Title | Bioinformatic Atlas of Radical SAM Enzyme-Modified RiPP Natural Products Reveals an Isoleucine-Tryptophan Crosslink. |
Publication Type | Journal Article |
Year of Publication | 2022 |
Authors | Clark, KA, Seyedsayamdost, MR |
Journal | J Am Chem Soc |
Volume | 144 |
Issue | 39 |
Pagination | 17876-17888 |
Date Published | 2022 Oct 05 |
ISSN | 1520-5126 |
Keywords | Amidines, Biological Products, Computational Biology, Iron, Isoleucine, Peptides, Protein Processing, Post-Translational, S-Adenosylmethionine, Sulfur, Tryptophan |
Abstract | <p>Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing family of natural products with diverse activities and structures. RiPP classes are defined by the tailoring enzyme, which can introduce a narrow range of modifications or a diverse set of alterations. In the latter category, RiPPs synthesized by radical -adenosylmethionine (SAM) enzymes, known as RaS-RiPPs, have emerged as especially divergent. A map of all RaS-RiPP gene clusters does not yet exist. Moreover, precursor peptides remain difficult to predict using computational methods. Herein, we have addressed these challenges and report a bioinformatic atlas of RaS-RiPP gene clusters in available microbial genome sequences. Using co-occurrence of RaS enzymes and transporters from varied families as a bioinformatic hook in conjunction with an in-house code to identify precursor peptides, we generated a map of ∼15,500 RaS-RiPP gene clusters, which reveal a remarkable diversity of syntenies pointing to a tremendous range of enzymatic and natural product chemistries that remain to be explored. To assess its utility, we examined one family of gene clusters encoding a YcaO enzyme and a RaS enzyme. We find the former is noncanonical, contains an iron-sulfur cluster, and installs a novel modification, a backbone amidine into the precursor peptide. The RaS enzyme was also found to install a new modification, a C-C crosslink between the unactivated terminal δ-methyl group of Ile and a Trp side chain. The co-occurrence search can be applied to other families of RiPPs, as we demonstrate with the emerging DUF692 di-iron enzyme superfamily.</p> |
DOI | 10.1021/jacs.2c06497 |
Alternate Journal | J Am Chem Soc |
PubMed ID | 36128669 |