Pub Date : 2025-11-17DOI: 10.1016/j.jbiosc.2025.10.010
Mingdong Chang , Ru Yin , Jianqiao Wang , Nana Wang , Pengfei Xiao
The understanding of white-rot fungi (WRF) and their role in degrading recalcitrant environmental pollutants has significantly advanced due to developments in bioremediation research. Considerable progress has been made in elucidating the degradation capabilities of WRF against lots of environmental pollutants. In this review, research hotspots on the degradation of WRF were identified through bibliometric analysis. Key findings from systematic studies on the degradation of polycyclic aromatic hydrocarbons (PAHs) and bisphenols by WRF are synthesized and discussed. Furthermore, insights into the molecular and genetic basis underlying the enzymatic systems responsible for the degradation of PAHs and bisphenols are highlighted. Advancements and challenges in understanding the degradation capabilities and degradation mechanisms are examined in order to identify opportunities for developing more effective strategies to harness the bioremediation potential of WRF.
{"title":"Biodegradation of recalcitrant environmental pollutants by white-rot fungi","authors":"Mingdong Chang , Ru Yin , Jianqiao Wang , Nana Wang , Pengfei Xiao","doi":"10.1016/j.jbiosc.2025.10.010","DOIUrl":"10.1016/j.jbiosc.2025.10.010","url":null,"abstract":"<div><div>The understanding of white-rot fungi (WRF) and their role in degrading recalcitrant environmental pollutants has significantly advanced due to developments in bioremediation research. Considerable progress has been made in elucidating the degradation capabilities of WRF against lots of environmental pollutants. In this review, research hotspots on the degradation of WRF were identified through bibliometric analysis. Key findings from systematic studies on the degradation of polycyclic aromatic hydrocarbons (PAHs) and bisphenols by WRF are synthesized and discussed. Furthermore, insights into the molecular and genetic basis underlying the enzymatic systems responsible for the degradation of PAHs and bisphenols are highlighted. Advancements and challenges in understanding the degradation capabilities and degradation mechanisms are examined in order to identify opportunities for developing more effective strategies to harness the bioremediation potential of WRF.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 2","pages":"Pages 81-89"},"PeriodicalIF":2.9,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145549307","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}
Pseudonocardia sp. D17 (D17) is a novel strain capable of aerobically metabolizing cis-1,2-dichloroethene (cDCE), a persistent contaminant in soil and groundwater. This study aimed to investigate the cDCE degradation characteristics of D17 with respect to kinetics, associated degradative enzymes, and degradation pathways. Degradation experiments with cDCE concentrations ranging from 0.267 to 91.3 μM revealed that D17 can efficiently degrade cDCE across this range. The maximum specific degradation rate and half saturation constant for cDCE degradation by D17 were estimated to be 0.418 ± 0.045 nmol/mg-protein/min and 38.5 ± 9.2 μM, respectively. Heterologous expression experiments demonstrated that both group 5 soluble di-iron monooxygenases in D17, namely tetrahydrofuran and propane monooxygenases, can catalyze cDCE degradation with higher catalytic activity observed in the former. This suggests their involvement in cDCE degradation by D17. It was also proposed that D17 completely dechlorinates cDCE through multiple pathways to generate glyoxylic acid, which is either mineralized or incorporated into the glyoxylate cycle, with a minor portion being converted to oxalic acid as a dead-end product. These findings provide novel insights into metabolic aerobic cDCE biodegradation and highlight the potential of D17 as a bioremediation agent.
{"title":"Aerobic degradation characteristics of cis-1,2-dichloroethene by Pseudonocardia sp. D17: Degradation kinetics, putative degradation pathways, and involvement of soluble di-iron monooxygenases in the initial oxidation","authors":"Ryugo Nishimine , Yuna Kaneko , Shinpei Fujiwara , Daisuke Inoue , Masahiro Takeo , Michihiko Ike","doi":"10.1016/j.jbiosc.2025.10.012","DOIUrl":"10.1016/j.jbiosc.2025.10.012","url":null,"abstract":"<div><div><em>Pseudonocardia</em> sp. D17 (D17) is a novel strain capable of aerobically metabolizing <em>cis</em>-1,2-dichloroethene (cDCE), a persistent contaminant in soil and groundwater. This study aimed to investigate the cDCE degradation characteristics of D17 with respect to kinetics, associated degradative enzymes, and degradation pathways. Degradation experiments with cDCE concentrations ranging from 0.267 to 91.3 μM revealed that D17 can efficiently degrade cDCE across this range. The maximum specific degradation rate and half saturation constant for cDCE degradation by D17 were estimated to be 0.418 ± 0.045 nmol/mg-protein/min and 38.5 ± 9.2 μM, respectively. Heterologous expression experiments demonstrated that both group 5 soluble di-iron monooxygenases in D17, namely tetrahydrofuran and propane monooxygenases, can catalyze cDCE degradation with higher catalytic activity observed in the former. This suggests their involvement in cDCE degradation by D17. It was also proposed that D17 completely dechlorinates cDCE through multiple pathways to generate glyoxylic acid, which is either mineralized or incorporated into the glyoxylate cycle, with a minor portion being converted to oxalic acid as a dead-end product. These findings provide novel insights into metabolic aerobic cDCE biodegradation and highlight the potential of D17 as a bioremediation agent.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 2","pages":"Pages 116-124"},"PeriodicalIF":2.9,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145512940","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}
Sake yeast exhibits remarkable fermentative capacity in mash environments, even under various stress conditions. Although breeding techniques aimed at improving the flavor of sake by modifying aroma compounds and organic acid composition have been employed, these approaches often result in reduced fermentative capacity. Furthermore, existing breeding methods aimed at enhancing fermentative capacity often result in increased acidity in the final product. In this study, we aimed to improve sake yeast fermentative capacity while limiting sake acidity. Depletion of intracellular ATP may enhance fermentative capacity, suggesting that strains with high vacuolar-type ATPase (V-ATPase) activity exhibit improved fermentative capacity. Thus, we subjected sake yeast to ultraviolet mutagenesis and bafilomycin A1 (Baf), a V-ATPase inhibitor, to select resistant strains. The selected Baf-resistant strains exhibited no changes in growth rate, cell morphology, or vacuolar morphology compared to the parent strain. However, increased vacuolar acidity and decreased intracellular ATP levels indicated enhanced V-ATPase activity. Moreover, evaluation of brewing characteristics confirmed improved fermentative capacity without increases in acidity or amino acid content. The results of this study suggest that obtaining a Baf-resistant strain can reduce intracellular ATP levels, thereby increasing fermentative capacity without increasing acidity.
{"title":"Breeding bafilomycin A1-resistant sake yeast to improve fermentative capacity","authors":"Mai Nakase , Hiroyuki Senjyu , Takuya Asai , Kaoru Takegawa , Takahiro Akashi","doi":"10.1016/j.jbiosc.2025.10.006","DOIUrl":"10.1016/j.jbiosc.2025.10.006","url":null,"abstract":"<div><div>Sake yeast exhibits remarkable fermentative capacity in mash environments, even under various stress conditions. Although breeding techniques aimed at improving the flavor of sake by modifying aroma compounds and organic acid composition have been employed, these approaches often result in reduced fermentative capacity. Furthermore, existing breeding methods aimed at enhancing fermentative capacity often result in increased acidity in the final product. In this study, we aimed to improve sake yeast fermentative capacity while limiting sake acidity. Depletion of intracellular ATP may enhance fermentative capacity, suggesting that strains with high vacuolar-type ATPase (V-ATPase) activity exhibit improved fermentative capacity. Thus, we subjected sake yeast to ultraviolet mutagenesis and bafilomycin A1 (Baf), a V-ATPase inhibitor, to select resistant strains. The selected Baf-resistant strains exhibited no changes in growth rate, cell morphology, or vacuolar morphology compared to the parent strain. However, increased vacuolar acidity and decreased intracellular ATP levels indicated enhanced V-ATPase activity. Moreover, evaluation of brewing characteristics confirmed improved fermentative capacity without increases in acidity or amino acid content. The results of this study suggest that obtaining a Baf-resistant strain can reduce intracellular ATP levels, thereby increasing fermentative capacity without increasing acidity.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 2","pages":"Pages 108-115"},"PeriodicalIF":2.9,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145512945","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}
Water-surface floating microalgae have a potential to be promising host organisms to produce useful compounds free from energy-consuming and costly harvesting processes. However, only a few water-surface floating microalgae have been studied for biotechnological applications. In this study, we investigated the potential of a chrysophycean alga Chromophyton sp., also known as Hikarimo in Japan, as a producer of fucoxanthin. The cells of this microalga float on the surface of freshwater in natural environments and can be harvested by attaching plastic film to the floating cells. Three strains, SH01, SH02, and SH03, were isolated from Japanese freshwater environments in Ibaraki, Nagano, and Chiba, and all three strains were identified as Chromophyton sp. by molecular phylogenetic analysis. After we prepared a less contaminated culture of these strains, culture conditions, namely medium concentrations, temperatures, and photon flux densities, were optimized to enhance the cell concentrations. As a result, the cell concentration of Chromophyton sp. reached 16.7 × 106 cells/ml, which is 10.7 times higher than that before the investigation. The cultured cells did not show a water-surface floating phenotype, and thus, we should identify the trigger(s) to induce this floating phenotype. High-performance liquid chromatography analyses revealed that Chromophyton sp. was rich in fucoxanthin. The fucoxanthin content and productivity were estimated to be 48.7 mg/g of dry cell weight and 2.31 mg/L/day, respectively. This is the highest level among the microalgal species studied so far. Since Chromophyton sp. was observed to be free from a cell wall, this microalga would also be favorable for food and feed applications.
{"title":"Production of fucoxanthin using a water surface-floating microalga Chromophyton sp. (Hikarimo)","authors":"Akira Umehara , Mardhiah Wahab , Kohei Yoneda , Fazrena Nadia Md Akhir , Koji Iwamoto , Ken-ichiro Ishida , Satomi Hiruta , Masahiro Suzuki , Izzah Nadzirah Rushdan Zaim , Tomoharu Sano , Masanobu Kawachi , Iwane Suzuki , Yoshiaki Maeda","doi":"10.1016/j.jbiosc.2025.10.009","DOIUrl":"10.1016/j.jbiosc.2025.10.009","url":null,"abstract":"<div><div>Water-surface floating microalgae have a potential to be promising host organisms to produce useful compounds free from energy-consuming and costly harvesting processes. However, only a few water-surface floating microalgae have been studied for biotechnological applications. In this study, we investigated the potential of a chrysophycean alga <em>Chromophyton</em> sp., also known as Hikarimo in Japan, as a producer of fucoxanthin. The cells of this microalga float on the surface of freshwater in natural environments and can be harvested by attaching plastic film to the floating cells. Three strains, SH01, SH02, and SH03, were isolated from Japanese freshwater environments in Ibaraki, Nagano, and Chiba, and all three strains were identified as <em>Chromophyton</em> sp. by molecular phylogenetic analysis. After we prepared a less contaminated culture of these strains, culture conditions, namely medium concentrations, temperatures, and photon flux densities, were optimized to enhance the cell concentrations. As a result, the cell concentration of <em>Chromophyton</em> sp. reached 16.7 × 10<sup>6</sup> cells/ml, which is 10.7 times higher than that before the investigation. The cultured cells did not show a water-surface floating phenotype, and thus, we should identify the trigger(s) to induce this floating phenotype. High-performance liquid chromatography analyses revealed that <em>Chromophyton</em> sp. was rich in fucoxanthin. The fucoxanthin content and productivity were estimated to be 48.7 mg/g of dry cell weight and 2.31 mg/L/day, respectively. This is the highest level among the microalgal species studied so far. Since <em>Chromophyton</em> sp. was observed to be free from a cell wall, this microalga would also be favorable for food and feed applications.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 1","pages":"Pages 49-57"},"PeriodicalIF":2.9,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145495566","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}
Aspergillus oryzae is used for brewing, and many strains with different brewing characteristics have been isolated. We compared enzymatic activities of eight A. oryzae strains, RIB40, 128, 143, 163, 301, 915, 1108, and 1178 strains, toward plant polysaccharides. The plant polysaccharide degradation-related enzymes produced by A. oryzae change depending on the monosaccharides and polysaccharides added to the culture medium. RIB915 produced more cellulolytic and hemicellulolytic enzymes, whereas RIB40, 128, and 301 produced less of these enzymes than the other strains. In addition, A. oryzae RIB128 produced different glycoside hydrolases in response to monosaccharides and polysaccharides compared with other strains. These results indicated that there is diversity in the production of plant polysaccharide degradation-related enzymes within A. oryzae species.
{"title":"Aspergillus oryzae strains heterogeneously produce plant polysaccharide degradation-related enzymes","authors":"Shimma Fujiwa , Ryousuke Kataoka , Kazuhiro Iwashita , Tomohiko Matsuzawa","doi":"10.1016/j.jbiosc.2025.10.008","DOIUrl":"10.1016/j.jbiosc.2025.10.008","url":null,"abstract":"<div><div><em>Aspergillus oryzae</em> is used for brewing, and many strains with different brewing characteristics have been isolated. We compared enzymatic activities of eight <em>A. oryzae</em> strains, RIB40, 128, 143, 163, 301, 915, 1108, and 1178 strains, toward plant polysaccharides. The plant polysaccharide degradation-related enzymes produced by <em>A. oryzae</em> change depending on the monosaccharides and polysaccharides added to the culture medium. RIB915 produced more cellulolytic and hemicellulolytic enzymes, whereas RIB40, 128, and 301 produced less of these enzymes than the other strains. In addition, <em>A. oryzae</em> RIB128 produced different glycoside hydrolases in response to monosaccharides and polysaccharides compared with other strains. These results indicated that there is diversity in the production of plant polysaccharide degradation-related enzymes within <em>A. oryzae</em> species.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 1","pages":"Pages 12-22"},"PeriodicalIF":2.9,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145495510","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}
Pub Date : 2025-11-04DOI: 10.1016/j.jbiosc.2025.10.007
Tengchang Li , Toshihisa Kajiwara , Hiroshi Mizumoto
Tissue engineering of thick hepatic tissues is limited by an inadequate oxygen supply, which causes hypoxia and cell death. Oxygen-generating materials have emerged to temporarily relieve hypoxia. However, quantitative analysis of their ability to generate oxygen is still lacking, hindering the precise evaluation of their efficacy. In this study, we developed an oxygen-generating collagen gel (oxy CG) containing calcium peroxide (CaO2) and quantitatively analyzed its oxygen release dynamics by measuring the oxygen generation rate and calculating its volumetric oxygen transfer coefficient (kLa). Using this method, we derived a theoretical threshold for cultivable cell density that was experimentally validated under hypoxic conditions using primary rat hepatocytes (PRHs). Oxy CG sustained oxygen release, while maintaining pH stability, supporting hepatocyte viability and liver-specific functions, such as urea synthesis and albumin secretion, within the predicted cell density range. This study provides a quantitative framework that balances oxygen supply and cellular demand, providing valuable insights for optimizing oxygen delivery in liver tissue engineering to overcome diffusion limitations in 3D constructs and improve clinical applicability.
{"title":"Production of oxygen-generating collagen gel and quantitative analysis of oxygen generation ability","authors":"Tengchang Li , Toshihisa Kajiwara , Hiroshi Mizumoto","doi":"10.1016/j.jbiosc.2025.10.007","DOIUrl":"10.1016/j.jbiosc.2025.10.007","url":null,"abstract":"<div><div>Tissue engineering of thick hepatic tissues is limited by an inadequate oxygen supply, which causes hypoxia and cell death. Oxygen-generating materials have emerged to temporarily relieve hypoxia. However, quantitative analysis of their ability to generate oxygen is still lacking, hindering the precise evaluation of their efficacy. In this study, we developed an oxygen-generating collagen gel (oxy CG) containing calcium peroxide (CaO<sub>2</sub>) and quantitatively analyzed its oxygen release dynamics by measuring the oxygen generation rate and calculating its volumetric oxygen transfer coefficient (<em>k</em><sub>L</sub><em>a</em>). Using this method, we derived a theoretical threshold for cultivable cell density that was experimentally validated under hypoxic conditions using primary rat hepatocytes (PRHs). Oxy CG sustained oxygen release, while maintaining pH stability, supporting hepatocyte viability and liver-specific functions, such as urea synthesis and albumin secretion, within the predicted cell density range. This study provides a quantitative framework that balances oxygen supply and cellular demand, providing valuable insights for optimizing oxygen delivery in liver tissue engineering to overcome diffusion limitations in 3D constructs and improve clinical applicability.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 1","pages":"Pages 74-80"},"PeriodicalIF":2.9,"publicationDate":"2025-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145451828","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}
Pub Date : 2025-11-01DOI: 10.1016/j.jbiosc.2025.10.005
Jian-Wei Dong, Meng Liu, Xue-Jiao Li, Ke-Wen Pan
1-(β-d-Ribofuranosyl)-1,2,4-triazole (RTA) is a nucleotide analog of 1,2,4-triazole that demonstrates broad-spectrum antiviral activity. It is currently the approved drug for treating chronic hepatitis E virus (HEV) infections. However, the production of RTA relies predominantly on chemical synthesis and extraction from plants and animals, with no report of microbial metabolic production. This study introduces a novel approach to producing RTA via solid-state fermentation (SSF) using Purpureocillium lavendulum DQWM-G4, with rice as the substrate. The chemical structure of RTA was elucidated through 1H and 13C nuclear magnetic resonance (NMR) spectroscopy. Fermentation conditions for producing RTA were optimized by investigating substrate type, temperature, and duration. Under optimized conditions, SSF with P. lavendulum DQWM-G4 on rice at 20 °C for 60 d yielded RTA at a high concentration of 3.46 ± 0.16 mg/g. This paper represents the first report on microbial production of RTA, offering an alternative to chemical synthesis and natural extraction.
{"title":"Production of 1-(β-d-ribofuranosyl)-1,2,4-triazole through solid-state fermentation with Purpureocillium lavendulum DQWM-G4","authors":"Jian-Wei Dong, Meng Liu, Xue-Jiao Li, Ke-Wen Pan","doi":"10.1016/j.jbiosc.2025.10.005","DOIUrl":"10.1016/j.jbiosc.2025.10.005","url":null,"abstract":"<div><div>1-(β-<span>d</span>-Ribofuranosyl)-1,2,4-triazole (RTA) is a nucleotide analog of 1,2,4-triazole that demonstrates broad-spectrum antiviral activity. It is currently the approved drug for treating chronic hepatitis E virus (HEV) infections. However, the production of RTA relies predominantly on chemical synthesis and extraction from plants and animals, with no report of microbial metabolic production. This study introduces a novel approach to producing RTA via solid-state fermentation (SSF) using <em>Purpureocillium lavendulum</em> DQWM-G4, with rice as the substrate. The chemical structure of RTA was elucidated through <sup>1</sup>H and <sup>13</sup>C nuclear magnetic resonance (NMR) spectroscopy. Fermentation conditions for producing RTA were optimized by investigating substrate type, temperature, and duration. Under optimized conditions, SSF with <em>P</em>. <em>lavendulum</em> DQWM-G4 on rice at 20 °C for 60 d yielded RTA at a high concentration of 3.46 ± 0.16 mg/g. This paper represents the first report on microbial production of RTA, offering an alternative to chemical synthesis and natural extraction.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 1","pages":"Pages 45-48"},"PeriodicalIF":2.9,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145426694","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}
Cellular innate fluorescence (IF) is a natural fluorescence derived from cellular metabolites and biomolecules within microbial cells. Although IF is suggested to be a promising tool for probing the physiology of cells in a non-invasive manner, the link between single-cell IF and heterogeneity in material production remains largely unexplored. This study aimed to examine the link between cellular IF in oleaginous yeasts and their lipid-producing capabilities at multiple taxonomic levels: intra-species, inter-species, and inter-genus. Briefly, we developed a novel microscopic method that can directly link cellular IF (a single-cell IF signature) and the lipid-producing capability of cells at single-cell resolution, thereby enabling the recognition of high heterogeneity in single-cell IF and lipid production in cells. At the intra-species level, the time-course analysis revealed a parallelism between the shifts in single-cell IF signatures and lipid production by Lipomyces starkeyi. The regression model constructed based on single-cell IF signatures could predict intracellular lipid contents. The link between IF and lipid production was also observed across the inter-strain, inter-species, and inter-genus levels, where the regression model constructed with single-cell IF signatures of different strains, species, and genera could predict lipid production. Machine learning models established a computational link to predict lipid productivity by relying on the single-cell IF signatures. These results indicate that the single-cell IF signature is a promising tool for lipid production analysis and prediction in oleaginous yeast species across taxa.
{"title":"Lipid metabolism prediction in oleaginous yeasts across taxonomic levels using single-cell innate fluorescence signature","authors":"Shiomi Yawata , Tomohiro Hirayama , Tatsuro Serita , Haruka Kazama , Koji Mori , Hiroaki Takaku , Nobuhiko Nomura , Yutaka Yawata","doi":"10.1016/j.jbiosc.2025.10.003","DOIUrl":"10.1016/j.jbiosc.2025.10.003","url":null,"abstract":"<div><div>Cellular innate fluorescence (IF) is a natural fluorescence derived from cellular metabolites and biomolecules within microbial cells. Although IF is suggested to be a promising tool for probing the physiology of cells in a non-invasive manner, the link between single-cell IF and heterogeneity in material production remains largely unexplored. This study aimed to examine the link between cellular IF in oleaginous yeasts and their lipid-producing capabilities at multiple taxonomic levels: intra-species, inter-species, and inter-genus. Briefly, we developed a novel microscopic method that can directly link cellular IF (a single-cell IF signature) and the lipid-producing capability of cells at single-cell resolution, thereby enabling the recognition of high heterogeneity in single-cell IF and lipid production in cells. At the intra-species level, the time-course analysis revealed a parallelism between the shifts in single-cell IF signatures and lipid production by <em>Lipomyces starkeyi</em>. The regression model constructed based on single-cell IF signatures could predict intracellular lipid contents. The link between IF and lipid production was also observed across the inter-strain, inter-species, and inter-genus levels, where the regression model constructed with single-cell IF signatures of different strains, species, and genera could predict lipid production. Machine learning models established a computational link to predict lipid productivity by relying on the single-cell IF signatures. These results indicate that the single-cell IF signature is a promising tool for lipid production analysis and prediction in oleaginous yeast species across taxa.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 1","pages":"Pages 37-44"},"PeriodicalIF":2.9,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145426712","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}
The biological treatment of selenium-containing wastewater has attracted attention as a cost-effective and eco-friendly technology. However, the inhibitory effect of high salinity and oxygen in wastewater on bacterial selenate/selenite-reducing abilities hinders their practical use. In this study, a unique halotolerant facultative anaerobe, Citrobacter koseri Y2, which can reduce selenate under both aerobic and anaerobic conditions, was isolated and characterized, including a whole genome analysis. Strain Y2 reduced 1 mM selenate and selenite, and 0.4 mM selenate and 1 mM selenite to elemental selenium within 4 d at 3 % (w/v) NaCl under aerobic and anaerobic conditions. Regarding the mechanisms underlying selenate reduction, genes for selenate reductases, YnfE and YnfF, and nitrate reductases were identified in the genome of strain Y2. Selenate reduction by strain Y2 was inhibited in the presence of tungstate, confirming the involvement of molybdoenzymes in this process. These results indicate that strain Y2 is a promising bioagent for the treatment of selenium-containing wastewater.
{"title":"Isolation and characterization of a novel halotolerant selenate-reducing bacterium, Citrobacter koseri Y2","authors":"Shunsuke Okahata , Yuya Ueda , Yuki Kikuchi , Takuya Naoe , Daisuke Inoue , Hideo Dohra , Hiroshi Nishikawa , Michihiko Ike","doi":"10.1016/j.jbiosc.2025.10.004","DOIUrl":"10.1016/j.jbiosc.2025.10.004","url":null,"abstract":"<div><div>The biological treatment of selenium-containing wastewater has attracted attention as a cost-effective and eco-friendly technology. However, the inhibitory effect of high salinity and oxygen in wastewater on bacterial selenate/selenite-reducing abilities hinders their practical use. In this study, a unique halotolerant facultative anaerobe, <em>Citrobacter koseri</em> Y2, which can reduce selenate under both aerobic and anaerobic conditions, was isolated and characterized, including a whole genome analysis. Strain Y2 reduced 1 mM selenate and selenite, and 0.4 mM selenate and 1 mM selenite to elemental selenium within 4 d at 3 % (w/v) NaCl under aerobic and anaerobic conditions. Regarding the mechanisms underlying selenate reduction, genes for selenate reductases, YnfE and YnfF, and nitrate reductases were identified in the genome of strain Y2. Selenate reduction by strain Y2 was inhibited in the presence of tungstate, confirming the involvement of molybdoenzymes in this process. These results indicate that strain Y2 is a promising bioagent for the treatment of selenium-containing wastewater.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 1","pages":"Pages 58-65"},"PeriodicalIF":2.9,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145421837","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}
In regenerative medicine, it is crucial to discover the key factors associated with erythroid differentiation for efficient production of artificial red blood cells. One such factor is erythroid metabolism as erythroid cells dynamically coordinate their metabolic processes to obtain energy for proper differentiation. However, the details of these metabolic changes are not well understood. In this study, we aimed to analyze the metabolism of K562, a cell line that differentiates into erythroid cells using 13C-metabolic flux analysis. The results showed that differentiated cells decreased glycolytic flux and increased TCA cycle flux compared with undifferentiated cells, indicating a shift to oxidative metabolism via differentiation. Based on the finding, the inhibition of ATP synthase by oligomycin treatment significantly suppressed differentiation of K562 cells, suggesting that the activation of oxidative metabolism is required for proper differentiation of K562 cells.
{"title":"13C-metabolic flux analysis of K562 cells before and after differentiation into erythroid reveals a metabolic shift toward oxidative metabolism","authors":"Eisuke Mochizuki , Nobuyuki Okahashi , Takeo Taniguchi , Fumio Matsuda","doi":"10.1016/j.jbiosc.2025.10.002","DOIUrl":"10.1016/j.jbiosc.2025.10.002","url":null,"abstract":"<div><div>In regenerative medicine, it is crucial to discover the key factors associated with erythroid differentiation for efficient production of artificial red blood cells. One such factor is erythroid metabolism as erythroid cells dynamically coordinate their metabolic processes to obtain energy for proper differentiation. However, the details of these metabolic changes are not well understood. In this study, we aimed to analyze the metabolism of K562, a cell line that differentiates into erythroid cells using <sup>13</sup>C-metabolic flux analysis. The results showed that differentiated cells decreased glycolytic flux and increased TCA cycle flux compared with undifferentiated cells, indicating a shift to oxidative metabolism via differentiation. Based on the finding, the inhibition of ATP synthase by oligomycin treatment significantly suppressed differentiation of K562 cells, suggesting that the activation of oxidative metabolism is required for proper differentiation of K562 cells.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 1","pages":"Pages 66-73"},"PeriodicalIF":2.9,"publicationDate":"2025-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145421906","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}
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