Metabolic engineering最新文献

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Metabolic engineering of Micromonospora for exploring useful natural products and phytobiotic interaction 利用小单孢子菌代谢工程探索有用的天然产物和植物共生相互作用
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-07-20 DOI: 10.1016/j.ymben.2025.07.005
Boncheol Gu, Jimin Lee, Duck Gyun Kim, Yu-jin Cha, Min-Kyu Oh
{"title":"Metabolic engineering of Micromonospora for exploring useful natural products and phytobiotic interaction","authors":"Boncheol Gu,&nbsp;Jimin Lee,&nbsp;Duck Gyun Kim,&nbsp;Yu-jin Cha,&nbsp;Min-Kyu Oh","doi":"10.1016/j.ymben.2025.07.005","DOIUrl":"10.1016/j.ymben.2025.07.005","url":null,"abstract":"<div><div><em>Micromonospora</em>, a genus within the Actinobacteria phylum, is recognized for its prolific production of bioactive secondary metabolites. It has important applications in the pharmaceutical, biotechnology, and agricultural fields. <em>Micromonospora</em> is renowned for generating antibiotics, anticancer agents, immunosuppressants, and plant growth-promoting compounds, making it a primary subject in natural product research. Advances in genome sequencing and mining technologies have revealed numerous biosynthetic gene clusters, many of which remain unexplored, underscoring their vast, untapped biosynthetic potential. This review presents an in-depth summary of the role of <em>Micromonospora</em> in the discovery of novel bioactive compounds and their biotechnological and industrial applications. Furthermore, we discuss the plant-microbe interactions of <em>Micromonospora</em>, consolidating current knowledge from its historical discovery to recent genomic insights, and outlines future research directions and challenges for optimizing the biotechnological potential of this promising yet underexploited microbial resource.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"92 ","pages":"Pages 39-50"},"PeriodicalIF":6.8,"publicationDate":"2025-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144669919","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
Biomass accumulation in chondrocyte metabolic modelling: Incorporating extracellular matrix proxies to predict tissue engineering outcomes 软骨细胞代谢模型中的生物量积累:结合细胞外基质代理来预测组织工程结果
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-07-13 DOI: 10.1016/j.ymben.2025.07.004
Roberto Tarantino , Halie Mei Jensen , Stephen D. Waldman
{"title":"Biomass accumulation in chondrocyte metabolic modelling: Incorporating extracellular matrix proxies to predict tissue engineering outcomes","authors":"Roberto Tarantino ,&nbsp;Halie Mei Jensen ,&nbsp;Stephen D. Waldman","doi":"10.1016/j.ymben.2025.07.004","DOIUrl":"10.1016/j.ymben.2025.07.004","url":null,"abstract":"<div><div>Metabolic modeling in chondrocytes plays a pivotal role in advancing our understanding of cellular function. These techniques have been used to study degenerative joint diseases (e.g. osteoarthritis), mechanotransduction, and more recently to optimize strategies for cartilage tissue engineering. Incorporating tissue formation into metabolic flux analysis is inherently challenging due to the complexity of linking metabolic activity to extracellular matrix (ECM) accumulation. Many ECM macromolecules are synthesized using metabolites derived from central carbon metabolism, but direct modeling of their accumulation remains complex. This study establishes a novel methodology for incorporating ECM synthesis into metabolic flux analysis (MFA). By utilizing chondroitin sulfate and hydroxyproline as measurable metabolic proxies for proteoglycan and collagen production, we demonstrate a framework for linking metabolic inputs with tissue formation. Extracellular flux data for glucose, lactate, carbon dioxide, glutamine, and glutamate, along with mass isotopomer distributions, were sourced from previous studies involving three-dimensional high-density cultures of articular cartilage tissue constructs. Additionally, the conditioned culture media used in these studies was used to quantify the production rates of chondroitin sulfate and hydroxyproline. Using a modular network model, proteoglycan and collagen metabolism were assessed independently, and in combination, with sensitivity analyses on ECM retention assumptions. Predicted proteoglycan production aligned well with previously observed trends; however, predicted collagen production was less consistent. These findings offer a novel approach for linking metabolic inputs with ECM production, advancing our ability to predict tissue formation and address key challenges in cartilage tissue engineering.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"92 ","pages":"Pages 1-12"},"PeriodicalIF":6.8,"publicationDate":"2025-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144622704","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
Establishing Vibrio natriegens as a high-performance host for acetate-based poly-3-hydroxybutyrate production 建立营养弧菌作为高效宿主生产基于醋酸酯的聚3-羟基丁酸酯
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-07-11 DOI: 10.1016/j.ymben.2025.07.003
Roland J. Politan , Simona Della Valle , Luke Pineda , Jitendra Joshi , Christian Euler , Gavin Flematti , Georg Fritz
{"title":"Establishing Vibrio natriegens as a high-performance host for acetate-based poly-3-hydroxybutyrate production","authors":"Roland J. Politan ,&nbsp;Simona Della Valle ,&nbsp;Luke Pineda ,&nbsp;Jitendra Joshi ,&nbsp;Christian Euler ,&nbsp;Gavin Flematti ,&nbsp;Georg Fritz","doi":"10.1016/j.ymben.2025.07.003","DOIUrl":"10.1016/j.ymben.2025.07.003","url":null,"abstract":"<div><div>Acetate can be a sustainable and renewable carbon source that holds significant promise for biotechnological production but is underutilized industrially due to limited microbial efficiency. <em>Vibrio natriegens</em>, recognized for exceptionally fast growth rates, represents a compelling host for developing efficient acetate-based bioprocesses. In this study, adaptive laboratory evolution significantly enhanced <em>V. natriegens</em>’ ability to grow on acetate as the sole carbon source, achieving an 89 % increase in growth rate. Genetic and transcriptomic analyses revealed key adaptations improving acetate uptake and metabolism via increased salt tolerance, boosted Pta/AckA pathway activity, and rewired quorum sensing. Further metabolic engineering and bioprocess optimization enabled the evolved strain to reach high cell densities and efficiently convert acetate into the bioplastic poly-3-hydroxybutyrate (PHB), with productivities up to 0.27 g/L/h and PHB accumulation reaching 45.66 % of cell biomass. These advances position <em>V. natriegens</em> as a highly promising microbial platform for sustainable, scalable, and cost-effective biomanufacturing using acetate as a green feedstock.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"92 ","pages":"Pages 22-38"},"PeriodicalIF":6.8,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144622705","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
Genome-scale overexpression screen reveals membrane homeostasis as a key determinant for free fatty acids overproduction in Escherichia coli 基因组尺度的过表达筛选揭示了膜稳态是大肠杆菌游离脂肪酸过量产生的关键决定因素。
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-07-10 DOI: 10.1016/j.ymben.2025.07.002
Lixia Fang , Xiaolei Liu , Zhongxiu Chen , Jiaqi Zhang , Lian Wang , Yingxiu Cao
{"title":"Genome-scale overexpression screen reveals membrane homeostasis as a key determinant for free fatty acids overproduction in Escherichia coli","authors":"Lixia Fang ,&nbsp;Xiaolei Liu ,&nbsp;Zhongxiu Chen ,&nbsp;Jiaqi Zhang ,&nbsp;Lian Wang ,&nbsp;Yingxiu Cao","doi":"10.1016/j.ymben.2025.07.002","DOIUrl":"10.1016/j.ymben.2025.07.002","url":null,"abstract":"<div><div>Genome-scale target identification is essential for optimizing microbial biosynthesis due to the highly complex and interconnected nature of cellular metabolism. Free fatty acids (FFAs), valuable precursors for biofuels and industrial chemicals, have been extensively studied in <em>Escherichia coli</em>. However, genome-wide exploration of beneficial targets that promote FFAs production remains limited, hindering efforts to fully unlock the potential of microbial biosynthetic capabilities. In this study, we performed genome-scale screening of upregulation targets for FFAs overproduction in <em>E. coli</em> by leveraging the ASKA (A Complete Set of <em>E. coli</em> K-12 ORF Archive) library in combination with fluorescence-activated cell sorting (FACS) and next-generation sequencing (NGS). We found that overexpression of <em>rfaY</em>, encoding a lipopolysaccharide (LPS) core heptose II phosphokinase, led to a 207.8% increase in FFAs production by enhancing membrane stability, as evidenced by reduced permeability and improved integrity. Further investigation revealed that overexpressing additional LPS biosynthesis-related genes similarly improved membrane robustness and FFAs production. Through iterative screening, <em>yafL</em> and <em>rimM</em> were identified as synergistic partners with <em>rfaY</em>, and subsequent integration of <em>fadR</em> overexpression ultimately yielded the optimal strain <em>rfaY</em><sup>+</sup>-<em>yafL</em><sup>+</sup>-<em>fadR</em><sup>+</sup>, which achieved a FFAs titer of 39.6 g/L under fed-batch fermentation—the highest reported to date in <em>E. coli</em>. This study highlights the significance of genome-scale mining potential genetic determinants for enhancing the biosynthesis of desired products.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"92 ","pages":"Pages 13-21"},"PeriodicalIF":6.8,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144613064","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 phenylpyruvate decarboxylase for controlled biosynthesis of aromatic amino acid derivatives 芳香族氨基酸衍生物控制生物合成的工程苯丙酮酸脱羧酶。
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-07-03 DOI: 10.1016/j.ymben.2025.07.001
Jian Li , Shiqing Zhang , Honghao Li , Xiaoran Dai , Chaoqun Huang , He Ma , Huayi Liu , Qi Qi , Xiang Sheng , Yunzi Luo
{"title":"Engineering phenylpyruvate decarboxylase for controlled biosynthesis of aromatic amino acid derivatives","authors":"Jian Li ,&nbsp;Shiqing Zhang ,&nbsp;Honghao Li ,&nbsp;Xiaoran Dai ,&nbsp;Chaoqun Huang ,&nbsp;He Ma ,&nbsp;Huayi Liu ,&nbsp;Qi Qi ,&nbsp;Xiang Sheng ,&nbsp;Yunzi Luo","doi":"10.1016/j.ymben.2025.07.001","DOIUrl":"10.1016/j.ymben.2025.07.001","url":null,"abstract":"<div><div>The biosynthetic pathway of aromatic amino acids (AAAs) and its branches are crucial for producing bioactive compounds. ARO10, a phenylpyruvate decarboxylase in yeast, catalyzes the decarboxylation of 2-keto acids to aldehydes, playing a key role in AAA-derivative biosynthesis in yeast. However, its broad substrate specificity hinders efficient target synthesis. Here, we engineered ARO10 to create three mutants (I335E, A628F/H339I/I335M, H339C/I335T/A628Q) with specificity for 4-hydroxyphenylpyruvic acid (4-HPP), phenylpyruvic acid (PPA), and indole-3-pyruvic acid (I3P) through a “Design-Build-Test-Learn” (DBTL) framework. Mechanisms were explored via enzyme kinetics and molecular dynamics. These mutants enabled high-yield production of AAA-derivatives in yeast strains: 11.08 g/L tyrosol, 2.77 g/L 2-phenylethanol, and 1.21 g/L tryptophol in 5 L fed-batch bioreactor. These are the highest reported <em>de novo</em> titers to date in yeast. This work highlights the potential for engineering promiscuous enzymes to enhance sustainable biosynthesis of AAA-derivatives and alkaloids.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"91 ","pages":"Pages 466-479"},"PeriodicalIF":6.8,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144565958","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
Tailoring Escherichia coli for high-yield production of O-acetyl-L-homoserine through multi-node metabolic regulation 通过多节点代谢调节使大肠杆菌高产o -乙酰- l-高丝氨酸
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-06-30 DOI: 10.1016/j.ymben.2025.06.010
Yuanyuan Chen , Lianggang Huang , Tao Yu , Mingming Zhao , Junping Zhou , Lijuan Wang , Zhiqiang Liu , Yuguo Zheng
{"title":"Tailoring Escherichia coli for high-yield production of O-acetyl-L-homoserine through multi-node metabolic regulation","authors":"Yuanyuan Chen ,&nbsp;Lianggang Huang ,&nbsp;Tao Yu ,&nbsp;Mingming Zhao ,&nbsp;Junping Zhou ,&nbsp;Lijuan Wang ,&nbsp;Zhiqiang Liu ,&nbsp;Yuguo Zheng","doi":"10.1016/j.ymben.2025.06.010","DOIUrl":"10.1016/j.ymben.2025.06.010","url":null,"abstract":"<div><div>O-acetyl-L-homoserine (OAH) is a key precursor for the biosynthesis of L-methionine and various C4 compounds, with significant industrial potential. However, efficient microbial production of OAH remains challenging due to complex metabolic regulation and precursor limitations. In this study, we rationally developed a plasmid-free, non-auxotrophic <em>Escherichia coli</em> strain to produce OAH. We modularized the OAH synthetic pathway into L-homoserine and acetyl-CoA modules, enhanced each module individually, and identified a highly efficient L-homoserine O-acetyltransferase (MetX) from <em>Cyclobacterium marinum</em>. Using small RNA screening, we pinpointed critical metabolic nodes and fine-tuned the pathway flux through promoter engineering and regulatory elements. Notably, we balanced the acetyl-CoA and L-homoserine synthesis with moderate expression of pyruvate carboxylase, weakened the TCA cycle by modulating citrate synthase and the branched-chain amino acid pathway by attenuating BCAA aminotransferase, thereby redirecting carbon flux towards OAH production. Additionally, we optimized the threonine attenuator for dynamic regulation of the threonine pathway and enhanced intracellular ATP turnover. Under a two-stage pH control fermentation strategy, the final plasmid-free and non-auxotrophic strain OAH37 achieved a titer of 94.1 g/L OAH, with a yield of 0.42 g/g glucose and a productivity of 1.37 g/L/h. Our work demonstrates the potential of metabolic engineering strategies for efficient microbial synthesis of OAH, providing a foundation for industrial-scale production of this important precursor.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"91 ","pages":"Pages 455-465"},"PeriodicalIF":6.8,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144534257","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
A multilayered biocontainment system for laboratory and probiotic yeast 实验室和益生菌酵母的多层生物防护系统。
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-06-25 DOI: 10.1016/j.ymben.2025.06.009
Carla Maneira , Sina Becker , Alexandre Chamas , Gerald Lackner
{"title":"A multilayered biocontainment system for laboratory and probiotic yeast","authors":"Carla Maneira ,&nbsp;Sina Becker ,&nbsp;Alexandre Chamas ,&nbsp;Gerald Lackner","doi":"10.1016/j.ymben.2025.06.009","DOIUrl":"10.1016/j.ymben.2025.06.009","url":null,"abstract":"<div><div>The containment of genetically engineered microorganisms to designated environments of action is a paramount step in preventing their spread to nature. Physical barriers were traditionally employed to solve this issue, nevertheless, the growing number of biotechnological operations in open dynamic environments calls for intrinsic biocontainment. Here we describe the development of genetically embedded safeguard systems for both a laboratory strain of <em>Saccharomyces cerevisiae</em> and the commercial probiotic <em>Saccharomyces cerevisiae</em> var. <em>boulardii</em>. In a stepwise approach, single-input metabolic circuits based either on a synthetic auxotrophy or a CRISPR-based kill switch were developed before their combination into an orthogonal two-input system. All circuits are based on gut-active molecules or environmental cues, making them amenable to microbiome therapy applications. The final two-input system is stable for more than a hundred generations while achieving less than one escapee in 10<sup>9</sup> CFUs after incubation under restrictive conditions for at least six days. Biocontained strains can robustly produce heterologous proteins under permissive conditions, supporting their future use in the most varied applications, like <em>in-situ</em> production and delivery of pharmaceutically active metabolites.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"91 ","pages":"Pages 442-454"},"PeriodicalIF":6.8,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144512159","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
Kinetic-model-guided engineering of multiple S. cerevisiae strains improves p-coumaric acid production 动力学模型引导的多酿酒酵母菌株工程提高了对香豆酸的产量
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-06-18 DOI: 10.1016/j.ymben.2025.06.008
Bharath Narayanan , Wei Jiang , Shengbao Wang , Javier Sáez-Sáez , Daniel Weilandt , Maria Masid Barcon , Viktor Hesselberg-Thomsen , Irina Borodina , Vassily Hatzimanikatis , Ljubisa Miskovic
{"title":"Kinetic-model-guided engineering of multiple S. cerevisiae strains improves p-coumaric acid production","authors":"Bharath Narayanan ,&nbsp;Wei Jiang ,&nbsp;Shengbao Wang ,&nbsp;Javier Sáez-Sáez ,&nbsp;Daniel Weilandt ,&nbsp;Maria Masid Barcon ,&nbsp;Viktor Hesselberg-Thomsen ,&nbsp;Irina Borodina ,&nbsp;Vassily Hatzimanikatis ,&nbsp;Ljubisa Miskovic","doi":"10.1016/j.ymben.2025.06.008","DOIUrl":"10.1016/j.ymben.2025.06.008","url":null,"abstract":"<div><div>The use of kinetic models of metabolism in design-build-learn-test cycles is limited despite their potential to guide and accelerate the optimization of cell factories. This is primarily due to difficulties in constructing kinetic models capable of capturing the complexities of the fermentation conditions. Building on recent advances in kinetic-model-based strain design, we present the rational metabolic engineering of an <em>S. cerevisiae</em> strain designed to overproduce <em>p</em>-coumaric acid (<em>p</em>-CA), an aromatic amino acid with valuable nutritional and therapeutic applications. To this end, we built nine kinetic models of an already engineered <em>p</em>-CA-producing strain by integrating different types of omics data and imposing physiological constraints pertinent to the strain. These nine models contained 268 mass balances involved in 303 reactions across four compartments and could reproduce the dynamic characteristics of the strain in batch fermentation simulations. We used constraint-based metabolic control analysis to generate combinatorial designs of 3 enzyme manipulations that could increase p-CA yield on glucose while ensuring that the resulting engineering strains did not deviate far from the reference phenotype. Among 39 unique designs, 10 proved robust across the phenotypic uncertainty of the models and could reliably increase <em>p</em>-CA yield in nonlinear simulations. We implemented these top 10 designs in a batch fermentation setting using a promoter-swapping strategy for down-regulations and plasmids for up-regulations. Eight out of the ten designs produced higher <em>p</em>-CA titers than the reference strain, with 19–32 % increases at the end of fermentation. All eight designs also maintained at least 90 % of the reference strain's growth rate, indicating the critical role of the phenotypic constraint. The high experimental success of our in-silico predictions lays the foundation for accelerated design-build-test-learn cycles enabled by large-scale kinetic modeling.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"91 ","pages":"Pages 430-441"},"PeriodicalIF":6.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337526","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
Modeling host–pathway dynamics at the genome scale with machine learning 用机器学习在基因组尺度上模拟动态宿主途径相互作用
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-06-17 DOI: 10.1016/j.ymben.2025.05.008
Charlotte Merzbacher , Oisin Mac Aodha , Diego A. Oyarzún
{"title":"Modeling host–pathway dynamics at the genome scale with machine learning","authors":"Charlotte Merzbacher ,&nbsp;Oisin Mac Aodha ,&nbsp;Diego A. Oyarzún","doi":"10.1016/j.ymben.2025.05.008","DOIUrl":"10.1016/j.ymben.2025.05.008","url":null,"abstract":"<div><div>Pathway engineering offers a promising avenue for sustainable chemical production. The design of efficient production systems requires understanding complex host–pathway interactions that shape the metabolic phenotype. While genome-scale metabolic models are widespread tools for studying static host–pathway interactions, it remains a challenge to predict dynamic effects such as metabolite accumulation or enzyme overexpression during the course of fermentation. Here, we propose a novel strategy to integrate kinetic pathway models with genome-scale metabolic models of the production host. Our method enables the simulation of the local nonlinear dynamics of pathway enzymes and metabolites, informed by the global metabolic state of the host as predicted by Flux Balance Analysis (FBA). To reduce computational costs, we make extensive use of surrogate machine learning models to replace FBA calculations, achieving simulation speed-ups of at least two orders of magnitude. Through case studies on two production pathways in <em>Escherichia coli</em>, we demonstrate the consistency of our simulations and the ability to predict metabolite dynamics under genetic perturbations and various carbon sources. We showcase the utility of our method for screening dynamic control circuits through large-scale parameter sampling and mixed-integer optimization. Our work links together genome-scale and kinetic models into a comprehensive framework for computational strain design.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"91 ","pages":"Pages 480-491"},"PeriodicalIF":6.8,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337538","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 genetic circuits for dynamic control of central metabolism 用于中枢代谢动态控制的工程遗传电路
IF 6.8 1区 生物学
Metabolic engineering Pub Date : 2025-06-16 DOI: 10.1016/j.ymben.2025.06.007
Yusong Zou, Xinyu Gong, Jianli Zhang, Qi Gan, Yajun Yan
{"title":"Engineering genetic circuits for dynamic control of central metabolism","authors":"Yusong Zou,&nbsp;Xinyu Gong,&nbsp;Jianli Zhang,&nbsp;Qi Gan,&nbsp;Yajun Yan","doi":"10.1016/j.ymben.2025.06.007","DOIUrl":"10.1016/j.ymben.2025.06.007","url":null,"abstract":"<div><div>Genetic regulation tools have been examined for their ability to enable sophisticated dynamic control of biosynthesis in microbial cell factories, enhancing the production performance of valuable compounds. However, most genetic tools are pathway- or intermediate-specific, hindering their broad applicability in synthetic biology. Moreover, their potential to balance metabolic fluxes in central metabolism between cell growth and product formation remains under-explored, raising the question of whether they can facilitate efficient biosynthesis. To answer this, we established the PdhR biosensor system that responds to pyruvate to dynamically regulate metabolic flux distribution in central metabolism. In this study, we first characterized the dose response of PdhR biosensor system by screening multiple PdhR homologs derived from various microorganisms. Computational analysis further guided the identification of key factors contributing to their functional differences, enabling the optimization of biosensor properties through site-directed mutagenesis. As proof of concept, we employed our biosensor system to improve the biosynthesis of trehalose and 4-hydroxycoumarin (4HC), respectively. Specifically, trehalose titer increased to 3.72 g/L, which is 2.33-fold higher than the control group. In addition, we improved the 4HC titer to 491.5 mg/L, which possessed a 1.63-fold increase over the static strategy. In summary, the established central metabolism-responsive biosensor system underlined the necessity of metabolic flux distribution and validated its broad applicability in the biosynthesis of central metabolism-derived compounds.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"91 ","pages":"Pages 405-414"},"PeriodicalIF":6.8,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144307991","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
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