Exploration, expansion and definition of the atropopeptide family of ribosomally synthesized and posttranslationally modified peptides
Friederike Biermann, Bin Tan, Milena Breitenbach, Yuya Kakumu, Pakjira Nanudorn, Yoana Dimitrova, Allison S. Walker, Reiko Ueoka, Eric J. N. Helfrich
Abstract
Ribosomally synthesized and posttranslationally modified peptides (RiPPs) constitute a diverse class of natural products. Atropopeptides are a recent addition to the class. Here we developed AtropoFinder, a genome mining algorithm to chart the biosynthetic landscape of the atropopeptides. AtropoFinder identified more than 650 atropopeptide biosynthetic gene clusters (BGCs). We pinpointed crucial motifs and residues in leader and core peptide sequences, prompting a refined definition of the atropopeptide RiPP family. Our study revealed that a substantial subset of atropopeptide BGCs harbors multiple tailoring genes, thus suggesting a broader structural diversity than previously anticipated. To verify AtropoFinder, we heterologously expressed four atropopeptide BGCs, which resulted in the identification of novel atropopeptides with varying peptide lengths, number and types of modifications. Atropopeptides serve as a proof-of-principle for the versatile genome mining approach developed in this study that can be repurposed for the identification of RiPP and other BGCs that currently evade detection.