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Retrofitting Escherichia coli for de novo production of rare L-sorbose from abundant D-glucose 改造大肠杆菌,使其从丰富的d -葡萄糖中重新生产稀有的l -山梨糖。
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-08-16 DOI: 10.1016/j.ymben.2025.08.006
Jayce E. Taylor , Trevor Gannalo , Bryant Luu , Dileep Sai Kumar Palur , Augustine Arredondo , Ian C. Anderson , Twisha Dasgupta , John Didzbalis , Justin B. Siegel , Shota Atsumi
Monosaccharides exist in either “D” or “L” conformations, with L-sugars being much less abundant in nature and therefore classified as “rare sugars.” Rare sugars hold significant potential due to their unique interactions with biological systems, offering health, food, and crop benefits. One such sugar, L-sorbose, serves as a critical precursor to Vitamin C and offers a low-calorie, moderately sweet alternative to table sugar, being 60–70 % as sweet but with only 25 % of the caloric value. However, the broader study and application of rare sugars, including L-sorbose, are constrained by their high cost and limited availability. To address this challenge, we developed a biosynthetic strategy to convert the abundant and inexpensive D-sugar D-glucose into the rare L-sugar L-sorbose using microbial production. By utilizing phosphorylation and dephosphorylation steps to thermodynamically drive carbon flux, efficient production of 14.5 g L−1 L-sorbose was achieved under test tube conditions. Additionally, this pathway results in the co-production of D-sedoheptulose, a non-sweet, rare sugar shown to inhibit C6 sugar consumption in humans by modulating energy metabolism. The dual production of L-sorbose and D-sedoheptulose presents unique opportunities for applications in food and health sciences. This study demonstrates microbial production as a promising platform for rare L-sugar biosynthesis and provides a generalizable strategy for converting abundant D-sugars into underexplored L-sugars. Expanding access to L-sugars enables deeper investigations into their biological functions, metabolic pathways, and industrial applications. By advancing both fundamental sugar metabolism research and microbial production strategies, this study broadens the scope of rare sugar utilization.
单糖以“D”或“L”构象存在,L糖在自然界中的含量要少得多,因此被归类为“稀有糖”。稀有糖具有巨大的潜力,因为它们与生物系统的独特相互作用,提供健康,食品和作物效益。其中一种糖,l -山梨糖,是维生素C的关键前体,提供了一种低热量、中等甜味的替代食糖,甜味为60-70%,但热量只有食糖的25%。然而,包括l -山梨糖在内的稀有糖的广泛研究和应用受到其高成本和有限可用性的限制。为了解决这一挑战,我们开发了一种生物合成策略,利用微生物生产将丰富而廉价的d -糖d -葡萄糖转化为稀有的l -糖L-sorbose。利用磷酸化和去磷酸化步骤热力学驱动碳通量,在试管条件下实现了14.5 g L-1 l -海马糖的高效生产。此外,这一途径导致D-sedoheptulose的共同产生,D-sedoheptulose是一种非甜的稀有糖,通过调节能量代谢来抑制人体对C6糖的消耗。l -山梨糖和d -糖庚糖的双重生产为食品和健康科学的应用提供了独特的机会。本研究证明微生物生产是稀有l糖生物合成的一个有前途的平台,并为将丰富的d糖转化为未开发的l糖提供了一种通用策略。扩大对l糖的获取,可以更深入地研究它们的生物学功能、代谢途径和工业应用。本研究通过推进糖代谢基础研究和微生物生产策略,拓宽了稀有糖利用的范围。
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引用次数: 0
Biosynthesis of 2,5-pyridinedicarboxylate from glucose via p-aminobenzoic acid in Escherichia coli 利用对氨基苯甲酸在大肠杆菌中由葡萄糖合成2,5-吡啶二羧酸酯
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-08-25 DOI: 10.1016/j.ymben.2025.08.011
Akinobu Katano , Ayana Mori , Daisuke Nonaka , Yutaro Mori , Shuhei Noda , Tsutomu Tanaka
Pyridine carboxylic acids, because of their structural similarity to aromatic carboxylic acids, have garnered increasing attention as alternative compounds in chemical synthesis. However, their broader utilization has been limited by challenges in biosynthetic production. In this study, we developed a metabolic pathway for biosynthesizing 2,5-pyridinedicarboxylate (2,5-PDCA) from glucose from p-aminobenzoate (PABA). The heterologous expression of 4-amino-3-hydroxybenzoate 2,3-dioxygenase (AhdA) in Escherichia coli enabled the conversion of 0.5 g/L of 4-amino-3-hydroxybenzoate (4A3HBA) into 0.47 g/L of 2,5-PDCA. Subsequent systematic evaluation of p-hydroxybenzoate hydroxylase (PobA) variants and optimization of pobA and ahdA co-expression facilitated the development of a 2,5-PDCA biosynthetic module for efficient production from PABA. Incorporating this module into a PABA biosynthesis pathway enabled direct 2,5-PDCA production from glucose. Further enhancements were achieved by increasing metabolic flux through the shikimate pathway and optimizing sodium pyruvate supplementation. Under optimized conditions, we achieved a titer of 1.84 g/L in test-tube cultures after 72 h and 10.6 g/L in bioreactor fermentation after 144 h. Overall, this study introduces a valuable strategy for the microbial production of pyridine carboxylates and establishes a promising platform for broader applications in aromatic compound biosynthesis.
吡啶羧酸由于其结构与芳香羧酸相似,在化学合成中作为替代化合物受到越来越多的关注。然而,它们的广泛利用受到生物合成生产挑战的限制。在这项研究中,我们开发了一个代谢途径,以葡萄糖为原料从对氨基苯甲酸酯(PABA)生物合成2,5-吡啶二羧酸(2,5- pdca)。4-氨基-3-羟基苯甲酸2,3-双加氧酶(AhdA)在大肠杆菌中的异源表达使0.5 g/L的4-氨基-3-羟基苯甲酸(4A3HBA)转化为0.47 g/L的2,5- pdca。随后对对羟基苯甲酸羟化酶(PobA)变异进行了系统评估,并优化了PobA和ahdA的共表达,促进了2,5- pdca生物合成模块的开发,从而有效地从PABA中生产。将该模块整合到PABA生物合成途径中,可以直接从葡萄糖中生产2,5- pdca。通过增加莽草酸途径的代谢通量和优化丙酮酸钠的补充,进一步增强了功能。在优化的条件下,试管培养72 h后滴度为1.84 g/L,生物反应器发酵144 h后滴度为10.6 g/L。总之,本研究为微生物生产吡啶羧酸酯提供了有价值的策略,并为芳香族化合物生物合成的广泛应用建立了一个有前景的平台。
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引用次数: 0
Sustainable production through spatial niche partitioning in engineered light-driven microbial community 工程光驱动微生物群落空间生态位分配的可持续生产
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-07-28 DOI: 10.1016/j.ymben.2025.07.012
Hao Gao , Yifan Song , Yujia Jiang , Wankui Jiang , Feng Guo , Ziyi Yu , Minjiao Chen , Guodong Luan , Jee Loon Foo , Wenming Zhang , Matthew Wook Chang , Fengxue Xin , Min Jiang
Light-driven microbial communities consisting of phototrophs and heterotrophs represent an emerging frontier for biochemicals production from carbon dioxide (CO2). However, the construction of stable and robust light-driven artificial microbial communities remains challenging because the dominant strain wins the competition for nutrient and leads to the instability of subpopulations. Inspired by natural ecosystems, one promising approach to assemble stable consortia is to construct spatial niches partitioning subpopulations—that is, physically separating different microbial members into distinct microenvironments to reduce competition and enable stable coexistence. Herein, a light-driven microbial community containing an autotrophic Synechococcus elongatus FL130 strain and a heterotrophic Meyerozyma guilliermondii strain was first constructed. Then, we developed spatially arranged core-shell microgels, enabling the precise control of subpopulations of different microbial members. Next, these microgels were integrated into macroscopic living material scaffold using extrusion bioprinting to advance bioprocessing applications, obtaining a well-coupled, robust and reusable light-driven microbial community. This resulted in a light-driven microbial communities with spatially compartmentalized distribution that can efficiently convert CO2 into valuable chemical products of 2-phenylethanol and tyrosol, representing a pioneering approach for sustainable high-value biochemical production.
由光养生物和异养生物组成的光驱动微生物群落代表了二氧化碳(CO2)生物化学生产的新兴前沿。然而,由于优势菌株赢得营养竞争并导致亚群的不稳定,构建稳定而强健的光驱动人工微生物群落仍然具有挑战性。受自然生态系统的启发,构建空间生态位划分亚种群是构建稳定群落的一种很有希望的方法,即物理上将不同的微生物成员分离到不同的微环境中,以减少竞争,实现稳定的共存。本文首先构建了一个包含自养长聚球菌FL130菌株和异养吉列mondii Meyerozyma菌株的光驱动微生物群落。然后,我们开发了空间排列的核壳微凝胶,可以精确控制不同微生物成员的亚群。接下来,利用挤出生物打印技术将这些微凝胶整合到宏观生物材料支架中,以推进生物加工应用,获得一个耦合良好、健壮且可重复使用的光驱动微生物群落。这就形成了一个具有空间分区分布的光驱动微生物群落,可以有效地将二氧化碳转化为有价值的2-苯乙醇和酪醇的化学产物,代表了可持续高价值生化生产的开创性方法。
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引用次数: 0
Microbial production of creatine using growth-coupled selection systems 使用生长偶联选择系统的微生物生产肌酸。
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-07-23 DOI: 10.1016/j.ymben.2025.07.009
Jinbei Li , Simon R. Krarup , Pascal Pieters , Tobias B. Alter , Paul Jacottin , Josefin Johnsen , Elsayed T. Mohamed , Thomas Harris , Linda Ahonen , Khem Bahadur Adhikari , Bernhard O. Palsson , Adam M. Feist , Lei Yang
Creatine is an important energy storage molecule produced exclusively in vertebrates and is crucial for muscle development. It is particularly valuable as a food supplement, especially for plant-based diets. Here, we present an alternative to chemical synthesis by developing a biosynthetic process using an Escherichia coli cell factory expressing a heterologous pathway. We employed a model-driven growth-coupled selection approach combined with adaptive laboratory evolution to overcome metabolic bottlenecks in the heterologous synthesis of creatine. We developed a novel growth-coupling strategy to optimize an important glycine amidinotransferase step guided by genome-scale modeling. We also improved creatine tolerance of E. coli by adaptive evolution. Several design-build-test-learn cycles of evolution and selection resulted in a 58 % increase in titer over the baseline strain from glycine and arginine. This study highlights the advantage of combining production with growth for efficient cell factory generation driven by evolutionary engineering and computational biology.
肌酸是一种重要的能量储存分子,仅在脊椎动物中产生,对肌肉发育至关重要。它是一种特别有价值的食物补充剂,特别是对植物性饮食。在这里,我们提出了一种替代化学合成的方法,即利用表达异源途径的大肠杆菌细胞工厂开发生物合成过程。我们采用模型驱动的生长耦合选择方法结合适应性实验室进化来克服异源合成肌酸的代谢瓶颈。我们开发了一种新的生长偶联策略,以基因组尺度建模为指导,优化重要的甘氨酸氨基转移酶步骤。我们还通过适应性进化提高了大肠杆菌的肌酸耐受性。几个设计-构建-测试-学习的进化和选择周期导致甘氨酸和精氨酸的滴度比基线菌株增加58%。这项研究强调了由进化工程和计算生物学驱动的高效细胞工厂生成的生产与生长相结合的优势。
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引用次数: 0
Engineering quorum-sensing circuits in Synechococcus elongatus PCC 7942 towards self-inducible systems 长聚球菌PCC 7942自诱导系统的工程群体感应电路。
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-07-25 DOI: 10.1016/j.ymben.2025.07.008
Emmanuel J. Kokarakis , María Santos-Merino , Sajjad Ghaffarinasab , Daniel Vocelle , Daniel C. Ducat
Despite significant potential for cyanobacteria as sustainable bioproduction chases, there are limited examples of scaled cyanobacterial bioproduction. In part, this is because most cyanobacterial species are poorly adapted to bioreactor cultivation conditions and lack features that facilitate biomass growth and harvesting at scale. We explored quorum sensing (QS) pathways derived from heterotrophic microbes as a method for autoinduction of gene expression circuits coordinated to population density in cyanobacteria. Here, we integrated genetic modules designed to produce and detect the diffusible QS signal, acyl-homoserine lactones (AHLs), in the cyanobacterial model, Synechococcus elongatus PCC 7942 (S. elongatus). We demonstrate that S. elongatus heterologously produces sufficient AHL signals to activate gene expression in a dose-dependent and population density-responsive manner. A hybrid combination of AHL synthesis enzyme from Vibrio fischeri (Lux system) with the transcription factor receiver from Pseudomonas aeruginosa (Las system) provides an ideal activation ratio and mitigates toxicity observed with some AHL systems. As a proof of concept, we coupled the QS pathway to the expression of a cell division inhibitory gene, cdv3, facilitating late-phase cell elongation, cell sedimentation, and improved biomass recovery. Our findings provide a foundation for the development of auto-induction systems leverageable to improve cyanobacterial biotechnology applications.
尽管蓝藻作为可持续生物生产追逐的巨大潜力,但规模蓝藻生物生产的例子有限。在某种程度上,这是因为大多数蓝藻物种对生物反应器培养条件的适应能力较差,缺乏促进生物量生长和大规模收获的特征。我们探索了来自异养微生物的群体感应(QS)途径,作为蓝藻中与种群密度协调的基因表达回路的自诱导方法。本研究中,我们在蓝藻模型长聚球菌(Synechococcus elongatus) PCC 7942 (S. elongatus)中整合了用于产生和检测可扩散QS信号酰基同丝氨酸内酯(AHLs)的遗传模块。我们证明,长叶卷叶蝉异源产生足够的AHL信号,以剂量依赖和种群密度响应的方式激活基因表达。费氏弧菌AHL合成酶(Lux系统)与铜绿假单胞菌(Las系统)转录因子受体的杂交组合提供了理想的激活比,并减轻了某些AHL系统所观察到的毒性。为了证明这一概念,我们将QS通路与细胞分裂抑制基因cdv3的表达结合起来,促进了后期细胞伸长、细胞沉积和提高生物质回收率。我们的发现为开发可用于提高蓝藻生物技术应用的自动诱导系统提供了基础。
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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 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub 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
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. Vibrio natriegens, recognized for exceptionally fast growth rates, represents a compelling host for developing efficient acetate-based bioprocesses. In this study, adaptive laboratory evolution significantly enhanced V. natriegens’ 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 V. natriegens as a highly promising microbial platform for sustainable, scalable, and cost-effective biomanufacturing using acetate as a green feedstock.
醋酸盐是一种可持续和可再生的碳源,在生物技术生产中具有重要的前景,但由于微生物效率有限,在工业上未得到充分利用。营养弧菌以其异常快速的生长速度而闻名,是开发高效的基于醋酸盐的生物过程的令人信服的宿主。在本研究中,适应性实验室进化显著增强了V. natrigens以醋酸盐为唯一碳源的生长能力,其生长速率提高了89%。遗传和转录组学分析表明,通过提高耐盐性,提高Pta/AckA途径活性,以及重新连接群体感应来改善醋酸盐摄取和代谢。进一步的代谢工程和生物工艺优化使进化菌株达到较高的细胞密度,并有效地将乙酸转化为生物塑料聚3-羟基丁酸酯(PHB),其产量高达0.27 g/L/h, PHB积累量达到细胞生物量的45.66%。这些进展使V. natriegens成为一个非常有前途的微生物平台,可以使用醋酸盐作为绿色原料进行可持续、可扩展和具有成本效益的生物制造。
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引用次数: 0
Development of a salt-enhanced promoter strategy for activating silent biosynthetic gene clusters from streptomycetes 盐增强启动子激活链霉菌沉默生物合成基因簇策略的开发。
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-07-25 DOI: 10.1016/j.ymben.2025.07.007
Lijuan Wang , Mengyi Zhu , Chunfang Yang , Siqi Zhu , Bin Tan , Shu-Hua Qi , Yiguang Zhu , Changsheng Zhang
Activating silent biosynthetic gene clusters (BGCs) within various microorganisms is an important approach to uncover valuable natural products. In this study, we reported the capture and activation of two large silent BGCs from a marine-derived Streptomyces sp. SCSGAA 0027 in the heterologous host Streptomyces albus J1074 by inserting a widely used constitutive promoter kasOp∗ upstream of the core biosynthetic genes, which led to the production of coprisamides (COPs) and padanamides (PADs), respectively. Interestingly, the yields of COPs and PADs were significantly enhanced when potassium or sodium salts were supplemented in the fermentation media, especially 1 % KCl. The promoting strength of kasOp∗ was found to be obviously increased upon KCl addition by using the eGFP (enhanced green fluorescent protein) as an indicator. These findings revealed for the first time that the exogenous promoter kasOp∗ performed unexpectedly as a salt-enhanced element in S. albus J1074. Consequently, a “kasOp∗-KCl” strategy was developed to achieve the highest production of COPs A/B at 97.9 mg/L in fermentation with shaking flasks, along with the coproduction of a pair of new analogues, COPs E/F at 151.8 mg/L, leading to a maximum isolation titer of COPs at 171.7 mg/L, about 170-fold improvement comparing to previous reports. Similarly, the strategy increased the titers of the antimalarial agent PAD A to 76.7 mg/L and the diisonitrile copper chelator SF2768 to 72.8 mg/L in S. albus J1074, representing the highest yields reported to date for both compounds. Moreover, a small library of kasOp∗ variants were generated and validated to also be KCl-responsive, expanding the promoter toolkits for metabolic engineering and genome mining. These findings provide new insights into the salt-enhancing property of the widely used promoter kasOp∗, and offer a simple “kasOp∗-KCl” approach to efficiently activate silent BGCs and improve the production of the encoding natural products in multiple commonly used Streptomyces hosts.
激活各种微生物中的沉默生物合成基因簇(BGCs)是发现有价值的天然产物的重要途径。在本研究中,我们通过在核心生物合成基因上游插入一个广泛使用的组成启动子kasOp*,从海洋来源链霉菌sp. SCSGAA 0027中捕获并激活了两个大型沉默bgc,分别产生了coprisamides (COPs)和padanamides (PADs)。有趣的是,当发酵培养基中添加钾或钠盐,特别是1% KCl时,cop和PADs的产量显著提高。以eGFP(增强型绿色荧光蛋白)为指标,发现KCl对kasOp*的促进作用明显增强。这些发现首次揭示了外源启动子kasOp*出乎意料地在S. albus J1074中作为盐增强元件发挥作用。因此,开发了“kasOp*-KCl”策略,在摇瓶发酵中实现了cop a /B的最高产量,为97.9 mg/L,同时共同生产了一对新的类似物,cop E/F,为151.8 mg/L,导致cop的最高分离滴度为171.7 mg/L,与之前的报道相比提高了约170倍。同样,该策略将抗疟药PAD A的滴度提高到76.7 mg/L,将二异腈铜螯合剂SF2768的滴度提高到72.8 mg/L,这是迄今为止报道的两种化合物的最高产量。此外,一个小的kasOp*变异库也被生成并验证为kcl响应,扩展了用于代谢工程和基因组挖掘的启动子工具包。这些发现为广泛使用的启动子kasOp*的盐增强特性提供了新的见解,并提供了一种简单的“kasOp*-KCl”方法来有效激活沉默BGCs,并提高多种常用链霉菌宿主中编码天然产物的产生。
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引用次数: 0
Heterologous integration-assisted metabolic engineering in Escherichia coli for elevated D-pantothenic acid production 外源整合辅助大肠杆菌代谢工程提高d -泛酸产量。
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-11-01 Epub Date: 2025-08-11 DOI: 10.1016/j.ymben.2025.08.003
Kuo Zhao , Hailin Gao , Mengnan Han , Bo Zhang , Zhiqiang Liu , Shuping Zou , Yuguo Zheng
D-pantothenic acid (D-PA) is a vital water-soluble vitamin with diverse industrial applications, driving the demand for efficient microbial production. Here, we rationally engineered an Escherichia coli strain to enhance D-PA production through metabolic engineering. First, to enhance carbon utilization efficiency, competing byproduct pathways were deleted and the pentose phosphate pathway was downregulated. Next, the glucose and β-alanine transport systems were strategically enhanced, and cofactor availability was improved through engineering NADPH regeneration and ATP recycling pathways. Subsequently, pathway engineering was applied to fine-tune the expression of heterologous enzymes, thereby enhancing the metabolic pull toward D-PA biosynthesis. To enhance the supply of one-carbon donor required by the rate-limiting enzyme ketopantoate hydroxymethyltransferase (KPHMT), a heterologous 5,10-methylenetetrahydrofolate biosynthesis module was introduced. Finally, dynamic regulation of isocitrate synthase and pantothenate kinase was implemented to balance cell growth and D-PA production. As a result of the integrated metabolic engineering strategies, the final strain DPZ28/P31 achieved a D-PA titer of 98.6 g/L and a yield of 0.44 g/g glucose in a two-stage fed-batch fermentation. These findings provide valuable insights for industrial-scale production of D-PA and related compounds.
d -泛酸(D-PA)是一种重要的水溶性维生素,具有多种工业应用,推动了对高效微生物生产的需求。本研究通过代谢工程对大肠杆菌菌株进行合理改造,提高D-PA的产量。首先,为了提高碳利用效率,删除竞争性副产物途径,下调戊糖磷酸途径。接下来,葡萄糖和β-丙氨酸运输系统被战略性地增强,通过工程NADPH再生和ATP循环途径提高辅助因子的可用性。随后,途径工程应用于微调异种酶的表达,从而增强对D-PA生物合成的代谢拉动。为了提高酮托酸羟甲基转移酶(KPHMT)所需的单碳供体的供应,引入了异源的5,10-亚甲基四氢叶酸生物合成模块。最后,通过动态调节异柠檬酸合成酶和泛酸激酶来平衡细胞生长和D-PA的产生。通过综合代谢工程策略,最终菌株DPZ28/P31在两段补料分批发酵中获得了D-PA滴度为98.6 g/L,葡萄糖产量为0.44 g/g。这些发现为D-PA及其相关化合物的工业规模生产提供了有价值的见解。
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引用次数: 0
Insights into the methanol utilization capacity of Y. lipolytica and improvements through metabolic engineering 解脂芽孢杆菌甲醇利用能力的研究及代谢工程改进。
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-03-28 DOI: 10.1016/j.ymben.2025.03.014
Wei Jiang , William Newell , Jingjing Liu , Lucas Coppens , Khushboo Borah Slater , Huadong Peng , David Bell , Long Liu , Victoria Haritos , Rodrigo Ledesma-Amaro
Methanol is a promising sustainable alternative feedstock for green biomanufacturing. The yeast Yarrowia lipolytica offers a versatile platform for producing a wide range of products but it cannot use methanol efficiently. In this study, we engineered Y. lipolytica to utilize methanol by overexpressing a methanol dehydrogenase, followed by the incorporation of methanol assimilation pathways from methylotrophic yeasts and bacteria. We also overexpressed the ribulose monophosphate (RuMP) and xylulose monophosphate (XuMP) pathways, which led to significant improvements in growth with methanol, reaching a consumption rate of 2.35 g/L in 24 h and a 2.68-fold increase in biomass formation. Metabolomics and Metabolite Flux Analysis confirmed methanol assimilation and revealed an increase in reducing power. The strains were further engineered to produce the valuable heterologous product resveratrol from methanol as a co-substrate. Unlike traditional methanol utilization processes, which are often resource-intensive and environmentally damaging, our findings represent a significant advance in green chemistry by demonstrating the potential of Y. lipolytica for efficient use of methanol as a co-substrate for energy, biomass, and product formation. This work not only contributes to our understanding of methanol metabolism in non-methylotrophic organisms but also paves the way for achieving efficient synthetic methylotrophy towards green biomanufacturing.
甲醇是一种有前途的可持续的绿色生物制造替代原料。酵母脂解耶氏酵母为生产多种产品提供了一个多功能平台,但它不能有效地利用甲醇。在这项研究中,我们通过过度表达甲醇脱氢酶来改造脂肪瘤,然后结合来自甲基营养酵母和细菌的甲醇同化途径来利用甲醇。我们还过度表达了单磷酸核酮糖(RuMP)和单磷酸木糖(XuMP)途径,这导致了甲醇对生长的显著改善,在24小时内达到2.35 g/L的消耗率,生物量形成增加了2.68倍。代谢组学和代谢物通量分析证实了甲醇同化,并显示还原能力增加。进一步对菌株进行工程改造,以甲醇为共底物生产有价值的外源产物白藜芦醇。传统的甲醇利用过程通常是资源密集型和环境破坏性的,而我们的研究结果表明,聚脂Y.酵母具有有效利用甲醇作为能源、生物质和产品形成的共同底物的潜力,这代表了绿色化学的重大进步。这项工作不仅有助于我们了解非甲基化营养生物的甲醇代谢,而且为实现高效合成甲基化生物制造铺平了道路。
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引用次数: 0
NEXT-FBA: A hybrid stoichiometric/data-driven approach to improve intracellular flux predictions NEXT-FBA:一种混合化学计量学/数据驱动的方法,用于改善细胞内通量预测。
IF 6.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2025-09-01 Epub Date: 2025-03-19 DOI: 10.1016/j.ymben.2025.03.010
James Morrissey , Gianmarco Barberi , Benjamin Strain , Pierantonio Facco , Cleo Kontoravdi
Genome-scale metabolic models (GEMs) have been widely utilized to understand cellular metabolism. The application of GEMs has been advanced by computational methods that enable the prediction and analysis of intracellular metabolic states. However, the accuracy and biological relevance of these predictions often suffer from the many degrees of freedom and scarcity of available data to constrain the models adequately. Here, we introduce Neural-net EXtracellular Trained Flux Balance Analysis, (NEXT-FBA), a novel computational methodology that addresses these limitations by utilizing exometabolomic data to derive biologically relevant constraints for intracellular fluxes in GEMs. We achieve this by training artificial neural networks (ANNs) with exometabolomic data from Chinese hamster ovary (CHO) cells and correlating it with 13C-labeled intracellular fluxomic data. By capturing the underlying relationships between exometabolomics and cell metabolism, NEXT-FBA predicts upper and lower bounds for intracellular reaction fluxes to constrain GEMs. We demonstrate the efficacy of NEXT-FBA across several validation experiments, where it outperforms existing methods in predicting intracellular flux distributions that align closely with experimental observations. Furthermore, a case study demonstrates how NEXT-FBA can guide bioprocess optimization by identifying key metabolic shifts and refining flux predictions to yield actionable process and metabolic engineering targets. Overall, NEXT-FBA aims to improve the accuracy and biological relevance of intracellular flux predictions in metabolic modelling, with minimal input data requirements for pre-trained models.
基因组尺度代谢模型(GEMs)已被广泛用于了解细胞代谢。GEMs的应用已经通过能够预测和分析细胞内代谢状态的计算方法得到了推进。然而,这些预测的准确性和生物学相关性经常受到许多自由度和可用数据稀缺的影响,无法充分约束模型。在这里,我们引入NEXT-FBA(神经网络细胞外训练通量平衡分析),这是一种新的计算方法,通过利用外代谢组学数据来获得GEMs细胞内通量的生物学相关限制,从而解决了这些限制。我们通过使用中国仓鼠卵巢(CHO)细胞的外代谢组学数据训练人工神经网络(ann),并将其与13c标记的细胞内通量组学数据相关联,实现了这一目标。通过捕获外代谢组学和细胞代谢之间的潜在关系,NEXT-FBA预测细胞内反应通量的上限和下限,以约束GEMs。我们通过几个验证实验证明了NEXT-FBA的有效性,在预测与实验观察密切相关的细胞内通量分布方面,它优于现有方法。此外,一个案例研究展示了NEXT-FBA如何通过识别关键的代谢变化和改进通量预测来指导生物过程优化,从而产生可操作的过程和代谢工程目标。总的来说,NEXT-FBA旨在提高生物过程优化代谢模型中细胞内通量预测的准确性和生物学相关性,对预训练模型的输入数据要求最小。
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Metabolic engineering
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