Search Results (2,065)

Acinetobacter baumannii is an opportunistic pathogen notable for multidrug resistance and environmental persistence. We characterized a clinical isolate, HKAB-1, which exhibits pronounced virulence-associated traits despite being highly susceptible to all tested antibiotics. HKAB-1 exhibited superior growth in MH2B, serum and desiccating conditions, robust biofilm formation, and active motility. Whole-genome sequencing identified two heme utilization clusters, multiple siderophore biosynthesis pathways, and other virulence-associated genes. Gene expression analysis revealed significant upregulation of heme utilization and siderophore biosynthetic gene clusters under serum exposure, indicating activation of iron uptake pathways under host-like conditions. Biofilm-associated genes, including bap, PNAG biosynthetic genes, and type IV pili components, were notably upregulated in biofilm-forming cells, supporting their role in driving the enhanced biofilm phenotype. Conversely, adeB, encoding a major RND efflux pump, was markedly downregulated, potentially explaining its drug-susceptible phenotype. Comparative genomic analysis highlighted differences in genes related to nutrient transport, metabolic pathways, and membrane biogenesis that may underpin its enhanced growth. These findings point to a potential trade-off between antibiotic resistance and virulence, underscoring the importance of monitoring antibiotic-susceptible yet highly virulent A. baumannii isolates as potential reservoirs for resistance evolution. Further investigation is warranted to elucidate the mechanisms underlying this phenotypic balance. Full article

Tubular aggregate myopathy (TAM) is an inherited skeletal muscle disease associated with progressive muscle weakness, cramps, and myalgia. Tubular aggregates (TAs) are regular arrays of highly ordered and densely packed straight-tubules observed in muscle biopsies; the extensive presence of TAs represent a key histopathological hallmark of this disease in TAM patients. TAM is caused by gain-of-function mutations in proteins that coordinate store-operated Ca²⁺ entry (SOCE): STIM1 Ca²⁺ sensor proteins in the sarcoplasmic reticulum (SR) and Ca²⁺-permeable ORAI1 channels in the surface membrane. Here, we assessed the therapeutic potential of endurance exercise in the form of voluntary wheel running (VWR) in mitigating TAs and muscle weakness in Orai1^G100S/+ (GS) mice harboring a gain-of-function mutation in the ORAI1 pore. Six months of VWR exercise significantly increased specific force production, upregulated biosynthetic and protein translation pathways, and normalized both mitochondrial protein expression and morphology in the soleus of GS mice. VWR also restored Ca²⁺ store content, reduced the incidence of TAs, and normalized pathways involving the formation of supramolecular complexes in fast twitch muscles of GS mice. In summary, sustained voluntary endurance exercise improved multiple skeletal muscle phenotypes observed in the GS mouse model of TAM. Full article

Cytosine and its derivatives are an important research topic in the fields of bioorganic chemistry, molecular biology and medicine due to their key role in the structure and function of nucleic acids. The article provides a detailed overview of the natural occurrence of cytosine, its biosynthetic and degradation pathways in living organisms, as well as its physicochemical and chemical properties. Particular attention was paid to the biological activity and therapeutic applications of cytosine derivatives, including their use in cancer, antiviral and epigenetic therapy. The analytical section describes high-performance liquid chromatography techniques as a major tool for identifying and determining cytosine and its derivatives in biological samples. Examples of separation conditions, column selection, mobile phases and detection parameters for these compounds are presented. The article also provides chemical structures, graphs, comparative tables and an up-to-date review of the scientific literature, presenting a comprehensive overview of the topic, including biological, chemical and analytical aspects. Full article

Despite the great structural diversity, plant lignans, coumarins, and xanthones share numerous biological activities, ranging from antimicrobial, anti-inflammatory, and antioxidant to antineoplastic and neuroprotective. The compounds, products of the shikimic acid biosynthetic pathway, also play an important role in plant–environment interactions. In a search for sustainable and renewable sources of these valuable plant products, numerous in vitro culture systems were investigated, including hairy root cultures. The Rhizobium rhizogenes-transformed root cultures of over 40 plant species representing 17 families of the plant kingdom were studied in this respect. The present review focuses on the hairy roots that may be efficient producers of valuable plant products with the prospect of use in the pharmaceutical, food, or cosmetics industry. In vitro culture systems based on hairy roots, which were used to elucidate the biosynthesis pathways of the high-added-value plant compounds, were also considered. Full article

Long non-coding RNAs (lncRNAs) have emerged as pivotal regulators in plant immune responses, yet their roles in rice resistance against Magnaporthe oryzae (M. oryzae) remain inadequately explored. In this study, we integrated translatome data with conventional genome annotations to construct an optimized protein-coding dataset. Subsequently, we developed a robust pipeline (“RiceLncRNA”) for the accurate identification of rice lncRNAs. Using strand-specific RNA-sequencing (ssRNA-seq) data from the resistant (IR25), susceptible (LTH), and Nipponbare (NPB) varieties under M. oryzae infection, we identified 9003 high-confidence lncRNAs, significantly improving identification accuracy over traditional methods. Among the differentially expressed lncRNAs (DELs), those unique to IR25 were enriched in the biosynthetic pathways of phenylalanine, tyrosine, and tryptophan, which suggests that they are associated with the production of salicylic acid (SA) and auxin (IAA) precursors, which may be involved in defense responses. Conversely, DELs specific to LTH primarily clustered within carbon metabolism pathways, indicating a metabolic reprogramming mechanism. Notably, 21 DELs responded concurrently in both IR25 and LTH at 12 h and 24 h post-inoculation, indicating a synergistic regulation of jasmonic acid (JA) and ethylene (ET) signaling while partially suppressing IAA pathways. Weighted gene co-expression network analysis (WGCNA) and competing endogenous RNA (ceRNA) network analysis revealed that key lncRNAs (e.g., LncRNA.9497.1) may function as miRNA “sponges”, potentially influencing the expression of receptor-like kinases (RLKs), resistance (R) proteins, and hormone signaling pathways. The reliability of these findings was confirmed through qRT-PCR and cloning experiments. In summary, our study provides an optimized rice lncRNA annotation framework and reveals the mechanism by which lncRNAs enhance rice blast resistance through the regulation of hormone signaling pathways. These findings offer an important molecular basis for rice disease-resistant breeding. Full article

High hydrostatic pressure (HHP) significantly modulates microbial metabolism, while chemical epigenetic modifiers are known to reactivate silent biosynthetic gene clusters and induce novel natural products. However, the mechanisms by which these epigenetic modifiers regulate fungal responses under differential pressure conditions, and how such regulation affects natural product biosynthesis, remain completely unexplored. Here, we investigated the hadal fungus Alternaria alternata CIEL23 isolated from 7332 m sediments in the Mariana Trench under epigenetic modifier treatment with contrasting pressures (0.1 MPa vs. 40 MPa). Our results revealed that epigenetic perturbations and high pressure significantly altered fungal phenotypes, gene expression, and secondary metabolite composition. Transcriptome-level analysis of epigenetic regulatory mechanisms under epigenetic modifiers in both pressure conditions (0.1 MPa and 40 MPa) demonstrated that the addition of epigenetic modifiers regulated MAPK pathway-related gene expression in response to the environment stimuli. Under dual stress conditions, the IG, CWI, and HOG branches of the MAPK pathway showed significantly altered activity patterns. These changes were associated with differential the regulation of genes related to hyphal growth, cell wall remodeling, cell cycle progression, and osmolyte synthesis, suggesting the coordinated modulation of multiple cellular processes. These findings provide the mechanistic link between epigenetic modification induced HHP-response changes and regulation in hadal fungi. Our study not only advances understanding of hadal fungal response to dual stressors but also unlocks new possibilities for harnessing their stress-driven metabolic versatility for biotechnological applications. Full article

Anesthesia has emerged as a critical strategy for maintaining fish viability during transport, with natural anesthetics gaining increasing attention in recent research. The active ingredients in Laurus nobilis L. have antioxidant effects and reduce cell apoptosis. Studies have shown that they can upregulate expression of Nrf2 in mitochondrial biosynthetic factors. This study aimed to investigate the effects of laurel (Laurus nobilis) essential oil on oxidative stress and apoptosis mechanisms during the live transport of hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂). The addition of laurel essential oil during transport activated the Nrf2-Keap1 antioxidant pathway, resulting in up-regulated expression of catalase (cat) and superoxide dismutase (sod) genes. This led to increased enzymatic activity and reduced levels of oxidative stress markers. The mitigation of oxidative stress contributed to physiological stability by downregulating apoptotic gene expression (Bax, Caspase 8), reducing gill and liver tissue damage, and lowering the activity of hepatocyte damage markers aspartate aminotransferase (AST) and alanine aminotransferase (ALT). Metabolomic analysis revealed several key metabolic pathways affected during transport, with the FoxO signaling pathway demonstrating the most significant impact. Within this pathway, reduced glutamate levels appeared to inhibit apoptosis, while decreased ADP and AMP levels potentially influenced antioxidant capacity. The addition of laurel essential oil to transport water proved beneficial in reducing biochemical markers of stress responses in hybrid grouper during keep live transport. Full article

Background: Medicago ruthenica, a perennial legume forage valuable for ecological restoration and improved breeding, suffers significant harvest losses due to pod shattering. Pod shattering is a trait not only linked to not only pod ventral suture, but also pericarp properties. In this study, we aimed to (1) elucidate the role of pericarp in explosive pod shattering by comparing shattering-susceptible (SPD) and shattering-resistant (RPD) M. ruthenica genotypes, and (2) identify key regulatory genes and pathways underlying this mechanism. Methods: We conducted comparative analyses of pericarp anatomy and physiological traits (pericarp components such as water content, cellulose, hemicellulose, pectin, and lignin; and the activities of enzymes such as cellulose synthase A (CesA), phenylalanine ammonia-lyase (PAL), 4-coumarate: CoA ligase (4CL), cinnamyl alcohol dehydrogenase (CAD), and peroxidase (POD) in SPD and RPD pods). Transcriptome of pod pericarps identified differentially expressed genes (DEGs) for the selection of candidates functional genes. Promoter analysis was performed on candidate functional genes to identify specific regulated factors. The functional role of auxin signaling was validated through exogenous auxin application and the assessment of pod shattering rates and gene expression. Results: SPD pod pericarps exhibited significantly higher lignification of endocarp, lignin, cellulose, hemicellulose and pectin content, but lower water content than RPD. Principal component analysis identified that lignin contributes the highest loading value (0.727) contributor to pod shattering. The activities of five cell wall biosynthesis enzymes were higher in SPD pod pericarps than RPD. Transcriptome analysis identified more than 3419 DEGs in SPD pericarps. KEGG enrichment highlighted “phenylpropanoid biosynthesis” as the most significant pathway. A total of 57 lignin-biosynthesis-related DEGs were upregulated in SPD, including 15 PODs. Promoters of 11 POD genes contained MYB-binding motifs and 8 contained auxin-responsive elements, a total of 76 MYB transcription factors (mostly upregulated) and 9 auxin biosynthesis genes (mostly downregulated) were differentially expressed in SPD. Exogenous auxin application significantly reduced SPD pod shattering to 23.6% and concurrently downregulated PODs expression. Conclusions: This study establishes that enhanced lignification within the pericarp endocarp by the upregulation of lignin biosynthetic genes (particularly PODs), coupled with upregulation by MYB transcription factors and downregulation by auxin, is a core mechanism of explosive pod shattering in M. ruthenica. The identified DEGs, especially MYBs, PODs, and auxin pathway genes, provide gene information for breeding shattering-resistant M. ruthenica varieties through molecular design or marker-assisted selection. Full article

Background: Streptomyces bacteria are prolific producers of secondary metabolites (SMs), including many antibiotics. However, most biosynthetic gene clusters (BGCs) remain silent under laboratory conditions. Global transcriptional regulators, such as AdpA, can activate these BGCs, but their roles in secondary metabolism are not fully understood. This study investigates the regulatory function of AdpA in Streptomyces venezuelae (AdpA_Sv), a fast-growing model species and natural chloramphenicol producer that encodes over 30 BGCs. Methods: We applied RNA-seq and ChIP-seq at 12 and 20 h—corresponding to vegetative and aerial hyphae stages—to profile the AdpA_Sv regulatory network. Results: AdpA_Sv influenced the expression of approximately 3000 genes, including those involved in primary metabolism, quorum sensing, sulfur metabolism, ABC transporters, and all annotated BGCs, and it bound to around 200 genomic sites. Integration of RNA-seq and ChIP-seq data identified a core regulon of 49–91 directly regulated genes, with additional effects likely mediated indirectly via other transcription factors or non-canonical binding sites. Motif analysis confirmed similarity to the canonical Streptomyces griseus AdpA-binding sequence, with a novel 5-bp 3′ extension. AdpA_Sv directly regulated several SM pathways, including chloramphenicol biosynthesis, potentially alleviating Lsr2-mediated repression. Conclusions: This study defines, for the first time, the direct AdpA regulon in S. venezuelae and establishes AdpA_Sv as a central regulator of secondary metabolism. Our findings highlight S. venezuelae as a promising chassis strain for heterologous expression and suggest strategies for activating silent BGCs in other Streptomyces species. Full article

Xanthophylls are carotenoids with diverse roles in stress protection across all taxa of life. This review highlights chloroplast-localized xanthophylls (with a focus on zeaxanthin) of plants by presenting an overview of the protective effects of xanthophylls as well as the role of carotenoids as precursors of multiple plant stress hormones. It also examines the roles of xanthophylls and stress hormones in signaling cascades between the chloroplast and nuclear genes that control plant growth, development, and stress defenses. This overview addresses the biosynthetic pathways of xanthophylls and carotenoid-derived plant stress hormones, functions of xanthophylls in photoprotection of photosynthesis, carotenoids as essential human micronutrients, and roles of xanthophylls in membrane integrity. Attention is given to the involvement of zeaxanthin in both abiotic and biotic defense as well as its impact on components of the biotic defense system with contrasting targets. Examples for the multiple principal loops of signaling cascades between the chloroplast and nucleus, which are based on chloroplast redox state and modulated by xanthophylls, are summarized. This review integrates the role of chloroplast carotenoids in controlling light-use efficiency and providing photoprotection with their system-wide regulatory effects as precursors of carotenoid-derived plant stress hormones and modulators of chloroplast redox state. A better understanding of these connections is needed to guide development of plant lines with improved resilience and productivity in complex, changing, and challenging environments. Full article

Streptococcus mutans (S. mutans) is a cariogenic bacterium in the oral cavity that plays a significant role in plaque formation and dental caries. In previous research by our group, we showed that the endocannabinoid anandamide (AEA) has anti-bacterial and anti-biofilm activities against S. mutans. Here, we aimed to investigate its effects on S. mutans through metabolomics analyses. S. mutans was cultivated in the absence or presence of AEA at a sub-minimum inhibitory concentration (MIC), and changes in metabolites and metabolic pathways were assessed through liquid chromatography–mass spectrometry (LC-MS). Treatment of S. mutans using AEA at 10 µg/mL significantly disturbed the glycolytic flux in the bacteria, which was indicated by a reduced glucose uptake into the cell, suppression of key glycolytic intermediates, reduced acid production into the media, imbalance of NAD⁺/NADH, and decreased adenosine triphosphate (ATP) production. The disruption of carbohydrate metabolism impacts critical cellular processes, including energy production, redox balance, and biosynthetic pathways, leading to metabolic stress and impaired cellular function. These results highlight the mode of action of AEA as an antimicrobial agent. Altogether, these findings suggest that AEA has potential as a novel antimicrobial agent in the development of therapeutics against S. mutans. Full article

Lactiplantibacillus pentosus is a lactic acid bacterium frequently detected in various fermented foods; however, the genomic traits related to its biotechnological potential have been underexplored. In this study, 34 catalase-negative isolates were obtained from pickled mustard greens, among which strain P7 exhibited the highest exopolysaccharide (EPS) yield (781.9 ± 14.7 mg/L) and was capable of growing in a chemically defined medium lacking riboflavin. Whole-genome sequencing revealed a 3,749,478 bp circular chromosome with 46.5% G + C content and 3389 protein-coding genes. A phylogenomic analysis identified P7 as L. pentosus. Functionally, 1 mg/mL EPS extracted from P7 demonstrated strong antioxidant activity, with DPPH and hydroxyl radical scavenging capacities of 89.8 ± 4.6% and 76.5 ± 9.5%, respectively. The use of 0.2 mg/mL EPS also protected Saccharomyces cerevisiae cells from oxidative stress. A comparative genomic analysis indicated the presence of nearly complete biosynthetic pathways for riboflavin, folate, and pyridoxine. High-performance liquid chromatography (HPLC) confirmed the production of 23.8 ± 0.4 µg/mL riboflavin, 36.6 ± 0.6 µg/mL folic acid, and 0.42 ± 0.02 µg/mL pyridoxine in the culture supernatant, which have not been previously reported. Additionally, strain P7 produced 91.2 ± 12.3 g/L of lactic acid after 24 h of incubation. These results support the potential of L. pentosus P7 as a candidate for industrial applications in the production of EPS, B-group vitamins, and lactic acid. Full article

Background/Objectives: Anaerobic gut fungi (Neocallimastigomycota) are biotechnologically relevant, lignocellulose-degrading microbes with under-explored biosynthetic potential for secondary metabolites. Untargeted metabolomic profiling with gas chromatography–mass spectrometry (GC-MS) was applied to two gut fungal strains, Anaeromyces robustus and Caecomyces churrovis, to establish a foundational metabolomic dataset to identify metabolites and provide insights into gut fungal metabolic capabilities. Methods: Gut fungi were cultured anaerobically in rumen-fluid-based media with a soluble substrate (cellobiose), and metabolites were extracted using the Metabolite, Protein, and Lipid Extraction (MPLEx) method, enabling metabolomic and proteomic analysis from the same cell samples. Samples were derivatized and analyzed via GC-MS, followed by compound identification by spectral matching to reference databases, molecular networking, and statistical analyses. Results: Distinct metabolites were identified between A. robustus and C. churrovis, including 2,3-dihydroxyisovaleric acid produced by A. robustus and maltotriitol, maltotriose, and melibiose produced by C. churrovis. C. churrovis may polymerize maltotriose to form an extracellular polysaccharide, like pullulan. GC-MS profiling potentially captured sufficiently volatile products of proteomically detected, putative non-ribosomal peptide synthetases and polyketide synthases of A. robustus and C. churrovis. The triterpene squalene and triterpenoid tetrahymanol were putatively identified in A. robustus and C. churrovis. Their conserved, predicted biosynthetic genes—squalene synthase and squalene tetrahymanol cyclase—were identified in A. robustus, C. churrovis, and other anaerobic gut fungal genera. Conclusions: This study provides a foundational, untargeted metabolomic dataset to unmask gut fungal metabolic pathways and biosynthetic potential and to prioritize future efforts for compound isolation and identification. Full article

Nicotinamide mononucleotide, known as NMN, is an important nicotinamide adenine dinucleotide (NAD⁺) precursor. It is integral in cellular metabolism, energy generation, and processes associated with aging. Since NMN provides healthy value, it becomes a major focus for the biotechnological industry. This study presents a new biosynthetic pathway for producing NMN without limits on intracellular PRPP (5′-phosphoribosyl pyrophosphate) metabolic flux. The route started by converting cytidine into 1-phosphoribose via pyrimidine-nucleoside phosphorylase (PyNP), after transforming into nicotinamide riboside (NR) through either purine-nucleoside phosphorylase (XapA) or nicotinate riboside kinase (NRK). NR was phosphorylated by NRK in the presence of nicotinamide (NAM) to produce NMN. We established an in vitro enzyme activity verification system for the feasibility check. The optimization of multienzyme cascade reactions was figured out for the NMN biosynthesis. Finally, the enzymes of PyNP and NRK were expressed in the cytidine-producing strain; we established a de novo biosynthesis pathway from glucose to NMN, achieving a production titer of 33.71 mg/L at a shake-flask scale. Full article

Fish reproduction requires suitable salinity and temperature, as well as sufficient energy. This study investigated temperature and salinity effects on ovarian development of Lateolabrax maculatus and energy metabolism differences between reproduction and growth. Two salinities (4‰ and 30‰) and temperatures (18 ± 1 °C and 30 ± 1 °C) formed four treatments: SWNT (30‰, 30 ± 1 °C), SWLT (30‰, 18 ± 1 °C), FWLT (4‰, 18 ± 1 °C), and FWNT (4‰, 30 ± 1 °C). GSI and sex hormones (FSH, LH, E2, and 17α,20β-DHP) were measured. Transcriptome analysis explored how temperature and salinity regulate ovarian development in L. maculatus, while integrated transcriptomic and targeted energy metabolomic analyses revealed energy metabolism differences between ovary and muscle during this process. The results showed that low salinity (4‰) and low temperature (18 ± 1 °C) synergistically promoted ovarian development in the FWLT group, as indicated by a significant increase in GSI and elevated levels of key sex hormones (FSH, LH, E2, and 17α,20β-DHP). Transcriptome analysis showed that low temperature activated pathways involved in steroidogenesis, oocyte maturation, and meiosis, and genes such as ADCY6, PRKACB, CPEB4, FZD7-A, and CCND2 were significantly upregulated. Salinity changes mainly affected amino acid metabolism, cholesterol metabolism, and the insulin signaling pathway. Genes such as PCSK9 and CKM may regulate ovarian development by regulating hormone synthesis and energy metabolism. Comprehensive transcriptome and metabolome analyses show that glycolysis is downregulated and oxidative phosphorylation is upregulated in the ovary, suggesting that ovarian oogenesis tends to be energized by aerobic metabolism. The TCA cycle may be used more for providing biosynthetic precursors and facilitating the transport of substrates between the mitochondrion and the cytoplasm rather than just as a source of ATP. Muscle tissue relies primarily on glycolysis for rapid energy production and may redistribute energy to the gonads, prioritizing the energy needs of the ovaries and contributing to the dynamic balance between reproduction and growth. This study provides insights into the molecular mechanisms of how environmental factors regulate fish reproduction, providing a theoretical basis and potential molecular targets for the regulation of reproduction and optimization of aquaculture environments. Full article