Basic Leucine Zipper Research Articles

Natural variation in a cortex/epidermis-specific transcription factor bZIP89 determines lateral root development and drought resilience in maize.

Lateral roots (LRs) branching is crucial for water and nutrient acquisition in plants, ultimately determining the overall plant performance and productivity. However, the transcriptional regulation of LR development in crops and its role in stress resilience remain largely unexplored. Leveraging integrated transcriptome-wide association study and single-cell RNA sequencing data, we identified a basic leucine zipper (bZIP) transcription factor ZmbZIP89 as an important regulator of LR elongation and mapped its spatial expression pattern in cortex/epidermis cell types. ZmbZIP89 can activate the expression of ZmPRX47 to regulate the production of root reactive oxygen species homeostasis, contributing to increased lateral root length (LRL) and enhanced drought resistance. Natural variations in the 3' untranslated region of ZmbZIP89 enhance gene expression by increasing mRNA stability, leading to increases in LRL and drought tolerance. These findings contribute to our understanding of the molecular mechanisms underlying LR development and provide potential gene targets for breeding stress-resilient crops.

Identification of RNAi efficiency-related gene in the green peach aphid, Myzus persicae (Hemiptera), based on comparative transcriptomics.

RNA interference (RNAi) is a promising strategy for aphid control; however, its practical application has been limited by low efficiency in aphids. To address this, we combined transcriptomic analysis with an 'RNAi of RNAi' approach to identify genes associated with RNAi efficiency in green peach aphid Myzus persicae. Using the artificial diet-mediated dsRNA delivery method, we observed that ingestion of both dsMpHunchback and dsfusion (a dsRNA targeting three genes) induced RNAi effects. These included significant gene silencing and reduced nymph production at 24, 36, and 48 h post-feeding compared to dsGFP. Expression profiling of core RNAi machinery revealed that samples from 36 and 48 h post-feeding were critical for RNAi efficiency, prompting their selection for transcriptome sequencing. Weighted gene co-expression network analysis (WGCNA) and analysis of Differentially Expressed Genes (DEGs) were employed to elucidate the RNA-seq data. Subsequent validation through RNAi of RNAi assay demonstrated functional roles for genes encoding basic region leucine zipper (gene11325), cathepsin B-like (gene12476), glucosidase KIAA1161-like (gene6489), and piggyBac transposable element-derived protein 3-like (gene7736). Notably, gene11325 and gene6489 were associated with RNAi efficiency, whereas gene12476 and gene7736 appeared to exert compensatory effects that counteracted the RNAi effects induced by dsMpHunchback and dsfusion. These findings highlight the functional diversity of genes influencing RNAi efficiency in green peach aphid, enhancing our understanding of RNAi mechanisms and establishing a foundation for optimizing RNAi-based aphid control strategies. © 2025 Society of Chemical Industry.

MAFF alleviates hepatic ischemia–reperfusion injury by regulating the CLCF1/STAT3 signaling pathway

BackgroundAlthough hepatic ischemia–reperfusion injury (IRI) frequently occurs during liver resection and transplantation, the underlying mechanisms remain incompletely understood. Through high-throughput sequencing, we found that v-maf musculoaponeurotic fibrosarcoma oncogene homolog F (MAFF) expression was significantly increased after hepatic IRI. The specific role of MAFF, a basic leucine zipper (bZIP) transcription factor, in hepatic IRI is unknown. In the present study, we aimed to explore the effect of MAFF on hepatic IRI injury.Approach and resultsAdenovirus vectors carrying the MAFF gene were administered to mice to explore the potential significance of MAFF. After ischemia–reperfusion, MAFF expression was significantly upregulated, suggesting a potential association between MAFF expression and hepatocyte apoptosis. A reduction in MAFF expression was demonstrated to worsen hepatic impairment and enhance the expression of proinflammatory cytokines in mice following ischemia–reperfusion. Conversely, MAFF overexpression had the opposite effect. Mechanistically, the combination of CUT&Tag and RNA sequencing technologies identified cardiotrophic factor-like cytokine 1 (CLCF1) as a direct transcriptional target for MAFF and BTB and CNC homology 1 (BACH1) heterodimers. This interaction subsequently triggers signal transducer and activator of transcription 3 (STAT3) signaling.ConclusionsMAFF alleviates hepatic ischemia–reperfusion injury by reducing hepatocyte apoptosis and the inflammatory response through the activation of the CLCF1/STAT3 signaling pathway, offering valuable insights into the impact of MAFF on liver protection and potential therapeutic targets for liver treatment.Graphical abstract

Gene Signature-Based Prognostic Model for Acute Myeloid Leukemia: The Role of BATF, EGR1, PD-1, PD-L1, and TIM-3.

Background: Acute myeloid leukemia (AML) is a malignancy of hematopoietic stem and progenitor cells, with T cell exhaustion linked to poor outcomes. Our previous research has shown that basic leucine zipper ATF-like transcription factor (BATF) and early growth response 1 (EGR1) play a role in chimeric antigen receptor T (CAR-T) cell exhaustion during AML tumor elimination. However, the roles of BATF and EGR1 and their association with immune checkpoint genes in AML prognosis remain underexplored. Methods: Bone marrow (BM) samples from 92 newly diagnosed AML patients at our clinical center (JUN-dataset) were analyzed to detect the expression levels of BATF, EGR1, programmed cell death 1 (PD-1), programmed death-ligand 1 (PD-L1), T cell immunoglobulin and mucin domain-containing protein 3 (TIM3) together with conducting a prognostic assessment. Our findings were validated using RNA sequencing data from 155 AML patients from the TCGA database and 199 AML patients from the Beat-AML database. Results: High BATF expression correlated with poor overall survival (OS) (P = 0.030), whereas high EGR1 expression indicated a favorable prognosis (P = 0.040). Patients with high BATF and low EGR1 expression had worst outcomes (P < 0.001). Among those receiving allogenic hematopoietic stem cell transplantation (allo-HSCT), high BATF expression was linked to shorter OS (P = 0.004). Moreover, a prognostic model incorporating BATF, EGR1, PD-1, PD-L1, and TIM-3 calculated a risk score, with high-risk patients demonstrating significantly shorter OS than low-risk patients in both total AML patients and allo-HSCT recipients (P < 0.001). Similar results were found in both the TCGA and Beat-AML datasets. Conclusions: We establish a prognostic model based on BATF, EGR1, PD-1, PD-L1, and TIM-3 expression that effectively predicts survival outcomes for AML patients and allo-HSCT recipients. This model may provide valuable insights for prognosis assessment and treatment strategies.

Genome-wide identification and expression analysis of TaFDL gene family responded to vernalization in wheat (Triticum aestivum L.)

BackgroundFLOWERING LOCUS D (FD) is a basic leucine zipper (bZIP) transcription factor known to be crucial in vernalization, flowering, and stress response across a variety of plants, including biennial and winter annual species. The TaFD-like (TaFDL) gene in wheat is the functional homologue of Arabidopsis FD, yet research on the TaFDL gene family in wheat is still lacking.ResultsIn this study, a total of 62 TaFDL gene family members were identified and classified into 4 main subfamilies, and these genes were located on 21 chromosomes. A comprehensive analysis of the basic physicochemical properties, gene structure, conservation motif, conserved domain, and advanced protein structure of TaFDL gene family revealed the conservation among its individual subfamily. The family members underwent purifying selection. The segmental duplication events were the main driving force behind the expansion of the TaFDL gene family. The TaFDL gene family underwent differentiation in the evolution of FD genes. Additionally, the subcellular localization and transcriptional activation activities of five key TaFDL members were demonstrated. Gene Ontology (GO) annotations and promoter cis-regulatory element analysis indicated that the TaFDL members may play potential roles in regulating flowering, hormone response, low-temperature response, light response, and stress response, which were verified by transcriptome data analysis. Specifically, quantitative real-time PCR (qRT-PCR) analysis revealed that five TaFDL genes exhibited differential responses to different vernalization conditions in winter wheat seeding. Finally, the homologous genes of the five key TaFDL genes across nine different wheat cultivars highlight significant genetic diversity.ConclusionThese findings enrich the research on FD and its homologous genes, providing valuable insights into the TaFDL gene family’s response to vernalization.

MsbZIP55 regulates salinity tolerance by modulating melatonin biosynthesis in alfalfa.

Soil salinity is a severe abiotic stress that damages plant growth and development. As an antioxidant and free radical scavenger, melatonin is well known for helping plants survive abiotic conditions, including salinity stress. Here, we report that the salt-related gene MsSNAT1, encoding a rate-limiting melatonin biosynthesis enzyme, is located in the chloroplast and contributes to salinity stress tolerance in alfalfa. We found that the MsSNAT1 overexpressing alfalfa lines exhibited higher endogenous melatonin levels and increased tolerance to salt stress by promoting antioxidant systems and improving ion homeostasis. Furthermore, through a combination of transcriptome sequencing, dual-luciferase assays and transgenic analysis, we identified that the basic leucine zipper (bZIP) transcription factor, MsbZIP55, is associated with salt response and MsSNAT1 expression. EMSA analysis and ChIP-qPCR uncovered that MsbZIP55 can recognize and directly bind to the MsSNAT1 promoter in vitro and in vivo. MsbZIP55 acts as a negative regulator of MsSNAT1 expression, thereby reducing melatonin biosynthesis. Morphological analysis revealed that overexpressing MsbZIP55 conferred salt sensitivity to transgenic alfalfa through a higher Na+/K+ ratio and lower antioxidant activities, which could be alleviated by applying exogenous melatonin. Silencing of MsbZIP55 by RNA interference in alfalfa resulted in higher expression of MsSNAT1 and promoted salt tolerance by enhancing the antioxidant system enzyme activities and ion homeostasis. Our findings indicate that the MsbZIP55-MsSNAT1 module plays a crucial role in regulating melatonin biosynthesis in alfalfa while facilitating protection against salinity stress. These results shed light on the regulatory mechanism of melatonin biosynthesis related to the salinity stress response in alfalfa.

Enhancement of grape heat tolerance through VvbZIP36-mediated quercetin production.

Enhancement of grape heat tolerance through VvbZIP36-mediated quercetin production.

Regulatory networks of bZIPs in drought, salt and cold stress response and signaling.

Regulatory networks of bZIPs in drought, salt and cold stress response and signaling.

USF2-Mediated Transcription of BZW2 Contributes to CRC Malignant Progression by Affecting LAMP3.

Colorectal cancer (CRC) is one of the most frequent causes of cancer death in China, and its occurrence, development, and prognosis are closely related to the living state of patients. Basic leucine zipper and W2 domains 2 (BZW2), also known as eIF5-mimin protein 1 (5MP1), is a translational regulatory protein and highly expressed in CRC and promotes malignant progression of CRC, but the specific mechanism has not been clarified. The databases were used to mine related genes. The expression levels of genes were detected by quantitative real-time PCR (qRT-PCR) and western blot. 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl tetrazolium bromide (MTT) assay, 5-ethynyl-2'-deoxyuridine (EdU) staining, flow cytometry, transwell assay, and sphere formation assay were employed to examine the effects of BZW2 on the phenotypes in CRC cells invitro. The mechanism of BZW2 in CRC progression was determined by chromatin immunoprecipitation (CHIP) and dual luciferase reporter assay. Invivo, xenograft animal model was performed to verify the results. BZW2 was elevated in CRC tissues and cells and was associated with poor prognosis of patients. Functionally, BZW2 enhanced CRC cell proliferation, invasion, and sphere formation but restrained apoptosis. CHIP and dual luciferase reporter assay confirmed that upstream transcription factor 2 (USF2) regulated BZW2 transcription. Also, BZW2 could attenuate the effects of USF2 defection in CRC progression. Meanwhile, lysosomal associated membrane protein 3 (LAMP3) acted as the target of BZW2 and restored the action of BZW2 knockdown. Similarly, BZW2 was involved in tumorigenesis invivo by the same mechanism invitro. These findings revealed a molecular basis for BZW2's promotion of CRC malignant progression and highlighted the role of BZW2 in promoting cancer stemness.

Fos genes in mainly invertebrate model systems: A review of commonalities and some diversities.

fos genes in mainly invertebrate model systems: A review of commonalities and some diversities.

Genome-wide identification of the bZIP family in Eutrema salsugineum and functional analysis of EsbZIP51 in regulating salt tolerance.

Genome-wide identification of the bZIP family in Eutrema salsugineum and functional analysis of EsbZIP51 in regulating salt tolerance.

Physiological responses and adaptive mechanisms of the harmful algal bloom species Heterosigma akashiwo to naphthalene exposure

Physiological responses and adaptive mechanisms of the harmful algal bloom species Heterosigma akashiwo to naphthalene exposure

Overexpression of the tomato nuclear-cytoplasmic shuttling bZIP transcription factor VSF-1 in Arabidopsis retards plant development under mannitol-stressed conditions.

VASCULAR SPECIFICITY FACTOR 1 (VSF-1) is a basic leucine zipper transcription factor identified in tomato (Solanum lycopersicum L.). VSF-1 regulates vascular-specific gene expression and is homologous to an Arabidopsis thaliana mechanical stress regulator, VIP1, but physiological roles for VSF-1 remain unclear. Here, we demonstrate that VSF-1 shuttles between the nucleus and the cytoplasm in response to hypo-osmotic stress. In Arabidopsis plants overexpressing the VSF-1-GFP fusion protein, VSF-1-GFP was mainly detected in the cytoplasm under unstressed conditions but in the nucleus under hypo-osmotically stressed conditions. VSF-1 contains three serine residues within HXRXXS motifs, which can serve as its phosphorylation and 14-3-3 protein-binding sites. In a transient gene expression system in Nicotiana benthamiana leaves, GFP-fused VSF-1 variants where those serine residues were replaced with alanine exhibited nuclear accumulation even under unstressed conditions. GFP-fused VSF-1 variants lacking those HXRXXS motifs also exhibited such nuclear accumulation. The VSF-1 variants lacking those HXRXXS motifs failed to interact with 14-3-3 proteins in a yeast two-hybrid system. These findings suggest that the nuclear accumulation of VSF-1 is triggered by hypo-osmotic stress through its dissociation from 14-3-3 proteins, similar to that of VIP1. The Arabidopsis VSF-1-GFP-overexpressing lines exhibited retarded germination and growth in the presence of mannitol, which can induce hyper-osmotic stress and repress nuclear accumulation of VSF-1. These results are consistent with phenotypes from VIP1-GFP-overexpressing lines in a previous study, indicating a conserved role for VIP1 and VSF-1 in regulating osmotic stress responses.

The Transcriptome Response of African and South American Cassava (Manihot esculenta) to Infection by East African Cassava Mosaic Virus‐Uganda

ABSTRACTCassava mosaic begomoviruses (CMBs) cause the economically important cassava mosaic disease (CMD) in cassava. In this research, we investigated potential new sources of resistance to CMD. Fourteen cassava varieties were tested for resistance to the major CMB, East African cassava mosaic virus‐Uganda (EACMV‐Ug). Six African cassava varieties (72‐TME 14, TME 204, TZ 130, Nase 1, Nase 3 and Nase 14) expressed no or mild disease symptoms with low viral load and therefore have been classified as resistant. South American varieties showed severe leaf symptoms and supported high viral load. Nase 3 (resistant), TZ 130 (resistant) and Ebwanateraka (susceptible) were subjected to RNA‐sequencing (RNA‐Seq) to identify putative CMD resistance genes and mechanisms. Transcriptome analysis of three cassava varieties at 2, 4, 7, and 28 days after grafting (DAG) revealed the largest number of differentially expressed genes (DEGs) upon virus infection in Nase 3 (4228) with 1725 genes uniquely over‐expressed. Additionally, early induction of heat shock proteins and transcription factors such as ethylene‐responsive transcription factor (ERF), teosinte‐like, cycloidea and PCF1 (TCPs), heat stress transcription factor and basic leucine zipper were observed in the resistant varieties. These results suggest that resistant varieties maintain a low titre of EACMV‐Ug by activating specific stress‐response genes early. The role of these genes in plants remains to be investigated but offers insights into the molecular mechanism of resistance to CMD.

Fine-Tuning of ATF4 DNA Binding Activity by a Secondary Basic Motif Unique to the ATF-X Subfamily of bZip Transcription Factors.

The fine-tuning of transcription factor DNA-binding activity is often governed by transient intramolecular interactions between the transactivation domain and the DNA-binding domain. An example of such interaction is found in the transcription factor ATF4, a central regulator of the Integrated Stress Response. In ATF4, dynamic coupling between the transactivation domain and the basic-leucine zipper (bZip) domain modulates the phosphorylation levels of the disordered transactivation domain by casein kinase 2. However, the structural and molecular basis of these interdomain interactions remains poorly understood. This study focuses on a secondary basic motif at the C-terminus of ATF4, which is shared exclusively with its closest paralogue, ATF5. Through a combination of solution NMR spectroscopy, fluorescence polarization assays, and long-timescale molecular simulations, we demonstrate that this secondary basic motif is the primary driver of interdomain coupling between the transactivation and bZip domains of ATF4. Moreover, this motif enhances ATF4's DNA-binding specificity via interaction with the transactivation domain while also potentially facilitating rapid DNA scanning. Our findings reveal the pivotal role of a conserved motif in establishing disorder-mediated interactions that critically modulate ATF4's DNA-binding activity.

Nfil3 contributes to renal fibrosis by activating fibroblasts through directly promoting the expression of Spp1.

Nfil3 contributes to renal fibrosis by activating fibroblasts through directly promoting the expression of Spp1.

Marek's Disease Virus (MDV) Meq Oncoprotein Plays Distinct Roles in Tumor Incidence, Distribution, and Size.

Marek's disease (MD), characterized by the rapid onset of T-cell lymphomas in chickens, is caused by Mardivirus gallidalpha2, an oncogenic alphaherpesvirus commonly known as Marek's disease virus (MDV). MDV encodes a bZIP protein, Meq, which contains a bZIP domain (basic DNA-binding and leucine zipper dimerization domain) at the amino terminus and a transcriptional regulatory domain at the carboxyl end. Meq can transform murine and chicken fibroblasts in vitro and is essential for tumor formation in chickens. Meq homodimerization and heterodimerization through its bZIP domain are involved in Meq-mediated transformation. However, the role of Meq DNA-binding and transcriptional regulatory domains in transformation has not been investigated. In this study, we constructed recombinant Md5 (very virulent MDV) viruses expressing chimeric Meq proteins generated by swapping the DNA-binding and transcriptional regulatory domains of Meq of Md5 and vaccine (CVI988/Rispens) strains. Our results show that these recombinant viruses, rMd5-Md5/CVI-Meq (Md5 DNA-binding domain and CVI transcriptional regulatory domain) and rMd5-CVI/Md5-Meq (CVI DNA-binding domain and Md5 transcriptional regulatory domain), replicated at levels similar to parental rMd5 in cell culture and chickens and could transmit efficiently among chickens. Interestingly, parental rMd5 and chimeric viruses exhibited distinct pathogenic phenotypes in chickens: rMd5 caused 100% mortality, a moderate level of tumor incidence in visceral organs and small visceral tumors; rMd5-Md5/CVI-Meq caused 100% mortality, a high level of tumor incidence in visceral organs, and very large visceral tumors; while rMd5-CVI/Md5-Meq caused an average of 37% mortality, rarely induced tumors in visceral organs, and the visceral tumors were small. In conclusion, our study suggests that the DNA-binding domain of Meq plays an essential role in transformation (tumor incidence), while the transcriptional regulatory domain of Meq influences the distribution and size of MDV-induced tumors.

Genome-Wide Profiling of bZIP Transcription Factors and FocbZIP11's Impact on Fusarium TR4 Pathogenicity.

The basic leucine zipper (bZIP) transcription factor (TF) family performs diverse functions in fungal processes, including vegetative growth, nutrient utilization, stress responses, and invasion. Despite their importance, little is known about the bZIP members in Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), a highly virulent banana pathogen. In this study, we systematically identified 17 bZIPs distributed across 10 Foc TR4 chromosomes and classified them into four types based on their protein sequences. Phylogenetic analysis of fungal bZIP TFs revealed that the FocbZIP proteins cluster into 12 groups shared across fungal species. A cis-element analysis showed that each bZIP promoter contains at least one type of stress response-related element. Furthermore, RNA-seq and RT-qPCR analyses of FocbZIP gene expression patterns demonstrated that these genes may serve distinct roles during infection. Notably, the deletion of FocbZIP11 led to reduced vegetative growth, heightened sensitivity to osmotic, oxidative, and cell wall stresses, and diminished virulence toward banana plantlets. Overall, our findings indicate that FocbZIP11 plays a critical role in growth, abiotic stress responses, and virulence in Foc TR4. This study provides a foundation for the further functional characterization of FocbZIP genes, and FocbZIP11 might serve as a promising target for RNA-based biopesticide control of FWB.

Genome-wide identification and characterization of the bZIP family in the Mangrove Plant Kandelia obovata and its role in response to stress

BackgroundThe basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and responses to environmental changes. The mangrove plant Kandelia obovata, native to subtropical and tropical coastal intertidal zones, has evolved various adaptive mechanisms to cope with unstable muddy substrates, tidal fluctuations, saltwater intrusion, and intense ultraviolet radiation. This study aims to provide a comprehensive characterization of the bZIP gene family in K. obovata and investigate its functional roles in response to environmental stresses.ResultsIn the K. obovata genome, 66 bZIP genes were identified and named KobZIP1 to KobZIP66, categorized based on their chromosomal locations. These KobZIP genes exhibited diversity in physicochemical properties, such as protein length, molecular weight, and isoelectric point, and were all predicted to localize to the nucleus. Phylogenetic and structural analyses classified the KobZIP genes into 12 subfamilies, with subfamily A containing the majority of members. Gene structure analysis revealed variations in the number and position of exons and introns among subfamilies, reflecting their evolutionary history and potential functional diversity. Conserved motif analysis showed that all bZIP family members contained motifs in the basic and hinge regions, with subfamily D displaying the greatest motif diversity. Promoter region analysis identified various cis-acting elements associated with responses to phytohormones (ABA, GA, ET, IAA, MeJA, SA) and environmental stress. The expression patterns of KobZIP genes across different tissues and under various abiotic stress conditions were analyzed using transcriptomic data and experimental validation.ConclusionThis study provides a comprehensive characterization and functional analysis of the bZIP gene family in K. obovata, offering new insights into their roles in plant development and environmental adaptation. The expression profiles of KobZIP genes during root development and post-embryonic stages, along with their responses to ABA, low temperature, and salt stress, underscore their potential significance in the adaptation of mangrove plants to the intertidal environment.

Echinocandin Adaptation in Candida albicans Is Accompanied by Altered Chromatin Accessibility at Gene Promoters and by Cell Wall Remodeling.

Infections by the major opportunistic pathogen of human Candida albicans are commonly treated with echinocandin (ECN) drugs. However, C. albicans can adapt to grow in the presence of certain amounts of ECNs. Prior studies by several laboratories have defined multiple genes, as well as mechanisms involving induced aneuploidy, that can govern this. Still, the mechanisms of ECN adaptation are not fully understood. Here, we use genome-wide profiling of chromatin accessibility by ATAC-seq to determine if ECN adaptation is reflected in changes in the chromatin landscape in the absence of aneuploidy. We find that drug adaptation is coupled with multiple changes in chromatin accessibility genome-wide, which occur predominantly in gene promoter regions. Areas of increased accessibilities in promoters are enriched with the binding motifs for at least two types of transcription factors: zinc finger and basic leucine zipper. We also find that chromatin changes are often associated with differentially expressed genes including genes with functions relevant to the ECN-adapted phenotype, such as cell wall biosynthesis. Consistent with this, we find that the cell wall is remodeled in ECN-adapted mutants, with chitin up and glucan down and increased cell surface exposure. A full understanding of ECN adaptation processes is of critical importance for the prevention of clinical resistance.