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

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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.**