1
|
Xu Y, Ruijne F, Diez MG, Stada JJ, Kuipers OP. Design and Production of Geranylated Cyclic Peptides by the RiPP Enzymes SyncM and PirF. Biomacromolecules 2025; 26:3186-3199. [PMID: 40189806 PMCID: PMC12076493 DOI: 10.1021/acs.biomac.5c00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2025] [Revised: 03/28/2025] [Accepted: 03/28/2025] [Indexed: 05/13/2025]
Abstract
The growing threat of antibiotic resistance highlights the urgent need for new antimicrobial agents. Nonribosomal peptides (NRPs) are potent antibiotics with complex structures, but generating novel NRP analogues is costly and inefficient. An emerging alternative is using ribosomally synthesized and post-translationally modified peptides (RiPPs), which are gene-encoded, allowing for easier mutagenesis and modification. This study aimed to produce peptides with two key structural elements of many NRP antibiotics: a macrocycle and an N-terminal lipid moiety. The RiPP enzymes SyncM and PirF were employed-SyncM introduced lanthionine or methyllanthionine macrocycles, while PirF incorporated isoprenyl chains to emulate the lipid moieties in NRPs. Both enzymes successfully modified the templates, and their combined use generated lipidated macrocyclic peptides, resembling lipopeptide antibiotics. These findings demonstrate the potential of SyncM and PirF as versatile tools for designing novel gene-encoded NRP mimics, enabling high-throughput screening for new bioactive peptides.
Collapse
Affiliation(s)
- Yanli Xu
- Department of Molecular Genetics,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Fleur Ruijne
- Department of Molecular Genetics,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Manel Garcia Diez
- Department of Molecular Genetics,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Jorrit Jilles Stada
- Department of Molecular Genetics,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen 9747 AG, The Netherlands
| |
Collapse
|
2
|
Zhang W, Ushimaru R, Kanaida M, Abe I. Pyrroline Ring Assembly via N-Prenylation and Oxidative Carbocyclization during Biosynthesis of Aeruginosin Derivatives. J Am Chem Soc 2025; 147:10853-10858. [PMID: 40080531 DOI: 10.1021/jacs.5c01994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2025]
Abstract
Aeruginosins are linear peptide natural products isolated from cyanobacteria and contain various arginine derivatives at their termini. 1-Amino-2-(N-amidino-3-Δ3-pyrrolinyl)ethane (Aeap) is a structurally unique arginine derivative, as it has an unusual pyrroline ring with two additional carbon atoms of unknown biosynthetic origin. Here, we demonstrate that Aer3, a member of a newly identified subfamily of prenyltransferases, catalyzes selective isopentenylation of the internal N atom of agmatine. Rieske oxygenase AerC then catalyzes both carbocyclization and C-C bond cleavage to construct the pyrroline ring in Aeap. This pyrroline ring formation in Aeap biosynthesis, involving two novel enzymes, represents a unique route for heterocycle formation in nature.
Collapse
Affiliation(s)
- Wenhe Zhang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- School of Life Sciences and Biopharmaceutical Sciences, Shenyang Pharmaceutical University, 103 Wenhua Road Shenhe, Shenyang 110016, China
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
- Institute for Advanced Study and Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- FOREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Masahiro Kanaida
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
| |
Collapse
|
3
|
Castelo-Branco R, Pereira JP, Freitas S, Preto M, Vieira AR, Morais J, Leão PN. Genome-informed Discovery of Monchicamides A-K: Cyanobactins from the Microcoleaceae Cyanobacterium LEGE 16532. JOURNAL OF NATURAL PRODUCTS 2025; 88:86-93. [PMID: 39718459 PMCID: PMC11774001 DOI: 10.1021/acs.jnatprod.4c01063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 12/10/2024] [Accepted: 12/10/2024] [Indexed: 12/25/2024]
Abstract
Genome mining has emerged as an important tool for the discovery of natural products and is particularly effective for the swift identification of ribosomally synthesized and post-translationally modified peptides (RiPPs). Among RiPPs, cyanobactins have gained attention due to their diverse structures and bioactive properties. Here, we explored the Microcoleaceae cyanobacterium LEGE 16532 strain and identified the mon biosynthetic gene cluster (BGC), which was predicted to encode cyanobactin-like molecules. This led to the detection of 11 macrocyclic cyanobactins, the monchicamides, some of which feature mono- or diprenylation. One of the compounds was isolated, monchicamides I (9), and its planar structure was established by LC-HRESIMS/MS data as well as 1D and 2D NMR spectroscopy, confirming forward O-prenylation in Tyr. In addition, the absolute configuration of compound 9 was determined by Marfey's method and chiral-phase HPLC. The structures of the additional cyanobactins were proposed from MS/MS data analysis. The bioactivity profile of the isolated compound was also evaluated, but no cytotoxic, antimicrobial, or antiamoebic activity was observed.
Collapse
Affiliation(s)
- Raquel Castelo-Branco
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n4450-208Matosinhos, Portugal
| | - João P. Pereira
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n4450-208Matosinhos, Portugal
| | - Sara Freitas
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n4450-208Matosinhos, Portugal
| | - Marco Preto
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n4450-208Matosinhos, Portugal
| | - Ana R. Vieira
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n4450-208Matosinhos, Portugal
| | - João Morais
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n4450-208Matosinhos, Portugal
| | - Pedro N. Leão
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n4450-208Matosinhos, Portugal
| |
Collapse
|
4
|
Weiss MB, Borges RM, Sullivan P, Domingues JPB, da Silva FHS, Trindade VGS, Luo S, Orjala J, Crnkovic CM. Chemical diversity of cyanobacterial natural products. Nat Prod Rep 2025; 42:6-49. [PMID: 39540765 PMCID: PMC11948988 DOI: 10.1039/d4np00040d] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
Covering: 2010 to 2023Cyanobacterial natural products are a diverse group of molecules with promising biotechnological applications. This review examines the chemical diversity of 995 cyanobacterial metabolites reported from 2010 to 2023. A computational analysis using similarity networking was applied to visualize the chemical space and to compare the diversity of cyanobacterial metabolites among taxonomic orders and environmental sources. Key examples are highlighted, detailing their sources, biological activities, and discovery processes.
Collapse
Affiliation(s)
- Márcio B Weiss
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil.
| | - Ricardo M Borges
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, CEP 21941-599, Rio de Janeiro, RJ, Brazil
| | - Peter Sullivan
- Helmholtz Institute for Pharmaceutical Research Saarland, Saarland University, 66123, Saarbrücken, Germany
| | - João P B Domingues
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil.
| | - Francisco H S da Silva
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil.
| | - Victória G S Trindade
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, CEP 21941-599, Rio de Janeiro, RJ, Brazil
| | - Shangwen Luo
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Jimmy Orjala
- College of Pharmacy, University of Illinois at Chicago, 60612, Chicago, IL, USA
| | - Camila M Crnkovic
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, CEP 05508-000, São Paulo, SP, Brazil.
| |
Collapse
|
5
|
Hubrich F, Kandy SK, Chepkirui C, Padhi C, Mordhorst S, Moosmann P, Zhu T, Gugger M, Chekan JR, Piel J. Ribosomal peptides with polycyclic isoprenoid moieties. Chem 2024; 10:3224-3242. [PMID: 39429465 PMCID: PMC11484575 DOI: 10.1016/j.chempr.2024.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2024]
Abstract
Isoprenoid modifications of proteins and peptides serve fundamental biological functions and are of therapeutic interest. While C15 (farnesyl) and C20 (geranylgeranyl) moieties are prevalent among proteins, known ribosomal peptide prenylations involve shorter-chain units not exceeding farnesyl in size. To our knowledge, cyclized terpene moieties have not been reported from either biomolecule class. Here we used targeted genome mining and heterologous pathway reconstitution to identify ribosomally synthesized and post-translationally modified peptides (RiPPs) with elaborate, cyclized geranylgeranyl modifications. The installing maturases commonly feature fused prenyltransferase-terpene cyclase architectures. We characterized two bifunctional maturases with distinct prenyltransferase folds and identified the terminal product of a cyanobacterial proteusin as an exceptionally complex pseudosteroid-annelated polycyclic peptide. Bioassays suggest modest anti-cyanobacterial activity with the modification being crucial for activity. Genome data predict cyclic isoprenoid units for various RiPP families including proteusin, Nif11, and lasso peptides and thus broader natural and biotechnological compatibility of the maturase system.
Collapse
Affiliation(s)
- Florian Hubrich
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog Weg 4, 8093 Zürich, Switzerland
- Present address: Pharmaceutical Institute, Saarland University; Helmholtz Institute for Pharmaceutical Research Saarland (HIPS); Campus Saarbrücken C2.3, 66123 Saarbrücken, Germany
| | - Sanath K. Kandy
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro; Greensboro, NC 27402-6170, United States of America
| | - Clara Chepkirui
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog Weg 4, 8093 Zürich, Switzerland
| | - Chandrashekhar Padhi
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog Weg 4, 8093 Zürich, Switzerland
- Present address: Department of Chemistry and Howard Hughes Medical Institute, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States of America
| | - Silja Mordhorst
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog Weg 4, 8093 Zürich, Switzerland
- Present address: Pharmaceutical Institute, University of Tübingen; Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Philipp Moosmann
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog Weg 4, 8093 Zürich, Switzerland
| | - Tao Zhu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences; Shandong Energy Institute; Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
| | - Muriel Gugger
- Institut Pasteur, Université Paris Cité, Collection of Cyanobacteria, F-75015 Paris, France
| | - Jonathan R. Chekan
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro; Greensboro, NC 27402-6170, United States of America
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog Weg 4, 8093 Zürich, Switzerland
- Lead contact: Jörn Piel
| |
Collapse
|
6
|
Inoue S, Thanh Nguyen D, Hamada K, Okuma R, Okada C, Okada M, Abe I, Sengoku T, Goto Y, Suga H. De Novo Discovery of Pseudo-Natural Prenylated Macrocyclic Peptide Ligands. Angew Chem Int Ed Engl 2024; 63:e202409973. [PMID: 38837490 DOI: 10.1002/anie.202409973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/07/2024]
Abstract
Prenylation of peptides is widely observed in the secondary metabolites of diverse organisms, granting peptides unique chemical properties distinct from proteinogenic amino acids. Discovery of prenylated peptide agents has largely relied on isolation or genome mining of naturally occurring molecules. To devise a platform technology for de novo discovery of artificial prenylated peptides targeting a protein of choice, here we have integrated the thioether-macrocyclic peptide (teMP) library construction/selection technology, so-called RaPID (Random nonstandard Peptides Integrated Discovery) system, with a Trp-C3-prenyltransferase KgpF involved in the biosynthesis of a prenylated natural product. This unique enzyme exhibited remarkably broad substrate tolerance, capable of modifying various Trp-containing teMPs to install a prenylated residue with tricyclic constrained structure. We constructed a vast library of prenylated teMPs and subjected it to in vitro selection against a phosphoglycerate mutase. This selection platform has led to the identification of a pseudo-natural prenylated teMP inhibiting the target enzyme with an IC50 of 30 nM. Importantly, the prenylation was essential for the inhibitory activity, enhanced serum stability, and cellular uptake of the peptide, highlighting the benefits of peptide prenylation. This work showcases the de novo discovery platform for pseudo-natural prenylated peptides, which is readily applicable to other drug targets.
Collapse
Affiliation(s)
- Sumika Inoue
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, 113-0033, Tokyo, Japan
| | - Dinh Thanh Nguyen
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, 113-0033, Tokyo, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, 236-0004, Yokohama, Japan
| | - Rika Okuma
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, 113-0033, Tokyo, Japan
| | - Chikako Okada
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, 236-0004, Yokohama, Japan
| | - Masahiro Okada
- Department of Material and Life Chemistry, Kanagawa University, Kanagawa-ku, 221-8686, Yokohama, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, 113-0033, Tokyo, Japan
| | - Toru Sengoku
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Kanazawa-ku, 236-0004, Yokohama, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, 113-0033, Tokyo, Japan
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, 606-8502, Kyoto, Japan
- Toyota Riken Rising Fellow, Toyota Physical and Chemical Research Institute, Sakyo, 606-8502, Kyoto, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, 113-0033, Tokyo, Japan
| |
Collapse
|
7
|
Chen XW, Liu Z, Dai S, Zou Y. Discovery, Characterization and Engineering of the Free l-Histidine C4-Prenyltransferase. J Am Chem Soc 2024; 146:23686-23691. [PMID: 39140691 DOI: 10.1021/jacs.4c08388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Prenylation of amino acids is a critical step for synthesizing building blocks of prenylated alkaloid family natural products, where the corresponding prenyltransferase that catalyzes prenylation on free l-histidine (l-His) has not yet been identified. Here, we first discovered and characterized a prenyltransferase FunA from the antifungal agent fungerin pathway that efficiently performs C4-dimethylallylation on l-His. Crystal structure-guided engineering of the prenyl-binding pocket of FunA, a single M181A mutation, successfully converted it into a C4-geranyltransferase. Furthermore, FunA and its variant FunA-M181A show broad substrate promiscuity toward substrates that vary in substituents of the imidazole ring. Our work furthers our knowledge of free amino acid prenyltransferase and expands the arsenal of alkylation biocatalysts for imidazole-containing small molecules.
Collapse
Affiliation(s)
- Xi-Wei Chen
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Zhiyong Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Shaobo Dai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Yi Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| |
Collapse
|
8
|
Richter D, Piel J. Novel types of RiPP-modifying enzymes. Curr Opin Chem Biol 2024; 80:102463. [PMID: 38729090 DOI: 10.1016/j.cbpa.2024.102463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 05/12/2024]
Abstract
Novel discoveries in natural product biosynthesis reveal hidden bioactive compounds and expand our knowledge in enzymology. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a rapidly growing class of natural products featuring diverse non-canonical amino acids introduced by maturation enzymes as a class-defining characteristic. Underexplored RiPP sources, such as the human microbiome, the oceans, uncultured microorganisms, and plants are rich hunting grounds for novel enzymology. Unusual α- and β-amino acids, peptide cleavages, lipidations, diverse macrocyclizations, and other features expand the range of chemical groups that are installed in RiPPs by often promiscuous enzymes. This review highlights the search for novelty in RiPP enzymology in the past two years, with respect to the discovery of new biochemical modifications but also towards novel applications.
Collapse
Affiliation(s)
- Daniel Richter
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland.
| |
Collapse
|
9
|
Mehjabin JJ, Phan CS, Okino T. Noducyclamides A1-A4, B1, and B2 from the Cyanobacterium Nodularia sp. NIES-3585. JOURNAL OF NATURAL PRODUCTS 2024; 87:984-993. [PMID: 38587271 DOI: 10.1021/acs.jnatprod.3c01272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A chemical investigation of the hydrophilic fraction of a cultured Nodularia sp. (NIES-3585) afforded six new cyclic lipopeptides, noducyclamides A1-A4 (1-4) containing 10 amino acid residues and dodecapeptides noducyclamides B1 and B2 (5 and 6). The planar structures of these lipopeptides were elucidated based on the combination of HRMS and 1D and 2D NMR spectroscopic data analyses. These peptides are structurally analogous to laxaphycins and contain the nonproteinogenic amino acids 3-hydroxyvaline and 3-hydroxyleucine and a β-amino decanoic acid residue. The absolute configurations of the noducyclamides (1-6) were determined by acid hydrolysis, followed by advanced Marfey's analysis. Noducyclamide B1 (5) showed cytotoxic activities against MCF7 breast cancer cell lines with an IC50 value of 3.0 μg/mL (2.2 μM).
Collapse
|
10
|
Harris LA, Saad H, Shelton K, Zhu L, Guo X, Mitchell DA. Tryptophan-Centric Bioinformatics Identifies New Lasso Peptide Modifications. Biochemistry 2024; 63:865-879. [PMID: 38498885 PMCID: PMC11197979 DOI: 10.1021/acs.biochem.4c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Lasso peptides are a class of ribosomally synthesized and post-translationally modified peptides (RiPPs) defined by a macrolactam linkage between the N-terminus and the side chain of an internal aspartic acid or glutamic acid residue. Instead of adopting a branched-cyclic conformation, lasso peptides are "threaded", with the C-terminal tail passing through the macrocycle to present a kinetically trapped rotaxane conformation. The availability of enhanced bioinformatics methods has led to a significant increase in the number of secondary modifications found on lasso peptides. To uncover new ancillary modifications in a targeted manner, a bioinformatic strategy was developed to discover lasso peptides with modifications to tryptophan. This effort identified numerous putative lasso peptide biosynthetic gene clusters with core regions of the precursor peptides enriched in tryptophan. Parsing of these tryptophan (Trp)-rich biosynthetic gene clusters uncovered several putative ancillary modifying enzymes, including halogenases and dimethylallyltransferases expected to act upon Trp. Characterization of two gene products yielded a lasso peptide with two 5-Cl-Trp modifications (chlorolassin) and another bearing 5-dimethylallyl-Trp and 2,3-didehydro-Tyr modifications (wygwalassin). Bioinformatic analysis of the requisite halogenase and dimethylallyltransferase revealed numerous other putative Trp-modified lasso peptides that remain uncharacterized. We anticipate that the Trp-centric strategy reported herein may be useful in discovering ancillary modifications for other RiPP classes and, more generally, guide the functional prediction of enzymes that act on specific amino acids.
Collapse
Affiliation(s)
- Lonnie A. Harris
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Hamada Saad
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kyle Shelton
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Lingyang Zhu
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Xiaorui Guo
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Douglas A. Mitchell
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| |
Collapse
|
11
|
Miyata A, Ito S, Fujinami D. Structure Prediction and Genome Mining-Aided Discovery of the Bacterial C-Terminal Tryptophan Prenyltransferase PalQ. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307372. [PMID: 38059776 PMCID: PMC10853753 DOI: 10.1002/advs.202307372] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/13/2023] [Indexed: 12/08/2023]
Abstract
Post-translational prenylations, found in eukaryotic primary metabolites and bacterial secondary metabolites, play crucial roles in biomolecular interactions. Employing genome mining methods combined with AlphaFold2-based predictions of protein interactions, PalQ , a prenyltransferase responsible for the tryptophan prenylation of RiPPs produced by Paenibacillus alvei, is identified. PalQ differs from cyanobactin prenyltransferases because of its evolutionary relationship to isoprene synthases, which enables PalQ to transfer extended prenyl chains to the indole C3 position. This prenylation introduces structural diversity to the tryptophan side chain and also leads to conformational dynamics in the peptide backbone, attributed to the cis/trans isomerization that arises from the formation of a pyrrolidine ring. Additionally, PalQ exhibited pronounced positional selectivity for the C-terminal tryptophan. Such enzymatic characteristics offer a toolkit for peptide therapeutic lipidation.
Collapse
Affiliation(s)
- Azusa Miyata
- Graduate Division of Nutritional and Environmental SciencesUniversity of Shizuoka52‐1 Yada, Suruga‐kuShizuoka422‐8526Japan
| | - Sohei Ito
- Graduate Division of Nutritional and Environmental SciencesUniversity of Shizuoka52‐1 Yada, Suruga‐kuShizuoka422‐8526Japan
| | - Daisuke Fujinami
- Graduate Division of Nutritional and Environmental SciencesUniversity of Shizuoka52‐1 Yada, Suruga‐kuShizuoka422‐8526Japan
| |
Collapse
|
12
|
Zhang Y, Hamada K, Satake M, Sengoku T, Goto Y, Suga H. Switching Prenyl Donor Specificities of Cyanobactin Prenyltransferases. J Am Chem Soc 2023; 145:23893-23898. [PMID: 37877712 DOI: 10.1021/jacs.3c07373] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Prenyltransferases in cyanobactin biosynthesis are of growing interest as peptide alkylation biocatalysts, but their prenylation modes characterized so far have been limited to dimethylallylation (C5) or geranylation (C10). Here we engaged in structure-guided engineering of the prenyl-binding pocket of a His-C2-geranyltransferase LimF to modulate its prenylation mode. Contraction of the pocket by a single mutation led to a His-C2-dimethylallyltransferase. More importantly, pocket expansion by a double mutation successfully repurposed LimF for farnesylation (C15), which is an unprecedented mode in this family. Furthermore, the obtained knowledge of the essential residues to construct the farnesyl-binding pocket has allowed for rational design of a Tyr-O-farnesyltransferase by a triple mutation of a Tyr-O-dimethylallyltransferase PagF. These results provide an approach to manipulate the prenyl specificity of cyanobactin prenyltransferases, broadening the chemical space covered by this class of enzymes and expanding the toolbox of peptide alkylation biocatalysts.
Collapse
Affiliation(s)
- Yuchen Zhang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama 236-0004, Japan
| | - Masayuki Satake
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Toru Sengoku
- Department of Biochemistry, Graduate School of Medicine, Yokohama City University, Yokohama 236-0004, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| |
Collapse
|
13
|
Ortiz-López FJ, Oves-Costales D, Carretero-Molina D, Martín J, Díaz C, de la Cruz M, Román-Hurtado F, Álvarez-Arévalo M, Jørgensen TS, Reyes F, Weber T, Genilloud O. Crossiellidines A-F, Unprecedented Pyrazine-Alkylguanidine Metabolites with Broad-Spectrum Antibacterial Activity from Crossiella sp. Org Lett 2023; 25:3502-3507. [PMID: 37162500 DOI: 10.1021/acs.orglett.3c01088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Crosiellidines are intriguing pyrazine-alkylguanidine metabolites isolated from the minor actinomycete genus Crossiella. Their structures present an unprecedented 2-methoxy-3,5,6-trialkyl pyrazine scaffold and uncommon guanidine prenylations, including an exotic O-prenylated N-hydroxyguanidine moiety. The novel substitution pattern of the 2-methoxypyrazine core inaugurates a new class of naturally occurring pyrazine compounds, the biosynthetic implications of which are discussed herein. Isotopic feeding and genome analysis allowed us to propose a biosynthetic pathway from arginine. The crossiellidines exhibited remarkable, broad-spectrum antibacterial activity.
Collapse
Affiliation(s)
- Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Daniel Carretero-Molina
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Caridad Díaz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Fernando Román-Hurtado
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - María Álvarez-Arévalo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, Denmark
| | - Tue Sparholt Jørgensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, Denmark
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, Denmark
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, Parque Tecnológico Ciencias de la Salud, 18016 Armilla, Granada, Spain
| |
Collapse
|
14
|
Colombano A, Dalponte L, Dall'Angelo S, Clemente C, Idress M, Ghazal A, Houssen WE. Chemoenzymatic Late-Stage Modifications Enable Downstream Click-Mediated Fluorescent Tagging of Peptides. Angew Chem Int Ed Engl 2023; 62:e202215979. [PMID: 36815722 PMCID: PMC10946513 DOI: 10.1002/anie.202215979] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 02/24/2023]
Abstract
Aromatic prenyltransferases from cyanobactin biosynthetic pathways catalyse the chemoselective and regioselective intramolecular transfer of prenyl/geranyl groups from isoprene donors to an electron-rich position in these macrocyclic and linear peptides. These enzymes often demonstrate relaxed substrate specificity and are considered useful biocatalysts for structural diversification of peptides. Herein, we assess the isoprene donor specificity of the N1-tryptophan prenyltransferase AcyF from the anacyclamide A8P pathway using a library of 22 synthetic alkyl pyrophosphate analogues, of which many display reactive groups that are amenable to additional functionalization. We further used AcyF to introduce a reactive moiety into a tryptophan-containing cyclic peptide and subsequently used click chemistry to fluorescently label the enzymatically modified peptide. This chemoenzymatic strategy allows late-stage modification of peptides and is useful for many applications.
Collapse
Affiliation(s)
- Alessandro Colombano
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Luca Dalponte
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - Sergio Dall'Angelo
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Claudia Clemente
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
| | - Mohannad Idress
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
- Abzena, Babraham Research CampusCambridgeUK
| | - Ahmad Ghazal
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| | - Wael E. Houssen
- Institute of Medical SciencesUniversity of Aberdeen Ashgrove Road WestAberdeenAB25 2ZDUK
- Department of ChemistryUniversity of AberdeenAberdeenAB24 3UEUK
| |
Collapse
|
15
|
Zhang Y, Goto Y, Suga H. Discovery, biochemical characterization, and bioengineering of cyanobactin prenyltransferases. Trends Biochem Sci 2023; 48:360-374. [PMID: 36564250 DOI: 10.1016/j.tibs.2022.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
Prenylation is a post-translational modification (PTM) widely found in primary and secondary metabolism. This modification can enhance the lipophilicity of molecules, enabling them to interact with lipid membranes more effectively. The prenylation of peptides is often carried out by cyanobactin prenyltransferases (PTases) from cyanobacteria. These enzymes are of interest due to their ability to add prenyl groups to unmodified peptides, thus making them more effective therapeutics through the subsequent acquisition of increased membrane permeability and bioavailability. Herein we review the current knowledge of cyanobactin PTases, focusing on their discovery, biochemistry, and bioengineering, and highlight the potential application of them as peptide alkylation biocatalysts to generate peptide therapeutics.
Collapse
Affiliation(s)
- Yuchen Zhang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan.
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan.
| |
Collapse
|
16
|
Albitz K, Csókás D, Dobi Z, Pápai I, Soós T. Late-Stage Formal Double C-H Oxidation of Prenylated Molecules to Alkylidene Oxetanes and Azetidines by Strain-Enabled Cross-Metathesis. Angew Chem Int Ed Engl 2023; 62:e202216879. [PMID: 36629402 DOI: 10.1002/anie.202216879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/12/2023]
Abstract
Prenylation is a ubiquitous late-stage modification in nature that often confers significantly improved bioactivity for secondary metabolites. While this lipophilic modification renders enhanced potency, the lipophilic tag(s) can diminish bioavailability and adversely alter drug transportation and metabolism. Thus, a functional-group-tolerant, mild, and selective late-stage C-H functionalization of prenyl tags would present a great potential in drug discovery programs but could also impact other fields, such as agrochemistry and chemical biology. Herein we report an exocyclic-strain-driven cross-metathesis reaction of prenyl tags, a formal double C-H oxidation protocol, that can be used for the selective late-stage derivatization of prenylated compounds and natural products. This methodology avoids the need for prefunctionalization of target molecules and affords ready access to an unprecedented library of oxo- and aza-prenylated complex molecules. Thus, in a broader context, this methodology extends late-stage functionalization beyond that available to nature.
Collapse
Affiliation(s)
- Krisztián Albitz
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, 1117, Budapest, Hungary.,Hevesy György PhD School of Chemistry, Eötvös Loránd University, 1/A Pázmány Péter sétány, 1117, Budapest, Hungary
| | - Dániel Csókás
- Theoretical Chemistry Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, 1117, Budapest, Hungary
| | - Zoltán Dobi
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, 1117, Budapest, Hungary
| | - Imre Pápai
- Theoretical Chemistry Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, 1117, Budapest, Hungary
| | - Tibor Soós
- Organocatalysis Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, 1117, Budapest, Hungary
| |
Collapse
|
17
|
Mordhorst S, Ruijne F, Vagstad AL, Kuipers OP, Piel J. Emulating nonribosomal peptides with ribosomal biosynthetic strategies. RSC Chem Biol 2023; 4:7-36. [PMID: 36685251 PMCID: PMC9811515 DOI: 10.1039/d2cb00169a] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Peptide natural products are important lead structures for human drugs and many nonribosomal peptides possess antibiotic activity. This makes them interesting targets for engineering approaches to generate peptide analogues with, for example, increased bioactivities. Nonribosomal peptides are produced by huge mega-enzyme complexes in an assembly-line like manner, and hence, these biosynthetic pathways are challenging to engineer. In the past decade, more and more structural features thought to be unique to nonribosomal peptides were found in ribosomally synthesised and posttranslationally modified peptides as well. These streamlined ribosomal pathways with modifying enzymes that are often promiscuous and with gene-encoded precursor proteins that can be modified easily, offer several advantages to produce designer peptides. This review aims to provide an overview of recent progress in this emerging research area by comparing structural features common to both nonribosomal and ribosomally synthesised and posttranslationally modified peptides in the first part and highlighting synthetic biology strategies for emulating nonribosomal peptides by ribosomal pathway engineering in the second part.
Collapse
Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Fleur Ruijne
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Nijenborgh 7, 9747 AG Groningen The Netherlands
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| |
Collapse
|
18
|
Phan CS, Mehjabin JJ, Anas ARJ, Hayasaka M, Onoki R, Wang J, Umezawa T, Washio K, Morikawa M, Okino T. Nostosin G and Spiroidesin B from the Cyanobacterium Dolichospermum sp. NIES-1697. JOURNAL OF NATURAL PRODUCTS 2022; 85:2000-2005. [PMID: 35948062 DOI: 10.1021/acs.jnatprod.2c00382] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chemical investigation of the cyanobacterium Dolichospermum sp. NIES-1697 afforded nostosin G (1), a linear tripeptide, spiroidesin B (2), and two known compounds, anabaenopeptins I (3) and J (4). Planar structures and absolute configurations for 1 and 2 were determined by 2D NMR, HRMS, Marfey's methodology, chiral-phase HPLC, and enzymatic degradation. Nostosin G (1) is a unique example of a linear peptide containing three subunits, 4-hydroxyphenyllactic acid (Hpla), homotyrosine (Hty), and argininal, with potent trypsin inhibitory properties. The biosynthetic gene clusters for nostosin G (1) and spiroidesin B (2) were investigated based on the genome sequence of Dolichospermum sp. NIES-1697.
Collapse
|
19
|
LimF is a versatile prenyltransferase for histidine-C-geranylation on diverse non-natural substrates. Nat Catal 2022. [DOI: 10.1038/s41929-022-00822-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
20
|
Sun C, Tian W, Lin Z, Qu X. Biosynthesis of pyrroloindoline-containing natural products. Nat Prod Rep 2022; 39:1721-1765. [PMID: 35762180 DOI: 10.1039/d2np00030j] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to 2022Pyrroloindoline is a privileged tricyclic indoline motif widely present in many biologically active and medicinally valuable natural products. Thus, understanding the biosynthesis of this molecule is critical for developing convenient synthetic routes, which is highly challenging for its chemical synthesis due to the presence of rich chiral centers in this molecule, especially the fully substituted chiral carbon center at the C3-position of its rigid tricyclic structure. In recent years, progress has been made in elucidating the biosynthetic pathways and enzymatic mechanisms of pyrroloindoline-containing natural products (PiNPs). This article reviews the main advances in the past few decades based on the different substitutions on the C3 position of PiNPs, especially the various key enzymatic mechanisms involved in the biosynthesis of different types of PiNPs.
Collapse
Affiliation(s)
- Chenghai Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Wenya Tian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhi Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xudong Qu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. .,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
21
|
Abstract
Biologically active peptides are a major growing class of drugs, but their therapeutic potential is constrained by several limitations including bioavailability and poor pharmacokinetics. The attachment of functional groups like lipids has proven to be a robust and effective strategy for improving their therapeutic potential. Biochemical and bioactivity-guided screening efforts have identified the cyanobactins as a large class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that are modified with lipids. These lipids are attached by the F superfamily of peptide prenyltransferase enzymes that utilize 5-carbon (prenylation) or 10-carbon (geranylation) donors. The chemical structures of various cyanobactins initially showed isoprenoid attachments on Ser, Thr, or Tyr. Biochemical characterization of the F prenyltransferases from the corresponding clusters shows that the different enzymes have different acceptor residue specificities but are otherwise remarkably sequence tolerant. Hence, these enzymes are well suited for biotechnological applications. The crystal structure of the Tyr O-prenyltransferase PagF reveals that the F enzyme shares a domain architecture reminiscent of a canonical ABBA prenyltransferase fold but lacks secondary structural elements necessary to form an enclosed active site. Binding of either cyclic or linear peptides is sufficient to close the active site to allow for productive catalysis, explaining why these enzymes cannot use isolated amino acids as substrates.Almost all characterized isoprenylated cyanobactins are modified with 5-carbon isoprenoids. However, chemical characterization demonstrates that the piricyclamides are modified with a 10-carbon geranyl moiety, and in vitro reconstitution of the corresponding PirF shows that the enzyme is a geranyltransferase. Structural analysis of PirF shows an active site nearly identical with that of the PagF prenyltransferase but with a single amino acid substitution. Of note, mutation at this residue in PagF or PirF can completely switch the isoprenoid donor specificity of these enzymes. Recent efforts have resulted in significant expansion of the F family with enzymes identified that can carry out C-prenylations of Trp, N-prenylations of Trp, and bis-N-prenylations of Arg. Additional genome-guided efforts based on the sequence of F enzymes identify linear cyanobactins that are α-N-prenylated and α-C-methylated by a bifunctional prenyltransferase/methyltransferase fusion and a bis-α-N- and α-C-prenylated linear peptide. The discovery of these different classes of prenyltransferases with diverse acceptor residue specificities expands the biosynthetic toolkit for enzymatic prenylation of peptide substrates.In this Account, we review the current knowledge scope of the F family of peptide prenyltransferases, focusing on the biochemical, structure-function, and chemical characterization studies that have been carried out in our laboratories. These enzymes are easily amenable for diversity-oriented synthetic efforts as they can accommodate substrate peptides of diverse sequences and are thus attractive catalysts for use in synthetic biology approaches to generate high-value peptidic therapeutics.
Collapse
Affiliation(s)
- Yiwu Zheng
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ying Cong
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Satish K. Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
22
|
Zhang SS, Xiong J, Cui JJ, Ma KL, Wu WL, Li Y, Luo S, Gao K, Dong SH. Lanthipeptides from the Same Core Sequence: Characterization of a Class II Lanthipeptide Synthetase from Microcystis aeruginosa NIES-88. Org Lett 2022; 24:2226-2231. [PMID: 35293207 DOI: 10.1021/acs.orglett.2c00573] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Class II lanthipeptide synthetases (LanMs) are relatively promiscuous to core peptide variations. Previous studies have shown that different LanMs catalyze identical reactions on the same core sequence fused to their respective cognate leaders. We characterized a new LanM enzyme from Microcystis aeruginosa NIES-88, MalM, and demonstrated that MalM and ProcM exhibited disparate dehydration and cyclization patterns on identical core peptides. Our study provided new insights into the regioselectivity of LanMs and showcased an appropriate strategy for lanthipeptide structural diversity engineering.
Collapse
Affiliation(s)
- Sha-Sha Zhang
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Jiang Xiong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Jiao-Jiao Cui
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Kai-Liang Ma
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Wen-Liang Wu
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Ya Li
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Shangwen Luo
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Kun Gao
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Shi-Hui Dong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
| |
Collapse
|
23
|
Biological Activity and Stability of Aeruginosamides from Cyanobacteria. Mar Drugs 2022; 20:md20020093. [PMID: 35200623 PMCID: PMC8878463 DOI: 10.3390/md20020093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Aeruginosamides (AEGs) are classified as cyanobactins, ribosomally synthesized peptides with post-translational modifications. They have been identified in cyanobacteria of genera Microcystis, Oscillatoria, and Limnoraphis. In this work, the new data on the in vitro activities of three AEG variants, AEG A, AEG625 and AEG657, and their interactions with metabolic enzymes are reported. Two aeruginosamides, AEG625 and AEG657, decreased the viability of human breast cancer cell line T47D, but neither of the peptides was active against human liver cancer cell line Huh7. AEGs also did not change the expression of MIR92b-3p, but for AEG625, the induction of oxidative stress was observed. In the presence of a liver S9 fraction containing microsomal and cytosolic enzymes, AEG625 and AEG657 showed high stability. In the same assays, quick removal of AEG A was recorded. The peptides had mild activity against three cytochrome P450 enzymes, CYP2C9, CYP2D6 and CYP3A4, but only at the highest concentration used in the study (60 µM). The properties of AEGs, i.e., cytotoxic activity and in vitro interactions with important metabolic enzymes, form a good basis for further studies on their pharmacological potential.
Collapse
|
24
|
Genome-Guided Discovery of the First Myxobacterial Biarylitide Myxarylin Reveals Distinct C-N Biaryl Crosslinking in RiPP Biosynthesis. Molecules 2021; 26:molecules26247483. [PMID: 34946566 PMCID: PMC8708641 DOI: 10.3390/molecules26247483] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022] Open
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a structurally diverse group of natural products. They feature a wide range of intriguing post-translational modifications, as exemplified by the biarylitides. These are a family of cyclic tripeptides found in Planomonospora, carrying a biaryl linkage between two aromatic amino acids. Recent genomic analyses revealed that the minimal biosynthetic prerequisite of biarylitide biosynthesis consists of only one ribosomally synthesized pentapeptide precursor as the substrate and a modifying cytochrome-P450-dependent enzyme. In silico analyses revealed that minimal biarylitide RiPP clusters are widespread among natural product producers across phylogenetic borders, including myxobacteria. We report here the genome-guided discovery of the first myxobacterial biarylitide MeYLH, termed Myxarylin, from Pyxidicoccus fallax An d48. Myxarylin was found to be an N-methylated tripeptide that surprisingly exhibits a C–N biaryl crosslink. In contrast to Myxarylin, previously isolated biarylitides are N-acetylated tripeptides that feature a C–C biaryl crosslink. Furthermore, the formation of Myxarylin was confirmed by the heterologous expression of the identified biosynthetic genes in Myxococcus xanthus DK1622. These findings expand the structural and biosynthetic scope of biarylitide-type RiPPs and emphasize the distinct biochemistry found in the myxobacterial realm.
Collapse
|
25
|
Amin DH, Sayed HAE, Elissawy AM, EL-Ghwas DE, Singab ANB. Antimicrobial Profile of Actinomycin D Analogs Secreted by Egyptian Desert Streptomyces sp. DH7. Antibiotics (Basel) 2021; 10:antibiotics10101264. [PMID: 34680844 PMCID: PMC8532959 DOI: 10.3390/antibiotics10101264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/18/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Egyptian deserts are an underexplored ecological niche, especially the Sinai Peninsula. In our recent study, we explored this extreme environment and shed light on the bioactive capabilities of desert Actinobacteria isolated from Sinai. Fifty desert Actinobacteria were isolated from the Sinai desert using mineral salt media, basal media, and starch casein media. The filtrate of Streptomyces sp. DH 7 displayed a high inhibitory effect against multidrug-resistant Staphylococcus aureus (MRSA) strains. The 16S rDNA sequencing confirmed that isolate DH7 belongs to the genus Streptomyces. The NJ phylogenetic tree showed relatedness to the Streptomyces flavofuscus strain NRRL B-2594 and Streptomyces pratensis strain ch24. The minimum inhibitory concentrations against MRSA were 16 and 32 μg/μL. Chemical investigation of the ethyl acetate extract of Streptomyces sp. DH7 led to the isolation and purification of natural products 1-4. Structure elucidation of the purified compounds was performed using detailed spectroscopic analysis including 1 and 2D NMR, and ESI-MS spectrometry. To the best of our knowledge, this is the first report for the isolation of compounds 1-4 from a natural source, while synthetic analogs were previously reported in the literature. Compounds 3-4 were identified as actinomycin D analogues and this is the first report for the production of actinomycin D analogs from the Sinai desert with an inhibitory effect against MRSA. We indorse further study for this analog that can develop enhanced antimicrobial activities. We confirm that the desert ecosystems in Egypt are rich sources of antibiotic-producing Actinobacteria.
Collapse
Affiliation(s)
- Dina H. Amin
- Department of Microbiology, Faculty of Science, Ain Shams University, Cairo 11566, Egypt;
- Correspondence:
| | - Hayam A. E. Sayed
- Department of Microbiology, Faculty of Science, Ain Shams University, Cairo 11566, Egypt;
| | - Ahmed M. Elissawy
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt; (A.M.E.); (A.N.B.S.)
- Center of Drug Discovery Research and Development, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Dina E. EL-Ghwas
- Pharmaceutical Industries Researches Division, Department of Chemistry of Natural and Microbial Products, National Research Centre, Giza 12622, Egypt;
| | - Abdel Nasser B. Singab
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt; (A.M.E.); (A.N.B.S.)
- Center of Drug Discovery Research and Development, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| |
Collapse
|