Informatics-Based Discovery of New Natural Products, Their Biosynthesis, and Their Biological Roles

In this work, genome mining and biosynthetic knowledge are applied for the discovery of new natural products, their biosynthetic pathways, and their promising biological activities and roles through the development of two unique new informatics-based approaches. In chapter one, an overview of microbial natural product biological functions and biosynthesis is provided. The use of bioinformatics leveraging microbial natural product biosynthetic knowledge is also introduced. This chapter highlights the importance and need for developing innovative approaches to accessing microbial natural products, a vastly untapped source of new molecules with promising biological activities. In chapter two, a correlational network linking the gene-encoded precursor peptides of lanthipeptide natural products, sometimes referred to as lantibiotics due to their antimicrobial properties, to the hidden unclustered proteases required for their maturation is constructed. Interrogation of the network results in the discovery of new lanthipeptide-associated proteases. Particularly, a family of M16B metallopeptidases with previously unclear function is established as class III lanthipeptide proteases. Heterologous expression of lanthipeptide BGCs alongside these proteases results in the discovery and characterization of several new class III lanthipeptides including unique new N,N-dimethylated lanthipeptides with antimicrobial activity. In chapter three, the specific biosynthetic enzymes involved in the biosynthesis of human gut microbial sulfonolipids, microbial mimics of human endogenous sphingolipids, are used in a large-scale genome mining effort across all available human gut microbial reference genomes to create clustered subfamilies of sulfonolipid biosynthetic enzyme homologs. These subfamilies are then used to construct a biosynthetic enzyme-disease correlation, linking the decreased biosynthesis of sulfonolipids to increased inflammatory parameters in human inflammatory bowel disease patient samples. This bioinformatic connection is then experimentally validated in a mouse model of colitis and foundational work is conducted demonstrating that naturally occurring human gut microbial sulfonolipids suppress toll-like receptor 4 (TLR4)-related inflammation through direct competition with lipopolysaccharide binding to the TLR4/myeloid differentiation factor-2 (MD-2) complex. Taken together, these two examples demonstrate the application of biosynthetic knowledge in the development of informatics-based approaches for discovery of natural products with promising biological activities.