{"title":"Study on authentication of ingredients and geographical origin of Japanese sake based on hydrogen stable isotope analysis by deuterium NMR.","authors":"Kenji Ogura, Ren Mizutani","doi":"10.1093/bbb/zbaf098","DOIUrl":"10.1093/bbb/zbaf098","url":null,"abstract":"<p><p>This study investigates the authentication of Japanese sake ingredients and geographical origin through the application of hydrogen stable isotope analysis by deuterium nuclear magnetic resonance (NMR) spectroscopy. Ethanol was purified from sake, and the hydrogen stable isotope ratios of its methyl and methylene groups of ethanol were measured. The results indicated that the (D/H)methyl ratio reflects differences in the ingredients, while the (D/H)methylene ratio reflects differences in the water utilized in the brewing process. This discrepancy was attributed to the different origins of hydrogen in these functional groups during ethanol biosynthesis by yeast. This study demonstrates that hydrogen stable isotope analysis by NMR can provide accurate information about sake ingredients and brewing water, thus providing a scientific basis for Japanese sake authentication.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"1373-1381"},"PeriodicalIF":1.3,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144583157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Characterization of N-malonylurea hydrolase in the pyrimidine oxidative degradation pathway of Rhodococcus erythropolis JCM 3132.","authors":"Kengo Deguchi, Nobuyuki Horinouchi, Michiki Takeuchi, Chee-Leong Soong, Sakayu Shimizu, Jun Ogawa","doi":"10.1093/bbb/zbaf083","DOIUrl":"10.1093/bbb/zbaf083","url":null,"abstract":"<p><p>Rhodococcus erythropolis JCM 3132 has the pyrimidine oxidative pathway consisting of uracil/thymine dehydrogenase, barbiturase, and N-malonylurea hydrolase (ureidomalonase, EC 3.5.1.95). In this study, we successfully purified to homogeneity a functional protein from Escherichia coli Rosetta2 overexpressing the N-malonylurea hydrolase gene from R. erythropolis JCM3132, and the purified enzyme showed the activity of amide hydrolysis of malonuric acid (ureidomalonic acid) to urea and malonic acid. The enzyme was also shown to have a strict specificity toward malonuric acid. The optimal reaction pH and temperature were 8.5 and 40 °C, respectively. Importantly, gene expression of the gene cluster of the pyrimidine oxidative degradation pathway was shown to be inducible by the addition of uracil. Pyrimidine oxidative degradation could be useful in the equilibrium control of ribose transfer between pyrimidine and purine bases, with an increase in the conversion yield of purine nucleoside synthesis.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"1286-1292"},"PeriodicalIF":1.3,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144301149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Discovery of a monomeric flavin-containing opine dehydrogenase from bacteria.","authors":"Seiya Watanabe, Kentaroh Yoshiwara, Mizue Date, Yasunori Watanabe","doi":"10.1093/bbb/zbaf096","DOIUrl":"10.1093/bbb/zbaf096","url":null,"abstract":"<p><p>Opines, such as nopaline and octopine, are specifically produced in the crown gall by Agrobacterium tumefaciens, and specifically catabolized by opine dehydrogenase (OpnDH) from them. Known OpnDH consists of α-, β-, and γ-subunits, which contain FAD, FMN, and 2 iron-sulfur clusters as cofactors. We herein identified a novel type of FAD-containing OpnDH from Aureimonas altamirensis (AaOdhB3), consisting of a single polypeptide and only ∼22% sequence identity with the β-subunit of the heteromeric enzyme. AaOdhB3, a monomeric structure, exhibited strict specificity toward nopaline. A crystallographic analysis revealed that the overall structure and binding mode of FAD were similar to those of D-amino acid oxidase superfamily members. A site-directed mutagenic analysis and structural comparisons with other members of this protein family indicated the significance of Arg312 (and Arg247) for substrate recognition, and fructosyl-amino acid oxidase, related to santhopine metabolism from A. tumefaciens, was phylogenetically and physiologically close to OdhB3.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"1329-1339"},"PeriodicalIF":1.3,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144526448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Therapeutic impact of polysaccharide from Chinese yam (Dioscorea opposita Thunb) on DSS-induced ulcerative colitis in mice.","authors":"Jianing Tan, Ziliang Zhuo, Ling Zhang, Xuemin Jin, Xiuyu Wang, Yanshuang Zhang, Yajun Zhou","doi":"10.1093/bbb/zbaf086","DOIUrl":"10.1093/bbb/zbaf086","url":null,"abstract":"<p><p>While yam polysaccharide (YP) demonstrates diverse biological activities, its anti-inflammatory mechanisms remain insufficiently characterized. This study systematically investigates the therapeutic efficacy of YP in ulcerative colitis (UC) through integrated in vitro and in vivo approaches. YP was purified from Dioscorea opposita Thunb. via ethanol precipitation, followed by cytotoxicity profiling. In Lipopolysaccharide (LPS)-stimulated intestinal epithelial cells (IEC-6), YP significantly attenuated proinflammatory responses. For in vivo validation, a murine colitis model was established through dextran sulfate sodium administration in drinking water. Systematic macroscopic and histopathological assessments revealed that YP treatment reduced colon shortening and mitigated crypt architectural distortion. Further analyses combining H&E staining, immunofluorescence, and western blotting demonstrated that YP exerts anti-inflammatory effects through upregulating interleukin-10 expression. These findings position YP as a multifaceted modulator of intestinal inflammation, suggesting its potential as a novel therapeutic agent for UC management.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"1362-1372"},"PeriodicalIF":1.3,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144265252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Development of a novel fatty acid-derived biopolymer with tunable polarity.","authors":"Takeshi Imai, Hiroto Achira, Akihiko Tanitame, Hisaaki Mihara","doi":"10.1093/bbb/zbaf095","DOIUrl":"10.1093/bbb/zbaf095","url":null,"abstract":"<p><p>A novel biopolymer, fatty acid-derived polyelectrolyte (FADP), was synthesized via oxidative polymerization and base-induced ionization of unsaturated fatty acids. We evaluated its ionization degree, molecular weight progression, and mechanical performance. FADP composites with optimal carboxylate content exhibited high flexural strength, suggesting the potential of producing sustainable, polarity-tunable polymers through a simple process.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"1357-1361"},"PeriodicalIF":1.3,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144511581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Seawater biodegradation of a microbial lactate-based polyester (LAHB) as an advanced version of non-degradable polylactide.","authors":"Sangho Koh, Miwa Suzuki, Ken-Ichi Kasuya, Seiichi Taguchi","doi":"10.1093/bbb/zbaf097","DOIUrl":"10.1093/bbb/zbaf097","url":null,"abstract":"<p><p>Here, we have demonstrated the good decomposition of microbially synthesized poly[45 mol% lactate (LA)-co-3-hydroxybutyrate (3HB)] (LAHB) in seawater, considered as a severe condition for plastic biodegradation. This provides the ecofriendly utility of LAHB over marine non-biodegradable polylactide (PLA). Accordingly, LAHB can be recognized as an advanced version sharing the beneficial properties of the biodegradable 3HB homopolymer and the widely used PLA.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"1405-1408"},"PeriodicalIF":1.3,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144526449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A unique tetrasaccharide-containing anchor glycolipid of lipoteichoic acid is commonly found in Lactobacillus gasseri and Lactobacillus paragasseri.","authors":"Tsukasa Shiraishi, Ryosuke Kutomi, Yamaha Sato, Akihito Endo, Satoru Fukiya, Satoshi Takahashi, Atsushi Yokota, Shin-Ichi Yokota","doi":"10.1093/bbb/zbaf081","DOIUrl":"10.1093/bbb/zbaf081","url":null,"abstract":"<p><p>Lipoteichoic acid (LTA) is a cell surface molecule with physiologically important roles in Gram-positive bacteria. Previously, we identified a novel tetrasaccharide-containing anchor glycolipid in the Lactobacillus gasseri JCM 1131T LTA. However, it is unclear whether this tetrasaccharide-containing anchor glycolipid structure is characteristic of JCM 1131T alone or is commonly found in other L. gasseri-related isolates. Lactobacillus paragasseri has been proposed as a new species, separated from the L. gasseri. In the present study, we characterized the chemical structures of LTA from 2 strains of L. gasseri and 4 strains of L. paragasseri. All 6 strains shared a polymer comprising repeating units of glycerophosphate with partial D-alanine substitutions, as well as L. gasseri JCM 1131T. Anchor glycolipid structure suggested that all strains shared a tetrasaccharide-containing glyceroglycolipid with 2 and 3 acyl groups. Focusing on LTA from L. gasseri and L. paragasseri species, a tetrasaccharide-containing anchor glycolipid is a specific feature.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"1382-1390"},"PeriodicalIF":1.3,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nana Wu, Ruyu Fu, Mingxu Dong, Xinyue Zhang, Jinzhu Zhang, Tao Yang, Jie Dong, Jinping Fan
{"title":"The effects of various CaCl2 concentrations on the physiological and growth responses of Asarin Scandens Rose under salt stress.","authors":"Nana Wu, Ruyu Fu, Mingxu Dong, Xinyue Zhang, Jinzhu Zhang, Tao Yang, Jie Dong, Jinping Fan","doi":"10.1093/bbb/zbaf061","DOIUrl":"10.1093/bbb/zbaf061","url":null,"abstract":"<p><p>Asarin Scandens Rose (\"F499\") is a perennial vine that is visually appealing, yet the salinization of the soil due to urban activity may reduce its potential as a landscaping plant. Our research utilized exogenous calcium to diminish the negative effects of salt stress on the growth of F499. Under salt stress, the application of 5 and 10 m m CaCl2 resulted in a considerable expansion of the leaf area, in addition to a heightened deposition of chlorophyll, thus improving the color of the leaves. Additionally, it was shown that F499's net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO2 concentration (Ci), transpiration rate (Tr), proline, and soluble protein levels all increased under the beneficial effects of CaCl2. Consequently, supplementation with appropriate amounts of exogenous calcium in urban saline soils is an effective way for plants to adapt to salt stress and maintain their ornamental value.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"1271-1278"},"PeriodicalIF":1.3,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shoki Fujita, Da Min Jeong, Takanori Ichikawa, Takahiro Shintani, Katsuya Gomi
{"title":"Presence of isomaltose transporters in Aspergilli demonstrated through nuclear translocation assays of the transcription factor AmyR.","authors":"Shoki Fujita, Da Min Jeong, Takanori Ichikawa, Takahiro Shintani, Katsuya Gomi","doi":"10.1093/bbb/zbaf085","DOIUrl":"10.1093/bbb/zbaf085","url":null,"abstract":"<p><p>Maltose is readily incorporated into Aspergillus oryzae cells. In contrast, isomaltose is unlikely to be incorporated into both A. oryzae and Aspergillus nidulans, even though extremely low concentrations of isomaltose can induce the nuclear translocation of AmyR. This suggests the presence of sensor-like proteins or isomaltose transporters in both Aspergilli. In this study, we showed that isomaltose can be incorporated via sugar/H+ symporters using AmyR nuclear translocation assays. Assuming that sugar transporters are proton-coupled symporters, we examined the effect of the protonophore carbonyl cyanide m-chlorophenyl hydrazone on isomaltose-induced AmyR nuclear translocation. Consequently, AmyR nuclear translocation was impaired by the addition of the protonophore in A. oryzae. This was confirmed under high pH conditions where AmyR nuclear translocation was abrogated in both Aspergilli. These results suggest that instead of sensors, isomaltose is most likely incorporated by sugar/H+ symporters with low isomaltose transport activity, triggering isomaltose-induced AmyR nuclear translocation.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"1391-1399"},"PeriodicalIF":1.3,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257382","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Generation of noncanonical fumagillin derivatives with a twisted cyclohexane conformation through engineered biosynthesis.","authors":"Yuta Tsunematsu, Yuji Ogata, Kanji Niwa, Namiko Ogata, Seiki Kobayashi, Michio Sato, Takuma Matsushita, Ryota Shizu, Kouichi Yoshinari, Mihoko Mori, Yumiko Saito-Nakano, Tomoyoshi Nozaki, Kenji Watanabe","doi":"10.1093/bbb/zbaf091","DOIUrl":"10.1093/bbb/zbaf091","url":null,"abstract":"<p><p>Fumagillin-class natural products, known as methionine aminopeptidase 2 inhibitors, have been explored as drug candidates for cancer, obesity, and infectious diseases such as amoebiasis. However, clinical development has been hindered by adverse effects. Here, we identified 2 fumagillin analogues via engineered biosynthesis in Saccharomyces cerevisiae, coupled with metabolomics and activity-guided isolation. Spectroscopic analysis revealed unique 6-oxabicyclo[3.2.1]octane scaffolds that are unprecedented among naturally occurring fumagillins. The compounds exhibited selective antiamoebic activity without cytotoxicity to human lung cells. Stereochemical and computational studies suggested that the unique bicyclic system arises from a twist-boat conformer that enables intramolecular ether formation. These findings demonstrate that biosynthetic pathway engineering can expand the chemical diversity of fumagillin-related molecules and provide new leads for antiparasitic drug discovery.</p>","PeriodicalId":9175,"journal":{"name":"Bioscience, Biotechnology, and Biochemistry","volume":" ","pages":"1264-1270"},"PeriodicalIF":1.3,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144504784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}