Natural Products and Synthetic Biology

While the phrasing of this tripartite classification was not intended to describe the current state of natural products research, it could have been, as it provides an apt description of the field today. The organic molecules lumped under the term natural products elude an easy definition. They are a structurally diverse collection of molecules produced by organisms in an idiosyncratic fashion, and their biological activities reflect the diversity of their producers and structures. Inclusion in or exclusion from the natural product family reflects the elasticity of classification. Consider three molecules that are closely related structurally and biosynthetically: tryptophan, serotonin, and psilocin (Figure 1a). Tryptophan’s universal distribution as a proteinogenic amino acid excludes it from being a natural product. Serotonin’s widespread distribution and well-understood biological activities result in its classification as a hormone or neurotransmitter, while psilocin, a hallucinogenic relative produced by only a few New World mushrooms, is a natural product. All natural products have one feature in common, biosyntheses by a genetically encoded pathway, and the possibilities for re-engineering these pathways connects natural products to synthetic biology. The opening quotation’s classification would differentiate natural products into the known knowns, such as the antibiotic erythromycin, for which we know the molecule (and in this case its genetically encoded biosynthetic pathway); the known unknowns or “cryptic metabolites”, which have never been isolated and characterized but whose existence can be inferred from biosynthetic pathways in sequenced genomes; and the unknown unknowns, or molecules whose existence has not been suspected through genomic or any other sort of analysis. We do not know how many natural products exist, but the Dictionary of Natural Products lists 170,000 known structures, which effectively represents today’s universe of known knowns. The biosynthetic pathways for most of these have not been definitively described, but progress on this front is extremely rapid, especially for molecules with significant biological activity produced by bacteria and fungi. The biosynthetic pathway encoding the genes that synthesize erythromycin’s core, a molecule called erythronolide, condenses seven three-carbon fragments with additional possible transformations following each condensation, and because of the modular and repetitive nature of the biosynthetic chemistry, the gene cluster is also large (∼50 kb) and highly repetitive (Figure 1b). Biosynthetic gene clusters like the one making erythromycin are relatively easy to identify in sequenced genomes, and their identification has been automated with programs like antiSMASH. The genes for many biosynthetic pathways can be manipulated relatively easily to create what have been called unnatural natural products. The erythromycin pathway is arguably the world’s best studied and most manipulated natural product biosynthetic pathway, and the Dictionary of Natural Products describes 34 biosynthetic relatives, some naturally occurring and some laboratory generated.