Zhang Ke, Zhao Weishu, Rodionov Dmitry A, Rubinstein Gabriel M, Nguyen Diep N, Tanwee Tania N N, Crosby James, Bing Ryan G, Kelly Robert M, Adams Michael W W, Zhang Ying
Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, USA.
Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, California, USA.
mSystems. 2021 Jun 29;6(3):e0135120. doi: 10.1128/mSystems.01351-20. Epub 2021 Jun 1.
Metabolic modeling was used to examine potential bottlenecks that could be encountered for metabolic engineering of the cellulolytic extreme thermophile Caldicellulosiruptor bescii to produce bio-based chemicals from plant biomass. The model utilizes subsystems-based genome annotation, targeted reconstruction of carbohydrate utilization pathways, and biochemical and physiological experimental validations. Specifically, carbohydrate transport and utilization pathways involving 160 genes and their corresponding functions were incorporated, representing the utilization of C5/C6 monosaccharides, disaccharides, and polysaccharides such as cellulose and xylan. To illustrate its utility, the model predicted that optimal production from biomass-based sugars of the model product, ethanol, was driven by ATP production, redox balancing, and proton translocation, mediated through the interplay of an ATP synthase, a membrane-bound hydrogenase, a bifurcating hydrogenase, and a bifurcating NAD- and NADP-dependent oxidoreductase. These mechanistic insights guided the design and optimization of new engineering strategies for product optimization, which were subsequently tested in the model, showing a nearly 2-fold increase in ethanol yields. The model provides a useful platform for investigating the potential redox controls that mediate the carbon and energy flows in metabolism and sets the stage for future design of engineering strategies aiming at optimizing the production of ethanol and other bio-based chemicals. The extremely thermophilic cellulolytic bacterium, Caldicellulosiruptor bescii, degrades plant biomass at high temperatures without any pretreatments and can serve as a strategic platform for industrial applications. The metabolic engineering of , however, faces potential bottlenecks in bio-based chemical productions. By simulating the optimal ethanol production, a complex interplay between redox balancing and the carbon and energy flow was revealed using a genome-scale metabolic model. New engineering strategies were designed based on an improved mechanistic understanding of the metabolism, and the new designs were modeled under different genetic backgrounds to identify optimal strategies. The model provided useful insights into the metabolic controls of this organism thereby opening up prospects for optimizing production of a wide range of bio-based chemicals.
代谢建模用于研究在对嗜热纤维素分解菌嗜热栖热放线菌进行代谢工程改造以从植物生物质生产生物基化学品时可能遇到的潜在瓶颈。该模型利用基于子系统的基因组注释、碳水化合物利用途径的靶向重建以及生化和生理实验验证。具体而言，纳入了涉及160个基因及其相应功能的碳水化合物运输和利用途径，代表了C5/C6单糖、二糖以及纤维素和木聚糖等多糖的利用。为说明其效用，该模型预测，模型产物乙醇基于生物质糖的最佳生产由ATP生成、氧化还原平衡和质子转运驱动，这是通过ATP合酶、膜结合氢化酶、分叉氢化酶以及分叉的依赖NAD和NADP的氧化还原酶之间的相互作用介导的。这些机制见解指导了用于产物优化的新工程策略的设计和优化，随后在模型中进行了测试，结果显示乙醇产量几乎提高了两倍。该模型为研究介导代谢中碳和能量流动的潜在氧化还原控制提供了一个有用的平台，并为未来旨在优化乙醇和其他生物基化学品生产的工程策略设计奠定了基础。嗜热纤维素分解菌嗜热栖热放线菌能够在无需任何预处理的情况下于高温下降解植物生物质，可作为工业应用的战略平台。然而其代谢工程在生物基化学品生产中面临潜在瓶颈。通过模拟最佳乙醇生产，利用基因组规模代谢模型揭示了氧化还原平衡与碳和能量流动之间的复杂相互作用。基于对该菌代谢的改进机制理解设计了新的工程策略，并在不同遗传背景下对新设计进行建模以确定最佳策略。该模型为该生物体的代谢控制提供了有用的见解，从而为优化多种生物基化学品的生产开辟了前景。
