A Prevalent Peptide-Binding Domain Guides Ribosomal Natural Product Biosynthesis

Abstract

Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a rapidly growing natural product class. RiPP precursor peptides can undergo extensive enzymatic tailoring, yielding structurally and functionally diverse products, and their biosynthetic logic makes them attractive bioengineering targets. Recent work suggests that unrelated RiPP modifying enzymes contain structurally similar precursor peptide-binding domains. Using profile hidden Markov model comparisons, we discovered related and previously unrecognized peptide-binding domains in proteins spanning the majority of known prokaryotic RiPP classes; thus, we named this conserved domain the RiPP precursor peptide recognition element (RRE). Through binding studies, we verify the role of the RRE for three distinct RiPP classes: linear azole-containing peptides, thiopeptides, and lasso peptides. Because numerous RiPP biosynthetic enzymes act on peptide substrates, our findings have powerful predictive value as to which protein(s) drive substrate binding, laying a foundation for further characterization of RiPP biosynthetic pathways and the rational engineering of new peptide-binding activities.