ArticlemSystems2020
RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery.
Article in mSystems, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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78 citing papers in PubMed.
- Evolutionary strategies of late-stage diversification in bacterial biosynthetic gene clusters.Essays in biochemistry · 2026Review
- Tangled Tail of Mechanically Interlocked Peptides.Journal of the American Chemical Society · 2026Review
- Biosynthesis, Structure, and Antibiotic Properties of Gelatinamin A, a Triculamin-Like Lasso Peptide.Chembiochem : a European journal of chemical biology · 2026Article
- RiPP recognition elements evolved to prevent pathway interference through leader peptide discrimination.Nature communications · 2026Article
- Biosynthesis of Peptidic Thiooxazole Metallophores Installed by Multinuclear Nonheme Iron Enzymes.ACS chemical biology · 2026Article
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- A Small-Molecular-Weight Bacteriocin-like Inhibitory Substance (BLIS) UI-11 Produced byVeterinary sciences · 2025Article
- Biosynthesis of peptidic thiooxazole metallophores installed by multinuclear nonheme iron enzymes.bioRxiv : the preprint server for biology · 2025Article
- ThiF-Like Enzyme Chemistry in Primary and Secondary Metabolism.Chembiochem : a European journal of chemical biology · 2025Review
- Characterizing and engineering post-translational modifications with high-throughput cell-free expression.Nature communications · 2025Article
- Sequence modeling tools to decode the biosynthetic diversity of the human microbiome.mSystems · 2025Review
- Biosynthesis of Biphenomycin-like Macrocyclic Peptides by Formation and Cross-Linking ofJournal of the American Chemical Society · 2025Article
- Indolylamide Macrocyclization by aOrganic letters · 2025Article
- Evolution-Guided Discovery of Antimycobacterial Triculamin-Like Lasso Peptides.Angewandte Chemie (International ed. in English) · 2025Article
- Large-scale transcriptome mining enables macrocyclic diversification and improved bioactivity of the stephanotic acid scaffold.Nature communications · 2025Article
- Biosynthesis of Macrocyclic Peptides by Formation and Crosslinking ofbioRxiv : the preprint server for biology · 2025Article
- Substrate recognition by a peptide-aminoacyl-tRNA ligase.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
18 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
Many ribosomally synthesized and posttranslationally modified peptide classes (RiPPs) are reliant on a domain called the RiPP recognition element (RRE). The RRE binds specifically to a precursor peptide and directs the posttranslational modification enzymes to their substrates. Given its prevalence across various types of RiPP biosynthetic gene clusters (BGCs), the RRE could theoretically be used as a bioinformatic handle to identify novel classes of RiPPs. In addition, due to the high affinity and specificity of most RRE-precursor peptide complexes, a thorough understanding of the RRE domain could be exploited for biotechnological applications. However, sequence divergence of RREs across RiPP classes has precluded automated identification based solely on sequence similarity. Here, we introduce RRE-Finder, a new tool for identifying RRE domains with high sensitivity. RRE-Finder can be used in precision mode to confidently identify RREs in a class-specific manner or in exploratory mode to assist in the discovery of novel RiPP classes. RRE-Finder operating in precision mode on the UniProtKB protein database retrieved ∼25,000 high-confidence RREs spanning all characterized RRE-dependent RiPP classes, as well as several yet-uncharacterized RiPP classes that require future experimental confirmation. Finally, RRE-Finder was used in precision mode to explore a possible evolutionary origin of the RRE domain. The results suggest RREs originated from a co-opted DNA-binding transcriptional regulator domain. Altogether, RRE-Finder provides a powerful new method to probe RiPP biosynthetic diversity and delivers a rich data set of RRE sequences that will provide a foundation for deeper biochemical studies into this intriguing and versatile protein domain.
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