1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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,
| |
Collapse
|
3
|
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.
Collapse
Affiliation(s)
- Wolfgang Hüttel
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstrasse 25, 79104 Freiburg, Germany.
| | | |
Collapse
|
4
|
Zhao Y, Ho YTC, Tailhades J, Cryle M. Understanding the Glycopeptide Antibiotic Crosslinking Cascade: In Vitro Approaches Reveal the Details of a Complex Biosynthesis Pathway. Chembiochem 2020; 22:43-51. [PMID: 32696500 DOI: 10.1002/cbic.202000309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/21/2020] [Indexed: 11/06/2022]
Abstract
The glycopeptide antibiotics (GPAs) are a fascinating example of complex natural product biosynthesis, with the nonribosomal synthesis of the peptide core coupled to a cytochrome P450-mediated cyclisation cascade that crosslinks aromatic side chains within this peptide. Given that the challenges associated with the synthesis of GPAs stems from their highly crosslinked structure, there is great interest in understanding how biosynthesis accomplishes this challenging set of transformations. In this regard, the use of in vitro experiments has delivered important insights into this process, including the identification of the unique role of the X-domain as a platform for P450 recruitment. In this minireview, we present an analysis of the results of in vitro studies into the GPA cyclisation cascade that have demonstrated both the tolerances and limitations of this process for modified substrates, and in turn developed rules for the future reengineering of this important antibiotic class.
Collapse
Affiliation(s)
- Yongwei Zhao
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Y T Candace Ho
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| | - Max Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,EMBL Australia, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
5
|
Greule A, Izoré T, Iftime D, Tailhades J, Schoppet M, Zhao Y, Peschke M, Ahmed I, Kulik A, Adamek M, Goode RJA, Schittenhelm RB, Kaczmarski JA, Jackson CJ, Ziemert N, Krenske EH, De Voss JJ, Stegmann E, Cryle MJ. Kistamicin biosynthesis reveals the biosynthetic requirements for production of highly crosslinked glycopeptide antibiotics. Nat Commun 2019; 10:2613. [PMID: 31197182 PMCID: PMC6565677 DOI: 10.1038/s41467-019-10384-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 05/07/2019] [Indexed: 01/25/2023] Open
Abstract
Kistamicin is a divergent member of the glycopeptide antibiotics, a structurally complex class of important, clinically relevant antibiotics often used as the last resort against resistant bacteria. The extensively crosslinked structure of these antibiotics that is essential for their activity makes their chemical synthesis highly challenging and limits their production to bacterial fermentation. Kistamicin contains three crosslinks, including an unusual 15-membered A-O-B ring, despite the presence of only two Cytochrome P450 Oxy enzymes thought to catalyse formation of such crosslinks within the biosynthetic gene cluster. In this study, we characterise the kistamicin cyclisation pathway, showing that the two Oxy enzymes are responsible for these crosslinks within kistamicin and that they function through interactions with the X-domain, unique to glycopeptide antibiotic biosynthesis. We also show that the kistamicin OxyC enzyme is a promiscuous biocatalyst, able to install multiple crosslinks into peptides containing phenolic amino acids.
Collapse
Affiliation(s)
- Anja Greule
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Thierry Izoré
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Dumitrita Iftime
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Melanie Schoppet
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Yongwei Zhao
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia
| | - Madeleine Peschke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Iftekhar Ahmed
- Department of Chemistry, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Martina Adamek
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Robert J A Goode
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Monash Biomedical Proteomics Facility, Monash University, Clayton, VIC, 3800, Australia
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Monash Biomedical Proteomics Facility, Monash University, Clayton, VIC, 3800, Australia
| | - Joe A Kaczmarski
- Research School of Chemistry, The Australian National University, Acton, ACT, 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, The Australian National University, Acton, ACT, 2601, Australia
| | - Nadine Ziemert
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Elizabeth H Krenske
- Department of Chemistry, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - James J De Voss
- Department of Chemistry, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
- German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076, Tübingen, Germany.
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
- EMBL Australia, Monash University, Clayton, VIC, 3800, Australia.
| |
Collapse
|
6
|
Brieke C, Tarnawski M, Greule A, Cryle MJ. Investigating Cytochrome P450 specificity during glycopeptide antibiotic biosynthesis through a homologue hybridization approach. J Inorg Biochem 2018; 185:43-51. [DOI: 10.1016/j.jinorgbio.2018.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/30/2018] [Accepted: 05/01/2018] [Indexed: 01/10/2023]
|
7
|
Rudolf JD, Chang CY, Ma M, Shen B. Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep 2017; 34:1141-1172. [PMID: 28758170 PMCID: PMC5585785 DOI: 10.1039/c7np00034k] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to January 2017Cytochrome P450 enzymes (P450s) are some of the most exquisite and versatile biocatalysts found in nature. In addition to their well-known roles in steroid biosynthesis and drug metabolism in humans, P450s are key players in natural product biosynthetic pathways. Natural products, the most chemically and structurally diverse small molecules known, require an extensive collection of P450s to accept and functionalize their unique scaffolds. In this review, we survey the current catalytic landscape of P450s within the Streptomyces genus, one of the most prolific producers of natural products, and comprehensively summarize the functionally characterized P450s from Streptomyces. A sequence similarity network of >8500 P450s revealed insights into the sequence-function relationships of these oxygen-dependent metalloenzymes. Although only ∼2.4% and <0.4% of streptomycete P450s have been functionally and structurally characterized, respectively, the study of streptomycete P450s involved in the biosynthesis of natural products has revealed their diverse roles in nature, expanded their catalytic repertoire, created structural and mechanistic paradigms, and exposed their potential for biomedical and biotechnological applications. Continued study of these remarkable enzymes will undoubtedly expose their true complement of chemical and biological capabilities.
Collapse
Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | | | | |
Collapse
|
8
|
Abstract
Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.
Collapse
Affiliation(s)
- Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Yi Zou
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| |
Collapse
|
9
|
Peschke M, Brieke C, Goode RJA, Schittenhelm RB, Cryle MJ. Chlorinated Glycopeptide Antibiotic Peptide Precursors Improve Cytochrome P450-Catalyzed Cyclization Cascade Efficiency. Biochemistry 2017; 56:1239-1247. [DOI: 10.1021/acs.biochem.6b01102] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Madeleine Peschke
- Department
of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Clara Brieke
- Department
of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Rob J. A. Goode
- Department
of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Monash
Biomedical Proteomics Facility, Monash University, Clayton, Victoria 3800, Australia
| | - Ralf B. Schittenhelm
- Department
of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Monash
Biomedical Proteomics Facility, Monash University, Clayton, Victoria 3800, Australia
| | - Max J. Cryle
- Department
of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Department
of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- ARC
Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
- EMBL
Australia, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
10
|
Mollo A, von Krusenstiern AN, Bulos JA, Ulrich V, Åkerfeldt KS, Cryle MJ, Charkoudian LK. P450 monooxygenase ComJ catalyses side chain phenolic cross-coupling during complestatin biosynthesis. RSC Adv 2017. [DOI: 10.1039/c7ra06518c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
P450 monooxygenase enzyme ComJ catalyzed biaryl ether bond formation with high efficiency and low stereoselectivity on selected complestatin-like peptide substrates.
Collapse
Affiliation(s)
- Aurelio Mollo
- Department of Chemistry
- Haverford College
- Haverford
- USA
| | | | | | - Veronika Ulrich
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69121 Heidelberg
- Germany
| | | | - Max J. Cryle
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69121 Heidelberg
- Germany
- EMBL Australia
| | | |
Collapse
|
11
|
Ulrich V, Brieke C, Cryle MJ. Biochemical and structural characterisation of the second oxidative crosslinking step during the biosynthesis of the glycopeptide antibiotic A47934. Beilstein J Org Chem 2016; 12:2849-2864. [PMID: 28144358 PMCID: PMC5238595 DOI: 10.3762/bjoc.12.284] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/09/2016] [Indexed: 12/24/2022] Open
Abstract
The chemical complexity and biological activity of the glycopeptide antibiotics (GPAs) stems from their unique crosslinked structure, which is generated by the actions of cytochrome P450 (Oxy) enzymes that affect the crosslinking of aromatic side chains of amino acid residues contained within the GPA heptapeptide precursor. Given the crucial role peptide cyclisation plays in GPA activity, the characterisation of this process is of great importance in understanding the biosynthesis of these important antibiotics. Here, we report the cyclisation activity and crystal structure of StaF, the D-O-E ring forming Oxy enzyme from A47934 biosynthesis. Our results show that the specificity of StaF is reduced when compared to Oxy enzymes catalysing C-O-D ring formation and that this activity relies on interactions with the non-ribosomal peptide synthetase via the X-domain. Despite the interaction of StaF with the A47934 X-domain being weaker than for the preceding Oxy enzyme StaH, StaF retains higher levels of in vitro activity: we postulate that this is due to the ability of the StaF/X-domain complex to allow substrate reorganisation after initial complex formation has occurred. These results highlight the importance of testing different peptide/protein carrier constructs for in vitro GPA cyclisation assays and show that different Oxy homologues can display significantly different catalytic propensities despite their overall similarities.
Collapse
Affiliation(s)
- Veronika Ulrich
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Clara Brieke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Max J Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
12
|
Peschke M, Gonsior M, Süssmuth RD, Cryle MJ. Understanding the crucial interactions between Cytochrome P450s and non-ribosomal peptide synthetases during glycopeptide antibiotic biosynthesis. Curr Opin Struct Biol 2016; 41:46-53. [DOI: 10.1016/j.sbi.2016.05.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 05/26/2016] [Indexed: 01/07/2023]
|
13
|
Peschke M, Brieke C, Cryle MJ. F-O-G Ring Formation in Glycopeptide Antibiotic Biosynthesis is Catalysed by OxyE. Sci Rep 2016; 6:35584. [PMID: 27752135 PMCID: PMC5067714 DOI: 10.1038/srep35584] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/04/2016] [Indexed: 12/19/2022] Open
Abstract
The glycopeptide antibiotics are peptide-based natural products with impressive antibiotic function that derives from their unique three-dimensional structure. Biosynthesis of the glycopeptide antibiotics centres of the combination of peptide synthesis, mediated by a non-ribosomal peptide synthetase, and the crosslinking of aromatic side chains of the peptide, mediated by the action of a cascade of Cytochrome P450s. Here, we report the first example of in vitro activity of OxyE, which catalyses the F-O-G ring formation reaction in teicoplanin biosynthesis. OxyE was found to only act after an initial C-O-D crosslink is installed by OxyB and to require an interaction with the unique NRPS domain from glycopeptide antibiotic - the X-domain - in order to display catalytic activity. We could demonstrate that OxyE displays limited stereoselectivity for the peptide, which mirrors the results from OxyB-catalysed turnover and is in sharp contrast to OxyA. Furthermore, we show that activity of a three-enzyme cascade (OxyB/OxyA/OxyE) in generating tricyclic glycopeptide antibiotic peptides depends upon the order of addition of the OxyA and OxyE enzymes to the reaction. This work demonstrates that complex enzymatic cascades from glycopeptide antibiotic biosynthesis can be reconstituted in vitro and provides new insights into the biosynthesis of these important antibiotics.
Collapse
Affiliation(s)
- Madeleine Peschke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Clara Brieke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Max J. Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
14
|
Guengerich FP, Waterman MR, Egli M. Recent Structural Insights into Cytochrome P450 Function. Trends Pharmacol Sci 2016; 37:625-640. [PMID: 27267697 PMCID: PMC4961565 DOI: 10.1016/j.tips.2016.05.006] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/07/2016] [Accepted: 05/11/2016] [Indexed: 02/08/2023]
Abstract
Cytochrome P450 (P450) enzymes are important in the metabolism of drugs, steroids, fat-soluble vitamins, carcinogens, pesticides, and many other types of chemicals. Their catalytic activities are important issues in areas such as drug-drug interactions and endocrine function. During the past 30 years, structures of P450s have been very helpful in understanding function, particularly the mammalian P450 structures available in the past 15 years. We review recent activity in this area, focusing on the past 2 years (2014-2015). Structural work with microbial P450s includes studies related to the biosynthesis of natural products and the use of parasitic and fungal P450 structures as targets for drug discovery. Studies on mammalian P450s include the utilization of information about 'drug-metabolizing' P450s to improve drug development and also to understand the molecular bases of endocrine dysfunction.
Collapse
Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.
| | - Michael R Waterman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.
| |
Collapse
|
15
|
Ulrich V, Peschke M, Brieke C, Cryle MJ. More than just recruitment: the X-domain influences catalysis of the first phenolic coupling reaction in A47934 biosynthesis by Cytochrome P450 StaH. MOLECULAR BIOSYSTEMS 2016; 12:2992-3004. [DOI: 10.1039/c6mb00373g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cytochrome P450 StaH catalyses the first cyclisation reaction in the biosynthesis of the glycopeptide antibiotic A47934 via recruitment to the NRPS machinery through interaction with the X-domain.
Collapse
Affiliation(s)
- Veronika Ulrich
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69121 Heidelberg
- Germany
| | - Madeleine Peschke
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69121 Heidelberg
- Germany
| | - Clara Brieke
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69121 Heidelberg
- Germany
| | - Max J. Cryle
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- 69121 Heidelberg
- Germany
- EMBL Australia
| |
Collapse
|