The production of bottromycin by S. bottropensis and S. scabies, as well as the production of a bottromycin analog termed bottromycin D, has been studied. It was independently confirmed in 2012 by multiple groups that bottromycin is produced as a ribosomal peptide natural product that it subsequently post-translationally modified. Before this, it was unclear whether bottromycin was produced by nonribosomal peptide synthetase machinery (NRPS). The presence of amino acids other than the 20 proteinogenic amino acids is often a feature of NRPS products because NRPS machinery can directly incorporate other amino acids, among other chemical building blocks. Ribosomal peptide synthesis, which is the same machinery that produces all proteins found in the cell, is limited to the 20 proteinogenic amino acids. However, bottromycin was found to be a highly modified ribosomal peptide by a combination of genome mining and gene deletion studies.
In ribosomal peptide synthesis, the final product results from modifications to a linear peptide starting material translated by the ribosome from an mRNA transcript. In S. scabies the precursor peptide, termed BtmD, is a 44-amino acid peptide. The precursor peptide is termed BmbC in S. bottropensis. The amino acids forming the bottromycin core are residues 2-9 in BtmD: Gly-Pro-Val-Val-Val-Phe-Asp-Cys. In bottromycin D, the sequence is Gly-Pro-Ala-Val-Val-Phe-Asp-Cys, and the precursor peptide is termed BstA. BstA shares high sequence homology with BtmD in the follower peptide region. Unlike other ribosomal peptide natural products, which are normally synthesized with a leader peptide that is cleaved, bottromycin is synthesized with a follower peptide. The presence of a follower peptide was identified by bioinformatic analysis of the bottromycin biosynthetic cluster.
The complete biosynthetic gene cluster for bottromycin has been identified. It is predicted to contain 13 genes, including the precursor peptide (notation will follow Crone and colleagues; other studies had similar results). One of the genes in the cluster, btmL, is proposed to be a transcriptional regulator. Another gene, btmA, is proposed to export bottromycin. The remaining ten genes are expected to modify the precursor peptide btmD from a linear peptide to the final macrocyclic product.
A biosynthetic pathway has been hypothesized based on proposed gene functions (see figure). btmM, with homology to Zn+2 aminopeptidases, is predicted to cleave the N-terminal methionine residue, which is not present in the bottromycin final product. btmE and btmF both contain YcaO-like domains. It is believed that one Although it is unclear which enzyme is responsible for which step, it is hypothesized that one catalyzes macrocyclic amidine formation while the other catalyzes thiazoline formation. btmJ, encoding an enzyme with cytochrome P450 homology, may oxidize the thiazoline to the thiazole. btmH or btmI both have homology to hydrolytic enzymes (α/β hydrolase and metallo-dependent hydrolase, respectively) may catalyze follower peptide hydrolysis. An alternative proposed role for btmH or btmI is to function as a cyclodehydratase in macrocyclization. Gene deletion studies failed to elucidate the function of other proteins within the cluster.