Chlamydomonas reinhardtii, which is a unicellular photosynthetic eukaryote, has long served as a model microalga for fundamental biological research and biotechnological applications. Recently, it has attracted attention as a promising biological resource for the sustainable production of bio-oils and high-value biomolecules. To enhance the biotechnological utility of this species, various genetic engineering tools have been developed in recent years. In this study, the tetracycline repressor (TetR)-based transactivation system, which is widely used in mammalian and other eukaryotic cells, was repurposed to establish a synthetic transcriptional activation system for exogenous gene expression in Chlamydomonas. We first constructed a transient expression-based evaluation platform to screen for transcriptional activation domains (TADs) that are functional in Chlamydomonas. Among the analyzed TADs, VP192 (tandem repeat of 12 copies of the core VP16 domain) had the highest transcriptional activity when fused to either TetR or Gal4 DNA-binding domains. Furthermore, fusion proteins comprising VP192 and either TetR or reverse TetR enabled doxycycline-dependent regulation of transgene expression in a dose-dependent manner. Notably, transcriptional inducibility was maintained even when the tetracycline-responsive element (TRE) was fused to the HSP70A promoter. Combining TetR-VP192 and this synthetic chimeric promoter (TRE-PHSP) yielded transgene expression levels that exceeded those resulting from the strong HSP70A/RbcS2 hybrid promoter by more than 14-fold. These findings suggest that artificial transcription factors and engineered promoters provide a versatile molecular toolkit for regulating exogenous gene expression in Chlamydomonas.
{"title":"Synthetic transactivator-promoter systems for exogenous gene expression in Chlamydomonas reinhardtii.","authors":"Yoshinori Kawabe, Tatsuki Akiyama, Kokoro Miyazoe, Masamichi Kamihira","doi":"10.1016/j.jbiosc.2026.02.003","DOIUrl":"https://doi.org/10.1016/j.jbiosc.2026.02.003","url":null,"abstract":"<p><p>Chlamydomonas reinhardtii, which is a unicellular photosynthetic eukaryote, has long served as a model microalga for fundamental biological research and biotechnological applications. Recently, it has attracted attention as a promising biological resource for the sustainable production of bio-oils and high-value biomolecules. To enhance the biotechnological utility of this species, various genetic engineering tools have been developed in recent years. In this study, the tetracycline repressor (TetR)-based transactivation system, which is widely used in mammalian and other eukaryotic cells, was repurposed to establish a synthetic transcriptional activation system for exogenous gene expression in Chlamydomonas. We first constructed a transient expression-based evaluation platform to screen for transcriptional activation domains (TADs) that are functional in Chlamydomonas. Among the analyzed TADs, VP192 (tandem repeat of 12 copies of the core VP16 domain) had the highest transcriptional activity when fused to either TetR or Gal4 DNA-binding domains. Furthermore, fusion proteins comprising VP192 and either TetR or reverse TetR enabled doxycycline-dependent regulation of transgene expression in a dose-dependent manner. Notably, transcriptional inducibility was maintained even when the tetracycline-responsive element (TRE) was fused to the HSP70A promoter. Combining TetR-VP192 and this synthetic chimeric promoter (TRE-P<sub>HSP</sub>) yielded transgene expression levels that exceeded those resulting from the strong HSP70A/RbcS2 hybrid promoter by more than 14-fold. These findings suggest that artificial transcription factors and engineered promoters provide a versatile molecular toolkit for regulating exogenous gene expression in Chlamydomonas.</p>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147326091","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}
Streptomyces rochei 7434AN4 carries three linear plasmids, pSLA2-L (211 kb), pSLA2-M (113 kb), and pSLA2-S (18 kb). Genome project of this strain revealed that the linear chromosome consists of 8.36 Mb in size and carries more than 35 biosynthetic gene clusters. Three plasmidless mutants (2-39, YN-P7, and YN-P145) showed their chromosomal telomere deletion, concomitantly with a loss of plasmids. To compare the metabolic profile of plasmidless mutants, each strain was cultivated in different mediums [YM and modified oatmeal broth (OMB) medium]. Remarkably, strain YN-P145 showed two distinct UV-active spots when it was grown in OMB medium. These UV-active compounds were purified using Sephadex LH-20 and silica gel chromatographies. The UV-active compound named YN-P145A has a molecular formula of C14H16N2O2 and was characterized to be cyclo(Phe-Pro), a diketopiperazine (cyclodipeptide) that is known to have an antifungal activity. Another UV-active compound from strain YN-P145, compound YN-P145B, has a molecular formula of C8H11NO. Extensive NMR analysis revealed that YN-P145B was identical to a cyclic enamide termed as YM3163-A, 2-(cyclohex-2-en-1-ylidene)acetamide, which has been isolated from the recombinant of SARP-type activator SRO_3163 in S. rochei. Thus, genome-wide deletion occasionally leads to accumulate natural products, whose expression was weak or not at all in its parent strain.
{"title":"Occasional production by genome-wide deletion through removal of linear plasmid harboring tap-tpg gene pair in Streptomycesrochei.","authors":"Mingge Zhang, Yosi Nindita, Amirudin Akhmad Fauzi, Sho Ogaki, Kota Fujita, Rikito Nishiura, Yiwen Zhang, Sisun Choi, Eung-Soo Kim, Kuninobu Inada, Aiko Teshima, Kenji Arakawa","doi":"10.1016/j.jbiosc.2026.01.012","DOIUrl":"https://doi.org/10.1016/j.jbiosc.2026.01.012","url":null,"abstract":"<p><p>Streptomyces rochei 7434AN4 carries three linear plasmids, pSLA2-L (211 kb), pSLA2-M (113 kb), and pSLA2-S (18 kb). Genome project of this strain revealed that the linear chromosome consists of 8.36 Mb in size and carries more than 35 biosynthetic gene clusters. Three plasmidless mutants (2-39, YN-P7, and YN-P145) showed their chromosomal telomere deletion, concomitantly with a loss of plasmids. To compare the metabolic profile of plasmidless mutants, each strain was cultivated in different mediums [YM and modified oatmeal broth (OMB) medium]. Remarkably, strain YN-P145 showed two distinct UV-active spots when it was grown in OMB medium. These UV-active compounds were purified using Sephadex LH-20 and silica gel chromatographies. The UV-active compound named YN-P145A has a molecular formula of C<sub>14</sub>H<sub>16</sub>N<sub>2</sub>O<sub>2</sub> and was characterized to be cyclo(Phe-Pro), a diketopiperazine (cyclodipeptide) that is known to have an antifungal activity. Another UV-active compound from strain YN-P145, compound YN-P145B, has a molecular formula of C<sub>8</sub>H<sub>11</sub>NO. Extensive NMR analysis revealed that YN-P145B was identical to a cyclic enamide termed as YM3163-A, 2-(cyclohex-2-en-1-ylidene)acetamide, which has been isolated from the recombinant of SARP-type activator SRO_3163 in S. rochei. Thus, genome-wide deletion occasionally leads to accumulate natural products, whose expression was weak or not at all in its parent strain.</p>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2026-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147321677","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":"2026-02-01","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}
Pub Date : 2026-02-01Epub Date: 2025-11-17DOI: 10.1016/j.jbiosc.2025.10.013
Shanthi Shanmugasundaram, Anitha Janet Roshni Yesudhas, Andrea Kagoo, Ramalingam Subramanian
A novel two-enzyme cascade one-pot synthesis of β-alanine from 1,3-diaminopropane (DAP) has been developed. In the first step, DAP was oxidized to 3-aminopropionaldehyde (3-APAL) by diamine oxidase (DAO). In the second step, 3-APAL was oxidized to β-alanine by 3-APAL dehydrogenase (APALDH). Catalase and NADH oxidase were employed to degrade the by-product, H2O2, and to regenerate the cofactor, NAD+. DAO specific to DAP has not been reported in any prokaryote. Therefore, initial proof of concept was established using commercial eukaryotic DAOpk (from porcine kidney) and catalase (from bovine liver), along with recombinant APALDH and NOX enzymes sourced from Arthrobacter crystallopoietes and Lactococcus lactis, respectively. β-Alanine was successfully produced via this pathway; 12.2 mM (1.1 g/L) was formed in 41 h with 12 % conversion. To increase the reaction rate, DAO with higher specific activity was identified from Arthrobacter pascens (DAOAp). The optimum pH and temperature of DAOAp were determined to be 9.0 and 37 °C, respectively. Batch enzymatic biotransformation achieved 6 % conversion, yielding 0.33 mM (29 mg/L) β-alanine in 4 h. The low titre in batch conversion was attributed to substrate inhibition affecting DAOAp, NOX, and catalase. Fed-batch enzymatic biotransformation was conducted to overcome substrate inhibition, yielding 47 % conversion, with 2.34 mM (63 mg/L) β-alanine formation in 4 h. Approximately a 7.5-fold increase in conversion was achieved using fed-batch enzymatic biotransformation. This study accomplished a novel two-enzyme cascade biotransformation strategy for one-pot β-alanine synthesis from DAP.
以1,3-二氨基丙烷（DAP）为原料，采用双酶级联一锅法合成β-丙氨酸。第一步，二胺氧化酶（DAO）将DAP氧化为3-氨基丙醛（3-APAL）。第二步，3-APAL脱氢酶（APALDH）将3-APAL氧化为β-丙氨酸。过氧化氢酶和NADH氧化酶被用来降解副产物H2O2，并再生辅助因子NAD+。在任何原核生物中未见DAP特异性DAO的报道。因此，最初的概念证明是使用商业真核DAOpk（来自猪肾）和过氧化氢酶（来自牛肝脏），以及分别来自节杆菌晶体和乳酸球菌的重组APALDH和NOX酶建立的。β-丙氨酸通过该途径成功生成；以12%的转化率，在41 h内形成12.2 mM （1.1 g/L）。为了提高反应速率，从pascens节杆菌（Arthrobacter pascens, DAOAp）中鉴定出具有较高比活性的DAO。测定了DAOAp的最佳pH为9.0℃，最佳温度为37℃。批量酶生物转化达到6%的转化率，在4小时内产生0.33 mM (29 mg/L) β-丙氨酸。批量转化的低滴度归因于底物对DAOAp、NOX和过氧化氢酶的抑制作用。为了克服底物抑制，进行了补料批式酶生物转化，转化率为47%，在4小时内生成2.34 mM (63 mg/L) β-丙氨酸。使用补料批式酶生物转化，转化率提高了约7.5倍。本研究完成了一种新的双酶级联生物转化策略，用于一锅法合成β-丙氨酸。
{"title":"One-pot synthesis of β-alanine from 1,3-diaminopropane using two-enzyme cascade in cell-free biotransformation","authors":"Shanthi Shanmugasundaram, Anitha Janet Roshni Yesudhas, Andrea Kagoo, Ramalingam Subramanian","doi":"10.1016/j.jbiosc.2025.10.013","DOIUrl":"10.1016/j.jbiosc.2025.10.013","url":null,"abstract":"<div><div>A novel two-enzyme cascade one-pot synthesis of β-alanine from 1,3-diaminopropane (DAP) has been developed. In the first step, DAP was oxidized to 3-aminopropionaldehyde (3-APAL) by diamine oxidase (DAO). In the second step, 3-APAL was oxidized to β-alanine by 3-APAL dehydrogenase (APALDH). Catalase and NADH oxidase were employed to degrade the by-product, H<sub>2</sub>O<sub>2</sub>, and to regenerate the cofactor, NAD<sup>+</sup>. DAO specific to DAP has not been reported in any prokaryote. Therefore, initial proof of concept was established using commercial eukaryotic DAO<sub>pk</sub> (from porcine kidney) and catalase (from bovine liver), along with recombinant APALDH and NOX enzymes sourced from <em>Arthrobacter crystallopoietes</em> and <em>Lactococcus lactis</em>, respectively. β-Alanine was successfully produced via this pathway; 12.2 mM (1.1 g/L) was formed in 41 h with 12 % conversion. To increase the reaction rate, DAO with higher specific activity was identified from <em>Arthrobacter pascens</em> (DAO<sub>Ap</sub>). The optimum pH and temperature of DAO<sub>Ap</sub> were determined to be 9.0 and 37 °C, respectively. Batch enzymatic biotransformation achieved 6 % conversion, yielding 0.33 mM (29 mg/L) β-alanine in 4 h. The low titre in batch conversion was attributed to substrate inhibition affecting DAO<sub>Ap</sub>, NOX, and catalase. Fed-batch enzymatic biotransformation was conducted to overcome substrate inhibition, yielding 47 % conversion, with 2.34 mM (63 mg/L) β-alanine formation in 4 h. Approximately a 7.5-fold increase in conversion was achieved using fed-batch enzymatic biotransformation. This study accomplished a novel two-enzyme cascade biotransformation strategy for one-pot β-alanine synthesis from DAP.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 2","pages":"Pages 90-97"},"PeriodicalIF":2.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145549243","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}
A high growth rate is essential for increasing protein production efficiency in liquid fermentation of filamentous fungi, such as Aspergillus oryzae. However, the increase in culture viscosity due to fungal growth constrains the overall yield. We have demonstrated that culture viscosity is lower in A. oryzae AGΔ-GAGΔ strains, which are deficient in the cell surface polysaccharides α-1,3-glucan (AG) and galactosaminogalactan (GAG), than in the wild-type (WT) strains. Nevertheless, even in aerated fermentation, an increase in AGΔ-GAGΔ viscosity results in oxygen depletion, which limits fungal growth and enzyme production. In this study, we investigated viscosity dynamics and protein production during high-cell-density fermentation of AGΔ-GAGΔ under pure oxygen aeration. Fed-batch cultivation of the WT and AGΔ-GAGΔ strains, expressing recombinant xylanase (XynF1), was used to compare the effects of air and pure oxygen aeration at the same flow rate. At 60 h, AGΔ-GAGΔ under pure oxygen aeration showed higher cell density (1.2× WT under pure oxygen aeration, 2.1× AGΔ-GAGΔ under air aeration) and XynF1 activity (1.8× WT under pure oxygen aeration, 2.3× AGΔ-GAGΔ under air aeration). Under pure oxygen aeration, AGΔ-GAGΔ showed lower viscosity (0.32×) and mixing time (0.50×) than WT. At 60 h, fine mycelial pellets (micropellets; 200–700 μm) were clearly observed in AGΔ-GAGΔ under pure oxygen but not under air aeration. These findings suggest that oxygen enrichment during AGΔ-GAGΔ cultivation mitigated the increase in viscosity, thereby promoting higher cell density and protein production. The formation of micropellets in AGΔ-GAGΔ likely contributed to a reduction in culture viscosity.
{"title":"Using pure oxygen aeration to increase recombinant protein production by an Aspergillus oryzae hyphal dispersion strain","authors":"Satoshi Ishibashi , Shunya Susukida , Kiyoaki Muto , Ken Miyazawa , Silai Zhang , Akira Yoshimi , Eiji Tabata , Keietsu Abe","doi":"10.1016/j.jbiosc.2025.10.011","DOIUrl":"10.1016/j.jbiosc.2025.10.011","url":null,"abstract":"<div><div>A high growth rate is essential for increasing protein production efficiency in liquid fermentation of filamentous fungi, such as <em>Aspergillus oryzae</em>. However, the increase in culture viscosity due to fungal growth constrains the overall yield. We have demonstrated that culture viscosity is lower in <em>A. oryzae</em> AGΔ-GAGΔ strains, which are deficient in the cell surface polysaccharides α-1,3-glucan (AG) and galactosaminogalactan (GAG), than in the wild-type (WT) strains. Nevertheless, even in aerated fermentation, an increase in AGΔ-GAGΔ viscosity results in oxygen depletion, which limits fungal growth and enzyme production. In this study, we investigated viscosity dynamics and protein production during high-cell-density fermentation of AGΔ-GAGΔ under pure oxygen aeration. Fed-batch cultivation of the WT and AGΔ-GAGΔ strains, expressing recombinant xylanase (XynF1), was used to compare the effects of air and pure oxygen aeration at the same flow rate. At 60 h, AGΔ-GAGΔ under pure oxygen aeration showed higher cell density (1.2× WT under pure oxygen aeration, 2.1× AGΔ-GAGΔ under air aeration) and XynF1 activity (1.8× WT under pure oxygen aeration, 2.3× AGΔ-GAGΔ under air aeration). Under pure oxygen aeration, AGΔ-GAGΔ showed lower viscosity (0.32×) and mixing time (0.50×) than WT. At 60 h, fine mycelial pellets (micropellets; 200–700 μm) were clearly observed in AGΔ-GAGΔ under pure oxygen but not under air aeration. These findings suggest that oxygen enrichment during AGΔ-GAGΔ cultivation mitigated the increase in viscosity, thereby promoting higher cell density and protein production. The formation of micropellets in AGΔ-GAGΔ likely contributed to a reduction in culture viscosity.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 2","pages":"Pages 98-107"},"PeriodicalIF":2.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145604529","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 : 2026-02-01Epub 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":"2026-02-01","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}
The natural abundances of stable isotopes were used to determine prey–predator relationships and material flows in a biological treatment reactor for municipal wastewater. The reactor used in this study was a down-flow hanging sponge (DHS), which is an alternative trickling filter that uses sponge as the packing material. The sponge retained sludge containing a wide variety of organisms, including microfauna. Stable isotope analysis revealed spatial, temporal, and biotic variations in the carbon and nitrogen stable isotope ratios (δ13C and δ15N) of the retained sludge and microfauna (water mites and fly larvae). In addition, adult flies and spiders were present and analyzed. The δ13C and δ15N in sludge were temporally and spatially similar along the reactor. The isotopic signature was associated with treatment characteristics such as a low nitrification efficiency in the DHS reactor. The δ13C and δ15N of sympatric fly larvae differed from those of water mites, which indicated dietary differences between the taxa. Interestingly, the water mites had higher δ13C and δ15N than the retained sludge, which indicated that they were in a higher trophic position in the food web. In addition, the δ13C and δ15N values of spiders were approximately 1 ‰–3‰ higher than those of adult flies. This strongly suggested that a prey–predator relationship existed between adult flies and spiders.
{"title":"Spatial, temporal, and biotic changes in the natural abundances of stable carbon and nitrogen isotopes in a biological treatment reactor","authors":"Takashi Onodera , Kengo Kubota , Akinori Iguchi , Akihiro Nagamachi , Tadashi Tagawa , Gen Kanaya , Ayato Kohzu , Kazuaki Syutsubo","doi":"10.1016/j.jbiosc.2025.11.002","DOIUrl":"10.1016/j.jbiosc.2025.11.002","url":null,"abstract":"<div><div>The natural abundances of stable isotopes were used to determine prey–predator relationships and material flows in a biological treatment reactor for municipal wastewater. The reactor used in this study was a down-flow hanging sponge (DHS), which is an alternative trickling filter that uses sponge as the packing material. The sponge retained sludge containing a wide variety of organisms, including microfauna. Stable isotope analysis revealed spatial, temporal, and biotic variations in the carbon and nitrogen stable isotope ratios (<em>δ</em><sup>13</sup>C and <em>δ</em><sup>15</sup>N) of the retained sludge and microfauna (water mites and fly larvae). In addition, adult flies and spiders were present and analyzed. The <em>δ</em><sup>13</sup>C and <em>δ</em><sup>15</sup>N in sludge were temporally and spatially similar along the reactor. The isotopic signature was associated with treatment characteristics such as a low nitrification efficiency in the DHS reactor. The <em>δ</em><sup>13</sup>C and <em>δ</em><sup>15</sup>N of sympatric fly larvae differed from those of water mites, which indicated dietary differences between the taxa. Interestingly, the water mites had higher <em>δ</em><sup>13</sup>C and <em>δ</em><sup>15</sup>N than the retained sludge, which indicated that they were in a higher trophic position in the food web. In addition, the <em>δ</em><sup>13</sup>C and <em>δ</em><sup>15</sup>N values of spiders were approximately 1 ‰–3‰ higher than those of adult flies. This strongly suggested that a prey–predator relationship existed between adult flies and spiders.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 2","pages":"Pages 135-141"},"PeriodicalIF":2.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145633959","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":"2026-02-01","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}
In this study, Pseudomonas sp. NGC7 was engineered to selectively produce vanillate (VA) from aromatic compounds in the sugarcane bagasse alkaline extract. A VA O-demethylase gene (vanA4B4)-disrupted strain derived from NGC7 grew and produced VA from the extract containing no saccharides. The organic acids in the extract promoted the strain to grow. The aromatics in the extract were further concentrated by the solid phase extraction with DIAION HP20 resin, and the organic acids were fractionated into the flow-through fraction. A fed-batch culture of NGC7ΔvanA4B4 strain using this concentrated alkaline extract exhibited increased VA production; however, the accumulation of syringate (SA) and 4-hydroxybenzoate (HBA) was also observed along with VA production, despite the strain possessing the genes responsible for SA and HBA degradation. Analysis of the mutants capable of degrading SA while producing VA revealed that mutations in vanR2, a transcriptional repressor of the genes responsible for SA degradation, enabled SA degradation during VA production. In addition, the expression of praI, an HBA hydroxylase derived from Paenibacillus sp. JJ-1b, was suitable for efficient HBA degradation. Thus, the mutation in vanR2 and the expression of praI represented the key engineering strategies for achieving the selective VA production. As the growth of the engineered strains was promoted by the organic acids present in the extract, VA production from the concentrated extract was evaluated in a flow-through-based medium supplemented with mineral salts and metals. Finally, the engineered VA-producing strain produced 4.30 mM VA selectively at a yield of 77 mol% in the practical medium.
本研究对假单胞菌sp. NGC7进行了工程改造，使其能够从甘蔗渣碱性提取物中的芳香化合物中选择性地产生香草酸（VA）。从NGC7衍生的VA o -去甲基化酶基因（vanA4B4）中断菌株生长并从不含糖的提取物中产生VA。提取物中的有机酸促进了菌株的生长。用DIAION HP20树脂固相萃取进一步浓缩提取液中的芳烃，将有机酸分馏成流动馏分。使用该浓缩碱性提取物对NGC7ΔvanA4B4菌株进行分批补料培养，VA产量增加；然而，尽管菌株具有负责SA和HBA降解的基因，但在产生VA的同时，也观察到紫丁香酸（SA）和4-羟基苯甲酸（HBA）的积累。对能够降解SA同时产生VA的突变体的分析表明，vanR2（负责SA降解的基因的转录抑制因子）的突变使SA在VA产生过程中降解。此外，源自Paenibacillus sp. JJ-1b的HBA羟化酶praI的表达适合于HBA的高效降解。因此，vanR2的突变和praI的表达代表了实现选择性VA产生的关键工程策略。由于提取物中存在的有机酸促进了工程菌株的生长，因此在添加无机盐和金属的流动培养基中评估了浓缩提取物的VA产量。最后，该工程产VA菌株在实际培养基中选择性地产生4.30 mM VA，产率为77 mol%。
{"title":"Selective vanillate production from sugarcane bagasse-derived aromatic compounds using an engineered Pseudomonas sp. NGC7-based strain","authors":"Md. Jahangir Alam , Naoya Kodama , Kazuma Ikeda , Kanami Muraki , Yudai Higuchi , Masaya Fujita , Naofumi Kamimura , Eiji Masai , Hiroyuki Kurihara , Tomonori Sonoki","doi":"10.1016/j.jbiosc.2025.11.001","DOIUrl":"10.1016/j.jbiosc.2025.11.001","url":null,"abstract":"<div><div>In this study, <em>Pseudomonas</em> sp. NGC7 was engineered to selectively produce vanillate (VA) from aromatic compounds in the sugarcane bagasse alkaline extract. A VA <em>O</em>-demethylase gene (<em>vanA4B4</em>)-disrupted strain derived from NGC7 grew and produced VA from the extract containing no saccharides. The organic acids in the extract promoted the strain to grow. The aromatics in the extract were further concentrated by the solid phase extraction with DIAION HP20 resin, and the organic acids were fractionated into the flow-through fraction. A fed-batch culture of NGC7Δ<em>vanA4B4</em> strain using this concentrated alkaline extract exhibited increased VA production; however, the accumulation of syringate (SA) and 4-hydroxybenzoate (HBA) was also observed along with VA production, despite the strain possessing the genes responsible for SA and HBA degradation. Analysis of the mutants capable of degrading SA while producing VA revealed that mutations in <em>vanR2</em>, a transcriptional repressor of the genes responsible for SA degradation, enabled SA degradation during VA production. In addition, the expression of <em>praI</em>, an HBA hydroxylase derived from <em>Paenibacillus</em> sp. JJ-1b, was suitable for efficient HBA degradation. Thus, the mutation in <em>vanR2</em> and the expression of <em>praI</em> represented the key engineering strategies for achieving the selective VA production. As the growth of the engineered strains was promoted by the organic acids present in the extract, VA production from the concentrated extract was evaluated in a flow-through-based medium supplemented with mineral salts and metals. Finally, the engineered VA-producing strain produced 4.30 mM VA selectively at a yield of 77 mol% in the practical medium.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"141 2","pages":"Pages 125-134"},"PeriodicalIF":2.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145581946","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":"2026-01-01","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}
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