Michael G. Thomas
Associate Professor of Bacteriology & Alfred Toepfer Faculty Fellow
Bacterial secondary metabolism has proven to be a rich source of natural products with medically and agriculturally relevant biological activities. Additionally, the enzymes employed by the producing organisms to generate these metabolites have proven to be a fascinating fusion of reactions that are typically seen in primary metabolism, with slight modifications to generate unusual enzymatic reactions. Thus, analysis of bacterial secondary metabolism offers the opportunity to study processes that have both basic and applied scientific interests. The overall goals of my research program are to discover, decipher, and harness bacterial secondary metabolism with these two scientific interests in mind.
One focus of my group is on the discovery of new bacterial secondary metabolic processes by mining both the sequenced genomes of cultured bacteria and the metagenome of uncultured bacteria for new secondary metabolites. In the first approach, we use bioinformatics to scan the putative proteome of sequenced bacterial genomes for proteins that have sequence similarity with enzymes known to be involved in secondary metabolism. We then target the gene coding the candidate protein for disruption using genetic techniques. Through a combination of transcriptional fusions, gene knockouts, and metabolite profiling we identify the metabolite and screen for potential biological activities. This approach has led to the identification of a new iron-chelating molecule from the plant pathogen Agrobacterium tumefaciens C58, and the identification of six lipopeptide biosurfactants produced by Pseudomonas syringae pv. tomato DC3000. We are currently extending this approach to other plant-associated bacteria. In the second approach, we collaborate with Dr. Jo Handelsman to generate and screen metagenomic libraries for the production of new antimicrobial compounds. Metagenomics is the functional and sequence-based analysis of the collective genomes of the microorganisms in an environmental sample, independent of laboratory culturing techniques. This is seen as one of the most promising directions for the identification of new natural products with desired biological activities.
Our goal of deciphering secondary metabolism focuses on the identification and analysis of biosynthetic pathways that produce known secondary metabolites. For this analysis, we clone, sequence, and analyze the biosynthetic gene cluster that codes for all of the enzymes involved in the production of a medically or agriculturally relevant secondary metabolite. We have recently deciphered the pathways for capreomycin and viomycin biosynthesis, members of the tuberactinomycin family of antituberculosis drugs. These drugs are included on the World Health Organization's "List of Essential Medicines" because of their potent activity against multidrug-resistant Mycobacterium tuberculosis. Our work has answered biosynthetic questions that have been investigated for over 50 years. In addition to the tuberactinomycins, we have also deciphered the pathway for zwittermicin A biosynthesis, an important agricultural antibiotic involved in the biocontrol activity of Bacillus cereus. Importantly, our work has identified two new extender units for the biosynthesis of polyketide natural products. This increases the number of known extender units from four to six and offers unique opportunities for metabolic engineering of polyketide biosynthetic pathways.
Once we have deciphered how a secondary metabolite is biosynthesized, we aim to harness this information for the production of "unnatural" derivatives of these metabolites. We use metabolic engineering of the corresponding biosynthetic pathways to generate new structural diversity in these metabolites that would not be easily attainable using more traditional chemical synthesis approaches. Through this approach, we aim to develop derivatives of these molecules that regain activity against resistant cells, have reduced side effects for a patient, and/or have enhanced biological activities. We are currently using this approach on multiple antibiotic biosynthetic pathways to develop new antituberculosis drugs.