1 Department of Bioengineering, Istanbul Medeniyet University, Istanbul, Turkey.
2 Department of Genetics and Bioengineering, Yeditepe University, Istanbul, Turkey.
OMICS. 2019 Apr;23(4):237-246. doi: 10.1089/omi.2019.0028. Epub 2019 Mar 30.
423 is a thermophilic bacterium capable of producing high levels of exopolysaccharide (EPS) that has broad applications in nutrition, feed, cosmetics, pharmaceutical, and chemical industries, not to mention in health and bionanotechnology sectors. EPS is a natural, nontoxic, and biodegradable polymer of sugar residues and plays pivotal roles in cell-to-cell interactions, adhesion, biofilm formation, and protection of cell against environmental extremes. This bacterium is a thermophilic EPS producer while exceeding other thermophilic producers by virtue of high level of polymer synthesis. Recently, 423 was noted for relevance to multiple industry sectors because of its capacity to use xylose, and produce EPS, isoprenoids, ethanol/butanol, lipases, proteases, cellulase, and glucoamylase enzymes as well as its resistance to arsenic. A key step in understanding EPS production with a systems-based approach is the knowledge of microbial genome sequence. To speed biotechnology and industrial applications, this study reports on a genome-scale metabolic model (GSMM) of 423, constructed using the recently available high-quality genome sequence that we have subsequently validated using physiological data on batch growth and EPS production on seven different carbon sources. The model developed contains 1454 reactions (of which 1127 are assigned an enzyme commission number) and 1410 metabolites from 925 genes. This GSMM offers the promise to enable and accelerate further systems biology and industrial scale studies, not to mention the ability to calculate metabolic flux distribution in large networks and multiomic data integration.
423 是一种嗜热细菌,能够产生高水平的胞外多糖 (EPS),在营养、饲料、化妆品、制药和化学工业中具有广泛的应用,更不用说在健康和生物纳米技术领域了。EPS 是一种天然的、无毒的、可生物降解的糖残基聚合物,在细胞间相互作用、粘附、生物膜形成以及保护细胞免受环境极端条件的影响方面发挥着关键作用。这种细菌是一种嗜热 EPS 产生菌,其聚合物合成水平高于其他嗜热产生菌。最近,由于其能够利用木糖和生产 EPS、类异戊二烯、乙醇/丁醇、脂肪酶、蛋白酶、纤维素酶和葡萄糖淀粉酶以及对砷的抗性,423 因其与多个行业部门的相关性而受到关注。采用系统方法理解 EPS 生产的关键步骤是了解微生物基因组序列。为了加速生物技术和工业应用,本研究报告了 423 的基因组规模代谢模型 (GSMM),该模型使用最近获得的高质量基因组序列构建,并使用七种不同碳源的分批生长和 EPS 生产的生理数据进行了后续验证。所开发的模型包含 1454 个反应(其中 1127 个反应分配了酶委员会编号)和 1410 种代谢物,来自 925 个基因。该 GSMM 有望实现并加速进一步的系统生物学和工业规模研究,更不用说能够计算大型网络中的代谢通量分布和多组学数据集成了。
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