Search Results (18,780)

The TCP (Teosinte branched 1/Cycloidea/Proliferating) gene family comprises plant-specific transcription factors essential for regulating growth, development, and environmental adaptation. Utilizing the high-quality ‘Rui Youpan 1’ (‘RYP1’) reference genome, we conducted a comprehensive genome-wide identification and characterization of the TCP family in peach (Prunus persica). We identified 20 PpTCP genes and systematically evaluated their physicochemical properties, chromosomal distribution, phylogeny, gene architecture, and promoter cis-regulatory elements. Notably, the enrichment of abscisic acid-responsive elements (ABREs) in their promoters suggests a significant role in abiotic stress signaling. Integrated RNA-seq and RT-qPCR analyses identified six putative candidates (PpTCP3, 5, 6, 11, 14, and 15) with pronounced differential expression under drought conditions. Subcellular localization confirmed that all tested PpTCPs function within the nucleus. Moreover, the results of STRING-based computer simulations predicting protein–protein interactions indicate that PpTCP3 and PpTCP5 interact with key hormone pathways and stress-related transcription factors (TFs), including auxin signaling and strigolactone signaling. Full article

Background/Objectives: Citrus sinensis, Olea europaea var. sylvestris, Populus nigra, Prunus dulcis, and Punica granatum are economically and medicinally important perennial plant species. Carotenoid cleavage oxygenase (CCO) genes encode key enzymes involved in carotenoid degradation and play essential roles in plant growth, development, and responses to environmental stresses. In this study, a comprehensive genome-wide comparative analysis of the CCO gene family was conducted in C. sinensis, O. europaea var. sylvestris, P. nigra, P. dulcis, and P. granatum to investigate their structural diversity, evolutionary relationships, and potential biological functions. Methods: Chromosomal distribution, phylogenetic relationships, gene structure, conserved protein motifs, homology modeling, subcellular localization, cis-regulatory elements, and miRNA interactions were analyzed. Results: A total of 12, 23, 22, 11, and 17 CCO genes were identified in C. sinensis, O. europaea var. sylvestris, P. nigra, P. dulcis, and P. granatum, respectively. Most CCO proteins were acidic, and genes were concentrated on specific chromosomes. Phylogenetic analysis grouped CCO genes into three main clades. Gene structure analysis revealed intronless and intron-containing genes of varying lengths. Some CCO proteins possessed all conserved motifs, while others lacked certain motifs or had multiple copies. β-sheets were the predominant secondary structural elements, and CCO proteins were predicted to be localized in chloroplasts, mitochondria, peroxisomes, the cytoplasm, and the nucleus. Stress-related cis-elements and miRNAs were identified. Conclusions: These findings provide valuable insights into the diversity and evolutionary characteristics of the CCO gene family and suggest that CCO genes may contribute to plant stress responses and metabolic processes. Overall, this study provides a comprehensive comparative analysis of the CCO gene family in these five perennial plant species and offers a valuable genomic resource for future functional characterization, comparative genomic studies, and molecular breeding applications. Full article

Oxidative stress is a central driver of atherosclerosis progression, promoting lipid peroxidation, vascular inflammation, and hepatic metabolic dysfunction. Forchlorfenuron (KT-30), a cytokinin-like plant growth regulator widely used on fruits such as kiwifruit, grapes, and watermelon, has been reported to elevate serum cholesterol levels, suggesting potential atherogenic effects. However, whether KT-30 induces oxidative stress and accelerates atherosclerosis remains unknown. Here, apolipoprotein E-deficient (apoE^−/−) mice were orally administered KT-30 (5 mg/kg/day) for four weeks. KT-30 significantly accelerated atherosclerotic lesion formation, elevated plasma cholesterol levels, upregulated scavenger receptors SR-A and CD36, and downregulated ABCA1 and LXRα, indicating impaired reverse cholesterol transport and enhanced foam cell formation. KT-30 also increased pro-inflammatory cytokines (IL-1β, IL-6, MIP-2) and aortic expression of F4/80 and VCAM-1. Critically, KT-30 exposure was associated with elevated oxidative stress markers, as evidenced by elevated plasma MDA levels, increased aortic 4-HNE immunostaining, and upregulation of NOX-1/4. In the liver, KT-30 induced lipid accumulation, characterized by elevated cholesterol and free fatty acids, accompanied by SREBP-1/2-driven de novo lipogenesis and impaired lipoprotein uptake. Proteomic analysis revealed significant alterations in mitochondrial oxidative phosphorylation- and sirtuin signaling-related protein expression. Taken together, KT-30-associated oxidative stress, accompanied by upregulation of NOX-1/4 and alterations in mitochondrial pathway-related protein expression, may represent an important mechanistic link between lipid homeostasis disruption and accelerated atherosclerosis in apoE^−/− mice, highlighting the potential pro-atherogenic effects of KT-30 in a susceptible experimental model and providing mechanistic evidence that warrants further investigation of its possible cardiovascular implications. Full article

The growing demand for sustainable protein sources has intensified interest in plant-based food systems. Pulses are well established and recognized as nutritious, sustainable protein sources (~15–30% dry weight), rich in lysine and limited in cysteine, methionine, and tryptophan amino acids. In contrast, Spirulina is characterized by a complete amino acid profile, high protein content (~50–70% dry weight), and bioactive potential. This comprehensive review explores the role of Spirulina as a complementary protein source in plant-based systems, with emphasis on its structural, technofunctional, and processing characteristics. A literature analysis was conducted to identify advances, trends, and gaps in their incorporation into food matrices. The findings indicate that, despite their nutritional and functional advantages, the application of microalgae and beans remains constrained by sensory and technological challenges, such as off-flavors and textural issues. The combination of microalgae with pulse-based ingredients represents a promising strategy to enhance amino acid balance, improve functionality, and develop nutritionally enriched products. Studies addressing multi-component systems remain scarce, especially in bakery and flour-based applications, as well as in understanding synergistic interactions between microalgae and pulse proteins in food matrices. This review highlights the potential of microalgae as key ingredients in next-generation food formulations. It identifies critical gaps that must be addressed to enable their broader application in food products. Full article

Background: Peanut (Arachis hypogaea) is a globally important legume crop with high nutritional and economic value. In the plant, the highly conserved 14-3-3 proteins participate in various biological functions. This study investigated the characterization and evolution of the 14-3-3 gene family in peanut and explores its potential roles in stress resistance. Methods: The 14-3-3 gene families in cultivated peanut and its ancestral species Arachis duranensis and Arachis ipaensis were identified and characterized via a genome-wide approach. We subsequently analyzed their structural features, conserved motifs, genomic distribution, phylogeny and promoter cis-acting elements. Results: A total of 22, 10, and 12 14-3-3 genes (also called general regulatory factors, GRFs) were identified in A. hypogaea, A. duranensis, and A. ipaensis, respectively. Cultivated peanut exhibits extensive genomic synteny with its progenitors, and segmental duplication appears to be a key mechanism underlying the expansion of this gene family. Moreover, according to cis-acting element prediction, these genes may contribute to stress tolerance under diverse environmental conditions. Conclusion: This comprehensive analysis enhances our understanding of the 14-3-3 (GRF) gene family in peanut and provides a valuable basis for further functional research on these genes. Full article

Plant-based cream cheese alternatives are gaining popularity, yet replicating the sensory and nutritional attributes of dairy cream cheese remains challenging. Plant proteins often impart undesirable flavors and differ structurally from dairy proteins, resulting in weaker emulsifying and gelling properties, as well as compromised product structure and texture. Hydrocolloids are commonly used to improve organoleptic properties and/or spreadability but may introduce gummy textures and conflict with clean-label expectations. Fermentation represents a promising strategy to address these challenges. Exopolysaccharide (EPS)-producing starter cultures can naturally enhance texture. Depending on EPS type, concentration, molecular structure, and interactions with the food matrix, fermentation can improve creaminess, viscosity, and water-holding capacity while supporting cleaner-label formulations. In addition, fermentation may improve flavor, protein digestibility, and amino acid bioavailability and reduce antinutritional factors, while EPS may confer health-related benefits. This review examines how fermentation, particularly EPS biosynthesis, can improve the overall quality and texture of plant-based cream cheese alternatives, considering current market formulations. The reviewed literature indicates that fermentation and in situ-formed EPS offer potential, although their effects depend on strain selection, matrix composition, and processing conditions. Pulsed electric fields and ultrasound may enhance EPS production, representing an underexplored field of research. Future studies should assess these strategies in complex plant-based matrices to clarify matrix-specific effects. Full article

The continued rise in fishmeal prices and the scarcity of fishery resources have led to an increase in the use of plant-based protein sources in compound feed, making mold contamination in compound feed a frequent occurrence. Aflatoxin B1 (AFB1) contamination in aquaculture feed can seriously harm fish growth and liver health; it is extremely toxic, posing an even greater risk to carnivorous fish such as grouper. Lycopene, a natural carotenoid, has antioxidant and anti-inflammatory physiological functions and may act as a functional feed additive to mitigate damage induced by mycotoxins. This study utilized hybrid grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) as the experimental model. An 8-week feeding trial was performed to systematically assess the impact of lycopene supplementation at levels of 0, 200, 400, 600, and 800 mg/kg to a basal diet containing 800 μg/kg AFB1 on the fish’s growth performance, antioxidant capacity, liver health, inflammation-related gene expression, and hepatic transcriptome. The results showed that adding 200 mg/kg lycopene to the feed significantly increased the FWB and SGR (p < 0.05) of hybrid grouper. An appropriate amount of lycopene could enhance the antioxidant capacity of serum and liver, significantly increase the activities of catalase (CAT) and superoxide dismutase (SOD), and significantly decrease serum alanine aminotransferase (ALT) activity while increasing albumin (ALB) levels (p < 0.05). An amount of 200 mg/kg lycopene significantly alleviated AFB1-induced hepatocyte vacuolation, steatosis, and inflammatory cell infiltration, while the protective effect of higher doses was weakened. The gene expression results showed that 200 mg/kg lycopene significantly upregulated the expression of antioxidant-related genes such as cat, sod, and nrf-2, and increased the expression level of the anti-inflammatory factor il10 (p < 0.05). The transcriptome analysis identified a total of 621 differentially expressed genes, which were mainly enriched in metabolic pathways, fatty acid metabolism, PPAR signaling pathway, redox process, ferroptosis, NF-κB signaling pathway, and Toll-like receptor signaling pathway. In summary, the addition of 200 mg/kg lycopene to the feed can effectively alleviate the growth inhibition and liver damage caused by AFB1 in hybrid grouper. Its mechanism of action may be related to enhancing antioxidant defenses, improving liver tissue structure, regulating lipid metabolism, and maintaining immune homeostasis. The research results indicate that lycopene can be used as a natural functional feed additive to alleviate AFB1 toxicity in hybrid grouper aquaculture. Full article

The plant epidermis, adorned with trichomes and root hairs, represents a critical interface where developmental programming and environmental responses converge. Although the genetic basis of epidermal patterning has been extensively characterized in model systems, how these pathways are modulated under abiotic stress remains incompletely understood. This review integrates recent advances in epidermal development and stress biology, focusing on MYB–bHLH–WD40 (MBW) complexes, GIS-family C2H2 zinc-finger proteins, and ROOT HAIR DEFECTIVE SIX-LIKE (RSL) transcription factors. These regulators participate in interconnected, organ-specific networks that coordinate trichome and root-hair development. Their activities are shaped by gibberellin–brassinosteroid interactions, ethylene–auxin coordination, jasmonate and abscisic acid signaling, and cytokinin- and nutrient-responsive pathways. We further discuss how reactive oxygen species and calcium oscillations translate transcriptional regulation into polarized cell growth. The resulting epidermal plasticity reflects trade-offs among growth, defense, resource acquisition, and conservation. By integrating single-cell transcriptomics, nutrient sensing, and evolutionary perspectives, this review provides a framework for understanding environmentally responsive epidermal development and identifies opportunities for improving crop resilience. The resulting framework identifies testable opportunities for crop improvement, while emphasizing that native network equivalence, pleiotropic effects, and field-level stress benefits remain to be established in crop species. Full article

Plant homeodomain (PHD) finger proteins are important histone modification readers that play broad roles in the epigenetic regulation of plant development and stress responses. However, the PHD finger gene family has not been systematically identified in Panax ginseng, and its association with ginsenoside biosynthesis remains unclear. In this study, we identified 63 PgPHD genes, corresponding to 163 transcripts, from the P. ginseng transcriptome using a combination of HMMER-based domain and BLAST-based homology searches (BLAST+ 2.16.0). Phylogenetic analysis classified these genes into 15 groups. Promoter cis-element prediction, co-expression network construction, and methyl jasmonate (MeJA) induction experiments were further performed to explore the possible regulatory associations of PgPHD genes. The PgPHD genes were distributed across all 24 chromosomes, and 18 segmentally duplicated gene pairs suggested that whole-genome duplication drove the expansion of this gene family. A total of 308 MeJA-responsive cis-elements were identified in the promoter regions, making them one of the most prevalent functional categories. Co-expression network analysis based on 42 landraces identified five candidate genes significantly associated with key enzyme genes involved in ginsenoside biosynthesis, among which PgPHD31-09 showed a significant expression correlation with nine key enzyme genes. qRT-PCR analysis showed that PgPHD31-09 was significantly upregulated in response to MeJA treatment, and its expression pattern was similar to that of several key enzyme-encoding genes related to ginsenoside biosynthesis. This study provides the first systematic analysis of the evolutionary and expression characteristics of the PHD gene family in P. ginseng, identifying PgPHD31-09 as a candidate gene potentially associated with MeJA responsiveness and ginsenoside biosynthesis. Full article

Salvia lavandulifolia Vahl. is an aromatic and medicinal plant cultivated as a rainfed crop for essential oil production in the western Mediterranean. New trends in the use of Lamiaceae seeds as functional ingredients warrant characterization of this species. Hence, studies were conducted to measure the proximate composition and amino acid profile, along with fatty acid profile, tocochromanol content, phenolic composition, and antioxidant activity in 10 wild populations. Defatted seed meal analysis demonstrates the potential usefulness of this species based on carbohydrate (50–60%), protein (13–21%), and oil (13–20%) content. The amino acid content ranged from 9.2 to 15.4 g/100 g. Seed oil analysis found a fatty acid content of 73–89 g/100 g with predominance of ω6 fatty acids, tocochromanol content of 62–89 mg/100 g, and a phenolic fraction of 7.5–148 mg/100 g with a high proportion of flavones. Antioxidant activity ranged from 10.6 to 23.1 µmol Trolox equivalents/100 g. Overall, seeds of S. lavandulifolia grown in subhumid conditions have strong nutritional and phytochemical profiles. These characteristics suggest opportunities for their use as functional ingredients. Further, strategies to minimize waste and maximize the availability of bioactive compounds will support the economic sustainability of this crop. Full article

The HAK/KUP/KT family represents a major group of plant potassium transporters involved in K⁺ uptake, ion homeostasis and stress responses. However, the accession-level diversity of HAK/KUP/KT genes in Brassica napus remains insufficiently characterized. In this study, we performed a pan-family analysis of HAK/KUP/KT genes across eight B. napus accessions. A total of 269 annotated HAK/KUP/KT family members were identified and classified into core, soft-core, dispensable and private orthogroups based on their representation across the analyzed genome annotations. Phylogenetic analysis grouped these proteins into four major clades together with reference HAK/KUP/KT members from Arabidopsis thaliana and rice. Ka/Ks analysis indicated that HAK/KUP/KT orthogroups were predominantly under purifying selection, while accession-variable orthogroups showed greater variation in sequence conservation. Gene structure, conserved domain, motif and predicted promoter cis-element analyses revealed conserved transporter-related protein features together with orthogroup-level structural and sequence variation. Expression profiling using the ZS11 BnIR dataset further revealed tissue-, hormone- and stress-responsive expression patterns among ZS11 HAK/KUP/KT genes. By integrating expression features, predicted promoter information, evolutionary characteristics, published salt GWAS context and BnVIR haplotype–phenotype information, BnaA08T0085800ZS was prioritized as a candidate locus located near salt-associated variation. This study provides a pan-genome perspective on HAK/KUP/KT family diversity in B. napus and establishes a framework for prioritizing candidate genes for future functional investigation. Full article

Background/Objectives: Allium atroviolaceum Boiss. is a functional food rich in phenolic compounds; however, the contribution of different plant organs to its bioactivity remains insufficiently understood. Methods: An integrated approach combining UHPLC-QTOF-IMS based metabolite profiling, network pharmacology, molecular docking, and experimental antioxidant assays was employed. Results: Metabolite profiling revealed that the flowers were rich in anthocyanins and flavonoids; leaves in flavonol glycosides; bulbs in flavonoids, phenolics, and lipids; and flower stalks in flavonoid glycosides and sterols. Interestingly, flowers exhibited the strongest antioxidant scavenging activity, with the lowest IC₅₀ values of 3.08 ± 0.21 µg/mL and 89 ± 2.8 µg/mL in the DPPH and ABTS assays, respectively. They also showed the highest FRAP response at 2 mg/mL (1.367 ± 0.010 at 2 mg/mL). Moreover, flower stalks were particularly effective in limiting lipid oxidation, displaying the greatest activity in the β-carotene bleaching assay, with an IC₅₀ value of 14.75 ± 0.29 µg/mL. Network-based target prioritization highlighted several oxidative stress/inflammation-associated proteins, including EGFR, HRAS, TGFB1, BCL2, JUN, TNF, TP53, MAPK1, and PTGS2. Additionally, Caffeoyl pinoresinol showed the strongest predicted interaction with PTGS2 and was therefore selected as a candidate ligand for further computational evaluation. Conclusions: A. atroviolaceum exhibits organ-specific phytochemical diversity and potent antioxidant activity mediated through multiple molecular targets. The in silico analyses identified candidate compound–target associations related to oxidative stress and inflammatory pathways, but these findings remain predictive and require biochemical and cell-based validation. Full article

Fruit-specific promoters (FSPs) are a class of regulatory DNA sequences that direct transgene expression exclusively in fruit tissues or during specific stages of fruit development. They are indispensable molecular tools in modern agricultural biotechnology, with broad applications in fruit quality improvement, nutritional enhancement, and shelf-life extension. By functioning as precise molecular switches that regulate fruit-specific gene expression, FSPs overcome the limitations of constitutive promoters and facilitate precision molecular breeding for fruit quality improvement. This review systematically summarizes recent advances in FSP research. First, based on their spatiotemporal expression patterns, FSPs are classified into four categories: immature fruit-specific, fruit ripening-specific, whole fruit development stage-specific, and dual-stage (immature fruit/ripening) promoters. Their origins, expression characteristics, and key cis-regulatory elements are comprehensively summarized. Second, the complex transcriptional regulatory network governing FSP activity is discussed from the perspectives of cis-regulatory elements, major transcription factor families (such as MADS-box and NAC proteins), and epigenetic regulation, including DNA methylation and histone modifications. Furthermore, recent advances in key methodologies, including promoter cloning, functional characterization, and CRISPR/Cas9-mediated precise editing of cis-regulatory elements, are reviewed, together with their applications in crop genetic improvement, plant molecular farming, and fundamental molecular biology research. Finally, this review highlights the major challenges limiting the application of FSPs, including the relatively weak transcriptional activity of natural promoters, insufficient tissue specificity, and limited cross-species applicability. Future perspectives are discussed, emphasizing the integration of artificial intelligence-assisted promoter design, high-throughput screening, and single-cell omics technologies to develop finely tunable synthetic promoters. These advances are expected to provide both a theoretical foundation and technical support for precision molecular breeding in fruit crops. Full article

Mitochondrial unfolded protein response (UPR^mt) is crucial in preserving mitochondrial health and, consequently, in prolonging healthspan. Natural bioactive polysaccharides have emerged as a central focus for delaying senescence, although their links to mitochondrial stress responses remain incompletely understood. In this study, a purified fraction of Lycii Fructus polysaccharide (FSP) significantly extended lifespan, improved healthspan-related phenotypes, and enhanced resistance to heat, oxidative, and ultraviolet stress in C. elegans. FSP also preserved mitochondrial abundance and morphology, increased adenosine triphosphate (ATP) levels and mitochondrial membrane potential, and reduced reactive oxygen species. Transcriptomic and qPCR analyses, together with hsp-60 and hsp-6 reporter assays, showed an enhanced UPR^mt-associated response after FSP treatment. FSP-mediated lifespan extension was not observed in the atfs-1 and ubl-5 mutant strains, supporting pathway involvement of ATFS-1/UBL-5-dependent UPR^mt signaling. FSP reduced senescence-associated β-galactosidase positivity and improved mitochondrial function in human dermal fibroblasts. Our findings provide a vision of regulating UPR^mt for anti-aging interventions with plant polysaccharides and highlight the anti-aging potential of FSP by improving mitochondrial health. Full article

Synergistic infections by different viruses exacerbate symptoms, broaden host ranges, and cause severe economic losses, becoming a critical factor in viral disease epidemics. Mixed-infection by Amalgavirus lycopersici (commonly known as southern tomato virus, STV) and Orthotospovirus tomatomaculae (commonly known as tomato spotted wilt virus, TSWV) results in leaf necrosis, fruit hardening, and severe yield loss in tomatoes. However, the mechanisms by which their synergistic infections aggravate tomato diseases remain unclear. From 2020 to 2023, the incidence of STV and TSWV was monitored by RT-PCR in a total of 572 tomato samples. The annual incidence of STV was 29.0%, 31.5%, 31.1%, and 45.2% in 2020, 2021, 2022, and 2023, respectively, while that of TSWV was 23.3%, 18.9%, 22.5% and 16.1%, respectively. Shoot tip detoxification technology was applied to cultivate virus-free seedlings of Ninghuang-1, and 80% of virus-free plants survived in large-scale cultivation experiments. Mixed-infection markedly increased viral RNA and TSWV N protein expression levels, accompanied by severe damage to chloroplasts, mitochondria, and other cellular structures. Putative STV virions were observed. This study provides a theoretical foundation and has practical implications for green prevention and control of viral diseases in the field. Full article