Search Results (633)

The transcription factor IRF5 maintains macrophages in the pro-inflammatory M1 state. We assessed the effects of siRNA-mediated knockdown of Irf5 on murine bone marrow-derived macrophages (BMDM) in M0, M1 and M2 states. Knockdown of Irf5 in M1 macrophages made them phenotypically similar to M2 macrophages, which was reflected in the decreased expression of the M1 marker iNOS, increased expression of the M2 marker CD206, increased mitochondrial content and respective morphological changes. Interestingly, the M2 phenotype was also affected by the reduction in Irf5. Using atomic force microscopy (AFM), we showed that Irf5 knockdown increases plasma membrane roughness, particularly in M2 macrophages. AFM-based stiffness measurements indicated that Irf5 knockdown altered macrophage elasticity, potentially influencing their functional behavior. Our data suggest a complex role of IRF5 in macrophage polarization, supporting its dual role as a transcriptional activator and repressor both in M1 and M2 states, and highlight the importance of IRF5 in the maintenance of metabolic and functional properties of macrophages. Full article

The Hedgehog (Hh) signaling pathway regulates key cellular processes, such as proliferation, differentiation, and morphogenesis. Although its canonical activation involves ligand binding to PTCH1, which activates Smoothened (SMO), noncanonical features of the pathway significantly contribute to cancer progression, particularly in prostate cancer (PCa). GLI3, a central transcription factor in the Hh pathway, can act as a repressor or activator depending on posttranslational modifications. In androgen-deprived PCa, GLI3 plays a critical role in driving castration-resistant phenotypes by interacting with the androgen receptor (AR), particularly the AR-V7 variant. This interaction enhances tumor survival and growth even under androgen deprivation therapy (ADT). Aberrant GLI3 activity is further driven by mutations in upstream regulators such as SPOP and MED12, which contribute to the progression of both prostate and other malignancies. Preclinical studies have shown promise in reducing tumor cell proliferation and migration, and in inducing apoptosis, by pharmacologically inhibiting the GLI3 pathway with SMO antagonists or GSK3β inhibitors. Recent evidence also highlights reciprocal interactions between Sonic Hedgehog (Shh) signaling and the AR that sustain tumor growth under ADT. GLI3 engagement with AR reinforces AR-dependent transcription, supporting tumor progression through noncanonical pathways. These findings suggest that targeting GLI3, particularly in combination with AR inhibition, could effectively overcome castration resistance and improve outcomes in patients with castration-resistant prostate cancer (CRPC). This review explores the role of GLI3 in both canonical and noncanonical Hh signaling, its potential as a therapeutic target, and future directions for overcoming resistance in Hh-driven cancers. Full article

Intrinsically disordered regions enable transcription factors (TFs) to undergo structural changes upon ligand binding, facilitating the transduction of environmental signals into gene expression. In this study, we applied molecular modeling methods to explore the hypothesis that unstructured inter-domain and subdomain linkers in bacterial TFs can function as sensors for carbohydrate signaling molecules. We combined molecular dynamics simulations and carbohydrate docking to analyze six repressors with GntR-type DNA-binding domains, including UxuR, GntR and FarR from Escherichia coli, as well as AraR, NagR and YydK from Bacillus subtilis. Protein models obtained from different time points of the dynamic simulations were subjected to sequential carbohydrate docking. We found that the inter-domain linker of the UxuR monomer binds D-fructuronate, D-galacturonate, D-glucose, and D-glucuronate with an affinity comparable to nonspecific interactions. However, these ligands formed multimolecular clusters, a feature absent in the UxuR dimer, suggesting that protein dimerization may depend on linker occupancy by cellular carbohydrates. D-glucose interacted with linkers connecting subdomains of the LacI/GalR-type E-domains in GntR and AraR, forming hydrogen bonds that connected distant structural modules of the proteins, while in NagR, FarR and YydK, it bridged the inter-domain linkers and a β-sheet within the HutC-type E-domains. Hence, our results establish flexible linkers as pivotal metabolic sensors that directly integrate nutritional cues to alter gene expression in bacteria. Full article

This study comprehensively characterizes the PEBP gene family in Cymbidium sinense, an orchid with a prolonged vegetative phase that limits its industrial production. Genome-wide analysis identified six CsPEBPs, classified into FT-like, TFL1-like, and MFT-like subfamilies. Evolutionary, gene structure, and collinearity analyses revealed both conservation and lineage-specific diversification of these genes. CsFTL3, a distinctive FT-like member, displayed notably high expression during the bud undifferentiated stage, followed by a sharp downregulation upon floral initiation. Functional studies identified CsFTL3 as a key floral repressor. Heterologous overexpression in Arabidopsis delayed flowering time from 32.0 days (wild-type) to 63.0–75.3 days (transgenic) and increased rosette leaf number from 12.6 to 33.0–34.5, while its knockdown via virus-induced gene silencing (VIGS) in C. sinense accelerated floral bud development and upregulated flowering-promoter genes. Phylogenetically, CsFTL3 falls within the flowering repressor FT-I clade, and multiple sequence alignment identified critical amino acid substitutions (Y134S, W138L, Q140E) that likely underpin its functional divergence from typical flowering promoters. Furthermore, promoter analysis revealed an enrichment of light-, hormone-, and stress-responsive cis-elements, and its expression was modulated by gibberellin (GA), abscisic acid (ABA), and low-temperature treatments. Predicted protein–protein interaction and transcriptional regulatory networks provide preliminary insights into its complex regulation. We conclude that CsFTL3 acts as a crucial floral inhibitor, integrating environmental and endogenous cues to repress flowering. These findings offer fundamental insights into the molecular mechanisms of flowering in orchids and provide a valuable genetic resource for molecular breeding programs aimed at achieving precise flowering time control. Full article

The transcription factor NRF2 orchestrates diverse cellular homeostatic networks, but its role in angiogenesis remains poorly understood. Genetic and pharmacological modulation of NRF2 in mouse neuroendothelial cells altered the expression of several genes involved in endothelial biology. Among these, the TIE2/Tek receptor, essential for vascular development and integrity, was downregulated upon NRF2 activation, accompanied by changes in adherens and tight junction gene expression. Hemin treatment and knockdown revealed that TIE2/Tek repression is independent of the NRF2 repressor BACH1. mRNA stability and ChIP analyses indicated no post-transcriptional or direct transcriptional repression by NRF2. These findings suggest an alternative NRF2-dependent mechanism affecting TIE2/Tek levels and potentially influencing angiogenic regulation. Full article

Disease-specific diversity in RNA transcripts stems from RNA splicing, ribosomal abnormalities, and other factors. However, the mechanisms underlying the regulation of rRNA expression in the nucleolus and mRNA expression in the cytoplasm during cancer and neuronal differentiation remain largely unknown. In this article, we review current knowledge and discuss the regulatory mechanisms of rRNA and mRNA expression in human diseases using the splicing model of PUF60 (poly(U) binding splicing factor 60)—also known as FUSE-binding protein-interacting repressor (FIR) (FUBP1-interacting repressor), RoBPI, SIAHBP1, and VRJS (Gene ID: 22827). Noncoding RNAs, much like coding RNAs, have been found to be translated into proteins with significant physiological functions. Splicing is also involved in dominant ORF RNAs implicated in the expression of both noncoding and coding RNAs. Here, we analyze recent findings regarding gene splicing, ribosome formation, and the determination of selected ORFs (dominant ORFs) in a system modeled on FIR splicing in two databases (RefSeq and ENSEMBL). rRNA transcription affects ribosomes, whereas mRNA expression and splicing affect the intracellular proteome. Our objective is to develop efficient methods for identifying biomarkers for disease diagnosis and therapeutic targets. In the field of cancer treatment, therapeutic drugs targeting intracellular signaling have proven effective. Full article

Candida albicans is the most prevalent opportunistic pathogenic fungus in humans, and its extracellular vesicles (EVs) play crucial roles in its growth and pathogenesis. Previously, we found that C. albicans EVs at low levels could promote its growth. However, the effects of EVs when accumulated at high concentrations in C. albicans remain unclear. This study revealed that a high concentration of EVs inhibited hyphal development in C. albicans in a time-dependent manner. Transcriptome and RT-qPCR analyses showed that EVs significantly upregulated the transcription repressor NRG1 and downregulated hyphal-specific genes in a laboratory strain and five clinical isolates, while EVs failed to repress nrg1Δ/Δ hyphae. Further experiments confirmed that EVs upregulated the upstream transcription factor SKO1 (but downregulated BRG1) to increase NRG1 expression, thereby inhibiting hyphal formation. Cargo proteins in EVs were key components that inhibited C. albicans hyphal growth. Additionally, EV-treated C. albicans showed improved mouse survival and reduced organ fungal burden in candidemia, but EVs did not attenuate virulence in nrg1Δ/Δ-infected mice. These results reveal that C. albicans EVs at high levels play an important role in its pathogenicity and highlight the potential for novel therapeutic strategies. Full article

1,5-Pentanediamine (PDA) is an important monomer for the synthesis of nylon materials. However, its microbial production from glucose is severely limited by product cytotoxicity, which slows the metabolism of both precursor lysine and glucose uptake. To overcome this limitation, a PDA-responsive dynamic regulatory switch (PDRS) was constructed using the transcriptional repressor CgmR and the P_cgmA promoter. By replacing promoters and ribosome-binding sites, the response window of the PDRS was optimized to a PDA concentration range of 38.9–87 g/L. Based on this system, the PDRS was employed to enhance lysine biosynthesis and glucose uptake. Following fermentation optimization, the optimal strain Corynebacterium glutamicum YY3.6 produced 105.5 g/L PDA within 36 h, achieving a PDA productivity of 2.93 g/L/h and a yield of 0.36 g/g glucose. Collectively, these results provide an effective strategy for the microbial production of PDA from glucose. Full article

Seed vitality is a key factor for successful germination of seeds and successful root establishment of crops. However, a cold environment can severely hinder the germination of soybean seeds, resulting in a significant decrease in yield. In this study, the cold tolerance of 205 chromosome segment substitution lines (CSSL) during the germination process was evaluated. CSSL_R22 exhibited higher seed vitality under low-temperature conditions. Five quantitative trait loci (QTL) related to cold tolerance during the germination stage were detected. By combining the QTL analysis results with transcriptome data, we determined that GmKAN1 (Glyma.20G108600) is an important regulatory factor for cold tolerance during seed germination. Preliminary studies have shown that GmKAN1, as a transcriptional repressor of GmARF2 and GmARF8, can regulate auxin synthesis to enhance the tolerance of seeds to cold stress. These results provide valuable insights into the regulatory network related to cold tolerance during soybean seed germination. Full article

Floral induction in late-maturing litchi is vulnerable to warm, humid winters with insufficient chilling. The late cultivar ‘Ziniangxi’ was evaluated during January–February 2024 in an experimental orchard in Hainan, China, when chilling accumulation was very low, with only seven days having a mean air temperature ≤ 15 °C. Under this marginal-chill context, the effects of plant growth regulator (PGR) applications on bud fate were assessed using six single-agent and thirteen composite PGR–nutrient treatments plus a water control, applied as four foliar sprays during floral induction. In the untreated control, the final flowering proportion of tagged shoots was 0.33 in the single-agent trial and 0.05 in the composite trial. In contrast, ABA (3.33 mg L⁻¹) increased flowering to 0.53, and ethephon- or brassinolide-based applications to 0.40–0.47. The most effective composite formulations raised flowering further to 0.50–0.63. These composite applications also increased leaf starch from about 4 mg g⁻¹ FW in the control to approximately 8–9 mg g⁻¹ FW ($p<0.05$), whereas sucrose concentrations showed only small differences among treatments. Across trials, shoots that became floral consistently exhibited higher leaf starch than vegetative shoots. Gene-expression analyses indicated that floral buds had higher transcript abundance of LcFUL and lower transcript levels of LcFLC and other floral repressors than vegetative buds, consistent with their assignment to floral versus vegetative categories. Overall, the results suggest that appropriately timed ethephon–ABA-based PGR programs, supplemented with BR or 6-BA and nutrients, can partially improve floral induction in ‘Ziniangxi’ under warm, low-chill winters and provide a basis for designing PGR strategies for late litchi cultivars facing insufficient winter chilling. Full article

Bolting and flowering time are critical agronomic traits affecting the commercial value and breeding efficiency of Chinese cabbage (Brassica rapa L. ssp. pekinensis). Although vernalization is a key environmental signal promoting flowering, its regulatory mechanisms remain poorly understood in this crop. Here, we identify the flowering repressor gene BrMAF5 and its antisense long non-coding RNA BrMAF5L as negative regulators of vernalization-induced flowering. During vernalization, transcript levels of both genes showed a decreasing trend as the vernalization period extended. Functional assays in Arabidopsis thaliana demonstrated that ectopic expression of BrMAF5 or BrMAF5L significantly delayed flowering, accompanied by increased expression of floral repressors (AtFLC, AtTEM1) and reduced expression of floral activators (AtFT, AtSOC1). Moreover, protein interaction analysis revealed that BrMAF5 associates with BrACP4 and BrRAB1A, linking it to fatty acid metabolism and membrane trafficking pathways. Collectively, our results reveal a novel regulatory module in vernalization-mediated flowering. These findings pave the way for developing bolting-resistant Brassicaceae crops by identifying promising molecular targets. Full article

Phytophthora root and stem rot is a destructive soybean disease worldwide, and thus improving soybean resistance to P. sojae is a major breeding target. However, the complex regulatory networks governing host defense remain unclear. Our previous study showed that GmWRKY40 positively regulates resistance of soybean to P. sojae. Here, to explore its molecular mechanism, we found that GmWRKY40 is induced by P. sojae in resistant cultivars and that the protein localizes in nucleus. RNA-seq and metabolomic analyses revealed that GmWRKY40 modulates the jasmonate (JA) signaling pathway. We then found that GmWRKY40 directly suppresses the key JA repressor GmJAZ1 by binding to the promoter. This leads to higher endogenous JA levels, and the overall state of enhanced resistance is also characterized by elevated SOD and POD antioxidant enzyme activity. Furthermore, we demonstrated that GmWRKY40 interacts with GmWRKY36, a transcription factor identified as a negative regulator of P. sojae infection in this research. Taken together, our study delineates a novel regulatory module where GmWRKY40 enhances resistance to P. sojae through a dual mechanism: activating the JA pathway by repressing its suppressor GmJAZ1, and engaging in a potentially antagonistic interaction with the negative regulator GmWRKY36, ultimately enhancing soybean resistance to P. sojae. Full article

Jasmonate ZIM-domain (JAZ) family genes, which belong to TIFY family, are plant-specific transcriptional repressors. As key regulators of the jasmonic acid signaling pathway, JAZ proteins play crucial roles in various aspects of plant biology. However, the identification and functional characterization of JAZ genes in sweet cherry (Prunus avium L.) fruit remain unknown. In the present study, we identified nine JAZ members in the sweet cherry genome. We systematically analyzed the gene structures, protein domains, evolutionary relationships, and physicochemical properties of these members and also evaluated their expression levels across different fruit developmental stages, as well as under methyl jasmonate (MeJA) treatment. Among these members, our results revealed a previously uncharacterized JAZ member, PavJAZ8, as a crucial regulator of fruit aroma traits. Specifically, RT-qPCR analysis showed that PavJAZ8 overexpression modulates the expression of genes involved in the biosynthesis of aroma volatiles, such as PavLOX2, PavLOX3, PavHPL1, PavADH1.1, PavADH1.2, and PavADH7, which are involved in the synthesis of aldehydes and alcohols. Consistent with the gene expression data, analysis of volatile metabolites revealed that PavJAZ8 overexpression significantly inhibited the accumulation of several related aldehydes and alcohols, including hexanal, geraniol, and benzyl alcohol. Furthermore, PavJAZ8 expression was highly responsive to phytohormone treatments, such as abscisic acid (ABA) and MeJA. Further analysis showed that PavJAZ8 interacts with PavMYC2, thereby mediating JA signal transduction. Our results highlight PavJAZ8 as a novel regulator of fruit aroma quality, offering a valuable genetic target for sweet cherry improvement. Full article

Actinidia valvata, a promising rootstock for kiwifruit cultivation, demonstrates superior waterlogging tolerance compared with commercial cultivars. Lateral organ boundaries domain (LBD) transcription factors (TFs) are known to be pivotal in plant responses to abiotic stress. Nevertheless, the characterization of the LBD family under waterlogging stress in A. valvata remains limited. In this study, 26 AvLBD genes were identified from a transcriptome dataset, with the majority classified into phylogenetic Class II. Under waterlogging stress, transcript accumulation of most AvLBD41 members, particularly AvLBD41_11 and AvLBD41_7, was markedly increased in roots. Bimolecular fluorescence complementation (BiFC) assays indicated that AvLBD41_7 heterodimerizes with both the AP2/ERF activator AvERF75 and the trihelix repressor AvHRA1, whereas AvLBD41_11 only interacts with AvERF75. Neither AvLBD41 isoform interacts with AvERF73, thereby defining distinct components of a waterlogging-responsive module. Yeast-based assays revealed an absence of transactivation activity for AvLBD41_7, and transient expression analyses confirmed its exclusive nuclear localization. The promoters of both AvLBD41_11 and AvLBD41_7 harbor numerous cis-elements responsive to hormones and abiotic stresses. An AvLBD41_7-derived PCR marker could be used to distinguish A. valvata from A. deliciosa accessions. Collectively, these findings provide a comprehensive functional annotation of the LBD gene family in A. valvata and establish AvLBD41_7 as a potential molecular target for future kiwifruit breeding programs aimed at waterlogging resilience. Full article

Heat stress caused by global climate change poses a significant threat to agricultural production. Phytohormones, as critical signaling molecules, play pivotal roles in modulating plant responses to heat stress. This review systematically summarizes the molecular mechanisms by which eight phytohormones (auxin, gibberellin, cytokinin, ethylene, abscisic acid, brassinosteroid, salicylic acid, and strigolactone) enhance plant thermotolerance through the regulation of heat shock protein (HSP) expression and function. Specifically, auxin enhances thermotolerance by inducing auxin signaling repressor (Aux/IAA) degradation to upregulate HSP transcription, facilitating the formation of the auxin receptor (TIR1)-HSP90 complex to stabilize TIR1, and forming the auxin exporter (PIN)-HSP22 complex to promote auxin transport. Cytokinin enhances thermotolerance by upregulating HSP transcription, with stronger effects in leaves than roots. Gibberellin, salicylic acid, and ethylene enhance thermotolerance primarily by activating heat shock factor (HSF) to induce HSP transcription. Abscisic acid and brassinosteroid improve thermotolerance by inducing HSP transcription and HSP phosphorylation, while strigolactone acts via D14-mediated upregulation of HSP transcription. These phytohormones collaboratively regulate HSPs, forming an intricate network to enhance plant thermotolerance. Deciphering these mechanisms provides a theoretical framework for developing heat-resistant crops and optimizing cultivation techniques. Full article