Search Results (792)

Rind color is an important quality trait in zucchini (Cucurbita pepo). As a core transcription factor in plant pigment biosynthesis, APRR2 plays a conserved yet mechanistically diverse regulatory role in the formation of rind color in various vegetables. However, the APRR2 transcription factor regulates rind color but has not been systematically identified in C. pepo. In this study, 50 APRR2 genes were defined by the presence of the conserved REC domain verified. These genes were identified and found to be unevenly distributed across the 20 chromosomes, primarily expanded through tandem duplication events. Phylogenetic and structural analysis classified these genes into three distinct subgroups, all featuring the conserved REC domain essential for pigment regulation but exhibiting variations in motifs and intron–exon structures. Promoter analysis revealed abundant light-responsive, hormone-responsive and stress-responsive elements that may contribute to environmental adaptation and photomorphogenesis. Crucially, transcriptome analysis during rind development (0 and 10 days after pollination) in green (GR) and white (WR) rind lines demonstrated profound functional divergence. Expression clusters indicated temporal shifts in metabolism and enriched “circadian rhythm-plant” and “photosynthesis” pathways in WR at 0 DAP. Specific APRR2 genes were tightly correlated with rind color. qPCR validation of the 24 selected APRR2 genes classified them into four trend groups based on the direction of expression change at 10 DAP. In total, 14 genes were upregulated in both GR and WR, 6 were downregulated in both lines, 1 was upregulated in GR but downregulated in WR, and 3 were downregulated in GR but upregulated in WR. Furthermore, protein–protein interaction prediction and yeast two-hybrid (Y2H) assays detected a physical interaction in yeast between a core APRR2 protein and a bHLH62 transcription factor, suggesting a potential interaction that may be involved in rind color regulation, pending in planta validation. The study first identified the members of the APRR2 gene family in C. pepo and conducted a bioinformatics analysis on them. The study establishes the molecular basis of APRR2 function and offers valuable resources for breeding improved C. pepo varieties. Full article

Microbial contamination remains a major challenge in food systems, creating demand for stable natural antimicrobials. This study investigates the inducible antibacterial response of Hermetia illucens and characterized the black soldier fly defensin-like peptide DLP4. Larvae were challenged with Staphylococcus aureus or Escherichia coli, and hemolymph activity, antimicrobial-peptide gene expression, C18 solid-phase extraction fractions, and LC–MS/MS profiles were evaluated. Synthetic mature DLP4 was further assessed for antibacterial spectrum, physicochemical stability, and structural properties. Hemolymph antibacterial activity varied with treatment and time, while DLP4 and CLP1 showed distinct transcriptional responses. Antibacterial activity was concentrated in early fractions, with F3 showing the greatest activity. LC–MS/MS detected a conserved DLP-family motif and a cysteine-rich defensin-like peptide in F3, whereas the complete 40-amino-acid sequence of synthetic DLP4 was confirmed. DLP4 showed strong, strain-dependent activity against Gram-positive bacteria, including Bacillus subtilis, Listeria ivanovii, and Staphylococcus spp., while no MIC endpoint was detected for the tested E. coli strains. DLP4 retained substantial activity after heat, ultraviolet, storage, pH, NaCl, and most metal-ion treatments, although Fe³⁺ reduced activity. These findings support DLP4 as a stable, Gram-positive-active antimicrobial candidate for further evaluation in food systems. Full article

Background: Glutathione S-transferases (GSTs) play pivotal roles in plant growth, abiotic stress responses, detoxification of xenobiotics, and maintenance of redox homeostasis. Methods: In this study, transcriptomic analysis was employed to identify differentially expressed genes (DEGs) in the pea cultivar DX27 under freezing stress (−4 °C) at 3, 6, and 12 h. Results:GO and KEGG enrichment analyses of global transcriptomic data further reveal that DEGs are significantly enriched in the following functional categories: oxidation–reduction processes, stress responses, glutathione metabolism, and secondary metabolite biosynthesis. A total of 52 PsatGST genes were identified and classified into nine subfamilies based on phylogenetic relationships. Chromosomal localization revealed a non-random distribution across seven chromosomes. Promoter cis-element analysis indicated that PsatGST genes harbor diverse regulatory elements associated with light responsiveness, hormone signaling (auxin, abscisic acid, gibberellin, salicylic acid, and MeJA), and abiotic/biotic stress responses. PsatGSTF2 expression analysis showed pronounced up-regulation under freezing stress (−4 °C) at 3, 6, and 12 h. Conclusions: These findings provide a foundational framework for understanding the evolutionary history and functional diversification of the PsatGST gene family and offer valuable candidate genes for the breeding of stress-tolerant pea varieties. Full article

The microphthalmia-associated transcription factor (Mitf) family is central to melanocyte biology. Teleosts possess two mitf paralogs, mitfa and mitfb, yet their functional divergence remains incompletely understood. Here, we characterized the coding sequences, phylogeny, tissue distribution, developmental expression, cellular localization, and stress responsiveness of mitfa and mitfb in Congjiang natural mutant crucian carp (NMCC). Both genes encoded proteins containing the characteristic bHLH-ZIP domain. Phylogenetic analysis revealed that teleost mitfb clustered with the tetrapod mitf clade, indicating closer evolutionary affinity than mitfa. mitfa was predominantly expressed in skin and eyes, whereas mitfb showed broad tissue distribution. Both paralogs were constitutively expressed in skin across developmental stages; mitfa levels remained consistently lower than mitfb. Both transcripts were localized to melanocyte-containing regions of the skin. Transcriptomic analysis following high temperature (34 °C), UV radiation, and combined stress (48 h) revealed that mitfa was significantly upregulated by thermal stress, while mitfb showed no significant changes. Profiling of DNA damage response pathways uncovered extensive, stress-specific transcriptional remodeling. High temperature broadly suppressed apoptotic genes while upregulating tsc2, gadd45b, and cdip1; UV triggered widespread apoptotic gene activation. Combined stress elicited a hybrid signature. Notably, robust DNA Damage Response pathway remodeling contrasted with muted mitf responses, suggesting that DNA Damage Response-to-pigmentation signaling may operate predominantly at post-transcriptional levels. These findings reveal a substantial regulatory divergence between mitfa and mitfb, with mitfa maintaining a conserved melanogenic role while mitfb has been co-opted for broader functions in non-pigmentary tissues. The differential stress responses of the two paralogs further provide new insights into tissue-specific genotoxic stress signaling and melanogenic regulation in teleosts. Full article

Background/Objectives: Soybean (Glycine max) productivity is increasingly constrained by soil salinity. WIP transcription factors, a subfamily of C2H2-type zinc finger proteins, regulate cell division, differentiation, and tissue patterning in several plant species, but this gene family had not previously been systematically characterized in soybean or any other major legume crop. This study aimed to identify and characterize the GmWIP gene family genome-wide and evaluate its potential involvement in the soybean salt-stress response. Methods: Genome-wide identification of GmWIP genes was performed using sequence similarity and domain-based searches against the Wm82.gnm4.ann1 reference genome, followed by characterization of physicochemical properties, chromosomal distribution, phylogenetic relationships, gene duplication, conserved motifs, gene structure, and promoter cis-acting elements. Tissue-specific expression was examined using transcriptome data, and GmWIP responses to salt stress were profiled by RT-qPCR in roots, stems, and leaves of a salt-tolerant cultivar (HN531) and a salt-sensitive cultivar (HN563), alongside physiological measurements of oxidative stress and osmotic adjustment. Results: Thirty GmWIP genes were identified, with molecular weights from 26.90 to 57.52 kDa, distributed unevenly across 15 soybean chromosomes, with chromosomes 11, 12, and 13 forming a major hotspot (53.3% of the family). Duplication analysis detected 54 reconciled segmental duplicate gene pairs, all exhibiting Ka/Ks values < 1 (ranging from 0.0351 to 0.4471; mean 0.214), consistent with purifying selection acting on this gene set. GmWIP promoters were enriched for ABRE, MBS, and MeJA cis-acting elements. RT-qPCR showed genotype- and tissue-dependent differential expression under salt stress (e.g., up to 14.9-fold induction of GmWIP22 in HN531 stems), paralleled by superior proline accumulation (+45%), soluble sugars, and CAT activity (+38%) alongside reduced MDA accumulation in the tolerant cultivar. Conclusions: The GmWIP gene family has expanded substantially in soybean relative to previously characterized species and shows genotype-dependent transcriptional responses to salt stress, suggesting that specific GmWIP members are candidate regulators of salt tolerance and warrant further functional investigation. Full article

GPR35 is a member of the G-protein-coupled receptor family and existing studies have shown that its expression may be negatively correlated with fat deposition in mice. However, the exact role of GPR35 in goat intramuscular preadipocytes’ adipogenic differentiation remains unknown. This study is the first to demonstrate that GPR35 inhibits the maturation and differentiation of goat intramuscular preadipocytes via activating the cAMP/PKA signaling pathway under in vitro culture conditions. The functional experimental results showed that GPR35 overexpression suppressed the adipogenic differentiation, lipid synthesis, and proliferation capacity of goat intramuscular preadipocytes, and concurrently downregulated the expression of adipogenic differentiation marker genes and cell proliferation marker genes. Conversely, GPR35 knockdown promoted lipid accumulation, reduced intracellular cAMP levels, and ultimately enhanced the differentiation and proliferation capacity of intramuscular preadipocytes. Treatment with the cAMP inhibitor SQ22536 and PKA phosphorylation inhibitor H89 successfully reversed the phenotypic changes induced by GPR35 overexpression, including abnormal lipid droplet morphology, decreased triglyceride (TG) content, and inhibition of the expression of genes related to adipocyte differentiation/proliferation/metabolism (such as CDK2, PCNA, and HSL). These results confirm that GPR35 mainly regulates intramuscular fat deposition in goats through the cAMP/PKA pathway, providing a new target for elucidating the molecular mechanism of lipid metabolism and goat molecular breeding. Full article

Background: Endophytic fungi are important sources of structurally diverse antimicrobial natural products, but their potential to yield antitubercular scaffolds remains insufficiently explored. This study aimed to uncover new decalin polyketides from the endophytic fungus, Trichoderma longicollum 17007, and to evaluate their biological activity. Methods: Feature-based molecular networking (FBMN) analysis of the ethyl acetate extract from rice-based cultures was performed using trichoharzin as a seed compound to guide targeted isolation. Structures were established by HRMS, 1D and 2D NMR spectroscopy, NOESY analysis, and quantum chemical ECD calculations. Cytotoxicity and activity against the avirulent Mycobacterium tuberculosis H37Ra strain were evaluated, and genome mining was performed to identify a candidate biosynthetic gene cluster. Results: Six new decalin polyketides, tandyukisins K–P (1–6), and two known analogues, trichoharzin (7) and tandyukisin J (8), were isolated. Compounds 1–6 are C1-O-acetylated analogues bearing a 3-methylpentenedioate-type acyl side chain. Comparative ¹³C NMR analysis revealed empirical features useful for assigning side-chain attachment site, double-bond position and geometry. Tandyukisins K (1) and P (6) showed moderate activity against the avirulent M. tuberculosis H37Ra strain, with a MIC value of 12.5 μg/mL. Conclusions: These findings expand the structural diversity of decalin polyketides and provide the first evidence of antitubercular activity by this compound family. Full article

The rubber tree (Hevea brasiliensis Müll. Arg), the primary source of natural rubber, faces severe constraints from low temperature stress in industrial production. To elucidate the molecular mechanisms underlying cold tolerance, this study identified and systematically analyzed 44 HbGATA transcription factor family members at the whole-genome level. Based on physicochemical property analysis, phylogenetic tree construction, chromosome localization, gene structure analysis, and profiling of promoter cis-elements, the characteristics of individual genes were determined. Using the cold-tolerant cultivar yunyan 77-2 subjected to 4 °C treatment (0, 2, 8, and 24 h), candidate genes were validated via quantitative real-time PCR analysis. The results demonstrate that HbGATA10, HbGATA13, and HbGATA27 were significantly up-regulated after 24 h treatment, whereas HbGATA44 exhibited down-regulated expression at 24 h, suggesting that these four genes represent core candidates in the response to cold stress in rubber trees. This study provides the first systematic insight into the potential functions of the HbGATA family in cold acclimation in rubber tree and offers novel theoretical foundations and genetic resources for molecular breeding aimed at improving cold tolerance. Full article

Hydrothermal systems contain diverse alkanes derived from biological and geological processes, providing potential carbon and energy sources for microorganisms. However, cultivated thermophilic alkane-utilizing bacteria from hydrothermal environments remain poorly characterized. In this study, a strain L01 was isolated from a deep-sea hydrothermal vent and identified as an alkane-degrading bacterium. The strain L01 grew at 55 °C and pH 7.0 in medium supplemented with n-hexadecane under microoxic conditions. Cells were elongated rods approximately 10–20 μm long and ~0.2 μm wide. Phylogenetic analyses based on 16S rRNA gene sequence similarity (93.11% to the closest described relative), average amino acid identity (AAI, 66.27–66.58%), average nucleotide identity (ANI, 80.80–83.05%), and digital DNA-DNA hybridization (dDDH, 12.5–20.8%) demonstrated that strain L01 represents a previously unrecognized genus within the family Symbiobacteriaceae, for which the provisional name “Thermalkanevorax longiformis” is proposed. An isotope tracing experiment together with genomics and transcriptomics revealed coordinated physiological and metabolic responses associated with n-hexadecane utilization by strain L01. These findings provide a cultivated representative of the family Symbiobacteriaceae with physiological and metabolic responses to n-hexadecane, thereby providing a basis for further investigation of hydrocarbon metabolism. Full article

Bryophytes possess a gene family repertoire substantially larger than vascular plants, yet the functional evolution of their transcription factors remains poorly understood. We conducted a nested analysis across 144 bryophyte genomes, cataloging 58 transcription factor families and deeply characterizing the C2H2 zinc-finger protein family. We identified 8246 C2H2 zinc-finger genes classified into four structural types based on zinc-finger architecture. Domain-level scanning of 11,565 zinc fingers revised Z-type frequency from ~20% to 4.2%. The plant-specific Q-type was most prevalent in mosses and least prevalent in liverworts, with the major Q-type radiation occurring in seed plants. C2H2 zinc-finger gene expansion in mosses was driven by whole-genome duplication, and gene count correlated with genome size. Through re-analysis of publicly available RNA-seq datasets, cross-species expression profiling showed that mosses mobilized 23–28% of their C2H2 zinc-finger repertoires under dehydration, whereas the liverwort Marchantia polymorpha showed no significant response to osmotic stress and only a weak, transient response to salt. Notably, the aluminum-tolerance regulator STOP1 was downregulated under dehydration. Together, these results suggest a marked divergence in stress-responsive C2H2-ZFP deployment between mosses and liverworts, although the underlying mechanisms remain to be validated functionally. Full article

Soursop (Annona muricata L.) is a climacteric tropical fruit belonging to the Annonaceae family, widely cultivated in tropical and subtropical regions due to its economic importance, nutritional value, and abundance of bioactive compounds. Its pulp is highly appreciated for fresh consumption and food processing; however, its high respiration rate and ethylene production accelerate ripening, resulting in rapid quality deterioration and a short postharvest shelf life. During ripening, soursop fruit undergoes physiological, biochemical, and molecular changes associated with organic acid metabolism, in which citrate synthase (CS) and malate dehydrogenase (MDH) play key roles within the tricarboxylic acid cycle. However, the transcriptional dynamics of genes associated with the tricarboxylic acid cycle during postharvest storage of tropical fruits remains poorly characterized. This study aimed to identify in silico genes encoding CS and MDH and to evaluate changes in physicochemical traits, enzymatic activity, and the expression of selected CS and MDH genes during postharvest storage of soursop (A. muricata) GUANAY-1 fruit. Fruits were stored at 26 ± 1 °C and evaluated on days 1, 2, 3, 4, and 5. Titratable acidity, pH, total soluble solids, CS activity, MDH activity, and the expression of selected CS and MDH genes were analyzed. Physicochemical analysis showed that the major changes in acidity, TSS, and pH occurred on day 3. In silico analysis identified 16 CS genes and 47 MDH genes in soursop, whereas transcriptome analysis identified four CS genes and three MDH genes with differential expression, designated as CS1, CS2, CS3, CS4, MDH1, MDH2, and MDH3, respectively. The Neighbor-Joining analysis grouped the CS sequences into two clusters and the MDH sequences into three clusters. Differential expression analysis revealed that CS1, CS2, CS3, CS4, MDH1, MDH2, and MDH3 were upregulated on day 3 relative to day 0 of postharvest storage. Functional enrichment analysis indicated that these genes were mainly associated with cellular respiration and the tricarboxylic acid cycle. The highest CS activity was recorded on day 3, coinciding with the maximum expression of CS1, CS2, and CS4. In contrast, MDH activity peaked on day 2, whereas MDH1 and MDH2 reached their highest expression on day 3. Correlation analysis showed positive associations between CS2 and CS4 expression and both TSS and titratable acidity. Overall, these results demonstrate temporal changes in physicochemical traits, CS and MDH enzymatic activities, and the expression of selected CS and MDH genes during postharvest storage of GUANAY-1 soursop fruit. Full article

Background/Objectives: β-Glucosidases from lactic acid bacteria are valuable biocatalysts for carbohydrate conversion, flavour enhancement, and bioactive glycoside biotransformation. Although GH3 family enzymes have been characterized from several Lactobacillus species, no systematic study exists for Lentilactobacillus buchneri—a GRAS strain with plant-polysaccharide-degrading potential. This work aimed to clone, heterologously express, and comprehensively characterize a novel GH3 β-glucosidase (LbBgl3) from L. buchneri, with a particular focus on its catalytic properties, substrate profile, stability, and the unexpected EDTA-mediated thermostabilization mechanism. Methods: A novel β-glucosidase gene (LbBgl3) from L. buchneri was successfully expressed in Escherichia coli. Results: Biochemical characterization revealed that LbBgl3 is a cold-adapted, moderately acidophilic enzyme, exhibiting optimal activity at 37 °C and pH 5.0, with a maximum specific activity of 799.67 U·mg⁻¹. Under optimal conditions, the enzyme displayed kinetic parameters toward pNPG with a K_m of 1.697 mM, V_max of 442.5 μmol·mg⁻¹·min⁻¹, k_cat of 634.32 s⁻¹, and k_cat/K_m of 373.79 mM⁻¹·s⁻¹. LbBgl3 exhibited high salt tolerance, with activity peaking at ~140% at 0.5 M NaCl and retaining ~68% at 2.0 M NaCl, while showing sensitivity to glucose inhibition. Notably, EDTA significantly enhanced both the activity and stability of LbBgl3. At 50 mM, the relative activity increased to 161%, and stability at 25 °C was prolonged. Molecular docking simulations suggested that EDTA binds near the substrate-binding pocket, forming hydrogen bonds with Ala57, Gln766, Ser768, and Lys770, thereby stabilizing the local conformation and enhancing thermal resistance. Conclusions: This study presents the first characterization of a GH3 β-glucosidase from L. buchneri and reveals a non-classical stabilizing effect of EDTA, offering valuable insights for enzyme engineering and biocatalytic applications. Full article

GDSL esterases/lipases constitute a large and functionally versatile gene family in plants, yet their systematic characterization in bamboo—perennial woody grasses with exceptionally rapid shoot elongation—remains scarce. Here, we performed a genome-wide identification of the GDSL family in allohexaploid Dendrocalamus farinosus and characterized the function of a candidate gene in secondary wall synthesis. A total of 265 DfGDSL genes were identified and classified into nine clades; rice xylan deacetylases BS1 and DARX1 fell within Clade VIII, which harbors 75 members. Chromosomal distribution, exon–intron organization, conserved motifs, and collinearity analyses indicated that whole-genome and tandem duplications drove family expansion, with purifying selection as the predominant evolutionary force. Expression profiling across tissues and shoot developmental stages pinpointed DfGDSL58 as the sole highly expressed OsDARX1 homolog in D. farinosus, showing specific upregulation during rapid elongation (50–400 cm). Its promoter contains auxin-responsive elements, and exogenous NAA treatment significantly induced its expression, with a peak at 6 h. Heterologous overexpression of DfGDSL58 (designated DfDACX1) in tobacco increased plant height and basal diameter while reducing lignin and hemicellulose deposition, xylem width, and transcript levels of xylan synthase (NtIRX9) and lignin biosynthetic genes (NtC4H, NtCOMT, NtCAD), whereas cellulose content and cellulose synthase genes (NtCESA4, NtCESA7) remained largely unchanged. Collectively, these findings demonstrate that DfDACX1 negatively regulates secondary wall thickening and promotes longitudinal growth, likely via modulating xylan deacetylation and downstream lignin biosynthesis. This study presents the first systematic characterization of the GDSL family in D. farinosus and identifies DfDACX1 as a key modulator of the trade-off between cell wall deposition and rapid shoot elongation, offering mechanistic insights into bamboo’s extraordinary growth and a potential target for engineering plant architecture. Full article

The ban on antibiotic growth promoters in livestock production has created an urgent demand for safe and effective probiotic alternatives derived from indigenous animal microbiota. Here, we isolated Enterococcus hirae HI3 from Hu sheep jejunum and confirmed its species assignment via whole-genome sequencing, with ANI analysis showing 98.92% identity to the E. hirae reference genome. HI3 showed moderate acid tolerance, with survival rates of 19.31% (95% CI: 15.83–22.78%) at pH 2 and 18.40% (95% CI: 17.87–18.94%) at pH 3 after 4 h, and maintained > 50% survival in 2% bile salts. It was susceptible to penicillin, ampicillin, erythromycin, and chloramphenicol. No hemolytic activity was observed, and major enterococcal virulence genes (gelE, cyl, esp, hyl) were absent from the HI3 genome. The HI3 genome (3.06 Mb) consists of one circular chromosome and three circular plasmids. Functional annotation identified 229 carbohydrate metabolism genes (including 65 glycoside hydrolases) and 43 probiotic-related genes involved in acid tolerance (atpA–G, nhaC), bile salt tolerance (cbh), stress responses (clp family, groEL, dnaK, cspA, sod2), and adhesion (ltaS, srtA, eno, epsA). Multiple bacteriocin biosynthetic gene clusters (enterolysin A, class II lanthipeptide, etc.) were identified. Plasmid-borne tetracycline resistance genes tet(M) and tet(L) were detected; however, their functional transferability requires experimental validation. No other known transferable resistance determinants were identified in the genomic analysis. These in vitro and genomic findings represent an initial characterization of E. hirae HI3 and support its potential as a ruminant probiotic candidate. However, in vivo studies are required to validate its colonization capacity, safety, and efficacy in the target ruminant species. Full article

The seeds of Polygonatum sibiricum exhibit dormancy, which poses a major challenge for its cultivation. To elucidate the regulatory mechanisms underlying dormancy release, we performed integrated transcriptomic and metabolomic analyses on seeds at 0, 5, 10, and 15 d after seed imbibition. Physiological assays revealed progressive declines in abscisic acid (ABA) and starch levels, alongside increases in gibberellin (GA) and soluble sugar contents, reflecting the metabolic changes accompanying the transition from dormancy to germination. Transcriptomic analysis identified 11,520 expressed genes, with 6753, 7775 and 9387 differentially expressed genes (DEGs) at T5, T10, and T15, respectively. KEGG enrichment highlighted starch and sucrose metabolism and plant hormone signal transduction as key pathways. Notably, the GA biosynthesis gene GA3ox was markedly upregulated, while the DELLA repressor (Isoform0012761) showed sustained downregulation, suggesting relieved GA signaling. In the ABA pathway, CYP707A catabolic genes exhibited biphasic expression, and ABA signaling components (PYL, PP2C, SnRK2) showed stage-specific remodeling. A total of 316, 412, and 479 differentially expressed transcription factors were identified across stages, with the GRAS family being the largest. Co-expression network analysis revealed 19 transcription factors integrating starch/sucrose metabolism with ABA and GA signaling, most of which were downregulated, except one C2H2 member showing sustained upregulation. These findings demonstrate that dormancy release in P. sibiricum is governed by coordinated hormonal reprogramming, metabolic mobilization, and transcription factor-mediated regulation, providing a theoretical foundation for improving seed germination in this medicinal plant. Full article