Structure Prediction and Genome Mining‐Aided Discovery of the Bacterial C‐Terminal Tryptophan Prenyltransferase PalQ

Abstract

Post‐translational prenylations, found in eukaryotic primary metabolites and bacterial secondary metabolites, play crucial roles in biomolecular interactions. Employing genome mining methods combined with AlphaFold2‐based predictions of protein interactions, PalQ , a prenyltransferase responsible for the tryptophan prenylation of RiPPs produced by Paenibacillus alvei, is identified. PalQ differs from cyanobactin prenyltransferases because of its evolutionary relationship to isoprene synthases, which enables PalQ to transfer extended prenyl chains to the indole C3 position. This prenylation introduces structural diversity to the tryptophan side chain and also leads to conformational dynamics in the peptide backbone, attributed to the cis/trans isomerization that arises from the formation of a pyrrolidine ring. Additionally, PalQ exhibited pronounced positional selectivity for the C‐terminal tryptophan. Such enzymatic characteristics offer a toolkit for peptide therapeutic lipidation.

Tryptophan-Centric Bioinformatics Identifies New Lasso Peptide Modifications

“…1,66−70 In contrast to the variation in the prenyl acceptor residue seen in the cyanobactins, ComX peptides share a conserved forward prenylation at the C3 position of an internal Trp of ComX, with certain strains performing geranylation and others farnesylation. 71 Unlike cyanobactins and ComX pheromones, wygwalassin A 1 is matured with TrpC5-forward dimethylallylation which has, to our knowledge, never been characterized in any RiPP-derived product. DMATs, particularly Trp-DMATs, are widespread in fungal biosynthetic (non-RiPP) pathways and perform similar reactions to those of the cyanobactin prenyltransferases.…”

“…Similarly, prenylation as an RiPP modification is known for classes like cyanobactins and the quorum-sensing ComX peptides. The former contains a rich chemical diversity, with forward/reverse O / N / C -prenylation to Ser, Thr, Tyr, Arg, Trp and His residues, as well as the N / C -terminus of linear cyanobactins. ,− In contrast to the variation in the prenyl acceptor residue seen in the cyanobactins, ComX peptides share a conserved forward prenylation at the C3 position of an internal Trp of ComX, with certain strains performing geranylation and others farnesylation . Unlike cyanobactins and ComX pheromones, wygwalassin A 1 is matured with TrpC5-forward dimethylallylation which has, to our knowledge, never been characterized in any RiPP-derived product.…”