Multiomic strategies towards the analysis of natural products, bacterial antimicrobial response, and non-canonical peptide translation

Organisms synthesize functionally diverse natural products through complex enzymatic transformations. In microbial environments, these metabolites are often secreted into the extracellular space to give the producing organism a distinct advantage against neighboring microbes in dynamic environments. These natural products have long been harvested, synthesized, and mass produced for applications outside of the environments in which they are produced naturally. Recently, the direct impact of natural products in their native environments have been realized. The fundamental goal of this dissertation is to develop strategies to analyze natural product production from bacteria, taking advantage of data-rich, mass spectrometry-centric experiments and publicly available sequencing information. Chapter 2 discloses detailed procedures for keystone experiments and analysis modes applied in later chapters of this dissertation. A vested interest in the proteomic response to antimicrobial treatment led to the discovery of increased colibactin production, and subsequent DNA damage in antibiotic resistant E. coli (Chapter 3). A unique antimicrobial peptide was discovered from the plant, C. majus, and multiple mass spectrometry techniques were used to determine the peptide sequence and mechanism of action (Chapter 4). Quantitative proteomics and metabolomics enabled the exploration of the relationship between natural product abundance and the abundance of the enzymes responsible for their biosynthesis (Chapter 5). Finally, a bioinformatic pipeline was built to aid in the identification of non-canonical coding regions of bacterial genomes.