1
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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: 13] [Impact Index Per Article: 13.0] [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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2
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Gene editing enables rapid engineering of complex antibiotic assembly lines. Nat Commun 2021; 12:6872. [PMID: 34824225 PMCID: PMC8616955 DOI: 10.1038/s41467-021-27139-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/02/2021] [Indexed: 11/08/2022] Open
Abstract
Re-engineering biosynthetic assembly lines, including nonribosomal peptide synthetases (NRPS) and related megasynthase enzymes, is a powerful route to new antibiotics and other bioactive natural products that are too complex for chemical synthesis. However, engineering megasynthases is very challenging using current methods. Here, we describe how CRISPR-Cas9 gene editing can be exploited to rapidly engineer one of the most complex megasynthase assembly lines in nature, the 2.0 MDa NRPS enzymes that deliver the lipopeptide antibiotic enduracidin. Gene editing was used to exchange subdomains within the NRPS, altering substrate selectivity, leading to ten new lipopeptide variants in good yields. In contrast, attempts to engineer the same NRPS using a conventional homologous recombination-mediated gene knockout and complementation approach resulted in only traces of new enduracidin variants. In addition to exchanging subdomains within the enduracidin NRPS, subdomains from a range of NRPS enzymes of diverse bacterial origins were also successfully utilized.
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3
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Niquille DL, Folger IB, Basler S, Hilvert D. Biosynthetic Functionalization of Nonribosomal Peptides. J Am Chem Soc 2021; 143:2736-2740. [PMID: 33570948 DOI: 10.1021/jacs.1c00925] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonribosomal peptides (NRPs) are a therapeutically important class of secondary metabolites that are produced by modular synthetases in assembly-line fashion. We previously showed that a single Trp-to-Ser mutation in the initial Phe-loading adenylation domain of tyrocidine synthetase completely switches the specificity toward clickable analogues. Here we report that this minimally invasive strategy enables efficient functionalization of the bioactive NRP on the pathway level. In a reconstituted tyrocidine synthetase, the W227S point mutation permitted selective incorporation of Phe analogues with alkyne, halogen, and benzoyl substituents by the initiation module. The respective W2742S mutation in module 4 similarly permits efficient incorporation of these functionalized substrate analogues at position 4, expanding this strategy to elongation modules. Efficient incorporation of an alkyne handle at position 1 or 4 of tyrocidine A allowed site-selective one-step fluorescent labeling of the corresponding tyrocidine analogues by Cu(I)-catalyzed alkyne-azide cycloaddition. By combining synthetic biology with bioorthogonal chemistry, this approach holds great potential for NRP isolation and molecular target elucidation as well as combinatorial optimization of NRP therapeutics.
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Affiliation(s)
- David L Niquille
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Ines B Folger
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Sophie Basler
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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4
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Kaniusaite M, Kittilä T, Goode RJA, Schittenhelm RB, Cryle MJ. Redesign of Substrate Selection in Glycopeptide Antibiotic Biosynthesis Enables Effective Formation of Alternate Peptide Backbones. ACS Chem Biol 2020; 15:2444-2455. [PMID: 32794694 DOI: 10.1021/acschembio.0c00435] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Nonribosomal peptide synthesis is capable of utilizing a wide range of amino acid residues due to the selectivity of adenylation (A)-domains. Changing the selectivity of A-domains could lead to new bioactive nonribosomal peptides, although remodeling efforts of A-domains are often unsuccessful. Here, we explored and successfully reengineered the specificity of the module 3 A-domain from glycopeptide antibiotic biosynthesis to change the incorporation of 3,5-dihydroxyphenylglycine into 4-hydroxyphenylglycine. These engineered A-domains remain selective in a functioning peptide assembly line even under substrate competition conditions and indicate a possible application of these for the future redesign of GPA biosynthesis.
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Affiliation(s)
- Milda Kaniusaite
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Tiia Kittilä
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Robert J. A. Goode
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria 3800, Australia
| | - Ralf B. Schittenhelm
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, Victoria 3800, Australia
| | - Max J. Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
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5
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Kaniusaite M, Goode RJA, Tailhades J, Schittenhelm RB, Cryle MJ. Exploring modular reengineering strategies to redesign the teicoplanin non-ribosomal peptide synthetase. Chem Sci 2020; 11:9443-9458. [PMID: 34094211 PMCID: PMC8162109 DOI: 10.1039/d0sc03483e] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/22/2020] [Indexed: 12/24/2022] Open
Abstract
Non-ribosomal peptide synthesis is an important biosynthesis pathway in secondary metabolism. In this study we have investigated modularisation and redesign strategies for the glycopeptide antibiotic teicoplanin. Using the relocation or exchange of domains within the NRPS modules, we have identified how to initiate peptide biosynthesis and explored the requirements for the functional reengineering of both the condensation/adenylation domain and epimerisation/condensation domain interfaces. We have also demonstrated strategies that ensure communication between isolated NRPS modules, leading to new peptide assembly pathways. This provides important insights into NRPS reengineering of glycopeptide antibiotic biosynthesis and has broad implications for the redesign of other NRPS systems.
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Affiliation(s)
- Milda Kaniusaite
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- EMBL Australia, Monash University Clayton Victoria 3800 Australia
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Monash University Clayton Victoria 3800 Australia
| | - Robert J A Goode
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- Monash Proteomics and Metabolomics Facility, Monash University Clayton Victoria 3800 Australia
| | - Julien Tailhades
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- EMBL Australia, Monash University Clayton Victoria 3800 Australia
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Monash University Clayton Victoria 3800 Australia
| | - Ralf B Schittenhelm
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- Monash Proteomics and Metabolomics Facility, Monash University Clayton Victoria 3800 Australia
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton Victoria 3800 Australia
- EMBL Australia, Monash University Clayton Victoria 3800 Australia
- The Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Monash University Clayton Victoria 3800 Australia
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6
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Chen D, Po KHL, Blasco P, Chen S, Li X. Convergent Synthesis of Calcium-Dependent Antibiotic CDA3a and Analogues with Improved Antibacterial Activity via Late-Stage Serine Ligation. Org Lett 2020; 22:4749-4753. [PMID: 32484680 DOI: 10.1021/acs.orglett.0c01544] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A convergent synthesis via the late-stage serine ligation of naturally occurring calcium-dependent antibiotic CDA3a and its analogues has been developed, which allowed us to readily synthesize the analogues with the variation on the lipid tail. Some analogues were found to show 100-500-fold higher antimicrobial activity than the natural compound CDA3a against drug resistant bacteria. This study will enhance our understanding of CDA3a and provide valuable antibacterial lead candidates for further development.
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Affiliation(s)
- Delin Chen
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Kathy Hiu Laam Po
- Department of Infectious Diseases Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, The City University of Hong Kong, Kowloon, Kowloon, Hong Kong, P. R. China
| | - Pilar Blasco
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China
| | - Sheng Chen
- Department of Infectious Diseases Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, The City University of Hong Kong, Kowloon, Kowloon, Hong Kong, P. R. China
| | - Xuechen Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, P. R. China
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7
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Kegler C, Bode HB. Artificial Splitting of a Non-Ribosomal Peptide Synthetase by Inserting Natural Docking Domains. Angew Chem Int Ed Engl 2020; 59:13463-13467. [PMID: 32329545 PMCID: PMC7496407 DOI: 10.1002/anie.201915989] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/18/2020] [Indexed: 12/13/2022]
Abstract
The interaction in multisubunit non‐ribosomal peptide synthetases (NRPSs) is mediated by docking domains that ensure the correct subunit‐to‐subunit interaction. We introduced natural docking domains into the three‐module xefoampeptide synthetase (XfpS) to create two to three artificial NRPS XfpS subunits. The enzymatic performance of the split biosynthesis was measured by absolute quantification of the products by HPLC‐ESI‐MS. The connecting role of the docking domains was probed by deleting integral parts of them. The peptide production data was compared to soluble protein amounts of the NRPS using SDS‐PAGE. Reduced peptide synthesis was not a result of reduced soluble NRPS concentration but a consequence of the deletion of vital docking domain parts. Splitting the xefoampeptide biosynthesis polypeptide by introducing docking domains was feasible and resulted in higher amounts of product in one of the two tested split‐module cases compared to the full‐length wild‐type enzyme.
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Affiliation(s)
- Carsten Kegler
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, 60438, Frankfurt, Germany.,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt, Germany
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8
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Kegler C, Bode HB. Artificial Splitting of a Non‐Ribosomal Peptide Synthetase by Inserting Natural Docking Domains. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Carsten Kegler
- Molekulare Biotechnologie, Fachbereich Biowissenschaften Goethe Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt am Main Germany
| | - Helge B. Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften Goethe Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt am Main Germany
- Buchmann Institute for Molecular Life Sciences (BMLS) Goethe-Universität Frankfurt 60438 Frankfurt Germany
- Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25 60325 Frankfurt Germany
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9
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Koomsiri W, Inahashi Y, Leetanasaksakul K, Shiomi K, Takahashi YK, O Mura S, Samborskyy M, Leadlay PF, Wattana-Amorn P, Thamchaipenet A, Nakashima T. Sarpeptins A and B, Lipopeptides Produced by Streptomyces sp. KO-7888 Overexpressing a Specific SARP Regulator. JOURNAL OF NATURAL PRODUCTS 2019; 82:2144-2151. [PMID: 31381320 DOI: 10.1021/acs.jnatprod.9b00074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Whole genome analysis of Streptomyces sp. KO-7888 has revealed various pathway-specific transcriptional regulatory genes associated with silent biosynthetic gene clusters. A Streptomyces antibiotic regulatory protein gene, speR, located adjacent to a novel nonribosomal peptide synthetase (NRPS) gene cluster, was overexpressed in the wild-type strain. The resulting recombinant strain of Streptomyces sp. KO-7888 produced two new lipopeptides, sarpeptins A and B. Their structures were elucidated by high-resolution electrospray ionization mass spectrometry, NMR analysis, and the advanced Marfey's method. The distinct modular sections of the corresponding NRPS biosynthetic gene cluster were characterized, and the assembly line for production of the lipopeptide chain was proposed.
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Affiliation(s)
- Wilaiwan Koomsiri
- Department of Genetics, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand
- Omics Center for Agriculture, Bioresources, Food and Health , Kasetsart University (OmiKU) , Bangkok 10900 , Thailand
| | - Yuki Inahashi
- Kitasato Institute for Life Sciences , Kitasato University , Tokyo 108-8641 , Japan
| | - Kantinan Leetanasaksakul
- Department of Genetics, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand
- Omics Center for Agriculture, Bioresources, Food and Health , Kasetsart University (OmiKU) , Bangkok 10900 , Thailand
| | - Kazuro Shiomi
- Kitasato Institute for Life Sciences , Kitasato University , Tokyo 108-8641 , Japan
| | - Yo Ko Takahashi
- Kitasato Institute for Life Sciences , Kitasato University , Tokyo 108-8641 , Japan
| | - Satoshi O Mura
- Kitasato Institute for Life Sciences , Kitasato University , Tokyo 108-8641 , Japan
| | - Markiyan Samborskyy
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1TN , U.K
| | - Peter F Leadlay
- Department of Biochemistry , University of Cambridge , Cambridge CB2 1TN , U.K
| | - Pakorn Wattana-Amorn
- Department of Chemistry, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand
- Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry , Kasetsart University , Bangkok 10900 , Thailand
| | - Arinthip Thamchaipenet
- Department of Genetics, Faculty of Science , Kasetsart University , Bangkok 10900 , Thailand
- Omics Center for Agriculture, Bioresources, Food and Health , Kasetsart University (OmiKU) , Bangkok 10900 , Thailand
| | - Takuji Nakashima
- Kitasato Institute for Life Sciences , Kitasato University , Tokyo 108-8641 , Japan
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10
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Izoré T, Cryle MJ. The many faces and important roles of protein-protein interactions during non-ribosomal peptide synthesis. Nat Prod Rep 2019; 35:1120-1139. [PMID: 30207358 DOI: 10.1039/c8np00038g] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Covering: up to July 2018 Non-ribosomal peptide synthetase (NRPS) machineries are complex, multi-domain proteins that are responsible for the biosynthesis of many important, peptide-derived compounds. By decoupling peptide synthesis from the ribosome, NRPS assembly lines are able to access a significant pool of amino acid monomers for peptide synthesis. This is combined with a modular protein architecture that allows for great variation in stereochemistry, peptide length, cyclisation state and further modifications. The architecture of NRPS assembly lines relies upon a repetitive set of catalytic domains, which are organised into modules responsible for amino acid incorporation. Central to NRPS-mediated biosynthesis is the carrier protein (CP) domain, to which all intermediates following initial monomer activation are bound during peptide synthesis up until the final handover to the thioesterase domain that cleaves the mature peptide from the NRPS. This mechanism makes understanding the protein-protein interactions that occur between different NRPS domains during peptide biosynthesis of crucial importance to understanding overall NRPS function. This endeavour is also highly challenging due to the inherent flexibility and dynamics of NRPS systems. In this review, we present the current state of understanding of the protein-protein interactions that govern NRPS-mediated biosynthesis, with a focus on insights gained from structural studies relating to CP domain interactions within these impressive peptide assembly lines.
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Affiliation(s)
- Thierry Izoré
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
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11
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Zhu M, Wang L, He J. Chemical Diversification Based on Substrate Promiscuity of a Standalone Adenylation Domain in a Reconstituted NRPS System. ACS Chem Biol 2019; 14:256-265. [PMID: 30673204 DOI: 10.1021/acschembio.8b00938] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A nonribosomal peptide synthetase (NRPS) assembly line ( sfa) in Streptomyces thioluteus that directs the formation of the diisonitrile chalkophore SF2768 (1) has been characterized by heterologous expression and directed gene knockouts. Herein, differential metabolic analysis of the heterologous expression strain and the original host led to the isolation of an SF2768 analogue (2, a byproduct of sfa) that possesses N-isovaleryl rather than 3-isocyanobutyryl side chains. The proposed biosynthetic logic of sfa and the structural difference between 1 and 2 suggested substrate promiscuity of the adenylate-forming enzyme SfaB. Further substrate scope investigation of SfaB and a successfully reconstituted NRPS system including a four-enzyme cascade enabled incorporation of diverse carboxylic acid building blocks into peptide scaffolds, and 30 unnatural products were thus generated. This structural diversification strategy based on substrate flexibility of the adenylation domain and in vitro reconstitution can be applied to other adenylation-priming pathways, thus providing a supplementary method for diversity-oriented total synthesis. Additionally, the biocatalytic process of the putative lysine δ-hydroxylase SfaE was validated through the derivatization of two key aldehyde intermediates (2a and 2b), thereby expanding the toolkit of enzymatic C-H bond activation.
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Affiliation(s)
- Mengyi Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lijuan Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, P. R. China
| | - Jing He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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12
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Greule A, Charkoudian LK, Cryle MJ. Studying trans-acting enzymes that target carrier protein-bound amino acids during nonribosomal peptide synthesis. Methods Enzymol 2019; 617:113-154. [PMID: 30784400 DOI: 10.1016/bs.mie.2018.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Nonribosomal peptide biosynthesis is a complex enzymatic assembly responsible for producing a great diversity of bioactive peptide natural products. Due to the recurring arrangement of catalytic domains within these machineries, great interest has been shown in reengineering these pathways to produce novel, designer peptide products. However, in order to realize such ambitions, it is first necessary to develop a comprehensive understanding of the selectivity, mechanisms, and structure of these complex enzymes, which in turn requires significant in vitro experiments. Within nonribosomal biosynthesis, some modifications are performed by enzymatic domains that are not linked to the main nonribosomal peptide synthetase but rather act in trans: these systems offer great potential for redesign, but in turn require detailed study. In this chapter, we present an overview of in vitro experiments that can be used to characterize examples of such trans-interacting enzymes from nonribosomal peptide biosynthesis: Cytochrome P450 monooxygenases and flavin-dependent halogenases.
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Affiliation(s)
- Anja Greule
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; EMBL Australia, Monash University, Clayton, VIC, Australia
| | | | - Max J Cryle
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; EMBL Australia, Monash University, Clayton, VIC, Australia.
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13
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Schoppet M, Peschke M, Kirchberg A, Wiebach V, Süssmuth RD, Stegmann E, Cryle MJ. The biosynthetic implications of late-stage condensation domain selectivity during glycopeptide antibiotic biosynthesis. Chem Sci 2019; 10:118-133. [PMID: 30713624 PMCID: PMC6333238 DOI: 10.1039/c8sc03530j] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/10/2018] [Indexed: 01/27/2023] Open
Abstract
Non-ribosomal peptide synthesis is a highly important biosynthetic pathway for the formation of many secondary metabolites of medical relevance. Due to the challenges associated with the chemical synthesis of many of the products of these assembly lines, understanding the activity and selectivity of non-ribosomal peptide synthetase (NRPS) machineries is an essential step towards the redesign of such machineries to produce new bioactive peptides. Whilst the selectivity of the adenylation domains responsible for amino acid activation during NRPS synthesis has been widely studied, the selectivity of the essential peptide bond forming domains - known as condensation domains - is not well understood. Here, we present the results of a combination of in vitro and in vivo investigations into the final condensation domain from the NRPS machinery that produces the glycopeptide antibiotics (GPAs). Our results show that this condensation domain is tolerant for a range of peptide substrates and even those with unnatural stereochemistry of the peptide C-terminus, which is in contrast to the widely ascribed role of these domains as a stereochemical gatekeeper during NRPS synthesis. Furthermore, we show that this condensation domain has a significant preference for linear peptide substrates over crosslinked peptides, which indicates that the GPA crosslinking cascade targets the heptapeptide bound to the final module of the NRPS machinery and reinforces the role of the unique GPA X-domain in this process. Finally, we demonstrate that the peptide bond forming activity of this condensation domain is coupled to the rate of amino acid activation performed by the subsequent adenylation domain. This is a significant result with implications for NRPS redesign, as it indicates that the rate of amino acid activation of modified adenylation domains must be maintained to prevent unwanted peptide hydrolysis from the NRPS due to a loss of the productive coupling of amino acid selection and peptide bond formation. Taken together, our results indicate that assessing condensation domain activity is a vital step in not only understanding the biosynthetic logic and timing of NRPS-mediated peptide assembly, but also the rules which redesign efforts must obey in order to successfully produce functional, modified NRPS assembly lines.
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Affiliation(s)
- Melanie Schoppet
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg , Germany
| | - Madeleine Peschke
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg , Germany
| | - Anja Kirchberg
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
| | - Vincent Wiebach
- Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany
| | - Roderich D Süssmuth
- Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen , Microbiology/Biotechnology , University of Tübingen , Auf der Morgenstelle 28, 72076 Tübingen , Germany .
- German Centre for Infection Research (DZIF) , Partner Site Tübingen, Tübingen , Germany
| | - Max J Cryle
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29, 69120 Heidelberg , Germany
- ARC Centre of Excellence in Advanced Molecular Imaging , Monash University , Clayton , Victoria 3800 , Australia
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14
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Payne JAE, Schoppet M, Hansen MH, Cryle MJ. Diversity of nature's assembly lines - recent discoveries in non-ribosomal peptide synthesis. MOLECULAR BIOSYSTEMS 2017; 13:9-22. [PMID: 27853778 DOI: 10.1039/c6mb00675b] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The biosynthesis of complex natural products by non-ribosomal peptide synthetases (NRPSs) and the related polyketide synthases (PKSs) represents a major source of important bioactive compounds. These large, multi-domain machineries are able to produce a fascinating range of molecules due to the nature of their modular architectures, which allows natural products to be assembled and tailored in a modular, step-wise fashion. In recent years there has been significant progress in characterising the important domains and underlying mechanisms of non-ribosomal peptide synthesis. More significantly, several studies have uncovered important examples of novel activity in many NRPS domains. These discoveries not only greatly increase the structural diversity of the possible products of NRPS machineries but - possibly more importantly - they improve our understanding of what is a highly important, yet complex, biosynthetic apparatus. In this review, several recent examples of novel NRPS function will be introduced, which highlight the range of previously uncharacterised activities that have now been detected in the biosynthesis of important natural products by these mega-enzyme synthetases.
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Affiliation(s)
- Jennifer A E Payne
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and 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.
| | - Melanie Schoppet
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and 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.
| | | | - Max J Cryle
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia and The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
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Süssmuth RD, Mainz A. Nonribosomal Peptide Synthesis-Principles and Prospects. Angew Chem Int Ed Engl 2017; 56:3770-3821. [PMID: 28323366 DOI: 10.1002/anie.201609079] [Citation(s) in RCA: 518] [Impact Index Per Article: 74.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Indexed: 01/05/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large multienzyme machineries that assemble numerous peptides with large structural and functional diversity. These peptides include more than 20 marketed drugs, such as antibacterials (penicillin, vancomycin), antitumor compounds (bleomycin), and immunosuppressants (cyclosporine). Over the past few decades biochemical and structural biology studies have gained mechanistic insights into the highly complex assembly line of nonribosomal peptides. This Review provides state-of-the-art knowledge on the underlying mechanisms of NRPSs and the variety of their products along with detailed analysis of the challenges for future reprogrammed biosynthesis. Such a reprogramming of NRPSs would immediately spur chances to generate analogues of existing drugs or new compound libraries of otherwise nearly inaccessible compound structures.
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Affiliation(s)
- Roderich D Süssmuth
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
| | - Andi Mainz
- Technische Universität Berlin, Institut für Chemie, Strasse des 17. Juni 124, 10623, Berlin, Germany
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16
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Süssmuth RD, Mainz A. Nicht-ribosomale Peptidsynthese - Prinzipien und Perspektiven. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609079] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Roderich D. Süssmuth
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Andi Mainz
- Technische Universität Berlin; Institut für Chemie; Straße des 17. Juni 124 10623 Berlin Deutschland
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Kittilä T, Mollo A, Charkoudian LK, Cryle MJ. New Structural Data Reveal the Motion of Carrier Proteins in Nonribosomal Peptide Synthesis. Angew Chem Int Ed Engl 2016; 55:9834-40. [PMID: 27435901 PMCID: PMC5113783 DOI: 10.1002/anie.201602614] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Indexed: 12/28/2022]
Abstract
The nonribosomal peptide synthetases (NRPSs) are one of the most promising resources for the production of new bioactive molecules. The mechanism of NRPS catalysis is based around sequential catalytic domains: these are organized into modules, where each module selects, modifies, and incorporates an amino acid into the growing peptide. The intermediates formed during NRPS catalysis are delivered between enzyme centers by peptidyl carrier protein (PCP) domains, which makes PCP interactions and movements crucial to NRPS mechanism. PCP movement has been linked to the domain alternation cycle of adenylation (A) domains, and recent complete NRPS module structures provide support for this hypothesis. However, it appears as though the A domain alternation alone is insufficient to account for the complete NRPS catalytic cycle and that the loaded state of the PCP must also play a role in choreographing catalysis in these complex and fascinating molecular machines.
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Affiliation(s)
- Tiia Kittilä
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Aurelio Mollo
- Department of Chemistry, Haverford College, Haverford, PA, 19041, USA
| | | | - 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, VIC, 3800, Australia.
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18
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Kittilä T, Mollo A, Charkoudian LK, Cryle MJ. Neue Strukturdaten geben Einblick in die Bewegungen von Transportproteinen in der nicht-ribosomalen Peptidsynthese. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Tiia Kittilä
- Abteilung Biomolekulare Mechanismen; Max-Planck-Institut für Medizinische Forschung; Jahnstraße 29 69120 Heidelberg Deutschland
| | - Aurelio Mollo
- Department of Chemistry; Haverford College; Haverford PA 19041 USA
| | | | - Max J. Cryle
- Abteilung Biomolekulare Mechanismen; Max-Planck-Institut für Medizinische Forschung; Jahnstraße 29 69120 Heidelberg Deutschland
- EMBL Australia; Monash University; Clayton Victoria 3800 Australien
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging; Monash University; Clayton VIC 3800 Australien
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19
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Uytterhoeven B, Appermans K, Song L, Masschelein J, Lathouwers T, Michiels CW, Lavigne R. Systematic analysis of the kalimantacin assembly line NRPS module using an adapted targeted mutagenesis approach. Microbiologyopen 2015; 5:279-86. [PMID: 26666990 PMCID: PMC4831472 DOI: 10.1002/mbo3.326] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/26/2015] [Accepted: 11/04/2015] [Indexed: 01/10/2023] Open
Abstract
Kalimantacin is an antimicrobial compound with strong antistaphylococcal activity that is produced by a hybrid trans‐acyltransferase polyketide synthase/nonribosomal peptide synthetase system in Pseudomonas fluorescens BCCM_ID9359. We here present a systematic analysis of the substrate specificity of the glycine‐incorporating adenylation domain from the kalimantacin biosynthetic assembly line by a targeted mutagenesis approach. The specificity‐conferring code was adapted for use in Pseudomonas and mutated adenylation domain active site sequences were introduced in the kalimantacin gene cluster, using a newly adapted ligation independent cloning method. Antimicrobial activity screens and LC‐MS analyses revealed that the production of the kalimantacin analogues in the mutated strains was abolished. These results support the idea that further insight in the specificity of downstream domains in nonribosomal peptide synthetases and polyketide synthases is required to efficiently engineer these strains in vivo.
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Affiliation(s)
- Birgit Uytterhoeven
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, B-3001, Belgium
| | - Kenny Appermans
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, B-3001, Belgium
| | - Lijiang Song
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, United Kingdom
| | - Joleen Masschelein
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, B-3001, Belgium.,Department of Chemistry, University of Warwick, Gibbet Hill, Coventry, CV4 7AL, United Kingdom
| | - Thomas Lathouwers
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, B-3001, Belgium
| | - Chris W Michiels
- Centre for Food and Microbial Technology, KU Leuven, Kasteelpark Arenberg 23 box 2457, Heverlee, B-3001, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, Heverlee, B-3001, Belgium
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20
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Labby KJ, Watsula SG, Garneau-Tsodikova S. Interrupted adenylation domains: unique bifunctional enzymes involved in nonribosomal peptide biosynthesis. Nat Prod Rep 2015; 32:641-53. [PMID: 25622971 DOI: 10.1039/c4np00120f] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nonribosomal peptides (NRPs) account for a large portion of drugs and drug leads currently available in the pharmaceutical industry. They are one of two main families of natural products biosynthesized on megaenzyme assembly-lines composed of multiple modules that are, in general, each comprised of three core domains and on occasion of accompanying auxiliary domains. The core adenylation (A) domains are known to delineate the identity of the specific chemical components to be incorporated into the growing NRPs. Previously believed to be inactive, A domains interrupted by auxiliary enzymes have recently been proven to be active and capable of performing two distinct chemical reactions. This highlight summarizes current knowledge on A domains and presents the various interrupted A domains found in a number of nonribosomal peptide synthetase (NRPS) assembly-lines, their predicted or proven dual functions, and their potential for manipulation and engineering for chemoenzymatic synthesis of new pharmaceutical agents with increased potency.
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Affiliation(s)
- Kristin J Labby
- Beloit College, Department of Chemistry, 700 College Street, Beloit, WI 53511, USA
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21
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Wu MC, Styles MQ, Law BJC, Struck AW, Nunns L, Micklefield J. Engineered biosynthesis of enduracidin lipoglycopeptide antibiotics using the ramoplanin mannosyltransferase Ram29. MICROBIOLOGY-SGM 2015; 161:1338-47. [PMID: 25878261 PMCID: PMC4635501 DOI: 10.1099/mic.0.000095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The lipopeptides ramoplanin from Actinoplanes sp. ATCC 33076 and enduracidin produced by Streptomyces fungicidicus are effective antibiotics against a number of drug-resistant Gram-positive pathogens. While these two antibiotics share a similar cyclic peptide structure, comprising 17 amino acids with an N-terminal fatty acid side chain, ramoplanin has a di-mannose moiety that enduracidin lacks. The mannosyl substituents of ramoplanin enhance aqueous solubility, which was important in the development of ramoplanin as a potential treatment for Clostridium difficile infections. In this study we have determined the function of the putative mannosyltransferase encoded by ram29 from the ramoplanin biosynthetic gene cluster. Bioinformatics revealed that Ram29 is an integral membrane protein with a putative DxD motif that is suggested to bind to, and activate, a polyprenyl phosphomannose donor and an extracytoplasmic C-terminal domain that is predicted to bind the ramoplanin aglycone acceptor. The ram29 gene was cloned into the tetracycline inducible plasmid pMS17 and integrated into the genome of the enduracidin producer S. fungicidicus. Induction of ram29 expression in S. fungicidicus resulted in the production of monomannosylated enduracidin derivatives, which are not present in the WT strain. Tandem MS analysis showed that mannosylation occurs on the Hpg11 residue of enduracidin. In addition to confirming the function of Ram29, these findings demonstrate how the less common, membrane-associated, polyprenyl phosphosugar-dependent glycosyltransferases can be used in natural product glycodiversification. Such a strategy may be valuable in future biosynthetic engineering approaches aimed at improving the physico-chemical and biological properties of bioactive secondary metabolites including antibiotics.
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Affiliation(s)
- Ming-Cheng Wu
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Matthew Q Styles
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Brian J C Law
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Anna-Winona Struck
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Laura Nunns
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
| | - Jason Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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22
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Miyanaga A, Cieślak J, Shinohara Y, Kudo F, Eguchi T. The crystal structure of the adenylation enzyme VinN reveals a unique β-amino acid recognition mechanism. J Biol Chem 2014; 289:31448-57. [PMID: 25246523 PMCID: PMC4223343 DOI: 10.1074/jbc.m114.602326] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/17/2014] [Indexed: 12/20/2022] Open
Abstract
Adenylation enzymes play important roles in the biosynthesis and degradation of primary and secondary metabolites. Mechanistic insights into the recognition of α-amino acid substrates have been obtained for α-amino acid adenylation enzymes. The Asp residue is invariant and is essential for the stabilization of the α-amino group of the substrate. In contrast, the β-amino acid recognition mechanism of adenylation enzymes is still unclear despite the importance of β-amino acid activation for the biosynthesis of various natural products. Herein, we report the crystal structure of the stand-alone adenylation enzyme VinN, which specifically activates (2S,3S)-3-methylaspartate (3-MeAsp) in vicenistatin biosynthesis. VinN has an overall structure similar to that of other adenylation enzymes. The structure of the complex with 3-MeAsp revealed that a conserved Asp(230) residue is used in the recognition of the β-amino group of 3-MeAsp similar to α-amino acid adenylation enzymes. A mutational analysis and structural comparison with α-amino acid adenylation enzymes showed that the substrate-binding pocket of VinN has a unique architecture to accommodate 3-MeAsp as a β-amino acid substrate. Thus, the VinN structure allows the first visualization of the interaction of an adenylation enzyme with a β-amino acid and provides new mechanistic insights into the selective recognition of β-amino acids in this family of enzymes.
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Affiliation(s)
| | - Jolanta Cieślak
- Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Yuji Shinohara
- Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | | | - Tadashi Eguchi
- Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
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23
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Genetic manipulation of non-ribosomal peptide synthetases to generate novel bioactive peptide products. Biotechnol Lett 2014; 36:2407-16. [DOI: 10.1007/s10529-014-1642-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/06/2014] [Indexed: 12/25/2022]
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24
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Synthetic fermentation of bioactive non-ribosomal peptides without organisms, enzymes or reagents. Nat Chem 2014; 6:877-84. [DOI: 10.1038/nchem.2048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 07/28/2014] [Indexed: 12/28/2022]
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25
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Zhang K, Nelson KM, Bhuripanyo K, Grimes KD, Zhao B, Aldrich CC, Yin J. Engineering the substrate specificity of the DhbE adenylation domain by yeast cell surface display. ACTA ACUST UNITED AC 2013; 20:92-101. [PMID: 23352143 DOI: 10.1016/j.chembiol.2012.10.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/19/2012] [Accepted: 10/25/2012] [Indexed: 01/30/2023]
Abstract
The adenylation (A) domains of nonribosomal peptide synthetases (NRPSs) activate aryl acids or amino acids to launch their transfer through the NRPS assembly line for the biosynthesis of many medicinally important natural products. In order to expand the substrate pool of NRPSs, we developed a method based on yeast cell surface display to engineer the substrate specificities of the A-domains. We acquired A-domain mutants of DhbE that have 11- and 6-fold increases in k(cat)/K(m) with nonnative substrates 3-hydroxybenzoic acid and 2-aminobenzoic acid, respectively and corresponding 3- and 33-fold decreases in k(cat)/K(m) values with the native substrate 2,3-dihydroxybenzoic acid, resulting in a dramatic switch in substrate specificity of up to 200-fold. Our study demonstrates that yeast display can be used as a high throughput selection platform to reprogram the "nonribosomal code" of A-domains.
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Affiliation(s)
- Keya Zhang
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
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26
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Davidsen JM, Townsend CA. In vivo characterization of nonribosomal peptide synthetases NocA and NocB in the biosynthesis of nocardicin A. ACTA ACUST UNITED AC 2012; 19:297-306. [PMID: 22365611 DOI: 10.1016/j.chembiol.2011.10.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/12/2011] [Accepted: 10/24/2011] [Indexed: 02/02/2023]
Abstract
Two nonribosomal peptide synthetases (NRPS), NocA and NocB, together comprising five modules, are essential for the biosynthesis of the D,L,D configured tripeptide backbone of the monocyclic β-lactam nocardicin A. We report a double replacement gene strategy in which point mutations were engineered in the two encoding NRPS genes without disruption of the nocABC operon by placing selective markers in adjacent genes. A series of mutants was constructed to inactivate the thiolation (T) domain of each module and to evaluate an HHxxxDR catalytic motif in NocA and an atypical extended histidine motif in NocB. The loss of nocardicin A production in each of the T domain mutants indicates that all five modules are essential for its biosynthesis. Conversely, production of nocardicin A was not affected by mutation of the NocB histidine motif or the R828G mutation in NocA.
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Affiliation(s)
- Jeanne M Davidsen
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA
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27
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Thirlway J, Lewis R, Nunns L, Al Nakeeb M, Styles M, Struck AW, Smith CP, Micklefield J. Introduction of a Non-Natural Amino Acid into a Nonribosomal Peptide Antibiotic by Modification of Adenylation Domain Specificity. Angew Chem Int Ed Engl 2012; 51:7181-4. [DOI: 10.1002/anie.201202043] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 05/18/2012] [Indexed: 01/22/2023]
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28
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Thirlway J, Lewis R, Nunns L, Al Nakeeb M, Styles M, Struck AW, Smith CP, Micklefield J. Introduction of a Non-Natural Amino Acid into a Nonribosomal Peptide Antibiotic by Modification of Adenylation Domain Specificity. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202043] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Giessen TW, Marahiel MA. Ribosome-independent biosynthesis of biologically active peptides: Application of synthetic biology to generate structural diversity. FEBS Lett 2012; 586:2065-75. [PMID: 22273582 DOI: 10.1016/j.febslet.2012.01.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 01/09/2012] [Accepted: 01/09/2012] [Indexed: 01/24/2023]
Abstract
Peptide natural products continue to play an important role in modern medicine as last-resort treatments of many life-threatening diseases, as they display many interesting biological activities ranging from antibiotic to antineoplastic. A large fraction of these microbial natural products is assembled by ribosome-independent mechanisms. Progress in sequencing technology and the mechanistic understanding of secondary metabolite pathways has led to the discovery of many formerly cryptic natural products and a molecular understanding of their assembly. Those advances enable us to apply protein and metabolic engineering approaches towards the manipulation of biosynthetic pathways. In this review we discuss the application potential of both templated and non-templated pathways as well as chemoenzymatic strategies for the structural diversification and tailoring of peptide natural products.
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Affiliation(s)
- Tobias W Giessen
- Department of Chemistry/Biochemistry, Philipps-University, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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30
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Bowers AA. Biochemical and biosynthetic preparation of natural product-like cyclic peptide libraries. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20068f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Natural product gene clusters are increasingly being used to compliment biochemical methods for production of cyclic peptide libraries.
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Affiliation(s)
- Albert A. Bowers
- Purdue University
- Dept. of Medicinal Chemistry and Molecular Pharmacology
- West Lafayette
- USA
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31
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Protein engineering towards natural product synthesis and diversification. J Ind Microbiol Biotechnol 2011; 39:227-41. [PMID: 22006344 DOI: 10.1007/s10295-011-1044-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 09/29/2011] [Indexed: 10/16/2022]
Abstract
A dazzling array of enzymes is used by nature in making structurally complex natural products. These enzymes constitute a molecular toolbox that may be used in the construction and fine-tuning of pharmaceutically active molecules. Aided by technological advancements in protein engineering, it is now possible to tailor the activities and specificities of these enzymes as biocatalysts in the production of both natural products and their unnatural derivatives. These efforts are crucial in drug discovery and development, where there is a continuous quest for more potent agents. Both rational and random evolution techniques have been utilized in engineering these enzymes. This review will highlight some examples from several large families of natural products.
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Villiers B, Hollfelder F. Directed Evolution of a Gatekeeper Domain in Nonribosomal Peptide Synthesis. ACTA ACUST UNITED AC 2011; 18:1290-9. [DOI: 10.1016/j.chembiol.2011.06.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 06/18/2011] [Accepted: 06/22/2011] [Indexed: 12/19/2022]
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Lewis RA, Nunns L, Thirlway J, Carroll K, Smith CP, Micklefield J. Active site modification of the β-ketoacyl-ACP synthase FabF3 of Streptomyces coelicolor affects the fatty acid chain length of the CDA lipopeptides. Chem Commun (Camb) 2011; 47:1860-2. [PMID: 21135931 DOI: 10.1039/c0cc03444d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Using site directed mutagenesis we altered an active site residue (Phe107) of the enzyme encoded by fabF3 (SCO3248) in the Streptomyces coelicolor gene cluster required for biosynthesis of the calcium dependent antibiotics (CDAs), successfully generating two novel CDA derivatives comprising truncated (C4) lipid side chains and confirming that fabF3 encodes a KAS-II homologue that is involved in determining CDA fatty acid chain length.
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Roongsawang N, Washio K, Morikawa M. Diversity of nonribosomal peptide synthetases involved in the biosynthesis of lipopeptide biosurfactants. Int J Mol Sci 2010; 12:141-72. [PMID: 21339982 PMCID: PMC3039948 DOI: 10.3390/ijms12010141] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/03/2010] [Accepted: 12/10/2010] [Indexed: 12/02/2022] Open
Abstract
Lipopeptide biosurfactants (LPBSs) consist of a hydrophobic fatty acid portion linked to a hydrophilic peptide chain in the molecule. With their complex and diverse structures, LPBSs exhibit various biological activities including surface activity as well as anti-cellular and anti-enzymatic activities. LPBSs are also involved in multi-cellular behaviors such as swarming motility and biofilm formation. Among the bacterial genera, Bacillus (Gram-positive) and Pseudomonas (Gram-negative) have received the most attention because they produce a wide range of effective LPBSs that are potentially useful for agricultural, chemical, food, and pharmaceutical industries. The biosynthetic mechanisms and gene regulation systems of LPBSs have been extensively analyzed over the last decade. LPBSs are generally synthesized in a ribosome-independent manner with megaenzymes called nonribosomal peptide synthetases (NRPSs). Production of active-form NRPSs requires not only transcriptional induction and translation but also post-translational modification and assemblage. The accumulated knowledge reveals the versatility and evolutionary lineage of the NRPSs system. This review provides an overview of the structural and functional diversity of LPBSs and their different biosynthetic mechanisms in Bacillus and Pseudomonas, including both typical and unique systems. Finally, successful genetic engineering of NRPSs for creating novel lipopeptides is also discussed.
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Affiliation(s)
- Niran Roongsawang
- Microbial Cell Factory Laboratory, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathumthani 12120, Thailand
- Authors to whom correspondence should be addressed; E-Mails: (N.R.); (M.M.); Tel.: +66-2564-6700 (N.R.); +81-11-706-2253 (M.M.); Fax: +66-2564-6707 (N.R.); +81-11-706-2253 (M.M.)
| | - Kenji Washio
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan; E-Mail:
| | - Masaaki Morikawa
- Division of Biosphere Science, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan; E-Mail:
- Authors to whom correspondence should be addressed; E-Mails: (N.R.); (M.M.); Tel.: +66-2564-6700 (N.R.); +81-11-706-2253 (M.M.); Fax: +66-2564-6707 (N.R.); +81-11-706-2253 (M.M.)
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Combinatorial and Synthetic Biosynthesis in Actinomycetes. FORTSCHRITTE DER CHEMIE ORGANISCHER NATURSTOFFE / PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS, VOL. 93 2010; 93:211-37. [DOI: 10.1007/978-3-7091-0140-7_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Micklefield J. Biosynthesis and biosynthetic engineering of calcium-dependent lipopeptide antibiotics. PURE APPL CHEM 2009. [DOI: 10.1351/pac-con-08-08-29] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biosynthetic engineering involves the reprogramming of genes that are involved in the biosynthesis of natural products to generate new "non-natural" products, which might otherwise not exist in nature. Potentially this approach can be used to provide large numbers of secondary metabolites variants, with altered biological activities, many of which are too complex for effective total synthesis. Recently we have been investigating the biosynthesis of the calcium-dependent antibiotics (CDAs) which are members of the therapeutically relevant class of acidic lipopeptide antibiotics. CDAs are assembled by nonribosomal peptide synthetase (NRPS) enzymes. These large modular assembly-line enzymes process intermediates that are covalently tethered to peptidyl carrier protein (PCP) domain bonds bonds, which makes them particularly amenable to reprogramming. The CDA producer, Streptomyces coelicolor, is also a genetically tractable model organism which makes CDA an ideal template for biosynthetic engineering. To this end we have elucidated many of the key steps in CDA biosynthesis and utilized this information to develop methods that have enabled the engineered biosynthesis of wide range of CDA-type lipopeptides.
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Affiliation(s)
- Jason Micklefield
- 1School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Zou Y, Yin J. Alkyne-functionalized chemical probes for assaying the substrate specificities of the adenylation domains in nonribosomal peptide synthetases. Chembiochem 2009; 9:2804-10. [PMID: 18988209 DOI: 10.1002/cbic.200800480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yekui Zou
- Department of Chemistry, The University of Chicago, 929 E. 57th Street, GCIS E505A, Chicago, IL 60637, USA
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Butz D, Schmiederer T, Hadatsch B, Wohlleben W, Weber T, Süssmuth RD. Module Extension of a Non-Ribosomal Peptide Synthetase of the Glycopeptide Antibiotic Balhimycin Produced byAmycolatopsis balhimycina. Chembiochem 2008; 9:1195-200. [DOI: 10.1002/cbic.200800068] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Nonribosomal biosynthesis of fusaricidins by Paenibacillus polymyxa PKB1 involves direct activation of a D-amino acid. ACTA ACUST UNITED AC 2008; 15:118-27. [PMID: 18291316 DOI: 10.1016/j.chembiol.2007.12.014] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 11/24/2007] [Accepted: 12/04/2007] [Indexed: 11/23/2022]
Abstract
Paenibacillus polymyxa PKB1 produces fusaricidins, a family of lipopeptide antibiotics that strongly inhibits the growth of many plant pathogenic fungi. The fusaricidin biosynthetic gene cluster was cloned and sequenced, and it spans 32.4 kb, including an open reading frame (fusA) encoding a six-module nonribosomal peptide synthetase. The second, fourth, and fifth modules of fusaricidin synthetase each contain an epimerization domain, consistent with the structure of fusaricidins. However, no epimerization domain is found in the sixth module, corresponding to D-Ala. This sixth adenylation domain was produced at a high level in Escherichia coli and is shown to activate D-Ala specifically, providing evidence for direct activation of a D-amino acid by a prokaryotic peptide synthetase. The fusaricidin gene cluster also includes genes involved in the biosynthesis of the lipid moiety, but no genes for resistance, regulation, or transport functions were encountered.
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Amir-Heidari B, Thirlway J, Micklefield J. Auxotrophic-precursor directed biosynthesis of nonribosomal lipopeptides with modified tryptophan residues. Org Biomol Chem 2008; 6:975-8. [DOI: 10.1039/b718766c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Powell A, Borg M, Amir-Heidari B, Neary JM, Thirlway J, Wilkinson B, Smith CP, Micklefield J. Engineered Biosynthesis of Nonribosomal Lipopeptides with Modified Fatty Acid Side Chains. J Am Chem Soc 2007; 129:15182-91. [DOI: 10.1021/ja074331o] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amanda Powell
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Mathew Borg
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Bagher Amir-Heidari
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Joanne M. Neary
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jenny Thirlway
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Barrie Wilkinson
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Colin P. Smith
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jason Micklefield
- Contribution from the School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom, and Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
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42
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Otten LG, Schaffer ML, Villiers BRM, Stachelhaus T, Hollfelder F. An optimized ATP/PP(i)-exchange assay in 96-well format for screening of adenylation domains for applications in combinatorial biosynthesis. Biotechnol J 2007; 2:232-40. [PMID: 17294409 DOI: 10.1002/biot.200600220] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We report a new format for measuring ATP/[(32)P]pyrophosphate exchange in a higher throughput assay of adenylation domains (A-domains) of non-ribosomal peptide synthetases. These enzymes are key specificity determinants in the assembly line biosynthesis of non-ribosomal peptides, an important class of natural products with an activity spectrum ranging from antibiotic to antitumor activities. Our assay in 96-well format allows the rapid measurement of approximately 1000 data points per week as a basis for precise assessment of the kinetics of A-domains. The assay also allows quantitative high-throughput screening of the substrate specificity of A-domains identifying alternative, promiscuous substrates. We show that our assay is able to give high quality data for the T278A mutant of the A-domain of the tyrocidine synthetase module TycA with a 330-fold lower k(cat)/K(M). The large dynamic range of this assay will be useful for the screening of libraries of mutant A-domains. Finally we describe and evaluate a procedure for the high-throughput purification of A-domains in 96-well format for the latter purpose. Our approach will be of utility for mechanistic analysis, substrate profiling and directed evolution of the A-domains, to ultimately enable the combinatorial biosynthesis of non-natural analogues of non-ribosomal peptides that may have potential as alternative drug candidates.
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Affiliation(s)
- Linda G Otten
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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Neary JM, Powell A, Gordon L, Milne C, Flett F, Wilkinson B, Smith CP, Micklefield J. An asparagine oxygenase (AsnO) and a 3-hydroxyasparaginyl phosphotransferase (HasP) are involved in the biosynthesis of calcium-dependent lipopeptide antibiotics. MICROBIOLOGY-SGM 2007; 153:768-776. [PMID: 17322197 DOI: 10.1099/mic.0.2006/002725-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nonribosomal peptides contain a wide range of unusual non-proteinogenic amino acid residues. As a result, these complex natural products are amongst the most structurally diverse secondary metabolites in nature, and possess a broad spectrum of biological activities. beta-Hydroxylation of amino acid precursors or peptidyl residues and their subsequent processing by downstream tailoring enzymes are some of the most common themes in the biosynthetic diversification of these therapeutically important peptides. Identification and characterization of the biosynthetic intermediates and enzymes involved in these processes are thus pivotal in understanding nonribosomal peptide assembly and modification. To this end, the putative asparaginyl oxygenase- and 3-hydroxyasparaginyl phosphotransferase-encoding genes hasP and asnO were separately deleted from the calcium-dependent antibiotic (CDA) biosynthetic gene cluster of Streptomyces coelicolor. Whilst the parent strains produce a number of 3-hydroxyasparagine- and 3-phosphohydroxyasparagine-containing CDAs, the DeltahasP mutants produce exclusively non-phosphorylated CDAs. On the other hand, DeltaasnO mutants produce several new Asn-containing CDAs not present in the wild-type, which retain calcium-dependent antimicrobial activity. This confirms that AsnO and HasP are required for the beta-hydroxylation and phosphorylation of the Asn residue within CDA.
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Affiliation(s)
- Joanne M Neary
- Department of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
- School of Chemistry, The University of Manchester, PO Box 88, Manchester M60 1QD, UK
| | - Amanda Powell
- School of Chemistry, The University of Manchester, PO Box 88, Manchester M60 1QD, UK
| | - Lyndsey Gordon
- Department of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
- School of Chemistry, The University of Manchester, PO Box 88, Manchester M60 1QD, UK
| | - Claire Milne
- School of Chemistry, The University of Manchester, PO Box 88, Manchester M60 1QD, UK
| | - Fiona Flett
- Department of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Barrie Wilkinson
- Biotica Technology Ltd, Chesterford Research Park, Little Chesterford, Saffron Walden, Essex CB10 1XL, UK
| | - Colin P Smith
- Department of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK
| | - Jason Micklefield
- School of Chemistry, The University of Manchester, PO Box 88, Manchester M60 1QD, UK
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Abstract
Natural products continue to fulfill an important role in the development of therapeutic agents. In addition, with the advent of chemical genetics and high-throughput screening platforms, these molecules have become increasingly valuable as tools for interrogating fundamental aspects of biological systems. To access the vast portion of natural-product structural diversity that remains unexploited for these and other applications, genome mining and microbial metagenomic approaches are proving particularly powerful. When these are coupled with recombineering and related genetic tools, large biosynthetic gene clusters that remain intractable or cryptic in the native host can be more efficiently cloned and expressed in a suitable heterologous system. For lead optimization and the further structural diversification of natural-product libraries, combinatorial biosynthetic engineering has also become indispensable. However, our ability to rationally redesign biosynthetic pathways is often limited by our lack of understanding of the structure, dynamics and interplay between the many enzymes involved in complex biosynthetic pathways. Despite this, recent structures of fatty acid synthases should allow a more accurate prediction of the likely architecture of related polyketide synthase and nonribosomal peptide synthetase multienzymes.
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Affiliation(s)
- Barrie Wilkinson
- Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK.
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Milne C, Powell A, Jim J, Al Nakeeb M, Smith CP, Micklefield J. Biosynthesis of the (2S,3R)-3-methyl glutamate residue of nonribosomal lipopeptides. J Am Chem Soc 2007; 128:11250-9. [PMID: 16925444 DOI: 10.1021/ja062960c] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The calcium-dependent antibiotics (CDAs) and daptomycin are therapeutically relevant nonribosomal lipopeptide antibiotics that contain penultimate C-terminal 3-methyl glutamate (3-MeGlu) residues. Comparison with synthetic standards showed that (2S,3R)-configured 3-MeGlu is present in both CDA and daptomycin. Deletion of a putative methyltransferase gene glmT from the cda biosynthetic gene cluster abolished the incorporation of 3-MeGlu and resulted in the production of Glu-containing CDA exclusively. However, the 3-MeGlu chemotype could be re-established through feeding synthetic 3-methyl-2-oxoglutarate and (2S,3R)-3-MeGlu, but not (2S,3S)-3-MeGlu. This indicates that methylation occurs before peptide assembly, and that the module 10 A-domain of the CDA peptide synthetase is specific for the (2S,3R)-stereoisomer. Further mechanistic analyses suggest that GlmT catalyzes the SAM-dependent methylation of alpha-ketoglutarate to give (3R)-methyl-2-oxoglutarate, which is transaminated to (2S,3R)-3-MeGlu. These insights will facilitate future efforts to engineer lipopeptides with modified glutamate residues, which may have improved bioactivity and/or reduced toxicity.
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Affiliation(s)
- Claire Milne
- School of Chemistry and Department of Biomolecular Sciences, The University of Manchester, P.O. Box 88, Manchester M60 1QD, United Kingdom
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Amir-Heidari B, Thirlway J, Micklefield J. Stereochemical Course of Tryptophan Dehydrogenation during Biosynthesis of the Calcium-Dependent Lipopeptide Antibiotics. Org Lett 2007; 9:1513-6. [PMID: 17355143 DOI: 10.1021/ol0701619] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] Hydrogen atoms are abstracted from the C2' and C3'-pro-S positions of an (S)-tryptophanyl precursor, with overall syn stereochemistry, during the biosynthesis of the C-terminal Z-2',3'-dehydrotryptophan residue of the calcium-dependent lipopeptide antibiotics (CDAs) in Streptomyces coelicolor. The absence of beta-hydroxytryptophanyl, or other possible intermediates, further suggests a direct dehydrogenation mechanism similar to that proposed for the l-tryptophan 2',3'-oxidase from Chromobacterium violaceum.
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Affiliation(s)
- Bagher Amir-Heidari
- School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7ND, UK
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47
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Powell A, Al Nakeeb M, Wilkinson B, Micklefield J. Precursor-directed biosynthesis of nonribosomal lipopeptides with modified glutamate residues. Chem Commun (Camb) 2007:2683-5. [PMID: 17594019 DOI: 10.1039/b706224a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Precursor-directed biosynthesis of calcium dependent antibiotics (CDAs) with modified 3-trifluoromethyl and 3-ethyl glutamate residues was achieved by feeding synthetic glutamate analogues to a mutant strain of Streptomyces coelicolor impaired in the biosynthesis of the natural precursor (2S,3R)-3-methyl glutamic acid.
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Affiliation(s)
- Amanda Powell
- School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester, UKM1 7ND
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Grünewald J, Marahiel MA. Chemoenzymatic and template-directed synthesis of bioactive macrocyclic peptides. Microbiol Mol Biol Rev 2006; 70:121-46. [PMID: 16524919 PMCID: PMC1393257 DOI: 10.1128/mmbr.70.1.121-146.2006] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Non-ribosomally synthesized peptides have compelling biological activities ranging from antimicrobial to immunosuppressive and from cytostatic to antitumor. The broad spectrum of applications in modern medicine is reflected in the great structural diversity of these natural products. They contain unique building blocks, such as d-amino acids, fatty acids, sugar moieties, and heterocyclic elements, as well as halogenated, methylated, and formylated residues. In the past decades, significant progress has been made toward the understanding of the biosynthesis of these secondary metabolites by nonribosomal peptide synthetases (NRPSs) and their associated tailoring enzymes. Guided by this knowledge, researchers genetically redesigned the NRPS template to synthesize new peptide products. Moreover, chemoenzymatic strategies were developed to rationally engineer nonribosomal peptides products in order to increase or alter their bioactivities. Specifically, chemical synthesis combined with peptide cyclization mediated by nonribosomal thioesterase domains enabled the synthesis of glycosylated cyclopeptides, inhibitors of integrin receptors, peptide/polyketide hybrids, lipopeptide antibiotics, and streptogramin B antibiotics. In addition to the synthetic potential of these cyclization catalysts, which is the main focus of this review, different enzymes for tailoring of peptide scaffolds as well as the manipulation of carrier proteins with reporter-labeled coenzyme A analogs are discussed.
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Affiliation(s)
- Jan Grünewald
- Fachbereich Chemie/Biochemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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Baltz RH, Miao V, Wrigley SK. Natural products to drugs: daptomycin and related lipopeptide antibiotics. Nat Prod Rep 2005; 22:717-41. [PMID: 16311632 DOI: 10.1039/b416648p] [Citation(s) in RCA: 272] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Daptomycin (Cubicin) is a lipopeptide antibiotic approved in the USA in 2003 for the treatment of skin and skin structure infections caused by Gram-positive pathogens. It is a member of the 10-membered cyclic lipopeptide family of antibiotics that includes A54145, calcium-dependent antibiotic (CDA), amphomycin, friulimicin, laspartomycin, and others. This review highlights research on this class of antibiotics from 1953 to 2005, focusing on more recent studies with particular emphasis on the interplay between structural features and antibacterial activities; chemical modifications to improve activity; the genetic organization and biosynthesis of lipopeptides; and the genetic engineering of the daptomycin biosynthetic pathway to produce novel derivatives for further chemical modification to develop candidates for clinical evaluation.
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Miao V, Brost R, Chapple J, She K, Gal MFCL, Baltz RH. The lipopeptide antibiotic A54145 biosynthetic gene cluster from Streptomyces fradiae. J Ind Microbiol Biotechnol 2005; 33:129-40. [PMID: 16208464 DOI: 10.1007/s10295-005-0028-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Accepted: 08/01/2005] [Indexed: 10/25/2022]
Abstract
Ca(2+)-dependent cyclic lipodepsipeptides are an emerging class of antibiotics for the treatment of infections caused by Gram-positive pathogens. These compounds are synthesized by nonribosomal peptide synthetase (NRPS) complexes encoded by large gene clusters. The gene cluster encoding biosynthetic pathway enzymes for the Streptomyces fradiae A54145 NRP was cloned from a cosmid library and characterized. Four NRPS-encoding genes, responsible for subunits of the synthetase, as well as genes for accessory functions such as acylation, methylation and hydroxylation, were identified by sequence analysis in a 127 kb region of DNA that appears to be located subterminally in the bacterial chromosome. Deduced epimerase domain-encoding sequences within the NRPS genes indicated a D: -stereochemistry for Glu, Lys and Asn residues, as observed for positionally analogous residues in two related compounds, daptomycin, and the calcium-dependent antibiotic (CDA) produced by Streptomyces roseosporus and Streptomyces coelicolor, respectively. A comparison of the structure and the biosynthetic gene cluster of A54145 with those of the related peptides showed many similarities. This information may contribute to the design of experiments to address both fundamental and applied questions in lipopeptide biosynthesis, engineering and drug development.
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Affiliation(s)
- Vivian Miao
- Cubist Pharmaceuticals Inc., 65 Hayden Av., Lexington, MA, 02421, USA
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