Genome mining with hypothetical proteins

Natural products are diverse compounds made by many organisms, though bacteria, fungi, and plants are particularly prolific producers. While they have a range of biological roles, bioactive natural products have long been of interest as drug candidates. With the advent of accessible genome mining tools like antiSMASH, it is possible to search through genomes and metagenomes, identifying genes associated with natural product production and even predicting potential structures for experimentally uncharacterized compounds. However, most genome mining tools rely on similarity to previously characterized natural product pathways, and so they can fail to detect unusual or novel pathways and pathways that rely on "hypothetical proteins" for key biosynthetic steps. This is unfortunate, because natural products from new classes or with potentially divergent scaffolds are of particular interest in efforts to identify compounds with antibiotic and anticancer activity. This chapter will document some of the approaches that can be used to explore and develop biosynthetic hypotheses for these challenging-to-detect natural product pathways.