From Genes to Molecules: Mining Bacterial Genomes for New Enzyme Reactions

从基因到分子：挖掘细菌基因组以实现新的酶反应

• 批准号: RGPIN-2016-03695
• 负责人: Zechel, David
• 金额: $ 4.44万
• 依托单位: Queen's University
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2019
• 资助国家: 加拿大
• 起止时间: 2019-01-01 至 2020-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=691036
• 关键词: Genes; Molecules; Mining; Bacterial; Genomes

The aim of this proposal is to use bacterial genome sequence data to identify new enzymes that can be used for the development of industrial biocatalysts. Bacteria comprise one of the largest and diverse forms of life on earth. Because of their relatively fragile structures and limited mobility, bacteria rely on novel chemical reactions, catalyzed by enzymes, to synthesize molecules for defence as well as obtain scarce nutrients from the environment. Therefore, harnessing the catalytic power of such enzymes will allow us to degrade pollutants or synthesize valuable molecules in an environmentally friendly manner. One half of this proposal will focus on a new enzyme pathway discovered by our lab, called PhnY-PhnZ, that degrades phosphonates, a class of molecule that include herbicides and chemical warfare agents. We will study the inner workings and structures of the enzymes PhnY and PhnZ so that we can engineer them to degrade phosphonates of environmental concern into harmless phosphate. We will first focus on engineering the PhnY-PhnZ pathway to degrade RoundUpTM, motivated by the fact that this is the most commonly used herbicide in the world. The second half of this proposal will look for bacterial enzymes that synthesize complex and bioactive molecules that may be developed into new drugs. We will specifically focus on a rare molecule called nucleocidin that is synthesized by a soil bacterium. Nucleocidin is notable for possessing two groups that are commonly used in drug design: a fluorine atom and a sulfamate. Fluorine in particular enjoys prominent use, with approximately 20% of currently used drugs and 30% of agrochemicals containing fluorine. In this proposal we will identify the enzymes that create the fluorine and sulfamate groups in nucleocidin and apply them to the synthesis of drugs or their precursors. We predict that these enzymes will have a major impact on the pharmaceutical industry. The installation of fluorine and sulfamate groups cannot be performed easily by chemists without using large volumes of solvents, high temperatures, multiple reaction steps, or toxic and reactive reagents. Moreover, the desired product often cannot be obtained in pure form or in high yield. In contrast, enzymes can perform these transformations in water as the solvent, with fewer steps, and at room temperature, thereby decreasing energy usage, environmental impact, and expense. The training that students will receive in these projects, ranging from microbiology to analytical chemistry to enzyme catalysis, will provide a solid foundation to enter the biotechnology and pharmaceutical fields.**

本提案的目的是利用细菌基因组序列数据来鉴定可用于工业生物催化剂开发的新酶。细菌是地球上最大、种类繁多的生命形式之一。由于其相对脆弱的结构和有限的流动性，细菌依靠酶催化的新型化学反应来合成防御分子，并从环境中获取稀缺的营养物质。因此，利用这种酶的催化能力将使我们能够以一种环保的方式降解污染物或合成有价值的分子。这个提议的一半将集中在我们实验室发现的一种新的酶途径上，叫做PhnY-PhnZ，它可以降解磷酸盐，磷酸盐是一类分子，包括除草剂和化学战剂。我们将研究PhnY和PhnZ酶的内部工作原理和结构，以便我们可以设计它们将环境关注的磷酸盐降解为无害的磷酸盐。我们将首先专注于设计PhnY-PhnZ途径来降解农达tm，这是由于这是世界上最常用的除草剂。该提案的后半部分将寻找合成复杂和生物活性分子的细菌酶，这些分子可能被开发成新药。我们将特别关注一种由土壤细菌合成的名为“杀核素”的稀有分子。在药物设计中，有两个常用的基团：一个氟原子和一个磺胺酸。氟的用途尤其突出，目前使用的药物中约有20%和30%的农用化学品含有氟。在本提案中，我们将确定在杀核素中产生氟和磺胺酸基团的酶，并将它们应用于药物或其前体的合成。我们预测这些酶将对制药行业产生重大影响。如果不使用大量溶剂、高温、多个反应步骤或有毒和活性试剂，化学家就不容易安装氟和氨基甲酸酯基团。此外，所需的产品往往不能以纯形式或高收率获得。相比之下，酶可以在水作为溶剂中进行这些转化，步骤更少，并且在室温下，从而减少能源使用，环境影响和费用。学生将在这些项目中接受从微生物学到分析化学到酶催化的培训，为进入生物技术和制药领域提供坚实的基础