Metabolic engineering最新文献_第3页

Enhancing oil feedstock utilization for high-yield low-carbon polyhydroxyalkanoates industrial bioproduction 提高石油原料利用率，促进高产低碳聚羟基烷酸酯工业生物生产

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2025-04-04 DOI: 10.1016/j.ymben.2025.04.001

Tianyu Jiang , Tingting Tan , Zhiyuan Zong , Dingding Fan , Jianxin Wang , Yanci Qiu , Xin Teng , Haoqian M. Zhang , Chitong Rao

{"title":"Enhancing oil feedstock utilization for high-yield low-carbon polyhydroxyalkanoates industrial bioproduction","authors":"Tianyu Jiang , Tingting Tan , Zhiyuan Zong , Dingding Fan , Jianxin Wang , Yanci Qiu , Xin Teng , Haoqian M. Zhang , Chitong Rao","doi":"10.1016/j.ymben.2025.04.001","DOIUrl":"10.1016/j.ymben.2025.04.001","url":null,"abstract":"<div><div>Polyhydroxyalkanoates (PHAs) are biodegradable and environmentally sustainable alternatives to conventional plastics, yet their adoption has been hindered by the high production costs and scalability challenges. This study employed unbiased genomics approaches to engineer <em>Cupriavidus necator H16, an industrial</em> strain with intrinsic capabilities for PHA biosynthesis<em>,</em> for enhanced utilization of oil-based feedstocks, including food-grade palm oil and crude waste cooking oil. The engineered strain demonstrated significant improvements in PHA production, achieving a 264 g/L yield (25.4 % increase) and a 100 g/g conversion rate of palm oil (12 % increase) in 60-h fed-batch fermentation at 150 m<sup>3</sup> production scale, the highest yield and conversion rate using food-grade palm oil as carbon source reported to the best of our knowledge. Notably, the carbon footprint of PHA production was reduced by 29.7 % using the engineered strain, and could be further reduced by adopting waste cooking oil. Mechanistic studies revealed that the <em>H16_A3043/H16_A3044</em> two-component system plays a central role in regulating stress response and biogenesis, the deletion of which unlocked the regulatory constraint and enhanced oil feedstock consumption. This mutation, supplemented with the necessary lipase engineering as revealed during the scale-up troubleshooting, confered higher PHA production in a robust fermentation process scalable through 0.5 L, 200 L, 15 m<sup>3</sup> and 150 m<sup>3</sup>. Additionally, the engineered strain demonstrated efficient utilization of waste cooking oil for PHA production. This study bridges laboratory-scale advancements and industrial feasibility, demonstrating a scalable, sustainable, and economically viable pathway for biopolymer production, contributing to the global shift toward a circular bioeconomy.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"91 ","pages":"Pages 44-58"},"PeriodicalIF":6.8,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143790853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Encapsulation of select violacein pathway enzymes in the 1,2-propanediol utilization bacterial microcompartment to divert pathway flux 1,2-丙二醇利用细菌微室中紫罗兰素途径酶的包封转移途径通量。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2025-04-03 DOI: 10.1016/j.ymben.2025.03.017

Brett Jeffrey Palmero , Emily Gamero , Niall M. Mangan , Danielle Tullman-Ercek

{"title":"Encapsulation of select violacein pathway enzymes in the 1,2-propanediol utilization bacterial microcompartment to divert pathway flux","authors":"Brett Jeffrey Palmero , Emily Gamero , Niall M. Mangan , Danielle Tullman-Ercek","doi":"10.1016/j.ymben.2025.03.017","DOIUrl":"10.1016/j.ymben.2025.03.017","url":null,"abstract":"<div><div>A continual goal in metabolic engineering is directing pathway flux to desired products and avoiding loss of pathway intermediates to competing pathways. Encapsulation of the pathway is a possible solution, as it creates a diffusion barrier between pathway intermediates and competing enzymes. It is hypothesized that bacteria use organelles known as bacterial microcompartments - proteinaceous shells encapsulating a metabolic pathway - for this purpose. We aim to determine to what degree this hypothesized benefit is conferred to encapsulated pathways. To this end, we used bacterial microcompartments to encapsulate select enzymes from the violacein pathway, which is composed of five enzymes that produce violacein as the main product and deoxyviolacein as a side product. Importantly, we studied the pathway in a cell-free context, allowing us to hold constant the concentration of unencapsulated and encapsulated enzymes and increase our control over reaction conditions. The VioE enzyme is a branch point in that it makes the precursor for both violacein and deoxyviolacein, the VioC enzyme is required for production of deoxyviolacein, and the VioD enzyme is required for violacein production. When we encapsulated VioE and VioC and left VioD unencapsulated, the product profile shifted toward deoxyviolacein and away from violacein compared to when VioC and VioD were both unencapsulated. This work provides the first fully quantitative evidence that microcompartment-based encapsulation can be used to divert pathway flux to the encapsulated pathway. It provides insight into why certain pathways are encapsulated natively and could be leveraged for metabolic engineering applications.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"91 ","pages":"Pages 91-102"},"PeriodicalIF":6.8,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Plasmid-based electroporation for efficient genetic engineering in immortalized T lymphocytes 基于质粒的电穿孔技术用于永生 T 淋巴细胞的高效基因工程。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2025-04-02 DOI: 10.1016/j.ymben.2025.03.019

Yu-Qing Xie , Martin Fussenegger

{"title":"Plasmid-based electroporation for efficient genetic engineering in immortalized T lymphocytes","authors":"Yu-Qing Xie , Martin Fussenegger","doi":"10.1016/j.ymben.2025.03.019","DOIUrl":"10.1016/j.ymben.2025.03.019","url":null,"abstract":"<div><div>The recent clinical success of genetically modified T-cell therapies underscores the urgent need to accelerate fundamental studies and functional screening methods in T lymphocytes. However, a facile and cost-effective method for efficient genetic engineering of T-cells remains elusive. Current approaches often rely on viral transduction, which is labor-intensive and requires stringent biosafety measures. Plasmid-based electroporation presents an affordable alternative, but remains underexplored in T-cells. Moreover, the availability of prototypical T-cell lines is limited. Here, we address these challenges by focusing on two immortalized murine T-cell lines, HT-2 and CTLL-2, which recapitulate key characteristics of primary T-cells, including cytotoxicity and cytokine-dependent proliferation. Alongside the widely used Jurkat T-cell line, HT-2 and CTLL-2 were successfully transfected with single or multiple genes with high efficiencies by means of optimized electroporation in a cuvette-based system. Notably, optimization of plasmid constructs enabled the delivery of large gene-of-interest (GOI) cargos of up to 6.5 kilobase pairs, as well as stable integration of a GOI into the genome via the Sleeping Beauty transposon system. We also developed advanced methodologies for CRISPR/Cas9-mediated gene editing in immortalized T lymphocytes, achieving knockout efficiencies of up to 97 % and homology-directed repair (HDR)-based targeted knock-in efficiencies of up to 70 %. We believe this optimized plasmid-based electroporation approach will contribute to advances in basic research on lymphocyte biology, as well as providing a practical, cost-effective tool for preclinical studies of T-cell therapies.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"91 ","pages":"Pages 77-90"},"PeriodicalIF":6.8,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Insights into the methanol utilization capacity of Y. lipolytica and improvements through metabolic engineering 解脂芽孢杆菌甲醇利用能力的研究及代谢工程改进。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2025-03-28 DOI: 10.1016/j.ymben.2025.03.014

Wei Jiang , William Newell , Jingjing Liu , Lucas Coppens , Khushboo Borah Slater , Huadong Peng , David Bell , Long Liu , Victoria Haritos , Rodrigo Ledesma-Amaro

{"title":"Insights into the methanol utilization capacity of Y. lipolytica and improvements through metabolic engineering","authors":"Wei Jiang , William Newell , Jingjing Liu , Lucas Coppens , Khushboo Borah Slater , Huadong Peng , David Bell , Long Liu , Victoria Haritos , Rodrigo Ledesma-Amaro","doi":"10.1016/j.ymben.2025.03.014","DOIUrl":"10.1016/j.ymben.2025.03.014","url":null,"abstract":"<div><div>Methanol is a promising sustainable alternative feedstock for green biomanufacturing. The yeast <em>Yarrowia lipolytica</em> offers a versatile platform for producing a wide range of products but it cannot use methanol efficiently. In this study, we engineered <em>Y. lipolytica</em> to utilize methanol by overexpressing a methanol dehydrogenase, followed by the incorporation of methanol assimilation pathways from methylotrophic yeasts and bacteria. We also overexpressed the ribulose monophosphate (RuMP) and xylulose monophosphate (XuMP) pathways, which led to significant improvements in growth with methanol, reaching a consumption rate of 2.35 g/L in 24 h and a 2.68-fold increase in biomass formation. Metabolomics and Metabolite Flux Analysis confirmed methanol assimilation and revealed an increase in reducing power. The strains were further engineered to produce the valuable heterologous product resveratrol from methanol as a co-substrate. Unlike traditional methanol utilization processes, which are often resource-intensive and environmentally damaging, our findings represent a significant advance in green chemistry by demonstrating the potential of <em>Y. lipolytica</em> for efficient use of methanol as a co-substrate for energy, biomass, and product formation. This work not only contributes to our understanding of methanol metabolism in non-methylotrophic organisms but also paves the way for achieving efficient synthetic methylotrophy towards green biomanufacturing.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"91 ","pages":"Pages 30-43"},"PeriodicalIF":6.8,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143753377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

BGC heteroexpression strategy for production of novel microbial secondary metabolites 新型微生物次生代谢产物的BGC异源表达策略。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2025-03-28 DOI: 10.1016/j.ymben.2025.03.018

Yuanyuan Liu, Yuqi Tang, Zhiyang Fu, Wangjie Zhu, Hong Wang, Huawei Zhang

引用次数: 0

Elucidation of the plant progesterone biosynthetic pathway and its application in a yeast cell factory 植物黄体酮生物合成途径的阐明及其在酵母细胞工厂中的应用。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2025-03-27 DOI: 10.1016/j.ymben.2025.03.016

Rongsheng Li , Shuang Guo , Dong Wang , Tingting Yang , Wenhao Li , Jie Wang , Luqi Huang , Xueli Zhang , Zhubo Dai

{"title":"Elucidation of the plant progesterone biosynthetic pathway and its application in a yeast cell factory","authors":"Rongsheng Li , Shuang Guo , Dong Wang , Tingting Yang , Wenhao Li , Jie Wang , Luqi Huang , Xueli Zhang , Zhubo Dai","doi":"10.1016/j.ymben.2025.03.016","DOIUrl":"10.1016/j.ymben.2025.03.016","url":null,"abstract":"<div><div>Progesterone and its steroidal derivatives, including androgens, estrogens, glucocorticoids and mineralocorticoids are extensively utilized in pharmacotherapy, serving as predominant agents in anti-inflammatory, contraceptive, and anticancer treatments. From the 1990s to the present, scientists attempted to biosynthesize steroids such as progesterone and hydrocortisone from sugars in engineered microbial strains expressing pathway enzymes derived from animal sources. However, the low activity of the cytochrome P450 sterol side-chain cleavage (P450scc) system and their mitochondrial compartmentalization have limited the development of this route. Therefore, discovering an efficient P450scc system and developing innovative strategies will be necessary to overcome this bottleneck. Here, we elucidated the complete biosynthetic pathway of progesterone in <em>Marsdenia tenacissima</em>, a medicinal plant rich in steroids. The pathway comprises four enzymes, the two P450scc enzymes MtCYP108 and MtCYP150, as well as the two 3β-hydroxysteroid dehydrogenase/Δ<sup>5</sup>-Δ<sup>4</sup> isomerases (HSDs) MtHSD5 and MtHSD6. Unlike their animal counterparts, the plant-derived P450scc enzymes were found to be localized to the endoplasmic reticulum in yeast and plants, and using the plant-type cytochrome P450 reductase (CPR) as electron transfer chain. The plant-derived HSDs are cytoplasmic in yeast and plants, whereas animal-derived HSDs localize to the endoplasmic reticulum. Based on this discovery, we engineered a yeast-based cell factory capable of synthesizing 1.06 g/L of progesterone from a simple carbon source. This discovery lays the groundwork for the sustainable synthesis of steroid hormone drugs through the use of plant-based systems or microbial host cells.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"90 ","pages":"Pages 197-208"},"PeriodicalIF":6.8,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143743649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Rhodotorula sp. as a promising host for microbial cell factories 红酵母是微生物细胞工厂的理想宿主。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2025-03-24 DOI: 10.1016/j.ymben.2025.03.015

Baisong Tong, Yi Yu, Shuobo Shi

{"title":"Rhodotorula sp. as a promising host for microbial cell factories","authors":"Baisong Tong, Yi Yu, Shuobo Shi","doi":"10.1016/j.ymben.2025.03.015","DOIUrl":"10.1016/j.ymben.2025.03.015","url":null,"abstract":"<div><div><em>Rhodotorula</em> sp. is a red yeast that has emerged as a promising host for microbial cell factories. Under specific conditions, <em>Rhodotorula</em> sp. can accumulate lipids that constitute over 70% of its dry cell weight, underscoring its potential in lipid compound production. Additionally, it can utilize a variety of carbon sources, including glucose, xylose, and volatile fatty acids, and exhibits high tolerance to low-cost carbon sources and industrial by-products, showcasing its excellent performance in industrial processes. Furthermore, the native mevalonate pathway of <em>Rhodotorula</em> sp. enables its efficient synthesis of antioxidant carotenoids and other terpenoids, which are widely applied in the food, pharmaceutical, and cosmetic industries. Due to its excellent accumulation ability of lipophilic compounds, metabolic diversity, and environmental adaptability, this review summarizes recent advances in genetic elements and metabolic engineering technologies for <em>Rhodotorula</em> sp., emphasizing its potential as a chassis cell factory for the production of lipids, carotenoids, and other chemicals. It also highlights key factors influencing commercial fermentation processes and concludes with challenges and solutions for further developing <em>Rhodotorula</em> sp. as microbial chassis.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"90 ","pages":"Pages 178-196"},"PeriodicalIF":6.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143730738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Strategic engineering for overproduction of oviedomycin, a Type II polyketide, in Escherichia coli 大肠杆菌中II型聚酮维多霉素过量生产的策略工程。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2025-03-22 DOI: 10.1016/j.ymben.2025.03.012

Boncheol Gu, Duck Gyun Kim, Yu-jin Cha, Min-Kyu Oh

{"title":"Strategic engineering for overproduction of oviedomycin, a Type II polyketide, in Escherichia coli","authors":"Boncheol Gu, Duck Gyun Kim, Yu-jin Cha, Min-Kyu Oh","doi":"10.1016/j.ymben.2025.03.012","DOIUrl":"10.1016/j.ymben.2025.03.012","url":null,"abstract":"<div><div>This study aimed to develop a metabolically engineered <em>Escherichia coli</em> strain capable of producing oviedomycin, a type II angucyclinone polyketide compound with anticancer activity. We first addressed the challenges of <em>in vivo</em> reassembly of the type II polyketide synthase machinery in <em>E. coli</em>. These included co-expressing molecular chaperones, rare tRNAs, and a fusion tag to enhance the solubility of all proteins from the oviedomycin biosynthetic gene cluster in <em>Streptomyces antibioticus</em>. After the soluble expression of all the proteins was confirmed, oviedomycin production was improved by reducing the accumulation of the intermediate 3-dehydrorabelomycin through substrate channeling using the CipB scaffold protein from <em>Photorhabdus luminescens</em>. In addition, the AcrAB-TolC efflux transporter system was introduced to enhance the growth of the producing strain, leading to higher oviedomycin yields. Ultimately, fed-batch fermentation with the final strain produced 120 mg/L oviedomycin from glucose within 24 h. These strategies have marked significant progress in the construction of biosynthetic pathways for the heterologous production of type II polyketides in <em>E. coli</em>, offering promising potential for producing various natural products with industrial applications.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"90 ","pages":"Pages 154-164"},"PeriodicalIF":6.8,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143700876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

Engineering Komagataella phaffii to produce lycopene sustainably from glucose or methanol 利用葡萄糖或甲醇可持续生产番茄红素。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2025-03-22 DOI: 10.1016/j.ymben.2025.03.013

Wei Zhou, Rui-Jing Ling, Yi-Chen Yang, Shu-Ting Hou, Feng-Qing Wang, Bei Gao, Dong-Zhi Wei

{"title":"Engineering Komagataella phaffii to produce lycopene sustainably from glucose or methanol","authors":"Wei Zhou, Rui-Jing Ling, Yi-Chen Yang, Shu-Ting Hou, Feng-Qing Wang, Bei Gao, Dong-Zhi Wei","doi":"10.1016/j.ymben.2025.03.013","DOIUrl":"10.1016/j.ymben.2025.03.013","url":null,"abstract":"<div><div>Lycopene, a potent carotenoid with high antioxidant capacity and extensive applications, holds significant potential for sustainable production via microbial engineering, particularly with the rising interest in methanol as an ideal non-grain feedstock for a carbon-negative economy. In this study, <em>Komagataella phaffii</em> was systematically engineered to enhance lycopene production using glucose and renewable methanol as alternative carbon sources. Firstly, we demonstrated that the cytoplasmic FPP could penetrate into the peroxisome, and thus achieved the dual-localized lycopene synthesis. Subsequently, the cytoplasmic FPP pool was expanded by dynamically regulating squalene synthase and enhancing the mevalonate pathway, and FPP was redirected to lycopene synthesis via assembling critical enzymes. Furthermore, the synthesis of lycopene from methanol was improved by reprogramming the methanol metabolic pathway. In the above process, we found that the engineered strains would degrade significantly in the process of passing culture. Comparative transcriptomic analysis revealed that nitrogen metabolism genes contributed significantly to strain degeneration, and a gene (PAS_chr2-2_0003) that positively influenced lycopene synthesis was identified. Finally, two strains were successfully engineered: strain zw327, which produced 8.4 g/L lycopene from glucose, and strain zw352, which achieved 10.2 g/L from methanol and glycerol. The latter represents the highest reported titer from methanol to date, underscoring the potential of <em>K. phaffii</em> as a robust one-carbon platform for industrial terpenoid biosynthesis.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"90 ","pages":"Pages 141-153"},"PeriodicalIF":6.8,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143692547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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

NEXT-FBA: A hybrid stoichiometric/data-driven approach to improve intracellular flux predictions NEXT-FBA：一种混合化学计量学/数据驱动的方法，用于改善细胞内通量预测。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2025-03-19 DOI: 10.1016/j.ymben.2025.03.010

James Morrissey , Gianmarco Barberi , Benjamin Strain , Pierantonio Facco , Cleo Kontoravdi

{"title":"NEXT-FBA: A hybrid stoichiometric/data-driven approach to improve intracellular flux predictions","authors":"James Morrissey , Gianmarco Barberi , Benjamin Strain , Pierantonio Facco , Cleo Kontoravdi","doi":"10.1016/j.ymben.2025.03.010","DOIUrl":"10.1016/j.ymben.2025.03.010","url":null,"abstract":"<div><div>Genome-scale metabolic models (GEMs) have been widely utilized to understand cellular metabolism. The application of GEMs has been advanced by computational methods that enable the prediction and analysis of intracellular metabolic states. However, the accuracy and biological relevance of these predictions often suffer from the many degrees of freedom and scarcity of available data to constrain the models adequately. Here, we introduce Neural-net EXtracellular Trained Flux Balance Analysis, (NEXT-FBA), a novel computational methodology that addresses these limitations by utilizing exometabolomic data to derive biologically relevant constraints for intracellular fluxes in GEMs. We achieve this by training artificial neural networks (ANNs) with exometabolomic data from Chinese hamster ovary (CHO) cells and correlating it with <sup>13</sup>C-labeled intracellular fluxomic data. By capturing the underlying relationships between exometabolomics and cell metabolism, NEXT-FBA predicts upper and lower bounds for intracellular reaction fluxes to constrain GEMs. We demonstrate the efficacy of NEXT-FBA across several validation experiments, where it outperforms existing methods in predicting intracellular flux distributions that align closely with experimental observations. Furthermore, a case study demonstrates how NEXT-FBA can guide bioprocess optimization by identifying key metabolic shifts and refining flux predictions to yield actionable process and metabolic engineering targets. Overall, NEXT-FBA aims to improve the accuracy and biological relevance of intracellular flux predictions in metabolic modelling, with minimal input data requirements for pre-trained models.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"91 ","pages":"Pages 130-144"},"PeriodicalIF":6.8,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143674154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"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