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Plasmid-based electroporation for efficient genetic engineering in immortalized T lymphocytes 基于质粒的电穿孔技术用于永生 T 淋巴细胞的高效基因工程。
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-04-02 DOI: 10.1016/j.ymben.2025.03.019
Yu-Qing Xie , Martin Fussenegger
The recent clinical success of genetically modified T-cell therapies underscores the urgent need to accelerate fundamental studies and functional screening methods in T lymphocytes. However, a facile and cost-effective method for efficient genetic engineering of T-cells remains elusive. Current approaches often rely on viral transduction, which is labor-intensive and requires stringent biosafety measures. Plasmid-based electroporation presents an affordable alternative, but remains underexplored in T-cells. Moreover, the availability of prototypical T-cell lines is limited. Here, we address these challenges by focusing on two immortalized murine T-cell lines, HT-2 and CTLL-2, which recapitulate key characteristics of primary T-cells, including cytotoxicity and cytokine-dependent proliferation. Alongside the widely used Jurkat T-cell line, HT-2 and CTLL-2 were successfully transfected with single or multiple genes with high efficiencies by means of optimized electroporation in a cuvette-based system. Notably, optimization of plasmid constructs enabled the delivery of large gene-of-interest (GOI) cargos of up to 6.5 kilobase pairs, as well as stable integration of a GOI into the genome via the Sleeping Beauty transposon system. We also developed advanced methodologies for CRISPR/Cas9-mediated gene editing in immortalized T lymphocytes, achieving knockout efficiencies of up to 97 % and homology-directed repair (HDR)-based targeted knock-in efficiencies of up to 70 %. We believe this optimized plasmid-based electroporation approach will contribute to advances in basic research on lymphocyte biology, as well as providing a practical, cost-effective tool for preclinical studies of T-cell therapies.
最近基因修饰T细胞疗法的临床成功强调了加速T淋巴细胞基础研究和功能筛选方法的迫切需要。然而,对t细胞进行高效基因工程的一种简单而经济的方法仍然是难以捉摸的。目前的方法通常依赖于病毒转导,这是劳动密集型的,需要严格的生物安全措施。基于质粒的电穿孔是一种经济实惠的替代方法,但在t细胞中仍未得到充分探索。此外,原型t细胞系的可用性是有限的。在这里,我们通过关注两种永生化小鼠t细胞系HT-2和CTLL-2来解决这些挑战,它们概括了原代t细胞的关键特征,包括细胞毒性和细胞因子依赖性增殖。与广泛使用的Jurkat t细胞系一起,HT-2和CTLL-2通过优化的电穿孔系统以高效率成功地转染了单个或多个基因。值得注意的是,质粒结构的优化使其能够递送多达6.5千碱基对的大型感兴趣基因(GOI)货物,并通过睡美人转座子系统将GOI稳定地整合到基因组中。我们还开发了CRISPR/ cas9介导的永生化T淋巴细胞基因编辑的先进方法,实现了高达97%的敲除效率和高达70%的基于同源定向修复(HDR)的靶向敲入效率。我们相信这种优化的基于质粒的电穿孔方法将有助于淋巴细胞生物学基础研究的进步,并为t细胞治疗的临床前研究提供实用、经济的工具。
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引用次数: 0
Carbon-conserving bioproduction of malate in an E. coli-based cell-free system 以大肠杆菌为基础的无细胞系统中苹果酸盐的碳保存生物生产
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-04-08 DOI: 10.1016/j.ymben.2025.03.020
Ryan A.L. Cardiff , Shaafique Chowdhury , Widianti Sugianto , Benjamin I. Tickman , Diego Alba Burbano , Pimphan A. Meyer , Margaret Cook , Brianne King , David Garenne , Alexander S. Beliaev , Vincent Noireaux , Peralta-Yahya Pamela , James M. Carothers
Formate, a biologically accessible form of CO2, has attracted interest as a renewable feedstock for bioproduction. However, approaches are needed to investigate efficient routes for biological formate assimilation due to its toxicity and limited utilization by microorganisms. Cell-free systems hold promise due to their potential for efficient use of carbon and energy sources and compatibility with diverse feedstocks. However, bioproduction using purified cell-free systems is limited by costly enzyme purification, whereas lysate-based systems must overcome loss of flux to background reactions in the cell extract. Here, we engineer an E. coli-based system for an eight-enzyme pathway from DNA and incorporate strategies to regenerate cofactors and minimize loss of flux through background reactions. We produce the industrial di-acid malate from glycine, bicarbonate, and formate by engineering the carbon-conserving reductive TCA and formate assimilation pathways. We show that in situ regeneration of NADH drives metabolic flux towards malate, improving titer by 15-fold. Background reactions can also be reduced 6-fold by diluting the lysate following expression and introducing chemical inhibitors of competing reactions. Together, these results establish a carbon-conserving, lysate-based cell-free platform for malate production, producing 64 μM malate after 8 h. This system conserves 43 % of carbon otherwise lost as CO2 through the TCA cycle and incorporates 0.13 mol CO2 equivalents/mol glycine fed. Finally, techno-economic analysis of cell-free malate production from formate revealed that the high cost of lysate is a key challenge to the economic feasibility of the process, even assuming efficient cofactor recycling. This work demonstrates the capabilities of cell-free expression systems for both the prototyping of carbon-conserving pathways and the sustainable bioproduction of platform chemicals.
甲酸盐是一种生物可获得的二氧化碳形式,作为生物生产的可再生原料引起了人们的兴趣。然而,由于甲酸酯的毒性和微生物利用有限,需要研究有效的生物同化途径。无细胞系统由于其有效利用碳和能源的潜力以及与各种原料的兼容性而具有前景。然而,使用纯化的无细胞系统的生物生产受到昂贵的酶纯化的限制,而基于裂解物的系统必须克服细胞提取物中背景反应的通量损失。在这里,我们设计了一个基于大肠杆菌的系统,用于DNA的八酶途径,并结合了再生辅助因子和通过背景反应最小化通量损失的策略。我们通过设计碳保护还原性TCA和甲酸同化途径,从甘氨酸、碳酸氢盐和甲酸酯中生产工业用苹果酸二酸酯。我们发现NADH的原位再生驱动了苹果酸盐的代谢通量,将滴度提高了15倍。通过在表达后稀释裂解物并引入竞争反应的化学抑制剂,背景反应也可以减少6倍。综上所述,这些结果建立了一个碳节约、基于裂解液的无细胞苹果酸生产平台,在8小时后生产64 μM苹果酸。该系统通过TCA循环节省了43%的碳,其他碳作为二氧化碳损失,并且每mol甘氨酸添加0.13 mol CO2当量。最后,对甲酸生产无细胞苹果酸的技术经济分析表明,裂解液的高成本是该工艺经济可行性的关键挑战。即使假设有效的辅因子回收。这项工作证明了无细胞表达系统在碳保存途径的原型设计和平台化学品的可持续生物生产方面的能力。
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引用次数: 0
Metabolic engineering in Hot Acid: Strategies enabling chemolithotrophy in thermoacidophilic archaea 热酸代谢工程:在嗜热酸古菌中实现化石化的策略
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-06-10 DOI: 10.1016/j.ymben.2025.06.005
Daniel J. Willard , Robert M. Kelly
A genome-scale metabolic model was developed to explore metabolic engineering strategies for thermoacidophilic archaea, with a focus on the genetically tractable Sulfolobus acidocaldarius (Topt 75 °C, pHopt 2.5). S. acidocaldarius is natively neither an autotroph nor a sulfur oxidizer, although its genome suggests that this might have been the case at some evolutionary point. Comparative genomics provided insights into key genes and pathways missing from S. acidocaldarius necessary for chemolithotrophy. Growth data for the chemolithotrophic sulfur oxidizer, Sulfurisphaera ohwakuensis (Topt 85 °C, pHopt 2.0), provided metabolic data to inform model development. Previous metabolic engineering efforts enabled sulfur oxidation by S. acidocaldarius, albeit at levels below native sulfur oxidizers. Model analysis pointed to active sulfur transport as a key missing complement to passive diffusion. Modelling results predicted that sulfur oxidation could drive production of a bio-based chemical, acetone, in engineered strains of S. acidocaldarius with concomitant fixation of CO2 into product via the 3-Hydroxybutyrate/4-Hydroxybutyrate cycle. The findings here provide new insights into the basis for thermoacidophile chemolithotrophy and motivate further efforts to develop S. acidocaldarius into a valuable metabolic engineering platform.
为了探索嗜热酸性古细菌的代谢工程策略,我们建立了一个基因组尺度的代谢模型,重点研究了遗传易感的Sulfolobus acidocalarius (Topt 75°C, pHopt 2.5)。S. acidocalarius既不是自养生物,也不是硫氧化剂,尽管它的基因组表明这可能是在某个进化点上的情况。比较基因组学提供了对S. acidocalarius趋化岩石形成所必需的关键基因和途径缺失的见解。化学岩石营养硫氧化剂,sulisphaera ohwakuensis (Topt 85°C, pHopt 2.0)的生长数据为模型开发提供了代谢数据。以前的代谢工程努力使硫氧化S. acidocalarius,尽管其水平低于天然硫氧化剂。模型分析指出,活性硫输运是被动扩散的关键缺失补充。模拟结果预测,硫氧化可以驱动工程菌株的生物基化学物质丙酮的生产,同时通过3-羟基丁酸盐/4-羟基丁酸盐循环将二氧化碳固定到产品中。本研究结果为热嗜酸菌的化学嗜石性提供了新的见解,并推动了将S. acidocalarius开发为有价值的代谢工程平台的进一步努力。
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引用次数: 0
Modulating fatty acid metabolism and composition of CHO cells by feeding high levels of fatty acids complexed using methyl-β-cyclodextrin 通过喂食高水平的甲基-β-环糊精脂肪酸络合物来调节脂肪酸代谢和CHO细胞的组成
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-04-25 DOI: 10.1016/j.ymben.2025.04.005
Bradley Priem , Xiangchen Cai , Yu-Jun Hong , Karl Gilmore , Zijun Deng , Sabrina Chen , Harnish Mukesh Naik , Michael J. Betenbaugh , Maciek R. Antoniewicz
Chinese Hamster Ovary (CHO) cells are widely used in the pharmaceutical industry to produce therapeutic proteins. Increasing the productivity of CHO cells through media development and genetic engineering is a significant industry objective. Past research demonstrated the benefits of modulating fatty acid composition of CHO cells through genetic engineering. In this study, we describe an alternative approach to modulate fatty acid composition by directly feeding high levels of fatty acids in CHO cell culture. To accomplish this, we developed and optimized a pharmaceutically relevant feeding strategy using methyl-β-cyclodextrin (MBCD) to solubilize fatty acids. To quantify fatty acid composition of CHO cells, a new GC-MS protocol was developed and validated. In fed batch cultures, we found that the degree of saturation of fatty acids in CHO cell mass, i.e. the relative abundances of saturated, monounsaturated and polyunsaturated fatty acids, can be controlled by the choice of fatty acid supplement and feeding strategy. Feeding unsaturated fatty acids such as palmitoleic acid, oleic acid, and linoleic acid had the greatest impact the fatty acid composition of CHO cells, increasing their respective abundances in cell mass by upwards of 25x, 1.5x, and 50x, respectively. 13C-Tracing further revealed that the supplemented fatty acids were involved in a range of elongation, desaturation, and β-oxidation reactions to yield both common and uncommon fatty acids such as vaccenic acid and hypogeic acid. Finally, we show that CHO-K1 and CHO-GS cells take up fatty acids solubilized with MBCD at rates comparable to delivery using bovine serum albumin. Taken together, this work paves the way for new feed media formulations containing fatty acids to optimize CHO cell physiology in industrial cell cultures.
中国仓鼠卵巢细胞(CHO)被广泛应用于制药行业,以生产治疗性蛋白。通过培养基开发和基因工程提高CHO细胞的生产力是一个重要的行业目标。过去的研究表明,通过基因工程调节脂肪酸组成的CHO细胞的好处。在这项研究中,我们描述了一种通过在CHO细胞培养中直接喂食高水平脂肪酸来调节脂肪酸组成的替代方法。为了实现这一目标,我们开发并优化了甲基β-环糊精(MBCD)对脂肪酸的增溶策略。为了量化CHO细胞的脂肪酸组成,我们开发并验证了一种新的GC-MS方案。在分批培养中,我们发现CHO细胞团中脂肪酸的饱和程度,即饱和脂肪酸、单不饱和脂肪酸和多不饱和脂肪酸的相对丰度可以通过脂肪酸补充和饲养策略的选择来控制。饲喂棕榈油酸、油酸和亚油酸等不饱和脂肪酸对CHO细胞脂肪酸组成的影响最大,使其在细胞质量中的丰度分别增加了25倍、1.5倍和50倍以上。13c示踪进一步显示,补充的脂肪酸参与了一系列的延伸、去饱和和β-氧化反应,生成了常见和不常见的脂肪酸,如异丙酸和次氯酸。最后,我们发现CHO-K1和CHO-GS细胞以与牛血清白蛋白相当的速度吸收与MBCD溶解的脂肪酸。综上所述,这项工作为含有脂肪酸的新饲料培养基配方铺平了道路,以优化工业细胞培养中的CHO细胞生理。
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引用次数: 0
Corrigendum to “Insights into the methanol utilization capacity of Y. lipolytica and improvements through metabolic engineering” [Metabol. Eng. (2025) 91 30–43] “解脂Y.酵母的甲醇利用能力及其通过代谢工程的改进”的勘误表[代谢。Eng。(2025) 91 - 43]
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-05-02 DOI: 10.1016/j.ymben.2025.04.004
Wei Jiang , William Newell , Jingjing Liu , Lucas Coppens , Khushboo Borah Slater , Huadong Peng , David Bell , Long Liu , Victoria Haritos , Rodrigo Ledesma-Amaro
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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 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-09-01 Epub 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
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 Escherichia coli 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 Cyclobacterium marinum. 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.
o -乙酰- l-高丝氨酸(OAH)是生物合成l-蛋氨酸和各种C4化合物的关键前体,具有重要的工业潜力。然而,由于复杂的代谢调节和前体的限制,高效的微生物生产OAH仍然具有挑战性。在这项研究中,我们合理地开发了一种无质粒、非营养大肠杆菌菌株来生产OAH。我们将OAH合成途径模块化为l-高丝氨酸和乙酰辅酶a模块,并分别对每个模块进行增强,从海洋环杆菌中鉴定出高效的l-高丝氨酸o -乙酰转移酶(MetX)。通过小RNA筛选,我们确定了关键的代谢节点,并通过启动子工程和调控元件微调了途径通量。值得注意的是,我们通过适度表达丙酮酸羧化酶来平衡乙酰辅酶a和l-高丝氨酸的合成,通过减弱BCAA转氨酶来调节柠檬酸合成酶和支链氨基酸途径,从而减弱TCA循环,从而将碳通量重定向到OAH的产生。此外,我们优化了苏氨酸衰减器,以动态调节苏氨酸途径并增强细胞内ATP的周转。在两阶段pH控制发酵策略下,最终无质粒、非营养不良菌株OAH37的OAH滴度为94.1 g/L,产率为0.42 g/g葡萄糖,产率为1.37 g/L/h。我们的工作证明了代谢工程策略在高效微生物合成OAH方面的潜力,为这种重要前体的工业规模生产提供了基础。
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引用次数: 0
Photosynthetic sorbitol production in Synechococcus sp. PCC 7002 is enhanced by addressing phosphatase promiscuity, nutrient availability and Calvin cycle bottlenecks 聚球菌PCC 7002通过解决磷酸酶混杂性、养分有效性和卡尔文循环瓶颈,提高了光合作用山梨醇的产量
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-05-02 DOI: 10.1016/j.ymben.2025.04.008
Cody Kamoku , Pranav Bhavaraju , Collin Travis , Luis Taquillo , David R. Nielsen
Cyanobacteria represent promising biocatalysts for producing carbohydrates, including sorbitol, a naturally-occurring, fermentable sugar alcohol with conventional uses as a sweetener, pharmaceutical additive, and biodegradable plasticizer. Previously, Synechocystis sp. PCC 6803 was engineered to produce sorbitol, reaching a final titer of 2.3 g/L after 18 days. To improve upon this performance, sorbitol production was herein engineered in the faster growing strain Synechococcus sp. PCC 7002. Upon introducing the sorbitol biosynthetic pathway, up to 500 mg/L sorbitol was initially produced after seven days. However, due to the initial use of two highly promiscuous sugar phosphatase variants, this also resulted in the unwanted co-production of ribose and growth inhibition due to depletion of ribose-5-phosphate from the Calvin cycle. This off-target effect was ultimately mitigated via the discovery that mannitol-1-phosphate phosphatase from Eimeria tenella also dephosphorylates sorbitol-6-phosphate to sorbitol with greater specificity, leading to improved growth and sorbitol production. Next, two bottleneck enzymes in the Calvin cycle, namely fructose-bisphosphate aldolase (FBA) and bifunctional fructose-1,6-bisphosphatase/sedoheptulose-1,7-bisphosphatase (BiBPase), were overexpressed both individually and in combination, resulting in sorbitol production up to 1.3 g/L. Finally, upon optimizing the culture media to address nutrient limitation, the final strain produced up to 3.6 g/L sorbitol in nine days, respectively representing 1.5- and 3-fold increases in titer and productivity relative to previously-engineered Synechocystis sp. PCC 6803.
蓝藻代表了生产碳水化合物的有前途的生物催化剂,包括山梨醇,一种天然存在的、可发酵的糖醇,通常用作甜味剂、药物添加剂和可生物降解的增塑剂。先前,Synechocystis sp. PCC 6803被改造成山梨糖醇,18天后达到2.3 g/L的最终滴度。为了提高这一性能,本文在生长速度更快的聚糖球菌(Synechococcus sp. pcc7002)中设计了山梨醇的生产。引入山梨糖醇生物合成途径后,7天后最初可生产高达500 mg/L的山梨糖醇。然而,由于最初使用了两种高度混杂的糖磷酸酶变体,这也导致了核糖的不必要的共同产生和由于卡尔文循环中核糖-5-磷酸的消耗而导致的生长抑制。这种脱靶效应最终通过发现来自柔韧性艾美耳球虫的甘露醇-1-磷酸磷酸酶也可以更特异性地将山梨醇-6-磷酸去磷酸化为山梨醇,从而改善生长和山梨醇的产量而得到缓解。接下来,卡尔文循环中的两个瓶颈酶,即果糖-二磷酸醛缩酶(FBA)和双功能果糖-1,6-二磷酸酶/sedoheptulose-1,7-二磷酸酶(BiBPase)单独或联合过表达,导致山梨醇产量高达1.3 g/L。最后,在优化培养基以解决营养限制后,最终菌株在9天内产生高达3.6 g/L的山梨糖醇,相对于先前设计的Synechocystis sp. PCC 6803,滴度和产量分别提高了1.5倍和3倍。
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引用次数: 0
Regulation of proenzyme activation and metabolic engineering for protein-glutaminase production in Bacillus subtilis 枯草芽孢杆菌蛋白谷氨酰胺酶原活化调控及代谢工程研究。
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-06-02 DOI: 10.1016/j.ymben.2025.06.001
Maofang Teng , Juan Zhang , Jingwen Zhou , Jianghua Li , Guocheng Du , Jian Chen , Guoqiang Zhang
The protein-glutaminase (PG, EC 3.5.1.44) specifically targets glutamine residues in proteins and peptides, and has significant potential for enhancing the functional characteristics and processing efficiency of plant proteins. However, natural PG production faces challenges such as low enzymatic yield and difficult genetic manipulation. To address these challenges, a novel self-activating PG expression system was developed in Bacillus subtilis. First, pro-PG (PPG)-activated proteases were identified in B. subtilis by constructing a series of engineered strains. Second, the co-expression of PPG and PPG-activated protease in B. subtilis WB800 for mature PG (mPG) production was analyzed, and it was found that the supply and activation of PPG during fermentation was insufficient. Therefore, the gene expression components of PPG and protease, including the promoter and RBS, were further optimized. In addition, the key genes of the maltose metabolic pathway were knocked out, and the engineered strain W8ΔM2-AE-Pmal380 showed the highest capacity for PG production. Finally, a 53.0 U/mL mPG yield was achieved in a 5-L bioreactor within 64 h. This study establishes an efficient platform for industrial PG production and provides a reference for the expression and activation of other proenzymes.
蛋白-谷氨酰胺酶(protein-glutaminase, PG, EC 3.5.1.44)专门针对蛋白质和多肽中的谷氨酰胺残基,在提高植物蛋白的功能特性和加工效率方面具有重要的潜力。然而,天然PG的生产面临着酶产率低和基因操作困难等挑战。为了解决这些挑战,在枯草芽孢杆菌中开发了一种新的自激活PG表达系统。首先,通过构建一系列工程菌株,鉴定了枯草芽孢杆菌中原pg (PPG)活化的蛋白酶。其次,分析了枯草芽孢杆菌WB800中PPG和PPG活化蛋白酶的共表达情况,发现发酵过程中PPG的供应和活化不足。因此,进一步优化PPG和蛋白酶的基因表达组分,包括启动子和RBS。此外,麦芽糖代谢途径的关键基因被敲除,工程菌株W8ΔM2-AE-Pmal380显示出最高的PG生产能力。最终在5-L的生物反应器中,在64 h内获得了53.0 U/mL的mPG产率。本研究为工业生产PG建立了一个高效的平台,并为其他原酶的表达和激活提供了参考。
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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 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-06-16 DOI: 10.1016/j.ymben.2025.06.007
Yusong Zou, Xinyu Gong, Jianli Zhang, Qi Gan, Yajun Yan
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.
遗传调控工具已经被研究,因为它们能够对微生物细胞工厂的生物合成进行复杂的动态控制,提高有价值化合物的生产性能。然而,大多数遗传工具是途径特异性或中间特异性的,阻碍了它们在合成生物学中的广泛应用。此外,它们在细胞生长和产物形成之间的中心代谢中平衡代谢通量的潜力仍未得到充分探索,这就提出了它们是否能促进有效的生物合成的问题。为此,我们建立了响应丙酮酸的PdhR生物传感器系统,动态调节中枢代谢的代谢通量分布。在这项研究中,我们首先通过筛选来自不同微生物的多个PdhR同源物来表征PdhR生物传感器系统的剂量效应。计算分析进一步指导识别导致其功能差异的关键因素,从而通过位点定向诱变优化生物传感器性能。作为概念验证,我们利用我们的生物传感器系统分别改善海藻糖和4-羟基香豆素(4HC)的生物合成。其中海藻糖滴度提高到3.72 g/L,是对照组的2.33倍。此外,我们将4HC滴度提高到491.5 mg/L,比静态策略提高了1.63倍。综上所述,建立的中枢代谢响应生物传感器系统强调了代谢通量分布的必要性,并验证了其在中枢代谢衍生化合物的生物合成中的广泛适用性。
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引用次数: 0
Metabolic engineering of acetogenic bacteria using CO gas-sensing transcriptional ON/OFF modules 利用CO气敏转录ON/OFF模块的产丙酮菌代谢工程。
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-05-10 DOI: 10.1016/j.ymben.2025.04.012
Sangrak Jin , Irisappan Ganesh , Jiyun Bae , Donghwi Lee , Seulgi Kang , Hyeonsik Lee , Jeong Wook Lee , Byung-Kwan Cho
Dynamic sensing of gas substrates like toxic carbon monoxide (CO) in living microbial cells is often limited due to the lack of suitable biosensors. Here, we integrated the CO-binding transcription activators, CooA and RcoM1, with an O2-independent fluorescent reporter system, Halo-tag, to develop CO-sensing modules (ON/OFF) capable of detecting CO concentrations in the strictly anaerobic acetogenic bacterium Eubacterium limosum. Furthermore, we employed CooA as the CO-sensing ON module to activate the target genes for 2,3-butanediol (2,3-BDO) biosynthesis, achieving a 1.7-fold increase in 2,3-BDO yield. These results indicate that the CO-ON module effectively redirects carbon flux toward target product biosynthesis pathway in acetogens. However, during CO gas with glucose mixotrophic fermentation, lactate emerged as the predominant product. To enhance target pathway flux using the CO-ON module, we deleted the lactate pathway in E. limosum using CRISPR/Cas9. The resulting engineered strain showed an 18.5 % increase in carbon utilization for 2,3-BDO production under CO sensing culture conditions. This optimized platform strain subsequently produced approximately 52 g/L of 2,3-BDO during two stage CO-glucose mixotrophic fermentation. Our results provide orthogonal CO-sensing transcriptional regulatory modules for engineering metabolic pathways that efficiently convert CO into value-added biochemicals using acetogenic biocatalysts.
由于缺乏合适的生物传感器,活体微生物细胞中有毒一氧化碳(CO)等气体底物的动态传感往往受到限制。在这里,我们将CO结合转录激活因子CooA和RcoM1与o2独立的荧光报告系统Halo-tag结合在一起,开发了CO传感模块(ON/OFF),能够检测严格厌氧产醋酸细菌(Eubacterium limosum)中的CO浓度。此外,我们利用CooA作为CO-sensing ON模块,激活目标基因进行2,3-丁二醇(2,3- bdo)的生物合成,使2,3- bdo的产量提高1.7倍。这些结果表明CO-ON模块有效地将碳通量重定向到目标产物生物合成途径。然而,在CO气体与葡萄糖混合营养发酵过程中,乳酸成为主要产物。为了使用CO-ON模块增强靶通路通量,我们使用CRISPR/Cas9删除了E. limosum中的乳酸通路。结果表明,在CO感应培养条件下,工程菌株对2,3- bdo的碳利用率提高了18.5%。该优化的平台菌株随后在两阶段co -葡萄糖混合营养发酵中产生约52 g/L的2,3- bdo。我们的研究结果为工程代谢途径提供了正交的CO传感转录调控模块,这些代谢途径利用产丙酮生物催化剂有效地将CO转化为增值的生化物质。
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Metabolic engineering
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