Targeted enzyme gene re-positioning: A computational approach for discovering alternative bacterial enzymes for the synthesis of plant-specific secondary metabolites
Targeted enzyme gene re-positioning: A computational approach for discovering alternative bacterial enzymes for the synthesis of plant-specific secondary metabolites
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DOI：
10.1016/j.mec.2019.e00102
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发表时间：
2019-09
影响因子：
5.2
通讯作者：
Yuya Nakamura;S. Hirose;Y. Taniguchi;Yuki Moriya;Takuji Yamada
中科院分区：
文献类型：
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作者：
Yuya Nakamura;S. Hirose;Y. Taniguchi;Yuki Moriya;Takuji Yamada
植物合成的次生代谢物是制药、食品添加剂和调味品的独特来源，以及其他工业用途。然而，由于这些代谢物结构复杂、对自然环境不友好、具有危险性，工业化生产十分困难，因此需要开发新的合成方法。在这项研究中，我们开发了一种新的方法来寻找替代细菌酶来产生植物生物合成的次生代谢物。基于酶反应的相似性，我们搜索了编码酶的候选细菌基因，这些基因可能取代KEGG数据库(酶重新定位)中包含的植物特异性次生代谢反应中的酶。结果，我们发现了447个植物特异性次级代谢反应的候选细菌替代酶基因。为了验证我们的方法，我们重点研究了天蓝色链霉菌A3(2)菌株的一种酶转化价烯为葡萄柚代谢物nootkatone的能力，并用气相色谱-质谱仪证实了它的酶活性。这种酶重新定位方法可能提供一种全新的方法来筛选酶，这是大多数其他传统方法无法实现的，它适用于各种其他代谢物，并可能使微生物生产目前难以工业化生产的化合物。
Plant-biosynthesised secondary metabolites are unique sources of pharmaceuticals, food additives, and flavourings, among other industrial uses. However, industrial production of these metabolites is difficult because of their structural complexity, dangerousness and unfriendliness to natural environment, so the development of new methods to synthesise them is required. In this study, we developed a novel approach to identifying alternative bacterial enzyme to produce plant-biosynthesised secondary metabolites. Based on the similarity of enzymatic reactions, we searched for candidate bacterial genes encoding enzymes that could potentially replace the enzymes in plant-specific secondary metabolism reactions that are contained in the KEGG database (enzyme re-positioning). As a result, we discovered candidate bacterial alternative enzyme genes for 447 plant-specific secondary metabolic reaction. To validate our approach, we focused on the ability of an enzyme fromStreptomyces coelicolorstrain A3(2) strain to convert valencene to the grapefruit metabolite nootkatone, and confirmed its enzymatic activity by gas chromatography-mass spectrometry. This enzyme re-positioning approach may offer an entirely new way of screening enzymes that cannot be achieved by most of other conventional methods, and it is applicable to various other metabolites and may enable microbial production of compounds that are currently difficult to produce industrially.