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SIGHT—A System for Solvent‐Tight Incubation and Growth Monitoring in High Throughput SIGHT--用于高通量溶剂密闭培养和生长监控的系统
IF 2.7 4区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-11 DOI: 10.1002/elsc.202400037
Jakob Rönitz, Felix Herrmann, Benedikt Wynands, Tino Polen, Nick Wierckx
Physiological characterization of microorganisms in the context of solvent tolerance is a tedious process with a high investment of manual labor while often being limited in throughput capability simultaneously. Therefore, we developed a small‐scale solvent‐impervious cultivation system consisting of screw cap‐sealed glass vials in combination with a 3D‐printed vial holder for the Growth Profiler (EnzyScreen) platform. Components and cultivation conditions were empirically tested, and a suitable setup was found for the intended application. To demonstrate the capability of this cultivation system, an adaptive laboratory evolution was performed to further increase the tolerance of Pseudomonas taiwanensis GRC3 toward styrene. This approach yielded heterogenic cultures with improved growth performances in the presence of styrene from which individual clones were isolated and characterized in high throughput. Several clones with improved growth in the presence of 1% (v/v) styrene were analyzed through whole‐genome sequencing, revealing mutations in the co‐chaperone‐encoding gene dnaJ, RNA polymerase α subunit‐encoding gene rpoA, and loss‐of‐function mutations in the ttgGHI solvent efflux pump repressor encoded by ttgV. The developed cultivation system has proven to be a very useful extension of the Growth Profiler, as it reduces manual workload and allows high‐throughput characterization.
耐溶剂微生物的生理学特征描述是一个繁琐的过程,需要投入大量的人工,同时通量能力往往有限。因此,我们开发了一种小规模不透溶剂培养系统,该系统由螺旋盖密封玻璃瓶和三维打印瓶架组成,适用于生长曲线仪(EnzyScreen)平台。根据经验对组件和培养条件进行了测试,找到了适合预期应用的设置。为了证明该培养系统的能力,进行了适应性实验室进化,以进一步提高台湾假单胞菌 GRC3 对苯乙烯的耐受性。这种方法产生了在苯乙烯存在下具有更好生长性能的异源培养物,从中分离出了单个克隆,并对其进行了高通量表征。通过全基因组测序分析了几个在 1%(v/v)苯乙烯存在下生长性能有所改善的克隆,发现了共伴侣蛋白编码基因 dnaJ、RNA 聚合酶 α 亚基编码基因 rpoA 的突变,以及由 ttgV 编码的 ttgGHI 溶剂外排泵抑制因子的功能缺失突变。事实证明,所开发的培养系统是生长曲线仪的一个非常有用的扩展,因为它减少了人工工作量,并能进行高通量表征。
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引用次数: 0
Stability of a Mutualistic Escherichia coli Co‐Culture During Violacein Production Depends on the Kind of Carbon Source 互助型大肠杆菌共培养菌群在生产维拉丝素过程中的稳定性取决于碳源种类
IF 2.7 4区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-09 DOI: 10.1002/elsc.202400025
Simon Schick, Tobias Müller, Ralf Takors, Georg A. Sprenger
The L‐tryptophan–derived purple pigment violacein (VIO) is produced in recombinant bacteria and studied for its versatile applications. Microbial synthetic co‐cultures are gaining more importance as efficient factories for synthesizing high‐value compounds. In this work, a mutualistic and cross‐feeding Escherichia coli co‐culture is metabolically engineered to produce VIO. The strains are genetically modified by auxotrophies in the tryptophan (TRP) pathway to enable a metabolic division of labor. Therein, one strain produces anthranilate (ANT) and the other transforms it into TRP and further to VIO. Population dynamics and stability depend on the choice of carbon source, impacting the presence and thus exchange of metabolites as well as overall VIO productivity. Four carbon sources (D‐glucose, glycerol, D‐galactose, and D‐xylose) were compared. D‐Xylose led to co‐cultures which showed stable growth and VIO production, ANT‐TRP exchange, and enhanced VIO production. Best titers were ∼126 mg L–1 in shake flasks. The study demonstrates the importance and advantages of a mutualistic approach in VIO synthesis and highlights the carbon source's role in co‐culture stability and productivity. Transferring this knowledge into an up‐scaled bioreactor system has great potential in improving the overall VIO production.
由 L-色氨酸衍生的紫色色素紫草素(VIO)是在重组细菌中生产出来的,其用途广泛。微生物合成共培养作为合成高价值化合物的高效工厂,正变得越来越重要。在这项工作中,通过代谢工程改造了一种互生和交叉进食的大肠杆菌共培养物,以生产 VIO。这些菌株通过色氨酸(TRP)途径中的辅助营养因子进行了基因改造,从而实现了代谢分工。其中,一个菌株生产蒽酸(ANT),另一个菌株将其转化为 TRP,再进一步转化为 VIO。种群的动态和稳定性取决于碳源的选择,这影响到代谢物的存在和交换,以及整个 VIO 的生产率。我们对四种碳源(D-葡萄糖、甘油、D-半乳糖和 D-木糖)进行了比较。D-木糖导致的共培养显示出稳定的生长和 VIO 产量、ANT-TRP 交换以及 VIO 产量的提高。在摇瓶中,最佳滴度为∼126 mg L-1。该研究证明了在 VIO 合成过程中采用互作方法的重要性和优势,并强调了碳源在共培养稳定性和生产率中的作用。将这些知识应用到大规模生物反应器系统中,对提高整体 VIO 产量具有巨大潜力。
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引用次数: 0
Cover Picture: Engineering in Life Sciences 9'24 封面图片:生命科学工程 9'24
IF 3.9 4区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-03 DOI: 10.1002/elsc.202470091
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引用次数: 0
Mini Bubble Columns for Miniaturizing Scale‐Down 微型气泡色谱柱实现小型化缩放
IF 2.7 4区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-02 DOI: 10.1002/elsc.202400051
Moritz Wild, Ralf Takors
The successful scale‐up of biotechnological processes from laboratory to industrial scale is crucial for translating innovation to practice. Scale‐down simulators have emerged as indispensable tools in this endeavor, enabling the evaluation of potential hosts’ adaptability to the dynamic conditions encountered in large‐scale fermenters. By simulating these real‐world scenarios, scale‐down simulators facilitate more accurate estimations of host productivity, thereby improving the process of selecting optimal strains for industrial production. Conventional scale‐down systems for detailed intracellular analysis necessitate an elaborate setup comprising interconnected lab‐scale reactors such as stirred tank reactors (STRs) and plug‐flow reactors (PFRs), often proving time‐consuming and resource‐intensive. This work introduces a miniaturized bubble column reactor setup (60 mL working volume), enabling individual and parallel carbon‐limited chemostat fermentations, offering a more efficient and streamlined approach. The industrially relevant organism Escherichia coli, chosen as a model organism, is continuously grown and subjected to carbon starvation for 150 s, followed by a return to carbon excess for another 150 s. The cellular response is characterized by the accumulation of the alarmone guanosine pentaphosphate (ppGpp) accompanied by a significant reduction in energy charge, from 0.8 to 0.7, which is rapidly replenished upon reintroduction of carbon availability. Transcriptomic analysis reveals a two‐phase response pattern, with over 200 genes upregulated and downregulated. The initial phase is dominated by the CRP–cAMP‐ and ppGpp‐mediated response to carbon limitation, followed by a shift to stationary phase‐inducing gene expression under the control of stress sigma factors. The system's validity is confirmed through a thorough comparison with a conventional STR/PFR setup. The analysis reveals the potential of the system to effectively reproduce data gathered from conventional STR/PFR setups, showcasing its potential use as a scale‐down simulator integrated in the process of strain development.
成功地将生物技术过程从实验室放大到工业规模,对于将创新转化为实践至关重要。缩小规模模拟器已成为这项工作中不可或缺的工具,可评估潜在宿主对大型发酵罐中动态条件的适应性。通过模拟这些真实世界的场景,缩比模拟器有助于更准确地估计宿主的生产率,从而改进为工业生产选择最佳菌株的过程。用于详细细胞内分析的传统缩比系统需要复杂的设置,包括相互连接的实验室级反应器,如搅拌罐反应器(STR)和塞流反应器(PFR),往往耗费大量时间和资源。这项研究引入了一种小型化的气泡柱反应器装置(工作容积为 60 毫升),可进行单独和并行的碳限制恒温发酵,提供了一种更高效、更简化的方法。细胞反应的特征是报警酮五磷酸鸟苷(ppGpp)的积累,同时伴随着能量电荷的显著降低,从 0.8 降至 0.7。转录组分析显示了两阶段的反应模式,有 200 多个基因上调和下调。初始阶段以 CRP-cAMP 和 ppGpp 介导的碳限制反应为主,随后在应激 sigma 因子的控制下转入静止阶段,诱导基因表达。通过与传统的 STR/PFR 设置进行全面比较,证实了该系统的有效性。分析结果表明,该系统具有有效再现从传统 STR/PFR 设置中收集的数据的潜力,展示了其作为集成在菌株开发过程中的缩放模拟器的潜在用途。
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引用次数: 0
Microbial Squalene: A Sustainable Alternative for the Cosmetics and Pharmaceutical Industry – A Review 微生物角鲨烯:化妆品和制药业的可持续替代品--综述
IF 2.7 4区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-08-27 DOI: 10.1002/elsc.202400003
Saseendran Shalu, Panam Kunnel Raveendranathan, Vinoth Kumar Vaidyanathan, Lars M. Blank, Andrea Germer, Palanisamy Athiyaman Balakumaran
Squalene is a natural triterpenoid and a biosynthetic precursor of steroids and hopanoids in microorganisms, plants, humans, and other animals. Squalene has exceptional properties, such as its antioxidant activity, a high penetrability of the skin, and the ability to trigger the immune system, promoting its application in the cosmetic, sustenance, and pharmaceutical industries. Because sharks are the primary source of squalene, there is a need to identify low‐cost, environment friendly, and sustainable alternatives for producing squalene commercially. This shift has prompted scientists to apply biotechnological advances to research microorganisms for synthesizing squalene. This review summarizes recent metabolic and bioprocess engineering strategies in various microorganisms for the biotechnological production of this valuable molecule.
角鲨烯是一种天然三萜类化合物,也是微生物、植物、人类和其他动物体内类固醇和类罂粟碱的生物合成前体。角鲨烯具有抗氧化活性、皮肤高渗透性和触发免疫系统的能力等优异特性,促进了其在化妆品、营养品和医药行业的应用。由于鲨鱼是角鲨烯的主要来源,因此需要找到低成本、环保和可持续的角鲨烯商业生产替代品。这一转变促使科学家们应用生物技术的进步来研究合成角鲨烯的微生物。本综述总结了最近在各种微生物中采用新陈代谢和生物过程工程策略,通过生物技术生产这种宝贵的分子。
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引用次数: 0
Cover Picture: Engineering in Life Sciences 8'24 封面图片:生命科学工程 8'24
IF 3.9 4区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-08-05 DOI: 10.1002/elsc.202470081
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引用次数: 0
Fungal Enzymes for Saccharification of Gamma-Valerolactone-Pretreated White Birch Wood: Optimization of the Production of Talaromyces amestolkiae Cellulolytic Cocktail 用于γ-戊内酯预处理白桦木糖化的真菌酵素:塔拉酵母菌纤维素分解鸡尾酒的优化生产
IF 3.9 4区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-07-11 DOI: 10.1002/elsc.202400029
Laura I. de Eugenio, Isabel de la Torre, Felipe de Salas, Francisco Vila, David Alonso, Alicia Prieto, María Jesús Martínez

Lignocellulosic biomass, the most abundant natural resource on earth, can be used for cellulosic ethanol production but requires a pretreatment to improve enzyme access to the polymeric sugars while obtaining value from the other components. γ-Valerolactone (GVL) is a promising candidate for biomass pretreatment since it is renewable and bio-based. In the present work, the effect of a pretreatment based on GVL on the enzymatic saccharification of white birch was evaluated at a laboratory scale and the importance of the washing procedure for the subsequent saccharification was demonstrated. Both the saccharification yield and the production of cellulosic ethanol were higher using a noncommercial enzyme crude from Talaromyces amestolkiae than with the commercial cocktail Cellic CTec2 from Novozymes. Furthermore, the production of extracellular cellulases by T. amestolkiae has been optimized in 2 L bioreactors, with improvements ranging from 40% to 75%. Finally, it was corroborated by isoelectric focus that optimization of cellulase secretion by T. amestolkiae did not affect the pattern production of the main β-glucosidases and endoglucanases secreted by this fungus.

木质纤维素生物质是地球上最丰富的自然资源,可用于生产纤维素乙醇,但需要进行预处理,以提高酶对聚合糖的利用率,同时从其他成分中获取价值。γ-戊内酯(GVL)是生物质预处理的理想候选物质,因为它是可再生的生物基。本研究在实验室规模上评估了基于 GVL 的预处理对白桦木酶法糖化的影响,并证明了洗涤程序对后续糖化的重要性。与诺维信公司的商品鸡尾酒 Cellic CTec2 相比,使用非商业性的羊角酵母菌酶粗品的糖化率和纤维素乙醇产量都更高。此外,在 2 升的生物反应器中,对羊角酵母菌生产胞外纤维素酶进行了优化,改进幅度在 40% 至 75% 之间。最后,等电聚焦法证实,优化 T. amestolkiae 的纤维素酶分泌并不影响该真菌分泌的主要 β-葡萄糖苷酶和内切葡聚糖酶的生产模式。
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引用次数: 0
Cover Picture: Engineering in Life Sciences 7'24 封面图片:生命科学工程 7'24
IF 3.9 4区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-07-04 DOI: 10.1002/elsc.202470071
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引用次数: 0
Improving Downstream Process Related Manufacturability Based on Protein Engineering—A Feasibility Study 基于蛋白质工程改善下游工艺的可制造性--可行性研究
IF 3.9 4区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-06-28 DOI: 10.1002/elsc.202400019
Florian Capito, Ting Hin Wong, Christine Faust, Kilian Brand, Werner Dittrich, Mark Sommerfeld, Garima Tiwari, Thomas Langer

While bioactivity and a favorable safety profile for biotherapeutics is of utmost importance, manufacturability is also worth of consideration to ease the manufacturing process. Manufacturability in the scientific literature is mostly related to stability of formulated drug substances, with limited focus on downstream process-related manufacturability, that is, how easily can a protein be purified. Process-related impurities or biological impurities like viruses and host cell proteins (HCP) are present in the harvest which have mostly acid isoelectric points and need to be removed to ensure patient safety. Therefore, during molecule design, the surface charge of the target molecule should preferably differ sufficiently from the surface charge of the impurities to enable an efficient purification strategy. In this feasibility study, we evaluated the possibility of improving manufacturability by adapting the surface charge of the target protein. We generated several variants of a GLP1-receptor-agonist-Fc-domain-FGF21-fusion protein and demonstrated proof of concept exemplarily for an anion exchange chromatography step which then can be operated at high pH values with maximal product recovery allowing removal of HCP and viruses. Altering the surface charge distribution of biotherapeutic proteins can thus be useful allowing for an efficient manufacturing process for removing HCP and viruses, thereby reducing manufacturing costs.

生物治疗药物的生物活性和良好的安全性是最重要的,但为了简化生产流程,可制造性也值得考虑。科学文献中的可制造性大多与配制药物的稳定性有关,对下游工艺相关的可制造性(即蛋白质的纯化难易程度)关注有限。收获物中存在与工艺相关的杂质或生物杂质,如病毒和宿主细胞蛋白(HCP),它们大多具有酸等电点,需要去除以确保患者安全。因此,在分子设计过程中,目标分子的表面电荷最好与杂质的表面电荷有足够大的差异,以便采用高效的纯化策略。在这项可行性研究中,我们评估了通过调整目标蛋白质的表面电荷来提高可制造性的可能性。我们生成了几种 GLP1 受体拮抗剂-Fc-结构域-FGF21 融合蛋白的变体,并示范了阴离子交换色谱步骤的概念验证,该步骤可在高 pH 值下操作,并能最大限度地回收产品,从而去除 HCP 和病毒。因此,改变生物治疗蛋白的表面电荷分布有助于实现去除 HCP 和病毒的高效生产工艺,从而降低生产成本。
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引用次数: 0
Editing Streptomyces genome using target AID system fused with UGI-degradation tag 利用融合了 UGI 降解标签的目标 AID 系统编辑链霉菌基因组
IF 3.9 4区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-06-24 DOI: 10.1002/elsc.202400005
Pamella Apriliana, Prihardi Kahar, Norimasa Kashiwagi, Akihiko Kondo, Chiaki Ogino

The utilization of Streptomyces as a microbial chassis for developing innovative drugs and medicinal compounds showcases its capability to produce bioactive natural substances. Recent focus on the clustered regularly interspaced short palindromic repeat (CRISPR) technology highlights its potential in genome editing. However, applying CRISPR technology in certain microbial strains, particularly Streptomyces, encounters specific challenges. These challenges include achieving efficient gene expression and maintaining genetic stability, which are critical for successful genome editing. To overcome these obstacles, an innovative approach has been developed that combines several key elements: activation-induced cytidine deaminase (AID), nuclease-deficient cas9 variants (dCas9), and Petromyzon marinus cytidine deaminase 1 (PmCDA1). In this study, this novel strategy was employed to engineer a Streptomyces coelicolor strain. The target gene was actVA-ORF4 (SCO5079), which is involved in actinorhodin production. The engineering process involved introducing a specific construct [pGM1190-dcas9-pmCDA-UGI-AAV-actVA-ORF4 (SCO5079)] to create a CrA10 mutant strain. The resulting CrA10 mutant strain did not produce actinorhodin. This outcome highlights the potential of this combined approach in the genetic manipulation of Streptomyces. The failure of the CrA10 mutant to produce actinorhodin conclusively demonstrates the success of gene editing at the targeted site, affirming the effectiveness of this method for precise genetic modifications in Streptomyces.

利用链霉菌作为开发创新药物和药用化合物的微生物底盘,展示了其生产生物活性天然物质的能力。最近对成簇规律性间隔短回文重复(CRISPR)技术的关注凸显了其在基因组编辑方面的潜力。然而,在某些微生物菌株(尤其是链霉菌)中应用 CRISPR 技术会遇到一些特定的挑战。这些挑战包括实现高效的基因表达和保持遗传稳定性,这对成功进行基因组编辑至关重要。为了克服这些障碍,我们开发了一种创新方法,该方法结合了几个关键要素:活化诱导胞苷脱氨酶(AID)、核酸酶缺陷cas9变体(dCas9)和Petromyzon marinus胞苷脱氨酶1(PmCDA1)。在本研究中,我们采用了这一新策略来改造一种链霉菌(Streptomyces coelicolor)菌株。目标基因是 actVA-ORF4 (SCO5079),它参与放线菌素的生产。工程过程包括引入一个特定的构建体[pGM1190-dcas9-pmCDA-UGI-AAV-actVA-ORF4 (SCO5079)]来创建一个 CrA10 突变菌株。产生的 CrA10 突变株不产生放线菌素。这一结果凸显了这种组合方法在链霉菌遗传操作方面的潜力。CrA10 突变体未能产生放线菌素,这最终证明在目标位点的基因编辑是成功的,从而肯定了这种方法在链霉菌中进行精确基因修饰的有效性。
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引用次数: 0
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