Radical S‐Adenosyl Methionine Epimerases: Regioselective Introduction of Diverse D‐Amino Acid Patterns into Peptide Natural Products

Abstract

PoyD is a radical S‐adenosyl methionine epimerase that introduces multiple D‐configured amino acids at alternating positions into the highly complex marine peptides polytheonamide A and B. This novel post‐translational modification contributes to the ability of the polytheonamides to form unimolecular minimalistic ion channels and its cytotoxic activity at picomolar levels. Using a genome mining approach we have identified additional PoyD homologues in various bacteria. Three enzymes were expressed in E. coli with their cognate as well as engineered peptide precursors and shown to introduce diverse D‐amino acid patterns into all‐L peptides. The data reveal a family of architecturally and functionally distinct enzymes that exhibit high regioselectivity, substrate promiscuity, and irreversible action and thus provide attractive opportunities for peptide engineering.

Natural Product Biosynthetic Diversity and Comparative Genomics of the Cyanobacteria

“…An unusual macrolide, nosperin, was discovered from symbiotic Nostoc commune strains in lichen through a targeted genome mining approach [33]. In addition, members of the proteusin family of peptides, produced through the action of architecturally and functionally distinct enzymes, were revealed by genome mining of unusual pathways found in cyanobacteria that exhibit high regioselectivity, substrate promiscuity, and irreversible action to introduce diverse D-amino acid patterns into all-L peptides [67]. This is an exciting trend as it truly hints at the power of genomics as a route to the discovery of new natural products and provides attractive opportunities for peptide engineering.…”

New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products

“…Other RiPPs contain D-amino acids that are introduced via epimerization. For example, the polytheonamides (Freeman et al, 2012) employ the use of a radical-SAM enzyme, which may have great biotechnological potential (Morinaka et al, 2014). In addition to D-amino acids, several additional PTMs have been characterized in lanthipeptides; the most recent one being an N-linked glycosylation of a Trp residue in the class III lanthipeptide NAI-112 (Iorio et al, 2014).…”

The Creatininase Homolog MftE from Mycobacterium smegmatis Catalyzes a Peptide Cleavage Reaction in the Biosynthesis of a Novel Ribosomally Synthesized Post-translationally Modified Peptide (RiPP)

“…A subset of RiPPs undergo maturation by radical-mediated routes leading to formation of thioether (4 -10), Lys-Trp (11) or Glu-Tyr (12) peptide cross-links, oxidative decarboxylation (13,14), or epimerization (15,16). These unusual transformations are catalyzed by enzymes of the radical S-adenosyl-L-methionine (SAM) superfamily (17) that leverage the reductive cleavage of SAM, generating a strong oxidant, 5Ј-deoxyadenosyl radical (5Ј-dAdo ⅐ ), to initiate radical-mediated transformations (18).…”