Metabolic engineering最新文献_第5页

Redefining HexR regulatory landscape in Pseudomonas putida KT2440 through integrative systems biology 通过整合系统生物学重新定义恶臭假单胞菌KT2440的HexR调控格局

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2026-03-01 Epub Date: 2025-11-17 DOI: 10.1016/j.ymben.2025.11.014

Linh Khanh Nong, Chandran Sathesh-Prabu, Sung Kuk Lee, Donghyuk Kim

{"title":"Redefining HexR regulatory landscape in Pseudomonas putida KT2440 through integrative systems biology","authors":"Linh Khanh Nong, Chandran Sathesh-Prabu, Sung Kuk Lee, Donghyuk Kim","doi":"10.1016/j.ymben.2025.11.014","DOIUrl":"10.1016/j.ymben.2025.11.014","url":null,"abstract":"<div><div><em>Pseudomonas putida</em> strains are prized biocatalysts, renowned for their versatility in degrading diverse chemicals, tolerating organic solvents, and withstanding environmental stressors. Central to their adaptive success is the precise regulation of primary carbon metabolism, with HexR emerging as a key regulator. While previous research has explored HexR binding through <em>in vitro</em> assays and comparative transcriptomics, the <em>in vivo</em> binding sites and genome-scale regulon remain uncharted. This study presents a comparative analysis of <em>P. putida</em> KT2440, comparing expression profiles of wild-type and <em>hexR</em> deletion mutant strains across distinct growth substrates: glucose (glycolytic), acetate, succinate (gluconeogenic), and glycerol (inducing both metabolic responses). Our findings revealed an extensive regulatory role of HexR in acetate metabolism, simultaneously suppressing the glycolytic pathway while enhancing pyruvate metabolism, glyoxylate shunt, and gluconeogenesis to support growth. Integration of ChIP-exo data identified 29 HexR binding locations in the KT2440 strain grown on acetate, directly regulating 75 genes. Complementing these findings, model-based <em>in silico</em> simulations provided contextual insight into metabolic flux states, deepening our understanding of carbon metabolism orchestrated by this transcription factor. This study thus offers a holistic view of the HexR regulatory landscape, highlighting its relevance in <em>P. putida</em> KT2440 metabolism and laying the groundwork for future metabolic engineering efforts in this versatile organism.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 77-89"},"PeriodicalIF":6.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145536219","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

Proteome constrained metabolic modeling of Sus scrofa muscle stem cells for cultured meat production 蛋白质组学约束下培养肉用Sus scrofa肌干细胞代谢模型的建立

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2026-03-01 Epub Date: 2026-01-03 DOI: 10.1016/j.ymben.2026.01.001

Sizhe Qiu , Eliska Kratochvilova , Wei E. Huang , Zhanfeng Cui , Tom Agnew , Aidong Yang , Hua Ye

{"title":"Proteome constrained metabolic modeling of Sus scrofa muscle stem cells for cultured meat production","authors":"Sizhe Qiu , Eliska Kratochvilova , Wei E. Huang , Zhanfeng Cui , Tom Agnew , Aidong Yang , Hua Ye","doi":"10.1016/j.ymben.2026.01.001","DOIUrl":"10.1016/j.ymben.2026.01.001","url":null,"abstract":"<div><div>Cultured meat has recently emerged as a sustainable alternative to traditional livestock farming and gained attention as a promising future protein source. Herein, the <em>Sus scrofa</em> muscle stem cell is a commonly used cell source in the cell proliferation step of cultured meat production. However, a major bottleneck of large-scale cultivation is the inhibition by secreted and accumulated lactate and ammonium in the process of <em>S. scrofa</em> cell proliferation. To simulate the growth and metabolism of <em>S. scrofa</em> muscle stem cells under different lactate and ammonium concentrations, this study constructed the first proteome constrained metabolic model for the core metabolism of <em>S. scrofa</em> muscle stem cells, pcPigMNet 2025. The relationship of lactate and ammonium levels with cellular metabolism was derived from growth and metabolomics data of two culture conditions with low and high initial ammonium concentrations, and then incorporated into metabolic flux simulation. Metabolic flux simulations for experimental conditions, along with perturbation simulations considering stressed non-growth associated maintenance and oxygen supply, demonstrated that pcPigMNet2025 could effectively characterize the response of the <em>S. scrofa</em> muscle stem cell's growth and metabolism to varying environmental conditions, shedding light on model-aided control and optimization of the cultured meat production process.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 252-263"},"PeriodicalIF":6.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145894425","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

De novo production of 1,3-olein-2-palmitin (OPO) and 1-olein-2-palmitin-3-linolein (OPL) by multiplexed reconstruction of lipid metabolism in yeasts 通过酵母脂质代谢的多重重建重新生产1,3-油素-2-棕榈素（OPO）和1-油素-2-棕榈素-3-亚油素(OPL

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2026-03-01 Epub Date: 2025-11-05 DOI: 10.1016/j.ymben.2025.11.005

Chenyang Zhang , Xuan Zhou , Wei Wei , Jiahui Yu , Yaokang Wu , Yanfeng Liu , Jianghua Li , Guocheng Du , Jian Chen , Tongcheng Xu , Xueqin Lv , Xianhao Xu , Long Liu

{"title":"De novo production of 1,3-olein-2-palmitin (OPO) and 1-olein-2-palmitin-3-linolein (OPL) by multiplexed reconstruction of lipid metabolism in yeasts","authors":"Chenyang Zhang , Xuan Zhou , Wei Wei , Jiahui Yu , Yaokang Wu , Yanfeng Liu , Jianghua Li , Guocheng Du , Jian Chen , Tongcheng Xu , Xueqin Lv , Xianhao Xu , Long Liu","doi":"10.1016/j.ymben.2025.11.005","DOIUrl":"10.1016/j.ymben.2025.11.005","url":null,"abstract":"<div><div>Human milk fats (HMFs) could facilitate nutrient absorption in the infant gut, with 1,3-olein-2-palmitin (OPO) and 1-olein-2-palmitin-3-linolein (OPL) being the most abundant components. The construction of microbial cell factories has garnered significant interest due to their potential to synthesize HMFs from cheap raw materials. However, the substrate preference of endogenous triglyceride (TAG) synthases and the complex fatty acid (FA) composition limit OPO and OPL synthesis. This study developed a microbial cell factory for OPO and OPL production by reconstructing and fine-tuning the lipid metabolic network in <em>Saccharomyces cerevisiae</em>. First, the TAG biosynthesis pathway of <em>S</em>. <em>cerevisiae</em> was reconstructed, resulting in more than 70 % of palmitic acid (C16:0) in TAG being esterified to the <em>sn</em>-2 position, while simultaneously achieving <em>de novo</em> OPO synthesis. Further optimization of intracellular FA composition improved the OPO proportion in TAG to 26.59 %. <em>De novo</em> synthesis of OPL was achieved by introducing a heterologous synthesis pathway of linoleic acid (C18:2). A push-pull strategy was employed to promote FA and TAG synthesis, resulting in a 3.86-fold increase in TAG production and reaching 81.2 mg/g dry cell weight in shake flask. In a 3-L bioreactor, the engineered strain HF-35 achieved OPO and OPL titers of 85.68 mg/L and 162.30 mg/L, respectively, representing the highest reported titers of OPO and OPL using glucose as the substrate to date. This study demonstrated that regulating lipid metabolism is an effective strategy for specific TAG synthesis and lays the foundation for large-scale production of OPO and OPL.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 1-14"},"PeriodicalIF":6.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145447230","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

An automated platform for accelerating and focusing adaptive laboratory evolution 加速和聚焦自适应实验室进化的自动化平台

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2026-03-01 Epub Date: 2025-12-25 DOI: 10.1016/j.ymben.2025.12.007

Peter Ruppen , Maximilian Ole Bahls , Michael Sebastian Gerlt , Martin Peter Edelmann , Tania Michelle Roberts , Philippe Marlière , Sven Panke

{"title":"An automated platform for accelerating and focusing adaptive laboratory evolution","authors":"Peter Ruppen , Maximilian Ole Bahls , Michael Sebastian Gerlt , Martin Peter Edelmann , Tania Michelle Roberts , Philippe Marlière , 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":"2026-03-01","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}

引用次数: 0

Establishing heterologous betaxanthin pigment biosynthesis in cyanobacteria 蓝藻中异源β -黄质色素的生物合成

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2026-03-01 Epub Date: 2026-01-05 DOI: 10.1016/j.ymben.2026.01.002

Sayali S. Hanamghar , David A. Russo , Silas Busck Mellor , Julie A.Z. Zedler

{"title":"Establishing heterologous betaxanthin pigment biosynthesis in cyanobacteria","authors":"Sayali S. Hanamghar , David A. Russo , Silas Busck Mellor , Julie A.Z. Zedler","doi":"10.1016/j.ymben.2026.01.002","DOIUrl":"10.1016/j.ymben.2026.01.002","url":null,"abstract":"<div><div>Betalains are water-soluble pigments with two major classes: red-violet betacyanins and yellow-orange betaxanthins. These pigments are increasingly being sought after as natural replacements for synthetic pigments in the food industry. Traditionally, betalains are extracted from cultivated plants. But due to low concentrations of native pigments, the process is inherently inefficient. Now, an increase in consumer demand calls for the development of scalable and sustainable betalain production routes. To address this challenge, we introduced a heterologous pathway for the production of betaxanthins into cyanobacteria. The pathway consists of an engineered variant of the cytochrome P450 CYP76AD1 (W13L, F309L) and the <span>l</span>-DOPA 4,5-dioxygenase DODA1 from <em>Beta vulgaris</em> (beet). Introduction of the two-enzyme betaxanthin pathway in <em>Synechocystis</em> sp. PCC 6803 did not result in detectable betaxanthins. Subsequent metabolic adjustments to the shikimate pathway, using a feedback resistant AroG<sup>fbr</sup> from <em>E. coli</em>, led to an overaccumulation of the aromatic amino acids phenylalanine, tryptophan, and tyrosine, and the production of low levels of phenylalanine-betaxanthin. Optimization of the cultivation conditions (i.e., growth in nutrient-rich medium and CO<sub>2</sub>-enriched air) increased titers approximately 165 times and led to the production of phenylalanine-betaxanthin with a final titer of 18.2 ± 5.1 mg L<sup>−1</sup>. Our work establishes a microbial system for photoautotrophic betaxanthin pigment production without the need for exogenous amino acid supplementation.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"94 ","pages":"Pages 264-272"},"PeriodicalIF":6.8,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145903384","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

Biosynthetic platform for orsellinic acid-derived meroterpenoids in Escherichia coli 大肠杆菌中奥塞利酸衍生巯基萜类化合物的生物合成平台

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2026-03-01 Epub Date: 2025-12-30 DOI: 10.1016/j.ymben.2025.12.008

Itsuki Tomita , Takahiro Bamba , Takanobu Yoshida , Lucília Domingues , Ryo Nasuno , Ryota Hidese , Tomohisa Hasunuma

{"title":"Biosynthetic platform for orsellinic acid-derived meroterpenoids in Escherichia coli","authors":"Itsuki Tomita , Takahiro Bamba , Takanobu Yoshida , Lucília Domingues , Ryo Nasuno , Ryota Hidese , 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":"2026-03-01","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}

引用次数: 0

Systems metabolic engineering of Klebsiella pneumoniae for high-level 1,3-propanediol production 高水平1,3-丙二醇生产肺炎克雷伯菌的系统代谢工程。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2026-01-01 Epub Date: 2025-09-01 DOI: 10.1016/j.ymben.2025.08.012

Shaolun Zhang , Fan Zhang , Jiake Sun , Hailang Yu , Peng Sun , Jia Liu , Xiaomin Li , Guipeng Hu , Jing Wu , Cong Gao , Liming Liu

{"title":"Systems metabolic engineering of Klebsiella pneumoniae for high-level 1,3-propanediol production","authors":"Shaolun Zhang , Fan Zhang , Jiake Sun , Hailang Yu , Peng Sun , Jia Liu , Xiaomin Li , Guipeng Hu , Jing Wu , Cong Gao , Liming Liu","doi":"10.1016/j.ymben.2025.08.012","DOIUrl":"10.1016/j.ymben.2025.08.012","url":null,"abstract":"<div><div>1,3-Propanediol (1,3-PDO) is an essential monomer used in the synthesis of polytrimethylene terephthalates. However, the microbial production of 1,3-PDO is limited by product tolerance and Vitamin B12 (VB<sub>12</sub>) supplementation. In this study, FMME-KP—a <em>Klebsiella pneumoniae</em> strain with a 1,3-PDO titer of 63.4 g/L. Through pathway reprogramming, the 1,3-PDO titer of strain FMME-14 was increased by 49.1 %. To enhance strain tolerance, a 1,3-PDO biosensor was developed to screen for high-yield strains during adaptive laboratory evolution. Reverse metabolic engineering of genes <em>ydaM</em><sup>L63V</sup> and <em>pgaD</em> improved the 1,3-PDO tolerance of strain FMME-38 by 62.5 %, leading to a 15.9 % increase in 1,3-PDO production. By enhancing the supply of cofactors VB<sub>12</sub> and NADH, strain FMME-51 produced 138.6 g/L 1,3-PDO, with a yield of 0.52 g/g within 48 h, without the need for external VB<sub>12</sub> supplementation. Additionally, this strain produced 122.7 g/L of 1,3-PDO using crude glycerol as a substrate. To the best of our knowledge, this is the highest reported titer and yield of microbial 1,3-PDO production.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"93 ","pages":"Pages 1-13"},"PeriodicalIF":6.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144960300","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

Feedstock-efficient conversion through hydrogen and formate-driven metabolism in Escherichia coli 在大肠杆菌中通过氢和甲酸驱动代谢实现原料高效转化。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2026-01-01 Epub Date: 2025-10-15 DOI: 10.1016/j.ymben.2025.10.003

Robert L. Bertrand , Justin Panich , Aidan E. Cowan , Jacob B. Roberts , Lesley J. Rodriguez , Juliana Artier , Emili Toppari , Edward E.K. Baidoo , Yan Chen , Christopher J. Petzold , Graham A. Hudson , Patrick M. Shih , Steven W. Singer , Jay D. Keasling

{"title":"Feedstock-efficient conversion through hydrogen and formate-driven metabolism in Escherichia coli","authors":"Robert L. Bertrand , Justin Panich , Aidan E. Cowan , Jacob B. Roberts , Lesley J. Rodriguez , Juliana Artier , Emili Toppari , Edward E.K. Baidoo , Yan Chen , Christopher J. Petzold , Graham A. Hudson , Patrick M. Shih , Steven W. Singer , Jay D. Keasling","doi":"10.1016/j.ymben.2025.10.003","DOIUrl":"10.1016/j.ymben.2025.10.003","url":null,"abstract":"<div><div>Product yields for biomanufacturing processes are often constrained by the tight coupling of cellular energy generation and carbon metabolism in sugar-based fermentation systems. To overcome this limitation, we engineered <em>Escherichia coli</em> to utilize hydrogen gas (H<sub>2</sub>) and formate (HCOO<sup>−</sup>) as alternative sources of energy and reducing equivalents, thereby decoupling energy generation from carbon metabolism. This approach enabled precise suppression of decarboxylative oxidation during acetate growth, with 86.6 ± 1.6 % of electrons from hydrogen gas (via soluble hydrogenase from <em>Cupriavidus necator</em> H16) and 98.4 ± 3.6 % of electrons from formate (via formate dehydrogenase from <em>Pseudomonas</em> sp. 101) offsetting acetate oxidation. Hydrogen gas supplementation led to a titratable and stoichiometric reduction in CO<sub>2</sub> evolution in acetate-fed cultures. Metabolomic analysis suggests that this metabolic decoupling redirects carbon flux through the glyoxylate shunt, partially bypassing two decarboxylative steps in the TCA cycle. We demonstrated the utility of this strategy by applying it to mevalonate biosynthesis, where formate supplementation during glucose fermentation increased titers by 57.6 % in our best-performing strain. Flux balance analysis further estimated that 99.0 ± 2.8 % of electrons from formate were used to enhance mevalonate production. These findings highlight a broadly applicable strategy for enhancing biomanufacturing efficiency by leveraging external reducing power to optimize feedstock and energy use.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"93 ","pages":"Pages 194-207"},"PeriodicalIF":6.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145313379","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

Multiplex base editing of RBSs rewires Bacillus subtilis metabolism for lycopene overproduction RBSs的多重碱基编辑重组枯草芽孢杆菌的代谢以过量生产番茄红素。

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2026-01-01 Epub Date: 2025-10-17 DOI: 10.1016/j.ymben.2025.10.005

Yang Liu , Xianhai Cao , Xiaojuan Wang , Ruirui Chen , Boxin Yuan , Shixin Li , Yu Wang , Xiaoping Liao , Xiaomeng Ni , Lixian Wang , Yanmei Guo , Hongwu Ma , Meng Wang

{"title":"Multiplex base editing of RBSs rewires Bacillus subtilis metabolism for lycopene overproduction","authors":"Yang Liu , Xianhai Cao , Xiaojuan Wang , Ruirui Chen , Boxin Yuan , Shixin Li , Yu Wang , Xiaoping Liao , Xiaomeng Ni , Lixian Wang , Yanmei Guo , Hongwu Ma , Meng Wang","doi":"10.1016/j.ymben.2025.10.005","DOIUrl":"10.1016/j.ymben.2025.10.005","url":null,"abstract":"<div><div><em>Bacillus subtilis</em> is a GRAS-certified chassis, yet scalable and precise multi-gene regulation remains a bottleneck in its metabolic engineering. Here, we present <em>bs</em>BETTER, a base editor-guided, template-free system enabling high-diversity expression tuning across multiple genomic loci. By editing ribosome binding sites (RBSs) of 12 lycopene biosynthetic genes, we generated thousands of combinatorial variants in situ, achieving up to 255 of 256 theoretical RBS combinations per gene. High-throughput screening identified variants exhibiting up to a 6.2-fold increase in lycopene production relative to strains carrying direct genomic overexpression of MEP pathway genes. RBS strength measurements revealed strong context dependence, highlighting the importance of genome-integrated expression optimization. Multi-omics analysis showed extensive transcriptional and metabolic rewiring, including enhanced MEP pathway flux and NADPH-generating capacity. <em>bs</em>BETTER offers a scalable, high-resolution approach for metabolic pathway engineering in <em>B. subtilis</em>, providing a generalizable framework for combinatorial gene expression modulation and metabolic pathway optimization.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"93 ","pages":"Pages 169-183"},"PeriodicalIF":6.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145314645","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 designed hybrid pathway for efficient synthesis of D-pantothenate in E. coli 大肠杆菌高效合成d -泛酸酯的杂交途径设计

IF 6.8 1区生物学

Metabolic engineering Pub Date : 2026-01-01 Epub Date: 2025-09-19 DOI: 10.1016/j.ymben.2025.09.007

Chenkai Cao , Jilong Wang , Mengzhen Nie , Jing Zhao , Yuchen Wang , Kechun Zhang

引用次数: 0