Search Results (71)

Cardiovascular diseases remain a leading cause of morbidity and mortality worldwide, underscoring the need to better understand cardiovascular physiology. A key aspect involves identifying regulatory molecules that govern metabolic shifts. Forkhead box protein O1 (FoxO1) has emerged as a potential regulator; however, its role and underlying mechanisms remain unclear. This study investigated FoxO1 in metabolic adaptation using Wistar rats divided into age groups (fetal, postnatal day 1, postnatal day 7, adult) and treatment groups (control, hypoxia, FoxO1 inhibitor, combination). Hypoxia (12–14% O₂) and FoxO1 inhibitor (AS1842856, 10 mg/kgBW/day) were administered accordingly. Parameters assessed included hypoxia inducible factor 1 α (HIF-1α), FoxO1 mRNA and protein, glucose transporter type 1 (GLUT1), glucose transporter type 4 (GLUT4), cluster of differentiation 36 (CD36), hexokinase, pyruvate dehydrogenase kinase isoform 4 (PDK4), phosphoenolpyruvate carboxykinase (PEPCK), lactic acid, malonyl-CoA, carnitine palmitoyltransferase 1 (CPT1), citrate synthase, cytochrome c, and adenosine triphosphate (ATP). ATP production increased with age, associated with higher FoxO1 expression and metabolic shifts. Hypoxia in fetal hearts reduced HIF-1α and FoxO1. FoxO1 inhibition elevated glycolytic and oxidative markers. In conclusion, FoxO1 regulates glycolysis and lipid metabolism, offering insights into cardiac adaptation to hypoxia and potential therapeutic strategies. Full article

Microorganisms are increasingly being used for the industrial production of raw materials for food, chemical products and pharmaceuticals. The unconventional yeast Yarrowia lipolytica has a rising profile as a platform for industrial biotechnology. It has attractive physiological and metabolic properties, including high terpene and lipid production, high tolerance to complex environments, and amenability to genetic modification. Y. lipolytica naturally produces sufficient levels of cytosolic acetyl-CoA and malonyl-CoA to achieve lipid accumulation. Engineering biology methods allow transformation of these native metabolites into synthetic precursors for high-value compounds such as terpenes and flavonoids. Gene-editing, expression, and regulation tools have been developed for Y. lipolytica, facilitating improvement in bio-manufacturing yields for this chassis. This review summarizes natural product yields in Y. lipolytica and strategies for improving productivity. We highlight morphological engineering, metabolic engineering, and adaptive laboratory evolution as key strategies that can be used to improve the future yield, productivity and controllability of target molecules for Y. lipolytica engineering. Full article

Malonyl-CoA decarboxylase (MCD) is an enzyme that controls malonyl-CoA levels and regulates fatty acid synthesis and oxidation. Although its physiological relevance in peripheral tissues is well known, the role of MCD in the central nervous system remains poorly understood. MCD is expressed in mitochondria, cytosol, and peroxisomes and may be regulated by PPAR-α, AMPK, and SIRT4 in tissues such as muscle, liver and kidney. In the brain, MCD expression varies during development and can respond to nutritional states. Inherited MCD deficiency (malonic aciduria) leads to the toxic accumulation of malonic acid and predominantly affects the central nervous system. The underlying mechanisms leading to brain damage in MCD patients remain unclear. Conversely, pharmacological modulation of MCD activity has been studied in obesity, diabetes, and ischemic injury, highlighting its therapeutic potential. There are still major gaps regarding MCD cellular distribution, regulatory pathways, and metabolic interaction with CPT1c (carnitine palmitoyltransferase 1c) in neural metabolism. A deeper understanding of the role of MCD in brain physiology and pathology may indicate novel therapeutic strategies targeting metabolic disorders that involve altered malonyl-CoA dynamics. Here, we discuss the current knowns and unknowns regarding MCD physiology, regulation, and pathophysiology, emphasizing brain aspects. Full article

The evolution of type I polyketide synthase (T1PKS) assembly lines remains poorly understood. Through systematic mining of polyene biosynthetic gene clusters, we identified a novel eurocidin biosynthetic pathway capable of producing identical compounds with divergent loading module architectures, thereby capturing an evolutionary transitional state. Biochemical analysis revealed unprecedented functional reprogramming of acyltransferase (AT) domains, shifting substrate specificity from extender units (malonyl-CoA) to starter units (acyl-CoA). This paradigm shift enables direct initiation of polyketide chain assembly via AT-mediated loading of starter units, thereby elucidating the origin of extant AT-initiated assembly lines and establishing AT functional plasticity as a novel mechanism for polyketide structural diversification. Parallel evolution of ketosynthase (KS) domains through KSS→KSQ mutations further diversified initiation strategies. Applying this evolutionary insight, we engineered the candicidin pathway by replacing its native aromatic-starting bimodule with a starter-selective monomodule from eurocidin, generating aliphatic-starting analogs. This demonstrates that evolution-inspired AT reprogramming provides a rational framework for modifying polyketide starter units, expanding structural diversity, and enhancing therapeutic potential. Full article

In modern bioinformatics, the analysis of high-dimensional data (genomic, metabolomic, etc.) remains a critical challenge due to the “curse of dimensionality,” where feature redundancy reduces classification efficiency and model interpretability. This study introduces a novel method, AIMarkerFinder (v0.1.0), for analyzing metabolomic data to identify key biomarkers. The method is based on a denoising autoencoder with an attention mechanism (DAE), enabling the extraction of informative features and the elimination of redundancy. Experiments on glioblastoma and adjacent tissue metabolomic data demonstrated that AIMarkerFinder reduces dimensionality from 446 to 4 key features while improving classification accuracy. Using the selected metabolites (Malonyl-CoA, Glycerophosphocholine, SM(d18:1/22:0 OH), GC(18:1/24:1)), the Random Forest and Kolmogorov–Arnold Networks (KAN) models achieved accuracies of 0.904 and 0.937, respectively. The analytical formulas derived by the KAN provide model interpretability, which is critical for biomedical research. The proposed approach is applicable to genomics, transcriptomics, proteomics, and the study of exogenous factors on biological processes. The study’s results open new prospects for personalized medicine and early disease diagnosis. Full article

Background/Objectives: In this work, a series of six new indazole-benzimidazole hybrids (M1–M6) were designed, synthesized, and fully characterized. The design of these compounds was based on the combination of two pharmacophoric units, indazole and benzimidazole, both known for their broad spectrum of biological activities. Methods: The molecular hybridization strategy was planned to combine these scaffolds through an effective synthetic pathway, using 6-nitroindazole, two 2-mercaptobenzimidazoles, and 1,3- or 1,5-dihaloalkanes as key precursors, affording the desired hybrids in good yields and with enhanced biological activity. Quantum chemical calculations were performed to investigate the structural, electronic, and electrostatic properties of M1–M6 molecules using Density Functional Theory (DFT) at the B3LYP/6-311++G(d,p) level. The antimicrobial activity efficacy of these compounds was assessed in vitro against four Gram-positive bacteria (Staphylococcus aureus, Enterococcus faecalis, Bacillus cereus, and Lactobacillus plantarum), four Gram-negative bacteria (Salmonella enteritidis, Escherichia coli, Campylobacter coli, Campylobacter jejuni), and four fungal strains (Saccharomyces cerevisiae, Candida albicans, Candida tropicalis, and Candida glabrata) using ampicillin and tetracycline as reference standard drugs. Results: Among the series, compound M6 exhibited remarkable antimicrobial activity, with minimum inhibitory concentrations (MIC) of 1.95 µg/mL against S. cerevisiae and C. tropicalis, and 3.90 µg/mL against S. aureus, B. cereus, and S. enteritidis, while the standards Ampicillin (AmB) (MIC ≥ 15.62 µg/mL) and Tetracycline (TET) (MIC ≥ 7.81 µg/mL) exhibited higher MIC values. To gain molecular insights into the compounds, an in silico docking study was performed to determine the interactions of M1–M6 ligands against the antimicrobial target beta-ketoacyl-acyl carrier protein (ACP) synthase III complexed with malonyl-COA (PDB ID: 1HNJ). Molecular modeling data provided valuable information on the structure-activity relationship (SAR) and the binding modes influencing the candidate ligand-protein recognition. Amino acid residues, such as Arg249, located in the solvent-exposed region, were essential for hydrogen bonding with the nitro group of the 6-nitroindazole moiety. Furthermore, polar side chains such as Asn274, Asn247, and His244 participated in interactions mediated by hydrogen bonding with the 5-nitrobenzimidazole moiety of these compound series. Conclusions: The hybridization of indazole and benzimidazole scaffolds produced compounds with promising antimicrobial activity, particularly M6, which demonstrated superior potency compared to standard antibiotics. Computational and docking analyses provided insights into the structure–activity relationships, highlighting these hybrids as potential candidates for antimicrobial drug development. Full article

Lipopolysaccharide (LPS) is an essential component of the outer membrane (OM) of Gram-negative bacteria, and its levels are tightly co-regulated with phospholipid (PL) amounts. This homeostatic regulation necessitates the involvement of numerous genes, including lapD in a poorly defined manner. To understand the function of LapD, we took advantage of the synthetic lethal phenotype conferred by the concomitant absence of LapD and myristoyltransferase LpxM or heptosyltransferase WaaC and isolated extragenic suppressors that could bypass this lethality. Suppressor analyses of Δ(lapD lpxM) bacteria identified five single amino acid exchanges in AccA and two in each of AccC and AccD. These proteins comprise different subunits of the acetyl-CoA carboxylase complex, which catalyzes the rate-limiting step in the initiation of fatty acid synthesis, mediating the conversion of acetyl-CoA to malonyl-CoA. Fatty acid analysis revealed that these mutations restored the ratio of saturated to unsaturated fatty acids and repressed elevated PL levels. Suppressor analyses of Δ(lapD waaC) identified a single amino acid substitution in LptD, which is required for LPS assembly in the OM, and in NlpI, which regulates the amount of peptidoglycan hydrolase MepS. These results posit LapD as the point of critical regulation of homeostatic control of three essential cell envelope components. Full article

The introduction of heterologous pathways into microbial cell compartments offers several potential advantages, including increasing enzyme concentrations and reducing competition with native pathways, making this approach attractive for producing complex metabolites like fatty acids and fatty alcohols. However, measuring subcellular concentrations of these metabolites remains technically challenging. Here, we explored 3-hydroxypropionic acid (3-HP), readily quantifiable and sharing the same precursors—acetyl-CoA, NADPH, and ATP—with the above-mentioned products, as a reporter metabolite for peroxisomal engineering in the yeast Komagataella phaffii. To this end, the malonyl-CoA reductase pathway for 3-HP production was targeted into the peroxisome of K. phaffii using the PTS1-tagging system, and further tested with different carbon sources. Thereafter, we used compartmentalized 3-HP production as a reporter system to showcase the impact of different strategies aimed at enhancing the peroxisomal NADPH pool. Co-overexpression of genes encoding a NADPH-dependent redox shuttle from Saccharomyces cerevisiae (IDP2/IDP3) significantly increased 3-HP yields across all substrates, whereas peroxisomal targeting of the S. cerevisiae NADH kinase Pos5 failed to improve 3-HP production. This study highlights the potential of using peroxisomal 3-HP production as a biosensor for evaluating peroxisomal acetyl-CoA and NAPDH availability by simply quantifying 3-HP, demonstrating its potential for peroxisome-based metabolic engineering in yeast. Full article

Bibenzyl compounds are one of the most important bioactive components of natural medicine. However, Dendrobium officinale as a traditional herbal medicine is rich in bibenzyl compounds and performs functions such as acting as an antioxidant, inhibiting cancer cell growth, and assisting in neuro-protection. The biosynthesis of bibenzyl products is regulated by bibenzyl synthase (BBS). In this study, we have cloned the cDNA gene of the bibenzyl synthase (DoBS1) from D. officinale using PCR with degenerate primers, and we have identified a novel type III polyketide synthase (PKS) gene by phylogenetic analyses. In a series of perfect experiments, DoBS1 was expressed in Escherichia coli, purified and some catalytic properties of the recombinant protein were investigated. The molecular weight of the recombinant protein was verified to be approximately 42.7 kDa. An enzyme activity analysis indicated that the recombinant DoBS1-HisTag protein was capable of using 4-coumaryol-CoA and 3 malonyl-CoA as substrates for dihydroresveratrol (DHR) in vitro. The Vmax and Km of the recombinant protein for DHR were 3.57 ± 0.23 nmol·min⁻¹·mg⁻¹ and 0.30 ± 0.08 mmol, respectively. The present study provides further insights into the catalytic mechanism of the active site in the biosynthetic pathway for the catalytic production of dihydroresveratrol by bibenzylase in D. officinale. The results can be used to optimize a novel biosynthetic pathway for the industrial synthesis of DHR. Full article

Diets containing higher-amylose-content starches were proved to have some beneficial effects on monogastric animals, such as promoting the proliferation of intestinal probiotics. However, current research on the effects of diets with different starch sources on animals at the extraintestinal level is still very limited. We hypothesized that diets with different starch sources may affect lipid-related gene expression and metabolism in the liver of pigs. This study aimed to use adult pig models to evaluate the effects of diets with different starch sources (tapioca starch, TS; pea starch, PS) on the liver gene expressions and metabolism. In total, 48 growing pigs were randomly assigned to the TS and PS diets with 8 replicate pens/group and 3 pigs per pen. On day 44 of the experiment, liver samples were collected for metabolome and transcriptome analysis. Metabolome data suggested that different starch sources affected (p < 0.05) the metabolic patterns of liver. Compared with the TS diet, the PS diet increased (p < 0.05) some unsaturated fatty acids and several amino acids or peptide levels in the liver of pigs. Moreover, transcriptome data indicated the PS diets elevated (p < 0.05) fatty acid β-oxidation-related gene expression in the liver of pigs, and reduced (p < 0.05) unsaturated fatty acid metabolism-related gene expression. The results of quantitative real-time PCR confirmed that the PS diet upregulated (p < 0.05) the expression of acyl-CoA dehydrogenase very long chain (ACADVL), carnitine palmitoyl transferase (CPT) 1A, and malonyl-CoA decarboxylase (MLYCD), and downregulated (p < 0.05) the expression level of cytochrome P450 2U1 (CYP2U1) and aldehyde dehydrogenase 1B1 (ALDH1B1) in the liver. In addition, the results of a Mantel test indicated the muscle fatty acids were significantly closely correlated (p < 0.05) with liver gene expressions and metabolites. In summary, these findings suggest that diets containing higher amylose starches improved the lipid degradation and the unsaturated fatty acid levels in pig livers, and thus can generate some potential beneficial effects (such as anti-inflammatory and antioxidant) on pig health. Full article

Isoflavones belong to the class of flavonoid compounds, which are important secondary metabolites that play a crucial role in plant development and defense. Acetyl-CoA carboxylase (ACCase) is a biotin-dependent enzyme that catalyzes the conversion of Acetyl-CoA into Malonyl-CoA in plants. It is a key enzyme in fatty acid synthesis and also catalyzes the production of various secondary metabolites. However, information on the ACC gene family in the soybean (Glycine max L. Merr.) genome and the specific members involved in isoflavone biosynthesis is still lacking. In this study, we identified 20 ACC family genes (GmACCs) from the soybean genome and further characterized their evolutionary relationships and expression patterns. Phylogenetic analysis showed that the GmACCs could be divided into five groups, and the gene structures within the same groups were highly conserved, indicating that they had similar functions. The GmACCs were randomly distributed across 12 chromosomes, and collinearity analysis suggested that many GmACCs originated from tandem and segmental duplications, with these genes being under purifying selection. In addition, gene expression pattern analysis indicated that there was functional divergence among GmACCs in different tissues. The GmACCs reached their peak expression levels during the early or middle stages of seed development. Based on the transcriptome and isoflavone content data, a weighted gene co-expression network was constructed, and three candidate genes (Glyma.06G105900, Glyma.13G363500, and Glyma.13G057400) that may positively regulate isoflavone content were identified. These results provide valuable information for the further functional characterization and application of GmACCs in isoflavone biosynthesis in soybean. Full article

A growing number of studies indicate that mitochondrial dysfunction serves as a pathological mechanism for periodontitis. Therefore, this two-sample Mendelian randomization (MR) study was carried out to explore the causal associations between mitochondrial biological function and periodontitis, because the specific nature of this causal relationship remains inconclusive in existing MR studies. Inverse variance weighting, Mendelian randomization-Egger, weighted mode, simple mode, and weighted median analyses were performed to assess the causal relationships between the exposure factors and periodontitis. The results of the present study revealed a causal association between periodontitis and medium-chain specific acyl-CoA dehydrogenase (MCAD), malonyl-CoA decarboxylase (MLYCD), glutaredoxin 2 (Grx2), oligoribonuclease (ORN), and pyruvate carboxylase (PC). Notably, MCAD and MLYCD are causally linked to periodontitis, and serve as protective factors. However, Grx2, ORN, and PC function as risk factors for periodontitis. Our study established a causal relationship between mitochondrial biological function and periodontitis, and such insights may provide a promising approach for treating periodontitis via mitochondrial regulation. Full article

Microbial melanins are a group of pigments with protective effects against harsh conditions, showing fascinating photoprotective activities, mainly due to their capability to absorb UV radiation. In bacteria, they are produced by the oxidation of L-tyrosine, generating eumelanin and pheomelanin. Meanwhile, allomelanin is produced by fungi through the decarboxylative condensation of malonyl-CoA. Moreover, melanins possess antioxidant and antimicrobial activities, revealing significant properties that can be used in different industries, such as cosmetic, pharmaceutical, and agronomical. In agriculture, melanins have potential applications, including the development of new biological products based on this pigment for the biocontrol of phytopathogenic fungi and bacteria to reduce the excessive and toxic levels of agrochemicals used in fields. Furthermore, there are possibilities to develop and improve new bio-based pesticides that control pest insects through the use of melanin-producing and toxin-producing Bacillus thuringiensis or through the application of melanin to insecticidal proteins to generate a new product with improved resistance to UV radiation that can then be applied to the plants. Melanins and melanin-producing bacteria have potential applications in agriculture due to their ability to improve plant growth. Finally, the bioremediation of water and soils is possible through the application of melanins to polluted soils and water, removing synthetic dyes and toxic metals. Full article

The marine Streptomyces harbor numerous biosynthetic gene clusters (BGCs) with exploitable potential. However, many secondary metabolites cannot be produced under laboratory conditions. Co-culture strategies of marine microorganisms have yielded novel natural products with diverse biological activities. In this study, we explored the metabolic profiles of co-cultures involving Streptomyces sp. 2-85 and Cladosporium sp. 3-22—derived from marine sponges. Combining Global Natural Products Social (GNPS) Molecular Networking analysis with natural product database mining, 35 potential antimicrobial metabolites annotated were detected, 19 of which were exclusive to the co-culture, with a significant increase in production. Notably, the Streptomyces-Fungus interaction led to the increased production of borrelidin and the discovery of several analogs via molecular networking. In this study, borrelidin was first applied to combat Saprolegnia parasitica, which caused saprolegniosis in aquaculture. We noted its superior inhibitory effects on mycelial growth with an EC₅₀ of 0.004 mg/mL and on spore germination with an EC₅₀ of 0.005 mg/mL compared to the commercial fungicide, preliminarily identifying threonyl-tRNA synthetase as its target. Further analysis of the associated gene clusters revealed an incomplete synthesis pathway with missing malonyl-CoA units for condensation within this strain, hinting at the presence of potential compensatory pathways. In conclusion, our findings shed light on the metabolic changes of marine Streptomyces and fungi in co-culture, propose the potential of borrelidin in the control of aquatic diseases, and present new prospects for antifungal applications. Full article

Resveratrol, a phenylpropanoid compound, exhibits diverse pharmacological properties, making it a valuable candidate for health and disease management. However, the demand for resveratrol exceeds the capacity of plant extraction methods, necessitating alternative production strategies. Microbial synthesis offers several advantages over plant-based approaches and presents a promising alternative. Yarrowia lipolytica stands out among microbial hosts due to its safe nature, abundant acetyl-CoA and malonyl-CoA availability, and robust pentose phosphate pathway. This study aimed to engineer Y. lipolytica for resveratrol production. The resveratrol biosynthetic pathway was integrated into Y. lipolytica by adding genes encoding tyrosine ammonia lyase from Rhodotorula glutinis, 4-coumarate CoA ligase from Nicotiana tabacum, and stilbene synthase from Vitis vinifera. This resulted in the production of 14.3 mg/L resveratrol. A combination of endogenous and exogenous malonyl-CoA biosynthetic modules was introduced to enhance malonyl-CoA availability. This included genes encoding acetyl-CoA carboxylase 2 from Arabidopsis thaliana, malonyl-CoA synthase, and a malonate transporter protein from Bradyrhizobium diazoefficiens. These strategies increased resveratrol production to 51.8 mg/L. The further optimization of fermentation conditions and the utilization of sucrose as an effective carbon source in YP media enhanced the resveratrol concentration to 141 mg/L in flask fermentation. By combining these strategies, we achieved a titer of 400 mg/L resveratrol in a controlled fed-batch bioreactor. These findings demonstrate the efficacy of Y. lipolytica as a platform for the de novo production of resveratrol and highlight the importance of metabolic engineering, enhancing malonyl-CoA availability, and media optimization for improved resveratrol production. Full article