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: 2016
• 资助国家: 加拿大
• 起止时间: 2016-01-01 至 2017-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=614559
• 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.

这项提议的目的是利用细菌基因组序列数据来识别可用于开发工业生物催化剂的新酶。细菌构成了地球上最大和最多样的生命形式之一。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颖化学反应来合成用于防御的分子，以及从环境中获得稀缺的营养。因此，利用这种酶的催化能力将使我们能够以环境友好的方式降解污染物或合成有价值的分子。这项提案的一半将专注于我们实验室发现的一种新的酶途径，称为PhnY-PhnZ，它可以降解包括除草剂和化学战剂在内的一类分子--磷酸盐。我们将研究PhnY和PhnZ酶的内部工作原理和结构，以便我们可以对它们进行改造，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RoundUpTM，动机是这是世界上最常用的除草剂。该提案的后半部分将寻找能够合成复杂的生物活性分子的细菌酶，这些分子可能会被开发成新药。我们将特别关注一种由土壤细菌合成的名为核杀菌素的罕见分子。值得注意的是，杀核素具有两个在药物设计中常用的基团：一个氟原子和一个磺酸盐。氟的用途尤其突出，目前使用的药物中约有20%含有氟，30%的农用化学品含有氟。在这项提案中，我们将确定在核杀菌素中产生氟基和氨基酸基的酶，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。化学家在不使用大量溶剂、高温、多个反应步骤或有毒和反应性试剂的情况下，不容易完成氟基和氨基酸基的安装。此外，所需的产品往往不能以纯形式或高产量获得。相比之下，酶可以在室温下以水为溶剂进行这些转化，步骤较少，从而减少了能源消耗、环境影响和费用。学生将在这些项目中接受培训，范围从微生物学到分析化学再到酶催化，将为进入生物技术和制药领域奠定坚实的基础。