3 Biotech最新文献

A novel Streptomyces violaceoruber strain BM-41, isolated from shellfish aquaculture waste, demonstrated potent chitinolytic activity (2.362 U/mL). Whole-genome sequencing revealed a 7.83 Mb genome (72.6% GC) encoding 238 carbohydrate-active enzymes (CAZymes), with 75 glycoside hydrolases (GHs). Significantly, seven chitinase genes were identified: six GH18 family members (ChiA-ChiF) and one GH19 member (Chi2a), displaying greater genetic diversity than S. albidoflavus ATCC 27,414 (45 GHs). Fermentation optimization via single-factor experiments and Box-Behnken response surface methodology yielded optimal enzyme production conditions: 4.5% colloidal chitin, 7 g/L yeast extract, 0.3 g/L MgSO₄, pH 5.0, 30 ℃, and 30% medium volume. This enhanced chitinase activity 2.37-fold (from 0.995 to 2.362 U/mL). Enzymatic characterization showed optimal activity at pH 5.0 and 50 ℃, stability across pH 4-8, and ion-specific modulation: Mg²⁺ and K⁺ increased activity by 25-30%, whereas Cu²⁺ strongly inhibited catalysis. Genomic analysis uncovered a synergistic degradation pathway involving extracellular chitinases (ChiA-ChiF) and 10 key metabolic enzymes, including N-acetylglucosaminidases (EC 3.2.1.52), deacetylases (EC 3.5.1.25), and UDP-N-acetylglucosamine pyrophosphorylases (EC 2.7.7.23). This enzymatic network facilitates efficient conversion of chitin to N-acetylglucosamine monomers and downstream metabolites. The findings contribute to the understanding of S. violaceoruber BM-41 genomic features and its potential as a source of industrially relevant enzymes.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04634-6.

Hydroxynitrile lyases (HNLs) are stereoselective biocatalysts that catalyze the addition of hydrogen cyanide to carbonyl compounds, yielding enantiopure cyanohydrins-valuable intermediates in pharmaceutical and agrochemical synthesis. Recent advances have expanded our understanding of HNLs across multiple dimensions, including their evolutionary origins, structural diversity, and catalytic mechanisms. High-throughput screening methods have accelerated the discovery and functional assessment of novel HNLs from diverse biological sources, revealing enzymes from lipocalin, α + β barrel, and cupin superfamilies. Structural and mechanistic studies have elucidated active site architectures, enabling rational design and protein engineering for improved stability, substrate scope, and catalytic efficiency. Recombinant expression systems now support scalable production and purification, while immobilization techniques enhance enzyme reusability for industrial applications. HNLs have proven especially valuable in the asymmetric synthesis of cyanohydrins under mild, environmentally friendly conditions. This review highlights recent progress in HNL research, emphasizing innovations in enzyme discovery, engineering, and application, while outlining key challenges and future directions for integrating HNLs into sustainable biocatalytic processes.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04653-3.

Rice microbiome plays a critical role in the growth, health, stress tolerance, nutrient uptake, root development, and productivity of its host. In this study, advanced machine learning algorithms were applied to analyze the genomic data from 1365 rice-associated bacteria sourced from Bacterial and Viral Bioinformatics Resource Center (BV-BRC) database. After filtering, the genomic data of 280 organisms were selected and annotated to identify their respective genes. These were further categorized into ortholog groups, and based on the presence and absence of the ortholog groups, the organisms were clustered into eight groups. Genes encoding amino acid transport, inorganic ion transport and metabolism were the most common Clusters of Orthologous Genes (COG) categories observed across the various clusters while cellular process, biological regulation, and response to stimuli were the most common gene ontology terms. However, the presence of a large proportion of genes having unknown functions suggests the distribution of novel genes which could facilitate the functions including the plant colonization. Further to this, machine learning models were used to classify the organisms as either beneficial or pathogenic. Here, Support Vector Machine based analysis showed the highest accuracy (92.98%) when compared to the Logistic Regression (90.16%) and Random Forest (57.80%). From the analysis, ABC-type transporters such as ABC-type oligopeptide transport system were more abundantly distributed in beneficial bacteria. On the other hand, transposase such as Transposase InsA were observed to be common among pathogenic strains. From the results obtained, the presence of genes responsible for the nutrient transport and metabolic versatility was found to be significant for the beneficial bacteria, while the genetic variability was remarkable for the pathogens. The information generated in this study hence highlights the power of AI for predicting the beneficial interactions between the rice and its microbiome, and thereby offer its applications in enhancing the crop resilience and productivity for the sustainable agricultural practices.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04665-z.

Statins are widely used in the treatment of hyperlipidemia; however, their specific mechanisms of action remain incompletely understood. To identify key therapeutic targets, we integrated differential expression analysis with machine learning and identified IL27RA as a pivotal candidate. IL27RA expression was significantly upregulated in atorvastatin-treated hyperlipidemia patients compared to healthy controls but decreased following statin intervention. Functional enrichment analysis revealed its association with immune-related pathways, and consistent with this, immune infiltration analysis showed significant correlations between IL27RA expression and the abundance of Th1 and plasmacytoid dendritic cells. Molecular docking and dynamics simulations further confirmed stable binding between IL27RA and atorvastatin. Collectively, these results establish IL27RA as a key therapeutic target for statins in hyperlipidemia and highlight its role in modulating the immune microenvironment.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04668-w.

Angiogenesis plays a crucial role in cancer progression. However, the role of PARP1 in regulating chromatin remodelers and activating pro-angiogenic factors in cancer stem cells (CSCs) remains poorly understood. This study systematically investigates the detailed molecular mechanism through which PARP1 and its associated chromatin remodelers, P300 and GCN5, regulate angiogenesis in ex vivo patient-derived oral mucosa cancer stem cells (PD-OMCSCs). To investigate this mechanism, we used a combination of experimental approaches, including CAM assays, tube formation assays, biochemical analyses (western blot, gelatin zymography, and ELISA), molecular imaging (tissue immunofluorescence), and protein-protein interaction (co-immunoprecipitation and in silico study). Comparative analyses revealed significantly higher expression of PARP1, P300, and GCN5 in oral cancer tissues compared to normal ones. Co-immunoprecipitation and docking studies confirmed their mutual interactions, forming a chromatin-remodeling complex (PARP1-P300-GCN5) that facilitates angiogenic gene activation and expression. Quinacrine (QC), in combination with PARP inhibitor Talazoparib, disrupted this complex, leading to significant downregulation of VEGFA expression, reduced MMP activity, and suppression of angiogenic markers (Ang-1, Ang-2, TGF-β, CXCL-12, VEGFC, HIF-1α, and IL-6). These effects collectively impaired endothelial cell tube formation and blood vessel development in both HUVECs and CAM models. Furthermore, individual knockdown of PARP1, P300, or GCN5 reduced VEGFA expression, indicating their important role in regulating tumor angiogenesis. In conclusion, the QC and Talazoparib combination effectively prevents the activation and secretion of angiogenic factors, thereby suppressing angiogenesis, and may serve as a promising therapeutic approach for oral cancer by targeting PARP1 and associated chromatin remodelers.

This investigation was intended to prepare lipid-polymer hybrid nanoparticles (LPHNPs) that are laden with Gemcitabine hydrochloride (GEM) for the controlled delivery to treat Hepatocellular carcinoma (HCC). LPHNPs were developed by the solvent evaporation technique employing polycaprolactone (PCL) as the biodegradable polymeric core and a phospholipid shell comprised of soya phosphatidylcholine (SPC) and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine (DSPE). This study presents a cost-effective, simple method for functionalizing LPHNPs with the carbohydrate ligand D-galactose (GA) using stearyl amine (SA) as a linker. To examine the impact of three independent factors on the particle size, percent entrapment efficiency (% EE), and percent drug loading (% DL), a three-factor, three-level Box-Behnken design (BBD) was implemented with Design-Expert 13 software. The nanoparticles' size range increased from 194.1 to 505.3 nm when the polymer content increased. GEM's percent drug release profile in the galactose functionalized gemcitabine-loaded lipid-polymer hybrid nanoparticles (GEM-LPHNPs-GA) suggests they are appropriate candidates for targeting the tumors microenvironment. In vitro drug release tests revealed a higher GEM release at pH 5.5 compared to the physiological pH of 7.4 for 48 h. Fourier transform infrared spectroscopy (FTIR) and proton nuclear magnetic resonance (¹H-NMR) spectroscopy verified that the conjugate GA-SA imine bond formed. The cytotoxicity of GEM-LPHNPs-GA was significantly greater than that of GEM-LPHNPs or GEM alone, as evidenced by the MTT assay conducted on HepG2 cells. Throughout the incubation period, HepG2 cells exhibit a markedly higher absorption of dye-loaded LPHNPs-GA than LPHNPs. GEM-LPHNPs-GA is an efficacious formulation for the targeted administration of anti-cancer therapeutics.

Petroleum refinery wastewater (PRWW) with 4% salinity was subjected to treatment and simultaneous generation of energy in air cathode-microbial fuel cell (MFC). Substrate load (SL) such as 0.41 gCOD/L, 0.84 gCOD/L, 1.26 gCOD/L, 1.78 gCOD/L and 2.25 gCOD/L was trialed in air cathode MFC. COD (chemical oxygen demand) reduction was 88% (total COD) and 87% (soluble COD) at optimized SL of 1.78 gCOD/L. Corresponding power and current density derived at optimized SL of 1.78 gCOD/L was 879 mW/m² and 1052 mA/m² respectively. Degradation of low and high molecular weight petroleum hydrocarbons in the PRWW was greater than 90% to 100%  and 71% to 82% respectively. Supplementation with a mild nutritional substrate in PRWW accelerated the hydrocarbon biodegradation with time reduction in MFC operated at 1.78 gCOD/L SL. Phylogenetic analysis revealed the dominancy of exo-electrogenic halophilic strains such as Ochrobactrum, Marinobacter, Bacillus and Stenotrophomonas in the reactor. Thus the bioaugmentation of halophiles in MFC efficiently treated PRWW and harvested bioenergy under saline condition.

[This corrects the article DOI: 10.1007/s13205-025-04587-w.].

The genomic characterization of phages is fundamental to the development of an effective phage therapy strategy for clinically important bacteria. This study is aimed at isolating and characterizing vB_PaeS_TUMS_P6, a new lytic Pseudomonas phage. The whole-genome sequencing revealed that it contains a Linear dsDNA genome of 73,885 bp with a G + C content of 53.5% and 106 predicted coding sequences. Genes related to virulence or lysogeny behavior were not found in the genome, so it is potentially safe in regard to therapeutic applications. Genomic and phylogenetic analysis indicated that vB_PaeS_TUMS_P6 is a member of the genus Luzseptimavirus, belonging to Schitoviridae family. The present study provides some basic information for further research on treatment of P. aeruginosa infections.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04528-7.

Membrane progesterone receptor α (mPRα)/ Progestin and adipoQ receptor family member 7(PAQR7), has been insufficiently studied in pan-cancer. This study analyzed its expression, diagnostic value, and correlations with clinical data, tumor stemness, genomic instability, prognosis, interacting molecules, RNA methylation phenotypes, and immune cell infiltration, immune-related genes, and immune checkpoints via multiple databases. It also evaluated mPRα's effects on LUSC cell malignancy using cell counting kit-8 (CCK-8), colony formation, transwell, and flow cytometry, detected its expression in lung squamous cell carcinoma (LUSC) tissue microarray by immunohistochemistry (IHC) staining, and analyzed its overall survival (OS) correlation in LUSC via Kaplan-Meier curves. Results showed PAQR7 up-regulated and down-regulated in some cancers. It had diagnostic value in some cancers and correlated with clinical data, tumor stemness, genomic instability, and prognosis in some tumors. PAQR7 interacted with various molecules, focusing on hormone-mediated signaling pathways in biological process (BP), steroid binding in molecular function (MF), and chemical carcinogenesis-receptor activation in Kyoto Encyclopedia of Genes and Genomes (KEGG). PAQR7 was related to tumor angiogenesis, differentiation, and stemness. PAQR7 expression further showed associations with immune cell infiltration, related immune genes, and immune checkpoints. More importantly, validation experiments demonstrated that mPRα was aberrantly overexpressed in LUSC cells, and its knockdown impaired the malignant characteristics of LUSCs. In addition, higher mPRα protein expression was associated with a poor OS in LUSC patients. In conclusion, mPRα/PAQR7 was abnormally expressed in various cancers, and its high expression was associated with malignant phenotypes and poor prognosis in LUSC.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04586-x.