1
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Dreckmann TM, Fritz L, Kaiser CF, Bouhired SM, Wirtz DA, Rausch M, Müller A, Schneider T, König GM, Crüsemann M. Biosynthesis of the corallorazines, a widespread class of antibiotic cyclic lipodipeptides. RSC Chem Biol 2024:d4cb00157e. [PMID: 39184525 PMCID: PMC11342130 DOI: 10.1039/d4cb00157e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024] Open
Abstract
Corallorazines are cyclic lipodipeptide natural products produced by the myxobacterium Corallococcus coralloides B035. To decipher the basis of corallorazine biosynthesis, the corallorazine nonribosomal peptide synthetase (NRPS) biosynthetic gene cluster crz was identified and analyzed in detail. Here, we present a model of corallorazine biosynthesis, supported by bioinformatic analyses and in vitro investigations on the bimodular NRPS synthesizing the corallorazine core. Corallorazine biosynthesis shows several distinct features, such as the presence of a dehydrating condensation domain, and a unique split adenylation domain on two open reading frames. Using an alternative fatty acyl starter unit, the first steps of corallorazine biosynthesis were characterized in vitro, supporting our biosynthetic model. The dehydrating condensation domain was bioinformatically analyzed in detail and compared to other modifying C domains, revealing unreported specific sequence motives for this domain subfamily. Using global bioinformatics analyses, we show that the crz gene cluster family is widespread among bacteria and encodes notable chemical diversity. Corallorazine A displays moderate antimicrobial activity against selected Gram-positive and Gram-negative bacteria. Mode of action studies comprising whole cell analysis and in vitro test systems revealed that corallorazine A inhibits bacterial transcription by targeting the DNA-dependent RNA polymerase.
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Affiliation(s)
- Teresa M Dreckmann
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Lisa Fritz
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
| | - Christian F Kaiser
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Sarah M Bouhired
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Daniel A Wirtz
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Marvin Rausch
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
| | - Anna Müller
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn Meckenheimer Allee 168 53115 Bonn Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne Bonn Germany
| | - Gabriele M König
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, University of Bonn Nussallee 6 53115 Bonn Germany
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2
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Voitsekhovskaia I, Ho YTC, Klatt C, Müller A, Machell DL, Tan YJ, Triesman M, Bingel M, Schittenhelm RB, Tailhades J, Kulik A, Maier ME, Otting G, Wohlleben W, Schneider T, Cryle M, Stegmann E. Altering glycopeptide antibiotic biosynthesis through mutasynthesis allows incorporation of fluorinated phenylglycine residues. RSC Chem Biol 2024:d4cb00140k. [PMID: 39247680 PMCID: PMC11376024 DOI: 10.1039/d4cb00140k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 08/10/2024] [Indexed: 09/10/2024] Open
Abstract
Glycopeptide antibiotics (GPAs) are peptide natural products used as last resort treatments for antibiotic resistant bacterial infections. They are produced by the sequential activities of a linear nonribosomal peptide synthetase (NRPS), which assembles the heptapeptide core of GPAs, and cytochrome P450 (Oxy) enzymes, which perform a cascade of cyclisation reactions. The GPAs contain proteinogenic and nonproteinogenic amino acids, including phenylglycine residues such as 4-hydroxyphenylglycine (Hpg). The ability to incorporate non-proteinogenic amino acids in such peptides is a distinctive feature of the modular architecture of NRPSs, with each module selecting and incorporating a desired amino acid. Here, we have exploited this ability to produce and characterise GPA derivatives containing fluorinated phenylglycine (F-Phg) residues through a combination of mutasynthesis, biochemical, structural and bioactivity assays. Our data indicate that the incorporation of F-Phg residues is limited by poor acceptance by the NRPS machinery, and that the phenol moiety normally present on Hpg residues is essential to ensure both acceptance by the NRPS and the sequential cyclisation activity of Oxy enzymes. The principles learnt here may prove useful for the future production of GPA derivatives with more favourable properties through mixed feeding mutasynthesis approaches.
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Affiliation(s)
- Irina Voitsekhovskaia
- Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen Tübingen Germany
| | - Y T Candace Ho
- 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
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Australia
| | - Christoph Klatt
- Institute of Organic Chemistry, University of Tübingen Tübingen Germany
| | - Anna Müller
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn Bonn Germany
| | - Daniel L Machell
- 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
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Australia
| | - Yi Jiun Tan
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Australia
- Research School of Chemistry, The Australian National University Acton ACT 2601 Australia
| | - Maxine Triesman
- 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
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Australia
| | - Mara Bingel
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn Bonn Germany
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Platform, Monash University Clayton VIC 3800 Australia
| | - 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
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Australia
| | - Andreas Kulik
- Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen Tübingen Germany
| | - Martin E Maier
- Institute of Organic Chemistry, University of Tübingen Tübingen Germany
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Australia
- Research School of Chemistry, The Australian National University Acton ACT 2601 Australia
| | - Wolfgang Wohlleben
- Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen Tübingen Germany
| | - Tanja Schneider
- Institute of Organic Chemistry, University of Tübingen Tübingen Germany
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn Bonn Germany
| | - Max 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
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Australia
| | - Evi Stegmann
- Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen Tübingen Germany
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Australia
- German Centre for Infection Research (DZIF), Partner Site Tübingen Tübingen Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections' (CMFI), University of Tübingen Tübingen Germany
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3
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Nguy AKL, Martinie RJ, Cai A, Seyedsayamdost MR. Detection of a Kinetically Competent Compound-I Intermediate in the Vancomycin Biosynthetic Enzyme OxyB. J Am Chem Soc 2024; 146:19629-19634. [PMID: 38989876 DOI: 10.1021/jacs.4c03102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Cytochrome P450 enzymes are abundantly encoded in microbial genomes. Their reactions have two general outcomes, one involving oxygen insertion via a canonical "oxygen rebound" mechanism and a second that diverts from this pathway and leads to a wide array of products, notably intramolecular oxidative cross-links. The antibiotic of-last-resort, vancomycin, contains three such cross-links, which are crucial for biological activity and are installed by the P450 enzymes OxyB, OxyA, and OxyC. The mechanisms of these enzymes have remained elusive in part because of the difficulty in spectroscopically capturing transient intermediates. Using stopped-flow UV/visible absorption and rapid freeze-quench electron paramagnetic resonance spectroscopies, we show that OxyB generates the highly reactive compound-I intermediate, which can react with a model vancomycin peptide substrate in a kinetically competent fashion to generate product. Our results have implications for the mechanism of OxyB and are in line with the notion that oxygen rebound and oxidative cross-links share early steps in their catalytic cycles.
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Affiliation(s)
- Andy K L Nguy
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Ryan J Martinie
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Hamilton College, Clinton, New York 13323, United States
| | - Amanda Cai
- 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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4
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Coe LJ, Zhao Y, Padva L, Keto A, Schittenhelm R, Tailhades J, Pierens G, Krenske EH, Crüsemann M, De Voss JJ, Cryle MJ. Reassignment of the Structure of a Tryptophan-Containing Cyclic Tripeptide Produced by the Biarylitide Crosslinking Cytochrome P450 blt. Chemistry 2024; 30:e202400988. [PMID: 38712638 DOI: 10.1002/chem.202400988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/08/2024]
Abstract
The structure of the sidechain crosslinked Tyr-Leu-Trp peptide produced by the biarylitide crosslinking cytochrome P450Blt from Micromonospora sp. MW-13 has been reanalysed by a series of NMR, computational and isotope labelling experiments and shown to contain a C-N rather than a C-O bond. Additional in vivo experiments using such a modified peptide show there is a general tolerance of biarylitide crosslinking P450 enzymes for histidine to tryptophan mutations within their minimal peptide substrate sequences despite the lack of such residues noted in natural biarylitide gene clusters. This work further highlights the impressive ability of P450s from biarylitide biosynthesis pathways to act as biocatalysts for the formation of a range of sidechain crosslinked tripeptides.
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Affiliation(s)
- Laura J Coe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, 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
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
| | - Leo Padva
- Institute of Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - Angus Keto
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ralf Schittenhelm
- Monash Proteomics and Metabolomics Platform, Monash University, Clayton, VIC, 3800, Australia
| | - 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
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
| | - Greg Pierens
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Max Crüsemann
- Institute of Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
| | - 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
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia
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5
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Yu Y, van der Donk WA. PEARL-Catalyzed Peptide Bond Formation after Chain Reversal by Ureido-Forming Condensation Domains. ACS CENTRAL SCIENCE 2024; 10:1242-1250. [PMID: 38947204 PMCID: PMC11212132 DOI: 10.1021/acscentsci.4c00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 07/02/2024]
Abstract
A subset of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are encoded in their biosynthetic gene clusters (BGCs) with enzymes annotated as lantibiotic dehydratases. The functions of these putative lantibiotic dehydratases remain unknown. Here, we characterize an NRPS-PKS BGC with a putative lantibiotic dehydratase from the bacterium Stackebrandtia nassauensis (sna). Heterologous expression revealed several metabolites produced by the BGC, and the omission of selected biosynthetic enzymes revealed the biosynthetic pathway toward these compounds. The final product is a bisarginyl ureidopeptide with an enone electrophile. The putative lantibiotic dehydratase catalyzes peptide bond formation to a Thr that extends the peptide scaffold opposite to the NRPS and PKS biosynthetic direction. The condensation domain of the NRPS SnaA catalyzes the formation of a ureido group, and bioinformatics analysis revealed a distinct active site signature EHHXXHDG of ureido-generating condensation (Curea) domains. This work demonstrates that the annotated lantibiotic dehydratase serves as a separate amide bond-forming machinery in addition to the NRPS, and that the lantibiotic dehydratase enzyme family possesses diverse catalytic activities in the biosynthesis of both ribosomal and nonribosomal natural products.
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Affiliation(s)
- Yue Yu
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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6
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Sakata S, Li J, Yasuno Y, Shinada T, Shin-Ya K, Katsuyama Y, Ohnishi Y. Identification of the Cirratiomycin Biosynthesis Gene Cluster in Streptomyces Cirratus: Elucidation of the Biosynthetic Pathways for 2,3-Diaminobutyric Acid and Hydroxymethylserine. Chemistry 2024; 30:e202400271. [PMID: 38456538 DOI: 10.1002/chem.202400271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024]
Abstract
Cirratiomycin, a heptapeptide with antibacterial activity, was isolated and characterized in 1981; however, its biosynthetic pathway has not been elucidated. It contains several interesting nonproteinogenic amino acids, such as (2S,3S)-2,3-diaminobutyric acid ((2S,3S)-DABA) and α-(hydroxymethyl)serine, as building blocks. Here, we report the identification of a cirratiomycin biosynthetic gene cluster in Streptomyces cirratus. Bioinformatic analysis revealed that several Streptomyces viridifaciens and Kitasatospora aureofaciens strains also have this cluster. One S. viridifaciens strain was confirmed to produce cirratiomycin. The biosynthetic gene cluster was shown to be responsible for cirratiomycin biosynthesis in S. cirratus in a gene inactivation experiment using CRISPR-cBEST. Interestingly, this cluster encodes a nonribosomal peptide synthetase (NRPS) composed of 12 proteins, including those with an unusual domain organization: a stand-alone adenylation domain, two stand-alone condensation domains, two type II thioesterases, and two NRPS modules that have no adenylation domain. Using heterologous expression and in vitro analysis of recombinant enzymes, we revealed the biosynthetic pathway of (2S,3S)-DABA: (2S,3S)-DABA is synthesized from l-threonine by four enzymes, CirR, CirS, CirQ, and CirB. In addition, CirH, a glycine/serine hydroxymethyltransferase homolog, was shown to synthesize α-(hydroxymethyl)serine from d-serine in vitro. These findings broaden our knowledge of nonproteinogenic amino acid biosynthesis.
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Affiliation(s)
- Shunki Sakata
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Jiafeng Li
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoko Yasuno
- Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Tetsuro Shinada
- Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi, Osaka, 558-8585, Japan
| | - Kazuo Shin-Ya
- National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
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7
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Treisman M, Coe L, Zhao Y, Sasi VM, Gullick J, Hansen MH, Ly A, Leichthammer V, Hess C, Machell DL, Schittenhelm RB, Hooper J, Jackson CJ, Tailhades J, De Voss JJ, Cryle MJ. An Engineered Biarylitide Cross-Linking P450 from RiPP Biosynthesis Generates Alternative Cyclic Peptides. Org Lett 2024; 26:1828-1833. [PMID: 38417822 DOI: 10.1021/acs.orglett.3c04366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Cytochrome-P450-mediated cross-linking of ribosomally encoded peptides (RiPPs) is rapidly expanding and displays great potential for biocatalysis. Here, we demonstrate that active site engineering of the biarylitide cross-linking enzyme P450Blt enables the formation of His-X-Tyr and Tyr-X-Tyr cross-linked peptides, thus showing how such P450s can be further exploited to produce alternate cyclic tripeptides with controlled cross-linking states.
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Affiliation(s)
- Maxine Treisman
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Laura Coe
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yongwei Zhao
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Vishnu Mini Sasi
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
| | - Jemma Gullick
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Mathias H Hansen
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Aviva Ly
- Department of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Victor Leichthammer
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Caroline Hess
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Daniel L Machell
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Platform, Monash University, Clayton, VIC 3800, Australia
| | - Joel Hooper
- Department of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Colin J Jackson
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Research School of Chemistry, The Australian National University, Acton, ACT 2601, Australia
- ARC Centre of Excellence in Synthetic Biology, Australian National University, Acton, ACT 2601, Australia
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, EMBL Australia, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
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8
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Liu CL, Wang ZJ, Shi J, Yan ZY, Zhang GD, Jiao RH, Tan RX, Ge HM. P450-Modified Multicyclic Cyclophane-Containing Ribosomally Synthesized and Post-Translationally Modified Peptides. Angew Chem Int Ed Engl 2024; 63:e202314046. [PMID: 38072825 DOI: 10.1002/anie.202314046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Indexed: 01/24/2024]
Abstract
Cyclic peptides with cyclophane linkers are an attractive compound type owing to the fine-tuned rigid three-dimensional structures and unusual biophysical features. Cytochrome P450 enzymes are capable of catalyzing not only the C-C and C-O oxidative coupling reactions found in vancomycin and other nonribosomal peptides (NRPs), but they also exhibit novel catalytic activities to generate cyclic ribosomally synthesized and post-translationally modified peptides (RiPPs) through cyclophane linkage. To discover more P450-modified multicyclic RiPPs, we set out to find cryptic and unknown P450-modified RiPP biosynthetic gene clusters (BGCs) through genome mining. Synergized bioinformatic analysis reveals that P450-modified RiPP BGCs are broadly distributed in bacteria and can be classified into 11 classes. Focusing on two classes of P450-modified RiPP BGCs where precursor peptides contain multiple conserved aromatic amino acid residues, we characterized 11 novel P450-modified multicyclic RiPPs with different cyclophane linkers through heterologous expression. Further mutation of the key ring-forming residues and combinatorial biosynthesis study revealed the order of bond formation and the specificity of P450s. This study reveals the functional diversity of P450 enzymes involved in the cyclophane-containing RiPPs and indicates that P450 enzymes are promising tools for rapidly obtaining structurally diverse cyclic peptide derivatives.
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Affiliation(s)
- Cheng Li Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zi Jie Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zhang Yuan Yan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Guo Dong Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Nanjing Drum Tower Hospital, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
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9
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Kries H, Trottmann F, Hertweck C. Novel Biocatalysts from Specialized Metabolism. Angew Chem Int Ed Engl 2024; 63:e202309284. [PMID: 37737720 DOI: 10.1002/anie.202309284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/23/2023]
Abstract
Enzymes are increasingly recognized as valuable (bio)catalysts that complement existing synthetic methods. However, the range of biotransformations used in the laboratory is limited. Here we give an overview on the biosynthesis-inspired discovery of novel biocatalysts that address various synthetic challenges. Prominent examples from this dynamic field highlight remarkable enzymes for protecting-group-free amide formation and modification, control of pericyclic reactions, stereoselective hetero- and polycyclizations, atroposelective aryl couplings, site-selective C-H activations, introduction of ring strain, and N-N bond formation. We also explore unusual functions of cytochrome P450 monooxygenases, radical SAM-dependent enzymes, flavoproteins, and enzymes recruited from primary metabolism, which offer opportunities for synthetic biology, enzyme engineering, directed evolution, and catalyst design.
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Affiliation(s)
- Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Department of Chemistry, University of Bayreuth, Universitätsstr. 30, 95440, Bayreuth, Germany
| | - Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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10
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Adhikari A, Shakya S, Shrestha S, Aryal D, Timalsina KP, Dhakal D, Khatri Y, Parajuli N. Biocatalytic role of cytochrome P450s to produce antibiotics: A review. Biotechnol Bioeng 2023; 120:3465-3492. [PMID: 37691185 DOI: 10.1002/bit.28548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/15/2023] [Accepted: 08/26/2023] [Indexed: 09/12/2023]
Abstract
Cytochrome P450s belong to a family of heme-binding monooxygenases, which catalyze regio- and stereospecific functionalisation of C-H, C-C, and C-N bonds, including heteroatom oxidation, oxidative C-C bond cleavages, and nitrene transfer. P450s are considered useful biocatalysts for the production of pharmaceutical products, fine chemicals, and bioremediating agents. Despite having tremendous biotechnological potential, being heme-monooxygenases, P450s require either autologous or heterologous redox partner(s) to perform chemical transformations. Randomly distributed P450s throughout a bacterial genome and devoid of particular redox partners in natural products biosynthetic gene clusters (BGCs) showed an extra challenge to reveal their pharmaceutical potential. However, continuous efforts have been made to understand their involvement in antibiotic biosynthesis and their modification, and this review focused on such BGCs. Here, particularly, we have discussed the role of P450s involved in the production of macrolides and aminocoumarin antibiotics, nonribosomal peptide (NRPSs) antibiotics, ribosomally synthesized and post-translationally modified peptide (RiPPs) antibiotics, and others. Several reactions catalyzed by P450s, as well as the role of their redox partners involved in the BGCs of various antibiotics and their derivatives, have been primarily addressed in this review, which would be useful in further exploration of P450s for the biosynthesis of new therapeutics.
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Affiliation(s)
- Anup Adhikari
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Sajan Shakya
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Shreesti Shrestha
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA
| | - Dipa Aryal
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Kavi Prasad Timalsina
- Department of Biotechnology, National College, Tribhuvan University, Kathmandu, Nepal
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida, USA
| | | | - Niranjan Parajuli
- Central Department of Chemistry, Tribhuvan University, Kirtipur, Kathmandu, Nepal
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11
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Hansen MH, Adamek M, Iftime D, Petras D, Schuseil F, Grond S, Stegmann E, Cryle MJ, Ziemert N. Resurrecting ancestral antibiotics: unveiling the origins of modern lipid II targeting glycopeptides. Nat Commun 2023; 14:7842. [PMID: 38030603 PMCID: PMC10687080 DOI: 10.1038/s41467-023-43451-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/09/2023] [Indexed: 12/01/2023] Open
Abstract
Antibiotics are central to modern medicine, and yet they are mainly the products of intra and inter-kingdom evolutionary warfare. To understand how nature evolves antibiotics around a common mechanism of action, we investigated the origins of an extremely valuable class of compounds, lipid II targeting glycopeptide antibiotics (GPAs, exemplified by teicoplanin and vancomycin), which are used as last resort for the treatment of antibiotic resistant bacterial infections. Using a molecule-centred approach and computational techniques, we first predicted the nonribosomal peptide synthetase assembly line of paleomycin, the ancestral parent of lipid II targeting GPAs. Subsequently, we employed synthetic biology techniques to produce the predicted peptide and validated its antibiotic activity. We revealed the structure of paleomycin, which enabled us to address how nature morphs a peptide antibiotic scaffold through evolution. In doing so, we obtained temporal snapshots of key selection domains in nonribosomal peptide synthesis during the biosynthetic journey from ancestral, teicoplanin-like GPAs to modern GPAs such as vancomycin. Our study demonstrates the synergy of computational techniques and synthetic biology approaches enabling us to journey back in time, trace the temporal evolution of antibiotics, and revive these ancestral molecules. It also reveals the optimisation strategies nature has applied to evolve modern GPAs, laying the foundation for future efforts to engineer this important class of antimicrobial agents.
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Affiliation(s)
- Mathias H Hansen
- 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
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, VIC, 3800, Australia
| | - Martina Adamek
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Dumitrita Iftime
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Daniel Petras
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Frauke Schuseil
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, 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.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, VIC, 3800, Australia.
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany.
- German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.
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12
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Heard SC, Diehl KL, Winter JM. Biosynthesis of the fungal nonribosomal peptide penilumamide A and biochemical characterization of a pterin-specific adenylation domain. RSC Chem Biol 2023; 4:748-753. [PMID: 37799585 PMCID: PMC10549243 DOI: 10.1039/d3cb00088e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/31/2023] [Indexed: 10/07/2023] Open
Abstract
We report the characterization of the penilumamide biosynthetic cluster from Aspergillus flavipes CNL-338. In vitro reconstitution experiments demonstrated that three nonribosomal peptide synthetases are required for constructing the tripeptide and studies with dissected adenylation domains allowed for the first biochemical characterization of a domain that selects a pterin-derived building block.
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Affiliation(s)
- Stephanie C Heard
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah Salt Lake City UT 84112 USA +1 (801) 585-7117
| | - Katharine L Diehl
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah Salt Lake City UT 84112 USA
| | - Jaclyn M Winter
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah Salt Lake City UT 84112 USA +1 (801) 585-7117
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13
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Patel KD, MacDonald MR, Ahmed SF, Singh J, Gulick AM. Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases. Nat Prod Rep 2023; 40:1550-1582. [PMID: 37114973 PMCID: PMC10510592 DOI: 10.1039/d3np00003f] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Indexed: 04/29/2023]
Abstract
Covering: up to fall 2022.Nonribosomal peptide synthetases (NRPSs) are a family of modular, multidomain enzymes that catalyze the biosynthesis of important peptide natural products, including antibiotics, siderophores, and molecules with other biological activity. The NRPS architecture involves an assembly line strategy that tethers amino acid building blocks and the growing peptides to integrated carrier protein domains that migrate between different catalytic domains for peptide bond formation and other chemical modifications. Examination of the structures of individual domains and larger multidomain proteins has identified conserved conformational states within a single module that are adopted by NRPS modules to carry out a coordinated biosynthetic strategy that is shared by diverse systems. In contrast, interactions between modules are much more dynamic and do not yet suggest conserved conformational states between modules. Here we describe the structures of NRPS protein domains and modules and discuss the implications for future natural product discovery.
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Affiliation(s)
- Ketan D Patel
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Monica R MacDonald
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Syed Fardin Ahmed
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Jitendra Singh
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
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14
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Gering HE, Li X, Tang H, Swartz PD, Chang WC, Makris TM. A Ferric-Superoxide Intermediate Initiates P450-Catalyzed Cyclic Dipeptide Dimerization. J Am Chem Soc 2023; 145:19256-19264. [PMID: 37611404 DOI: 10.1021/jacs.3c04542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
The cytochrome P450 (CYP) AspB is involved in the biosynthesis of the diketopiperazine (DKP) aspergilazine A. Tryptophan-linked dimeric DKP alkaloids are a large family of natural products that are found in numerous species and exhibit broad and often potent bioactivity. The proposed mechanisms for C-N bond formation by AspB, and similar C-C bond formations by related CYPs, have invoked the use of a ferryl-intermediate as an oxidant to promote substrate dimerization. Here, the parallel application of steady-state and transient kinetic approaches reveals a very different mechanism that involves a ferric-superoxide species as a primary oxidant to initiate DKP-assembly. Single turnover kinetic isotope effects and a substrate analog suggest the probable nature and site for abstraction. The direct observation of CYP-superoxide reactivity rationalizes the atypical outcome of AspB and reveals a new reaction manifold in heme enzymes.
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Affiliation(s)
- Hannah E Gering
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Xiaojun Li
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Haoyu Tang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Paul D Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thomas M Makris
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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15
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Zhao X, Chen Y, Long T, Liu Z, Zhang Q, Zhang H, Yan Y, Zhang C, Zhu Y. Genome Mining and Biosynthetic Reconstitution of Fungal Depsidone Mollicellins Reveal a Dual Functional Cytochrome P450 for Ether Formation. JOURNAL OF NATURAL PRODUCTS 2023; 86:2046-2053. [PMID: 37566707 DOI: 10.1021/acs.jnatprod.3c00609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Depsidones are significant in structural diversity and broad in biological activities; however, their biosynthetic pathways have not been well understood and have attracted considerable attention. Herein, we heterologously reconstituted a depsidone encoding gene cluster from Ovatospora sp. SCSIO SY280D in Aspergillus nidulans A1145, leading to production of mollicellins, a representative family of depsidones, and discovering a bifunctional P450 monooxygenase that catalyzes both ether formation and hydroxylation in the biosynthesis of the mollicellins. The functions of a decarboxylase and an aromatic prenyltransferase are also characterized to understand the tailoring modification steps. This work provides important insights into the biosynthesis of mollicellins.
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Affiliation(s)
- Xiaoyang Zhao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youzhe Chen
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Ting Long
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiying Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Haibo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Yan Yan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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16
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Zhang S, Zhang L, Greule A, Tailhades J, Marschall E, Prasongpholchai P, Leng DJ, Zhang J, Zhu J, Kaczmarski JA, Schittenhelm RB, Einsle O, Jackson CJ, Alberti F, Bechthold A, Zhang Y, Tosin M, Si T, Cryle MJ. P450-mediated dehydrotyrosine formation during WS9326 biosynthesis proceeds via dehydrogenation of a specific acylated dipeptide substrate. Acta Pharm Sin B 2023; 13:3561-3574. [PMID: 37655329 PMCID: PMC10465960 DOI: 10.1016/j.apsb.2023.03.021] [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: 02/06/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
WS9326A is a peptide antibiotic containing a highly unusual N-methyl-E-2-3-dehydrotyrosine (NMet-Dht) residue that is incorporated during peptide assembly on a non-ribosomal peptide synthetase (NRPS). The cytochrome P450 encoded by sas16 (P450Sas) has been shown to be essential for the formation of the alkene moiety in NMet-Dht, but the timing and mechanism of the P450Sas-mediated α,β-dehydrogenation of Dht remained unclear. Here, we show that the substrate of P450Sas is the NRPS-associated peptidyl carrier protein (PCP)-bound dipeptide intermediate (Z)-2-pent-1'-enyl-cinnamoyl-Thr-N-Me-Tyr. We demonstrate that P450Sas-mediated incorporation of the double bond follows N-methylation of the Tyr by the N-methyl transferase domain found within the NRPS, and further that P450Sas appears to be specific for substrates containing the (Z)-2-pent-1'-enyl-cinnamoyl group. A crystal structure of P450Sas reveals differences between P450Sas and other P450s involved in the modification of NRPS-associated substrates, including the substitution of the canonical active site alcohol residue with a phenylalanine (F250), which in turn is critical to P450Sas activity and WS9326A biosynthesis. Together, our results suggest that P450Sas catalyses the direct dehydrogenation of the NRPS-bound dipeptide substrate, thus expanding the repertoire of P450 enzymes that can be used to produce biologically active peptides.
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Affiliation(s)
- Songya Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg 79104, Germany
| | - Anja Greule
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
- EMBL Australia, Monash University, Clayton 3800, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton 3800, VIC, Australia
| | - Edward Marschall
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
- EMBL Australia, Monash University, Clayton 3800, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton 3800, VIC, Australia
| | | | - Daniel J. Leng
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jingfan Zhang
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Jing Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Joe A. Kaczmarski
- Research School of Chemistry, the Australian National University, Acton 2601, ACT, Australia
| | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton 3800, VIC, Australia
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg 79104, Germany
| | - Colin J. Jackson
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton 3800, VIC, Australia
- Research School of Chemistry, the Australian National University, Acton 2601, ACT, Australia
| | - Fabrizio Alberti
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK
| | - Andreas Bechthold
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg 79104, Germany
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Manuela Tosin
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Max J. Cryle
- Department of Biochemistry and Molecular Biology, the Monash Biomedicine Discovery Institute, Monash University, Clayton 3800, VIC, Australia
- EMBL Australia, Monash University, Clayton 3800, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton 3800, VIC, Australia
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17
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Hauser N, Ireland KA, Chioti VT, Forneris CC, Davis KM, Seyedsayamdost MR. Robust Chemoenzymatic Synthesis of Keratinimicin Aglycone Analogues Facilitated by the Structure and Selectivity of OxyB. ACS Chem Biol 2023. [PMID: 37405871 PMCID: PMC10399570 DOI: 10.1021/acschembio.3c00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The emergence of multidrug-resistant pathogens poses a threat to public health and requires new antimicrobial agents. As the archetypal glycopeptide antibiotic (GPA) used against drug-resistant Gram-positive pathogens, vancomycin provides a promising starting point. Peripheral alterations to the vancomycin scaffold have enabled the development of new GPAs. However, modifying the core remains challenging due to the size and complexity of this compound family. The recent successful chemoenzymatic synthesis of vancomycin suggests that such an approach can be broadly applied. Herein, we describe the expansion of chemoenzymatic strategies to encompass type II GPAs bearing all aromatic amino acids through the production of the aglycone analogue of keratinimicin A, a GPA that is 5-fold more potent than vancomycin against Clostridioides difficile. In the course of these studies, we found that the cytochrome P450 enzyme OxyBker boasts both broad substrate tolerance and remarkable selectivity in the formation of the first aryl ether cross-link on the linear peptide precursors. The X-ray crystal structure of OxyBker, determined to 2.8 Å, points to structural features that may contribute to these properties. Our results set the stage for using OxyBker broadly as a biocatalyst toward the chemoenzymatic synthesis of diverse GPA analogues.
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Affiliation(s)
- Nicole Hauser
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Kendra A Ireland
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Vasiliki T Chioti
- 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
| | - Katherine M Davis
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, 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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18
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Goldfinger V, Spohn M, Rodler JP, Sigle M, Kulik A, Cryle MJ, Rapp J, Link H, Wohlleben W, Stegmann E. Metabolic engineering of the shikimate pathway in Amycolatopsis strains for optimized glycopeptide antibiotic production. Metab Eng 2023; 78:84-92. [PMID: 37244369 DOI: 10.1016/j.ymben.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Glycopeptide antibiotics (GPA) consist of a glycosylated heptapeptide backbone enriched in aromatic residues originating from the shikimate pathway. Since the enzymatic reactions within the shikimate pathway are highly feedback-regulated, this raises the question as to how GPA producers control the delivery of precursors for GPA assembly. We chose Amycolatopsis balhimycina, the producer of balhimycin, as a model strain for analyzing the key enzymes of the shikimate pathway. A. balhimycina contains two copies each of the key enzymes of the shikimate pathway, deoxy-d-arabino-heptulosonate-7-phosphate synthase (Dahp) and prephenate dehydrogenase (Pdh), with one pair (Dahpsec and Pdhsec) encoded within the balhimycin biosynthetic gene cluster and one pair (Dahpprim and Pdhprim) in the core genome. While overexpression of the dahpsec gene resulted in a significant (>4-fold) increase in balhimycin yield, no positive effects were observed after overexpression of the pdhprim or pdhsec genes. Investigation of allosteric enzyme inhibition revealed that cross-regulation between the tyrosine and phenylalanine pathways plays an important role. Tyrosine, a key precursor of GPAs, was found to be a putative activator of prephenate dehydratase (Pdt), which catalyzes the first step reaction from prephenate to phenylalanine in the shikimate pathway. Surprisingly, overexpression of pdt in A. balhimycina led to an increase in antibiotic production in this modified strain. In order to demonstrate that this metabolic engineering approach is generally applicable to GPA producers, we subsequently applied this strategy to Amycolatopsis japonicum and improved the production of ristomycin A, which is used in diagnosis of genetic disorders. Comparison of "cluster-specific" enzymes with the isoenzymes from the primary metabolism's pathway provided insights into the adaptive mechanisms used by producers to ensure adequate precursor supply and GPA yields. These insights further demonstrate the importance of a holistic approach in bioengineering efforts that takes into account not only peptide assembly but also adequate precursor supply.
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Affiliation(s)
- Valentina Goldfinger
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Marius Spohn
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Jens-Peter Rodler
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbial Bioactive Compounds, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Melanie Sigle
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbial Bioactive Compounds, University of Tübingen, Auf der Morgenstelle 28, 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; ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, VIC, 3800, Australia
| | - Johanna Rapp
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Bacterial Metabolomics, University of Tübingen, Auf der Morgenstelle 25, 72076, Tübingen, Germany
| | - Hannes Link
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Bacterial Metabolomics, University of Tübingen, Auf der Morgenstelle 25, 72076, Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Cluster of Excellence CMFI, Bacterial Metabolomics University of Tübingen, Auf der Morgenstelle 25, 72076, Tübingen, Germany
| | - Wolfgang Wohlleben
- 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
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbial Bioactive Compounds, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
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19
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Zhang S, Chen Y, Zhu J, Lu Q, Cryle MJ, Zhang Y, Yan F. Structural diversity, biosynthesis, and biological functions of lipopeptides from Streptomyces. Nat Prod Rep 2023; 40:557-594. [PMID: 36484454 DOI: 10.1039/d2np00044j] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2022Streptomyces are ubiquitous in terrestrial and marine environments, where they display a fascinating metabolic diversity. As a result, these bacteria are a prolific source of active natural products. One important class of these natural products is the nonribosomal lipopeptides, which have diverse biological activities and play important roles in the lifestyle of Streptomyces. The importance of this class is highlighted by the use of related antibiotics in the clinic, such as daptomycin (tradename Cubicin). By virtue of recent advances spanning chemistry and biology, significant progress has been made in biosynthetic studies on the lipopeptide antibiotics produced by Streptomyces. This review will serve as a comprehensive guide for researchers working in this multidisciplinary field, providing a summary of recent progress regarding the investigation of lipopeptides from Streptomyces. In particular, we highlight the structures, properties, biosynthetic mechanisms, chemical and chemoenzymatic synthesis, and biological functions of lipopeptides. In addition, the application of genome mining techniques to Streptomyces that have led to the discovery of many novel lipopeptides is discussed, further demonstrating the potential of lipopeptides from Streptomyces for future development in modern medicine.
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Affiliation(s)
- Songya Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yunliang Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
- The Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 1000050, China.
| | - Jing Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qiujie Lu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - 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
| | - Youming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
| | - Fu Yan
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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20
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Ho YTC, Schittenhelm RB, Iftime D, Stegmann E, Tailhades J, Cryle MJ. Exploring the Flexibility of the Glycopeptide Antibiotic Crosslinking Cascade for Extended Peptide Backbones. Chembiochem 2023; 24:e202200686. [PMID: 36534957 DOI: 10.1002/cbic.202200686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/23/2022]
Abstract
The glycopeptide antibiotics (GPAs) are a clinically approved class of antimicrobial agents that classically function through the inhibition of bacterial cell-wall biosynthesis by sequestration of the precursor lipid II. The oxidative crosslinking of the core peptide by cytochrome P450 (Oxy) enzymes during GPA biosynthesis is both essential to their function and the source of their synthetic challenge. Thus, understanding the activity and selectivity of these Oxy enzymes is of key importance for the future engineering of this important compound class. Recent reports of GPAs that display an alternative mode of action and a wider range of core peptide structures compared to classic lipid II-binding GPAs raises the question of the tolerance of Oxy enzymes for larger changes in their peptide substrates. In this work, we explore the ability of Oxy enzymes from the biosynthesis pathways of lipid II-binding GPAs to accept altered peptide substrates based on a vancomycin template. Our results show that Oxy enzymes are more tolerant of changes at the N terminus of their substrates, whilst C-terminal extension of the peptide substrates is deleterious to the activity of all Oxy enzymes. Thus, future studies should prioritise the study of Oxy enzymes from atypical GPA biosynthesis pathways bearing C-terminal peptide extension to increase the substrate scope of these important cyclisation enzymes.
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Affiliation(s)
- Y T Candace Ho
- 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.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, 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 Proteomics and Metabolomics Facility, Monash University, Clayton, VIC 3800, Australia
| | - Dumitrita Iftime
- Interfaculty Institute of Microbiology and Infection Medicine, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, 72076, Tübingen, Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine, Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, 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.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
| | - 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.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC 3800, Australia
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21
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A Genomic Survey of the Natural Product Biosynthetic Potential of Actinomycetes Isolated from New Zealand Lichens. mSystems 2023; 8:e0103022. [PMID: 36749048 PMCID: PMC10134820 DOI: 10.1128/msystems.01030-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Actinomycetes are prolific producers of industrially valuable and medically important compounds. Historically, the most efficient method of obtaining compounds has been bioactivity-guided isolation and characterization of drug-like molecules from culturable soil actinomycetes. Unfortunately, this pipeline has been met with an increasing number of rediscoveries, to the point where it is no longer considered an attractive approach for drug discovery. To address this challenge and to continue finding new compounds, researchers have increasingly focused on alternative environmental niches and screening methods. Here, we report the genetic investigation of actinomycetes from an underexplored source, New Zealand lichens. In this work, we obtain draft genome sequences for 322 lichen-associated actinomycetes. We then explore this genetic resource with an emphasis on biosynthetic potential. By enumerating biosynthetic gene clusters (BGCs) in our data sets and comparing these to various reference collections, we demonstrate that actinomycetes sourced from New Zealand lichens have the genetic capacity to produce large numbers of natural products, many of which are expected to be broadly different from those identified in previous efforts predominantly based on soil samples. Our data shed light on the actinomycete assemblage in New Zealand lichens and demonstrate that lichen-sourced actinobacteria could serve as reservoirs for discovering new secondary metabolites. IMPORTANCE Lichens are home to complex and distinctive microbial cohorts that have not been extensively explored for the ability to produce novel secondary metabolites. Here, we isolate and obtain genome sequence data for 322 actinomycetes from New Zealand lichens. In doing so, we delineate at least 85 potentially undescribed species, and show that lichen associated actinomycetes have the potential to yield many new secondary metabolites, and as such, might serve as a productive starting point for drug discovery efforts.
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22
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Zhai G, Zhu Y, Sun G, Zhou F, Sun Y, Hong Z, Dong C, Leadlay PF, Hong K, Deng Z, Zhou F, Sun Y. Insights into azalomycin F assembly-line contribute to evolution-guided polyketide synthase engineering and identification of intermodular recognition. Nat Commun 2023; 14:612. [PMID: 36739290 PMCID: PMC9899208 DOI: 10.1038/s41467-023-36213-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 01/20/2023] [Indexed: 02/06/2023] Open
Abstract
Modular polyketide synthase (PKS) is an ingenious core machine that catalyzes abundant polyketides in nature. Exploring interactions among modules in PKS is very important for understanding the overall biosynthetic process and for engineering PKS assembly-lines. Here, we show that intermodular recognition between the enoylreductase domain ER1/2 inside module 1/2 and the ketosynthase domain KS3 inside module 3 is required for the cross-module enoylreduction in azalomycin F (AZL) biosynthesis. We also show that KS4 of module 4 acts as a gatekeeper facilitating cross-module enoylreduction. Additionally, evidence is provided that module 3 and module 6 in the AZL PKS are evolutionarily homologous, which makes evolution-oriented PKS engineering possible. These results reveal intermodular recognition, furthering understanding of the mechanism of the PKS assembly-line, thus providing different insights into PKS engineering. This also reveals that gene duplication/conversion and subsequent combinations may be a neofunctionalization process in modular PKS assembly-lines, hence providing a different case for supporting the investigation of modular PKS evolution.
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Affiliation(s)
- Guifa Zhai
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Yan Zhu
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Guo Sun
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Fan Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Yangning Sun
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Zhou Hong
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Chuan Dong
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Peter F Leadlay
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Kui Hong
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Zixin Deng
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China
| | - Yuhui Sun
- Department of Hematology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, 430071, Wuhan, People's Republic of China. .,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, 430071, Wuhan, People's Republic of China. .,Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, 430071, Wuhan, People's Republic of China.
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23
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Ma X, Tang Z, Ding W, Liu T, Yang D, Liu W, Ma M. Structure-Based Mechanistic Insights into ColB1, a Flavoprotein Functioning in-trans in the 2,2'-Bipyridine Assembly Line for Cysteine Dehydrogenation. ACS Chem Biol 2023; 18:18-24. [PMID: 36603145 DOI: 10.1021/acschembio.2c00785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The recruitment of trans-acting enzymes by nonribosomal peptide synthetase (NRPS) assembly line is rarely reported. ColB1 is a flavin-dependent dehydrogenase that is recruited by an NRPS terminal condensation domain (Ct domain) and catalyzes peptidyl carrier protein (PCP)-tethered cysteine dehydrogenation in collismycin biosynthesis. We here report the crystal structure of ColB1 complexed with FAD and reveal a typical structural fold of acyl-CoA dehydrogenases (ACADs). However, ColB1 shows distinct structural features from ACADs in substrate recognition both at the entrance of and inside the active site. Site-directed mutagenesis and substrate modeling establish a Glu393-mediated catalytic mechanism, by which the cysteine substrate is sandwiched between Glu393 and FAD to facilitate Cα proton abstraction and Cβ hydride migration. A ColB1-PCP-Ct complex model is generated, providing structural basis for the unique recruitment interactions between ColB1 and the associated NRPS. These results add insights into the mechanisms by which trans-acting enzymes function in an assembly line.
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Affiliation(s)
- Xueyang Ma
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wenping Ding
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Tan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
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24
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Tian L, Shi S, Zhang X, Han F, Dong H. Newest perspectives of glycopeptide antibiotics: biosynthetic cascades, novel derivatives, and new appealing antimicrobial applications. World J Microbiol Biotechnol 2023; 39:67. [PMID: 36593427 PMCID: PMC9807434 DOI: 10.1007/s11274-022-03512-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
Glycopeptide antibiotics (GPAs) are a family of non-ribosomal peptide natural products with polypeptide skeleton characteristics, which are considered the last resort for treating severe infections caused by multidrug-resistant Gram-positive pathogens. Over the past few years, an increasing prevalence of Gram-positive resistant strain "superbugs" has emerged. Therefore, more efforts are needed to study and modify the GPAs to overcome the challenge of superbugs. In this mini-review, we provide an overview of the complex biosynthetic gene clusters (BGCs), the ingenious crosslinking and tailoring modifications, the new GPA derivatives, the discoveries of new natural GPAs, and the new applications of GPAs in antivirus and anti-Gram-negative bacteria. With the development and interdisciplinary integration of synthetic biology, next-generation sequencing (NGS), and artificial intelligence (AI), more GPAs with new chemical structures and action mechanisms will constantly be emerging.
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Affiliation(s)
- Li Tian
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
| | - Shi Shi
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
| | - Xiangmei Zhang
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
| | - Fubo Han
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
| | - Huijun Dong
- School of Pharmaceutical Sciences, Liaocheng University, 252000 Liaocheng, China
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25
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Ho YTC, Zhao Y, Tailhades J, Cryle MJ. A Chemoenzymatic Approach to Investigate Cytochrome P450 Cross-Linking in Glycopeptide Antibiotic Biosynthesis. Methods Mol Biol 2023; 2670:187-206. [PMID: 37184705 DOI: 10.1007/978-1-0716-3214-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Glycopeptide antibiotics (GPAs) are important and medically relevant peptide natural products. In the context of antimicrobial resistance (AMR), understanding and manipulating GPA biosynthesis is essential to discover new bioactive derivatives of these peptides. Among all the enzymatic steps in GPA biosynthesis, the most complex occurs during the maturation (cross-linking) of the peptide aglycone. This is achieved-while the peptide remains attached to the nonribosomal peptide synthetase (NRPS) machinery-through the action of a cytochrome P450 (CYP450 or Oxy)-mediated cyclization cascade. There is great interest in understanding the formation of the cross-links between the aromatic side chains in GPAs as this process leads to the cup-shaped aglycone, which is itself a requirement for antibiotic activity. In this regard, the use of in vitro experiments is crucial to study this process. To address the process of peptide cyclization during GPA biosynthesis, a series of peptide substrates and different Oxy enzymes are required. In this chapter, we describe a practical and efficient route for the synthesis of peptidyl-CoAs, the expression of proteins/enzymes involved in the in vitro cyclization assay, the loading of the PCP with peptidyl-CoAs, an optimized CYP450-mediated cyclization cascade and assay workup followed by mass spectrometry (MS) characterization. This in vitro assay affords high conversion to cyclic peptides and demonstrates the tolerance of the P450s for novel GPA precursor peptide substrates.
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Affiliation(s)
- Y T Candace Ho
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Yongwei Zhao
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Julien Tailhades
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Max J Cryle
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
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26
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Zhao Y, Marschall E, Treisman M, McKay A, Padva L, Crüsemann M, Nelson DR, Steer DL, Schittenhelm RB, Tailhades J, Cryle MJ. Cytochrome P450 Blt Enables Versatile Peptide Cyclisation to Generate Histidine- and Tyrosine-Containing Crosslinked Tripeptide Building Blocks. Angew Chem Int Ed Engl 2022; 61:e202204957. [PMID: 35851739 PMCID: PMC9542247 DOI: 10.1002/anie.202204957] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Indexed: 12/05/2022]
Abstract
We report our investigation of the utility of peptide crosslinking cytochrome P450 enzymes from biarylitide biosynthesis to generate a range of cyclic tripeptides from simple synthons. The crosslinked tripeptides produced by this P450 include both tyrosine-histidine (A-N-B) and tyrosine-tryptophan (A-O-B) crosslinked tripeptides, the latter a rare example of a phenolic crosslink to an indole moiety. Tripeptides are easily isolated following proteolytic removal of the leader peptide and can incorporate a wide range of amino acids in the residue inside the crosslinked tripeptide. Given the utility of peptide crosslinks in important natural products and the synthetic challenge that these can represent, P450 enzymes have the potential to play roles as important tools in the generation of high-value cyclic tripeptides for incorporation in synthesis, which can be yet further diversified using selective chemical techniques through specific handles contained within these tripeptides.
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Affiliation(s)
- Yongwei Zhao
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Edward Marschall
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Maxine Treisman
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Alasdair McKay
- Department of ChemistryMonash UniversityClaytonVIC 3800Australia
| | - Leo Padva
- Institute of Pharmaceutical BiologyUniversity of Bonn53115BonnGermany
| | - Max Crüsemann
- Institute of Pharmaceutical BiologyUniversity of Bonn53115BonnGermany
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of TennesseeMemphisTN 38163USA
| | - David L. Steer
- Monash Proteomics and Metabolomics FacilityMonash UniversityClaytonVIC 3800Australia
| | - Ralf B. Schittenhelm
- Monash Proteomics and Metabolomics FacilityMonash UniversityClaytonVIC 3800Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
| | - Max J. Cryle
- Department of Biochemistry and Molecular BiologyThe Monash Biomedicine Discovery InstituteMonash UniversityClaytonVIC 3800Australia
- EMBL AustraliaMonash UniversityClaytonVIC 3800Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceClaytonVIC 3800Australia
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27
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Chen H, Zhong L, Zhou H, Sun T, Zhong G, Tu Q, Zhuang Y, Bai X, Wang X, Xu J, Xia L, Shen Y, Zhang Y, Bian X. Biosynthesis of Glidomides and Elucidation of Different Mechanisms for Formation of β-OH Amino Acid Building Blocks. Angew Chem Int Ed Engl 2022; 61:e202203591. [PMID: 35689369 DOI: 10.1002/anie.202203591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 11/06/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) can incorporate nonproteinogenic amino acids into peptidyl backbones to increase structural diversity. Genome mining of Schlegelella brevitalea led to the identification of a class of linear lipoheptapeptides, glidomides, featuring two unusual residues: threo-β-OH-L-His and threo-β-OH-D-Asp. The β-hydroxylation of Asp and His is catalyzed by the nonheme FeII /α-ketoglutarate-dependent β-hydroxylases GlmD and GlmF, respectively. GlmD independently catalyzes the hydroxylation of L-Asp to primarily produce threo-β-OH-L-Asp on the thiolation domain, and then undergoes epimerization to form threo-β-OH-D-Asp in the final products. However, β-hydroxylation of His requires the concerted action of GlmF and the interface (I) domain, a novel condensation domain family clade. The key sites of I domain for interaction with GlmF were identified, suggesting that the mechanism for hydroxylation of His depends on the collaboration between hydroxylase and NRPS.
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Affiliation(s)
- Hanna Chen
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Lin Zhong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Tao Sun
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Guannan Zhong
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Qiang Tu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yan Zhuang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xianping Bai
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Xingyan Wang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Jiaying Xu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yuemao Shen
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
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28
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Hansen MH, Stegmann E, Cryle MJ. Beyond vancomycin: recent advances in the modification, reengineering, production and discovery of improved glycopeptide antibiotics to tackle multidrug-resistant bacteria. Curr Opin Biotechnol 2022; 77:102767. [PMID: 35933924 DOI: 10.1016/j.copbio.2022.102767] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/01/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Glycopeptide antibiotics (GPAs), which include vancomycin and teicoplanin, are important last-resort antibiotics used to treat multidrug-resistant Gram-positive bacterial infections. Whilst second-generation GPAs - generated through chemical modification of natural GPAs - have proven successful, the emergence of GPA resistance has underlined the need to develop new members of this compound class. Significant recent advances have been made in GPA research, including gaining an in-depth understanding of their biosynthesis, improving titre in production strains, developing new derivatives via novel chemical modifications and identifying a new mode of action for structurally diverse type-V GPAs. Taken together, these advances demonstrate significant untapped potential for the further development of GPAs to tackle the growing threat of multidrug-resistant bacteria.
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Affiliation(s)
- Mathias H Hansen
- 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, 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, Tübingen, Germany; Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - 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; ARC Centre of Excellence for Innovations in Peptide and Protein Science, Australia.
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29
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Zhu HJ, Zhang B, Wei W, Liu SH, Xiang L, Zhu J, Jiao RH, Igarashi Y, Bashiri G, Liang Y, Tan RX, Ge HM. AvmM catalyses macrocyclization through dehydration/Michael-type addition in alchivemycin A biosynthesis. Nat Commun 2022; 13:4499. [PMID: 35922406 PMCID: PMC9349299 DOI: 10.1038/s41467-022-32088-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 07/15/2022] [Indexed: 11/21/2022] Open
Abstract
Macrocyclization is an important process that affords morphed scaffold in biosynthesis of bioactive natural products. Nature has adapted diverse biosynthetic strategies to form macrocycles. In this work, we report the identification and characterization of a small enzyme AvmM that can catalyze the construction of a 16-membered macrocyclic ring in the biosynthesis of alchivemycin A (1). We show through in vivo gene deletion, in vitro biochemical assay and isotope labelling experiments that AvmM catalyzes tandem dehydration and Michael-type addition to generate the core scaffold of 1. Mechanistic studies by crystallography, DFT calculations and MD simulations of AvmM reveal that the reactions are achieved with assistance from the special tenuazonic acid like moiety of substrate. Our results thus uncover an uncharacterized macrocyclization strategy in natural product biosynthesis. Macrocyclization is an important process in bioactive natural product synthesis. Here, the authors report on the study of a macrocyclic ring constructing enzyme in the biosynthesis of alchivemycin A and using gene deletion, biochemical assays and isotope labelling show the enzyme catalyses tandem dehydration and Michael-type addition.
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Affiliation(s)
- Hong Jie Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Wanqing Wei
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Centre, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Shuang He Liu
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Lang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jiapeng Zhu
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Medicine and Life Sciences, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, 939-0398, Japan
| | - Ghader Bashiri
- Laboratory of Molecular and Microbial Biochemistry, School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Centre, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Centre, Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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30
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Patteson JB, Fortinez CM, Putz AT, Rodriguez-Rivas J, Bryant LH, Adhikari K, Weigt M, Schmeing TM, Li B. Structure and Function of a Dehydrating Condensation Domain in Nonribosomal Peptide Biosynthesis. J Am Chem Soc 2022; 144:14057-14070. [PMID: 35895935 DOI: 10.1021/jacs.1c13404] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dehydroamino acids are important structural motifs and biosynthetic intermediates for natural products. Many bioactive natural products of nonribosomal origin contain dehydroamino acids; however, the biosynthesis of dehydroamino acids in most nonribosomal peptides is not well understood. Here, we provide biochemical and bioinformatic evidence in support of the role of a unique class of condensation domains in dehydration (CmodAA). We also obtain the crystal structure of a CmodAA domain, which is part of the nonribosomal peptide synthetase AmbE in the biosynthesis of the antibiotic methoxyvinylglycine. Biochemical analysis reveals that AmbE-CmodAA modifies a peptide substrate that is attached to the donor carrier protein. Mutational studies of AmbE-CmodAA identify several key residues for activity, including four residues that are mostly conserved in the CmodAA subfamily. Alanine mutation of these conserved residues either significantly increases or decreases AmbE activity. AmbE exhibits a dimeric conformation, which is uncommon and could enable transfer of an intermediate between different protomers. Our discovery highlights a central dehydrating function for CmodAA domains that unifies dehydroamino acid biosynthesis in diverse nonribosomal peptide pathways. Our work also begins to shed light on the mechanism of CmodAA domains. Understanding CmodAA domain function may facilitate identification of new natural products that contain dehydroamino acids and enable engineering of dehydroamino acids into nonribosomal peptides.
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Affiliation(s)
- Jon B Patteson
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Camille Marie Fortinez
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Andrew T Putz
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Juan Rodriguez-Rivas
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biologie Computationnelle et Quantitative - LCQB, Paris 75005, France
| | - L Henry Bryant
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kamal Adhikari
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Martin Weigt
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine, Biologie Computationnelle et Quantitative - LCQB, Paris 75005, France
| | - T Martin Schmeing
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, Canada H3G 0B1
| | - Bo Li
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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31
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Zhao Y, Marschall E, Treisman M, McKay A, Padva L, Crüsemann M, Nelson DR, Steer DL, Schittenhelm RB, Tailhades J, Cryle MJ. Cytochrome P450Blt Enables Versatile Peptide Cyclisation to Generate Histidine and Tyrosine Containing Crosslinked Tripeptide Building Blocks. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | | | | | | | - Leo Padva
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Institute of Pharmaceutical Biology GERMANY
| | - Max Crüsemann
- University of Bonn: Rheinische Friedrich-Wilhelms-Universitat Bonn Pharmaceutical Biology GERMANY
| | - David R Nelson
- University of Tennessee College of Medicine: The University of Tennessee Health Science Center College of Medicine Microbiology UNITED STATES
| | - David L Steer
- Monash University Biochemistry and Molecular Biology AUSTRALIA
| | | | | | - Max J. Cryle
- Monash University Department of Biochemistry and Molecular Biology 15 Innovation WalkMonash University 3800 Melbourne AUSTRALIA
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32
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Chen H, Zhong L, Zhou H, Sun T, Zhong G, Tu Q, Zhuang Y, Bai X, Wang X, Xu J, Xia L, Shen Y, Zhang Y, Bian X. Biosynthesis of Glidomides and Elucidation of Different Mechanisms for Formation of β‐OH Amino Acid Building Blocks. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203591] [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)
- Hanna Chen
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Lin Zhong
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- Faculty of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Tao Sun
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Guannan Zhong
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Qiang Tu
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- Faculty of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Yan Zhuang
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Xianping Bai
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Xingyan Wang
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Jiaying Xu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology State Key Laboratory of Developmental Biology of Freshwater Fish College of Life Science Hunan Normal University Changsha 410081 China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology State Key Laboratory of Developmental Biology of Freshwater Fish College of Life Science Hunan Normal University Changsha 410081 China
| | - Yuemao Shen
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
- CAS Key Laboratory of Quantitative Engineering Biology Shenzhen Institute of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- Faculty of Synthetic Biology Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-infectives Shandong University-Helmholtz Institute of Biotechnology State Key Laboratory of Microbial Technology Shandong University Qingdao Shandong 266237 China
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33
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Xu M, Wang W, Waglechner N, Culp EJ, Guitor AK, Wright GD. Phylogeny-Informed Synthetic Biology Reveals Unprecedented Structural Novelty in Type V Glycopeptide Antibiotics. ACS CENTRAL SCIENCE 2022; 8:615-626. [PMID: 35647273 PMCID: PMC9136965 DOI: 10.1021/acscentsci.1c01389] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Indexed: 06/01/2023]
Abstract
The rise and dissemination of glycopeptide antibiotic (GPA)-resistant pathogens in healthcare settings fuel efforts to discover GPAs that can overcome resistance. Members of the type V subclass of GPAs can evade common GPA resistance mechanisms and offer promise as new drug leads. We characterize five new type V GPAs-rimomycin-A/B/C and misaugamycin-A/B-discovered through a phylogeny-guided genome mining strategy coupled with heterologous production using our GPAHex synthetic biology platform. Rimomycin is a heptapeptide similar to kistamicin but includes an N-methyl-tyrosine at amino acid 6 (AA6) and substitutes 4-hydroxyphenylglycine for tyrosine and 3,5-dihydroxyphenylglycine at positions AA1 and AA3. Misaugamycin is characterized by an unprecedented N-C cross-link between AA2 and AA4 and unique N-terminal acylation by malonyl (misaugamycin-A) or 2-sulfoacetyl (misaugamycin-B) groups. We demonstrate that rimomycin-A/B/C and misaugamycin-A/B are potent antibiotics with activity against GPA-resistant clinical isolates and that the mode of action is consistent with the inhibition of cell division by the evasion of autolysin activity. These discoveries expand the chemical diversity of the type V GPAs, offer new chemical scaffolds for drug development, and demonstrate the application of the GPAHex platform in mining GPA chemical "dark matter".
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Affiliation(s)
- Min Xu
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Wenliang Wang
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Nicholas Waglechner
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Elizabeth J. Culp
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Allison K. Guitor
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Gerard D. Wright
- David Braley Center for Antibiotic
Discovery, Michael G. DeGroote Institute for Infectious Disease Research,
Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
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34
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An JS, Kim MS, Han J, Jang SC, Im JH, Cui J, Lee Y, Nam SJ, Shin J, Lee SK, Yoon YJ, Oh DC. Nyuzenamide C, an Antiangiogenic Epoxy Cinnamic Acid-Containing Bicyclic Peptide from a Riverine Streptomyces sp. JOURNAL OF NATURAL PRODUCTS 2022; 85:804-814. [PMID: 35294831 DOI: 10.1021/acs.jnatprod.1c00837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A new nonribosomal peptide, nyuzenamide C (1), was discovered from riverine sediment-derived Streptomyces sp. DM14. Comprehensive analysis of the spectroscopic data of nyuzenamide C (1) revealed that 1 has a bicyclic backbone composed of six common amino acid residues (Asn, Leu, Pro, Gly, Val, and Thr) and four nonproteinogenic amino acid units, including hydroxyglycine, β-hydroxyphenylalanine, p-hydroxyphenylglycine, and 3,β-dihydroxytyrosine, along with 1,2-epoxypropyl cinnamic acid. The absolute configuration of 1 was proposed by J-based configuration analysis, the advanced Marfey's method, quantum mechanics-based DP4 calculations, and bioinformatic analysis of its nonribosomal peptide synthetase biosynthetic gene cluster. Nyuzenamide C (1) displayed antiangiogenic activity in human umbilical vein endothelial cells and induced quinone reductase in murine Hepa-1c1c7 cells.
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Affiliation(s)
- Joon Soo An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Myoun-Su Kim
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jaeho Han
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Chul Jang
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Hyeon Im
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeonjin Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang-Jip Nam
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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35
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Greule A, Izoré T, Machell D, Hansen MH, Schoppet M, De Voss JJ, Charkoudian LK, Schittenhelm RB, Harmer JR, Cryle MJ. The Cytochrome P450 OxyA from the Kistamicin Biosynthesis Cyclization Cascade is Highly Sensitive to Oxidative Damage. Front Chem 2022; 10:868240. [PMID: 35464232 PMCID: PMC9023744 DOI: 10.3389/fchem.2022.868240] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/01/2022] [Indexed: 11/17/2022] Open
Abstract
Cytochrome P450 enzymes (P450s) are a superfamily of monooxygenases that utilize a cysteine thiolate–ligated heme moiety to perform a wide range of demanding oxidative transformations. Given the oxidative power of the active intermediate formed within P450s during their active cycle, it is remarkable that these enzymes can avoid auto-oxidation and retain the axial cysteine ligand in the deprotonated—and thus highly acidic—thiolate form. While little is known about the process of heme incorporation during P450 folding, there is an overwhelming preference for one heme orientation within the P450 active site. Indeed, very few structures to date contain an alternate heme orientation, of which two are OxyA homologs from glycopeptide antibiotic (GPA) biosynthesis. Given the apparent preference for the unusual heme orientation shown by OxyA enzymes, we investigated the OxyA homolog from kistamicin biosynthesis (OxyAkis), which is an atypical GPA. We determined that OxyAkis is highly sensitive to oxidative damage by peroxide, with both UV and EPR measurements showing rapid bleaching of the heme signal. We determined the structure of OxyAkis and found a mixed population of heme orientations present in this enzyme. Our analysis further revealed the possible modification of the heme moiety, which was only present in samples where the alternate heme orientation was present in the protein. These results suggest that the typical heme orientation in cytochrome P450s can help prevent potential damage to the heme—and hence deactivation of the enzyme—during P450 catalysis. It also suggests that some P450 enzymes involved in GPA biosynthesis may be especially prone to oxidative damage due to the heme orientation found in their active sites.
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Affiliation(s)
- Anja Greule
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
| | - Thierry Izoré
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
| | - Daniel Machell
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
| | - Mathias H. Hansen
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
| | - Melanie Schoppet
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
| | - James J. De Voss
- Department of Chemistry, The University of Queensland, St Lucia, QLD, Australia
| | | | - Ralf B. Schittenhelm
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, VIC, Australia
| | - Jeffrey R. Harmer
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia
| | - Max J. Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
- *Correspondence: Max J. Cryle,
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36
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Xu M, Wang W, Wright GD. Glycopeptide antibiotic discovery in the genomic era. Methods Enzymol 2022; 665:325-346. [PMID: 35379441 DOI: 10.1016/bs.mie.2021.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Glycopeptide antibiotics are essential drugs used to treat infections caused by multi-drug resistant Gram-positive pathogens. There is a continuous need for new antibiotics, including GPAs, to address emerging resistance and offer desirable pharmacological profiles for improved efficacy. Microbial natural products are proven sources of antibiotics, and this source has dominated drug discovery over the past century. Bacteria from the phylum Actinobacteria are particularly renowned for producing a diverse range of bioactive natural products including glycopeptide antibiotics. The traditional approach to mining this resource is through the culture and extraction of natural products followed by assay for cell-killing activity. Unfortunately, this method no longer efficiently yields new antibiotic leads, delivering instead known compounds. Whole-genome sequencing programs on the other hand are revealing thousands of unexplored natural product biosynthetic gene clusters in the chromosomes of Actinobacteria. These gene clusters encode the necessary enzymes, transport and resistance mechanisms, along with regulatory elements for the biosynthesis of a variety of antibiotics. Identification of uncharacterized or cryptic biosynthetic gene clusters to unlock the chemical "dark matter" represents a new direction for the discovery of new drug candidates. This chapter discusses the identification of glycopeptide antibiotic biosynthetic gene clusters in microbial genomes, the improved production of these antibiotics using the GPAHex synthetic biology platform, and methods for their purification.
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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
| | - 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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37
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Duban M, Cociancich S, Leclère V. Nonribosomal Peptide Synthesis Definitely Working Out of the Rules. Microorganisms 2022; 10:577. [PMID: 35336152 PMCID: PMC8949500 DOI: 10.3390/microorganisms10030577] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 12/04/2022] Open
Abstract
Nonribosomal peptides are microbial secondary metabolites exhibiting a tremendous structural diversity and a broad range of biological activities useful in the medical and agro-ecological fields. They are built up by huge multimodular enzymes called nonribosomal peptide synthetases. These synthetases are organized in modules constituted of adenylation, thiolation, and condensation core domains. As such, each module governs, according to the collinearity rule, the incorporation of a monomer within the growing peptide. The release of the peptide from the assembly chain is finally performed by a terminal core thioesterase domain. Secondary domains with modifying catalytic activities such as epimerization or methylation are sometimes included in the assembly lines as supplementary domains. This assembly line structure is analyzed by bioinformatics tools to predict the sequence and structure of the final peptides according to the sequence of the corresponding synthetases. However, a constantly expanding literature unravels new examples of nonribosomal synthetases exhibiting very rare domains and noncanonical organizations of domains and modules, leading to several amazing strategies developed by microorganisms to synthesize nonribosomal peptides. In this review, through several examples, we aim at highlighting these noncanonical pathways in order for the readers to perceive their complexity.
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Affiliation(s)
- Matthieu Duban
- Université de Lille, Université de Liège, UMRT 1158 BioEcoAgro, Métabolites Secondaires d’origine Microbienne, Institut Charles Viollette, F-59000 Lille, France;
| | - Stéphane Cociancich
- CIRAD, UMR PHIM, F-34398 Montpellier, France;
- PHIM, Université Montpellier, CIRAD, INRAE, Institut Agro, IRD, F-34398 Montpellier, France
| | - Valérie Leclère
- Université de Lille, Université de Liège, UMRT 1158 BioEcoAgro, Métabolites Secondaires d’origine Microbienne, Institut Charles Viollette, F-59000 Lille, France;
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38
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Wenski SL, Thiengmag S, Helfrich EJ. Complex peptide natural products: Biosynthetic principles, challenges and opportunities for pathway engineering. Synth Syst Biotechnol 2022; 7:631-647. [PMID: 35224231 PMCID: PMC8842026 DOI: 10.1016/j.synbio.2022.01.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/03/2023] Open
Abstract
Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties. As a result, many peptides have entered the clinics for various applications. Two main routes for the biosynthesis of complex peptides have evolved in nature: ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic pathways and non-ribosomal peptide synthetases (NRPSs). Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes. These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides. In this review, we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications. In addition, the influence of the fundamentally different biosynthetic principles on past, current and future engineering approaches is illustrated. Despite the different biosynthetic principles of both peptide biosynthetic routes, the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping. The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.
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Affiliation(s)
- Sebastian L. Wenski
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
| | - Sirinthra Thiengmag
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
| | - Eric J.N. Helfrich
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
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39
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Fortinez CM, Bloudoff K, Harrigan C, Sharon I, Strauss M, Schmeing TM. Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module. Nat Commun 2022; 13:548. [PMID: 35087027 PMCID: PMC8795117 DOI: 10.1038/s41467-022-28221-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/19/2021] [Indexed: 12/15/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and additional proteins that introduce chemical modifications before, during or after assembly-line synthesis. The bacillamide biosynthetic pathway is a common, three-protein system, with a decarboxylase that prepares an NRPS substrate, an NRPS, and an oxidase. Here, the pathway is reconstituted in vitro. The oxidase is shown to perform dehydrogenation of the thiazoline in the peptide intermediate while it is covalently attached to the NRPS, as the penultimate step in bacillamide D synthesis. Structural analysis of the oxidase reveals a dimeric, two-lobed architecture with a remnant RiPP recognition element and a dramatic wrapping loop. The oxidase forms a stable complex with the NRPS and dimerizes it. We visualized co-complexes of the oxidase bound to the elongation module of the NRPS using X-ray crystallography and cryo-EM. The three active sites (for adenylation, condensation/cyclization, and oxidation) form an elegant arc to facilitate substrate delivery. The structures enabled a proof-of-principle bioengineering experiment in which the BmdC oxidase domain is embedded into the NRPS.
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Affiliation(s)
- Camille Marie Fortinez
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Kristjan Bloudoff
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Connor Harrigan
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Itai Sharon
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Mike Strauss
- Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada.,Department of Anatomy and Cell Biology, McGill University, Montréal, QC, H3A 0C7, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada. .,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada.
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40
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Aldemir H, Shu S, Schaefers F, Hong H, Richarz R, Harteis S, Einsiedler M, Milzarek TM, Schneider S, Gulder TAM. Carrier Protein-Free Enzymatic Biaryl Coupling in Arylomycin A2 Assembly and Structure of the Cytochrome P450 AryC. Chemistry 2022; 28:e202103389. [PMID: 34725865 PMCID: PMC9299028 DOI: 10.1002/chem.202103389] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Indexed: 12/16/2022]
Abstract
The arylomycin antibiotics are potent inhibitors of bacterial type I signal peptidase. These lipohexapeptides contain a biaryl structural motif reminiscent of glycopeptide antibiotics. We herein describe the functional and structural evaluation of AryC, the cytochrome P450 performing biaryl coupling in biosynthetic arylomycin assembly. Unlike its enzymatic counterparts in glycopeptide biosynthesis, AryC converts free substrates without the requirement of any protein interaction partner, likely enabled by a strongly hydrophobic cavity at the surface of AryC pointing to the substrate tunnel. This activity enables chemo-enzymatic assembly of arylomycin A2 that combines the advantages of liquid- and solid-phase peptide synthesis with late-stage enzymatic cross-coupling. The reactivity of AryC is unprecedented in cytochrome P450-mediated biaryl construction in non-ribosomal peptides, in which peptidyl carrier protein (PCP)-tethering so far was shown crucial both in vivo and in vitro.
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Affiliation(s)
- Hülya Aldemir
- Chair of Technical BiochemistryTechnical University of DresdenBergstraße 6601069DresdenGermany
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
| | - Shuangjie Shu
- Chair of Technical BiochemistryTechnical University of DresdenBergstraße 6601069DresdenGermany
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
| | - Francoise Schaefers
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
| | - Hanna Hong
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
| | - René Richarz
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
| | - Sabrina Harteis
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
| | - Manuel Einsiedler
- Chair of Technical BiochemistryTechnical University of DresdenBergstraße 6601069DresdenGermany
| | - Tobias M. Milzarek
- Chair of Technical BiochemistryTechnical University of DresdenBergstraße 6601069DresdenGermany
| | - Sabine Schneider
- Department of ChemistryLudwig-Maximillians-University MunichButenandtstraße 5–1381377MunichGermany
| | - Tobias A. M. Gulder
- Chair of Technical BiochemistryTechnical University of DresdenBergstraße 6601069DresdenGermany
- Biosystems Chemistry, Faculty of ChemistryTechnical University of MunichLichtenbergstraße 485748GarchingGermany
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41
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Iacovelli R, Bovenberg RAL, Driessen AJM. Nonribosomal peptide synthetases and their biotechnological potential in Penicillium rubens. J Ind Microbiol Biotechnol 2021; 48:6324005. [PMID: 34279620 PMCID: PMC8788816 DOI: 10.1093/jimb/kuab045] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/12/2021] [Indexed: 01/23/2023]
Abstract
Nonribosomal peptide synthetases (NRPS) are large multimodular enzymes that synthesize a diverse variety of peptides. Many of these are currently used as pharmaceuticals, thanks to their activity as antimicrobials (penicillin, vancomycin, daptomycin, echinocandin), immunosuppressant (cyclosporin) and anticancer compounds (bleomycin). Because of their biotechnological potential, NRPSs have been extensively studied in the past decades. In this review, we provide an overview of the main structural and functional features of these enzymes, and we consider the challenges and prospects of engineering NRPSs for the synthesis of novel compounds. Furthermore, we discuss secondary metabolism and NRP synthesis in the filamentous fungus Penicillium rubens and examine its potential for the production of novel and modified β-lactam antibiotics.
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Affiliation(s)
- Riccardo Iacovelli
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Roel A L Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands.,DSM Biotechnology Centre, 2613 AX Delft, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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42
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Ye Y, Fu H, Hyster TK. Activation modes in biocatalytic radical cyclization reactions. J Ind Microbiol Biotechnol 2021; 48:kuab021. [PMID: 33674826 PMCID: PMC8210684 DOI: 10.1093/jimb/kuab021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/26/2021] [Indexed: 12/17/2022]
Abstract
Radical cyclizations are essential reactions in the biosynthesis of secondary metabolites and the chemical synthesis of societally valuable molecules. In this review, we highlight the general mechanisms utilized in biocatalytic radical cyclizations. We specifically highlight cytochrome P450 monooxygenases (P450s) involved in the biosynthesis of mycocyclosin and vancomycin, nonheme iron- and α-ketoglutarate-dependent dioxygenases (Fe/αKGDs) used in the biosynthesis of kainic acid, scopolamine, and isopenicillin N, and radical S-adenosylmethionine (SAM) enzymes that facilitate the biosynthesis of oxetanocin A, menaquinone, and F420. Beyond natural mechanisms, we also examine repurposed flavin-dependent "ene"-reductases (ERED) for non-natural radical cyclization. Overall, these general mechanisms underscore the opportunity for enzymes to augment and enhance the synthesis of complex molecules using radical mechanisms.
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Affiliation(s)
- Yuxuan Ye
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Haigen Fu
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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43
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Pang B, Liao R, Tang Z, Guo S, Wu Z, Liu W. Caerulomycin and collismycin antibiotics share a trans-acting flavoprotein-dependent assembly line for 2,2'-bipyridine formation. Nat Commun 2021; 12:3124. [PMID: 34035275 PMCID: PMC8149447 DOI: 10.1038/s41467-021-23475-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 04/28/2021] [Indexed: 11/09/2022] Open
Abstract
Linear nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) template the modular biosynthesis of numerous nonribosomal peptides, polyketides and their hybrids through assembly line chemistry. This chemistry can be complex and highly varied, and thus challenges our understanding in NRPS and PKS-programmed, diverse biosynthetic processes using amino acid and carboxylate building blocks. Here, we report that caerulomycin and collismycin peptide-polyketide hybrid antibiotics share an assembly line that involves unusual NRPS activity to engage a trans-acting flavoprotein in C-C bond formation and heterocyclization during 2,2'-bipyridine formation. Simultaneously, this assembly line provides dethiolated and thiolated 2,2'-bipyridine intermediates through differential treatment of the sulfhydryl group arising from L-cysteine incorporation. Subsequent L-leucine extension, which does not contribute any atoms to either caerulomycins or collismycins, plays a key role in sulfur fate determination by selectively advancing one of the two 2,2'-bipyridine intermediates down a path to the final products with or without sulfur decoration. These findings further the appreciation of assembly line chemistry and will facilitate the development of related molecules using synthetic biology approaches.
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Affiliation(s)
- Bo Pang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Rijing Liao
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Shengjie Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Zhuhua Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China. .,Huzhou Center of Bio-Synthetic Innovation, Huzhou, China.
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44
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Izoré T, Candace Ho YT, Kaczmarski JA, Gavriilidou A, Chow KH, Steer DL, Goode RJA, Schittenhelm RB, Tailhades J, Tosin M, Challis GL, Krenske EH, Ziemert N, Jackson CJ, Cryle MJ. Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity. Nat Commun 2021; 12:2511. [PMID: 33947858 PMCID: PMC8097023 DOI: 10.1038/s41467-021-22623-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/23/2021] [Indexed: 02/08/2023] Open
Abstract
Non-ribosomal peptide synthetases are important enzymes for the assembly of complex peptide natural products. Within these multi-modular assembly lines, condensation domains perform the central function of chain assembly, typically by forming a peptide bond between two peptidyl carrier protein (PCP)-bound substrates. In this work, we report structural snapshots of a condensation domain in complex with an aminoacyl-PCP acceptor substrate. These structures allow the identification of a mechanism that controls access of acceptor substrates to the active site in condensation domains. The structures of this complex also allow us to demonstrate that condensation domain active sites do not contain a distinct pocket to select the side chain of the acceptor substrate during peptide assembly but that residues within the active site motif can instead serve to tune the selectivity of these central biosynthetic domains.
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Affiliation(s)
- Thierry Izoré
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- EMBL Australia, Monash University, Clayton, VIC, Australia.
| | - Y T Candace Ho
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Joe A Kaczmarski
- Research School of Chemistry, The Australian National University, Acton, ACT, Australia
| | - Athina Gavriilidou
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Tübingen, Germany
| | - Ka Ho Chow
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - David L Steer
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, VIC, Australia
| | - Robert J A Goode
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, VIC, Australia
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, VIC, Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
| | - Manuela Tosin
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Gregory L Challis
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
- Department of Chemistry, University of Warwick, Coventry, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Partnersite Tübingen, Tübingen, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Colin J Jackson
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
- Research School of Chemistry, The Australian National University, Acton, ACT, Australia
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- EMBL Australia, Monash University, Clayton, VIC, Australia.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia.
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45
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Yuan C, Ouyang Q, Wang X, Li X, Tan H, Chen G. Interactive Regulation between Aliphatic Hydroxylation and Aromatic Hydroxylation of Thaxtomin D in TxtC: A Theoretical Investigation. Inorg Chem 2021; 60:6433-6445. [PMID: 33861573 DOI: 10.1021/acs.inorgchem.1c00154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
TxtC is an unusual bifunctional cytochrome P450 that is able to perform sequential aliphatic and aromatic hydroxylation of the diketopiperazine substrate thaxtomin D in two distinct sites to produce thaxtomin A. Though the X-ray structure of TxtC complexed with thaxtomin D revealed a binding mode for its aromatic hydroxylation, the preferential hydroxylation site is aliphatic C14. It is thus intriguing to unravel how TxtC accomplishes such two-step catalytic hydroxylation on distinct aliphatic and aromatic carbons and why the aliphatic site is preferred in the hydroxylation step. In this work, by employing molecular docking and molecular dynamics (MD) simulation, we revealed that thaxtomin D could adopt two different conformations in the TxtC active site, which were equal in energy with either the aromatic C20-H or aliphatic C14-H pointing toward the active Cpd I oxyferryl moiety. Further ONIOM calculations indicated that the energy barrier for the rate-limiting hydroxylation step on the aliphatic C14 site was 9.6 kcal/mol more favorable than that on the aromatic C20 site. The hydroxyl group on the monohydroxylated intermediate thaxtomin B C14 site formed hydrogen bonds with Ser280 and Thr385, which induced the l-Phe moiety to rotate around the Cβ-Cγ bond of the 4-nitrotryptophan moiety. Thus, it adopted an energetically favorable conformation with aromatic C20 adjacent to the oxyferryl moiety. In addition, the hydroxyl group induced solvent water molecules to enter the active site, which propelled thaxtomin B toward the heme plane and resulted in heme distortion. Based on this geometrical layout, the rate-limiting aromatic hydroxylation energy barrier decreased to 15.4 kcal/mol, which was comparable to that of the thaxtomin D aliphatic hydroxylation process. Our calculations indicated that heme distortion lowered the energy level of the lowest Cpd I α-vacant orbital, which promoted electron transfer in the rate-limiting thaxtomin B aromatic hydroxylation step in TxtC.
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Affiliation(s)
- Chang Yuan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Qingwen Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Xixi Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Hongwei Tan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing 100875, China
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46
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Leng DJ, Greule A, Cryle MJ, Tosin M. Chemical probes reveal the timing of early chlorination in vancomycin biosynthesis. Chem Commun (Camb) 2021; 57:2293-2296. [PMID: 33533358 DOI: 10.1039/d0cc07421g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycopeptides such as vancomycin are antibiotics of last resort whose biosynthetic pathways still hold undefined details. Chemical probes were used to capture biosynthetic intermediates generated in the nonribosomal peptide formation of vancomycin in vivo. The putative intercepted intermediates were characterised via HR-LC-MS2. These species provided insights into the timing of the first chlorination of the peptide backbone by the halogenase VhaA: this holds significant interest for enzyme engineering towards the making of novel glycopeptides.
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Affiliation(s)
- Daniel J Leng
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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47
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Shi J, Xu X, Liu PY, Hu YL, Zhang B, Jiao RH, Bashiri G, Tan RX, Ge HM. Discovery and biosynthesis of guanipiperazine from a NRPS-like pathway. Chem Sci 2021; 12:2925-2930. [PMID: 34164059 PMCID: PMC8179380 DOI: 10.1039/d0sc06135b] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are modular enzymes that use a thiotemplate mechanism to assemble the peptide backbones of structurally diverse and biologically active natural products in bacteria and fungi. Unlike these canonical multi-modular NRPSs, single-module NRPS-like enzymes, which lack the key condensation (C) domain, are rare in bacteria, and have been largely unexplored to date. Here, we report the discovery of a gene cluster (gup) encoding a NRPS-like megasynthetase through genome mining. Heterologous expression of the gup cluster led to the production of two unprecedented alkaloids, guanipiperazines A and B. The NRPS-like enzyme activates two l-tyrosine molecules, reduces them to the corresponding amino aldehydes, and forms an unstable imine product. The subsequent enzymatic reduction affords piperazine, which can be morphed by a P450 monooxygenase into a highly strained compound through C–O bond formation. Further intermolecular oxidative coupling forming the C–C or C–O bond is catalyzed by another P450 enzyme. This work reveals the huge potential of NRPS-like biosynthetic gene clusters in the discovery of novel natural products. Genome mining of a NRPS-like gene cluster led to the identification of two novel alkaloids with antimicrobial activity. This work reveals the huge potential of NRPS-like biosynthetic gene clusters in the discovery of novel natural products.![]()
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Affiliation(s)
- Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Xiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Pei Yi Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Yi Ling Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Ghader Bashiri
- Laboratory of Structural Biology, Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland Auckland 1010 New Zealand
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China
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Dekimpe S, Masschelein J. Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis. Nat Prod Rep 2021; 38:1910-1937. [DOI: 10.1039/d0np00098a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.
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Affiliation(s)
- Sofie Dekimpe
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
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Hüttel W, Müller M. Regio- and stereoselective intermolecular phenol coupling enzymes in secondary metabolite biosynthesis. Nat Prod Rep 2020; 38:1011-1043. [PMID: 33196733 DOI: 10.1039/d0np00010h] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 2005 to 2020Phenol coupling is a key reaction in the biosynthesis of important biopolymers such as lignin and melanin and of a plethora of biarylic secondary metabolites. The reaction usually leads to several different regioisomeric products due to the delocalization of a radical in the reaction intermediates. If axial chirality is involved, stereoisomeric products are obtained provided no external factor influences the selectivity. Hence, in non-enzymatic organic synthesis it is notoriously difficult to control the selectivity of the reaction, in particular if the coupling is intermolecular. From biosynthesis, it is known that especially fungi, plants, and bacteria produce biarylic compounds regio- and stereoselectively. Nonetheless, the involved enzymes long evaded discovery. First progress was made in the late 1990s; however, the breakthrough came only with the genomic era and, in particular, in the last few years the number of relevant publications has dramatically increased. The discoveries reviewed in this article reveal a remarkable diversity of enzymes that catalyze oxidative intermolecular phenol coupling, including various classes of laccases, cytochrome P450 enzymes, and heme peroxidases. Particularly in the case of laccases, the catalytic systems are often complex and additional proteins, substrates, or reaction conditions have a strong influence on activity and regio- and atroposelectivity. Although the field of (selective) enzymatic phenol coupling is still in its infancy, the diversity of enzymes identified recently could make it easier to select suitable candidates for biotechnological development and to approach this challenging reaction through biocatalysis.
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Affiliation(s)
- Wolfgang Hüttel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104 Freiburg, Germany.
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50
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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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