Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway.
Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway.
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DOI：
10.1038/ncomms10005
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发表时间：
2015-11-24
影响因子：
16.6
通讯作者：
Siegel JB
中科院分区：
文献类型：
--
作者：
Mak WS;Tran S;Marcheschi R;Bertolani S;Thompson J;Baker D;Liao JC;Siegel JB
生物合成生产超出自然界常见化学物质的能力需要发现新的酶功能。在这里，我们利用两种方法来发现能够从糖中特异性生产长链 (C5–C8) 醇的酶。第一种方法将生物信息学和分子建模结合起来挖掘序列数据库，产生能够催化目标反应的多种酶。通过计算选择的酶的中值催化效率比一组简单选择的同系物高 75 倍。这种综合基因组挖掘方法为在快速扩展的序列数据库中发现酶功能建立了独特的途径。第二种方法使用计算酶设计来重新编程特异性。这两种方法都能使酶的目标反应特异性提高 100 倍以上。当两种方法中的酶在体内整合时，长链酒精的产量会增加 10 倍以上，占总酒精产品的 95% 以上。 通过非自然途径修饰酶以产生所需化合物是生产商品化学品的有用途径。在这里，作者展示了两种从糖中生成高级醇的方法——基因组挖掘和计算酶设计。
The ability to biosynthetically produce chemicals beyond what is commonly found in Nature requires the discovery of novel enzyme function. Here we utilize two approaches to discover enzymes that enable specific production of longer-chain (C5–C8) alcohols from sugar. The first approach combines bioinformatics and molecular modelling to mine sequence databases, resulting in a diverse panel of enzymes capable of catalysing the targeted reaction. The median catalytic efficiency of the computationally selected enzymes is 75-fold greater than a panel of naively selected homologues. This integrative genomic mining approach establishes a unique avenue for enzyme function discovery in the rapidly expanding sequence databases. The second approach uses computational enzyme design to reprogramme specificity. Both approaches result in enzymes with >100-fold increase in specificity for the targeted reaction. When enzymes from either approach are integrated in vivo, longer-chain alcohol production increases over 10-fold and represents >95% of the total alcohol products. The modification of enzymes to generate desired compounds by non-natural pathways is a useful route for the production of commodity chemicals. Here, the authors show two approaches—genome mining and computational enzyme design—to generate higher alcohols from sugar.