Discovery and biosynthesis of tricyclic copper-binding ribosomal peptides containing histidine-to-butyrine crosslinks

Abstract

Cyclic peptide natural products represent an important class of bioactive compounds and clinical drugs. Enzymatic side-chain macrocyclization of ribosomal peptides is a major strategy developed by nature to generate these chemotypes, as exemplified by the superfamily of ribosomally synthesized and post-translational modified peptides. Despite the diverse types of side-chain crosslinks in this superfamily, the participation of histidine residues is rare. Herein, we report the discovery and biosynthesis of bacteria-derived tricyclic lanthipeptide noursin, which is constrained by a tri amino acid labionin crosslink and an unprecedented histidine-to-butyrine crosslink, named histidinobutyrine. Noursin displays copper-binding ability that requires the histidinobutyrine crosslink and represents the first copper-binding lanthipeptide. A subgroup of lanthipeptide synthetases, named LanKCHbt, were identified to catalyze the formation of both the labionin and the histidinobutyrine crosslinks in precursor peptides and produce noursin-like compounds. The discovery of the histidinobutyrine-containing lanthipeptides expands the scope of post-translational modifications, structural diversity and bioactivity of ribosomally synthesized and post-translational modified peptides.

A widespread family of ribosomal peptide metallophores involved in bacterial adaptation to metal stress

“…Peptide natural products with other heterocycles are known to bind transition metals and fulfil different functions [45][46][47][48] . Most prominently, the RiPP methanobactins scavenge copper from the milieu to feed it to cuproenzymes, and some of them also protect bacteria from toxic metals such as mercury 49 .…”

Dehydroamino acid residues in bioactive natural products

“…9C ). 50 It is likely that the constraints generated by the Lab motif in the peptidyl intermediates as they are processed contribute the increased reactivity of Dhb-8. Phylogenetic analysis has indicated that NorKC and its homologues form a separate cluster distinct from LanKC enzymes for the typical class III lanthipeptides.…”

Genome Mining for New Enzyme Chemistry

“…A RiPP displaying an unusual His-Dhb (Hbt) cross-link was discovered during genome mining efforts for new class III lanthipeptides using the class-defining lanthipeptide synthetase LanKC (IPR000719 and IPR007822). A putative class III lanthipeptide BGC ( nor ) was identified in Streptomyces noursei ATCC 11455, with the precursor peptide NorA containing three Ser/Thr and only one Cys . Heterologous expression in Streptomyces lividans and in vitro reconstitution demonstrated that the lanthipeptide synthetase NorKC (ANZ21440.1) catalyzes the dehydration of all three Ser/Thr to the corresponding Dha/Dhb as well as the formation of a canonical labionin between the Cys and Dha residues.…”

“…A putative class III lanthipeptide BGC ( nor ) was identified in Streptomyces noursei ATCC 11455, with the precursor peptide NorA containing three Ser/Thr and only one Cys. 69 Heterologous expression in Streptomyces lividans and in vitro reconstitution demonstrated that the lanthipeptide synthetase NorKC (ANZ21440.1) catalyzes the dehydration of all three Ser/Thr to the corresponding Dha/Dhb as well as the formation of a canonical labionin between the Cys and Dha residues. Unexpectedly, NorKC also formed an unprecedented cross-link between the N τ of His and C β of an aminobutyric acid residue via a Michael addition of His to dehydrobutyrine ( Figure 3 B).…”