enhancing rice and soybean resilience under abiotic stress. Both microbial and non-microbial biostimulants including phytohormones such as salicylic acid; melatonin; humic and fulvic substances; seaweed extracts; nanoparticles; and beneficial microbes have been discussed. Biostimulants enhance antioxidant defenses, improve photosynthesis and nutrient uptake, regulate hormones, and activate stress-responsive genes, thereby supporting growth and yield. Moreover, biostimulants regulate molecular pathways such as ABA- and ROS-mediated signaling and activate key transcription factors (e.g., WRKY, DREB, NAC), linking molecular responses with physiological and phenotypic resilience. The effectiveness of biostimulants depends on crop species, growth stage, stress severity and application method. This review summarizes recent findings on the role of biostimulants in enhancing the mechanisms underlying growth, yield, and stress tolerance of rice and soybean under abiotic stress. Additionally, the incorporation of biostimulants into sustainable farming practices to increase productivity in the context of climate-related challenges has been discussed. Furthermore, the necessity for additional research to elucidate the underlying mechanisms, refine application methods, and verify their effectiveness in field conditions has been highlighted. Full article

Salt stress is a major abiotic factor limiting wolfberry (Lycium barbarum) growth. As a high-value medicinal and edible crop, wolfberry relies on its carotenoid content, a critical determinant of fruit quality and nutritional value. To elucidate the expression regulatory mechanisms of key genes in the carotenoid biosynthesis pathway under salt stress, this study systematically identified 17 structural genes within the L. barbarum carotenoid pathway using genomic and transcriptomic approaches. Comprehensive analyses were conducted on gene structure, chromosomal distribution, conserved domains, and cis-acting elements. The results revealed that these genes were clustered on chromosomes Chr08 and Chr10 and exhibit strong collinearity with tomato (18 syntenic pairs). Their promoters were enriched with light-responsive (G-box) and stress-responsive (ABRE, DRE) elements. Tissue-specific expression analysis demonstrated high expression in mid-to-late fruit developmental stages (LbaPSY1, LbaPDS) and in photoprotective genes (LbaZEP, LbaVDE) in leaves. Under 300 mM NaCl stress treatment, the genes exhibited a staged response: Early stage (1–3 h): upstream MEP pathway genes (LbaDXS, LbaGGPS) were rapidly induced to supply precursors. Mid-stage (6–12 h): midstream genes (LbaPSY, LbaPDS, LbaZDS) were continuously upregulated, promoting lycopene synthesis and preferentially activating the β-branch (LbaLCYB). Late stage (12–24 h): downstream xanthophyll cycle genes (LbaBCH, LbaZEP, LbaVDE) were significantly enhanced, facilitating the accumulation of antioxidant compounds like violaxanthin and neoxanthin. This coordinated regulation formed a synergistic “precursor supply–antioxidant product” network. This study revealed the phased and coordinated regulatory network of carotenoid biosynthesis genes under salt stress in L. barbarum. It also provided potential target genes for the new cultivar selection with enhanced salt tolerance and nutritional quality. Full article

Abiotic stresses severely impair plant growth and productivity. To counteract stress, plants have evolved intricate strategies, including the induction of stress-responsive proteins. The Arabidopsis thaliana Salt Tolerance-Related Protein (STRP) has recently emerged as a key player in abiotic stress tolerance. STRP is a small, hydrophilic, intrinsically disordered protein that exhibits the potential to adopt distinct conformations depending on the cellular context. STRP is localized in the cytosol and nucleus and is associated with the plasma membrane. Stress induces the subcellular redistribution of STRP, accompanied by a significant increase (up to ten-fold) in its levels due to reduced degradation by the 26S proteasome. Reverse genetics studies have demonstrated that STRP can mitigate the detrimental effects of oxidative stress and participate in modulating stress-related gene expression. Although the exact mechanism of STRP remains unclear, its physicochemical properties suggest a dual role as a molecular shield, interacting with macromolecules without a fixed conformation, and as a binder of specific defense-related client proteins, adopting a defined tertiary structure. This review provides a comprehensive overview of STRP and its emerging role as a multifunctional player in abiotic stress responses, also highlighting its potential for strengthening crop resilience and maintaining agricultural productivity under global climate challenges. Full article

Members of the WRKY transcription factors (TFs) family play crucial roles in biotic and abiotic stress responses in plants, but their roles in response to drought stress in maize (Zea mays L.) have not been fully elucidated. Maize ZmWRKY82, a group IIc WRKY gene, was isolated from maize using reverse transcription polymerase chain reaction (RT-PCR). Using the UniProt online database, we found that ZmWRKY82 encodes a 222-amino protein with conserved WRKYGKK and C-X₄-C-X₂₃-H-X₁-H motifs. ZmWRKY82 is strongly induced by polyethylene glycol (PEG), abscisic acid (ABA), methyl jasmonate (MeJA), salicylic acid (SA), and ethephon (ETH) treatments. The ZmWRKY82 protein was located in the cell nucleus. ZmWRKY82 had transcriptional activation capability and was able to bind to the W-box element. ZmWRKY82-overexpressing Arabidopsis and maize exhibited stronger drought resilience, which was associated with enhanced antioxidant enzyme activity and altered transcription level of drought-related genes. These findings suggest that ZmWRKY82 plays a central role in conferring drought tolerance in maize and may contribute to crop improvement and sustainable agricultural practices. Full article

JmjC domain proteins play crucial roles in plant growth and development, regulation of epigenetic processes, flowering control, and stress defence. However, these proteins have not been systematically identified or characterised in tomato. Here, we performed a genome-wide identification of JmjC domain-containing genes (JMJ family) in tomato and identified 23 SlJMJ genes within the tomato genome. Expression analysis indicated that SlJMJ15 was responsive to drought stress, prompting us to investigate its functional role in tomato plants. We found that SlJMJ15-RNAi lines displayed a severe dwarf phenotype, whereas SlJMJ15-overexpression lines exhibited increased drought sensitivity compared to wild-type plants, indicating that SlJMJ15 negatively regulates drought tolerance in tomatoes. Further investigation suggests that SlJMJ15 may reduce drought tolerance in tomatoes by modulating the expression of key genes involved in abscisic acid signalling pathways through its demethylation activity. This study deepens our understanding of the roles of SlJMJ family genes in tomato growth and abiotic stress responses, laying the foundation for developing strategies to improve drought stress tolerance in tomatoes. Full article

The PLATZ gene family influences plant growth, development, and responses to both biotic and abiotic stresses. Flax (Linum usitatissimum L.), an important oilseed and fiber crop, has not been extensively studied for its PLATZ genes. In this study, 27 LuPLATZ genes were identified in the recently assembled T2T (Telomere-to-Telomere) flax genome through bioinformatics analyses. Phylogenetic analysis grouped these genes into five subfamilies. Examination of gene structure and motifs showed conserved exon–intron arrangements and similar motif compositions within the same clade. Promoter analysis revealed that most cis-elements are associated with plant hormone responses (such as MeJA and ABA) and abiotic stresses, including anaerobic induction, drought, and low temperature. Duplication analysis identified 33 segmental duplication events, and miRNA target prediction indicated that lus-miR167 is the primary regulator of LuPLATZ genes. Expression profiling based on RNA-seq data showed high expression levels of most LuPLATZ genes in leaves and roots, and qRT-PCR confirmed their stress-responsive expression under cold, drought, and salt conditions, with LuPLATZ14 and LuPLATZ21 significantly upregulated in all treatments. Furthermore, overexpression of these two genes enhanced drought tolerance in yeast transformants. Full article

Glycyrrhiza uralensis is an important medicinal plant exhibiting strong tolerance to abiotic stresses, including drought and salinity. DREB (Dehydration-Responsive Element-Binding) transcription factors, key members of the AP2/ERF family, play crucial roles in plant growth, development, and stress responses. Based on transcriptome data, we identified 18 DREB transcription factors in G. uralensis, designated GuDREB1 to GuDREB18. Bioinformatics analysis revealed genomic sequences ranging from 534 to 2864 bp and coding sequence (CDS) lengths between 525 and 1509 bp. All GuDREB proteins contain a single AP2 domain, including the conserved YRG and RAYD elements, and were predicted to localize to the nucleus. Phylogenetic analysis clustered the G. uralensis DREBs with 61 Arabidopsis thaliana DREBs into five subgroups, indicating evolutionary conservation. Promoter analysis detected seventeen stress-responsive cis-acting elements, encompassing hormone-responsive and abiotic stress-responsive motifs, suggesting diverse biological functions. Tissue-specific expression profiling revealed GuDREB transcription in both aerial and underground parts. Drought stress induced varying degrees of GuDREB expression, confirming their involvement in stress responses. Notably, GuDREB10 expression increased significantly in underground parts, while GuDREB15 showed pronounced upregulation in aerial parts under drought; the GuDREB15 promoter contained the highest number of light-responsive elements (23), potentially explaining its aerial tissue specificity. Drought stress significantly increased abscisic acid (ABA) content. Underground parts exhibited higher initial sensitivity to drought, whereas aerial parts displayed a more sustained response; ABA levels overall showed an initial increase followed by a decline. This study expands the G. uralensis DREB gene database, provides a foundation for selecting stress-resistance genes, and offers insights into DREB functional roles in abiotic stress responses in this key medicinal species. Full article

The RNA-directed DNA methylation (RdDM) pathway is a crucial epigenetic mechanism governing plant responses to environmental stress. While the RdDM pathway has been extensively studied in Arabidopsis thaliana, the comprehensive understanding of its components in cucumber (Cucumis sativus L.) remains lacking. In this study, we performed a genome-wide identification and characterization of RdDM pathway genes in cucumber, followed by an analysis of their expression patterns across various tissues and under multiple abiotic stress conditions. A total of 67 putative CsRdDM genes were identified, which are unevenly distributed across the cucumber’s chromosomes. Phylogenetic and gene structure analyses revealed considerable evolutionary divergence, particularly within the key Argonaute gene family (CsAGO). Crucially, the promoter regions of CsRdDM genes were found to contain cis-regulatory elements associated with abiotic stress, light signaling, and development, suggesting their potential involvement in complex regulatory networks. RT-qPCR assays confirmed that CsRdDM genes exhibit distinct and stress-specific transcriptional patterns. Notably, several genes such as CsAGO4 and CsIDN2 showed antagonistic expression between roots and leaves under drought (PEG-6000) stress, implying a sophisticated, tissue-specific defense mechanism. Among them, CsAGO4 emerged as a candidate gene responsive to abiotic stress. Those findings provide new insights into the regulatory roles of CsRdDM genes under abiotic stress and highlight candidate genes for the genetic improvement of stress tolerance in cucumber. Full article

Chilling stress is a major abiotic factor that limits chili pepper (Capsicum annuum L.) cultivation by disrupting redox homeostasis, thereby impairing growth and fruit productivity. Superoxide dismutases (SODs), which catalyze the conversion of superoxide radicals into hydrogen peroxide and oxygen, serve as key components of the plant antioxidant defense system. However, the SOD gene family in chili pepper has not been comprehensively characterized. Therefore, this study aimed to characterize the SOD gene family in chili pepper and investigate their responses to chilling stress. We identified nine putative CaSOD genes and classified them into CZSOD, FeSOD, and MnSOD clades based on phylogenetic relationships and conserved domain architecture. Bioinformatic analyses revealed variation in physicochemical properties and predicted subcellular localizations, suggesting functional diversification. Transcriptome profiling indicated tissue-specific expression, with several CaSODs preferentially expressed in fruits and floral buds, while qRT-PCR analysis demonstrated that six CaSODs were transcriptionally induced under chilling stress. Functional validation in Nicotiana benthamiana leaves showed that transient expression of four selected CaSODs significantly enhanced SOD activity in an isoform-specific manner. Future studies should validate these genes across diverse chili pepper cultivars under field conditions and assess their potential for integration into breeding programs. Collectively, these findings provide new insights into the molecular and functional diversity of CaSODs, highlight their role in maintaining redox balance under chilling stress, and provide useful genetic resources for breeding stress-tolerant chili pepper and related crops. Full article

Protein identity and functional roles within the cell provide the landscape of proteomics and other high-throughput technologies. However, not all protein sequences are cataloged with an identity or a functional protein family. The lack of identity and functional role of a set of proteins are collectively named as the dark proteome. Key structural features are, for example, ordered sequences (with a defined structural arrangement) and disordered sequences (presenting one or more intrinsically disordered stretches). Here, we reanalyzed eight proteomic datasets and the subset of the “unknown” proteome of S. lycopersicum to describe if there is a relationship between disorder, length, and tissue-specific abundance of proteins with key structural features in the relation of ordered/disordered abundance in the protein sequences. Intriguingly, we unveil that from the S. lycopersicum proteome, the “unknown” subset represents around 10% only. We further cataloged dark proteome in terms of ordered and disordered sequences and found that proteins with disorder represent around 23% of the total “unknown” proteins. Also, we describe an amino acid composition and sequence length enrichment both, in the ordered and disordered fraction of the dark proteome. Finally, we describe that proteins within the dark proteome can be related to a specific location and abundance in an organ or tissue. An unknown protein sequence presenting a combination of specific length and degree of disorder can be explored with other biotechnological alternatives to improve responses or tolerate abiotic stress, also serving as sensors during development or ripening stages. These findings suggest an opportunity to study “protein darkness” in terms of disorder and functional associations. Full article

Saussurea involucrata, a rare and endangered medicinal plant of the Asteraceae family, is primarily distributed in high-altitude rocky slopes and meadows at elevations of 2400–4100 m. In nature, this herb endures various abiotic stresses, including intense cold and ultraviolet radiation. In our study, transcriptomic profiles revealed that most of the differentially expressed genes (DEGs) enriched in stress response pathways, such as “response to water”, “response to abscisic acid”, “cold acclimation”, and “response to water deprivation”, were significantly upregulated after low-temperature treatment. In contrast, the majority of genes with lower expression were related to “photosynthesis”, “protein–chromophore linkage”, and “chloroplast thylakoid membrane”. Among them, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) database analysis revealed that approximately 20 DEGs were identified and annotated as dehydrin genes (DHNs). Quantitative PCR (qPCR) validation also confirmed that these DHNs were upregulated under cold stress. Moreover, SiDHN3, a new dehydrin gene, was cloned by Rapid Amplification of cDNA Ends (RACE). SiDHN3’s heterologous expression in E. coli showed enhanced salt, osmotic, freeze–thaw, and cold stress tolerance. A functional analysis of SiDHN3’s truncated derivatives revealed that the K-segment was critical for its protective function under freeze–thaw and cold stresses. Collectively, our study demonstrated the potential role of various DHNs as a functional protein, enhancing tolerance to cold stress in the high-altitude adaptation of plants. Full article