YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function

Abstract

With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.

Radical S-Adenosylmethionine Enzymes Involved in RiPP Biosynthesis

“…2,3 In general, RiPP biosynthesis commences with the post-translational modification (PTM) of a precursor peptide, typically consisting of N -terminal leader and C -terminal core regions. 1–4 The RiPP precursor peptide gene is often encoded adjacent to other genes responsible for regulation, biosynthesis, and export. Collectively, these genes comprise the biosynthetic gene cluster (BGC) for the natural product.…”

Chimeric Leader Peptides for the Generation of Non-Natural Hybrid RiPP Products

“…HcaD/F is a thiazoline-forming cyclodehydratase (Figure 1d) 31,38 and was chosen in part because the RS of the precursor peptide (HcaA) was previously defined. 38 The other enzyme, NisB/C, originates from the nisin biosynthetic gene cluster and was chosen because of the large body of knowledge pertaining to how the peptide substrate (NisA) is recognized and processed (Figure S2).…”

In Vitro Biosynthesis of Peptides Containing Exotic Azoline Analogues

“…During biosynthesis, precursor peptides, which generally consist of an N‐terminal leader peptide (LP) region and a following core peptide (CP) region, are produced by the translation machinery. Subsequently, Cys, Ser, and Thr residues in the CP region undergo post‐translational cyclodehydration catalyzed by a YcaO‐family enzyme, resulting in peptides bearing the corresponding azolines. Because the incorporation of azolines into the backbone bestows proteolytic stability, conformational strain, and unique hydrogen‐bonding sites on peptides, azoline‐containing peptides (Az‐peptides) are an attractive class of compounds for the development of biologically active peptides.…”