Applied Biological Chemistry最新文献

Greenhouse gas emissions (GHG) are contributing significantly to climate change, particularly from rice paddy fields. However, agricultural management practices such as silicate application can mitigate GHG emissions by altering soil properties and microbial activities. Therefore, the study objective was to analyze the effects of silicate and different fertilizers on GHG emissions in rice paddy fields. The experimental design included five treatments: no fertilizer (NF), inorganic fertilizer (NPK), NPK with rice straw compost (NPKC), NPK with silicate fertilizer (NPKS), and NPK with both rice straw compost and silicate fertilizer (NPKCS). Results demonstrated that the combined application of silicate and compost fertilizers (NPKCS) reduced methane (CH₄) emissions by approximately 14.08% and significantly lowered nitrous oxide (N₂O) (37.15%) emissions compared to NPKC. Additionally, the rice yield increased under all treatments compared to the control (NF), with a greater yield observed under the NPKCS (158.14%). These results underscore the importance of the synergistic use of silicate with compost to mitigate GHG emissions and improve crop productivity.

Faecalibacterium prausnitzii is a predominant anaerobic bacterium in the human gut microbiome, contributing to host intestinal health through butyrate production and anti-inflammatory effects. The L2-6 strain serves as a representative model for genomic and metabolic research, with high potential for therapeutic modulation of the gut microbiota. Butyrate biosynthesis in this organism proceeds through the butyryl-CoA dehydrogenase (BCD) and electron transferring flavoprotein (Etf) system, which is a key enzymatic step linking fatty acid metabolism and redox equilibrium. So far, structural information on F. prausnitzii BCD has been lacking, limiting our mechanistic comprehension of its catalytic cycle. Here, we report the crystal structures of F. prausnitzii L2-6 BCD in both apo and FAD-bound states. The catalytic glutamate is positioned approximately 8.0 Å from the FAD isoalloxazine ring, suggesting that crotonyl-CoA likely enters through the space between E373 and the re-face of FAD. To compare the structure with other species, we obtained a modeling structure of BCD and Etf complexes in the Fp L2-6 strain. Comparative analysis with structurally characterized BCDs and Etf complexes from other butyrate-producing species reveals that F. prausnitzii L2-6 follows a similar electron transfer and catalytic cycle, reinforcing its role in energy conservation and redox balance under anaerobic conditions. These findings deepen our molecular understanding of butyrate metabolism in F. prausnitzii, with broader implications for host-microbiome interactions. Furthermore, the structural framework provided here can serve as a basis for future studies aiming to modulate butyrate production across strains, potentially informing the development of microbiome-based therapeutics.

Background

Ubiquitination, a crucial post-translational modification, plays a vital role in cancer progression. The present research focused on the function of ubiquitin-specific protease 13 (USP13) and its potential mechanism related to leucine-rich repeat-containing G-protein-coupled receptor 4 (LGR4) in cisplatin (DDP) resistance and ferroptosis of ovarian cancer (OC).

Methods

Real-time quantitative PCR and Western blotting were used for mRNA and protein detection. The half-maximal inhibitory concentration (IC50) of DDP was determined using CCK-8 assay. Cell proliferation, apoptosis, and migration were assessed through colony formation/EdU assays, flow cytometry, and transwell/wound healing assays, respectively. Ferroptosis was analyzed by detecting reactive oxygen species (ROS), malondialdehyde (MDA), glutathione (GSH), Fe²⁺ level and protein marker expression. Co-immunoprecipitation (Co-IP) assay was applied for protein interaction and ubiquitination analysis. Xenograft studies were constructed for in vivo research.

Results

LGR4 expression was increased in DDP-resistant OC tissues and cell lines. After LGR4 was downregulated, chemoresistance and malignant characteristics such as proliferation and migration were suppressed while ferroptosis was promoted in DDP-resistant OC cells. USP13 served as a deubiquitinating enzyme to enhance LGR4 protein stability. USP13 inhibition attenuated DDP resistance and promoted ferroptosis by targeting LGR4. LGR4 knockdown could enhance chemosensitivity of tumor tissues to DDP in mice.

Conclusion

These findings elucidated that USP13 stabilized LGR4 protein to regulate DDP resistance and ferroptosis in OC. Targeting the USP13/LGR4 axis represents a potential therapeutic strategy to overcome DDP resistance in OC.

Highlights

1. 1.

   LGR4 inhibition reduces chemoresistance and promotes ferroptosis in cisplatin-resistant ovarian cancer cells.

2. 2.

   USP13 stabilizes LGR4 protein by deubiquitination.

3. 3.

   LGR4 can reverse the effects of USP13 knockdown on cisplatin resistance and ferroptosis

Food waste contributes significantly to environmental challenges, such as greenhouse gas (GHG) emissions and soil and water contamination through conventional disposal methods. Converting food waste into food waste compost (FWC) offers an alternative that reduces GHG emissions and enriches soil carbon stocks, supporting sustainable agriculture. However, the high sodium (Na) levels in FWC can adversely impact soil health and crop growth. Therefore, the objective was to thoroughly investigate the effect of different amounts of FWC on soil chemical properties, soil carbon stock (SOC), nitrogen use efficiency (NUE), growth, and yield of Chinese cabbage over three crop seasons. The treatments included: ⅰ) No fertilization (NF), ⅱ) inorganic fertilization (NPK, control), ⅲ) NPK + FWC-1 time (FWC1, optimal amount of food waste compost), ⅳ) NPK + FWC-2 times (FWC2), and ⅴ) NPK + FWC-3 times (FWC3). The results showed that excessive FWC application decreased NUE (27.1%) and negatively affected cabbage yield. The FWC3 treatment during second and third crop seasons (CS) increased soil electrical conductivity (EC), Na content, and exchangeable sodium percentage (ESP). Initial FWC applications enhanced SOC stocks by 8.2%; however, continuous use declined SOC stocks. The FWC2 of the second CS increased the NUE and yield of Chinese cabbage, while growth improved in the FWC2 of the first CS. This study provides valuable insights into the balanced use of FWC to improve soil properties, crop growth, and soil carbon sequestration and promote sustainable agriculture.

Sarcopenia starts around age 40, with individuals losing more than 30% of muscle mass by age 70. Due to the absence of approved pharmacological treatments, current management primarily relies on exercise and protein supplementations. Schizonepeta tenuifolia is a medicinal plant commonly found in Korea, China, Japan and is traditionally used for headaches, colds and allergies. However, its preventive effect against sarcopenia have not yet been explored. This study to investigate whether the ethanol extract of Schizonepeta tenuifolia (DKB138) enhances muscle strength in a dexamethasone (DEX)-muscle atrophy mice model. The preventive effects of DKB138 against muscle atrophy were evaluated in DEX-induced models both in vitro and in vivo. In vitro, DEX-induced myotubes were assessed for cell viability to determine cytoprotective effects. In vivo, a DEX-induced muscle atrophy mouse model was used evaluate muscle strength and functional performance. Using UPLC and comparison with reference standards, seven components of DKB138 were identified. DKB138 effectively prevented DEX-induced death in C2C12 skeletal muscle cells. In vivo, mice treated with DKB138 exhibited 28.5% increase in grip strength (***p < 0.001) and a threefold significant increase in running distance (**p < 0.01) compared to the DEX-induced mice. Additionally, DKB138 treatment resulted in downregulation of Murf-1 and Atrogin mRNA while upregulating of MyoD mRNA expression. These finding demonstrate that DKB138 protects against DEX-induced muscle atrophy by suppressing muscle degradation factors and enhancing muscle strength. These results suggest that DKB138 has potential as functional food against muscle dysfunction and atrophy.

Graphical Abstract

This study aimed to investigate the anti-obesity effects of Lactobacillus fermentum TKSN02 and its role in modulating gut microbiota. Biochemical assays, tissue section analysis, and qPCR were employed to evaluate serum and tissue parameters in mice. Additionally, mRNA expression of specific microorganisms in fecal samples was measured to assess changes in gut microbiota composition. The results demonstrated that both L-carnitine and L. fermentum TKSN02 significantly reduced body weight in obese mice. These treatments also decreased liver and epididymal fat organ indices, and lowered serum and hepatic levels of ALT, AST, AKP, TC, TG, and LDL-C. Meanwhile, they increased HDL-C levels, as well as fecal contents of TC, TG, and total protein (TP). H&E staining revealed that L-carnitine and L. fermentum TKSN02 ameliorated obesity-induced liver tissue damage and reduced adipocyte hypertrophy and accumulation. qPCR analysis further indicated that both interventions upregulate the mRNA expression of CPT-1, LPL, PPAR-α, and CYP7A1, while downregulating PPAR-γ and C/EBPα in the liver of high-fat diet-fed mice. Moreover, they promoted the abundance of Bacteroidetes, Lactobacillus, and Bifidobacterium, but suppressed Firmicutes in the gut microbiota. Together, these results suggest that L-carnitine and L. fermentum TKSN02 exert anti-obesity effects, with the high-dose L. fermentum TKSN02 (TKSN02H) showing the most pronounced outcomes. In conclusion, L. fermentum TKSN02 may help control obesity by positively modulating gut microbiota.

Reactive oxygen species (ROS), particularly hydrogen peroxide (H₂O₂), are implicated in oxidative stress and kidney tubular injury. Daphne jejudoensis (DJ), a plant native to Jeju Island, has demonstrated anti-inflammatory properties, but its effects on kidney diseases remain unexplored. This study investigated the impact of DJ extract and its compounds, daphnin and daphnetin, on H₂O₂-induced cell death and ROS production in kidney proximal tubular HK-2 cells. Extracts from the DJ plant parts significantly enhanced cell viability in H₂O₂-exposed cells. The DJ leaf extract significantly reduced levels of superoxide anion and hydroxyl radical and prevented the decrease in superoxide dismutase (SOD) activity. Fractions from 70% ethanol DJ leaf extract exhibited protective effects against H₂O₂-induced injury, with the ethyl acetate fraction standing out for its ability to enhance antioxidant enzyme activities. Daphnin and daphnetin, major bioactive compounds of DJ extract, significantly increased cell viability and reduced ROS production in H₂O₂-exposed cells, restoring SOD and catalase activities. Conclusively, DJ extract and the main compounds, daphnin and daphnetin, protect kidney proximal tubular cells against H₂O₂-induced oxidative stress by reducing ROS production and enhancing antioxidant defenses. These findings suggest the potential therapeutic use of DJ in kidney diseases associated with oxidative stress.

Kale (Brassica oleracea) is a cruciferous vegetable known for health benefits, primarily due to sulforaphane, a compound with notable anticancer properties. Recently, we reported that the application of geraniol can significantly increase sulforaphane content in kale. However, the molecular mechanisms underlying this enhancement remain unexplored. In this study, we aimed to elucidate the metabolic pathways by which geraniol influences sulforaphane biosynthesis. Geraniol was applied as a 500-ppm solution, sprayed on the leaves of kale cultivated in an indoor aeroponic farm, once daily for two consecutive days, one week prior to harvest. As a result, we found that the sulforaphane content in the geraniol-treated group was 2.2 times higher than in the control group. Moreover, gene expression analysis demonstrated significant upregulation of CYP83, SUR1, and UGT, which are key genes involved in sulforaphane biosynthesis, with increases of 1.7, 1.3, and 1.1-fold, respectively, in the geraniol-treated group compared to the control group. These findings suggest that geraniol enhances sulforaphane content by upregulating genes critical to its biosynthesis.

Dysbiosis of the gut microbiota has increasingly been associated with atopic dermatitis (AD), a chronic inflammatory dermatological disorder. Butyrate, a short-chain fatty acid recognized for its significant anti-inflammatory capabilities, has garnered particular interest among gut microbial metabolites. The process that converts acetoacetyl-CoA to 3-hydroxybutyryl-CoA, which is important for making butyrate, is carried out by L26HBD, an enzyme from F. prausnitzii L2-6 that depends on NAD⁺. We determined the crystal structure of L26HBD in association with NAD⁺ and acetoacetyl-CoA to clarify the structural information of its catalytic action. The monomeric enzyme consists of two distinct domains: a C-terminal domain responsible for dimerization and an N-terminal Rossmann fold that binds NAD⁺. The enclosure of the active site arises from a significant conformational shift in the clamp-lid domain induced by substrate binding, with a root-mean-square deviation of 2.88 Å. The induced fit mechanism was corroborated by structural comparisons between the ligand-free and substrate-bound forms, revealing substrate-driven cavity contraction. Despite the identification of the acetoacetyl-CoA binding mechanism, electron density and B-factor measurements indicated that it exhibited lower stability compared to NAD⁺ binding. These findings enhance our understanding of butyrate biosynthesis in commensal gut bacteria by providing mechanistic insights into substrate detection and catalysis by L26HBD.

We investigated microbial community dynamics and potential pathogen persistence across treatment stages in a livestock manure treatment plant (LMTP) and a municipal wastewater treatment plant (WWTP). To quantify taxon-specific absolute abundances, we used quantitative microbiome profiling (QMP) by combining 16 S rRNA gene amplicon sequencing with quantitative PCR (qPCR) and 16 S rRNA gene copy number (16 S GCN) correction. The LMTP influent was enriched with fermentative and methanogenic taxa such as Candidatus Cloacamonas and Methanobrevibacter and showed a consistent decline in the total microbial load through successive stages. In contrast, the WWTP influent was dominated by gut-associated bacteria, including Lactococcus and Segatella. During sludge treatment and anaerobic digestion, genera such as Xylanibacter and Methanothermobacter became enriched. Functional predictions indicated that anaerobic chemoheterotrophy generally predominated from influent to effluent in both facilities. Although total microbial abundance decreased substantially in the final effluents, potentially pathogenic genera such as Moraxella, Acinetobacter, and Mycobacterium remained detectable at low levels. Integrating absolute abundance data with microbial profiling revealed significant taxon shifts that were missed by relative abundance analysis. These findings provide a more robust basis for assessing microbial dynamics and pathogen persistence, and offer practical insights for risk-based management of wastewater treatment processes.