1
|
Matsuda K. Macrocyclizing-thioesterases in bacterial non-ribosomal peptide biosynthesis. J Nat Med 2024:10.1007/s11418-024-01841-y. [PMID: 39214926 DOI: 10.1007/s11418-024-01841-y] [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] [Received: 05/30/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
Macrocyclization of peptides reduces conformational flexibilities, potentially leading to improved drug-like properties. However, side reactions such as epimerization and oligomerization often pose synthetic challenges. Peptide-cyclizing biocatalysts in the biosynthesis of non-ribosomal peptides (NRPs) have remarkable potentials as chemoenzymatic tools to facilitate more straightforward access to complex macrocycles. This review highlights the biocatalytic potentials of NRP cyclases, especially those of cis-acting thioesterases, the most general cyclizing machinery in NRP biosynthesis. Growing insights into penicillin-binding protein-type thioesterases, a relatively new group of trans-acting thioesterases, are also summarized.
Collapse
Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo, 060-0812, Japan.
| |
Collapse
|
2
|
Matsuda K, Wakimoto T. Penicillin-binding protein-type thioesterases: An emerging family of non-ribosomal peptide cyclases with biocatalytic potentials. Curr Opin Chem Biol 2024; 80:102465. [PMID: 38759287 DOI: 10.1016/j.cbpa.2024.102465] [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: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024]
Abstract
Macrocyclization of peptides reduces conformational flexibilities, potentially leading to improved drug-like properties, such as target specificities and metabolic stabilities. As chemical methodologies often allow side reactions like epimerization and oligomerization, keen attention has been directed toward enzymatic peptide cyclization using peptide cyclases from specialized metabolic pathways. Penicillin-binding protein-type thioesterases (PBP-type TEs) are a recently identified family of peptide cyclases involved in the biosynthesis of non-ribosomal peptides in actinobacteria. PBP-type TEs have undergone intensive investigation due to their outstanding potential as biocatalysts. This review summarizes the rapidly growing knowledge on PBP-type TEs, with special emphasis on their functions, scopes, and structures, and efforts towards their biocatalytic applications.
Collapse
Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan.
| |
Collapse
|
3
|
Wang H, Yi X, Zhou Z, Yang J, Pei Y, Shi S, Gao C, Tian X, Ju J, Li Q. Metabolic blockade-based genome mining of Streptomyces cacaoi SCSIO 68063: Isolation and identification of BE-18257 and pentaminomycin analogues. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
4
|
Booth TJ, Bozhüyük KAJ, Liston JD, Batey SFD, Lacey E, Wilkinson B. Bifurcation drives the evolution of assembly-line biosynthesis. Nat Commun 2022; 13:3498. [PMID: 35715397 PMCID: PMC9205934 DOI: 10.1038/s41467-022-30950-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 05/18/2022] [Indexed: 11/09/2022] Open
Abstract
Reprogramming biosynthetic assembly-lines is a topic of intense interest. This is unsurprising as the scaffolds of most antibiotics in current clinical use are produced by such pathways. The modular nature of assembly-lines provides a direct relationship between the sequence of enzymatic domains and the chemical structure of the product, but rational reprogramming efforts have been met with limited success. To gain greater insight into the design process, we wanted to examine how Nature creates assembly-lines and searched for biosynthetic pathways that might represent evolutionary transitions. By examining the biosynthesis of the anti-tubercular wollamides, we uncover how whole gene duplication and neofunctionalization can result in pathway bifurcation. We show that, in the case of the wollamide biosynthesis, neofunctionalization is initiated by intragenomic recombination. This pathway bifurcation leads to redundancy, providing the genetic robustness required to enable large structural changes during the evolution of antibiotic structures. Should the new product be non-functional, gene loss can restore the original genotype. However, if the new product confers an advantage, depreciation and eventual loss of the original gene creates a new linear pathway. This provides the blind watchmaker equivalent to the design, build, test cycle of synthetic biology.
Collapse
Affiliation(s)
- Thomas J Booth
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
- School of Molecular Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Kenan A J Bozhüyük
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
| | - Jonathon D Liston
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Sibyl F D Batey
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
| |
Collapse
|
5
|
Cociancich S, Leclère V. Editorial for the Special Issue “Microbial Nonribosomal Synthesis of Secondary Metabolites”. Microorganisms 2022; 10:microorganisms10051064. [PMID: 35630506 PMCID: PMC9146935 DOI: 10.3390/microorganisms10051064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 12/04/2022] Open
Affiliation(s)
- Stéphane Cociancich
- CIRAD, UMR PHIM, F-34398 Montpellier, France
- PHIM, Université Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
- Correspondence:
| | - Valérie Leclère
- Université de Lille, Université de Liège, UMRT 1158 BioEcoAgro, Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, F-59000 Lille, France;
| |
Collapse
|
6
|
Carretero-Molina D, Ortiz-López FJ, Martín J, González I, Sánchez-Hidalgo M, Román-Hurtado F, Díaz C, de la Cruz M, Genilloud O, Reyes F. Pentaminomycins F and G, Nonribosomal Peptides Containing 2-Pyridylalanine. JOURNAL OF NATURAL PRODUCTS 2021; 84:1127-1134. [PMID: 33793225 DOI: 10.1021/acs.jnatprod.0c01199] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pentaminomycins F-H (1-3), a group of three new hydroxyarginine-containing cyclic pentapeptides, were isolated from cultures of a Streptomyces cacaoi subsp. cacaoi strain along with the known pentaminomycins A-E. The structures of the new peptides were determined by a combination of mass spectrometry, NMR, and Marfey's analyses. Pentaminomycins F (1) and G (2) were shown to contain the rare amino acid 3-(2-pyridyl)-alanine. This finding represents the first reported examples of nonribosomal peptides containing this residue. The ldlld chiral sequence found for the three compounds was in agreement with that reported for previously isolated pentaminomycins and consistent with the epimerization domains present in the putative nonribosomal peptide synthetase (NRPS) biosynthetic gene cluster.
Collapse
Affiliation(s)
- Daniel Carretero-Molina
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, 18016 Armilla (Granada), Spain
| | - Francisco Javier Ortiz-López
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, 18016 Armilla (Granada), Spain
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, 18016 Armilla (Granada), Spain
| | - Ignacio González
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, 18016 Armilla (Granada), Spain
| | - Marina Sánchez-Hidalgo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, 18016 Armilla (Granada), Spain
| | - Fernando Román-Hurtado
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, 18016 Armilla (Granada), Spain
| | - Caridad Díaz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, 18016 Armilla (Granada), Spain
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, 18016 Armilla (Granada), Spain
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, 18016 Armilla (Granada), Spain
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento 34, 18016 Armilla (Granada), Spain
| |
Collapse
|
7
|
Matsuda K, Fujita K, Wakimoto T. PenA, a penicillin-binding protein-type thioesterase specialized for small peptide cyclization. J Ind Microbiol Biotechnol 2021; 48:6169712. [PMID: 33713128 PMCID: PMC9113502 DOI: 10.1093/jimb/kuab023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/19/2021] [Indexed: 12/31/2022]
Abstract
Penicillin-binding protein-type thioesterases (PBP-type TEs) are a recently identified group of peptide cyclases that catalyze head-to-tail macrolactamization of nonribosomal peptides. PenA, a new member of this group, is involved in the biosyntheses of cyclic pentapeptides. In this study, we demonstrated the enzymatic activity of PenA in vitro, and analyzed its substrate scope with a series of synthetic substrates. A comparison of the reaction profiles between PenA and SurE, a representative PBP-type TE, showed that PenA is more specialized for small peptide cyclization. A computational model provided a possible structural rationale for the altered specificity for substrate chain lengths.
Collapse
Affiliation(s)
- Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Kei Fujita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12, Nishi 6, Kita-ku, Sapporo 060-0812, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Kita 12, Nishi 6, Sapporo 060-0812, Japan
| |
Collapse
|