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
|
Miles CO, McCarron P, Thomas K, Al-Sinawi B, Liu T, Neilan BA. Microcystins with Modified Adda 5-Residues from a Heterologous Microcystin Expression System. ACS OMEGA 2024; 9:27618-27631. [PMID: 38947807 PMCID: PMC11209926 DOI: 10.1021/acsomega.4c03332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024]
Abstract
Microcystins are hepatotoxic cyclic heptapeptides produced by some cyanobacterial species and usually contain the unusual β-amino acid 3S-amino-9S-methoxy-2S,6,8S-trimethyl-10-phenyl-4E,6E-decadienoic acid (Adda) at position-5. The full microcystin gene cluster from Microcystis aeruginosa PCC 7806 has been expressed in Escherichia coli. In an earlier study, the engineered strain was shown to produce MC-LR and [d-Asp3]MC-LR, the main microcystins reported in cultures of M. aeruginosa PCC 7806. However, analysis of the engineered strain of E. coli using semitargeted liquid chromatography with high-resolution tandem mass spectrometry (LC-HRMS/MS) and thiol derivatization revealed the presence of 15 additional microcystin analogues, including four linear peptide variants and, in total, 12 variants with modifications to the Adda moiety. Four of the Adda-variants lacked the phenyl group at the Adda-terminus, a modification that has not previously been reported in cyanobacteria. Their HRMS/MS spectra contained the product-ion from Adda at m/z 135.1168, but the commonly observed product-ion at m/z 135.0804 from Adda-containing microcystins was almost completely absent. In contrast, three of the variants were missing a methyl group between C-2 and C-8 of the Adda moiety, and their LC-HRMS/MS spectra displayed the product-ion from Adda at m/z 135.0804. However, instead of the product-ion at m/z 135.1168, these three variants gave product-ions at m/z 121.1011. These observations, together with spectra from microcystin standards using in-source fragmentation, showed that the product-ion at m/z 135.1168 found in the HRMS/MS spectra of most microcystins originated from the C-2 to C-8 region of the Adda moiety. Identification of the fragmentation pathways for the Adda side chain will facilitate the detection of microcystins containing modifications in their Adda moieties that could otherwise easily be overlooked with standard LC-MS screening methods. Microcystin variants containing Abu at position-1 were also prominent components of the microcystin profile of the engineered bacterium. Microcystin variants with Abu1 or without the phenyl group on the Adda side chain were not detected in the original host cyanobacterium. This suggests not only that the microcystin synthase complex may be affected by substrate availability within its host organism but also that it possesses an unexpected degree of biosynthetic flexibility.
Collapse
Affiliation(s)
- Christopher O. Miles
- Biotoxin
Metrology, National Research Council Canada, Halifax, Nova Scotia B3H 3Z1, Canada
- Norwegian
Veterinary Institute, Postboks 64, 1431 Ås, Norway
| | - Pearse McCarron
- Biotoxin
Metrology, National Research Council Canada, Halifax, Nova Scotia B3H 3Z1, Canada
| | - Krista Thomas
- Biotoxin
Metrology, National Research Council Canada, Halifax, Nova Scotia B3H 3Z1, Canada
| | - Bakir Al-Sinawi
- Diagnostic
Technology Pty. Ltd., Sydney 2085, NSW, Australia
- School
of Environmental and Life Sciences, The
University of Newcastle, Callaghan 2308, NSW, Australia
| | - Tianzhe Liu
- Diagnostic
Technology Pty. Ltd., Sydney 2085, NSW, Australia
- Department
of Chemistry and Food Chemistry, Technical
University of Dresden, 01069 Dresden, Germany
| | - Brett A. Neilan
- School
of Environmental and Life Sciences, The
University of Newcastle, Callaghan 2308, NSW, Australia
- ARC Centre
of Excellence in Synthetic Biology, Sydney, NSW 2019, Australia
| |
Collapse
|
3
|
Kobayashi M, Fujita K, Matsuda K, Wakimoto T. Chemo-Enzymatic Synthesis of Non-ribosomal Macrolactams by a Penicillin-Binding Protein-Type Thioesterase. Methods Mol Biol 2023; 2670:127-144. [PMID: 37184702 DOI: 10.1007/978-1-0716-3214-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Penicillin-binding protein-type thioesterases (PBP-type TEs) are an emerging family of non-ribosomal peptide cyclases. PBP-type TEs exhibit distinct substrate scopes from the well-exploited ribosomal peptide cyclases and traditional non-ribosomal peptide cyclases. Their unique properties, as well as their stand-alone nature, highlight PBP-type TEs as valuable candidates for development as biocatalysts for peptide macrocyclization. Here in this chapter, we describe the scheme for the chemoenzymatic synthesis of non-ribosomal macrolactam by SurE, a representative member of PBP-type TEs.
Collapse
Affiliation(s)
| | - Kei Fujita
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Kenichi Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan.
| | - Toshiyuki Wakimoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan.
| |
Collapse
|
4
|
Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
Collapse
Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| |
Collapse
|
5
|
Adrover-Castellano ML, Schmidt JJ, Sherman DH. Biosynthetic Cyclization Catalysts for the Assembly of Peptide and Polyketide Natural Products. ChemCatChem 2021; 13:2095-2116. [PMID: 34335987 PMCID: PMC8320681 DOI: 10.1002/cctc.202001886] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 12/13/2022]
Abstract
Many biologically active natural products are synthesized by nonribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and their hybrids. These megasynthetases contain modules possessing distinct catalytic domains that allow for substrate initiation, chain extension, processing and termination. At the end of a module, a terminal domain, usually a thioesterase (TE), is responsible for catalyzing the release of the NRPS or PKS as a linear or cyclized product. In this review, we address the general cyclization mechanism of the TE domain, including oligomerization and the fungal C-C bond forming Claisen-like cyclases (CLCs). Additionally, we include examples of cyclization catalysts acting within or at the end of a module. Furthermore, condensation-like (CT) domains, terminal reductase (R) domains, reductase-like domains that catalyze Dieckmann condensation (RD), thioesterase-like Dieckmann cyclases, trans-acting TEs from the penicillin binding protein (PBP) enzyme family, product template (PT) domains and others will also be reviewed. The studies summarized here highlight the remarkable diversity of NRPS and PKS cyclization catalysts for the production of biologically relevant, complex cyclic natural products and related compounds.
Collapse
Affiliation(s)
| | - Jennifer J Schmidt
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
| | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
| |
Collapse
|