Journal of bioscience and bioengineering最新文献_第3页

Role of the Pho regulon and genetic reconstruction of a phosphite-dependent Escherichia coli. Pho调控子的作用和亚磷酸依赖大肠杆菌的基因重建。

IF 2.9 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-09-01 Epub Date: 2025-06-16 DOI: 10.1016/j.jbiosc.2025.05.012

Naoki Momokawa, Takeshi Ikeda, Takenori Ishida, Kaori Nimura-Matsune, Hisakage Funabashi, Satoru Watanabe, Akio Kuroda, Ryuichi Hirota

{"title":"Role of the Pho regulon and genetic reconstruction of a phosphite-dependent Escherichia coli.","authors":"Naoki Momokawa, Takeshi Ikeda, Takenori Ishida, Kaori Nimura-Matsune, Hisakage Funabashi, Satoru Watanabe, Akio Kuroda, Ryuichi Hirota","doi":"10.1016/j.jbiosc.2025.05.012","DOIUrl":"10.1016/j.jbiosc.2025.05.012","url":null,"abstract":"<p><p>A phosphite (Pt)-dependent biological containment strategy, achieved by introducing a Pt-metabolic pathway and disrupting endogenous phosphate transporters, renders Escherichia coli growth strictly dependent on Pt, a compound rarely detected in natural environments, thereby preventing unintended environmental spread. In this study, we demonstrated that expression of phosphate regulon (Pho regulon) genes was markedly upregulated in a Pt-dependent E. coli strain due to the elimination of phoU, a negative regulator of the Pho regulon, along with the high-affinity phosphate transporter pstSCAB. However, further genetic modification of this strain for detailed analysis was hindered by the presence of multiple antibiotic resistance markers. To overcome this limitation, we reconstructed a Pt-dependent E. coli strain using CRISPR-Cas12a-mediated genome editing, enabling the removal of the antibiotic resistance markers and facilitating subsequent genetic manipulation. Using this strain, we disrupted the PhoBR two-component regulatory genes and found that deletion of phoBR alleviated the constitutive overexpression of Pho regulon genes and partially restored growth of the Pt-dependent strain. These findings provide mechanistic insights and technical advances for the refinement and practical application of Pt-dependent biocontainment strategy.</p>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":"117-122"},"PeriodicalIF":2.9,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144317019","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}

引用次数: 0

Reproducing in vitro artificial gut microbiota using glycerol stocks of fecal cultures combined with different prebiotic additives. 利用粪便培养物的甘油原液结合不同益生元添加剂进行体外人工肠道菌群的繁殖。

IF 2.9 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-09-01 Epub Date: 2025-07-01 DOI: 10.1016/j.jbiosc.2025.06.002

Kengo Sasaki, Yasunobu Takeshima, Ayami Fujino

{"title":"Reproducing in vitro artificial gut microbiota using glycerol stocks of fecal cultures combined with different prebiotic additives.","authors":"Kengo Sasaki, Yasunobu Takeshima, Ayami Fujino","doi":"10.1016/j.jbiosc.2025.06.002","DOIUrl":"10.1016/j.jbiosc.2025.06.002","url":null,"abstract":"<p><p>Artificial human microbiota can be produced in gut simulators from cryopreserved stocks. They are used for in vitro fermentation models and as alternative material for fecal microbiota transplantation therapy. However, current methods have limited information on microbial structure at the genus level and present challenges during cryopreservation. In this study, we used an edible glycerol stock of fecal batch culture instead of fresh feces to create artificial gut microbiota. Three glycerol stocks, generated through in vitro fecal fermentation with different prebiotic additives (such as fructooligosaccharide, xylan, pectin, and guar gum), were combined. Profiling via 16S rRNA gene amplicon sequencing revealed that the artificial gut microbiota derived from the combined glycerol stocks showed more amplicon sequence variants than those from a single glycerol stock. In the artificial microbiota, relative abundance values of common genera such as Bifidobacterium, Bacteroides, Prevotella, Faecalibacterium, and Escherichia were more than 10 % of those found in the original feces. Other commensal genera such as Collinsella, Anaerobutyricum hallii (formerly Eubacterium hallii) group, Anaerostipes, Blautia, Dorea, Lachnospiraceae UCG-004, and Oscillospiraceae UCG-003 were similarly maintained. Our data indicated that combining glycerol stocks of fecal cultures with different additives in a batch-type gut simulator is a useful option for producing artificial gut microbiota, the taxonomic compositions of which are comparable to those of the original feces.</p>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":" ","pages":"154-161"},"PeriodicalIF":2.9,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540340","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}

引用次数: 0

High productivity of cellulase and xylanase enzymes in the mycelial-dispersed Pleurotus ostreatus Δpkac2 strain 菌丝分散平菇Δpkac2菌株纤维素酶和木聚糖酶高产性研究。

IF 2.9 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-08-29 DOI: 10.1016/j.jbiosc.2025.08.001

Yuitsu Otsuka , Moriyuki Kawauchi , Vladimir Elisashvili , Saori Endo , Kenya Tsuji , Akira Yoshimi , Chihiro Tanaka , Takehito Nakazawa , Toshikazu Irie , Yoichi Honda

{"title":"High productivity of cellulase and xylanase enzymes in the mycelial-dispersed Pleurotus ostreatus Δpkac2 strain","authors":"Yuitsu Otsuka , Moriyuki Kawauchi , Vladimir Elisashvili , Saori Endo , Kenya Tsuji , Akira Yoshimi , Chihiro Tanaka , Takehito Nakazawa , Toshikazu Irie , Yoichi Honda","doi":"10.1016/j.jbiosc.2025.08.001","DOIUrl":"10.1016/j.jbiosc.2025.08.001","url":null,"abstract":"<div><div>White-rot fungi secrete unique enzymes to degrade plant cell wall components. These enzymes have the potential to improve the effective utilization of lignocellulosic biomass in a bio-based society. In our previous study, <em>pkac2</em>-disrupted strains of <em>Pleurotus ostreatus</em> were applied for high-density liquid culture by improving mycelial dispersibility. In this study, we investigated the productivity and transcriptional profiles of wood-degrading enzymes of the Δ<em>pkac2</em> strain in the high-density liquid cultivation. Cellulase and xylanase activities in the culture filtrate of Δ<em>pkac2</em> strains in liquid shaking culture were 7.8- and 49-fold higher than those of the wild-type (WT) strain, respectively. In this condition, the mycelial dry weight of Δ<em>pkac2</em> strains was two-fold higher than that of the WT, showing their greater efficiencies for cellulase and xylanase production than the WT. RNA-Seq analysis indicated that 9 of 35 predicted cellulase genes and two of five predicted xylanase genes were significantly upregulated in the Δ<em>pkac2</em> strains. On the contrary, the transcript levels of laccase-encoding genes were significantly decreased, indicating that <em>pkac2</em> is involved in their transcriptional regulation. These results indicate that the Δ<em>pkac2</em> strains have high potential to produce cellulase and xylanase in the high-density liquid cultivation by increasing mycelial growth as well as upregulating the expression of relevant genes.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"140 5","pages":"Pages 277-283"},"PeriodicalIF":2.9,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955368","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}

引用次数: 0

Injectability of temperature-responsive hydrogel derived from elastin-like polypeptide for cell delivery 由弹性蛋白样多肽衍生的温度响应水凝胶的可注射性。

IF 2.9 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-08-23 DOI: 10.1016/j.jbiosc.2025.08.003

Mutawakil Al Muqadasi , Keitaro Ii , Kei Nishida , Masayasu Mie , Eiry Kobatake

{"title":"Injectability of temperature-responsive hydrogel derived from elastin-like polypeptide for cell delivery","authors":"Mutawakil Al Muqadasi , Keitaro Ii , Kei Nishida , Masayasu Mie , Eiry Kobatake","doi":"10.1016/j.jbiosc.2025.08.003","DOIUrl":"10.1016/j.jbiosc.2025.08.003","url":null,"abstract":"<div><div>Injectable hydrogels are promising biomaterials for tissue engineering applications due to their ability to deliver bioactive compounds or cells with minimal invasiveness. Temperature-responsive <em>in situ</em> gelling hydrogels, which undergo transition from liquid to gel in response to temperature stimuli, are desirable candidates for injectable hydrogels. Elastin-like polypeptides (ELPs) are well-known temperature-responsive biomaterials for cell scaffolds, drug delivery, and tissue engineering, due to their biocompatibility, biodegradability, and tunable mechanical properties. However, due to high hydrophobicity and heterogeneous aggregation, the development of injectable hydrogel-derived ELPs remains limited. In our previous study, we designed coiled-coil unit-bound ELPs (CUBEs) hydrogel systems, which integrate ELPs, a polyaspartic acid (polyD) chain, a functional peptide, and a coiled-coil peptide. In this study, we evaluated the injectability and cell delivery potential of a basic CUBE hydrogel system, called O-CUBE (AVGVP)<sub>42</sub>-D<sub>88</sub>-CL. The O-CUBE protein solution was mixed with human cervical cancer (HeLa) cells, serving as a cell model, and subsequently injected into culture medium pre-warmed to 37 °C to initiate <em>in situ</em> gelation. O-CUBE protein was successfully gelled at an approximately 90 % gelation rate after injection at 37 °C within pH ranges of 6–8. Encapsulated HeLa cells exhibited spheroid morphology, indicating that the hydrogel facilitated cell–cell interactions in three-dimensional culture. Further evaluation using a DNA assay revealed that HeLa cells can survive and proliferate within the hydrogel. These results demonstrate that the CUBE hydrogel system is a promising candidate to deliver cells with minimal invasiveness.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"140 5","pages":"Pages 350-356"},"PeriodicalIF":2.9,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955452","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}

引用次数: 0

Identification of toluene degradation genes in Acinetobacter sp. Tol 5 不动杆菌Tol 5中甲苯降解基因的鉴定。

IF 2.9 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-08-21 DOI: 10.1016/j.jbiosc.2025.07.010

Shogo Yoshimoto , Maiko Hattori , Shori Inoue , Sakura Mori , Yuki Ohara , Katsutoshi Hori

{"title":"Identification of toluene degradation genes in Acinetobacter sp. Tol 5","authors":"Shogo Yoshimoto , Maiko Hattori , Shori Inoue , Sakura Mori , Yuki Ohara , Katsutoshi Hori","doi":"10.1016/j.jbiosc.2025.07.010","DOIUrl":"10.1016/j.jbiosc.2025.07.010","url":null,"abstract":"<div><div>Microbial degradation of aromatic compounds provides sustainable solutions for environmental remediation and bioconversion. <em>Acinetobacter</em> sp. Tol 5 is notable for its strong adhesiveness and potential as a biocatalyst for toluene degradation; however, its toluene metabolic pathway has not been fully elucidated. In this study, genomic analysis identified a cluster of genes in Tol 5 highly similar to the well-known <em>tod</em> operon of <em>Pseudomonas putida</em>, encoding enzymes responsible for toluene metabolism. Phylogenetic analyses indicated that these <em>tod</em> genes, unusual among <em>Acinetobacter</em> species, were likely acquired through horizontal gene transfer. Transcriptomic analyses revealed that <em>todF</em> and <em>todC1</em> are co-transcribed, while the adjacent <em>fadL2</em> gene, encoding a putative outer membrane transporter corresponding to <em>P. putida todX</em>, is independently transcribed. Growth experiments using gene-knockout mutants revealed that TodC1, the large subunit of dioxygenase, is essential for growth on toluene, whereas FadL2 is not essential. Growth curves on each carbon source further showed that the <em>todC1</em> knockout mutant could metabolize benzoate, but not toluene or benzene, confirming that the TOD pathway is the primary route for toluene and benzene degradation in Tol 5. The identification of the functional TOD pathway, which is unique within <em>Acinetobacter</em>, provides genetic and biochemical insights for the development of Tol 5 as an efficient immobilized biocatalyst for the bioremediation and bioconversion of aromatic compounds.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"140 5","pages":"Pages 284-289"},"PeriodicalIF":2.9,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955288","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}

引用次数: 0

Application of a mitigation method for nitrous oxide emission in a full-scale Carrousel reactor: Carbon footprint assessment 一种减缓氧化亚氮排放方法在全尺寸Carrousel反应堆中的应用：碳足迹评估。

IF 2.9 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-08-21 DOI: 10.1016/j.jbiosc.2025.07.009

Shohei Otomo , Akihiko Terada , Satoru Shibata , Tomoyuki Hori , Eisuke Tamura , Masahiro Ito , Yu-You Li , Fumiaki Takakai , Kunihiro Okano , Naoyuki Miyata , Shuhei Masuda

{"title":"Application of a mitigation method for nitrous oxide emission in a full-scale Carrousel reactor: Carbon footprint assessment","authors":"Shohei Otomo , Akihiko Terada , Satoru Shibata , Tomoyuki Hori , Eisuke Tamura , Masahiro Ito , Yu-You Li , Fumiaki Takakai , Kunihiro Okano , Naoyuki Miyata , Shuhei Masuda","doi":"10.1016/j.jbiosc.2025.07.009","DOIUrl":"10.1016/j.jbiosc.2025.07.009","url":null,"abstract":"<div><div>Nitrous oxide (N<sub>2</sub>O) emissions from biological nitrogen removal processes in sewage treatment plants greatly contribute to their overall carbon footprint. The present study aimed to mitigate N<sub>2</sub>O emissions from an elliptical Carrousel bioreactor in a full-scale plant. The oxygen supply agitators equipped at the influent point and the opposite side of the reactor was operated alternately. The dissolved N<sub>2</sub>O (DN<sub>2</sub>O) concentrations were lowered when the agitator at the influent point was suspended while that on the opposite side was running. This scenario was associated with high levels of complementary DNA (RNA) from potential complete denitrifying bacteria, indicating increased N<sub>2</sub>O reduction activity utilizing influent organic matter. However, during periods of reduced influent organic load, dissolved oxygen (DO) levels temporarily increased; thereafter, DN<sub>2</sub>O increased, accompanied by a decrease in DO. This fluctuation was associated with the accumulation of nitrite and nitrate resulting from ammonia oxidation during the high-DO periods. Based on these findings, an N<sub>2</sub>O mitigation strategy was implemented: reducing the oxygen supply and increasing the running time of the opposite-side agitator during the low-organic-loading periods. This approach effectively decreased the DN<sub>2</sub>O levels, although a certain degree of instability remained during rainfall events. The median N<sub>2</sub>O emission factor decreased from 0.86 % to 0.28 %, reducing the annual carbon footprint of the plant by 14 %. This study provides valuable insights into N<sub>2</sub>O mitigation for full-scale plants and demonstrates the great impact of N<sub>2</sub>O reduction on their carbon footprint.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"140 5","pages":"Pages 332-340"},"PeriodicalIF":2.9,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144955371","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}

引用次数: 0

Nitrogen removal and N2O emissions in anammox reactors: Influence of reactor design on process performance and microbial communities 厌氧氨氧化反应器中的氮去除和N2O排放：反应器设计对工艺性能和微生物群落的影响。

IF 2.9 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-08-14 DOI: 10.1016/j.jbiosc.2025.07.007

Jean De Dieu Shema , Satoshi Nakai , Takehiko Gotoh , Wataru Nishijima , Toshikazu Suenaga

{"title":"Nitrogen removal and N2O emissions in anammox reactors: Influence of reactor design on process performance and microbial communities","authors":"Jean De Dieu Shema , Satoshi Nakai , Takehiko Gotoh , Wataru Nishijima , Toshikazu Suenaga","doi":"10.1016/j.jbiosc.2025.07.007","DOIUrl":"10.1016/j.jbiosc.2025.07.007","url":null,"abstract":"<div><div>The assessment and mitigation of N<sub>2</sub>O emissions from anammox-related processes is challenging for environmentally friendly wastewater treatment. This study evaluated the nitrogen removal efficiency (NRE), N<sub>2</sub>O emissions, and microbial diversity in three laboratory-scale anammox reactors: a sequencing batch reactor (SBR) with a recirculation line, a continuous stirred tank reactor (CSTR) without a recirculation line (CSTR1), and a CSTR with a recirculation line (CSTR2). Across two operational phases with anammox biomass (dry weight) of 1.63 g L<sup>−1</sup> (phase I) and 5.44 g L<sup>−1</sup> (phase II), the SBR had a higher NRE and lower N<sub>2</sub>O emissions than the CSTRs. The NREs in phase II were 70.7 ± 14.1 % for the SBR, 68.9 ± 15.7 % for CSTR2, and 41.9 ± 15.8 % for CSTR1. N<sub>2</sub>O emissions from the SBR were reduced by 56 % in phase II relative to phase I. Microbial diversity declined, and community composition shifted during reactor operation. In phase II, the Shannon entropy indices were 4.77 (SBR), 4.61 (CSTR2), and 5.04 (CSTR1); higher diversity in CSTR1 correlated with lower anammox abundance and thus lower performance. <em>Candidatus</em> Jettenia caeni became the predominant anammox species. Gene analysis revealed a positive correlation between the abundance of anammox-specific 16S rRNA genes (targeted by <em>Amx809f/Amx1066r</em>) and NRE, while <em>nirS</em> and <em>nirK</em> gene copy numbers were inversely related to reactor performance (NRE and N<sub>2</sub>O emissions). The copy numbers of <em>nosZ</em> genes (clade I and clade II) varied in phase II across different reactors, which potentially contributed to the differences in N<sub>2</sub>O emission reductions observed during this phase.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"140 5","pages":"Pages 320-331"},"PeriodicalIF":2.9,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859243","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}

引用次数: 0

Establishment of genome editing techniques in the marine oleaginous diatom Fistulifera solaris for improved oil accumulation 海洋产油硅藻fisstulifera solaris基因组编辑技术的建立，以改善油脂积累。

IF 2.9 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-08-13 DOI: 10.1016/j.jbiosc.2025.07.008

Satoshi Murata , Natsuno Kushiyama , Yusuke Yabu , Kahori Watanabe , Taiga Fujii , Rein Yasui , Daisuke Nojima , Yoshiaki Maeda , Tomoko Yoshino , Yusuke Matsuda , Tsuyoshi Tanaka

{"title":"Establishment of genome editing techniques in the marine oleaginous diatom Fistulifera solaris for improved oil accumulation","authors":"Satoshi Murata , Natsuno Kushiyama , Yusuke Yabu , Kahori Watanabe , Taiga Fujii , Rein Yasui , Daisuke Nojima , Yoshiaki Maeda , Tomoko Yoshino , Yusuke Matsuda , Tsuyoshi Tanaka","doi":"10.1016/j.jbiosc.2025.07.008","DOIUrl":"10.1016/j.jbiosc.2025.07.008","url":null,"abstract":"<div><div>Biofuel production using microalgae has attracted considerable attention owing to high growth rate and lipid accumulation properties. However, further enhancement in lipid productivity is required to render this economically feasible. CRISPR/Cas9, which is one of the powerful genome editing tools, is an essential technique that may solve this problem. The marine diatom <em>Fistulifera solaris</em> JPCC DA0580 is a promising candidate of the biofuel production, since it accumulates significant amount of lipids. However, genome editing techniques have not yet been established for <em>F. solaris</em>, which prevent the construction of valuable strains. In this study, CRISPR/Cas9-mediated specific gene knockout technique was established in <em>F. solaris</em>, through targeting adenine phosphoribosyl transferase gene (<em>apt</em>) and triacylglycerol (TAG) lipase gene (<em>tgl1</em>). Mutations in the target sequence were detected in <em>apt</em>- and <em>tgl1</em>-edited mutants. Moreover, the mutants showed distinct phenotypes, such as suppression of TAG degradation and resistance to 2-fluoroadenine. These results indicate the successful demonstration of CRISPR/Cas9-mediated genome editing in the oleaginous marine diatom <em>F. solaris</em>. Furthermore, oil degradation was successfully suppressed by knocking-out <em>tgl1</em>. The CRISPR/Cas9-mediated genome editing established in this study provides key molecular tools for both the basic biology and the future biotechnological applications of <em>F. solaris</em>, such as biofuel production.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"140 5","pages":"Pages 271-276"},"PeriodicalIF":2.9,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144846630","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}

引用次数: 0

Metabolomics-based investigation of the differences between traditional and modern soy sauce 基于代谢组学的传统酱油与现代酱油差异研究。

IF 2.9 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-08-11 DOI: 10.1016/j.jbiosc.2025.07.004

Yoshika Maekawa , Miki Nakamura , Miho Imamura , Eiichiro Fukusaki

{"title":"Metabolomics-based investigation of the differences between traditional and modern soy sauce","authors":"Yoshika Maekawa , Miki Nakamura , Miho Imamura , Eiichiro Fukusaki","doi":"10.1016/j.jbiosc.2025.07.004","DOIUrl":"10.1016/j.jbiosc.2025.07.004","url":null,"abstract":"<div><div>Soy sauces can be classified into three categories based on the production method used: <em>honjozo</em>, <em>kongojozo</em> (mixed-brewing, amino acid-decomposed), and <em>kongo</em> (mixed, amino acid-decomposed) soy sauces. Although differences in flavor between traditional (<em>honjozo</em>) and modern (amino acid-decomposed) soy sauces are clear, knowledge of the differences in compound profiles and the relationship between these and the sensory characteristics that affect soy sauce quality is limited. Therefore, this study aimed to investigate the differences between traditional and modern soy sauce compounds using metabolomic analysis, and to investigate the compounds that may be correlated with differences in flavor. Non-targeted gas chromatography/mass spectrometry (GC/MS) metabolomics analysis was performed on nine traditional and six modern soy sauces to annotate 239 soy sauce compounds. Principal component analysis suggested that the production methods used formed clusters that affected the types and amounts of soy sauce compounds, and that the production method had a greater effect on soy sauce composition than did the aging barrels or type of soybean used. Traditional soy sauce was characterized by alcohols and esters, whereas modern soy sauce was characterized by pyrazines. A sensory evaluation revealed that traditional soy sauce was characterized by bitterness and astringency, whereas modern soy sauce was characterized by sweetness and viscosity, suggesting that the method of soy sauce production influences flavor differences. This is the first study to comprehensively characterize the effects of production methods, aging barrels, and soybean types on soy sauce compounds and how these compounds contribute to differences in flavor.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"140 5","pages":"Pages 290-297"},"PeriodicalIF":2.9,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144835200","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}

引用次数: 0

Ribonucleoprotein-based CRISPR/Cas9 genome co-editing in Aspergillus luchuensis mut. kawachii 基于核糖核蛋白的CRISPR/Cas9基因组共编辑在葡曲霉中的应用kawachii。

IF 2.9 4区生物学

Journal of bioscience and bioengineering Pub Date : 2025-08-06 DOI: 10.1016/j.jbiosc.2025.07.006

Takefumi Karashima , Ken Oda , Taiki Futagami , Hideki Hokazono , Hideharu Takashita

{"title":"Ribonucleoprotein-based CRISPR/Cas9 genome co-editing in Aspergillus luchuensis mut. kawachii","authors":"Takefumi Karashima , Ken Oda , Taiki Futagami , Hideki Hokazono , Hideharu Takashita","doi":"10.1016/j.jbiosc.2025.07.006","DOIUrl":"10.1016/j.jbiosc.2025.07.006","url":null,"abstract":"<div><div>In this study, we established a ribonucleoprotein-based clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome co-editing method for the white koji fungus, <em>Aspergillus luchuensis</em> mut. <em>kawachii</em>. To introduce the single guide RNA-Cas9 ribonucleoprotein complex into protoplast cells of <em>A. luchuensis</em> mut. <em>kawachii</em>, we investigated the conditions for protoplast preparation using Yatalase -Plus-. Subsequently, we employed the ribonucleoprotein-based method to knockout the ATP sulfurylase-encoding <em>sC</em> gene, which imparts selenate resistance in the model strain NBRC 4308 and the industrial strain No. 8046. Furthermore, we explored genome co-editing by simultaneously targeting <em>sC</em> along with either the orotidine 5′-phosphate decarboxylase-encoding <em>pyrG</em> gene or the transcriptional activator of protease genes-encoding <em>prtR</em> gene in NBRC 4308. The transformants were selected in medium containing selenate, resulting in the successful generation of <em>pyrG</em>- and <em>prtR</em>-knockout strains. Similarly, transformants were selected on medium containing selenate, resulting in the successful generation of <em>prtR</em>-knockout strain in No. 8046. These results demonstrate that the ribonucleoprotein-based genome co-editing method is applicable not only to the model strain but also to industrial strains, making it a promising approach for manipulating <em>A. luchuensis</em> mut. <em>kawachii</em>.</div></div>","PeriodicalId":15199,"journal":{"name":"Journal of bioscience and bioengineering","volume":"140 5","pages":"Pages 298-305"},"PeriodicalIF":2.9,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144799199","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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