From genes to molecules: mining bacterial genomes for new enzyme reactions

一把土壤或一桶海水就有可能解决当今世界面临的一些紧迫的环境和人类健康问题吗？大规模DNA测序的出现揭示了一个分子世界，它可能确实为清理污染物提供了答案，或者为研发下一种特效药提供了途径。受DNA驱动的新化学反应和分子发现的新时代的启发，我们建议探索有可能改善环境和人类健康的酶。具体来说，我们将研究碳磷裂解酶中显著的碳磷键裂解反应。我们还将研究PhnY / PhnZ有机膦酸盐降解系统，该系统最近通过筛选海洋DNA发现，似乎通过一种新的反应机制来切割碳磷键。这两种酶系统都有可能降解被称为有机膦酸盐的环境污染物，有机膦酸盐是除草剂、杀虫剂、化学战剂和表面活性剂的组成部分。我们还将研究参与“卤化”天然产物生物合成的酶，这是一大类生物活性分子，具有很大的潜力，可以提供新的抗癌和抗生素药物。具体来说，我们研究了由“卤化酶”催化的独特反应，该反应涉及20世纪第一个神奇药物之一——抗生素氯霉素的生物合成。利用从基因组测序中获得的信息，我们还将描述杀核素的生物合成，这是一种罕见的氟取代天然产物。鉴定包含氟原子的酶，即“氟酶”，可能导致合成含氟核苷的生物催化剂，这些核苷作为抗病毒抑制剂非常有兴趣。总体而言，我们的提案包含4个研究领域，将培养4名研究生，以及每年的暑期学生，从分子生物学和微生物学到合成化学的各种技能。在制药和生物技术公司日益多学科的环境中，这些技能的需求量很大。

Is it possible that a handful of soil or a pail of seawater could hold the solution to some of the pressing environmental and human health issues facing the world today? The advent of large scale DNA sequencing has revealed a molecular world that may indeed provide the answer to cleaning up pollutants or the path to the next wonder drug. Inspired by this new era of DNA driven discovery of new chemical reactions and molecules, we propose to explore enzymes that have the potential to improve environmental and human health. Specifically, we will study the remarkable carbon-phosphorus bond cleaving reaction of carbon-phosphorus lyase. We will also study the PhnY / PhnZ organophosphonate degradation system, recently identified through screening of marine DNA, which appears to cleave carbon-phosphorus bonds through a new reaction mechanism. Both enzyme systems have the potential to degrade environmental pollutants known as organophosphonates, a component of herbicides, insecticides, chemical warfare agents, and surfactants. We will also study enzymes that are involved in the biosynthesis of 'halogenated' natural products, a large family of bioactive molecules that have great potential to provide new anticancer and antibiotic drugs. Specifically we examine the unique reaction catalyzed by the 'halogenase' involved in the biosynthesis of one of the first wonder drugs of the 20th century, the antibiotic chloramphenicol. Using information gained from genome sequencing, we will also characterize the biosynthesis of, nucleocidin, a rare example of a fluorine substituted natural product. Identification of the enzyme that incorporates the fluorine atom, a 'fluorinase', could lead to a biocatalyst for the synthesis of fluorine containing nucleosides, which are of great interest as antiviral inhibitors. Overall our proposal contains 4 areas of study that will train 4 graduate students, as well as a yearly summer student, in a variety of skills, from molecular biology and microbiology to synthetic chemistry. These skills are in high demand in the increasingly multidisciplinary environment that exists in pharmaceutical and biotechnology companies.