Maxime Maton , Baptiste Leroy , Alain Vande Wouwer
{"title":"A constructive bottom-up approach for the elaboration of metabolic networks: Case study of photosynthetic cyanobacteria Arthrospira spirulina platensis PCC 8005","authors":"Maxime Maton , Baptiste Leroy , Alain Vande Wouwer","doi":"10.1016/j.bej.2025.109770","DOIUrl":"10.1016/j.bej.2025.109770","url":null,"abstract":"<div><div>Mathematical modeling has proven to be a highly effective tool for understanding microbial metabolism for which in-silico and experimental studies help to quantify intracellular mechanisms and pave the way for optimizing the production of molecules of interest. In that context, the development of metabolic networks turns out to be particularly interesting despite the challenges underlying their reconstruction. While the elaboration of genome-scale networks is computationally costly, small networks are often oversimplified and important biological mechanisms might be omitted, which limits their use in industrial applications. For this purpose, this study proposes a constructive bottom-up approach for the identification of metabolic networks of intermediate size, typically comprised of a couple of hundred reactions. It combines basic biological knowledge and a series of constraint-based methods in an iterative strategy, enabling the refinement of the network definition. The network is first validated using in-silico data, and subsequently refined using experimental data to enhance its biological relevance. Several case studies have been addressed to assess the efficiency of the methodology, and this paper focuses on the modeling of photosynthetic cyanobacteria <em>Arthrospira</em> sp. PCC 8005. The procedure is effective and provides promising results and metabolic analyses show consistent predictive capabilities of the network, in concordance with existing studies.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109770"},"PeriodicalIF":3.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143941238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yiwei Zhou , Shaochen Bian , Hua Wang , Yixuan Chu , Lei Zheng , Yali Song , Chengran Fang
{"title":"Corrigendum to: “Responses of nitrogen removal, microbial community and antibiotic resistance genes to biodegradable microplastics during biological wastewater treatment” [Biochem. Eng. J. 219 (2025) 109732]","authors":"Yiwei Zhou , Shaochen Bian , Hua Wang , Yixuan Chu , Lei Zheng , Yali Song , Chengran Fang","doi":"10.1016/j.bej.2025.109774","DOIUrl":"10.1016/j.bej.2025.109774","url":null,"abstract":"","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"220 ","pages":"Article 109774"},"PeriodicalIF":3.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Development of an artificial biosynthetic pathway for biosynthesis of cinnamyl cinnamate in engineered Escherichia coli","authors":"Jin Yang , Qiuli Wang , Hong Pan , Daoyi Guo","doi":"10.1016/j.bej.2025.109771","DOIUrl":"10.1016/j.bej.2025.109771","url":null,"abstract":"<div><div>Cinnamyl cinnamate is a key flavoring and bioactive compound present in various plants. It is used in a variety of products including fragrances for decorative cosmetics, fine fragrances, shampoos, toilet soaps, and other toiletries, as well as in non-cosmetic items such as household cleaners and detergents. The production of cinnamyl cinnamate through plant extraction and chemical synthesis is inefficient and environmentally unfriendly. Therefore, a promising and attractive alternative is the production of cinnamyl cinnamate from renewable carbon sources using microbial cell factories. In this study, the construction of a <em>de novo</em> cinnamyl cinnamate pathway in <em>Escherichia coli</em> has been demonstrated for the first time. Subsequently, by increasing the supply of precursor substrates, we have further improved the biosynthesis of cinnamyl cinnamate. Finally, by knocking out the <em>tyrA</em> gene to block the competitive pathway, the cinnamyl cinnamate production was increased to 769 mg/L. It represents a sustainable and environmentally friendly alternative for the synthesis of cinnamyl cinnamate.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109771"},"PeriodicalIF":3.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143927752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Emmanuel Chimeh Ezeako , Barine Innocent Nwiloh , Malachy Chigozie Odo , Vincent E. Ozougwu
{"title":"Harnessing synthetic biology for sustainable industrial innovation: Advances, challenges, and future direction","authors":"Emmanuel Chimeh Ezeako , Barine Innocent Nwiloh , Malachy Chigozie Odo , Vincent E. Ozougwu","doi":"10.1016/j.bej.2025.109777","DOIUrl":"10.1016/j.bej.2025.109777","url":null,"abstract":"<div><div>Synthetic biology (Synbiology) is an emerging science that leverages the genetic engineering of biological systems to accomplish industrial operations and produce valuable and desired products. Synbiology-inspired fabrication and reprogramming of biological systems has opened avenues for unearthing critical questions in chemical and biological engineering and harnessing the production of value-added chemicals, including biotherapeutics, food items, biocosmetics, biopolymers, and biofuels. However, engineering biological systems still lags far behind designing physical systems in precision, scalability, and market viability. Tackling these limitations is essential to unlocking the full industrial potential of Synbiology, from molecular compound selection to large-scale commercial production. This review x-rays the innovative contributions of Synbiology to industrial operations, emphasizing its role in advancing sustainable production of high-value chemicals, enhancing industrial efficiency, optimizing biofuel production, and enabling carbon capture and utilization. The findings highlight the pivotal role of Synbiology-based technology in driving a bio-based economy and fostering a sustainable future while identifying technical bottlenecks that must be addressed to elevate bioengineering practices to match other engineering disciplines.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109777"},"PeriodicalIF":3.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144084145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Linsong Luo , Xiao Han , Xiaoyan Dong , Qinghong Shi , Yan Sun
{"title":"Polyvinylpyrrolidone-assisted in situ enzymes encapsulation within ZIF-8 for enhanced glycerol conversion","authors":"Linsong Luo , Xiao Han , Xiaoyan Dong , Qinghong Shi , Yan Sun","doi":"10.1016/j.bej.2025.109778","DOIUrl":"10.1016/j.bej.2025.109778","url":null,"abstract":"<div><div>The growth of biodiesel and oleochemical industries results in substantial surpluses of glycerol and consistently low prices. To absorb this surplus, we report a polymer-assisted <em>in situ</em> enzymes encapsulation strategy in which glycerol dehydrogenase (GDH) is encapsulated with polyvinylpyrrolidone (PVP) and cysteine (Cys) within ZIF-8 for glycerol conversion. The results showed that the encapsulated GDH/ZIF-8 composites presented stronger substrate affinities and higher catalytic efficiencies than free GDH as well as good stability. Among the free GDH and GDH/ZIF-8 composites, GDH/Cys/PVP@ZIF-8 presented the highest relative activity of 300.7 %. This could be attributed to the structural evolution of the encapsulated GDH and the formation of a more hydrophilic microenvironment around GDH during complexation with PVP. To increase cofactor utilization, a cofactor self-sufficient cascade system was constructed by encapsulating GDH and forming H<sub>2</sub>O NADH oxidase (Nox) with PVP and Cys within ZIF-8 for the conversion of glycerol to 1,3-dihydroxyacetone (DHA). At the optimal GDH:Nox molar ratio (4:1) and a substrate concentration of 100 mM, the DHA yield reached approximately 4.2 mM in GDH-Nox/Cys/PVP@ZIF-8, and the total turnover number of GDH-Nox/Cys/PVP@ZIF-8 reached 2787 at 0.05 µM NAD<sup>+</sup>, indicating its feasibility for large-scale DHA production. This work has thus provided a promising procedure of co-immobilizing enzymes via Cys/PVP-assisted <em>in situ</em> encapsulation within ZIF-8 for the development of economically viable multienzyme biocatalysts for glycerol conversion.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109778"},"PeriodicalIF":3.7,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143924737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yajie Li , Yuyao Zhang , Ou Wang , Weikang Kong , Salma Tabassum
{"title":"Anodic modification-enhanced microbial electrolysis cell coupled with anaerobic digestion for coal gasification wastewater treatment","authors":"Yajie Li , Yuyao Zhang , Ou Wang , Weikang Kong , Salma Tabassum","doi":"10.1016/j.bej.2025.109767","DOIUrl":"10.1016/j.bej.2025.109767","url":null,"abstract":"<div><div>The treatment of coal gasification wastewater (CGW) by anodic modification enhanced microbial electrolysis cell coupled with anaerobic digestion was discussed. In this study, iron sulfate was used to load modified biochar to obtain anode modified materials. The results showed that the electrode modification effectively improved the specific surface area of the graphite felt electrode, The conductivity of modified Fe<sub>2</sub>(SO<sub>4</sub>)<sub>3</sub> activated carbon was 191.4 ± 0.16 μS/cm, Fe-O-C functional groups boost electrode surface electron transfer. Three reactors were set up as the experimental groups: the anaerobic (AD) reactor (R1) as the control group, the microbial electrolysis cell coupled anaerobic digestion (MEC-AD) reactor (R2) and, the anode modified microbial electrolysis cell coupled anaerobic digestion (MEC-AD) reactor (R3). The results showed that R1, R2 and R3 had average removal rates of total phenol by 41 %, 48 % and 67 %, respectively. The degradation trend of quinoline and indole in R1, R2 and R3 was similar to that of total phenol. The degradation rates of quinoline and indole in R3 were the highest, reaching 86 % and 89 %, respectively. The electrode modification is beneficial to improve the treatment effect of MEC-AD. In addition, electrode modification promoted the enrichment of electroactive microorganisms such as <em>Syntrophus</em> and <em>Pseudomonas</em>, which was conducive to promoting direct interspecies electron transfer (DIET) and enhancing the degradation of organic pollutants.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"220 ","pages":"Article 109767"},"PeriodicalIF":3.7,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143923865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qibin Wang , Jing Yang , Weijie Cao , Hu Liu , Chun Li
{"title":"Engineering robust β-glucuronidase via protein assembly and immobilization for enhanced glycyrrhizin hydrolysis","authors":"Qibin Wang , Jing Yang , Weijie Cao , Hu Liu , Chun Li","doi":"10.1016/j.bej.2025.109772","DOIUrl":"10.1016/j.bej.2025.109772","url":null,"abstract":"<div><div><em>β</em>-Glucuronidase (GUS) plays a crucial role in modifying glycyrrhizin (GL) to enhance its physicochemical properties and biological activities. However, most enzymes suffer from poor thermostability and high production costs, limiting their industrial applications. In this study, we utilized the SpyTag-SpyCatcher pair to assemble tetrameric <em>Aspergillus oryzae</em> GUS (PGUS) into higher-order structures. The thermostability of PGUS was significantly improved by optimizing the assembly sites. Furthermore, we coated an organosilica network (OSN) onto <em>Escherichia coli</em> cells expressing PGUS assemblies using tetraethoxysilane (TEOS) and 3-aminopropyltriethoxysilane (APTES), constructing an immobilized PGUS system. This integrated approach not only enhanced PGUS thermostability without compromising its catalytic activity but also improved the reusability and long-term operational stability, offering a sustainable solution for industrial biocatalysis.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"221 ","pages":"Article 109772"},"PeriodicalIF":3.7,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143927753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lin Li , Jiahua Li , Xiaoying Yu , Bo Wei , Yizhan Liu , Jingyi Zhu , Huaji Sun , Gang Zhou
{"title":"N-octanoyl-DL-homoserine lactone-mediated quorum sensing enhances microbial degradation of petroleum hydrocarbons in saline-alkali soils","authors":"Lin Li , Jiahua Li , Xiaoying Yu , Bo Wei , Yizhan Liu , Jingyi Zhu , Huaji Sun , Gang Zhou","doi":"10.1016/j.bej.2025.109768","DOIUrl":"10.1016/j.bej.2025.109768","url":null,"abstract":"<div><div>Bioremediation of petroleum-contaminated soil is limited by the inherent capacity of indigenous microorganisms to metabolize petroleum hydrocarbons. Microbial proliferation could stimulate the biodegradation of pollutants. This study investigated the ability of exogenous N-octanoyl-DL-homoserine lactone (C8-HSL) to improve hydrocarbon degradation through quorum sensing (QS) regulation. <em>Pseudomonas Stutzeri</em> M3 was inoculated into petroleum-contaminated soil to elucidate the regulatory mechanisms of C8-HSL-mediated QS on several key factors of petroleum degradation. Specifically, it affects soil respiration activity, the activity of key degradation enzymes, and the role of extracellular polymeric substances (EPS). The findings demonstrate that adding 100 nM C8-HSL significantly increased the degradation rate of petroleum hydrocarbons in soil by 37.83 % and markedly abbreviated the overall bioremediation time. Concurrently, exogenous acyl-homoserine lactone (AHL) has been shown to augment the quantity and diversify the composition of EPS in the system. The interaction between 100 nM C8-HSL and predominant degrading bacteria (<em>Pseudomonas</em>) facilitates the enrichment of petroleum hydrocarbon-degrading microbial populations. This study elucidates the QS-driven mechanisms underlying efficient total petroleum hydrocarbon (TPH) degradation in soil matrices, demonstrating the pivotal role of C8-HSL in stimulating indigenous microorganisms for oilfield bioremediation. Our findings provide novel mechanistic insights into AHL-mediated QS regulation of microbial petroleum degradation. The petroleum-contaminated soil remediation technology has dual advantages in treatment efficiency and economic benefits, and it is economically and practically significant.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"220 ","pages":"Article 109768"},"PeriodicalIF":3.7,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143906764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dan-Feng Liu , Xin Xin , Ru-Jie Shang , Zi Wei Luo , Bing-Zhi Li , Zhi-Hua Liu
{"title":"Microbial synthesis of terephthalic acid via Saccharomyces cerevisiae cell factories","authors":"Dan-Feng Liu , Xin Xin , Ru-Jie Shang , Zi Wei Luo , Bing-Zhi Li , Zhi-Hua Liu","doi":"10.1016/j.bej.2025.109766","DOIUrl":"10.1016/j.bej.2025.109766","url":null,"abstract":"<div><div>Terephthalic acid (TPA) is a key industrial chemical widely used in plastic films, bottle containers, pharmaceutical intermediates, and various other applications. Microbial synthesis of TPA has significant potential for sustainable development. In this study, a <em>Saccharomyces cerevisiae</em> cell factory was successfully designed to synthesize TPA using multiple engineering techniques. A genetically engineered <em>S. cerevisiae</em> strain was first constructed and used as the chassis by knocking out six alcohol dehydrogenases to block the branched metabolic pathways of intermediate metabolites such as <em>p</em>-tolualdehyde and 4-carboxybenzaldehyde. Screening of the integration loci helped to improve the titer of <em>p</em>-toluic acid in <em>S. cerevisiae</em>. Through several rounds of integration and enzyme fusion engineering, the heterogeneous TsaMB enzyme was successfully expressed in <em>S. cerevisiae</em>, enabling TPA biosynthesis via a well-planned two-stage biphasic fermentation strategy. Stepwise fermentation optimization revealed critical factors for increasing the TPA yield, with a 2.6-fold increase in the 4-carboxybenzyl alcohol titer and 33.5 % increase in the TPA titer by multiplying the copy number of <em>tsaC</em> gene. Ultimately, a <em>S. cerevisiae</em> cell factory achieved a TPA titer of 131.5 mg/L, corresponding to a conversion yield of 24.1 mol%. These results demonstrate the viability of microbial cell factory for TPA biosynthesis and provide new opportunities for the sustainable production of TPA.</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"220 ","pages":"Article 109766"},"PeriodicalIF":3.7,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143899435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Anjan Kumar , Ahmed M. Naglah , Yashwantsinh Jadeja , Suhas Ballal , Shaker Al-Hasnaawei , Abhayveer Singh , T. Krithiga , Subhashree Ray , Chou-Yi Hsu
{"title":"Developing novel photoactive bimetal Cr/Ag-codoped CeO2 nanozymes with synergistic activity toward biophotodegradation of organic dyes from real water media and textile wastewater","authors":"Anjan Kumar , Ahmed M. Naglah , Yashwantsinh Jadeja , Suhas Ballal , Shaker Al-Hasnaawei , Abhayveer Singh , T. Krithiga , Subhashree Ray , Chou-Yi Hsu","doi":"10.1016/j.bej.2025.109765","DOIUrl":"10.1016/j.bej.2025.109765","url":null,"abstract":"<div><div>A novel biophotodegradation method of organic dyes was developed using photoactive bimetal Cr/Ag-codoped CeO<sub>2</sub> nanozymes with synergistic activity toward dye biophotodegradation from real water media and textile wastewater. The photoactive bimetal Cr/Ag-codoped CeO<sub>2</sub> nanozymes were synthesized and then comprehensively identified using several characterization methods. The developed bimetal Cr/Ag-codoped CeO<sub>2</sub> nanozymes revealed enhanced peroxidase-like activity. The introduced bimetal Cr/Ag-codoped CeO<sub>2</sub> nanozymes exhibited 6.66-order, 3.53-fold, and 2.0-order higher enzyme-like activity than the CeO<sub>2,</sub> Ag-CeO<sub>2,</sub> and Cr-CeO<sub>2</sub>, respectively, revealing the synergistic effect of bimetal-codoping on their catalytic activity. The photonanozymatic activity of the nanozymes was found to be 1.47-fold and 2.48-order higher than their nanozymatic and photocatalytic activity, respectively. Hence, they were applied for environmental mineralization applications via biophotodegradation of methylene blue. The effective factors on the yield of biodegradation were optimized by the one-factor-at-a-time method, providing maximal biophotodegradation of 99.95 % within 7.0 min. The storage and cycling stability of the developed photoactive bimetal Cr/Ag-codoped CeO<sub>2</sub> nanozymes were assessed, exhibiting that they are sable for at-least 30 days and 10 recycles without any change in their activity. The method was then practically applied for the treatment of water media (biophotodegradation, 98.7–99.6 %) and textile wastewater (biophotodegradation, 89.6–99.5 %).</div></div>","PeriodicalId":8766,"journal":{"name":"Biochemical Engineering Journal","volume":"220 ","pages":"Article 109765"},"PeriodicalIF":3.7,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143868684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}