Expanding the biosynthetic scope of peptides

The "Ribosomally synthesized and Post-translationally modified Peptides" (RiPPs) are a large and diverse natural product class. A major focus of our work is to characterize novel types of RiPP modifying enzymes and to discover new RiPPs.

Our studies on uncultivated bacteria revealed RiPP pathways that encode giant peptide toxins of the proteusin-family. Their biosynthesis involves 48 modifications catalyzed by only 6 enzymes. These and further compounds, that we identified by genome mining, belong to various new natural product families that use unprecedented peptide maturases to install for example:

D-amino acids,
ornithine,
fatty acids,
tert-butyl groups,
N-methylations,
and beta-amino acids.

The latter modification was applied in synthetic biology to introduce diverse and multiple beta-amino acids in proteins.

Enlarged view: Dissection and utilization of natural product pathways — Modifying enzymes act post-translationally on ribosomal peptides. Cleavage of the leader peptide by a protease releases the modified core peptide.

Related publications (selection)

Mordhorst S, Ruijne F, Vagstad AL, Kuipers OP, Piel J. "Emulating nonribosomal peptides with ribosomal biosynthetic strategies." RSC Chem. Biol. (2022) 4, 1, 7-36. external pageAbstract

Hubrich F, Lotti A, Scott TA, Piel J. "Uncovering Novel Peptide Chemistry from Bacterial Natural Products." Chimia (Aarau). (2021) 75, 6, 543-547. Abstract

Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. "New developments in RiPP discovery, enzymology and engineering." Nat. Prod. Rep. (2021) 38, 1, 130-239. external pageAbstract

Scott TA, Piel J. "The hidden enzymology of bacterial natural product biosynthesis." Nat. Rev. Chem. (2019) 7, 404-425. external pageAbstract

Freeman MF, Vagstad AL, Piel J. "Polytheonamide biosynthesis showcasing the metabolic potential of sponge-associated uncultivated 'Entotheonella' bacteria." Curr. Opin. Chem. Biol. (2016) 8-14. external pageAbstract

Richter D, Lakis E, Piel J. "Site-specific bioorthogonal protein labelling by tetrazine ligation using endogenous β-amino acid dienophiles." Nat. Chem. (2023) doi: 10.1038/s41557-023-01252-8. external pageAbstract

Lakis E, Magyari S, Piel J. "In Vivo Production of Diverse β-Amino Acid-Containing Proteins." Angew. Chem. Int. Ed. (2022), 61, 29, e202202695. external pageAbstract

Scott TA, Verest M, Farnung J, Forneris CC, Robinson SL, Ji X, Hubrich F, Chepkirui C, Richter DU, Huber S, Rust P, Streiff AB, Zhang Q, Bode JW, Piel J. "Widespread microbial utilization of ribosomal β-amino acid-containing peptides and proteins" Chem (2022) 8, 10, 2659-2677. external pageAbstract

Morinaka BI, Lakis E, Verest M, Helf MJ, Scalvenzi T, Vagstad AL, Sims J, Sunagawa S, Gugger M, Piel J. "Natural noncanonical protein splicing yields products with diverse β-amino acid residues." Science. (2018) 359, 6377, 779-782. external pageAbstract

Mordhorst S, Badmann T, Bösch NM, Morinaka BI, Rauch H, Piel J, Groll M, Vagstad AL. "Structural and Biochemical Insights into Post-Translational Arginine-to-Ornithine Peptide Modifications by an Atypical Arginase." ACS Chem. Biol. (2023) 18, 3, 528-536. external pageAbstract

Hubrich F, Bösch NM, Chepkirui C, Morinaka BI, Rust M, Gugger M, Robinson SL, Vagstad AL, Piel J. "Ribosomally derived lipopeptides containing distinct fatty acyl moieties." Proc. Natl. Acad. Sci. U. S. A. (2022) 119, 3, e2113120119. external pageAbstract

Mordhorst S, Morinaka BI, Vagstad AL, Piel J. "Posttranslationally Acting Arginases Provide a Ribosomal Route to Non-proteinogenic Ornithine Residues in Diverse Peptide Sequences." Angew. Chem. Int. Ed. (2020) 59, 48, 21442-21447. external pageAbstract

Bösch NM, Borsa M, Greczmiel U, Morinaka BI, Gugger M, Oxenius A, Vagstad AL, Piel J. "Landornamides: Antiviral Ornithine-Containing Ribosomal Peptides Discovered through Genome Mining." Angew. Chem. Int. Ed. (2020) 59, 29, 11763-11768. external pageAbstract

Korneli M, Fuchs SW, Felder K, Ernst C, Zinsli LV, Piel J. "Promiscuous Installation of D-Amino Acids in Gene-Encoded Peptides." ACS Synth. Biol. (2021) 10, 2, 236-242. external pageAbstract

Vagstad AL, Kuranaga T, Püntener S, Pattabiraman VR, Bode JW, Piel J. "Introduction of D-Amino Acids in Minimalistic Peptide Substrates by an S-Adenosyl-l-Methionine Radical Epimerase." Angew. Chem. Int. Ed. (2019) 58, 8, 2246-2250. external pageAbstract

Morinaka BI, Vagstad AL, Piel J. "Radical S-Adenosylmethionine Peptide Epimerases: Detection of Activity and Characterization of D-Amino Acid Products." Methods Enzymol. (2018) 604, 237-257. external pageAbstract

Morinaka BI, Verest M, Freeman MF, Gugger M, Piel J. "An Orthogonal D₂O-Based Induction System that Provides Insights into D-Amino Acid Pattern Formation by Radical S-Adenosylmethionine Peptide Epimerases." Angew. Chem. Int. Ed. (2017) 56, 3, 762-766. external pageAbstract

Fuchs SW, Lackner G, Morinaka BI, Morishita Y, Asai T, Riniker S, Piel J. "A Lanthipeptide-like N-Terminal Leader Region Guides Peptide Epimerization by Radical SAM Epimerases: Implications for RiPP Evolution." Angew. Chem. Int. Ed. (2016) 55, 40, 12330-3. external pageAbstract

Morinaka BI, Vagstad AL, Helf MJ, Gugger M, Kegler C, Freeman MF, Bode HB, Piel J "Radical S-adenosyl methionine epimerases: regioselective introduction of diverse D-amino acid patterns into peptide natural products" Angew Chem Int Ed Engl. (2014) 53, 8503-7. external pageAbstract

Cogan DP, Bhushan A, Reyes R, Zhu L, Piel J, Nair SK. "Structure and mechanism for iterative amide N-methylation in the biosynthesis of channel-forming peptide cytotoxins." Proc. Natl. Acad. Sci. U. S. A. (2022) 119, 13, e2116578119. external pageAbstract

Helf MJ, Freeman MF, Piel J. "Investigations into PoyH, a promiscuous protease from polytheonamide biosynthesis." J. Ind. Microbiol. Biotechnol. (2019) 46, 3-4, 551-563. external pageAbstract

Helf MJ, Jud A, Piel J. "Enzyme from an Uncultivated Sponge Bacterium Catalyzes S-Methylation in a Ribosomal Peptide." Chembiochem. (2017) 18, 5, 444-450. external pageAbstract

Freeman MF, Helf MJ, Bhushan A, Morinaka BI, Piel J. "Seven enzymes create extraordinary molecular complexity in an uncultivated bacterium." Nat. Chem. (2017) 4, 387-395. external pageAbstract

Freeman MF, Gurgui C, Helf MJ, Morinaka BI, Uria AR, Oldham NJ, Sahl HG, Matsunaga S, Piel J. "Metagenome mining reveals polytheonamides as posttranslationally modified ribosomal peptides." Science (2012) 338, 6105, 387-90. external pageAbstract