Metabolic engineering最新文献

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 124-135"},"PeriodicalIF":6.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146630347","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}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 57-66"},"PeriodicalIF":6.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146630355","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}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 213-222"},"PeriodicalIF":6.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146630359","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}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 252-263"},"PeriodicalIF":6.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146630367","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}

{"title":"Biosynthetic platform for orsellinic acid-derived meroterpenoids in Escherichia coli","authors":"Itsuki Tomita ,&nbsp;Takahiro Bamba ,&nbsp;Takanobu Yoshida ,&nbsp;Lucília Domingues ,&nbsp;Ryo Nasuno ,&nbsp;Ryota Hidese ,&nbsp;Tomohisa Hasunuma","doi":"10.1016/j.ymben.2025.12.008","DOIUrl":"10.1016/j.ymben.2025.12.008","url":null,"abstract":"<div><div>Orsellinic acid (OSA)-derived meroterpenoids, that have an OSA backbone, are plant-derived natural products that have attracted considerable attention as pharmaceutical precursors because of their diverse pharmacological activities. Therefore, developing efficient microbial production methods is highly desirable. However, to date, only a few reports on the microbial production of OSA-derived meroterpenoids are available, and even for the precursor OSA, only minimal production levels (approximately 5 mg/L) have been achieved using engineered microbes. In this study, <em>Escherichia coli</em> was engineered to enable the <em>de novo</em> biosynthesis of OSA to establish an alternative production platform for OSA-derived meroterpenoids. The introduction of type III polyketide synthase and cyclase resulted in 1.4 mg/L production. CRISPR interference aimed at enhancing OSA production revealed that the knockdown of <em>fadR</em>, which is involved in malonyl-CoA consumption, was effective. Metabolome analysis was performed to evaluate the metabolic impact of the engineering strategies revealed malonyl-CoA depletion, indicating that its supply constituted a major bottleneck. Based on this insight, the overexpression of acetyl-CoA carboxylase, pantothenate kinase, and ATP citrate lyase was implemented, which increased OSA production to 202 mg/L under optimized cultivation conditions, representing a 145-fold improvement. Finally, introducing a plant-derived prenyltransferase enabled grifolic acid biosynthesis (2.5 μg/g-DCW), representing the first <em>de novo</em> production of OSA-derived meroterpenoids in <em>E. coli</em>. This study establishes <em>E. coli</em> as a versatile and scalable host for the biosynthesis of pharmacologically valuable meroterpenoids.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 231-240"},"PeriodicalIF":6.8,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145883466","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}

{"title":"An automated platform for accelerating and focusing adaptive laboratory evolution","authors":"Peter Ruppen ,&nbsp;Maximilian Ole Bahls ,&nbsp;Michael Sebastian Gerlt ,&nbsp;Martin Peter Edelmann ,&nbsp;Tania Michelle Roberts ,&nbsp;Philippe Marlière ,&nbsp;Sven Panke","doi":"10.1016/j.ymben.2025.12.007","DOIUrl":"10.1016/j.ymben.2025.12.007","url":null,"abstract":"<div><div>The rate of change in adaptive laboratory evolution (ALE), in which a population of microorganisms is continuously cultivated under a specific selective pressure, is controlled by the cellular mutagenesis rate and the randomness of where in the genetic material mutations are introduced. The constant selection pressure makes it a crucial, yet slow, method in developing microorganisms with novel phenotypes for which a rational engineering pathway is either too complex or unknown.</div><div>A variety of targeted genome editing methods to accelerate evolution and facilitate the engineering of complex novel traits are available. However, these protocols require (nearly) as many successive transformation steps as loci they target, leaving the actual engineering process quite labor-intense, cumbersome, and at odds with the continuous nature of ALE. Here, we provide a fully integrated microfluidic platform that automates and accelerates bacterial transformation by electroporation to the mere push of a button. We demonstrate the functionality and effect by using oligonucleotide-directed mutagenesis in an ALE experiment to accelerate the engineering of riboflavin prototrophy into <em>Escherichia coli</em>.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 241-251"},"PeriodicalIF":6.8,"publicationDate":"2025-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145845093","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}

{"title":"Systematic metabolic engineering of an industrial Penicillium citrinum for one-step pravastatin production","authors":"Mengyi Xiong ,&nbsp;Zhiqiang Du ,&nbsp;Zehao Fan ,&nbsp;Beibei Wang ,&nbsp;Wenjiao Diao ,&nbsp;Min Wang ,&nbsp;Xuenian Huang ,&nbsp;Xuefeng Lu","doi":"10.1016/j.ymben.2025.12.005","DOIUrl":"10.1016/j.ymben.2025.12.005","url":null,"abstract":"<div><div>Pravastatin is a widely prescribed cholesterol-lowering drug known for its superior water solubility and favorable pharmacokinetics. However, its industrial production remains constrained by an inefficient two-step fermentation process, particularly the second biotransformation step involving <em>Streptomyces fermentation</em>. In this study, we engineered the industrial mevastatin-producing strain <em>Penicillium citrinum</em> MEFC10 to achieve efficient one-step pravastatin biosynthesis. Through systematic screening and integration of optimal cytochrome P450-redox partner modules, a one-step pravastatin production cell factory was constructed in industrial <em>Penicillium citrinum</em> MEFC10. Next, NADP⁺-dependent <em>g6pd3</em> was overexpressed to increase statin biosynthesis via NADPH regeneration. Further manipulation of pathway transcriptional regulator, self-resistance gene and minimization of byproduct formation, a high-performance Pra2.0 strain was constructed. The Pra2.0 strain produced 8.48 g/L pravastatin and 15.06 g/L total statins in a 50-L bioreactor under fed-batch fermentation. This work established a one-step fermentation process for pravastatin production with markedly improved efficiency over the conventional methods. This work not only establishes an efficient, green production route for pravastatin but also provides a versatile engineering framework for the sustainable biosynthesis of other complex fungal polyketides.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 223-230"},"PeriodicalIF":6.8,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145777265","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}

{"title":"Engineering Escherichia coli for the production of saturated archaeal lipids","authors":"Jiayi Jiang ,&nbsp;Mirthe Hoekzema ,&nbsp;Ruben Andringa ,&nbsp;Adriaan J. Minnaard ,&nbsp;Arnold J.M. Driessen","doi":"10.1016/j.ymben.2025.12.004","DOIUrl":"10.1016/j.ymben.2025.12.004","url":null,"abstract":"<div><div>Archaeal membrane phospholipids have a different chemical composition than the phospholipids found in bacteria and eukaryotes. Typically, in archaea, phospholipids consist of saturated isoprenoid chains that are ether-bonded to glycerol 1-phosphate whereas in bacteria and eukaryotes, the main phospholipids are fatty acyl chains ester-bonded to glycerol 3-phosphate. This distinct chemical structure of phospholipids is believed to play a crucial role in enabling archaea to survive extreme environments and energy-limited conditions. <em>Escherichia coli</em> has previously been engineered to synthesize archaeal phospholipids next to its endogenous bacterial phospholipids. Cells equipped with these mixed heterochiral membranes were found to be viable with some improvement in robustness. However, a complete biosynthetic pathway for the production of substantial amounts of saturated archaeal lipids has not yet been realized in <em>E. coli</em>. Here, we engineered <em>E. coli</em> for the production of saturated archaeal phospholipids by introducing next to the geranylgeranyl reductase (GGR) and ferredoxin (Fd) from <em>Methanosarcina acetivorans</em>, the pyruvate-ferredoxin oxidoreductase (PFOR) from <em>E. coli</em> to allow for an efficient reduction of Fd. This resulted in a strain where approximately 75 % of the produced archaeal lipids are partially or completely saturated. Importantly, <em>E. coli</em> cells containing this mixed heterochiral membrane showed improved resistance to both heat and cold shock as compared to native <em>E. coli</em> strain. This <em>E. coli</em> strain with saturated archaeal phospholipids can serve as a valuable model for further engineering to incorporate different types of more complex archaeal membrane lipids.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 213-222"},"PeriodicalIF":6.8,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145777266","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}

{"title":"Lacto-N-tetraose biosynthesis from lactose via metabolically rewired Escherichia coli","authors":"Dileep Sai Kumar Palur ,&nbsp;Shannon R. Pressley ,&nbsp;Alex McGill ,&nbsp;Yuanyuan Bai ,&nbsp;Hai Yu ,&nbsp;Xi Chen ,&nbsp;Shota Atsumi","doi":"10.1016/j.ymben.2025.12.001","DOIUrl":"10.1016/j.ymben.2025.12.001","url":null,"abstract":"<div><div>Human milk oligosaccharides (HMOs), such as lacto-<em>N</em>-tetraose (LNT), play critical roles in infant health by shaping gut microbiota and modulating immune function. While LNT is already produced at industrial scales, efficient microbial routes to more complex HMOs derived from LNT remain limited. Here, we established a simplified microbial platform in <em>Escherichia coli</em> that produces LNT directly from lactose as the sole carbon and precursor source. A key innovation was construction of a strain library with tunable β-galactosidase (LacZ) activity, enabling controlled lactose hydrolysis to generate glucose and galactose for UDP-sugar biosynthesis while preserving sufficient intact lactose as the scaffold for LNT assembly. Quantitative profiling of intracellular UDP-sugars further guided identification of metabolic bottlenecks. The optimized strain achieved co-production of 2.4 g/L LNT and 2.0 g/L lacto-<em>N</em>-triose II (LNT II) from 10 g/L lactose. This streamlined strategy demonstrates the feasibility of producing LNT from a single substrate and provides a versatile foundation for scalable microbial biosynthesis of more complex HMOs.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 182-191"},"PeriodicalIF":6.8,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145731784","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}

{"title":"PET-FBA: A lightweight enzyme allocation and thermodynamics-constrained flux analysis approach to explore Escherichia coli metabolic adaptation to intracellular acidification","authors":"Chao Wu ,&nbsp;Jeffrey N. Law ,&nbsp;Onyeka Onyenemezu ,&nbsp;Jetendra K. Roy ,&nbsp;Peter C. St. John ,&nbsp;Robert L. Jernigan ,&nbsp;Yannick J. Bomble ,&nbsp;Laura Jarboe","doi":"10.1016/j.ymben.2025.12.003","DOIUrl":"10.1016/j.ymben.2025.12.003","url":null,"abstract":"<div><div><em>Escherichia coli</em> employs diverse strategies to adapt to acidic environments that disrupt enzyme activity and the thermodynamic feasibility of essential reactions. To understand the impact of pH stress on cell metabolism, we present the PET-FBA (pH-, Enzyme protein allocation-, and Thermodynamics-constrained Flux Balance Analysis) framework. PET-FBA extends genome-scale modeling by integrating enzyme protein costs and reaction Gibbs free energy changes. Additionally, by incorporating pH-dependent enzyme kinetics in response to intracellular acidification, this framework enables the simulation of <em>E. coli</em>'s metabolic adjustments across varying external pH levels. The model's accuracy is validated by comparing <em>in silico</em> growth simulations with experimental measurements under both anaerobic and aerobic conditions, as well as <em>in silico</em> gene knockouts of essential genes. By explicitly incorporating pH effects, our model accurately replicates the metabolic shift towards lactate production as the primary fermentation product at low pH in anaerobic conditions. This shift is only predicted when enzyme kinetics are dynamically adjusted as a function of pH. Further analysis revealed that this shift can be attributed to the reduced protein efficiency of the acetyl-CoA branch compared to lactate dehydrogenase under acidic stress, which then becomes crucial for maintaining NAD regeneration and cell growth at low pH. Furthermore, we identified strategies for enhancing cell growth under acidic anaerobic conditions by improving the enzyme activity of lactate dehydrogenase and pyruvate formate lyase, which increases NAD production efficiency and reduces enzyme protein allocation costs. Designed as a lightweight yet versatile framework, PET-FBA enables efficient genome-scale metabolic analysis. Using <em>E. coli</em> as a model system, our framework provides a systematic approach to understanding metabolic responses to environmental stress, pinpointing key metabolic bottlenecks, and identifying potential targets for strain optimization. This work also highlights the critical role of intracellular acidification in shaping enzyme performance and microbial adaptation. The PET-FBA framework is implemented as a Python package at <span><span>https://github.com/Chaowu88/etfba</span><svg><path></path></svg></span>, with detailed documentation provided at <span><span>https://etfba.readthedocs.io</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 202-212"},"PeriodicalIF":6.8,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145731099","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}