Search Results (349)

C3H-type zinc finger proteins play essential roles in plant responses to abiotic stresses, as well as in the regulation of growth, development, and signal transduction. Birch (Betula platyphylla Suk.), an ecologically adaptable tree species widely distributed in northern regions, has not yet been systematically characterized for its C3H gene family. In this study, a total of 15 BpC3Hs were identified from a genome-wide analysis of birch. Their physiochemical properties, gene structures, conserved motifs and domains were systematically analyzed. Promoter analysis identified cis-acting elements associated with stress responses, hormone signaling, and developmental regulation. Transcriptome data further showed that most BpC3Hs were responsive to salt, drought, high/low-temperature stresses, and light/dark treatment, and showed differential expression patterns in tension wood and opposite wood. Additionally, they displayed stage-specific expression patterns during male inflorescence development. This study lays a foundation for future functional characterization of the C3H gene family in birch and its application in molecular breeding for stress resistance. Full article

SHORT INTERNODE (SHI)-related sequence (SRS) transcription factors are plant-specific zinc-finger proteins increasingly implicated in growth and abiotic stress responses. Despite their diverse vital role in plants, they are largely unexplored in bread wheat. In this study, we identified 15 TaSRS genes and classified them into five homoeologous groups in the bread wheat genome. Each TaSRS protein consisted of conserved RING-like zinc-finger and IGGH domains. The synteny and phylogenetic analyses provided insight into the evolutionary divergence and conservation of TaSRS proteins. Promoter analysis revealed the presence of stress-responsive cis-regulatory elements along with various transcription factor binding sites, indicating their plausible roles in drought and salinity stress responses and signalling. Additionally, the predicted regulation of a few TaSRS genes through certain miRNAs involved in hormone and stress responses, plant development, and nutrient uptake suggested their diverse functions. In silico protein–protein interaction and gene ontology analyses further anticipated an association of TaSRS proteins with organ development and hormone and stress response. High-throughput transcriptomic profiling revealed differential expression of TaSRS genes across various vegetative and reproductive stages and abiotic stress conditions. The qRT-PCR analyses confirmed the stress-responsive role of TaSRS1-1D, TaSRS2-3D, TaSRS4-7A, and TaSRS5-7A under drought and salinity conditions. These results indicated the potential role of TaSRS genes in stress adaptation and opened up opportunities for their detailed functional characterization and applications in the development of salinity and drought resilience in crops. Full article

Background: Cymbidium goeringii, one of China’s traditional and valuable orchids, possesses significant ornamental and economic value. However, it is relatively sensitive to low temperature and other abiotic stresses, which severely restrict its application in landscaping and industrial development. WRKY transcription factors play important roles in plant responses to abiotic stresses, yet related research in C. goeringii remains limited. Methods: In this study, based on transcriptome data of C. goeringii under four different stresses, we identified and cloned the WRKY transcription factor gene CgWRKY53. Through bioinformatics analysis, quantitative real-time PCR, and heterologous transformation in Arabidopsis thaliana, we systematically investigated its structural characteristics, expression patterns, and function under cold stress. Results: The full-length CDS of CgWRKY53 is 1080 bp, encoding a protein of 359 amino acids with a molecular weight of 39.95 kDa. Group III subfamily of the WRKY family, possessing the conserved WRKYGQK domain and a C2HC-type zinc finger motif. CgWRKY53 is expressed in roots, pseudobulbs, leaves, and flowers of C. goeringii, with the highest expression observed in flowers. Under cold, heat, waterlogging, and ABA treatments, CgWRKY53 displayed significant changes in expression, with the most pronounced response occurring under cold stress, where its expression was significantly upregulated. Homozygous transgenic A. thaliana lines overexpressing CgWRKY53 exhibited dwarfed stature, with smaller and deformed leaves and notably shorter roots compared to wild-type plants. The overexpression lines also showed cold-sensitive phenotypes under low-temperature stress, and the expression of several cold-responsive genes was suppressed, suggesting that CgWRKY53 may act as a negative regulator in the response to cold stress. Conclusions: These results identify CgWRKY53 as a negative regulator of cold stress response in C. goeringii. This study provides important genetic resources and theoretical foundations for molecular breeding of stress-resistant orchids. Full article

The PRDM (PR domain-containing) family consists of transcriptional regulators characterized by a PR (PRDI-BF1 and RIZ homology) domain, a subtype of the SET domain, and a variable number of zinc finger motifs. Nineteen PRDM family members have been identified in both mice and humans, and increasing evidence supports their roles as epigenetic regulators in development and disease. PRDM proteins share a conserved structure, comprising an N-terminal PR domain with potential histone methyltransferase activity and C-terminal C2H2-type zinc fingers involved in protein–protein, protein–RNA, and protein–DNA interactions. Recent studies indicate that multiple PRDM family members are involved in the regulation of the neuro-motor system, including neural lineage specification, neuronal differentiation, motor function maintenance, and neuromuscular-related pathological processes. This review summarizes current evidence on the functions and regulatory mechanisms of PRDM family members in the neuro-motor system. Overall, PRDM family members act as important epigenetic regulators in the neuro-motor system. Clarifying their molecular mechanisms may contribute to a better understanding of neuro-motor regulation and provide a theoretical basis for future research in exercise and movement science. Full article

Zinc finger proteins (ZFPs) are a diverse group of plant transcription factors essential for regulating development, signaling, and stress responses. In this study, we performed a genome-wide identification and integrative analysis of 140 C3H-type zinc finger transcription factor genes in the soybean genome, exhibiting an uneven distribution across all 20 chromosomes. These C3H-ZFPs contained one (37), two (58), three (19), four (7), five (17), or six (2) C3H domains and were classified into 14 subsets based on their domain architecture. All C3H genes encoding proteins harbored the conserved C3H-ZFP domain and displayed various physicochemical characteristics. Phylogenetic analysis grouped them into 10 clades, closely related to other species like Arabidopsis, rice and alfalfa. Promoter analysis revealed cis-elements associated with stress response (~39.1%), light response (~37.3%), phytohormones (~18.5%), and development (~4.97%). Duplication analysis revealed 78 pairs of segmental and eight tandem duplication events, with purifying selection indicated by Ka/Ks (nonsynonymous/synonymous) ratios, indicating that these C3H-ZFP duplicates were largely maintained under purifying selection. A total of 388 miRNAs from 196 gene families were predicted to target 140 C3H-ZFP genes, with most enriched miRNAs targeting C3H-ZFP genes, including the miR156, miR395, and miR396 families. Transcription factor binding sites for MYB, AP2, MIKC_MADS, BBR-BPC, ERF, C2H2, and Dof were found upstream of most C3H-ZFP genes. RNA-Seq and qRT-PCR analyses showed tissue-specific expression and stress-responsive expression patterns, with several C3H-ZFP genes, especially GmC3H1, GmC3H63, GmC3H124, and GmC3H127, being significantly upregulated under abiotic stress conditions. Together, these results provide a comprehensive overview of soybean C3H-ZFP genes and identify promising candidates for future functional studies on development and abiotic stress adaptation. Full article

Cadmium (Cd) is a highly toxic heavy metal that severely impairs plant growth and poses ecological and health risks. Chrysanthemum indicum (L.), a dominant species in Cd-contaminated regions, represents a valuable germplasm for phytoremediation. In this study, we cloned and characterized CiWRKY50, a WRKY transcription factor containing a conserved WRKY domain and C2H2-type zinc finger. CiWRKY50 was localized to the nucleus but lacked intrinsic transcriptional activation activity. Overexpression of CiWRKY50 in Arabidopsis thaliana and C. indicum significantly enhanced Cd tolerance, as shown by reduced root Cd accumulation, improved transport efficiency, lower ROS and MDA levels, and increased chlorophyll, proline, and soluble protein contents. Antioxidant enzyme activities and Cd-chelating compounds (GSH, NPT, PCs) were also upregulated. Furthermore, combined Cd and ABA treatments promoted Cd sequestration in roots and activated ABA-responsive genes (CiABF1, CiABF2, CiABF4), alleviating shoot toxicity. These findings indicate that CiWRKY50 enhances Cd tolerance in association with enhanced ABA-mediated signaling and redox homeostasis, providing new insights for breeding Cd-resistant plants and improving phytoremediation strategies. Full article

Background/Objectives: ASXL1 is a chromatin-associated gene implicated in both hematologic malignancies and neurodevelopmental disorders, including Bohring–Opitz syndrome (BOS). Although many ASXL1 variants are well classified, a substantial proportion remain variants of uncertain significance (VUS), complicating molecular diagnosis and genetic counseling. The objective of this study was to evaluate whether structural context can inform the interpretation of selected ASXL1 missense variants in a clinical setting. Methods: We describe a 17-year-old female with clinical features consistent with BOS carrying the heterozygous ASXL1 variant p.Q1448R, currently classified as benign under ACMG/AMP guidelines. Three-dimensional in silico structural modeling was performed using AlphaFold3 and available crystallographic data. Three additional ASXL1 missense variants classified as VUS in ClinVar (p.R265H, p.T297M, and p.Y358C) were also analyzed. Evolutionary conservation, domain localization, and residue-level interactions were assessed. Results: Structural modeling indicated that the p.Q1448R substitution alters polar interactions and introduces a steric constraint near a conserved PHD-type zinc finger domain. Variants p.R265H and p.T297M affected stabilizing interactions within the DEUBAD, which is involved in BAP1 activation, while p.Y358C altered a polar microenvironment adjacent to a chromatin-interacting region. All analyzed variants, except p.T297M, localized to evolutionarily conserved regions. Conclusions: This study demonstrates that in silico structural analysis can provide complementary, domain-level insights for the interpretation of ASXL1 missense variants that remain classified as benign, likely benign or VUS under current frameworks. Such approaches may assist in prioritizing variants for further functional evaluation and refining molecular interpretation when experimental data are limited. Full article

Papain-like protease (PLpro), a crucial functional domain of the SARS-CoV-2 non-structural protein 3 (nsp3), plays a dual role in both hydrolyzing viral polyprotein precursors and modulating host immune responses. These critical functions position PLpro as a key target in the ongoing development of antiviral therapies for SARS-CoV-2. This review analyzes more than 100 PLpro-ligand co-crystal structures and summarizes the major binding modes between these ligands and PLpro. Most of these ligands bind to sites analogous to those targeted by the classical non-covalent inhibitor GRL0617, primarily involving the P3 and P4 subsites and the BL2 loop. Based on these structural insights, optimized inhibitors have expanded targeting beyond the canonical binding site to auxiliary regions such as the BL2 groove and the Val70 site, and in some cases toward the catalytic Cys111 buried within a narrow pocket. Certain ligands identified through various screening approaches bind to non-canonical or allosteric regions, such as the S1 and S2 sites or the zinc-finger domain, engaging PLpro through distinct interaction modes and thereby offering additional opportunities for PLpro inhibitor design. The review also discusses potential strategies for future PLpro inhibitor development informed by recent structural advances. Taken together, these structural and functional insights support ongoing efforts in the structure-guided design and optimization of PLpro inhibitors. Full article

The Dof (DNA binding with one finger) transcription factor family is a plant-specific group of transcription factors that play critical roles in plant growth and development, stress response, and the regulation of secondary metabolism. Prunella vulgaris (P. vulgaris) has attracted considerable attention due to its medicinal value, with rosmarinic acid being one of its key bioactive components. However, the systematic identification of the Dof transcription factor family in P. vulgaris and its regulatory role in rosmarinic acid biosynthesis remains poorly understood. In this study, based on the whole-genome data of P. vulgaris, we identified 48 Dof transcription factor genes distributed across 14 chromosomes using bioinformatics approaches. Physicochemical analysis revealed that the encoded proteins have molecular weights ranging from 15,482.44 to 55,875.53 Da, amino acid lengths between 142 and 509, and theoretical isoelectric points from 4.84 to 10.2. All proteins were predicted to be hydrophilic and localized in the nucleus. Phylogenetic analysis classified them into four subfamilies, and multiple sequence alignment confirmed that all members contain a conserved C2-C2-type zinc finger domain. Analysis of cis-regulatory elements in the promoter regions identified numerous elements related to light responsiveness, hormone response, and development. Transcriptomic expression profiling demonstrated distinct tissue-specific expression patterns of Dof genes, with some showing high expression in spikes and seeds. Correlation analysis between gene expression and rosmarinic acid content identified three candidate genes potentially involved in the regulation of rosmarinic acid biosynthesis, which were further validated by RT-qPCR. Moreover, protein–protein interaction network predictions indicated 242 interactions among 23 Dof proteins. This study provides the first systematic identification of the Dof transcription factor family in P. vulgaris, offering important insights into the transcriptional regulation of rosmarinic acid biosynthesis and presenting potential genetic targets for enhancing rosmarinic acid production through genetic engineering. Full article

Methyl farnesoate (MF) is a sesquiterpenoid hormone that controls a variety of physiological processes in crustaceans, including morphogenesis, development, reproduction, and molting. MF action is mediated by a transcriptional signaling cascade consisting of Methoprene-tolerant (Met), Steroid receptor coactivator (Src), Krüppel homolog 1 (Kr-h1), and Ecdysone response gene 93 (E93) transcription factors (TFs), and transcriptional co-regulators CREB-binding protein (CBP) and C-terminal-binding protein (CtBP). Phylogenetic and sequence analyses revealed that these genes were highly conserved across pancrustacean species. Met and Src were characterized as basic helix-loop-helix, Period (Per)-Aryl Hydrocarbon Nuclear Translocator (ARNT)-Single-minded (Sim) protein (bHLH-PAS) TFs; Kr-h1 was characterized as a C₂H₂ zinc finger TF with seven zinc finger motifs; E93 was characterized as a helix-turn-helix, pipsqueak (HTH_Psq) TF. CBP was identified by several zinc finger-binding regions with Transcription Adaptor Zinc Finger 1 and 2, Really Interesting New Gene, Plant homeodomain, and Z-type zinc finger domains; the Kinase-inducible Domain Interacting-transcription factor docking site; the Bromodomain-acetylated lysine recognition and binding site; the histone acetyltransferase domain; and a C-terminal CREB-binding region containing a nuclear receptor co-activator-binding domain. CtBP had a dehydrogenase domain with arginine-glutamate-histidine catalytic triad. 81 Met contigs, 45 Src contigs, 136 Kr-h1 contigs, 66 E93 contigs, 60 CBP contigs, and 172 CtBP contigs were identified across pancrustacean taxa, including decapod crustaceans. Bioinformatic identification and annotation of these TFs and co-regulators in brachyuran Y-organ (YO) transcriptomes suggests that MF signaling influences YO ecdysteroidogenesis; functional tests in the YO are needed to establish causality. Full article

Background: The zinc finger-homeodomain (ZF-HD) transcription factor family exerts pivotal regulatory functions in plant development and stress responses, yet a systematic genome-wide survey is lacking for Rosa chinensis. Methods: In this study, we performed a comprehensive genome-wide identification and analysis of RcZF-HD genes in R. chinensis using bioinformatics approaches. Nine RcZF-HD loci were mined from the rose genome and comprehensively profiled for physicochemical parameters, phylogenetic affiliations, chromosomal positions, exon–intron architectures, conserved motifs, and spatiotemporal expression landscapes. Results: The results showed that RcZF-HD genes were unevenly distributed across four chromosomes (Chr2, Chr4, Chr6, and Chr7), with tandem duplication events detected on chromosomes 2 and 7, suggesting their contribution to gene family expansion. Maximum-likelihood phylogeny placed RcZF-HD proteins within nine well-supported sub-clades alongside Arabidopsis orthologs, implying both evolutionary conservation and lineage-specific divergence. All members retain canonical zinc-finger domains, yet acquire unique motif signatures predictive of functional specialization. Gene structure analysis revealed considerable diversity in exon–intron organization. Expression profiling across six different tissues (root, stem, leaf, bud, flower, and fruit) demonstrated remarkable tissue-specific expression patterns. Notably, RchiOBHm_Chr2g0168531 exhibited extremely high expression in stem tissue, while RchiOBHm_Chr7g0181371 showed preferential expression in flower tissue, suggesting specialized roles in stem development and floral organ formation, respectively. The cold-stress challenge of ‘Old Blush’ petals further disclosed pronounced up-regulation of seven RcZF-HD genes, attesting to their critical contribution to low-temperature tolerance. Conclusions: Integrative analyses furnish a multidimensional blueprint of the rose RcZF-HD repertoire, providing molecular landmarks for future functional dissection and ornamental trait engineering. Full article

Annual wild soybean, the ancestor of cultivated soybean, underwent a significant increase in seed oil content during domestication. To elucidate the genetic basis of this change, a chromosome segment substitution line population (177 lines) constructed with cultivated soybean NN1138-2 as recipient and wild soybean N24852 as donor was used in this study. Phenotypic evaluation across three distinct environments led to the identification of two major QTL/segments, qOC14 on chromosome 14 and qOC20 on chromosome 20, which collectively explained 39.46% of the phenotypic variation, with individual contributions of 17.87% and 21.59%, respectively. Both wild alleles exhibited negative additive effects, with values of −0.35% and −0.42%, respectively, consistent with the inherently low oil content of wild soybeans. Leveraging transcriptome and genome data from the two parents, two candidate genes were predicted. Notably, Glyma.14G179800 is a novel candidate gene encoding a PHD-type zinc finger domain-containing protein, and the hap-A haplotype exhibits a positive effect on oil content. In contrast, Glyma.20G085100 is a reported POWR1 gene, known to regulate protein and oil content. Our findings not only validate the role of known gene but, more importantly, unveil a new candidate gene, offering valuable genetic resources and theoretical targets for molecular breeding of high-oil soybean. Full article

The described features of dinoflagellate gene expression indicate the predominance of post-transcriptional and translational regulation over transcriptional control. These microorganisms also exhibit extensive RNA editing and distinctive splicing characteristics. This regulatory landscape underscores the central role of RNA-binding proteins in dinoflagellate biology. In this review, we summarize current knowledge on major RNA-binding protein groups identified or bioinformatically annotated in dinoflagellates, including RNA recognition motif domain-containing proteins, Sm and Sm-like family, KH domain-containing proteins, zinc-finger proteins, and Pumilio family proteins, S1 domain-containing and cold shock domain-containing proteins, DEAD/DEAH-box RNA helicases, and pentatricopeptide repeat proteins. We focus on the features of their conserved domains, their functions in eukaryotes, and available data on their presence and putative roles in dinoflagellate cells. Integrating genomic, transcriptomic, and proteomic evidence, and where possible experimental data, we highlight both their overall conservation and potential lineage-specific traits. Our aim is to provide a concise synthesis of current knowledge, identify key uncertainties, and outline promising directions for future research into the evolution and cellular roles of RNA-binding proteins in this ecologically and biologically remarkable group. Full article

GATA transcription factors, defined by their zinc finger DNA-binding domains, are central regulators of tissue development. They modulate gene expression by activating or repressing transcription, thereby coordinating cellular differentiation and cell cycle exit to maintain homeostasis. In progenitor cells, GATA factors promote proliferation, whereas in differentiating cells, they drive maturation and induce cell cycle arrest. Dysregulation of GATA factors has been linked to tumorigenesis and contributes significantly to cancer progression and metastasis. Mutations in GATA factor genes correlate with poor prognosis in multiple cancers, where they influence key oncogenic processes, including sustained proliferative signaling, activation of epithelial–mesenchymal transition, angiogenesis, resistance to cell death, and immune escape. Importantly, their context-dependent roles across tumor types highlight the complexity of their functions in malignancies. Meanwhile, non-coding RNAs have emerged as critical regulators of gene expression, acting as either tumor suppressors or oncogenes by modulating chromatin dynamics, transcription factor activity, and mRNA stability. Despite this, the regulation of GATA transcriptional activity by non-coding RNAs remains largely unexplored. This review highlights the role of GATA factors in regulating EMT and metastasis and focuses on the interplay between non-coding RNAs and GATA transcription factors in cancer progression, proposing a novel regulatory axis with potential implications for biomarker discovery and therapeutic targeting. Full article

Salt stress causes harm to plants through multiple aspects, such as osmotic pressure, ion poisoning, nutrient imbalance, and oxidative damage. Zinc finger proteins harboring two B-box domains, known as double B-box (DBB) proteins, constitute the DBB family. While DBB genes have been implicated in regulating circadian rhythms and stress responses in various plant species, their functions in cotton remain largely unexplored. The present study characterized the DBB gene family across the genomes of Gossypium hirsutum L., Gossypium raimondii L., and Gossypium arboreum L., revealing a complement of 58 members. These DBB genes were assigned to three separate clades based on phylogenetic analysis. Members possessing close phylogenetic relationships have similar conserved protein motifs and gene structures. All DBB proteins were predicted to be nuclear-localized, consistent with their roles as transcription factors. Furthermore, the presence of multiple cis-acting elements related to light, hormone, and stress responses in the promoters implies that GhDBBs are integral to cotton’s environmental stress adaptation. Expression pattern analysis indicated that the expression of GhDBB genes was associated with the plant’s response to multiple abiotic stresses, such as salt, drought, heat (37 °C), and cold (4 °C). The reliability of the expression data was confirmed by qPCR analysis of eight selected GhDBBs. Under 200 mM NaCl, Arabidopsis plants overexpressing GhDBB22 displayed longer roots and healthier true leaves than the wild-type controls. Conversely, VIGS-mediated silencing of GhDBB22 in G. hirsutum led to significantly reduced salt tolerance, accompanied by exacerbated oxidative damage. Taken together, the findings from our integrated genomic and functional analyses provide a foundational understanding of the molecular mechanisms through which proteins encoded by DBB genes are involved in the plant’s response to salt stress. Full article