51
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Alonzo DA, Schmeing TM. Biosynthesis of depsipeptides, or Depsi: The peptides with varied generations. Protein Sci 2020; 29:2316-2347. [PMID: 33073901 DOI: 10.1002/pro.3979] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022]
Abstract
Depsipeptides are compounds that contain both ester bonds and amide bonds. Important natural product depsipeptides include the piscicide antimycin, the K+ ionophores cereulide and valinomycin, the anticancer agent cryptophycin, and the antimicrobial kutzneride. Furthermore, database searches return hundreds of uncharacterized systems likely to produce novel depsipeptides. These compounds are made by specialized nonribosomal peptide synthetases (NRPSs). NRPSs are biosynthetic megaenzymes that use a module architecture and multi-step catalytic cycle to assemble monomer substrates into peptides, or in the case of specialized depsipeptide synthetases, depsipeptides. Two NRPS domains, the condensation domain and the thioesterase domain, catalyze ester bond formation, and ester bonds are introduced into depsipeptides in several different ways. The two most common occur during cyclization, in a reaction between a hydroxy-containing side chain and the C-terminal amino acid residue in a peptide intermediate, and during incorporation into the growing peptide chain of an α-hydroxy acyl moiety, recruited either by direct selection of an α-hydroxy acid substrate or by selection of an α-keto acid substrate that is reduced in situ. In this article, we discuss how and when these esters are introduced during depsipeptide synthesis, survey notable depsipeptide synthetases, and review insight into bacterial depsipeptide synthetases recently gained from structural studies.
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Affiliation(s)
- Diego A Alonzo
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
| | - T Martin Schmeing
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
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52
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Xu M, Wang W, Waglechner N, Culp EJ, Guitor AK, Wright GD. GPAHex-A synthetic biology platform for Type IV-V glycopeptide antibiotic production and discovery. Nat Commun 2020; 11:5232. [PMID: 33067466 PMCID: PMC7567792 DOI: 10.1038/s41467-020-19138-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/23/2020] [Indexed: 11/09/2022] Open
Abstract
Glycopeptide antibiotics (GPAs) are essential for the treatment of severe infectious diseases caused by Gram-positive bacteria. The emergence and spread of GPA resistance have propelled the search for more effective GPAs. Given their structural complexity, genetic intractability, and low titer, expansion of GPA chemical diversity using synthetic or medicinal chemistry remains challenging. Here we describe a synthetic biology platform, GPAHex (GPA Heterologous expression), which exploits the genes required for the specialized GPA building blocks, regulation, antibiotic transport, and resistance for the heterologous production of GPAs. Application of the GPAHex platform results in: (1) a 19-fold increase of corbomycin titer compared to the parental strain, (2) the discovery of a teicoplanin-class GPA from an Amycolatopsis isolate, and (3) the overproduction and characterization of a cryptic nonapeptide GPA. GPAHex provides a platform for GPA production and mining of uncharacterized GPAs and provides a blueprint for chassis design for other natural product classes. Expansion of the chemical diversity of glycopeptide antibiotics (GPAs) to deal with the emergence and spread of GPA resistance is challenging. Here, the authors report a GPA synthetic biology platform in Streptomyces coelicolor for Type IV–V glycopeptide antibiotic production and discovery.
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Affiliation(s)
- Min Xu
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Wenliang Wang
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Nicholas Waglechner
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Elizabeth J Culp
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Allison K Guitor
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Gerard D Wright
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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53
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Characterization of inthomycin biosynthetic gene cluster revealing new insights into carboxamide formation. Chin J Nat Med 2020; 18:677-683. [PMID: 32928511 DOI: 10.1016/s1875-5364(20)60006-1] [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: 04/25/2020] [Indexed: 11/20/2022]
Abstract
Inthomycins are polyketide antibiotics which contain a terminal carboxamide group and a triene chain. Inthomycin B (1) and its two new analogues 2 and 3 were isolated from the crude extract of Streptomyces pactum L8. Identification of the gene cluster for inthomycin biosynthesis as well as the 15N-labeled glycine incorporation into inthomycins are described. Combined with the gene deletion of the rare P450 domain in the NRPS module, a formation mechanism of carboxamide moiety in inthomycins was proposed via an oxidative release of the assembly chain assisted by the P450 domain.
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54
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Zhao Y, Ho YTC, Tailhades J, Cryle M. Understanding the Glycopeptide Antibiotic Crosslinking Cascade: In Vitro Approaches Reveal the Details of a Complex Biosynthesis Pathway. Chembiochem 2020; 22:43-51. [PMID: 32696500 DOI: 10.1002/cbic.202000309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/21/2020] [Indexed: 11/06/2022]
Abstract
The glycopeptide antibiotics (GPAs) are a fascinating example of complex natural product biosynthesis, with the nonribosomal synthesis of the peptide core coupled to a cytochrome P450-mediated cyclisation cascade that crosslinks aromatic side chains within this peptide. Given that the challenges associated with the synthesis of GPAs stems from their highly crosslinked structure, there is great interest in understanding how biosynthesis accomplishes this challenging set of transformations. In this regard, the use of in vitro experiments has delivered important insights into this process, including the identification of the unique role of the X-domain as a platform for P450 recruitment. In this minireview, we present an analysis of the results of in vitro studies into the GPA cyclisation cascade that have demonstrated both the tolerances and limitations of this process for modified substrates, and in turn developed rules for the future reengineering of this important antibiotic class.
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Affiliation(s)
- Yongwei Zhao
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Y T Candace Ho
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Max Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
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55
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Kaniusaite M, Goode RJA, Tailhades J, Schittenhelm RB, Cryle MJ. Exploring modular reengineering strategies to redesign the teicoplanin non-ribosomal peptide synthetase. Chem Sci 2020; 11:9443-9458. [PMID: 34094211 PMCID: PMC8162109 DOI: 10.1039/d0sc03483e] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/22/2020] [Indexed: 12/24/2022] Open
Abstract
Non-ribosomal peptide synthesis is an important biosynthesis pathway in secondary metabolism. In this study we have investigated modularisation and redesign strategies for the glycopeptide antibiotic teicoplanin. Using the relocation or exchange of domains within the NRPS modules, we have identified how to initiate peptide biosynthesis and explored the requirements for the functional reengineering of both the condensation/adenylation domain and epimerisation/condensation domain interfaces. We have also demonstrated strategies that ensure communication between isolated NRPS modules, leading to new peptide assembly pathways. This provides important insights into NRPS reengineering of glycopeptide antibiotic biosynthesis and has broad implications for the redesign of other NRPS systems.
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Affiliation(s)
- Milda Kaniusaite
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- EMBL Australia, Monash University Clayton Victoria 3800 Australia
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Monash University Clayton Victoria 3800 Australia
| | - Robert J A Goode
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- Monash Proteomics and Metabolomics Facility, Monash University Clayton Victoria 3800 Australia
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- EMBL Australia, Monash University Clayton Victoria 3800 Australia
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Monash University Clayton Victoria 3800 Australia
| | - Ralf B Schittenhelm
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- Monash Proteomics and Metabolomics Facility, Monash University Clayton Victoria 3800 Australia
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- EMBL Australia, Monash University Clayton Victoria 3800 Australia
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Monash University Clayton Victoria 3800 Australia
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56
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Forneris CC, Nguy AKL, Seyedsayamdost MR. Mapping and Exploiting the Promiscuity of OxyB toward the Biocatalytic Production of Vancomycin Aglycone Variants. ACS Catal 2020; 10:9287-9298. [PMID: 34422446 PMCID: PMC8378672 DOI: 10.1021/acscatal.0c01719] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vancomycin is one of the most important clinical antibiotics in the fight against infectious disease. Its biological activity relies on three aromatic cross-links, which create a cup-shaped topology and allow tight binding to nascent peptidoglycan chains. The cytochrome P450 enzymes OxyB, OxyA, and OxyC have been shown to introduce these synthetically challenging aromatic linkages. The ability to utilize the P450 enzymes in a chemo-enzymatic scheme to generate vancomycin derivatives is appealing but requires a thorough understanding of their reactivities and mechanisms. Herein, we systematically explore the scope of OxyB biocatalysis and report installation of diverse diaryl ether and biaryl cross-links with varying macrocycle sizes and compositions, when the enzyme is presented with modified vancomycin precursor peptides. The structures of the resulting products were determined using one-dimensional/two-dimensional nuclear magnetic resonance spectroscopy, high-resolution mass spectrometry (HR-MS), tandem HR-MS, and isotopic labeling, as well as ultraviolet-visible light absorption and fluorescence emission spectroscopies. An exploration of the biological activities of these alternative OxyB products surprisingly revealed antifungal properties. Taking advantage of the promiscuity of OxyB, we chemo-enzymatically generated a vancomycin aglycone variant containing an expanded macrocycle. Mechanistic implications for OxyB and future directions for creating vancomycin analogue libraries are discussed.
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Affiliation(s)
- Clarissa C Forneris
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Andy K L Nguy
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R Seyedsayamdost
- Department of Chemistry and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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57
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Xu ZF, Bo ST, Wang MJ, Shi J, Jiao RH, Sun Y, Xu Q, Tan RX, Ge HM. Discovery and biosynthesis of bosamycins from Streptomyces sp. 120454. Chem Sci 2020; 11:9237-9245. [PMID: 34094195 PMCID: PMC8161544 DOI: 10.1039/d0sc03469j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Nonribosomal peptides (NRPs) that are synthesized by modular megaenzymes known as nonribosomal peptide synthetases (NRPSs) are a rich source for drug discovery. By targeting an unusual NRPS architecture, we discovered an unusual biosynthetic gene cluster (bsm) from Streptomyces sp. 120454 and identified that it was responsible for the biosynthesis of a series of novel linear peptides, bosamycins. The bsm gene cluster contains a unique monomodular NRPS, BsmF, that contains a cytochrome P450 domain at the N-terminal. BsmF (P450 + A + T) can selectively activate tyrosine with its adenylation (A) domain, load it onto the thiolation (T) domain, and then hydroxylate tyrosine to form 5-OH tyrosine with the P450 domain. We demonstrated a NRPS assembly line for the formation of bosamycins by genetic and biochemical analysis and heterologous expression. Our work reveals a genome mining strategy targeting a unique NRPS domain for the discovery of novel NRPs.
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Affiliation(s)
- Zi Fei Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University 210023 P. R. China
| | - Sheng Tao Bo
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University 210023 P. R. China
| | - Mei Jing Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University 210023 P. R. China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University 210023 P. R. China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University 210023 P. R. China
| | - Yang Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University 210023 P. R. China .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University Nanjing 210023 P. R. China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University 210023 P. R. China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University 210023 P. R. China .,State Key Laboratory Cultivation Base for TCM Quality and Efficacy, Nanjing University of Chinese Medicine Nanjing 210023 P. R. China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University 210023 P. R. China .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University Nanjing 210023 P. R. China
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58
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Kaniusaite M, Tailhades J, Kittilä T, Fage CD, Goode RJA, Schittenhelm RB, Cryle MJ. Understanding the early stages of peptide formation during the biosynthesis of teicoplanin and related glycopeptide antibiotics. FEBS J 2020; 288:507-529. [PMID: 32359003 DOI: 10.1111/febs.15350] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 02/02/2023]
Abstract
The biosynthesis of the glycopeptide antibiotics (GPAs) demonstrates the exceptional ability of nonribosomal peptide (NRP) synthesis to generate diverse and complex structures from an expanded array of amino acid precursors. Whilst the heptapeptide cores of GPAs share a conserved C terminus, including the aromatic residues involved cross-linking and that are essential for the antibiotic activity of GPAs, most structural diversity is found within the N terminus of the peptide. Furthermore, the origin of the (D)-stereochemistry of residue 1 of all GPAs is currently unclear, despite its importance for antibiotic activity. Given these important features, we have now reconstituted modules (M) 1-4 of the NRP synthetase (NRPS) assembly lines that synthesise the clinically relevant type IV GPA teicoplanin and the related compound A40926. Our results show that important roles in amino acid modification during the NRPS-mediated biosynthesis of GPAs can be ascribed to the actions of condensation domains present within these modules, including the incorporation of (D)-amino acids at position 1 of the peptide. Our results also indicate that hybrid NRPS assembly lines can be generated in a facile manner by mixing NRPS proteins from different systems and that uncoupling of peptide formation due to different rates of activity seen for NRPS modules can be controlled by varying the ratio of NRPS modules. Taken together, this indicates that NRPS assembly lines function as dynamic peptide assembly lines and not static megaenzyme complexes, which has significant implications for biosynthetic redesign of these important biosynthetic systems.
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Affiliation(s)
- Milda Kaniusaite
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia.,EMBL Australia, Monash University, Clayton, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia.,EMBL Australia, Monash University, Clayton, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Australia
| | - Tiia Kittilä
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | - Robert J A Goode
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia.,Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Australia
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia.,Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Australia
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia.,EMBL Australia, Monash University, Clayton, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Australia
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59
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Tailhades J, Zhao Y, Ho YTC, Greule A, Ahmed I, Schoppet M, Kulkarni K, Goode RJA, Schittenhelm RB, De Voss JJ, Cryle MJ. A Chemoenzymatic Approach to the Synthesis of Glycopeptide Antibiotic Analogues. Angew Chem Int Ed Engl 2020; 59:10899-10903. [DOI: 10.1002/anie.202003726] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/14/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Julien Tailhades
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Yongwei Zhao
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Y. T. Candace Ho
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Anja Greule
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Iftekhar Ahmed
- School of Chemistry and Molecular Biosciences The University of Queensland St Lucia Queensland 4072 Australia
| | - Melanie Schoppet
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - Rob J. A. Goode
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- Monash Proteomics & Metabolomics Facility Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- Monash Proteomics & Metabolomics Facility Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences The University of Queensland St Lucia Queensland 4072 Australia
| | - Max J. Cryle
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
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60
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Tailhades J, Zhao Y, Ho YTC, Greule A, Ahmed I, Schoppet M, Kulkarni K, Goode RJA, Schittenhelm RB, De Voss JJ, Cryle MJ. A Chemoenzymatic Approach to the Synthesis of Glycopeptide Antibiotic Analogues. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Julien Tailhades
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Yongwei Zhao
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Y. T. Candace Ho
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Anja Greule
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Iftekhar Ahmed
- School of Chemistry and Molecular Biosciences The University of Queensland St Lucia Queensland 4072 Australia
| | - Melanie Schoppet
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - Rob J. A. Goode
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- Monash Proteomics & Metabolomics Facility Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- Monash Proteomics & Metabolomics Facility Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences The University of Queensland St Lucia Queensland 4072 Australia
| | - Max J. Cryle
- Department of Biochemistry and Molecular Biology Monash Biomedicine Discovery Institute Monash University Clayton Victoria 3800 Australia
- EMBL Australia Monash University Clayton Victoria 3800 Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Monash University Clayton Victoria 3800 Australia
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61
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Wang M, Zhou M, Zhang L, Zhang Z, Zhang W. A step-economic and one-pot access to chiral C α-tetrasubstituted α-amino acid derivatives via a bicyclic imidazole-catalyzed direct enantioselective C-acylation. Chem Sci 2020; 11:4801-4807. [PMID: 34122937 PMCID: PMC8159231 DOI: 10.1039/d0sc00808g] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cα-Tetrasubstituted α-amino acids are ubiquitous and unique structural units in bioactive natural products and pharmaceutical compounds. The asymmetric synthesis of these molecules has attracted a lot of attention, but a more efficient method is still greatly desired. Here we describe the first sequential four-step acylation reaction for the efficient synthesis of chiral Cα-tetrasubstituted α-amino acid derivatives from simple N-acylated amino acids via an auto-tandem catalysis using a single nucleophilic catalyst. The synthetic efficiency is improved via a direct enantioselective C-acylation; the methodology affords the corresponding Cα-tetrasubstituted α-amino acid derivatives with excellent enantioselectivities (up to 99% ee). This step-economic, one-pot, and auto-tandem strategy provides facile access to important chiral building blocks, such as peptides, serines, and oxazolines, which are often used in medicinal and synthetic chemistry. The first four-step sequential reaction for the synthesis of Cα-tetrasubstituted chiral α-amino acid derivatives via auto-tandem catalysis has been developed.![]()
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Affiliation(s)
- Mo Wang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University Shanghai 200240 China .,School of Pharmacy, Shanghai Jiao Tong University Shanghai 200240 China
| | - Muxing Zhou
- School of Pharmacy, Shanghai Jiao Tong University Shanghai 200240 China
| | - Lu Zhang
- School of Pharmacy, Shanghai Jiao Tong University Shanghai 200240 China
| | - Zhenfeng Zhang
- School of Pharmacy, Shanghai Jiao Tong University Shanghai 200240 China
| | - Wanbin Zhang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University Shanghai 200240 China .,School of Pharmacy, Shanghai Jiao Tong University Shanghai 200240 China
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62
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Di Nardo G, Gilardi G. Natural Compounds as Pharmaceuticals: The Key Role of Cytochromes P450 Reactivity. Trends Biochem Sci 2020; 45:511-525. [PMID: 32413326 DOI: 10.1016/j.tibs.2020.03.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/28/2020] [Accepted: 03/06/2020] [Indexed: 12/16/2022]
Abstract
The design of drugs from natural products is a re-emerging area due to the need for bioactive compounds. The exploitation of natural products and their derivatives obtained by biocatalysis is in line with the higher attention given today to new sustainable technologies that better preserve the environment (green chemistry). The research field of cytochromes P450 (CYPs) is continuously providing new enzymes and mutants that produce metabolites suitable for late-stage functionalization for new potential drugs. This review provides an overview of the exploitation of CYPs as biocatalysts in drug synthesis. Additionally, recent progress in protein and metabolic engineering is provided to show how these enzymes offer a toolbox that can be combined with other biocatalytic or chemical processes to build new platforms for the green production of new drugs.
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Affiliation(s)
- Giovanna Di Nardo
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Gianfranco Gilardi
- Department of Life Sciences and Systems Biology, University of Torino, Via Accademia Albertina 13, 10123, Torino, Italy.
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Teicoplanin biosynthesis: unraveling the interplay of structural, regulatory, and resistance genes. Appl Microbiol Biotechnol 2020; 104:3279-3291. [PMID: 32076781 DOI: 10.1007/s00253-020-10436-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/26/2020] [Accepted: 02/04/2020] [Indexed: 01/10/2023]
Abstract
Teicoplanin (Tcp) is a clinically relevant glycopeptide antibiotic (GPA) that is produced by the actinobacterium Actinoplanes teichomyceticus. Tcp is a front-line therapy for treating severe infections caused by multidrug-resistant Gram-positive pathogens in adults and infants. In this review, we provide a detailed overview of how Tcp is produced by A. teichomyceticus by describing Tcp biosynthesis, regulation, and resistance. We summarize the knowledge gained from in vivo and in vitro studies to provide an integrated model of teicoplanin biosynthesis. Then, we discuss genetic and nutritional factors that contribute to the regulation of teicoplanin biosynthesis, focusing on those that have been successfully applied for improving teicoplanin production. A current view on teicoplanin self-resistance mechanisms in A. teichomyceticus is given, and we compare the Tcp biosynthetic gene cluster with other glycopeptide gene clusters from actinoplanetes and from unidentified isolates/metagenomics samples. Finally, we provide an outlook for further directions in studying Tcp biosynthesis and regulation.
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64
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Culp EJ, Waglechner N, Wang W, Fiebig-Comyn AA, Hsu YP, Koteva K, Sychantha D, Coombes BK, Van Nieuwenhze MS, Brun YV, Wright GD. Evolution-guided discovery of antibiotics that inhibit peptidoglycan remodelling. Nature 2020; 578:582-587. [DOI: 10.1038/s41586-020-1990-9] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 12/12/2019] [Indexed: 11/09/2022]
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65
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Tan K, Zhou M, Jedrzejczak RP, Wu R, Higuera RA, Borek D, Babnigg G, Joachimiak A. Structures of teixobactin-producing nonribosomal peptide synthetase condensation and adenylation domains. Curr Res Struct Biol 2020; 2:14-24. [PMID: 34235466 PMCID: PMC8244413 DOI: 10.1016/j.crstbi.2020.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 11/28/2022] Open
Abstract
The recently discovered antibiotic teixobactin is produced by uncultured soil bacteria. The antibiotic inhibits cell wall synthesis of Gram-positive bacteria by binding to precursors of cell wall building blocks, and therefore it is thought to be less vulnerable to development of resistance. Teixobactin is synthesized by two nonribosomal peptide synthetases (NRPSs), encoded by txo1 and txo2 genes. Like other NRPSs, the Txo1 and Txo2 synthetases are large, multifunctional, and comprised of several modules. Each module is responsible for catalysis of a distinct step of teixobactin synthesis and contains specific functional units, commonly including a condensation (C) domain, an adenylation (A) domain, and a peptidyl carrier protein (PCP) domain. Here we report the structures of the C-A bidomains of the two L-Ser condensing modules, from Txo1 and Txo2, respectively. In the structure of the C domain of the L-Ser subunit of Txo1, a large conformational change is observed, featuring an outward swing of its N-terminal α-helix. This repositioning, if functionally validated, provides the necessary conformational change for the condensation reaction in C domain, and likely represents a regulatory mechanism. In an Acore subdomain, a well-coordinated Mg2+ cation is observed, which is required in the adenylation reaction. The Mg2+-binding site is defined by a largely conserved amino acid sequence motif and is coordinated by the α-phosphate group of AMP (or ATP) when present, providing some structural evidence for the role of the metal cation in the catalysis of A domain.
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Key Words
- A domain, Adenylation domain
- Acore subdomain, Large N-terminal subdomain of A domain
- Adenylation domain
- Asub subdomain, Small C-terminal subdomain of A domain
- C domain, Condensation domain
- CCterm subdomain, C-terminal subdomain of C domain
- CNterm subdomain, N-terminal subdomain of C domain
- COMA domain, Acceptor communication-mediating domain
- COMD domain, Donor communication-mediating domain
- Condensation domain
- Conformational change
- MES, 2- morpholinoethane sulfonic acid
- Mg2+-binding
- NRPS, Nonribosomal peptide synthetase
- Nonribosomal peptide synthetase
- PCP domain, Peptidyl carrier domain
- RMSD, Root-mean-square deviation
- SAD, Single wavelength diffraction
- SSM, Secondary-structure matching
- Teixobactin
- Txo1
- Txo2
- α-helix regulation
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Affiliation(s)
- Kemin Tan
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, IL 60439, USA
| | - Min Zhou
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
- Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Robert P. Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, IL 60439, USA
| | - Ruiying Wu
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, IL 60439, USA
| | - Raul A. Higuera
- BUILDing SCHOLARS, The University of Texas at El Paso, 500 W. University Ave, El Paso, TX 79968, USA
| | - Dominika Borek
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gyorgy Babnigg
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
- Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637, USA
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave. Lemont, IL 60439, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60367, USA
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66
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Yushchuk O, Andreo-Vidal A, Marcone GL, Bibb M, Marinelli F, Binda E. New Molecular Tools for Regulation and Improvement of A40926 Glycopeptide Antibiotic Production in Nonomuraea gerenzanensis ATCC 39727. Front Microbiol 2020; 11:8. [PMID: 32038594 PMCID: PMC6985074 DOI: 10.3389/fmicb.2020.00008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/06/2020] [Indexed: 12/12/2022] Open
Abstract
Genome sequencing has revealed that Nonomuraea spp. represent a still largely unexplored source of specialized metabolites. Nonomuraea gerenzanensis ATCC 39727 is the most studied representative species since it produces the glycopeptide antibiotic (GPA) A40926 – the precursor of the clinically relevant antibiotic dalbavancin, approved by the FDA in 2014 for the treatment of acute skin infections caused by multi-drug resistant Gram-positive pathogens. The clinical relevance of dalbavancin has prompted increased attention on A40926 biosynthesis and its regulation. In this paper, we investigated how to enhance the genetic toolkit for members of the Nonomuraea genus, which have proved quite recalcitrant to genetic manipulation. By constructing promoter-probe vectors, we tested the activity of 11 promoters (heterologous and native) using the GusA reporter system in N. gerenzanensis and in Nonomuraea coxensis; this latter species is phylogenetically distant from N. gerenzanesis and also possesses the genetic potential to produce A40926 or a very similar GPA. Finally, the strongest constitutive promoter analyzed in this study, aac(3)IVp, was used to overexpress the cluster-situated regulatory genes controlling A40926 biosynthesis (dbv3 and dbv4 from N. gerenzanensis and nocRI from N. coxensis) in N. gerenzanensis, and the growth and productivity of the best performing strains were assessed at bioreactor scale using an industrial production medium. Overexpression of positive pathway-specific regulatory genes resulted in a significant increase in the level of A40926 production in N. gerenzanensis, providing a new knowledge-based approach to strain improvement for this valuable glycopeptide antibiotic.
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Affiliation(s)
- Oleksandr Yushchuk
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Andres Andreo-Vidal
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | | | - Mervyn Bibb
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elisa Binda
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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67
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Kaniusaite M, Goode RJA, Schittenhelm RB, Makris TM, Cryle MJ. The Diiron Monooxygenase CmlA from Chloramphenicol Biosynthesis Allows Reconstitution of β-Hydroxylation during Glycopeptide Antibiotic Biosynthesis. ACS Chem Biol 2019; 14:2932-2941. [PMID: 31774267 PMCID: PMC6929969 DOI: 10.1021/acschembio.9b00862] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022]
Abstract
β-Hydroxylation plays an important role in the nonribosomal peptide biosynthesis of many important natural products, including bleomycin, chloramphenicol, and the glycopeptide antibiotics (GPAs). Various oxidative enzymes have been implicated in such a process, with the mechanism of incorporation varying from installation of hydroxyl groups in amino acid precursors prior to adenylation to direct amino acid oxidation during peptide assembly. In this work, we demonstrate the in vitro utility and scope of the unusual nonheme diiron monooxygenase CmlA from chloramphenicol biosynthesis for the β-hydroxylation of a diverse range of carrier protein bound substrates by adapting this enzyme as a non-native trans-acting enzyme within NRPS-mediated GPA biosynthesis. The results from our study show that CmlA has a broad substrate specificity for modified phenylalanine/tyrosine residues as substrates and can be used in a practical strategy to functionally cross complement compatible NRPS biosynthesis pathways in vitro.
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Affiliation(s)
- Milda Kaniusaite
- The
Monash Biomedicine Discovery Institute, Department of Biochemistry
and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL
Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Robert J. A. Goode
- The
Monash Biomedicine Discovery Institute, Department of Biochemistry
and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Monash
Biomedical Proteomics Facility, Monash University, Clayton, Victoria 3800, Australia
| | - Ralf B. Schittenhelm
- The
Monash Biomedicine Discovery Institute, Department of Biochemistry
and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Monash
Biomedical Proteomics Facility, Monash University, Clayton, Victoria 3800, Australia
| | - Thomas M. Makris
- Department
of Chemistry and Biochemistry, University
of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Max J. Cryle
- The
Monash Biomedicine Discovery Institute, Department of Biochemistry
and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL
Australia, Monash University, Clayton, Victoria 3800, Australia
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68
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Zhao Y, Goode RJA, Schittenhelm RB, Tailhades J, Cryle MJ. Exploring the Tetracyclization of Teicoplanin Precursor Peptides through Chemoenzymatic Synthesis. J Org Chem 2019; 85:1537-1547. [DOI: 10.1021/acs.joc.9b02640] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Yongwei Zhao
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Robert J. A. Goode
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria 3800, Australia
| | - Ralf B. Schittenhelm
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria 3800, Australia
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Max J. Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
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69
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DeMars MD, Samora NL, Yang S, Garcia-Borràs M, Sanders JN, Houk KN, Podust LM, Sherman DH. Exploring the molecular basis for substrate specificity in homologous macrolide biosynthetic cytochromes P450. J Biol Chem 2019; 294:15947-15961. [PMID: 31488542 PMCID: PMC6827315 DOI: 10.1074/jbc.ra119.010352] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/30/2019] [Indexed: 11/06/2022] Open
Abstract
Cytochromes P450 (P450s) are nature's catalysts of choice for performing demanding and physiologically vital oxidation reactions. Biochemical characterization of these enzymes over the past decades has provided detailed mechanistic insight and highlighted the diversity of substrates P450s accommodate and the spectrum of oxidative transformations they catalyze. Previously, we discovered that the bacterial P450 MycCI from the mycinamicin biosynthetic pathway in Micromonospora griseorubida possesses an unusually broad substrate scope, whereas the homologous P450 from tylosin-producing Streptomyces fradiae (TylHI) exhibits a high degree of specificity for its native substrate. Here, using biochemical, structural, and computational approaches, we aimed to understand the molecular basis for the disparate reactivity profiles of these two P450s. Turnover and equilibrium binding experiments with substrate analogs revealed that TylHI strictly prefers 16-membered ring macrolides bearing the deoxyamino sugar mycaminose. To help rationalize these results, we solved the X-ray crystal structure of TylHI in complex with its native substrate at 1.99-Å resolution and assayed several site-directed mutants. We also conducted molecular dynamics simulations of TylHI and MycCI and biochemically characterized a third P450 homolog from the chalcomycin biosynthetic pathway in Streptomyces bikiniensis These studies provided a basis for constructing P450 chimeras to gain further insight into the features dictating the differences in reaction profile among these structurally and functionally related enzymes, ultimately unveiling the central roles of key loop regions in influencing substrate binding and turnover. Our work highlights the complex nature of P450/substrate interactions and raises interesting questions regarding the evolution of functional diversity among biosynthetic enzymes.
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Affiliation(s)
- Matthew D DeMars
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
| | - Nathan L Samora
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093
| | - Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Marc Garcia-Borràs
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Larissa M Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, Michigan 48109
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109
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70
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Marschall E, Cryle MJ, Tailhades J. Biological, chemical, and biochemical strategies for modifying glycopeptide antibiotics. J Biol Chem 2019; 294:18769-18783. [PMID: 31672921 DOI: 10.1074/jbc.rev119.006349] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Since the discovery of vancomycin in the 1950s, the glycopeptide antibiotics (GPAs) have been of great interest to the scientific community. These nonribosomally biosynthesized peptides are highly cross-linked, often glycosylated, and inhibit bacterial cell wall assembly by interfering with peptidoglycan synthesis. Interest in glycopeptide antibiotics covers many scientific disciplines, due to their challenging total syntheses, complex biosynthesis pathways, mechanism of action, and high potency. After intense efforts, early enthusiasm has given way to a recognition of the challenges in chemically synthesizing GPAs and of the effort needed to study and modify GPA-producing strains to prepare new GPAs to address the increasing threat of microbial antibiotic resistance. Although the preparation of GPAs, either by modifying the pendant groups such as saccharides or by functionalizing the N- or C-terminal moieties, is readily achievable, the peptide core of these molecules-the GPA aglycone-remains highly challenging to modify. This review aims to present a summary of the results of GPA modification obtained with the three major approaches developed to date: in vivo strain manipulation, total chemical synthesis, and chemoenzymatic synthesis methods.
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Affiliation(s)
- Edward Marschall
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.
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71
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Tailhades J, Zhao Y, Schoppet M, Greule A, Goode RJA, Schittenhelm RB, De Voss JJ, Cryle MJ. Enzymatic Cascade To Evaluate the Tricyclization of Glycopeptide Antibiotic Precursor Peptides as a Prequel to Biosynthetic Redesign. Org Lett 2019; 21:8635-8640. [DOI: 10.1021/acs.orglett.9b03245] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Julien Tailhades
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Yongwei Zhao
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Melanie Schoppet
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Anja Greule
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Robert J. A. Goode
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ralf B. Schittenhelm
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - James J. De Voss
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Max J. Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
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72
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Genomic analysis of siderophore β-hydroxylases reveals divergent stereocontrol and expands the condensation domain family. Proc Natl Acad Sci U S A 2019; 116:19805-19814. [PMID: 31527229 DOI: 10.1073/pnas.1903161116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Genome mining of biosynthetic pathways streamlines discovery of secondary metabolites but can leave ambiguities in the predicted structures, which must be rectified experimentally. Through coupling the reactivity predicted by biosynthetic gene clusters with verified structures, the origin of the β-hydroxyaspartic acid diastereomers in siderophores is reported herein. Two functional subtypes of nonheme Fe(II)/α-ketoglutarate-dependent aspartyl β-hydroxylases are identified in siderophore biosynthetic gene clusters, which differ in genomic organization-existing either as fused domains (IβHAsp) at the carboxyl terminus of a nonribosomal peptide synthetase (NRPS) or as stand-alone enzymes (TβHAsp)-and each directs opposite stereoselectivity of Asp β-hydroxylation. The predictive power of this subtype delineation is confirmed by the stereochemical characterization of β-OHAsp residues in pyoverdine GB-1, delftibactin, histicorrugatin, and cupriachelin. The l-threo (2S, 3S) β-OHAsp residues of alterobactin arise from hydroxylation by the β-hydroxylase domain integrated into NRPS AltH, while l-erythro (2S, 3R) β-OHAsp in delftibactin arises from the stand-alone β-hydroxylase DelD. Cupriachelin contains both l-threo and l-erythro β-OHAsp, consistent with the presence of both types of β-hydroxylases in the biosynthetic gene cluster. A third subtype of nonheme Fe(II)/α-ketoglutarate-dependent enzymes (IβHHis) hydroxylates histidyl residues with l-threo stereospecificity. A previously undescribed, noncanonical member of the NRPS condensation domain superfamily is identified, named the interface domain, which is proposed to position the β-hydroxylase and the NRPS-bound amino acid prior to hydroxylation. Through mapping characterized β-OHAsp diastereomers to the phylogenetic tree of siderophore β-hydroxylases, methods to predict β-OHAsp stereochemistry in silico are realized.
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73
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Tsutsumi H, Katsuyama Y, Ohnishi Y. Formation of 5- or 6-Membered Ring via Nitrene Formation and Addition by a Cytochrome P450 in Benzastatin Biosynthesis. J SYN ORG CHEM JPN 2019. [DOI: 10.5059/yukigoseikyokaishi.77.912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo
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74
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Kaniusaite M, Tailhades J, Marschall EA, Goode RJA, Schittenhelm RB, Cryle MJ. A proof-reading mechanism for non-proteinogenic amino acid incorporation into glycopeptide antibiotics. Chem Sci 2019; 10:9466-9482. [PMID: 32055321 PMCID: PMC6993612 DOI: 10.1039/c9sc03678d] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 08/29/2019] [Indexed: 01/09/2023] Open
Abstract
A complex interplay of non-ribosomal peptide synthetase domains works together with trans-acting enzymes to ensure effective GPA biosynthesis.
Non-ribosomal peptide biosynthesis produces highly diverse natural products through a complex cascade of enzymatic reactions that together function with high selectivity to produce bioactive peptides. The modification of non-ribosomal peptide synthetase (NRPS)-bound amino acids can introduce significant structural diversity into these peptides and has exciting potential for biosynthetic redesign. However, the control mechanisms ensuring selective modification of specific residues during NRPS biosynthesis have previously been unclear. Here, we have characterised the incorporation of the non-proteinogenic amino acid 3-chloro-β-hydroxytyrosine during glycopeptide antibiotic (GPA) biosynthesis. Our results demonstrate that the modification of this residue by trans-acting enzymes is controlled by the selectivity of the upstream condensation domain responsible for peptide synthesis. A proofreading thioesterase works together with this process to ensure that effective peptide biosynthesis proceeds even when the selectivity of key amino acid activation domains within the NRPS is low. Furthermore, the exchange of condensation domains with altered amino acid specificities allows the modification of such residues within NRPS biosynthesis to be controlled, which will doubtless prove important for reengineering of these assembly lines. Taken together, our results indicate the importance of the complex interplay of NRPS domains and trans-acting enzymes to ensure effective GPA biosynthesis, and in doing so reveals a process that is mechanistically comparable to the hydrolytic proofreading function of tRNA synthetases in ribosomal protein synthesis.
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Affiliation(s)
- Milda Kaniusaite
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia
| | - Edward A Marschall
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia
| | - Robert J A Goode
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,Monash Proteomics and Metabolomics Facility , Monash University , Clayton , Victoria 3800 , Australia
| | - Ralf B Schittenhelm
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,Monash Proteomics and Metabolomics Facility , Monash University , Clayton , Victoria 3800 , Australia
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia . .,EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia
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75
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Greule A, Stok JE, De Voss JJ, Cryle MJ. Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism. Nat Prod Rep 2019; 35:757-791. [PMID: 29667657 DOI: 10.1039/c7np00063d] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: 2000 up to 2018 The cytochromes P450 (P450s) are a superfamily of heme-containing monooxygenases that perform diverse catalytic roles in many species, including bacteria. The P450 superfamily is widely known for the hydroxylation of unactivated C-H bonds, but the diversity of reactions that P450s can perform vastly exceeds this undoubtedly impressive chemical transformation. Within bacteria, P450s play important roles in many biosynthetic and biodegradative processes that span a wide range of secondary metabolite pathways and present diverse chemical transformations. In this review, we aim to provide an overview of the range of chemical transformations that P450 enzymes can catalyse within bacterial secondary metabolism, with the intention to provide an important resource to aid in understanding of the potential roles of P450 enzymes within newly identified bacterial biosynthetic pathways.
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Affiliation(s)
- Anja Greule
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Jeanette E Stok
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane 4072, Australia.
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia. and EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.
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76
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Brown AS, Calcott MJ, Owen JG, Ackerley DF. Structural, functional and evolutionary perspectives on effective re-engineering of non-ribosomal peptide synthetase assembly lines. Nat Prod Rep 2019; 35:1210-1228. [PMID: 30069573 DOI: 10.1039/c8np00036k] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to May 2018 Non-ribosomal peptide synthetases (NRPSs) are mega-enzymes that form modular templates to assemble specific peptide products, independent of the ribosome. The autonomous nature of the modules in the template offers prospects for re-engineering NRPS enzymes to generate modified peptide products. Although this has clearly been a primary mechanism of natural product diversification throughout evolution, equivalent strategies have proven challenging to implement in the laboratory. In this review we examine key examples of successful and less-successful re-engineering of NRPS templates to generate novel peptides, with the aim of extracting practical guidelines to inform future efforts. We emphasise the importance of maintaining effective protein-protein interactions in recombinant NRPS templates, and identify strengths and limitations of diverse strategies for achieving different engineering outcomes.
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Affiliation(s)
- Alistair S Brown
- School of Biological Sciences, Victoria University of Wellington, New Zealand.
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77
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Izoré T, Cryle MJ. The many faces and important roles of protein-protein interactions during non-ribosomal peptide synthesis. Nat Prod Rep 2019; 35:1120-1139. [PMID: 30207358 DOI: 10.1039/c8np00038g] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Covering: up to July 2018 Non-ribosomal peptide synthetase (NRPS) machineries are complex, multi-domain proteins that are responsible for the biosynthesis of many important, peptide-derived compounds. By decoupling peptide synthesis from the ribosome, NRPS assembly lines are able to access a significant pool of amino acid monomers for peptide synthesis. This is combined with a modular protein architecture that allows for great variation in stereochemistry, peptide length, cyclisation state and further modifications. The architecture of NRPS assembly lines relies upon a repetitive set of catalytic domains, which are organised into modules responsible for amino acid incorporation. Central to NRPS-mediated biosynthesis is the carrier protein (CP) domain, to which all intermediates following initial monomer activation are bound during peptide synthesis up until the final handover to the thioesterase domain that cleaves the mature peptide from the NRPS. This mechanism makes understanding the protein-protein interactions that occur between different NRPS domains during peptide biosynthesis of crucial importance to understanding overall NRPS function. This endeavour is also highly challenging due to the inherent flexibility and dynamics of NRPS systems. In this review, we present the current state of understanding of the protein-protein interactions that govern NRPS-mediated biosynthesis, with a focus on insights gained from structural studies relating to CP domain interactions within these impressive peptide assembly lines.
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Affiliation(s)
- Thierry Izoré
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
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78
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Gulick AM, Aldrich CC. Trapping interactions between catalytic domains and carrier proteins of modular biosynthetic enzymes with chemical probes. Nat Prod Rep 2019; 35:1156-1184. [PMID: 30046790 DOI: 10.1039/c8np00044a] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to early 2018 The Nonribosomal Peptide Synthetases (NRPSs) and Polyketide Synthases (PKSs) are families of modular enzymes that produce a tremendous diversity of natural products, with antibacterial, antifungal, immunosuppressive, and anticancer activities. Both enzymes utilize a fascinating modular architecture in which the synthetic intermediates are covalently attached to a peptidyl- or acyl-carrier protein that is delivered to catalytic domains for natural product elongation, modification, and termination. An investigation of the structural mechanism therefore requires trapping the often transient interactions between the carrier and catalytic domains. Many novel chemical probes have been produced to enable the structural and functional investigation of multidomain NRPS and PKS structures. This review will describe the design and implementation of the chemical tools that have proven to be useful in biochemical and biophysical studies of these natural product biosynthetic enzymes.
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Affiliation(s)
- Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 955 Main St, Buffalo, NY 14203, USA.
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79
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Greule A, Izoré T, Iftime D, Tailhades J, Schoppet M, Zhao Y, Peschke M, Ahmed I, Kulik A, Adamek M, Goode RJA, Schittenhelm RB, Kaczmarski JA, Jackson CJ, Ziemert N, Krenske EH, De Voss JJ, Stegmann E, Cryle MJ. Kistamicin biosynthesis reveals the biosynthetic requirements for production of highly crosslinked glycopeptide antibiotics. Nat Commun 2019; 10:2613. [PMID: 31197182 PMCID: PMC6565677 DOI: 10.1038/s41467-019-10384-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 05/07/2019] [Indexed: 01/25/2023] Open
Abstract
Kistamicin is a divergent member of the glycopeptide antibiotics, a structurally complex class of important, clinically relevant antibiotics often used as the last resort against resistant bacteria. The extensively crosslinked structure of these antibiotics that is essential for their activity makes their chemical synthesis highly challenging and limits their production to bacterial fermentation. Kistamicin contains three crosslinks, including an unusual 15-membered A-O-B ring, despite the presence of only two Cytochrome P450 Oxy enzymes thought to catalyse formation of such crosslinks within the biosynthetic gene cluster. In this study, we characterise the kistamicin cyclisation pathway, showing that the two Oxy enzymes are responsible for these crosslinks within kistamicin and that they function through interactions with the X-domain, unique to glycopeptide antibiotic biosynthesis. We also show that the kistamicin OxyC enzyme is a promiscuous biocatalyst, able to install multiple crosslinks into peptides containing phenolic amino acids.
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Affiliation(s)
- Anja Greule
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Thierry Izoré
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Dumitrita Iftime
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Melanie Schoppet
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Yongwei Zhao
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Madeleine Peschke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Iftekhar Ahmed
- Department of Chemistry, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Martina Adamek
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Robert J A Goode
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Monash Biomedical Proteomics Facility, Monash University, Clayton, VIC, 3800, Australia
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Monash Biomedical Proteomics Facility, Monash University, Clayton, VIC, 3800, Australia
| | - Joe A Kaczmarski
- Research School of Chemistry, The Australian National University, Acton, ACT, 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, The Australian National University, Acton, ACT, 2601, Australia
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Elizabeth H Krenske
- Department of Chemistry, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - James J De Voss
- Department of Chemistry, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
- German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076, Tübingen, Germany.
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia.
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80
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Santa Maria KC, Chan AN, O'Neill EM, Li B. Targeted Rediscovery and Biosynthesis of the Farnesyl-Transferase Inhibitor Pepticinnamin E. Chembiochem 2019; 20:1387-1393. [PMID: 30694017 PMCID: PMC6750724 DOI: 10.1002/cbic.201900025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Indexed: 11/08/2022]
Abstract
The natural product pepticinnamin E potently inhibits protein farnesyl transferases and has potential applications in treating cancer and malaria. Pepticinnamin E contains a rare N-terminal cinnamoyl moiety as well as several nonproteinogenic amino acids, including the unusual 2-chloro-3-hydroxy-4-methoxy-N-methyl-L-phenylalanine. The biosynthesis of pepticinnamin E has remained uncharacterized because its original producing strain is no longer available. Here we identified a gene cluster (pcm) for this natural product in a new producer, Actinobacteria bacterium OK006, by means of a targeted rediscovery strategy. We demonstrated that the pcm cluster is responsible for the biosynthesis of pepticinnamin E, a nonribosomal peptide/polyketide hybrid. We also characterized a key O-methyltransferase that modifies 3,4-dihydroxy-l-phenylalanine. Our work has identified the gene cluster for pepticinnamins for the first time and sets the stage for elucidating the unique chemistry required for biosynthesis.
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Affiliation(s)
- Kevin C Santa Maria
- Department of Chemistry, University of North Carolina at Chapel Hill, CB#3290, Chapel Hill, NC, 27514, USA
| | - Andrew N Chan
- Department of Chemistry, University of North Carolina at Chapel Hill, CB#3290, Chapel Hill, NC, 27514, USA
| | - Erinn M O'Neill
- Department of Chemistry, University of North Carolina at Chapel Hill, CB#3290, Chapel Hill, NC, 27514, USA
| | - Bo Li
- Department of Chemistry, University of North Carolina at Chapel Hill, CB#3290, Chapel Hill, NC, 27514, USA
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81
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Abstract
Landmark achievements in chemical and structural biology have advanced our understanding of nonribosomal peptide synthetase mechanisms. However, nature's proven ability to re-engineer these enzymes remains difficult to recapitulate synthetically. In a recent issue of Cell Chemical Biology, Meyer et al. (2016) sought to extract new clues from old (evolutionary) evidence.
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Affiliation(s)
- David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6140, New Zealand.
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82
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Abstract
Enzyme-mediated cascade reactions are widespread in biosynthesis. To facilitate comparison with the mechanistic categorizations of cascade reactions by synthetic chemists and delineate the common underlying chemistry, we discuss four types of enzymatic cascade reactions: those involving nucleophilic, electrophilic, pericyclic, and radical reactions. Two subtypes of enzymes that generate radical cascades exist at opposite ends of the oxygen abundance spectrum. Iron-based enzymes use O2 to generate high valent iron-oxo species to homolyze unactivated C-H bonds in substrates to initiate skeletal rearrangements. At anaerobic end, enzymes reversibly cleave S-adenosylmethionine (SAM) to generate the 5'-deoxyadenosyl radical as a powerful oxidant to initiate C-H bond homolysis in bound substrates. The latter enzymes are termed radical SAM enzymes. We categorize the former as "thwarted oxygenases".
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Affiliation(s)
- Christopher T Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H), Stanford University, Stanford, CA, 94305, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
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83
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McErlean M, Overbay J, Van Lanen S. Refining and expanding nonribosomal peptide synthetase function and mechanism. J Ind Microbiol Biotechnol 2019; 46:493-513. [PMID: 30673909 PMCID: PMC6460464 DOI: 10.1007/s10295-018-02130-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/20/2018] [Indexed: 12/14/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are involved in the biosynthesis of numerous peptide and peptide-like natural products that have been exploited in medicine, agriculture, and biotechnology, among other fields. As a consequence, there have been considerable efforts aimed at understanding how NRPSs orchestrate the assembly of these natural products. This review highlights several recent examples that continue to expand upon the fundamental knowledge of NRPS mechanism and includes (1) the discovery of new NRPS substrates and the mechanism by which these sometimes structurally complex substrates are made, (2) the characterization of new NRPS activities and domains that function during the process of peptide assembly, and (3) the various catalytic strategies that are utilized to release the NRPS product. These findings continue to strengthen the predictive power for connecting genes to products, thereby facilitating natural product discovery and development in the Genomics Era.
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Affiliation(s)
- Matt McErlean
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - Jonathan Overbay
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - Steven Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA.
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84
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Affiliation(s)
- Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (CheM-H)Stanford University Stanford CA 94305 USA
| | - Bradley S. Moore
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California, San Diego La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California, San Diego La Jolla CA 92093 USA
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85
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Greule A, Charkoudian LK, Cryle MJ. Studying trans-acting enzymes that target carrier protein-bound amino acids during nonribosomal peptide synthesis. Methods Enzymol 2019; 617:113-154. [PMID: 30784400 DOI: 10.1016/bs.mie.2018.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Nonribosomal peptide biosynthesis is a complex enzymatic assembly responsible for producing a great diversity of bioactive peptide natural products. Due to the recurring arrangement of catalytic domains within these machineries, great interest has been shown in reengineering these pathways to produce novel, designer peptide products. However, in order to realize such ambitions, it is first necessary to develop a comprehensive understanding of the selectivity, mechanisms, and structure of these complex enzymes, which in turn requires significant in vitro experiments. Within nonribosomal biosynthesis, some modifications are performed by enzymatic domains that are not linked to the main nonribosomal peptide synthetase but rather act in trans: these systems offer great potential for redesign, but in turn require detailed study. In this chapter, we present an overview of in vitro experiments that can be used to characterize examples of such trans-interacting enzymes from nonribosomal peptide biosynthesis: Cytochrome P450 monooxygenases and flavin-dependent halogenases.
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Affiliation(s)
- Anja Greule
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; EMBL Australia, Monash University, Clayton, VIC, Australia
| | | | - Max J Cryle
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; EMBL Australia, Monash University, Clayton, VIC, Australia.
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86
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Drosophila melanogaster nonribosomal peptide synthetase Ebony encodes an atypical condensation domain. Proc Natl Acad Sci U S A 2019; 116:2913-2918. [PMID: 30705105 DOI: 10.1073/pnas.1811194116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The protein Ebony from Drosophila melanogaster plays a central role in the regulation of histamine and dopamine in various tissues through condensation of these amines with β-alanine. Ebony is a rare example of a nonribosomal peptide synthetase (NRPS) from a higher eukaryote and contains a C-terminal sequence that does not correspond to any previously characterized NRPS domain. We have structurally characterized this C-terminal domain and have discovered that it adopts the aryl-alkylamine-N-acetyl transferase (AANAT) fold, which is unprecedented in NRPS biology. Through analysis of ligand-bound structures, activity assays, and binding measurements, we have determined how this atypical condensation domain is able to provide selectivity for both the carrier protein-bound amino acid and the amine substrates, a situation that remains unclear for standard condensation domains identified to date from NRPS assembly lines. These results demonstrate that the C terminus of Ebony encodes a eukaryotic example of an alternative type of NRPS condensation domain; they also illustrate how the catalytic components of such assembly lines are significantly more diverse than a minimal set of conserved functional domains.
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87
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Schoppet M, Peschke M, Kirchberg A, Wiebach V, Süssmuth RD, Stegmann E, Cryle MJ. The biosynthetic implications of late-stage condensation domain selectivity during glycopeptide antibiotic biosynthesis. Chem Sci 2019; 10:118-133. [PMID: 30713624 PMCID: PMC6333238 DOI: 10.1039/c8sc03530j] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/10/2018] [Indexed: 01/27/2023] Open
Abstract
Non-ribosomal peptide synthesis is a highly important biosynthetic pathway for the formation of many secondary metabolites of medical relevance. Due to the challenges associated with the chemical synthesis of many of the products of these assembly lines, understanding the activity and selectivity of non-ribosomal peptide synthetase (NRPS) machineries is an essential step towards the redesign of such machineries to produce new bioactive peptides. Whilst the selectivity of the adenylation domains responsible for amino acid activation during NRPS synthesis has been widely studied, the selectivity of the essential peptide bond forming domains - known as condensation domains - is not well understood. Here, we present the results of a combination of in vitro and in vivo investigations into the final condensation domain from the NRPS machinery that produces the glycopeptide antibiotics (GPAs). Our results show that this condensation domain is tolerant for a range of peptide substrates and even those with unnatural stereochemistry of the peptide C-terminus, which is in contrast to the widely ascribed role of these domains as a stereochemical gatekeeper during NRPS synthesis. Furthermore, we show that this condensation domain has a significant preference for linear peptide substrates over crosslinked peptides, which indicates that the GPA crosslinking cascade targets the heptapeptide bound to the final module of the NRPS machinery and reinforces the role of the unique GPA X-domain in this process. Finally, we demonstrate that the peptide bond forming activity of this condensation domain is coupled to the rate of amino acid activation performed by the subsequent adenylation domain. This is a significant result with implications for NRPS redesign, as it indicates that the rate of amino acid activation of modified adenylation domains must be maintained to prevent unwanted peptide hydrolysis from the NRPS due to a loss of the productive coupling of amino acid selection and peptide bond formation. Taken together, our results indicate that assessing condensation domain activity is a vital step in not only understanding the biosynthetic logic and timing of NRPS-mediated peptide assembly, but also the rules which redesign efforts must obey in order to successfully produce functional, modified NRPS assembly lines.
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Affiliation(s)
- Melanie Schoppet
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg , Germany
| | - Madeleine Peschke
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg , Germany
| | - Anja Kirchberg
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
| | - Vincent Wiebach
- Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany
| | - Roderich D Süssmuth
- Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen , Microbiology/Biotechnology , University of Tübingen , Auf der Morgenstelle 28, 72076 Tübingen , Germany .
- German Centre for Infection Research (DZIF) , Partner Site Tübingen, Tübingen , Germany
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg , Germany
- ARC Centre of Excellence in Advanced Molecular Imaging , Monash University , Clayton , Victoria 3800 , Australia
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88
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89
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Abdel Monaim SAH, Somboro AM, El-Faham A, de la Torre BG, Albericio F. Bacteria Hunt Bacteria through an Intriguing Cyclic Peptide. ChemMedChem 2018; 14:24-51. [PMID: 30394699 DOI: 10.1002/cmdc.201800597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/10/2018] [Indexed: 12/15/2022]
Abstract
In the last few decades, peptides have been victorious over small molecules as therapeutics due to their broad range of applications, high biological activity, and high specificity. However, the main challenges to overcome if peptides are to become effective drugs is their low oral bioavailability and instability under physiological conditions. Cyclic peptides play a vital role in this context because they show higher stability under physiological conditions, higher membrane permeability, and greater oral bioavailability than that of their corresponding linear analogues. In this regard, cyclic antimicrobial peptides (AMPs) have gained considerable attention in the field of novel antibiotic development. Bacterial strains produce cyclic AMPs through two pathways: ribosomal and nonribosomal. This review provides an overview of the chemical classification of cyclic AMPs isolated from bacteria, and provides a description of their biological activity and mode of action.
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Affiliation(s)
- Shimaa A H Abdel Monaim
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.,Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Anou M Somboro
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Ayman El-Faham
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia.,Chemistry Department, Faculty of Science, Alexandria University, P.O. Box 426, Ibrahimia, Alexandria, 12321, Egypt
| | - Beatriz G de la Torre
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Fernando Albericio
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa.,Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia.,CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, and Department of Organic Chemistry, University of Barcelona, Barcelona, 08028, Spain
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90
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Alkhalaf LM, Barry SM, Rea D, Gallo A, Griffiths D, Lewandowski JR, Fulop V, Challis GL. Binding of Distinct Substrate Conformations Enables Hydroxylation of Remote Sites in Thaxtomin D by Cytochrome P450 TxtC. J Am Chem Soc 2018; 141:216-222. [DOI: 10.1021/jacs.8b08864] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lona M. Alkhalaf
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K
| | - Sarah M. Barry
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K
| | - Dean Rea
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - Angelo Gallo
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K
| | - Daniel Griffiths
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K
| | | | - Vilmos Fulop
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - Gregory L. Challis
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, U.K
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, CV4 7AL, U.K
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
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91
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Wang L, Yuan M, Zheng J. Crystal structure of the condensation domain from lovastatin polyketide synthase. Synth Syst Biotechnol 2018; 4:10-15. [PMID: 30533541 PMCID: PMC6260248 DOI: 10.1016/j.synbio.2018.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/01/2018] [Accepted: 11/15/2018] [Indexed: 12/03/2022] Open
Abstract
The highly reducing iterative polyketide synthases responsible for lovastatin biosynthesis contains a section homologous to condensation (CON) domain observed in nonribosomal peptide synthetases (NRPSs). In the present study, we expressed the isolated lovastatin CON domain and solved the crystal structure to 1.79 Å resolution. The overall structure shows similarity to canonical condensation domains of NRPSs, containing the N-terminal and C-terminal subdomains that resemble enzymes of chloramphenicol acetyltransferase family, whereas distinct structural features are observed at the active site. The acceptor entry of the substrate channel is blocked by a flexible loop, thereby preventing the loading of substrate for a new round of chain elongation. The mutation of conserved catalytic motif located at the midpoint of substrate channel agrees with the incapability of CON to catalyzed amide-bond formation. The structure helps to understand the function of CON in lovastatin biosynthesis.
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92
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Guzmán-Chávez F, Zwahlen RD, Bovenberg RAL, Driessen AJM. Engineering of the Filamentous Fungus Penicillium chrysogenum as Cell Factory for Natural Products. Front Microbiol 2018; 9:2768. [PMID: 30524395 PMCID: PMC6262359 DOI: 10.3389/fmicb.2018.02768] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022] Open
Abstract
Penicillium chrysogenum (renamed P. rubens) is the most studied member of a family of more than 350 Penicillium species that constitute the genus. Since the discovery of penicillin by Alexander Fleming, this filamentous fungus is used as a commercial β-lactam antibiotic producer. For several decades, P. chrysogenum was subjected to a classical strain improvement (CSI) program to increase penicillin titers. This resulted in a massive increase in the penicillin production capacity, paralleled by the silencing of several other biosynthetic gene clusters (BGCs), causing a reduction in the production of a broad range of BGC encoded natural products (NPs). Several approaches have been used to restore the ability of the penicillin production strains to synthetize the NPs lost during the CSI. Here, we summarize various re-activation mechanisms of BGCs, and how interference with regulation can be used as a strategy to activate or silence BGCs in filamentous fungi. To further emphasize the versatility of P. chrysogenum as a fungal production platform for NPs with potential commercial value, protein engineering of biosynthetic enzymes is discussed as a tool to develop de novo BGC pathways for new NPs.
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Affiliation(s)
- Fernando Guzmán-Chávez
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Reto D Zwahlen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Roel A L Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,DSM Biotechnology Centre, Delft, Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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93
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Meng S, Tang GL, Pan HX. Enzymatic Formation of Oxygen-Containing Heterocycles in Natural Product Biosynthesis. Chembiochem 2018; 19:2002-2022. [PMID: 30039582 DOI: 10.1002/cbic.201800225] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Indexed: 01/12/2023]
Abstract
Oxygen-containing heterocycles are widely encountered in natural products that display diverse pharmacological properties and have potential benefits to human health. The formation of O-heterocycles catalyzed by different types of enzymes in the biosynthesis of natural products not only contributes to the structural diversity of these compounds, but also enriches our understanding of nature's ability to construct complex molecules. This minireview focuses on the various modes of enzymatic O-heterocyclization identified in natural product biosynthesis and summarizes the possible mechanisms involved in ring closure.
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Affiliation(s)
- Song Meng
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Gong-Li Tang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Hai-Xue Pan
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of the Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
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94
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Brieke C, Tarnawski M, Greule A, Cryle MJ. Investigating Cytochrome P450 specificity during glycopeptide antibiotic biosynthesis through a homologue hybridization approach. J Inorg Biochem 2018; 185:43-51. [DOI: 10.1016/j.jinorgbio.2018.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/30/2018] [Accepted: 05/01/2018] [Indexed: 01/10/2023]
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95
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Forneris CC, Seyedsayamdost MR. In Vitro Reconstitution of OxyC Activity Enables Total Chemoenzymatic Syntheses of Vancomycin Aglycone Variants. Angew Chem Int Ed Engl 2018; 57:8048-8052. [DOI: 10.1002/anie.201802856] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/13/2018] [Indexed: 11/10/2022]
Affiliation(s)
| | - Mohammad R. Seyedsayamdost
- Department of ChemistryPrinceton University Princeton NJ 08544 USA
- Department of Molecular BiologyPrinceton University Princeton NJ 08544 USA
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96
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Forneris CC, Seyedsayamdost MR. In Vitro Reconstitution of OxyC Activity Enables Total Chemoenzymatic Syntheses of Vancomycin Aglycone Variants. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802856] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Mohammad R. Seyedsayamdost
- Department of ChemistryPrinceton University Princeton NJ 08544 USA
- Department of Molecular BiologyPrinceton University Princeton NJ 08544 USA
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97
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Ozturk S, Forneris CC, Nguy AKL, Sorensen EJ, Seyedsayamdost MR. Modulating OxyB-Catalyzed Cross-Coupling Reactions in Vancomycin Biosynthesis by Incorporation of Diverse d-Tyr Analogues. J Org Chem 2018; 83:7309-7317. [DOI: 10.1021/acs.joc.8b00916] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Seyma Ozturk
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Clarissa C. Forneris
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Andy K. L. Nguy
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Erik J. Sorensen
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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98
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Schoppet M, Tailhades J, Kulkarni K, Cryle MJ. Precursor Manipulation in Glycopeptide Antibiotic Biosynthesis: Are β-Amino Acids Compatible with the Oxidative Cyclization Cascade? J Org Chem 2018; 83:7206-7214. [DOI: 10.1021/acs.joc.8b00418] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Melanie Schoppet
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | | | | | - Max J. Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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99
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Forneris CC, Ozturk S, Sorensen EJ, Seyedsayamdost MR. Installation of Multiple Aryl Ether Crosslinks onto Non-Native Substrate Peptides by the Vancomycin OxyB. Tetrahedron 2018; 74:3231-3237. [PMID: 30386000 DOI: 10.1016/j.tet.2018.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biosynthesis of glycopeptide antibiotics (GPAs) has been an active area of research for decades. Nonetheless, insights into the activity of the cytochrome P450 enzymes required for installing the aromatic crosslinks, which form their cup-shaped topologies and render GPAs bioactive, have only recently emerged. Presently, little is known about the substrate scope and promiscuity of the P450 enzymes. Herein, we report that OxyBvan, the P450 enzyme that installs the first crosslink in vancomycin biosynthesis, is capable of catalyzing the formation of its conventional C-O-D bis-aryl ether bond in non-natural substrates and, furthermore, the formation of a second, novel linkage when D-Trp is incorporated at position 6. HR-MS/MS and isotope labeling studies indicate the second crosslink is formed between rings A and B, resulting in a novel GPA-type scaffold. OxyB is also capable of installing two crosslinks in kistamicin- and complestatin-like substrate peptides. These findings highlight the utility of OxyBvan in creating crosslinked GPA derivatives and provide clues regarding the unusual biosynthesis of kistamicin.
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Affiliation(s)
| | - Seyma Ozturk
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Erik J Sorensen
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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100
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Wolff H, Bode HB. The benzodiazepine-like natural product tilivalline is produced by the entomopathogenic bacterium Xenorhabdus eapokensis. PLoS One 2018; 13:e0194297. [PMID: 29596433 PMCID: PMC5875774 DOI: 10.1371/journal.pone.0194297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/28/2018] [Indexed: 01/05/2023] Open
Abstract
The pyrrolobenzodiazepine tilivalline (1) was originally identified in the human gut pathobiont Klebsiella oxytoca, the causative agent of antibiotic-associated hemorrhagic colitis. Here we show the identification of tilivalline and analogs thereof in the entomopathogenic bacterium Xenorhabdus eapokensis as well as the identification of its biosynthesis gene cluster encoding a bimodular non-ribosomal peptide synthetase. Heterologous expression of both genes in E. coli resulted in the production of 1 and from mutasynthesis and precursor directed biosynthesis 11 new tilivalline analogs were identified in X. eapokensis. These results allowed the prediction of the tilivalline biosynthesis being similar to that in K. oxytoca.
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Affiliation(s)
- Hendrik Wolff
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B. Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- * E-mail:
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