Search Results (1,911)

The plant-specific TCP transcription factor family originated before the emergence of land plants. However, the timing of the appearance of their specific transcriptional repressor family, the TCP Interactor containing EAR motif protein (TIE), remains unknown. Here, through phylogenetic analyses, we traced the origin of the TIE family to the early evolution of the embryophyte, while an earlier diversification in algae cannot be ruled out. Strikingly, we found that the number of TIE members is highly constrained compared to the expansion of TCPs in angiosperms. We used co-expression data to identify potential TIE-TCP regulatory targets across Arabidopsis thaliana and rice. Notably, the expression pattern between these species is remarkably similar. TCP Class I and Class II genes formed two distinct clusters, and TIE genes cluster within the TCP Class I group. This study provides a comprehensive evolutionary analysis of the TIE family, shedding light on its conserved role in the regulation of gene transcription in flowering plant development. Full article

Candida albicans and Staphylococcus aureus are opportunistic pathogens that cause life-threatening infections. This study focused on using photodynamic inactivation (PDI) to eliminate mixed biofilms of C. albicans–S. aureus formed on poly (urethane) (PU) discs functionalized with a nanocomposite layer containing phloxine B (PhB). Additionally, the effect of PDI on the ALS3 and HWP1 genes of C. albicans was examined in mixed biofilms. Spectral analysis showed a continuous release of PhB from the nanocomposite in Mueller–Hinton broth within 48 h, with a released amount of PhB < 5% of the total amount. The anti-biofilm effectiveness of the light-activated nanocomposite with PhB showed a reduction in the survival rate of biofilm cells to 0.35% and 31.79% for S. aureus and C. albicans, respectively, compared to the control biofilm on PU alone. Scanning electron microscopy images showed that the nanocomposite effectively reduced the colonization and growth of the mixed biofilm. While PDI reduced the regulation of the ALS3 gene, the HWP1 gene was upregulated. Nevertheless, the cell survival of the C. albicans–S. aureus biofilm was significantly reduced, showing great potential for the elimination of mixed biofilms. Full article

DNA methylation, mediated by DNA methyltransferases (DMTs) and demethylases (DMLs), is an important epigenetic modification that maintains genomic stability and regulates gene expression in plant growth, development, and stress responses. However, a comprehensive characterization of these gene families in Populus sect. Turanga remains lacking. In this study, eight PeDMT and two PeDML genes were identified in Populus euphratica, and six PpDMT and three PpDML genes in Populus pruinosa. Phylogenetic analysis revealed that DMTs and DMLs could be classified into four and three subfamilies, respectively. The analysis of cis-acting elements indicated that the promoter regions of both DMTs and DMLs were enriched with elements responsive to growth and development, light, phytohormones, and stress. Collinearity analysis detected three segmentally duplicated gene pairs (PeDMT5/8, PeDML1/2, and PpDML2/3), suggesting potential functional diversification. Transcriptome profiling showed that several PeDMTs and PeDMLs exhibited leaf shape- and developmental stage-specific expression patterns, with PeDML1 highly expressed during early stages and in broad-ovate leaves. Whole-genome bisulfite sequencing revealed corresponding decreases in DNA methylation levels, suggesting that active demethylation may contribute to heteromorphic leaf formation. Overall, this study provides significant insights for exploring the functions and expression regulation of plant DMTs and DMLs and will contribute to future research unraveling the molecular mechanisms of epigenetic regulation in P. euphratica. Full article

Objectives: Light intensity is a critical environmental factor regulating plant growth, development, and stress adaptation. However, the physiological and molecular mechanisms underlying light responses in Aconitum kusnezoffii, a valuable alpine medicinal plant, remain poorly understood. This study aimed to elucidate the adaptive strategies of A. kusnezoffii under different light intensities through integrated physiological and transcriptomic analyses. Methods: Two-year-old A. kusnezoffii plants were exposed to three controlled light regimes (790, 620, and 450 lx). Leaf anatomical traits were assessed via histological sectioning and microscopic imaging. Antioxidant enzyme activities (CAT, POD, and SOD), membrane lipid peroxidation (MDA content), osmoregulatory substances, and carbon metabolites were quantified using standard biochemical assays. Transcriptomic profiling was conducted using Illumina RNA-seq, with differentially expressed genes (DEGs) identified through DESeq2 and functionally annotated via GO and KEGG enrichment analyses. Results: Moderate light (620 lx) promoted optimal leaf structure by enhancing palisade tissue development and epidermal thickening, while reducing membrane lipid peroxidation. Antioxidant defense capacity was elevated through higher CAT, POD, and SOD activities, alongside increased accumulation of soluble proteins, sugars, and starch. Transcriptomic analysis revealed DEGs enriched in photosynthesis, monoterpenoid biosynthesis, hormone signaling, and glutathione metabolism pathways. Key positive regulators (PHY and HY5) were upregulated, whereas negative regulators (COP1 and PIFs) were suppressed, collectively facilitating chloroplast development and photomorphogenesis. Trend analysis indicated a “down–up” gene expression pattern, with early suppression of stress-responsive genes followed by activation of photosynthetic and metabolic processes. Conclusions: A. kusnezoffii employs a coordinated, multi-level adaptation strategy under moderate light (620 lx), integrating leaf structural optimization, enhanced antioxidant defense, and dynamic transcriptomic reprogramming to maintain energy balance, redox homeostasis, and photomorphogenic flexibility. These findings provide a theoretical foundation for optimizing artificial cultivation and light management of alpine medicinal plants. Full article

Banana fruits are harvested and then undergo rapid ripening and senescence, sharply limiting their shelf-life and marketability. Myo-inositol (MI) is an important regulator in ethylene production and reactive oxygen species (ROS) accumulation; however, its involvement in the postharvest ripening process of banana remains to be determined. This study found that postharvest application of MI could efficiently delay the fruit ripening and extend the time in which the luster, color, and hardness were maintained in two cultivars with contrasting storage characteristics, storable ‘Brazil’ and unstorable ‘Fenza No. 1’, when stored at room temperature (23 °C ± 2 °C). Moreover, physiological, metabolic, and gene expression analyses indicated that MI application improved MI metabolism and postponed ethylene biosynthesis and cell wall loosening. The decrease in ethylene production was associated with a reduction in the expression of ACS1 and ACO1 genes. MI treatment decreased the expressions of PL1/2, PG, and EXP1/7/8, which may account for the delay in softening. In addition, the application of MI could alleviate ROS-mediated senescence and cell membrane damage by promoting the activities of SOD, POD, and anti-O₂⁻ and decreasing PPO activity. This study shed light on the function of MI in regulating the postharvest ripening and senescence of bananas and provided an efficient strategy for extending shelf-life and reduce losses. Full article

Background/Objectives: Emerging studies have indicated the importance of intra-tumoral neuronal signals in tumor progression and immune modulation. However, there is limited insight into neuroimmune crosstalk, and the molecules involved are largely unknown. This study investigates the relationship between tumor-derived neuropeptides and immune modulation in head and neck squamous cell carcinoma (HNSC). Methods: By utilizing neuropeptide databases and web tools leveraging TCGA data, neuropeptides’ expression and their associations with neurotrophic factors, immune cell infiltration, and immune checkpoints were analyzed, followed by survival analysis. Results: Over half of the neuropeptides were expressed in HNSC, with 16% exhibiting differential expression compared to normal counterparts. Notably, differentially expressed neuropeptides showed significant correlations with neurotrophic factors, immune cell infiltration, and checkpoint genes. Further, their expression was significantly different in responder and non-responder patient samples subjected to immune checkpoint therapy. Neuropeptide genes—PTHLH, NMB, GAST, APLN, and LYNX1—were identified and emerged as crucial mediators in neuroimmune crosstalk. Additionally, the neurotrophic gene NTRK1 exhibited extensive correlation with immune checkpoint genes, underscoring the prevalence of neuroimmune crosstalk in HNSC. Conclusions: These findings shed light on the role of tumor-derived neuropeptides in neuroimmune regulation in HNSC, offering valuable insights for future studies to decode the cancer neuroscience of HNSC progression and therapy. Full article

UDP-glycosyltransferases (UGTs) play essential roles in various biological processes, such as phytohormone homeostasis, abiotic stress adaptation, and secondary metabolite biosynthesis. Populus euphratica is a model species for investigating stress adaptation; however, the PeUGT gene family has yet to be systematically characterized. Here, we identified 134 UGT genes in P. euphratica. Phylogenetic analysis classified these genes into 16 major groups (A–P), and UGT genes within the same groups showed similar structural characteristics. Tandem duplication events were identified as the predominant mechanism driving the expansion of the PeUGT family. Cis-acting element analysis revealed an enrichment of motifs associated with developmental regulation, light response, phytohormone signaling, and abiotic stress in the promoters of PeUGT genes. Expression profiling demonstrated spatiotemporal regulation of the PeUGT genes under drought stress. Among them, PeUGT110 was significantly induced by PEG treatment in the leaf, root, and stem tissues of P. euphratica. Overexpression of PeUGT110 enhanced drought tolerance in transgenic Arabidopsis. Furthermore, the PeUGT110-OE lines exhibited reduced malonaldehyde accumulation, elevated proline content, higher superoxide dismutase activity, and upregulated expression of stress-related genes under drought stress. The results demonstrated that PeUGT110 plays a critical role in plant drought resistance. These findings establish a foundation for elucidating the function of PeUGT genes. Full article

Apomixis-mediated fixation of heterosis could transform hybrid breeding in alfalfa (Medicago sativa), a globally important forage crop. The parthenogenesis-inducing morphogenetic regulator BABY BOOM (BBM) represents a promising candidate for enabling this advancement. Here, we identified BBM homologs from three alfalfa genomes, characterized their promoter regions, and cloned a 2082 bp MsBBM gene encoding a 694-amino acid nuclear-localized protein. Three alfalfa BBM gene promoters primarily contained light- and hormone-responsive elements. Phylogenetic and conserved domain analyses of the MsBBM protein revealed a high sequence similarity with M. truncatula BBM. Expression profiling demonstrated tissue-specific accumulation of MsBBM transcripts, with the highest expression in the roots and developing pods. Hormonal treatments differentially regulated MsBBM. Expression was upregulated by GA₃ (except at 4 h) and SA, downregulated by NAA, MeJA (both except at 8 h), and ABA (except at 4 h), while ETH treatment induced a transient expression peak at 2 h. As an AP2/ERF family transcription factor showing preferential expression in young embryos, MsBBM likely participates in reproductive development and may facilitate apomixis. These findings establish a molecular framework for exploiting MsBBM to enhance alfalfa breeding efficiency through heterosis fixation. Full article

B-box (BBX) transcription factors are critical regulators of light-mediated anthocyanin biosynthesis, influencing peel coloration in plants. To explore their role in red mango cultivars, we identified 32 BBX genes (MiBBX1–MiBBX32) in the mango (Mangifera indica L.) genome using a genome-wide analysis. Phylogenetic and structural analyses classified these genes into five subfamilies based on conserved domains. A collinearity analysis revealed segmental duplication as the primary mechanism of MiBBX gene family expansion, with purifying selection shaping their evolution. A promoter analysis identified numerous light- and hormone-responsive cis-elements, indicating regulatory roles in the light and hormonal signaling pathways. Expression profiling in the ‘Sensation’ cultivar revealed organ-specific patterns, with several MiBBX genes showing higher expression in the peel than in the flesh. Many of these genes also consistently exhibited elevated expression in the peel of red-skinned cultivars (‘Sensation’ and ‘Guifei’) compared to yellow and green cultivars, suggesting their role in red peel pigmentation. Furthermore, postharvest light treatment of ‘Hongmang No. 6’ fruit significantly upregulated multiple MiBBX genes, suggesting their involvement in light-induced anthocyanin accumulation in red mango peel. These findings provide valuable insights into the molecular mechanisms governing light-regulated peel coloration in mango and establish a foundation for functional studies of MiBBX genes in fruit pigmentation. Full article

Stargardt’s disease (STGD1) is an autosomal recessive juvenile macular degeneration caused by mutations in the ABCA4 gene, impairing clearance of toxic retinoid byproducts in the retinal pigment epithelium (RPE). This leads to lipofuscin accumulation, oxidative stress, photoreceptor degeneration, and central vision loss. Over 1200 pathogenic/likely pathogenic ABCA4 variants highlight the genetic heterogeneity of STGD1, which manifests as progressive central vision loss, with phenotype influenced by deep intronic variants, modifier genes, and environmental factors like light exposure. ABCA4 variants also show variable penetrance and geographical prevalence. With no approved treatment, investigational therapies target different aspects of disease pathology. Small-molecule therapies target vitamin A dimerization (e.g., ALK-001), inhibit lipofuscin accumulation (e.g., soraprazan), or modulate the visual cycle (e.g., emixustat hydrochloride). Gene therapy trials explore ABCA4 supplementation including strategies like RNA exon editing (ACDN-01) and bioengineered ambient light-activated OPSIN. RORA gene therapy (Phase 2/3) addresses oxidative stress, inflammation, lipid metabolism, and complement system dysregulation. Trials like DRAGON (Phase 3, tinlarebant), STARLIGHT (phase 2, bioengineered OPSIN) show promise, but optimizing efficacy remains challenging. With the key problem of establishing genotype–phenotype correlations, the future of STGD1 therapy may rely on approaches targeting oxidative stress, lipid metabolism, inflammation, complement regulation, and genetic repair. Full article

As a plant-specific peroxidase family, class III peroxidase (PRX) plays an important role in plant growth, development, and stress response. In this study, a preliminary functional analysis of CqPRX9L1 was conducted. Bioinformatics analysis revealed that CqPRX9L1 encodes a 349-amino acid protein belonging to the plant-peroxidase-like superfamily, featuring a transmembrane domain and cytoplasmic localization. The promoter region of CqPRX9L1 harbors various cis-acting elements associated with stress responses, hormone signaling, light regulation, and meristem-specific expression. The tissue-specific expression pattern of the CqPRX9L1 gene and its characteristics in response to different stresses were explored using subcellular localization, quantitative real-time PCR (qRT-PCR), and heterologous transformation into Arabidopsis thaliana. The results showed that CqPRX9L1, with a transmembrane structure, was localized in the cytoplasm, which encodes 349 amino acids and belongs to the plant-peroxisome-like superfamily. The promoter region contains stress-response elements, hormone-response elements, light-response elements, and meristem expression-related elements. The expression of CqPRX9L1 was relatively higher in ears and roots at the panicle stage than in stems and leaves. CqPRX9L1 showed a dynamic expression pattern of first decreasing and then increasing under abiotic stresses such as 15% PEG 6000, low temperature, and salt damage, with differences in response time and degree. CqPRX9L1 plays an important role in response to abiotic stress by affecting the activity of antioxidant enzymes such as superoxide dismutase (SOD) and peroxidase (POD), as well as the synthesis and decomposition of proline (Pro). CqPRX9L1 also affects plant bolting and flowering by regulating key flowering genes (such as FT and AP1) and gibberellin (GA)-related pathways. The results establish a foundation for revealing the functions and molecular mechanisms of the CqPRX9L1 gene. Full article

The WRKY gene family comprises important transcription factors widely distributed in plants and plays significant roles in the growth and development, diverse (biotic and abiotic) stress responses, and various biological processes. In the current study, 96 identified HvLWRKY genes were classified into three groups and seven subgroups. Among these, 89 genes possessed the conserved domain WRKYGQK. A total of ten motifs were harbored in HvLWRKY genes with two to four introns. Fragmental duplication was suggested to be the prime force that drove the evolution of HvLWRKY genes. A high degree of collinearity was observed between barley and Triticum spelta. Cis-elements of HvLWRKYs were closely associated with abiotic stress, light response, and hormone response; however, there were differences in the numbers among groups. HvLWRKY genes, even the paralogous gene pairs, from different clades were differentially regulated under cold treatments in two landraces. HvLWRKY33, 43, 44, 57, 65, and 77 were homologous with the relative AtWRKY genes in Arabidopsis thaliana. They are suggested to regulate abiotic and pathogen resistance of two barley landraces via SA and JA pathways. Meanwhile, some genes (for example, HvLWRKY1 and HvLWRKY32) were specifically expressed in either cold-tolerant or cold-sensitive landraces. Under cold stress, different cold-responsive patterns occurred in different barley landraces. These findings provide a foundation for further studies on cold resistance in barley landraces and offer new insights for application of WRKY genes in barley breeding. Full article

The role of G-quadruplexes (G4s) in gene regulation has been widely documented, especially in gene promoters. However, the transcriptional mechanisms involving G4s in other regulatory regions remain largely unexplored. In this study, we integrated the G4-DNA data derived from 22 breast cancer patient-derived tumor xenograft (PDTX) models and MCF7 cell line as potential breast cancer-associated G4s (BC-G4s). Genome-wide analysis showed that BC-G4s are more prevalent in gene promoters and the first introns. The genes accommodating promoter or intronic BC-G4s show significantly higher transcriptional output than their non-G4 counterparts. The biased distribution of BC-G4s in close proximity to the transcription start site (TSS) is associated with an enrichment of transcription factor (TF) interactions. A significant negative correlation was detected between the G4–TF interactions within the first introns and their cognate promoters. These different interactions are complementary rather than redundant. Furthermore, the differentially expressed genes (DEGs) harboring promoter and first intron BC-G4s are significantly enriched in the cell cycle pathway. Notably, promoter BC-G4s of DEGs could be a central hub for TF–TF co-occurrence. Our analysis also revealed that G4-related single nucleotide variants (SNVs) affect the stability of G4 structures and the transcription of disease-related genes. Collectively, our results shed light on how BC-G4s within promoters and first introns regulate gene expression and reinforce the critical role of G4s and G4-related genes in breast cancer-associated processes. Full article

The circadian clock is a self-sustaining oscillator with a period of approximately 24 h, enabling organisms to anticipate daily recurring events, such as sunrise and sunset. Since the circadian period is not exactly 24 h and the environmental day length varies throughout the year, the clock must be periodically reset to align an organism’s physiology with the natural light/dark cycle. This synchronization, known as entrainment, is primarily regulated by nocturnal light, which can be replicated in laboratory settings using a 15 min light pulse (LP) and by assessing locomotor activity. An LP during the early part of the dark phase delays the onset of locomotor activity, resulting in a phase delay, whereas an LP in the late dark phase advances activity onset, causing a phase advance. The clock gene Period 2 (Per2) plays a key role in this process. To investigate its contributions, we examined the effects of Per2 deletion in neurons versus astrocytes using glia-specific GPer2 (Per2/GfapCre) knockout (KO) and neuronal-specific NPer2KO (Per2/NesCre) mice. All groups were subjected to Aschoff type II protocol, where an LP was applied at ZT14 or ZT22 and the animals were released into constant darkness. As control, no LP was applied. Phase shift, period, amplitude, total activity count, and rhythm instability were assessed. Our findings revealed that mice lacking Per2 in neurons (NPer2) exhibited smaller phase delays and larger phase advances compared to control animals. In contrast, mice with Per2 deletion specifically in glial cells including astrocytes (GPer2) displayed normal clock resetting. Interestingly, the absence of Per2 in either of the cell types resulted in a shorter circadian period compared to control animals. These results suggest that astrocytic Per2 is important for maintaining the circadian period but is not required for phase adaptation to light stimuli. Full article

In farmed animals, body color is not only an ecological trait but also an important trait that influences the commercial value of the animals. Melanin plays an important role in the formation of body color in animals, while the tyrosinase (TYR) gene family is a group of key enzymes that regulate melanogenesis. The Chinese soft-shelled turtle (Pelodiscus sinensis) is one of the most important reptiles in freshwater aquaculture. However, the potential role of the TYR gene family in the body color formation of P. sinensis remains unclear. This study aimed to investigate the expression and conservation of the TYR gene family in relation to body color variation in P. sinensis. Three core members of this gene family were identified from the P. sinensis genome. Following identification, the genomic features were analyzed. They shared similar physicochemical properties and conserved domains. Chromosome mapping showed that the three genes of P. sinensis were all located on the autosomes, while phylogenetic and collinearity analysis suggested that the protein functions of the three genes in the studied species were highly conserved. Amino acid sequence alignment indicated high conservation among the three TYR gene family proteins (TYR, TYRP1, and DCT) in multiple critical regions, particularly in their hydrophobic N-/C-terminal regions and cysteine/histidine-rich conserved domains. The qRT-PCR revealed that the TYR and DCT genes were highly expressed in the eyes of individuals with different body colors. The expression levels of TYR and TYRP1 genes in the skin were significantly higher in dark-colored individuals than in light-colored ones (p < 0.05). These results will lay the groundwork for functional studies and breeding programs targeting color traits in aquaculture. Full article