Cacaoidin, First Member of the New Lanthidin RiPP Family

Abstract

Lantibiotics are ribosomally synthesized and post‐translationally modified peptides (RiPPs) characterized by the presence of lanthionine or methyllanthionine rings and their antimicrobial activity. Cacaoidin, a novel glycosylated lantibiotic, was isolated from a Streptomyces cacaoi strain and fully characterized by NMR, mass spectrometry, chemical derivatization approaches and genome analysis. The new molecule combines outstanding structural features, such as a high number of d‐amino acids, an uncommon glycosylated tyrosine residue and an unprecedented N,N‐dimethyl lanthionine. This latter feature places cacaoidin within a new RiPP family located between lanthipeptides and linaridins, here termed lanthidins. Cacaoidin displayed potent antibacterial activity against Gram‐positive pathogens including Clostridium difficile. The biosynthetic gene cluster showed low homology with those of other known lanthipeptides or linaridins, suggesting a new RiPP biosynthetic pathway.

Understanding Thioamitide Biosynthesis Using Pathway Engineering and Untargeted Metabolomics

“…Our insights are supported by parallel studies of individual enzymes in other thioamitide pathways 10,11 , as well as the recent discoveries of cacaoidin 33 and lexapeptide 34 , which contain AviMeCys macrocycles, as predicted from our experimental and informatic analyses. We anticipate that the data reported here will inform further experimental work on the thioamitides and related RiPPs to determine key biosynthetic steps, including the true roles of HopA1 and TfuA domain proteins in their respective steps, given that neither protein features a known catalytic domain.…”

“…Most of the putative precursor peptides from Cyanobacteria and Actinobacteria belong to two major subnetworks that are loosely related between themselves (Families 1A and 1B). The main precursor peptide network associated to Actinobacteria (272 precursor peptides, Family 1B) includes the precursor peptide for the antibiotic cacaoidin, the first member or the recently described lanthidin RiPP family 33 . Genes cao7, cao9 and caoD in the cacaoidin BCG encode a HopA1-like protein, a phosphotransferase and a cysteine decarboxylase homologous to TsaD, TsaC and TsaF respectively, which suggests that the AviMeCys group found in this molecule is installed following a similar mechanism as in the thioamitides.…”

Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides

“…The NH signals in the 1 H NMR spectrum were very broad using DMSO-d 6 as solvent. We therefore changed to CD 3 CN:H 2 O 9:1 as the solvent, which showed very good NH signals for the recently identified similar peptide cacaoidin [81]. Indeed, sharper peaks and better heteronuclear multiple bond correlation (HMBC) signals could be observed (S14B Fig).…”

“…Thus, the primary sequence of the peptide, the MS/MS fragmentation data, the NMR data, acid hydrolysis, and labeling experiments (Table 3) allowed us to elucidate the 2D structure of pristinin A3 (1) as shown in Fig 3E. The RiPPs characterized here contain a number of modifications which have been previously identified in different other RiPPs. A recent study, which appeared around the time of submission for this paper, describes a RiPP found by activity-based screening called cacaoidin, which has many of the same modifications [81] and is additionally glycosylated. The serines converted to alanines in cacaoidin were all D-alanines.…”

Combating Antimicrobial Resistance With New-To-Nature Lanthipeptides Created by Genetic Code Expansion

“…classified based on the biosynthetic mechanisms involved in their structural maturation, the recently discovered modified peptides, including Cocaoidin and Lexapeptide, exhibited novel modification features such as different biosynthetic gene clusters and have been introduced as class V lanthipeptides (Ortiz-López et al, 2020;Xu et al, 2020).…”