Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors
Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors
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DOI：
10.1021/acssynbio.8b00049
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发表时间：
2018-08-01
影响因子：
4.7
通讯作者：
Hatzimanikatis, Vassily
中科院分区：
文献类型：
--
作者：
Tokic, Milenko;Hadadi, Noushin;Hatzimanikatis, Vassily
有限的化石燃料供应和新的环境政策的建立，使工业界和学术界的研究转向第二代生物燃料的可持续生产，甲基乙基酮（MEK）是一种有前途的燃料候选者。MEK是一种具有商业价值的石油化工产品，作为溶剂具有广泛的应用。然而，到目前为止，尽管多次尝试在工业微生物中引入生物合成途径，但尚未实现MEK的可持续和经济上可行的生产。我们使用BNICE.ch作为逆转录生物合成工具来发现MEK周围的所有新途径。在1325个鉴定的化合物中，我们选择了3-氧代戊酸酯、丁-3-烯-2-酮、丁-1-烯-2-醇酯、丁胺和2-羟基-2-甲基丁腈进行进一步研究。我们重建了3 679 610个新的生物合成途径，这5个化合物。然后我们将这些通路嵌入到E.大肠杆菌，和一组18 622被认为是最生物学上可行的热力学和他们的产量的基础上。对于可行途径中的每个新反应，我们提出了最相似的KEGG反应及其基因和蛋白质序列，作为直接实验实施或酶工程基础的候选反应。通过途径相似性分析，我们对途径进行了分类，并确定了目标分子产生所必需的酶和前体。这些逆生物合成研究证明了BNICE.ch在合成生物学和代谢工程研究中发现、系统评价和分析新途径的潜力。
The limited supply of fossil fuels and the establishment of new environmental policies shifted research in industry and academia toward sustainable production of the second generation of biofuels, with methyl ethyl ketone (MEK) being one promising fuel candidate. MEK is a commercially valuable petrochemical with an extensive application as a solvent. However, as of today, a sustainable and economically viable production of MEK has not yet been achieved despite several attempts of introducing biosynthetic pathways in industrial microorganisms. We used BNICE.ch as a retrobiosynthesis tool to discover all novel pathways around MEK. Out of 1325 identified compounds connecting to MEK with one reaction step, we selected 3-oxopentanoate, but-3-en-2-one, but-1-en-2-olate, butylamine, and 2-hydroxy-2-methylbutanenitrile for further study. We reconstructed 3 679 610 novel biosynthetic pathways toward these 5 compounds. We then embedded these pathways into the genome-scale model of E. coli, and a set of 18 622 were found to be the most biologically feasible ones on the basis of thermodynamics and their yields. For each novel reaction in the viable pathways, we proposed the most similar KEGG reactions, with their gene and protein sequences, as candidates for either a direct experimental implementation or as a basis for enzyme engineering. Through pathway similarity analysis we classified the pathways and identified the enzymes and precursors that were indispensable for the production of the target molecules. These retrobiosynthesis studies demonstrate the potential of BNICE.ch for discovery, systematic evaluation, and analysis of novel pathways in synthetic biology and metabolic engineering studies.