Bioinformatic prediction and experimental validation of RiPP recognition elements

Bioinformatics-guided discovery of biaryl-linked lasso peptides

“…To shed light on the sequence-function relatedness of NopF/LopF versus known P450-modified RiPPs, a sequence similarity network (SSN) was constructed using the top 1000 non-redundant BLAST-P hits of NopF, predicted atropeptide- and biarylitide-associated cytochrome P450 proteins, and 883 P450 proteins encoded within 10 ORFs of an RRE domain. 5 c ,21 b ,24 The SSN and similarity/identity analysis (Fig. S51 and S52†) suggested that NopF/LopF are rare examples of P450 proteins within lasso peptide BGCs.…”

“…As observed for nearly all discrete RRE domains (as opposed to fused cases), the RRE binding to NopA is governed by a characteristic YxxP-containing recognition sequence. 5 c ,16,24 Furthermore, the BGC includes a putative ABC transporter (NopD, PF00005). Notably, and as the principal criterion for target selection, a cytochrome P450 protein (NopF, PF00067) is locally encoded (Table S1†).…”

Discovery and engineering of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products

“…Also, as many PTM enzymes share significant homology with enzymes in other metabolic pathways, mining efforts can usually yield products that are unrelated to RiPPs. 78 In recent years, strategies for exploring RiPPs using the PTM enzyme as the gene mining hallmark have been further developed. These methods have emerged to overcome the limitations of traditional approaches and discover new classes of RiPPs.…”

Genome mining unveils a class of ribosomal peptides with two amino termini

“…One unexploited approach to identify first-in-class RiPPs is to leverage the RiPP precursor recognition element (RRE), a domain responsible for recruiting the precursor peptide to RiPP biosynthetic enzymes 22,23,24 . As the most common domain involved in RiPP biosynthesis, the RRE has been found in 19 of the 41 known prokaryotic RiPP classes, and its frequency suggests it could be used as a class-independent handle for RiPP genome mining.…”