Exploring De Novo metabolic pathways from pyruvate to propionic acid
Exploring De Novo metabolic pathways from pyruvate to propionic acid
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DOI：
10.1002/btpr.2233
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发表时间：
2016-03
影响因子：
2.9
通讯作者：
A. Stine;Miaomin Zhang;S. Ro;S. Clendennen;M. C. Shelton;Keith E. J. Tyo;L. Broadbelt
中科院分区：
文献类型：
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作者：
A. Stine;Miaomin Zhang;S. Ro;S. Clendennen;M. C. Shelton;Keith E. J. Tyo;L. Broadbelt
工业生物技术为化工生产提供了一种高效、可持续的解决方案。然而，仅根据已知反应设计生化途径并不能充分发挥其潜力。已知酶接受非天然底物，这可能允许新的，有利的反应。我们之前已经开发了一个名为生物网络集成计算资源管理器（BNICE）的计算程序，使用从生化反应数据库中提取的广义反应规则来预测混杂酶的活性并设计合成途径。在这里，我们使用BNICE设计丙酮酸合成丙酸的途径。目前已知的自然途径产生不良副产物乳酸和琥珀酸，降低了它们的经济可行性。BNICE预测了7条包含4个或更少反应步骤的途径，其中5条避免了这些副产物。在包含这些途径的16个生化反应中，有44%被文献证实。这些已知反应中超过28%不在BNICE训练数据集中，这表明BNICE能够预测新的酶底物。大多数途径包括中间的丙烯酸。随着丙烯酸生物生产技术的发展，我们重点研究了将丙烯酸还原为丙酸的关键步骤。我们通过实验验证了来自酿酒酵母的Oye2p可以以较慢的周转率（10−3 s−1）催化该反应，这是该酶未知的，这是进一步丙酸代谢工程的重要发现。这些结果验证了BNICE作为一种途径搜索工具，可以预测以前未知的混杂酶活性，并表明计算方法可以阐明工业应用的新型生化途径。©2016美国化学工程师协会生物技术。掠夺。， 32:303-311, 2016
Industrial biotechnology provides an efficient, sustainable solution for chemical production. However, designing biochemical pathways based solely on known reactions does not exploit its full potential. Enzymes are known to accept non‐native substrates, which may allow novel, advantageous reactions. We have previously developed a computational program named Biological Network Integrated Computational Explorer (BNICE) to predict promiscuous enzyme activities and design synthetic pathways, using generalized reaction rules curated from biochemical reaction databases. Here, we use BNICE to design pathways synthesizing propionic acid from pyruvate. The currently known natural pathways produce undesirable by‐products lactic acid and succinic acid, reducing their economic viability. BNICE predicted seven pathways containing four reaction steps or less, five of which avoid these by‐products. Among the 16 biochemical reactions comprising these pathways, 44% were validated by literature references. More than 28% of these known reactions were not in the BNICE training dataset, showing that BNICE was able to predict novel enzyme substrates. Most of the pathways included the intermediate acrylic acid. As acrylic acid bioproduction has been well advanced, we focused on the critical step of reducing acrylic acid to propionic acid. We experimentally validated that Oye2p from Saccharomyces cerevisiae can catalyze this reaction at a slow turnover rate (10−3 s−1), which was unknown to occur with this enzyme, and is an important finding for further propionic acid metabolic engineering. These results validate BNICE as a pathway‐searching tool that can predict previously unknown promiscuous enzyme activities and show that computational methods can elucidate novel biochemical pathways for industrial applications. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:303–311, 2016