Metabolic engineering最新文献_第8页

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

Metabolic engineering

Pub 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

Quantifying supply and demand in the pea aphid-Buchnera symbiosis reveals the metabolic Achilles’ heels of this interaction 定量的供应和需求在豌豆蚜虫- buchnera共生揭示了代谢的阿基里斯之踵，这种相互作用。

IF 6.8 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Metabolic engineering

Pub Date : 2025-07-26 DOI: 10.1016/j.ymben.2025.07.011

Léo Gerlin, Karen Gaget, Garance Lapetoule, Yohann Quivet, Patrice Baa-Puyoulet, Isabelle Rahioui, Mélanie Ribeiro Lopes, Pedro Da Silva, Federica Calevro, Hubert Charles

Many herbivorous insects feed on unbalanced diets and rely on bacterial endosymbionts to meet all their nutritional needs. This is the case for the pea aphid (Acyrthosiphon pisum), a plant pest whose remarkable growth and reproductive capacities cannot be sustained by its sole nutritional resource, the plant phloem sap, and which relies on a symbiotic relationship maintained over millions of years with the intracellular bacterium Buchnera aphidicola for the biosynthesis of amino acids and vitamins. Exploiting original experimental data and metabolic reconstructions, we have built a quantitative genome-scale metabolic model of B. aphidicola and used it to quantify amino acid exchanges between the bacterium and its host. We found metabolites that can rewire pathways, influencing the balance between selfish (growth-focused) and mutualist (amino acid synthesis) behavior. Among the products synthesized by Buchnera, phenylalanine, tyrosine and leucine are the main matter sinks and consume more than 60 % of imported glucose and serine. Finally, we compared the predicted bacterial supply to the aphid demand in amino acids. We found that the pea aphid may efficiently regulate its symbiont population density depending on its metabolic requirements, but that embryos are quantitatively not self-sustaining, with embryonic bacteria supply falling short of demand by 50 %. Overall, our study highlights candidate compounds and pathways to target for destabilizing this symbiosis or predicting its resilience to environmental or nutritional perturbations.

许多草食性昆虫以不平衡的饮食为食，依靠细菌内共生体来满足它们所有的营养需求。豌豆蚜虫（Acyrthosiphon pisum）就是这种情况，这种植物害虫的显著生长和繁殖能力不能靠其唯一的营养来源——植物韧皮部汁液来维持，它依赖于与细胞内细菌蚜虫（Buchnera aphidicola）维持了数百万年的共生关系来合成氨基酸和维生素。利用原始实验数据和代谢重建，我们建立了一个定量的蚜虫基因组尺度的代谢模型，并利用它来量化细菌与宿主之间的氨基酸交换。我们发现代谢物可以重新连接通路，影响自私（以生长为中心）和互惠（氨基酸合成）行为之间的平衡。在Buchnera合成的产品中，苯丙氨酸、酪氨酸和亮氨酸是主要的物质汇，消耗了60%以上的进口葡萄糖和丝氨酸。最后，我们比较了预测的细菌供应和蚜虫对氨基酸的需求。我们发现豌豆蚜虫可以根据其代谢需求有效地调节其共生体的种群密度，但胚胎在数量上不能自我维持，胚胎细菌供应不足需求的50%。总的来说，我们的研究突出了候选化合物和途径，以破坏这种共生关系或预测其对环境或营养扰动的恢复能力。

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引用次数: 0

Enhancing ε-poly-L-lysine production in Streptomyces albulus through L-lysine importer engineering 利用l -赖氨酸进口工程提高白球链霉菌的ε-聚l -赖氨酸产量。

IF 6.8 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Metabolic engineering

Pub Date : 2025-07-25 DOI: 10.1016/j.ymben.2025.07.010

Daojun Zhu , Jiawei Zhang , Shangyu Li, Liang Wang, Hongjian Zhang, Jianhua Zhang, Zhang, Xusheng Chen

ε-Poly-L-lysine (ε-PL) is a homopolymer of L-lysine residues produced by microorganisms, widely utilized in the food, pharmaceutical, and cosmetic industries. However, the development of efficient microbial cell factories (MCFs) for ε-PL production remains challenging. In this study, L-lysine importers were systematically screened, identified, and engineered to enhance ε-PL biosynthesis. First, an ε-PL-producing strain, Streptomyces albulus GS114, efficiently utilizing exogenous L-lysine, was selected. Bioinformatics analysis identified seven putative L-lysine importers in GS114, among which GL6157 was confirmed as the primary importer through molecular docking, transcriptional analysis, and genetic manipulation. Through combinatorial optimization of GL6157 expression coupled with overexpression of ε-poly-L-lysine synthase (pls), we engineered the GS114/pls-GL6157 strain, which achieved a ε-PL of 94.0 g/L in fed-batch fermentation. To our knowledge, this represents the highest reported yield to date. These findings demonstrate that transporter engineering is an effective strategy for enhancing ε-PL biosynthesis in industrial MCFs.

ε-聚l -赖氨酸（ε-PL）是一种由微生物产生的l -赖氨酸残基的均聚物，广泛应用于食品、制药和化妆品等行业。然而，开发高效的微生物细胞工厂（mcf）生产ε-PL仍然具有挑战性。在本研究中，l -赖氨酸导入物被系统筛选、鉴定和改造以促进ε-PL的生物合成。首先，选择了一株能高效利用外源l -赖氨酸的产ε- pl菌株——白链霉菌GS114。生物信息学分析在GS114中鉴定出7个假定的l -赖氨酸进口蛋白，通过分子对接、转录分析和基因操作确定GL6157为主要进口蛋白。通过对GL6157的表达和过表达ε-聚L-赖氨酸合成酶（pls）的组合优化，构建了菌株GS114/pls-GL6157，该菌株在补料分批发酵条件下的ε-PL为94.0 g/L。据我们所知，这是迄今为止报道的最高产量。这些发现表明，转运体工程是促进工业MCFs中ε-PL生物合成的有效策略。

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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

Metabolic engineering

Pub 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

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

Metabolic engineering

Pub 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

Improving recombinant antibody production using FcBAR: An in situ approach to detect and amplify protein-protein interactions 利用FcBAR提高重组抗体的生产：一种原位检测和扩增蛋白质相互作用的方法。

IF 6.8 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Metabolic engineering

Pub Date : 2025-07-23 DOI: 10.1016/j.ymben.2025.07.006

Mina Ying Min Wu , Frances Rocamora , Mojtaba Samoudi , Caressa M. Robinson , Chih-Chung Kuo , Nuša Pristovšek , Lise Marie Grav , Helene Faustrup Kildegaard , Gyun Min Lee , Alexandre Rosa Campos , Nathan E. Lewis

Recombinant proteins, in particular monoclonal antibodies and related molecules, have become dominant therapeutics. As they are produced in mammalian cells, they require the concerted function of hundreds of host cell proteins in the protein secretion pathway. However, the comprehensive set of host cell machinery involved remains unclear. Thus, it is often unknown why some recombinant proteins fail to express well. Here we present and deploy an approach called Fc-targeting Biotinylation by Antibody Recognition (FcBAR), which allows for the in situ detection of protein-protein interactions for any recombinant protein with Fc domain. Briefly, cells are permeabilized and incubated with an anti-Fc antibody, conjugated with horseradish peroxidase. All proteins interacting with Fc-bearing proteins are then biotinylated, pulled down and identified via mass spectrometry. We applied this method on a panel of rituximab-producing CHO-S clones with a range of productivity levels. Through analysis of FcBAR protein-protein interactions and RNA-Seq, we identified protein interactions positively correlated with rituximab secretion, and tested 7 of these targets. We found overexpression of AGPAT4, EPHX1, and NSDHL significantly increased rituximab production. Thus, FcBAR provides an unbiased approach to measure PPIs supporting recombinant antibody production in situ, and can guide efforts to boost production of biotherapeutics and biosimilars by addressing production bottlenecks.

重组蛋白，特别是单克隆抗体和相关分子，已经成为主要的治疗方法。由于它们是在哺乳动物细胞中产生的，因此在蛋白质分泌途径中需要数百种宿主细胞蛋白协同作用。然而，宿主细胞机制的综合机制仍不清楚。因此，通常不知道为什么一些重组蛋白不能很好地表达。在这里，我们提出并部署了一种称为Fc靶向生物素化抗体识别（FcBAR）的方法，该方法允许原位检测任何具有Fc结构域的重组蛋白的蛋白质相互作用。简单地说，细胞渗透和培养抗fc抗体，结合辣根过氧化物酶。然后，所有与含fc蛋白相互作用的蛋白质都被生物素化，并通过质谱法进行鉴定。我们将这种方法应用于一组具有不同生产水平的产生利妥昔单抗的CHO-S克隆。通过FcBAR蛋白-蛋白相互作用和RNA-Seq分析，我们发现蛋白相互作用与利妥昔单抗分泌呈正相关，并对其中7个靶点进行了检测。我们发现过表达AGPAT4、EPHX1和NSDHL显著增加了利妥昔单抗的产量。因此，FcBAR提供了一种公正的方法来测量支持原位重组抗体生产的PPIs，并可以通过解决生产瓶颈来指导促进生物治疗药物和生物仿制药的生产。

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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

Metabolic engineering

Pub 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

Metabolic engineering of Micromonospora for exploring useful natural products and phytobiotic interaction 利用小单孢子菌代谢工程探索有用的天然产物和植物共生相互作用

IF 6.8 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Metabolic engineering

Pub Date : 2025-07-20 DOI: 10.1016/j.ymben.2025.07.005

Boncheol Gu, Jimin Lee, Duck Gyun Kim, Yu-jin Cha, Min-Kyu Oh

Micromonospora, a genus within the Actinobacteria phylum, is recognized for its prolific production of bioactive secondary metabolites. It has important applications in the pharmaceutical, biotechnology, and agricultural fields. Micromonospora is renowned for generating antibiotics, anticancer agents, immunosuppressants, and plant growth-promoting compounds, making it a primary subject in natural product research. Advances in genome sequencing and mining technologies have revealed numerous biosynthetic gene clusters, many of which remain unexplored, underscoring their vast, untapped biosynthetic potential. This review presents an in-depth summary of the role of Micromonospora in the discovery of novel bioactive compounds and their biotechnological and industrial applications. Furthermore, we discuss the plant-microbe interactions of Micromonospora, consolidating current knowledge from its historical discovery to recent genomic insights, and outlines future research directions and challenges for optimizing the biotechnological potential of this promising yet underexploited microbial resource.

小单孢子菌是放线菌门中的一个属，以其多产的生物活性次生代谢物而闻名。它在制药、生物技术和农业领域有着重要的应用。小单孢子菌以产生抗生素、抗癌剂、免疫抑制剂和植物生长促进化合物而闻名，使其成为天然产物研究的主要课题。基因组测序和挖掘技术的进步揭示了许多生物合成基因簇，其中许多仍未被探索，强调了它们巨大的、未开发的生物合成潜力。本文综述了小单孢子菌在新型生物活性化合物的发现及其生物技术和工业应用中的作用。此外，我们讨论了小单孢菌的植物与微生物的相互作用，从其历史发现到最近的基因组见解，巩固了当前的知识，并概述了未来的研究方向和挑战，以优化这一有前途但尚未开发的微生物资源的生物技术潜力。

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引用次数: 0

Biomass accumulation in chondrocyte metabolic modelling: Incorporating extracellular matrix proxies to predict tissue engineering outcomes 软骨细胞代谢模型中的生物量积累：结合细胞外基质代理来预测组织工程结果

IF 6.8 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Metabolic engineering

Pub Date : 2025-07-13 DOI: 10.1016/j.ymben.2025.07.004

Roberto Tarantino , Halie Mei Jensen , Stephen D. Waldman

Metabolic modeling in chondrocytes plays a pivotal role in advancing our understanding of cellular function. These techniques have been used to study degenerative joint diseases (e.g. osteoarthritis), mechanotransduction, and more recently to optimize strategies for cartilage tissue engineering. Incorporating tissue formation into metabolic flux analysis is inherently challenging due to the complexity of linking metabolic activity to extracellular matrix (ECM) accumulation. Many ECM macromolecules are synthesized using metabolites derived from central carbon metabolism, but direct modeling of their accumulation remains complex. This study establishes a novel methodology for incorporating ECM synthesis into metabolic flux analysis (MFA). By utilizing chondroitin sulfate and hydroxyproline as measurable metabolic proxies for proteoglycan and collagen production, we demonstrate a framework for linking metabolic inputs with tissue formation. Extracellular flux data for glucose, lactate, carbon dioxide, glutamine, and glutamate, along with mass isotopomer distributions, were sourced from previous studies involving three-dimensional high-density cultures of articular cartilage tissue constructs. Additionally, the conditioned culture media used in these studies was used to quantify the production rates of chondroitin sulfate and hydroxyproline. Using a modular network model, proteoglycan and collagen metabolism were assessed independently, and in combination, with sensitivity analyses on ECM retention assumptions. Predicted proteoglycan production aligned well with previously observed trends; however, predicted collagen production was less consistent. These findings offer a novel approach for linking metabolic inputs with ECM production, advancing our ability to predict tissue formation and address key challenges in cartilage tissue engineering.

软骨细胞的代谢模型在促进我们对细胞功能的理解方面起着关键作用。这些技术已被用于研究退行性关节疾病（如骨关节炎）、机械转导，以及最近用于优化软骨组织工程的策略。由于将代谢活动与细胞外基质（ECM）积累联系起来的复杂性，将组织形成纳入代谢通量分析本身就具有挑战性。许多ECM是利用源自中心碳代谢的代谢物合成的，但对其积累的直接建模仍然很复杂。本研究建立了一种将ECM合成纳入代谢通量分析（MFA）的新方法。通过利用硫酸软骨素和羟脯氨酸作为蛋白聚糖和胶原蛋白生产的可测量代谢代用物，我们展示了一个将代谢输入与组织形成联系起来的框架。葡萄糖、乳酸、二氧化碳、谷氨酰胺和谷氨酸的细胞外通量数据，以及质量同位素分布，来源于先前涉及关节软骨组织构建的三维高密度培养的研究。此外，在这些研究中使用的条件培养基被用来量化硫酸软骨素和羟脯氨酸的产量。使用模块化网络模型，分别评估蛋白聚糖和胶原代谢，并结合ECM保留假设的敏感性分析。预测的蛋白多糖产量与先前观察到的趋势一致；然而，预测的胶原蛋白生成不太一致。这些发现为将代谢输入与ECM产生联系起来提供了一种新的方法，提高了我们预测组织形成的能力，并解决了软骨组织工程中的关键挑战。

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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

Metabolic engineering

Pub Date : 2025-07-11 DOI: 10.1016/j.ymben.2025.07.003

Roland J. Politan , Simona Della Valle , Luke Pineda , Jitendra Joshi , Christian Euler , Gavin Flematti , Georg Fritz

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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