Salinipeptins: Integrated Genomic and Chemical Approaches Reveal Unusual d-Amino Acid-Containing Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs) from a Great Salt Lake Streptomyces sp.

Abstract

Analysis of the full genome of an environmentally unique, halotolerant Streptomyces sp. strain GSL-6C, isolated from the Great Salt Lake, revealed a gene cluster encoding the biosynthesis of the salinipeptins, d-amino-acid-containing members of the rare linaridin subfamily of ribosomally synthesized and post-translationally modified peptides (RiPPs). The sequence organization of the unmodified amino acid residues in salinipeptins A–D (1–4) were suggested by genome annotation, and subsequently, their sequence and post-translational modifications were defined using a range of spectroscopic techniques and chemical derivatization approaches. The salinipeptins are unprecedented linaridins bearing nine d-amino acids, which are uncommon in RiPP natural products and are the first reported in the linaridin subfamily. Whole genome mining of GSL-6C did not reveal any homologues of the reported genes responsible for amino acid epimerization in RiPPs, inferring new epimerases may be involved in the conversion of l- to d-amino acids. In addition, the N-oxide and dimethylimidazolidin-4-one moieties in salinipeptins B and C, which are modified from N,N-dimethylalanine, are unknown in bacterial peptides. The three-dimensional structure of salinipeptin A, possessing four loops generated by significant hydrogen bonding, was established on the basis of observed nuclear Overhauser effect (NOE) correlations. This study demonstrates that integration of genomic information early in chemical analysis significantly facilitates the discovery and structure characterization of novel microbial secondary metabolites.

Cacaoidin, First Member of the New Lanthidin RiPP Family

“…The planar structure of 1 confirmed the dehydration of genetically encoded Ser‐1, Ser‐2 and Thr‐18 and the subsequent addition of Cys‐5 and (decarboxylated) Cys‐23 to the transients Dha‐1 and Dhb‐18 respectively (to ultimately originate the N‐terminus Lan and the C‐terminus AviMeCys rings) (SI, Figure S48). The biosynthetic origin of AviMeCys in 1 is therefore the same as that described for lanthipeptides and lipolanthines, and different to that reported for linaridins, in which the AviCys is formed between two cysteine residues …”

“…Furthermore, an unprecedented N , N ‐dimethyl lanthionine system (NMe 2 Lan) was found to be present in 1 , based on the characteristic chemical shifts in the HSQC and the key cross‐peaks in the HMBC spectrum (SI, sections 2.3 and 2.11; Figure S28). Thus far, the N‐terminus dimethylation has been reported only for the rare linaridin family, whose members lack lanthionine rings. The involvement of a dimethylated N‐terminus in a Lan ring (NMe 2 Ala‐S‐Ala) is reported here for the first time within RiPPs and further highlights the structural novelty of cacaoidin.…”

LanD-like Flavoprotein-Catalyzed Aminovinyl-Cysteine Formation through Oxidative Decarboxylation and Cyclization of a Peptide at the C-Terminus

“…Together, CypD activity prefers a dethiolated/dehydrated substrate (rather than hijacking the L-Cys19/L-Ser19functionalized intermediate) and tends to produce a D-AviCys-containing product. In fact, D-AviCys residue was found exclusively in related natural products that were characterized in stereochemistry 31,32 . The above results argue against the recent report by Zhang et al who failed to observe AviCys formation in the conversion of a Dhacontaining peptide and thus concluded that CypD has no cyclase activity 33 .…”

Advances in actinomycete research: an ActinoBase review of 2019

“…Further analysis into the possible mechanism of amino acid isomerization suggested that novel enzymology may be involved in the generation of salinipeptide d -amino acids, as homologues of known isomerases could not be identified in the Streptomyces sp. GSL-6C genome [28]. As well as amino acid reconfiguration, additional PTMs in salinipeptide A include formation of an aminovinyl-cysteine end group and dehydration of threonine residues to dehydrobutyrine (Dhb).…”