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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 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY 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
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, Escherichia coli was engineered to enable the de novo 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 fadR, 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 de novo production of OSA-derived meroterpenoids in E. coli. This study establishes E. coli as a versatile and scalable host for the biosynthesis of pharmacologically valuable meroterpenoids.
Orsellinic acid (OSA)-derived meroterpenoids,是一种具有OSA主干的植物源性天然产物,由于其多种药理活性,作为药物前体受到了广泛关注。因此,开发高效的微生物生产方法是非常必要的。然而,到目前为止,只有少数关于OSA衍生的美罗萜类化合物的微生物生产的报道,甚至对于前体OSA,也只有最小的生产水平(约5毫克/升)已经使用工程微生物实现。在本研究中,我们对大肠杆菌进行了改造,使其能够重新生物合成OSA,从而建立了OSA衍生的巯基萜类化合物的替代生产平台。引入III型聚酮合成酶和环化酶,产量为1.4 mg/L。CRISPR干扰旨在增强OSA的产生,结果表明,抑制参与丙二酰辅酶a消耗的fadR是有效的。代谢组学分析评估了工程策略的代谢影响,发现丙二酰辅酶a耗竭,表明其供应构成了主要瓶颈。在此基础上,对乙酰辅酶a羧化酶、泛酸激酶和ATP柠檬酸裂解酶进行过表达,在优化的培养条件下,OSA产量提高到202 mg/L,提高了145倍。最后,引入一种植物源戊烯基转移酶,实现了沙棘酸的生物合成(2.5 μg/g-DCW),这是首次在大肠杆菌中重新生产沙棘酸衍生的巯基萜类化合物。本研究建立了大肠杆菌作为一个多功能和可扩展的宿主,用于生物合成具有药理价值的美罗萜类化合物。
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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 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY 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
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 (VB12) supplementation. In this study, FMME-KP—a Klebsiella pneumoniae 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 ydaML63V and pgaD 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 VB12 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 VB12 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.
1,3-丙二醇(1,3- pdo)是合成聚对苯二甲酸三亚甲基酯的重要单体。然而,1,3- pdo的微生物生产受到产品耐受性和维生素B12 (VB12)补充的限制。本研究FMME-KP-a肺炎克雷伯菌1,3- pdo滴度为63.4 g/L。通过途径重编程,菌株FMME-14的1,3- pdo滴度提高了49.1%。为了提高菌株的耐受性,开发了一种1,3- pdo生物传感器,用于筛选实验室适应性进化过程中的高产菌株。通过基因ydaML63V和pgaD的反向代谢工程,菌株FMME-38对1,3- pdo的耐受性提高了62.5%,1,3- pdo产量提高了15.9%。通过增加辅因子VB12和NADH的供给,菌株FMME-51在48 h内产生138.6 g/L 1,3- pdo,产量为0.52 g/g,无需外部补充VB12。此外,该菌株以粗甘油为底物产生122.7 g/L的1,3- pdo。据我们所知,这是报道的微生物1,3- pdo生产的最高滴度和产量。
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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 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY 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
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 Escherichia coli to utilize hydrogen gas (H2) and formate (HCOO) 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 Cupriavidus necator H16) and 98.4 ± 3.6 % of electrons from formate (via formate dehydrogenase from Pseudomonas sp. 101) offsetting acetate oxidation. Hydrogen gas supplementation led to a titratable and stoichiometric reduction in CO2 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.
生物制造过程的产品产量通常受到糖基发酵系统中细胞能量产生和碳代谢的紧密耦合的限制。为了克服这一限制,我们设计了大肠杆菌,利用氢气(H2)和甲酸(HCOO-)作为替代能源和还原物,从而将能量产生与碳代谢解耦。这种方法能够精确抑制乙酸生长过程中的脱羧氧化,86.6±1.6%的电子来自氢气(通过Cupriavidus necator H16的可溶性氢化酶)和98.4±3.6%的电子来自甲酸(通过Pseudomonas sp. 101的甲酸脱氢酶)抵消乙酸氧化。氢气的补充导致醋酸盐培养物中CO2演化的可滴定和化学计量减少。代谢组学分析表明,这种代谢解耦通过乙醛酸分流重定向碳通量,部分绕过TCA循环中的两个脱羧步骤。我们通过将其应用于甲羟戊酸生物合成证明了这一策略的实用性,在葡萄糖发酵期间补充甲酸盐使我们表现最好的菌株的滴度提高了57.6%。通量平衡分析进一步估计,甲酸盐中99.0±2.8%的电子被用于提高甲羟戊酸的产量。这些发现强调了一种广泛适用的策略,通过利用外部减少功率来优化原料和能源使用,从而提高生物制造效率。
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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 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY 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
Bacillus subtilis is a GRAS-certified chassis, yet scalable and precise multi-gene regulation remains a bottleneck in its metabolic engineering. Here, we present bsBETTER, 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. bsBETTER offers a scalable, high-resolution approach for metabolic pathway engineering in B. subtilis, providing a generalizable framework for combinatorial gene expression modulation and metabolic pathway optimization.
枯草芽孢杆菌(Bacillus subtilis)是grass认证的“底盘”,但可扩展和精确的多基因调控仍然是其代谢工程的瓶颈。在这里,我们提出了bsBETTER,这是一个碱基编辑器引导的无模板系统,可以跨多个基因组位点进行高多样性表达调节。通过编辑12个番茄红素生物合成基因的核糖体结合位点(RBSs),我们原位生成了数千个组合变体,每个基因获得256个理论RBS组合中的255个。高通量筛选发现,与携带MEP通路基因直接基因组过表达的菌株相比,番茄红素产量增加了6.2倍。RBS强度测量显示了强烈的上下文依赖性,突出了基因组整合表达优化的重要性。多组学分析显示广泛的转录和代谢重新布线,包括增强的MEP途径通量和nadph生成能力。bsBETTER为枯草芽孢杆菌的代谢途径工程提供了一个可扩展的、高分辨率的方法,为组合基因表达调节和代谢途径优化提供了一个可推广的框架。
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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 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY 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
D-Pantothenate (D-PA), a crucial precursor for coenzyme A, is widely used in various industries. Traditional chemical synthesis of D-PA involves toxic inputs, including cyanide, and generates environmental pollution. Total biosynthesis from glucose still has limitation in long reaction time and low titer. To provide a new approach to D-PA, we designed a hybrid pathway. First, we used green chemical method to convert inexpensive glyoxylate and isobutyaldehyde into 2-hydroxy-3-methyl-3-formylbutyric acid (HMFBA). Then we established a biosynthetic pathway to transform HMFBA into D-PA. Specifically, we engineered a malate dehydrogenase to achieve the efficient stereospecific conversion step. Optimization efforts led to a strain producing 116.5 g/L D-PA in 48 h, which is the highest rate and titier reported so far. This new approach offers a potentially economic and high-rate production route of D-PA.
d -泛酸酯(D-PA)是辅酶a的重要前体,广泛应用于各个工业领域。传统的D-PA化学合成涉及有毒物质,包括氰化物,并产生环境污染。葡萄糖全生物合成仍存在反应时间长、效价低的局限性。为了提供一种新的途径,我们设计了一种混合途径。首先,我们采用绿色化学方法将廉价的乙醛酸酯和异丁醛转化为2-羟基-3-甲基-3-甲酰基丁酸(HMFBA)。然后我们建立了将HMFBA转化为D-PA的生物合成途径。具体来说,我们设计了苹果酸脱氢酶来实现高效的立体特异性转化步骤。经过优化,菌株在48小时内产生116.5 g/L D-PA,这是迄今为止报道的最高速率和滴度。该方法为D-PA的经济高效生产提供了一条新的途径。
{"title":"A designed hybrid pathway for efficient synthesis of D-pantothenate in E. coli","authors":"Chenkai Cao ,&nbsp;Jilong Wang ,&nbsp;Mengzhen Nie ,&nbsp;Jing Zhao ,&nbsp;Yuchen Wang ,&nbsp;Kechun Zhang","doi":"10.1016/j.ymben.2025.09.007","DOIUrl":"10.1016/j.ymben.2025.09.007","url":null,"abstract":"<div><div>D-Pantothenate (D-PA), a crucial precursor for coenzyme A, is widely used in various industries. Traditional chemical synthesis of D-PA involves toxic inputs, including cyanide, and generates environmental pollution. Total biosynthesis from glucose still has limitation in long reaction time and low titer. To provide a new approach to D-PA, we designed a hybrid pathway. First, we used green chemical method to convert inexpensive glyoxylate and isobutyaldehyde into 2-hydroxy-3-methyl-3-formylbutyric acid (HMFBA). Then we established a biosynthetic pathway to transform HMFBA into D-PA. Specifically, we engineered a malate dehydrogenase to achieve the efficient stereospecific conversion step. Optimization efforts led to a strain producing 116.5 g/L D-PA in 48 h, which is the highest rate and titier reported so far. This new approach offers a potentially economic and high-rate production route of D-PA.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"93 ","pages":"Pages 73-79"},"PeriodicalIF":6.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145103539","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
Reusable and modular combinatorial libraries for iterative metabolic engineering of Saccharomyces cerevisiae 用于酿酒酵母迭代代谢工程的可重用和模块化组合库。
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-01 Epub Date: 2025-09-19 DOI: 10.1016/j.ymben.2025.09.006
Philip Tinggaard Thomsen, Peter Gockel, Christina Vasileiou, Ingrid Mohr, Marc Cernuda Pastor, Irina Borodina
Efficiently rewiring microbial metabolism for molecule production lies at the core of industrial metabolic engineering. Combinatorial libraries are useful for directing metabolism towards molecule production; however, their construction is labor-intensive, and their use in iterative strain engineering campaigns is often restricted by site-specific genomic integration. Here we present an automation-friendly framework for generating reusable and modular integration-based combinatorial libraries that can be used repeatedly to build high-performing strains. We apply this approach to engineer the production of betacyanins, a commonly used red food colorant extracted from beetroots, in Saccharomyces cerevisiae. Iterative implementation of combinatorial libraries targeting the betacyanin biosynthesis pathway (design space: ∼25,000), precursors (design space: ∼43,000), and cofactors (design space: ∼26,000) consistently improved pigment production by 1.2–5.7-fold per cycle over seven rounds of engineering. Sequencing of high-performing library isolates from each round revealed unique insights into betacyanin and yeast metabolism, e.g. we found strong evidence implicating the S. cerevisiae cytochrome b5 in heterologous red beet pigment production. Altogether, this study demonstrates a framework for combinatorial library engineering well-suited for accelerating the development of high-performing cell factories for industrial fermentation processes.
有效地重组微生物代谢以生产分子是工业代谢工程的核心。组合文库有助于将代谢导向分子生成;然而,它们的构建是劳动密集型的,并且它们在迭代菌株工程活动中的使用经常受到特定位点基因组整合的限制。在这里,我们提出了一个自动化友好的框架,用于生成可重用的和模块化的基于集成的组合库,可以重复使用来构建高性能的菌株。我们将这种方法应用于酿酒酵母中甜菜青素的工程生产,甜菜青素是一种常用的从甜菜根中提取的红色食品着色剂。针对甜菜花青素生物合成途径(设计空间:~ 25,000)、前体(设计空间:~ 43,000)和辅因子(设计空间:~ 26,000)的组合文库的迭代实施在七轮工程中不断提高色素产量,每个周期提高1.2-5.7倍。对每一轮的高效文库分离物进行测序,揭示了甜菜青素和酵母代谢的独特见解,例如,我们发现了强有力的证据,表明酿酒酵母细胞色素b5参与了异源红甜菜色素的生产。总之,本研究展示了一个组合文库工程框架,非常适合于加速工业发酵过程高性能细胞工厂的开发。
{"title":"Reusable and modular combinatorial libraries for iterative metabolic engineering of Saccharomyces cerevisiae","authors":"Philip Tinggaard Thomsen,&nbsp;Peter Gockel,&nbsp;Christina Vasileiou,&nbsp;Ingrid Mohr,&nbsp;Marc Cernuda Pastor,&nbsp;Irina Borodina","doi":"10.1016/j.ymben.2025.09.006","DOIUrl":"10.1016/j.ymben.2025.09.006","url":null,"abstract":"<div><div>Efficiently rewiring microbial metabolism for molecule production lies at the core of industrial metabolic engineering. Combinatorial libraries are useful for directing metabolism towards molecule production; however, their construction is labor-intensive, and their use in iterative strain engineering campaigns is often restricted by site-specific genomic integration. Here we present an automation-friendly framework for generating reusable and modular integration-based combinatorial libraries that can be used repeatedly to build high-performing strains. We apply this approach to engineer the production of betacyanins, a commonly used red food colorant extracted from beetroots, in <em>Saccharomyces cerevisiae</em>. Iterative implementation of combinatorial libraries targeting the betacyanin biosynthesis pathway (design space: ∼25,000), precursors (design space: ∼43,000), and cofactors (design space: ∼26,000) consistently improved pigment production by 1.2–5.7-fold per cycle over seven rounds of engineering. Sequencing of high-performing library isolates from each round revealed unique insights into betacyanin and yeast metabolism, <em>e.g.</em> we found strong evidence implicating the <em>S. cerevisiae</em> cytochrome <em>b</em>5 in heterologous red beet pigment production. Altogether, this study demonstrates a framework for combinatorial library engineering well-suited for accelerating the development of high-performing cell factories for industrial fermentation processes.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"93 ","pages":"Pages 100-114"},"PeriodicalIF":6.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145103543","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 a biosensor based high-throughput screening platform for high-yield caffeic acid production in Escherichia coli 设计一个基于生物传感器的高通量筛选平台,用于大肠杆菌高产咖啡酸的生产。
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-01 Epub Date: 2025-09-30 DOI: 10.1016/j.ymben.2025.09.010
Daoguang Tian , Zhen Qin , Weilin Liu , Qinggele Caiyin , Weiguo Li , Guang-Rong Zhao , Jianjun Qiao
Caffeic acid (CA) is a valuable phenolic compound with wide applications in pharmaceuticals, food additives, and materials. However, its microbial production faces several challenges, including low heterologous enzyme activity and product toxicity. Here, we report the development of an integrated biosensor-driven high-throughput screening (HTS) platform for the efficient production of CA in Escherichia coli. We first identified and characterized CarR, a novel phenolic acid-responsive transcription factor from Acetobacterium woodii, and engineered it into a p-coumaric acid (p-CA) biosensor. Systematic optimization of the p-CA biosensor, resulting in reduced background, extended dynamic range and increased sensitivity. By coupling this biosensor with fluorescence-activated cell sorting, we established an efficient HTS platform that enabled the rapid selection of an improved FjTALG85S mutant with a 6.85-fold enhancement in catalytic activity and a robust p-CA-producing strain (M5) with enhanced tolerance to p-CA and CA. Subsequent bottom-up metabolic engineering in strain CA8 achieved a CA titer of 9.61 g L−1 in a 5-L bioreactor, the highest reported titer to date. Our work not only overcomes key bottlenecks in CA biosynthesis (low tyrosine ammonia-lyase activity, CA and p-CA cytotoxicity) but also provides a powerful tool to accelerate the engineering of microbial cell factories for the production of p-CA and other derived chemicals.
咖啡酸(cafic acid, CA)是一种有价值的酚类化合物,在医药、食品添加剂和材料等方面有着广泛的应用。然而,其微生物生产面临着一些挑战,包括低外源酶活性和产品毒性。在这里,我们报道了一种集成的生物传感器驱动的高通量筛选(HTS)平台的开发,用于在大肠杆菌中高效生产CA。我们首先从woodii乙杆菌中鉴定并表征了一种新的酚酸反应转录因子CarR,并将其设计成对香豆酸(p-CA)生物传感器。系统优化p-CA生物传感器,减少背景,扩大动态范围,提高灵敏度。通过将这种生物传感器与荧光激活的细胞分选相结合,我们建立了一个高效的HTS平台,能够快速选择催化活性提高6.85倍的FjTALG85S突变体和对p-CA和CA耐受性增强的强大的p-CA产生菌株(M5)。随后对菌株CA8进行自下而上的代谢工程,在5-L生物反应器中获得了9.61 g L-1的CA滴度,这是迄今为止报道的最高滴度。我们的工作不仅克服了CA生物合成的关键瓶颈(低酪氨酸解氨酶活性,CA和对CA的细胞毒性),而且为加速微生物细胞工厂的工程生产对CA和其他衍生化学品提供了有力的工具。
{"title":"Engineering a biosensor based high-throughput screening platform for high-yield caffeic acid production in Escherichia coli","authors":"Daoguang Tian ,&nbsp;Zhen Qin ,&nbsp;Weilin Liu ,&nbsp;Qinggele Caiyin ,&nbsp;Weiguo Li ,&nbsp;Guang-Rong Zhao ,&nbsp;Jianjun Qiao","doi":"10.1016/j.ymben.2025.09.010","DOIUrl":"10.1016/j.ymben.2025.09.010","url":null,"abstract":"<div><div>Caffeic acid (CA) is a valuable phenolic compound with wide applications in pharmaceuticals, food additives, and materials. However, its microbial production faces several challenges, including low heterologous enzyme activity and product toxicity. Here, we report the development of an integrated biosensor-driven high-throughput screening (HTS) platform for the efficient production of CA in <em>Escherichia coli</em>. We first identified and characterized CarR, a novel phenolic acid-responsive transcription factor from <em>Acetobacterium woodii</em>, and engineered it into a <em>p</em>-coumaric acid (<em>p</em>-CA) biosensor. Systematic optimization of the <em>p</em>-CA biosensor, resulting in reduced background, extended dynamic range and increased sensitivity. By coupling this biosensor with fluorescence-activated cell sorting, we established an efficient HTS platform that enabled the rapid selection of an improved FjTAL<sup>G85S</sup> mutant with a 6.85-fold enhancement in catalytic activity and a robust <em>p</em>-CA-producing strain (M5) with enhanced tolerance to <em>p</em>-CA and CA. Subsequent bottom-up metabolic engineering in strain CA8 achieved a CA titer of 9.61 g L<sup>−1</sup> in a 5-L bioreactor, the highest reported titer to date. Our work not only overcomes key bottlenecks in CA biosynthesis (low tyrosine ammonia-lyase activity, CA and <em>p</em>-CA cytotoxicity) but also provides a powerful tool to accelerate the engineering of microbial cell factories for the production of <em>p</em>-CA and other derived chemicals.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"93 ","pages":"Pages 128-144"},"PeriodicalIF":6.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145203458","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-wide CRISPR screening identifies genes in recombinant human embryonic kidney 293 cells for increased ammonia resistance 全基因组CRISPR筛选鉴定重组人胚胎肾293细胞中增加氨抗性的基因
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-01 Epub Date: 2025-10-21 DOI: 10.1016/j.ymben.2025.10.008
Sang Yoon Lee , Hyun Seung Kim , Yeon Gu Kim , Seunghyeon Shin , Seokchan Kweon , Jae Jun Lee , Gyun Min Lee
Ammonia, a byproduct of glutamine metabolism, inhibits cell growth and reduces product yield and quality in mammalian cell culture. To identify novel genes associated with ammonia resistance, a genome-wide CRISPR knockout screening was conducted in monoclonal antibody (mAb)-producing human embryonic kidney 293 (HEK-mAb) cells using a virus-free, recombinase-mediated cassette exchange-based gRNA interrogation method. The knockout cell library was subcultured for five consecutive passages under 20 mM NH4Cl, enriching cells with a sgRNA that conferred a proliferation advantage under high-ammonia conditions. Next-generation sequencing analysis of the enriched population identified three target genes -WNT3, TSPAN1, and CYHR1-among 19,114 genes. Knockout of these genes in HEK-mAb cells resulted in a 1.33- to 1.56-fold increase in maximum viable cell concentration and a 1.28- to 1.58-fold increase in maximum mAb concentration under 20 mM NH4Cl. Notably, WNT3 knockout maintained N-glycan galactosylation proportions of mAb despite ammonia stress. These findings highlight the effectiveness of genome-wide CRISPR knockout screening in identifying novel gene targets for ammonia-resistant HEK293 cell, offering a promising strategy for improving mAb production.
氨是谷氨酰胺代谢的副产物,在哺乳动物细胞培养中抑制细胞生长,降低产品产量和质量。为了鉴定与氨抗性相关的新基因,采用无病毒、重组酶介导的基于盒式交换的gRNA询问方法,在产生单克隆抗体(mAb)的人胚胎肾293 (HEK-mAb)细胞中进行了全基因组CRISPR敲除筛选。将敲除细胞文库在20 mM NH4Cl下连续传代5代,富集具有高氨条件下增殖优势的sgRNA细胞。下一代测序分析富集群体在19,114个基因中鉴定出三个靶基因- wnt3, TSPAN1和CYHR1。在20 mM NH4Cl条件下,敲除HEK-mAb细胞中的这些基因导致最大活细胞浓度增加1.33- 1.56倍,最大mAb浓度增加1.28- 1.58倍。值得注意的是,尽管氨胁迫,敲除WNT3仍能维持单抗的n -聚糖半乳糖化比例。这些发现强调了全基因组CRISPR敲除筛选在鉴定氨抗性HEK293细胞的新基因靶点方面的有效性,为提高单克隆抗体的生产提供了一种有希望的策略。
{"title":"Genome-wide CRISPR screening identifies genes in recombinant human embryonic kidney 293 cells for increased ammonia resistance","authors":"Sang Yoon Lee ,&nbsp;Hyun Seung Kim ,&nbsp;Yeon Gu Kim ,&nbsp;Seunghyeon Shin ,&nbsp;Seokchan Kweon ,&nbsp;Jae Jun Lee ,&nbsp;Gyun Min Lee","doi":"10.1016/j.ymben.2025.10.008","DOIUrl":"10.1016/j.ymben.2025.10.008","url":null,"abstract":"<div><div>Ammonia, a byproduct of glutamine metabolism, inhibits cell growth and reduces product yield and quality in mammalian cell culture. To identify novel genes associated with ammonia resistance, a genome-wide CRISPR knockout screening was conducted in monoclonal antibody (mAb)-producing human embryonic kidney 293 (HEK-mAb) cells using a virus-free, recombinase-mediated cassette exchange-based gRNA interrogation method. The knockout cell library was subcultured for five consecutive passages under 20 mM NH<sub>4</sub>Cl, enriching cells with a sgRNA that conferred a proliferation advantage under high-ammonia conditions. Next-generation sequencing analysis of the enriched population identified three target genes -<em>WNT3</em>, <em>TSPAN1</em>, and <em>CYHR1</em>-among 19,114 genes. Knockout of these genes in HEK-mAb cells resulted in a 1.33- to 1.56-fold increase in maximum viable cell concentration and a 1.28- to 1.58-fold increase in maximum mAb concentration under 20 mM NH<sub>4</sub>Cl. Notably, <em>WNT3</em> knockout maintained <em>N</em>-glycan galactosylation proportions of mAb despite ammonia stress. These findings highlight the effectiveness of genome-wide CRISPR knockout screening in identifying novel gene targets for ammonia-resistant HEK293 cell, offering a promising strategy for improving mAb production.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"93 ","pages":"Pages 184-193"},"PeriodicalIF":6.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145351710","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
Emerging hosts for metabolic engineering 代谢工程的新宿主。
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-01 Epub Date: 2025-10-21 DOI: 10.1016/j.ymben.2025.10.009
Hal S. Alper
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引用次数: 0
Edible fungus Fusarium venenatum: advances, challenges, and engineering strategies for future food production 食用菌镰刀菌:未来食品生产的进展、挑战和工程策略
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2026-01-01 Epub Date: 2025-09-25 DOI: 10.1016/j.ymben.2025.09.009
Sheng Tong, Qiyu Qiu, Jiaying Gao, Jiali Yu, Yaobo Xu, Zhihua Liao
By 2050, the global population is projected to reach 9.7 billion, necessitating a 70 % increase in traditional agricultural output to meet growing demands. However, critical constraints are emerging as arable land and water resources approach their sustainable utilization thresholds. In this context, ensuring safe, efficient, and sustainable food production has become a pivotal issue intertwined with national economy and people's livelihood. Microbial manufacturing based on microbial chassis and synthetic biology technology represents a transformative approach to future food production. Notably, the edible filamentous fungus Fusarium venenatum serves as an ideal chassis for next-generation future food biomanufacturing. However, there has been a lack of systematic reviews specifically focusing on the development of synthetic biology tools, chassis engineering, and chassis applications for this strain. This paper systematically summarizes the latest significant progress, from the perspectives mentioned above, in the use of F. venenatum for future food biomanufacturing. Furthermore, it discusses potential development directions and challenges, and proposes some available strategies, intending to provide ideas and guidance for the further development of F. venenatum-based future food production systems.
到2050年,全球人口预计将达到97亿,传统农业产量必须提高70%才能满足日益增长的需求。然而,随着耕地和水资源接近其可持续利用阈值,关键的制约因素正在出现。在此背景下,确保安全、高效、可持续的粮食生产已成为关系国计民生的关键问题。基于微生物底盘和合成生物学技术的微生物制造代表了未来食品生产的变革性方法。值得注意的是,可食用丝状真菌镰刀菌是下一代未来食品生物制造的理想基础。然而,对于该菌株的合成生物学工具、底盘工程和底盘应用的开发,一直缺乏系统的综述。本文从以上几个方面系统地总结了维氏霉霉在未来食品生物制造中的应用的最新重大进展。探讨了潜在的发展方向和挑战,并提出了一些可行的策略,旨在为未来以黄曲霉为基础的粮食生产系统的进一步发展提供思路和指导。
{"title":"Edible fungus Fusarium venenatum: advances, challenges, and engineering strategies for future food production","authors":"Sheng Tong,&nbsp;Qiyu Qiu,&nbsp;Jiaying Gao,&nbsp;Jiali Yu,&nbsp;Yaobo Xu,&nbsp;Zhihua Liao","doi":"10.1016/j.ymben.2025.09.009","DOIUrl":"10.1016/j.ymben.2025.09.009","url":null,"abstract":"<div><div>By 2050, the global population is projected to reach 9.7 billion, necessitating a 70 % increase in traditional agricultural output to meet growing demands. However, critical constraints are emerging as arable land and water resources approach their sustainable utilization thresholds. In this context, ensuring safe, efficient, and sustainable food production has become a pivotal issue intertwined with national economy and people's livelihood. Microbial manufacturing based on microbial chassis and synthetic biology technology represents a transformative approach to future food production. Notably, the edible filamentous fungus <em>Fusarium venenatum</em> serves as an ideal chassis for next-generation future food biomanufacturing. However, there has been a lack of systematic reviews specifically focusing on the development of synthetic biology tools, chassis engineering, and chassis applications for this strain. This paper systematically summarizes the latest significant progress, from the perspectives mentioned above, in the use of <em>F. venenatum</em> for future food biomanufacturing. Furthermore, it discusses potential development directions and challenges, and proposes some available strategies, intending to provide ideas and guidance for the further development of <em>F. venenatum</em>-based future food production systems.</div></div>","PeriodicalId":18483,"journal":{"name":"Metabolic engineering","volume":"93 ","pages":"Pages 115-127"},"PeriodicalIF":6.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145156005","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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Metabolic engineering
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