1
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Karanth MN, Kirkpatrick JP, Krausze J, Schmelz S, Scrima A, Carlomagno T. The specificity of intermodular recognition in a prototypical nonribosomal peptide synthetase depends on an adaptor domain. SCIENCE ADVANCES 2024; 10:eadm9404. [PMID: 38896613 PMCID: PMC11186497 DOI: 10.1126/sciadv.adm9404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
In the quest for new bioactive substances, nonribosomal peptide synthetases (NRPS) provide biodiversity by synthesizing nonproteinaceous peptides with high cellular activity. NRPS machinery consists of multiple modules, each catalyzing a unique series of chemical reactions. Incomplete understanding of the biophysical principles orchestrating these reaction arrays limits the exploitation of NRPSs in synthetic biology. Here, we use nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry to solve the conundrum of how intermodular recognition is coupled with loaded carrier protein specificity in the tomaymycin NRPS. We discover an adaptor domain that directly recruits the loaded carrier protein from the initiation module to the elongation module and reveal its mechanism of action. The adaptor domain of the type found here has specificity rules that could potentially be exploited in the design of engineered NRPS machinery.
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Affiliation(s)
- Megha N. Karanth
- Laboratory of Integrative Structural Biology, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Institute of Organic Chemistry and Center of Biomolecular Drug Research, Leibniz University Hannover, Hannover D-30167, Germany
| | - John P. Kirkpatrick
- Institute of Organic Chemistry and Center of Biomolecular Drug Research, Leibniz University Hannover, Hannover D-30167, Germany
- Laboratory of Integrative Structural Biology, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
| | - Joern Krausze
- Institute of Organic Chemistry and Center of Biomolecular Drug Research, Leibniz University Hannover, Hannover D-30167, Germany
| | - Stefan Schmelz
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
| | - Andrea Scrima
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
| | - Teresa Carlomagno
- Laboratory of Integrative Structural Biology, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Institute of Organic Chemistry and Center of Biomolecular Drug Research, Leibniz University Hannover, Hannover D-30167, Germany
- Laboratory of Integrative Structural Biology, School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
- Department of Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
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2
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Folger IB, Frota NF, Pistofidis A, Niquille DL, Hansen DA, Schmeing TM, Hilvert D. High-throughput reprogramming of an NRPS condensation domain. Nat Chem Biol 2024; 20:761-769. [PMID: 38308044 PMCID: PMC11142918 DOI: 10.1038/s41589-023-01532-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 12/19/2023] [Indexed: 02/04/2024]
Abstract
Engineered biosynthetic assembly lines could revolutionize the sustainable production of bioactive natural product analogs. Although yeast display is a proven, powerful tool for altering the substrate specificity of gatekeeper adenylation domains in nonribosomal peptide synthetases (NRPSs), comparable strategies for other components of these megaenzymes have not been described. Here we report a high-throughput approach for engineering condensation (C) domains responsible for peptide elongation. We show that a 120-kDa NRPS module, displayed in functional form on yeast, can productively interact with an upstream module, provided in solution, to produce amide products tethered to the yeast surface. Using this system to screen a large C-domain library, we reprogrammed a surfactin synthetase module to accept a fatty acid donor, increasing catalytic efficiency for this noncanonical substrate >40-fold. Because C domains can function as selectivity filters in NRPSs, this methodology should facilitate the precision engineering of these molecular assembly lines.
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Affiliation(s)
- Ines B Folger
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Natália F Frota
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
| | - Angelos Pistofidis
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
| | - David L Niquille
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Douglas A Hansen
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - T Martin Schmeing
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland.
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3
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Cook GD, Stasulli NM. Employing synthetic biology to expand antibiotic discovery. SLAS Technol 2024; 29:100120. [PMID: 38340893 DOI: 10.1016/j.slast.2024.100120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/04/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Antimicrobial-resistant (AMR) bacterial pathogens are a continually growing threat as our methods for combating these infections continue to be overcome by the evolution of resistance mechanisms. Recent therapeutic methods have not staved off the concern of AMR infections, so continued research focuses on new ways of identifying small molecules to treat AMR pathogens. While chemical modification of existing antibiotics is possible, there has been rapid development of resistance by pathogens that were initially susceptible to these compounds. Synthetic biology is becoming a key strategy in trying to predict and induce novel, natural antibiotics. Advances in cloning and mutagenesis techniques applied through a synthetic biology lens can help characterize the native regulation of antibiotic biosynthetic gene clusters (BGCs) to identify potential modifications leading to more potent antibiotic activity. Additionally, many cryptic antibiotic BGCs are derived from non-ribosomal peptide synthase (NRPS) and polyketide synthase (PKS) biosynthetic pathways; complex, clustered genetic sequences that give rise to amino acid-derived natural products. Synthetic biology can be applied to modify and metabolically engineer these enzyme-based systems to promote rapid and sustainable production of natural products and their variants. This review will focus on recent advances related to synthetic biology as applied to genetic pathway characterization and identification of antibiotics from naturally occurring BGCs. Specifically, we will summarize recent efforts to characterize BGCs via general genomic mutagenesis, endogenous gene expression, and heterologous gene expression.
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Affiliation(s)
- Greta D Cook
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA
| | - Nikolas M Stasulli
- Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Rd, Dodds Hall 316, West Haven 06516 USA.
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4
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Bozhüyük KAJ, Präve L, Kegler C, Schenk L, Kaiser S, Schelhas C, Shi YN, Kuttenlochner W, Schreiber M, Kandler J, Alanjary M, Mohiuddin TM, Groll M, Hochberg GKA, Bode HB. Evolution-inspired engineering of nonribosomal peptide synthetases. Science 2024; 383:eadg4320. [PMID: 38513038 DOI: 10.1126/science.adg4320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/09/2024] [Indexed: 03/23/2024]
Abstract
Many clinically used drugs are derived from or inspired by bacterial natural products that often are produced through nonribosomal peptide synthetases (NRPSs), megasynthetases that activate and join individual amino acids in an assembly line fashion. In this work, we describe a detailed phylogenetic analysis of several bacterial NRPSs that led to the identification of yet undescribed recombination sites within the thiolation (T) domain that can be used for NRPS engineering. We then developed an evolution-inspired "eXchange Unit between T domains" (XUT) approach, which allows the assembly of NRPS fragments over a broad range of GC contents, protein similarities, and extender unit specificities, as demonstrated for the specific production of a proteasome inhibitor designed and assembled from five different NRPS fragments.
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Affiliation(s)
- Kenan A J Bozhüyük
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Myria Biosciences AG, Tech Park Basel, Hochbergstrasse 60C, 4057 Basel, Switzerland
| | - Leonard Präve
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Carsten Kegler
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Leonie Schenk
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Sebastian Kaiser
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Christian Schelhas
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
| | - Yan-Ni Shi
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Wolfgang Kuttenlochner
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Max Schreiber
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Joshua Kandler
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - T M Mohiuddin
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
| | - Helge B Bode
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) & Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt, Germany
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5
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Ishikawa F, Nakamura S, Nakanishi I, Tanabe G. Recent progress in the reprogramming of nonribosomal peptide synthetases. J Pept Sci 2024; 30:e3545. [PMID: 37721208 DOI: 10.1002/psc.3545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/19/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) biosynthesize nonribosomal peptide (NRP) natural products, which belong to the most promising resources for drug discovery and development because of their wide range of therapeutic applications. The results of genetic, biochemical, and bioinformatics analyses have enhanced our understanding of the mechanisms of the NRPS machinery. A major goal in NRP biosynthesis is to reprogram the NRPS machinery to enable the biosynthetic production of designed peptides. Reprogramming strategies for the NRPS machinery have progressed considerably in recent years, thereby increasing the yields and generating modified peptides. Here, the recent progress in NRPS reprogramming and its application in peptide synthesis are described.
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Affiliation(s)
| | | | | | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, Osaka, Japan
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6
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Messenger SR, McGuinniety EMR, Stevenson LJ, Owen JG, Challis GL, Ackerley DF, Calcott MJ. Metagenomic domain substitution for the high-throughput modification of nonribosomal peptides. Nat Chem Biol 2024; 20:251-260. [PMID: 37996631 DOI: 10.1038/s41589-023-01485-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/12/2023] [Indexed: 11/25/2023]
Abstract
The modular nature of nonribosomal peptide biosynthesis has driven efforts to generate peptide analogs by substituting amino acid-specifying domains within nonribosomal peptide synthetase (NRPS) enzymes. Rational NRPS engineering has increasingly focused on finding evolutionarily favored recombination sites for domain substitution. Here we present an alternative evolution-inspired approach that involves large-scale diversification and screening. By amplifying amino acid-specifying domains en masse from soil metagenomic DNA, we substitute more than 1,000 unique domains into a pyoverdine NRPS. Initial fluorescence and mass spectrometry screens followed by sequencing reveal more than 100 functional domain substitutions, collectively yielding 16 distinct pyoverdines as major products. This metagenomic approach does not require the high success rates demanded by rational NRPS engineering but instead enables the exploration of large numbers of substitutions in parallel. This opens possibilities for the discovery and production of nonribosomal peptides with diverse biological activities.
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Affiliation(s)
- Sarah R Messenger
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Edward M R McGuinniety
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Luke J Stevenson
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Jeremy G Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, Victoria, Australia
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
| | - Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
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7
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Platt AJ, Padrick S, Ma AT, Beld J. A dissected non-ribosomal peptide synthetase maintains activity. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140972. [PMID: 37951518 DOI: 10.1016/j.bbapap.2023.140972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) generate chemically complex compounds and their modular architecture suggests that changing their domain organization can predictably alter their products. Ebony, a small three-domain NRPS, catalyzes the formation of β-alanine containing amides from biogenic amines. To examine the necessity of interdomain interactions, we modeled and docked domains of Ebony to reveal potential interfaces between them. Testing the same domain combinations in vitro showed that 8 % of activity was preserved after Ebony was dissected into a di-domain and a detached C-terminal domain, suggesting that sufficient interaction was maintained after dissection. Our work creates a model to identify domain interfaces necessary for catalysis, an important step toward utilizing Ebony as a combinatorial engineering platform for novel amides.
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Affiliation(s)
- Amanda J Platt
- Department of Microbiology and Immunology, Institute of Molecular Medicine and Infectious Disease, Center for Advanced Microbial Processing, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Shae Padrick
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15(th) Street, Philadelphia, PA 19102, USA
| | - Amy T Ma
- Department of Microbiology and Immunology, Institute of Molecular Medicine and Infectious Disease, Center for Advanced Microbial Processing, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Joris Beld
- Department of Microbiology and Immunology, Institute of Molecular Medicine and Infectious Disease, Center for Advanced Microbial Processing, Drexel University College of Medicine, Philadelphia, PA, USA.
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8
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Camus A, Gantz M, Hilvert D. High-Throughput Engineering of Nonribosomal Extension Modules. ACS Chem Biol 2023; 18:2516-2523. [PMID: 37983914 PMCID: PMC10728897 DOI: 10.1021/acschembio.3c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/22/2023]
Abstract
Nonribosomal peptides constitute an important class of natural products that display a wide range of bioactivities. They are biosynthesized by large assembly lines called nonribosomal peptide synthetases (NRPSs). Engineering NRPS modules represents an attractive strategy for generating customized synthetases for the production of peptide variants with improved properties. Here, we explored the yeast display of NRPS elongation and termination modules as a high-throughput screening platform for assaying adenylation domain activity and altering substrate specificity. Depending on the module, display of A-T bidomains or C-A-T tridomains, which also include an upstream condensation domain, proved to be most effective. Reprograming a tyrocidine synthetase elongation module to accept 4-propargyloxy-phenylalanine, a noncanonical amino acid that is not activated by the native protein, illustrates the utility of this approach for altering NRPS specificity at internal sites.
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Affiliation(s)
- Anna Camus
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Maximilian Gantz
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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9
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Patel KD, MacDonald MR, Ahmed SF, Singh J, Gulick AM. Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases. Nat Prod Rep 2023; 40:1550-1582. [PMID: 37114973 PMCID: PMC10510592 DOI: 10.1039/d3np00003f] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Indexed: 04/29/2023]
Abstract
Covering: up to fall 2022.Nonribosomal peptide synthetases (NRPSs) are a family of modular, multidomain enzymes that catalyze the biosynthesis of important peptide natural products, including antibiotics, siderophores, and molecules with other biological activity. The NRPS architecture involves an assembly line strategy that tethers amino acid building blocks and the growing peptides to integrated carrier protein domains that migrate between different catalytic domains for peptide bond formation and other chemical modifications. Examination of the structures of individual domains and larger multidomain proteins has identified conserved conformational states within a single module that are adopted by NRPS modules to carry out a coordinated biosynthetic strategy that is shared by diverse systems. In contrast, interactions between modules are much more dynamic and do not yet suggest conserved conformational states between modules. Here we describe the structures of NRPS protein domains and modules and discuss the implications for future natural product discovery.
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Affiliation(s)
- Ketan D Patel
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Monica R MacDonald
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Syed Fardin Ahmed
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Jitendra Singh
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
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10
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Sztain T, Corpuz JC, Bartholow TG, Hernandez JOS, Jiang Z, Mellor DA, Heberlig GW, La Clair JJ, McCammon JA, Burkart MD. Interface Engineering of Carrier-Protein-Dependent Metabolic Pathways. ACS Chem Biol 2023; 18:2014-2022. [PMID: 37671411 PMCID: PMC10807135 DOI: 10.1021/acschembio.3c00238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Carrier-protein-dependent metabolic pathways biosynthesize fatty acids, polyketides, and non-ribosomal peptides, producing metabolites with important pharmaceutical, environmental, and industrial properties. Recent findings demonstrate that these pathways rely on selective communication mechanisms involving protein-protein interactions (PPIs) that guide enzyme reactivity and timing. While rational design of these PPIs could enable pathway design and modification, this goal remains a challenge due to the complex nature of protein interfaces. Computational methods offer an encouraging avenue, though many score functions fail to predict experimental observables, leading to low success rates. Here, we improve upon the Rosetta score function, leveraging experimental data through iterative rounds of computational prediction and mutagenesis, to design a hybrid fatty acid-non-ribosomal peptide initiation pathway. By increasing the weight of the electrostatic score term, the computational protocol proved to be more predictive, requiring fewer rounds of iteration to identify mutants with high in vitro activity. This allowed efficient design of new PPIs between a non-ribosomal peptide synthetase adenylation domain, PltF, and a fatty acid synthase acyl carrier protein, AcpP, as validated by activity and structural studies. This method provides a promising platform for customized pathway design, establishing a standard for carrier-protein-dependent pathway engineering through PPI optimization.
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Affiliation(s)
| | | | - Thomas G. Bartholow
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Javier O. Sanlley Hernandez
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ziran Jiang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Desirae A. Mellor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Graham W. Heberlig
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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11
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Stephan P, Langley C, Winkler D, Basquin J, Caputi L, O'Connor SE, Kries H. Directed Evolution of Piperazic Acid Incorporation by a Nonribosomal Peptide Synthetase. Angew Chem Int Ed Engl 2023; 62:e202304843. [PMID: 37326625 DOI: 10.1002/anie.202304843] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/17/2023]
Abstract
Engineering of biosynthetic enzymes is increasingly employed to synthesize structural analogues of antibiotics. Of special interest are nonribosomal peptide synthetases (NRPSs) responsible for the production of important antimicrobial peptides. Here, directed evolution of an adenylation domain of a Pro-specific NRPS module completely switched substrate specificity to the non-standard amino acid piperazic acid (Piz) bearing a labile N-N bond. This success was achieved by UPLC-MS/MS-based screening of small, rationally designed mutant libraries and can presumably be replicated with a larger number of substrates and NRPS modules. The evolved NRPS produces a Piz-derived gramicidin S analogue. Thus, we give new impetus to the too-early dismissed idea that widely accessible low-throughput methods can switch the specificity of NRPSs in a biosynthetically useful fashion.
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Affiliation(s)
- Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Chloe Langley
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Daniela Winkler
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Jérôme Basquin
- Department of Structural Cell Biology, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Planegg Martinsried, Germany
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
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12
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Puja H, Mislin GLA, Rigouin C. Engineering Siderophore Biosynthesis and Regulation Pathways to Increase Diversity and Availability. Biomolecules 2023; 13:959. [PMID: 37371539 DOI: 10.3390/biom13060959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Siderophores are small metal chelators synthesized by numerous organisms to access iron. These secondary metabolites are ubiquitously present on Earth, and because their production represents the main strategy to assimilate iron, they play an important role in both positive and negative interactions between organisms. In addition, siderophores are used in biotechnology for diverse applications in medicine, agriculture and the environment. The generation of non-natural siderophore analogs provides a new opportunity to create new-to-nature chelating biomolecules that can offer new properties to expand applications. This review summarizes the main strategies of combinatorial biosynthesis that have been used to generate siderophore analogs. We first provide a brief overview of siderophore biosynthesis, followed by a description of the strategies, namely, precursor-directed biosynthesis, the design of synthetic or heterologous pathways and enzyme engineering, used in siderophore biosynthetic pathways to create diversity. In addition, this review highlights the engineering strategies that have been used to improve the production of siderophores by cells to facilitate their downstream utilization.
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Affiliation(s)
- Hélène Puja
- CNRS-UMR7242, Biotechnologie et Signalisation Cellulaire, 300 Bld Sébastien Brant, 67412 Illkirch, France
- Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), Université de Strasbourg, 300 Bld Sébastien Brant, 67412 Illkirch, France
| | - Gaëtan L A Mislin
- CNRS-UMR7242, Biotechnologie et Signalisation Cellulaire, 300 Bld Sébastien Brant, 67412 Illkirch, France
- Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), Université de Strasbourg, 300 Bld Sébastien Brant, 67412 Illkirch, France
| | - Coraline Rigouin
- CNRS-UMR7242, Biotechnologie et Signalisation Cellulaire, 300 Bld Sébastien Brant, 67412 Illkirch, France
- Institut de Recherche de l'Ecole de Biotechnologie de Strasbourg (IREBS), Université de Strasbourg, 300 Bld Sébastien Brant, 67412 Illkirch, France
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13
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He R, Zhang J, Shao Y, Gu S, Song C, Qian L, Yin WB, Li Z. Knowledge-guided data mining on the standardized architecture of NRPS: Subtypes, novel motifs, and sequence entanglements. PLoS Comput Biol 2023; 19:e1011100. [PMID: 37186644 DOI: 10.1371/journal.pcbi.1011100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 05/25/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Non-ribosomal peptide synthetase (NRPS) is a diverse family of biosynthetic enzymes for the assembly of bioactive peptides. Despite advances in microbial sequencing, the lack of a consistent standard for annotating NRPS domains and modules has made data-driven discoveries challenging. To address this, we introduced a standardized architecture for NRPS, by using known conserved motifs to partition typical domains. This motif-and-intermotif standardization allowed for systematic evaluations of sequence properties from a large number of NRPS pathways, resulting in the most comprehensive cross-kingdom C domain subtype classifications to date, as well as the discovery and experimental validation of novel conserved motifs with functional significance. Furthermore, our coevolution analysis revealed important barriers associated with re-engineering NRPSs and uncovered the entanglement between phylogeny and substrate specificity in NRPS sequences. Our findings provide a comprehensive and statistically insightful analysis of NRPS sequences, opening avenues for future data-driven discoveries.
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Affiliation(s)
- Ruolin He
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jinyu Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yuanzhe Shao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Shaohua Gu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Long Qian
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, PR China
| | - Zhiyuan Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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14
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Tseng CC, Chen L, Lee C, Tu Z, Lin CH, Lin HC. Characterization and catalytic investigation of fungal single-module nonribosomal peptide synthetase in terpene-amino acid meroterpenoid biosynthesis. J Ind Microbiol Biotechnol 2023; 50:kuad043. [PMID: 38049376 PMCID: PMC10720950 DOI: 10.1093/jimb/kuad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
Hybrid natural products are compounds that originate from diverse biosynthetic pathways and undergo a conjugation process, which enables them to expand their chemical diversity and biological functionality. Terpene-amino acid meroterpenoids have garnered increasing attention in recent years, driven by the discovery of noteworthy examples such as the anthelmintic CJ-12662, the insecticidal paeciloxazine, and aculene A (1). In the biosynthesis of terpene-amino acid natural products, single-module nonribosomal peptide synthetases (NRPSs) have been identified to be involved in the esterification step, catalyzing the fusion of modified terpene and amino acid components. Despite prior investigations into these NRPSs through gene deletion or in vivo experiments, the enzymatic basis and mechanistic insights underlying this family of single-module NRPSs remain unclear. In this study, we performed biochemical characterization of AneB by in vitro characterization, molecular docking, and site-directed mutagenesis. The enzyme reaction analyses, performed with L-proline and daucane/nordaucane sesquiterpene substrates, revealed that AneB specifically esterifies the C10-OH of aculenes with L-proline. Notably, in contrast to ThmA in CJ-12662 biosynthesis, which exclusively recognizes oxygenated amorpha-4,11-diene sesquiterpenes for L-tryptophan transfer, AneB demonstrates broad substrate selectivity, including oxygenated amorpha-4,11-diene and 2-phenylethanol, resulting in the production of diverse unnatural prolyl compounds. Furthermore, site-directed mutagenesis experiments indicated the involvement of H794 and D798 in the esterification catalyzed by AneB. Lastly, domain swapping between AneB and ThmA unveiled that the A‒T domains of ThmA can be effectively harnessed by the C domain of AneB for L-tryptophan transfer, thus highlighting the potential of the C domain of AneB for generating various terpene-amino acid meroterpenoid derivatives. ONE-SENTENCE SUMMARY The enzymatic basis and mechanistic insights into AneB, a single-module NRPS, highlight its capacity to generate various terpene-amino acid meroterpenoid derivatives.
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Affiliation(s)
- Cheng-Chung Tseng
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- School of Pharmacy, National Taiwan University, Taipei 100, Taiwan R.O.C
| | - Li‐Xun Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan R.O.C
| | - Chi‐Fang Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan R.O.C
| | - Zhijay Tu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
| | - Chun-Hung Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan R.O.C
| | - Hsiao-Ching Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan R.O.C
- School of Pharmacy, National Taiwan University, Taipei 100, Taiwan R.O.C
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan R.O.C
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15
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Zhang L, Wang C, Chen K, Zhong W, Xu Y, Molnár I. Engineering the biosynthesis of fungal nonribosomal peptides. Nat Prod Rep 2023; 40:62-88. [PMID: 35796260 DOI: 10.1039/d2np00036a] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 2011 up to the end of 2021.Fungal nonribosomal peptides (NRPs) and the related polyketide-nonribosomal peptide hybrid products (PK-NRPs) are a prolific source of bioactive compounds, some of which have been developed into essential drugs. The synthesis of these complex natural products (NPs) utilizes nonribosomal peptide synthetases (NRPSs), multidomain megaenzymes that assemble specific peptide products by sequential condensation of amino acids and amino acid-like substances, independent of the ribosome. NRPSs, collaborating polyketide synthase modules, and their associated tailoring enzymes involved in product maturation represent promising targets for NP structure diversification and the generation of small molecule unnatural products (uNPs) with improved or novel bioactivities. Indeed, reprogramming of NRPSs and recruiting of novel tailoring enzymes is the strategy by which nature evolves NRP products. The recent years have witnessed a rapid development in the discovery and identification of novel NRPs and PK-NRPs, and significant advances have also been made towards the engineering of fungal NRP assembly lines to generate uNP peptides. However, the intrinsic complexities of fungal NRP and PK-NRP biosynthesis, and the large size of the NRPSs still present formidable conceptual and technical challenges for the rational and efficient reprogramming of these pathways. This review examines key examples for the successful (and for some less-successful) re-engineering of fungal NRPS assembly lines to inform future efforts towards generating novel, biologically active peptides and PK-NRPs.
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Affiliation(s)
- Liwen Zhang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Chen Wang
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Kang Chen
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Weimao Zhong
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA
| | - Yuquan Xu
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, 250 E. Valencia Rd., Tucson, AZ 85706, USA.,VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
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16
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Abbood N, Präve L, Bozhueyuek KAJ, Bode HB. A Practical Guideline to Engineering Nonribosomal Peptide Synthetases. Methods Mol Biol 2023; 2670:219-234. [PMID: 37184707 DOI: 10.1007/978-1-0716-3214-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The bioengineering of nonribosomal peptide synthetases (NRPSs) is a rapidly developing field to access natural product derivatives and new-to-nature natural products like scaffolds with changed or improved properties. However, the rational (re-)design of these often gigantic assembly-line proteins is by no means trivial and needs in-depth insights into structural flexibility, inter-domain communication, and the role of proofreading by catalytic domains-so it is not surprising that most previous rational reprogramming efforts have been met with limited success. With this practical guide, the result of nearly one decade of NRPS engineering in the Bode lab, we provide valuable insights into the strategies we have developed during this time for the successful engineering and cloning of these fascinating molecular machines.
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Affiliation(s)
- Nadya Abbood
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Leonard Präve
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kenan A J Bozhueyuek
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany.
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Myria Biosciences AG, Basel, Switzerland.
| | - Helge B Bode
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany.
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Philipps-Universität Marburg, Chemische Biologie, Marburg, Germany.
- Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany.
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17
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Miyanaga A, Kudo F, Eguchi T. Cross-Linking of the Nonribosomal Peptide Synthetase Adenylation Domain with a Carrier Protein Using a Pantetheine-Type Probe. Methods Mol Biol 2023; 2670:207-217. [PMID: 37184706 DOI: 10.1007/978-1-0716-3214-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Adenylation domains (A-domains) are responsible for the selective incorporation of carboxylic acid substrates in the biosynthesis of nonribosomal peptides and related natural products. The A-domain transfers an acyl substrate onto its cognate carrier protein (CP). The proper interactions between an A-domain and the cognate CP are important for functional substrate transfer. To stabilize the transient interactions sufficiently for structural analysis of A-domain-CP complex, vinylsulfonamide adenosine inhibitors have been traditionally used as molecular probes. Recently, we have developed an alternative strategy using a synthetic pantetheine-type probe that enables site-specific cross-linking between an A-domain and a CP. In this chapter, we describe the laboratory protocols for this cross-linking reaction.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, Japan.
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, Japan.
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18
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Miyanaga A, Kudo F, Eguchi T. Recent advances in the structural analysis of adenylation domains in natural product biosynthesis. Curr Opin Chem Biol 2022; 71:102212. [PMID: 36116190 DOI: 10.1016/j.cbpa.2022.102212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 01/27/2023]
Abstract
Adenylation (A) domains catalyze the biosynthetic incorporation of acyl building blocks into nonribosomal peptides and related natural products by selectively transferring acyl substrates onto cognate carrier proteins (CP). The use of noncanonical acyl units, such as nonproteinogenic amino acids and keto acids, by A domains expands the structural diversity of natural products. Furthermore, interrupted A domains, which have embedded auxiliary domains, are able to modify the incorporated acyl units. Structural information on A domains is important for rational protein engineering to generate unnatural compounds. In this review, we summarize recent advances in the structural analysis of A domains. First, we discuss the mechanisms by which A domains recognize noncanonical acyl units. We then focus on the interactions of A domains with CP domains and embedded auxiliary domains.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, 152-8551, Japan.
| | - Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, 152-8551, Japan
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19
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Rüschenbaum J, Steinchen W, Mayerthaler F, Feldberg A, Mootz HD. FRET Monitoring of a Nonribosomal Peptide Synthetase Elongation Module Reveals Carrier Protein Shuttling between Catalytic Domains. Angew Chem Int Ed Engl 2022; 61:e202212994. [PMID: 36169151 PMCID: PMC9828546 DOI: 10.1002/anie.202212994] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Indexed: 01/12/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) employ multiple domains, specifically arranged in modules, for the assembly-line biosynthesis of a plethora of bioactive peptides. It is poorly understood how catalysis is correlated with the domain interplay and associated conformational changes. We developed FRET sensors of an elongation module to study in solution the intramodular interactions of the peptidyl carrier protein (PCP) with adenylation (A) and condensation (C) domains. Backed by HDX-MS analysis, we discovered dynamic mixtures of conformations that undergo distinct population changes in favor of the PCP-A and PCP-C interactions upon completion of the adenylation and thiolation reactions, respectively. To probe this model we blocked PCP binding to the C domain by photocaging and triggered peptide bond formation with light. Changing intramodular domain affinities of the PCP appear to result in conformational shifts according to the logic of the templated assembly process.
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Affiliation(s)
- Jennifer Rüschenbaum
- University of MünsterInstitute of BiochemistryCorrensstraße 3648149MünsterGermany
| | - Wieland Steinchen
- Philipps-University MarburgSYNMIKRO Research Center & Faculty of ChemistryKarl-von-Frisch-Straße 1435043MarburgGermany
| | - Florian Mayerthaler
- University of MünsterInstitute of BiochemistryCorrensstraße 3648149MünsterGermany
| | - Anna‐Lena Feldberg
- University of MünsterInstitute of BiochemistryCorrensstraße 3648149MünsterGermany
| | - Henning D. Mootz
- University of MünsterInstitute of BiochemistryCorrensstraße 3648149MünsterGermany
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20
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Corpuz JC, Patel A, Davis TD, Podust LM, McCammon JA, Burkart MD. Essential Role of Loop Dynamics in Type II NRPS Biomolecular Recognition. ACS Chem Biol 2022; 17:2890-2898. [PMID: 36173802 PMCID: PMC9808923 DOI: 10.1021/acschembio.2c00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Non-ribosomal peptides play a critical role in the clinic as therapeutic agents. To access more chemically diverse therapeutics, non-ribosomal peptide synthetases (NRPSs) have been targeted for engineering through combinatorial biosynthesis; however, this has been met with limited success in part due to the lack of proper protein-protein interactions between non-cognate proteins. Herein, we report our use of chemical biology to enable X-ray crystallography, molecular dynamics (MD) simulations, and biochemical studies to elucidate binding specificities between peptidyl carrier proteins (PCPs) and adenylation (A) domains. Specifically, we determined X-ray crystal structures of a type II PCP crosslinked to its cognate A domain, PigG and PigI, and of PigG crosslinked to a non-cognate PigI homologue, PltF. The crosslinked PCP-A domain structures possess large protein-protein interfaces that predominantly feature hydrophobic interactions, with specific electrostatic interactions that orient the substrate for active site delivery. MD simulations of the PCP-A domain complexes and unbound PCP structures provide a dynamical evaluation of the transient interactions formed at PCP-A domain interfaces, which confirm the previously hypothesized role of a PCP loop as a crucial recognition element. Finally, we demonstrate that the interfacial interactions at the PCP loop 1 region can be modified to control PCP binding specificity through gain-of-function mutations. This work suggests that loop conformational preferences and dynamism account for improved shape complementary in the PCP-A domain interactions. Ultimately, these studies show how crystallographic, biochemical, and computational methods can be used to rationally re-engineer NRPSs for non-cognate interactions.
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Affiliation(s)
- Joshua C. Corpuz
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0332, USA
| | - Ashay Patel
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0332, USA
| | - Tony D. Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0332, USA
| | - Larissa M. Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0332, USA
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0332, USA
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0332, USA
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21
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Pourmasoumi F, De S, Peng H, Trottmann F, Hertweck C, Kries H. Proof-Reading Thioesterase Boosts Activity of Engineered Nonribosomal Peptide Synthetase. ACS Chem Biol 2022; 17:2382-2388. [PMID: 36044980 PMCID: PMC9486807 DOI: 10.1021/acschembio.2c00341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are a vast source of valuable natural products, and re-engineering them is an attractive path toward structurally diversified active compounds. NRPS engineering often requires heterologous expression, which is hindered by the enormous size of NRPS proteins. Protein splitting and docking domain insertion have been proposed as a strategy to overcome this limitation. Here, we have applied the splitting strategy to the gramicidin S NRPS: Despite better production of the split proteins, gramicidin S production almost ceased. However, the addition of type II thioesterase GrsT boosted production. GrsT is an enzyme encoded in the gramicidin S biosynthetic gene cluster that we have produced and characterized for this purpose. We attribute the activity enhancement to the removal of a stalled intermediate from the split NRPS that is formed due to misinitiation. These results highlight type II thioesterases as useful tools for NRPS engineering.
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Affiliation(s)
- Farzaneh Pourmasoumi
- Independent
Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and
Infection Biology e.V., Hans Knöll Institute (HKI Jena), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Sayantan De
- Independent
Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and
Infection Biology e.V., Hans Knöll Institute (HKI Jena), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Huiyun Peng
- Independent
Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and
Infection Biology e.V., Hans Knöll Institute (HKI Jena), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Felix Trottmann
- Biomolecular
Chemistry, Leibniz Institute for Natural
Product Research and Infection Biology e.V., Hans Knöll Institute
(HKI Jena), Beutenbergstr.
11a, 07745 Jena, Germany
| | - Christian Hertweck
- Biomolecular
Chemistry, Leibniz Institute for Natural
Product Research and Infection Biology e.V., Hans Knöll Institute
(HKI Jena), Beutenbergstr.
11a, 07745 Jena, Germany,Faculty
of Biological Sciences, Friedrich Schiller
University Jena, 07743 Jena, Germany
| | - Hajo Kries
- Independent
Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and
Infection Biology e.V., Hans Knöll Institute (HKI Jena), Beutenbergstr. 11a, 07745 Jena, Germany,E-mail:
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22
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Corpuz JC, Sanlley JO, Burkart MD. Protein-protein interface analysis of the non-ribosomal peptide synthetase peptidyl carrier protein and enzymatic domains. Synth Syst Biotechnol 2022; 7:677-688. [PMID: 35224236 PMCID: PMC8857579 DOI: 10.1016/j.synbio.2022.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/16/2022] Open
Abstract
Non-ribosomal peptide synthetases (NRPSs) are attractive targets for biosynthetic pathway engineering due to their modular architecture and the therapeutic relevance of their products. With catalysis mediated by specific protein-protein interactions formed between the peptidyl carrier protein (PCP) and its partner enzymes, NRPS enzymology and control remains fertile ground for discovery. This review focuses on the recent efforts within structural biology by compiling high-resolution structural data that shed light into the various protein-protein interfaces formed between the PCP and its partner enzymes, including the phosphopantetheinyl transferase (PPTase), adenylation (A) domain, condensation (C) domain, thioesterase (TE) domain and other tailoring enzymes within the synthetase. Integrating our understanding of how the PCP recognizes partner proteins with the potential to use directed evolution and combinatorial biosynthetic methods will enhance future efforts in discovery and production of new bioactive compounds.
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Affiliation(s)
- Joshua C. Corpuz
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Javier O. Sanlley
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
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23
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Chu Yuan Kee MJ, Bharath SR, Wee S, Bowler MW, Gunaratne J, Pan S, Zhang L, Song H. Structural insights into the substrate-bound condensation domains of non-ribosomal peptide synthetase AmbB. Sci Rep 2022; 12:5353. [PMID: 35354859 PMCID: PMC8968710 DOI: 10.1038/s41598-022-09188-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 03/15/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractNon-ribosomal peptide synthetases (NRPS) are multi-modular/domain enzymes that catalyze the synthesis of bioactive peptides. A crucial step in the process is peptide elongation accomplished by the condensation (C) domain with the aid of a peptidyl carrier or thiolation (T) domain. Here, we examined condensation reaction carried out by NRPS AmbB involved in biosynthesis of l-2-amino-4-methoxy-trans-3-butenoic acid (AMB) in P. aeruginosa. We determined crystal structures of the truncated T–C bidomain of AmbB in three forms, the apo enzyme with disordered T domain, the holo form with serine linked phosphopantetheine (Ppant) and a holo form with substrate (l-alanine) loaded onto Ppant. The two holo forms feature the T domain in a substrate-donation conformation. Mutagenesis combined with functional assays identified residues essential for the attachment of Ppant, anchoring the Ppant-l-Ala in the donor catalytic channel and the role of the conserved His953 in condensation activity. Altogether, these results provide structural insights into the condensation reaction at the donor site with a substrate-bound C domain of AmbB and lay the foundation for understanding the molecular mechanism of condensation which is crucial for AMB synthesis.
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24
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Kim WE, Ishikawa F, Re RN, Suzuki T, Dohmae N, Kakeya H, Tanabe G, Burkart MD. Developing crosslinkers specific for epimerization domain in NRPS initiation modules to evaluate mechanism. RSC Chem Biol 2022; 3:312-319. [PMID: 35359491 PMCID: PMC8905534 DOI: 10.1039/d2cb00005a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/18/2022] [Indexed: 12/16/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are complex multi-modular enzymes containing catalytic domains responsible for the loading and incorporation of amino acids into natural products. These unique molecular factories can produce peptides with nonproteinogenic d-amino acids in which the epimerization (E) domain catalyzes the conversion of l-amino acids to d-amino acids, but its mechanism remains not fully understood. Here, we describe the development of pantetheine crosslinking probes that mimic the natural substrate l-Phe of the initiation module of tyrocidine synthetase, TycA, to elucidate and study the catalytic residues of the E domain. Mechanism-based crosslinking assays and MALDI-TOF MS were used to identify both H743 and E882 as the crosslinking site residues, demonstrating their roles as catalytic bases. Mutagenesis studies further validated these results and allowed the comparison of reactivity between the catalytic residues, concluding that glutamate acts as the dominant nucleophile in the crosslinking reaction, resembling the deprotonation of the Cα-H of amino acids in the epimerization reaction. The crosslinking probes employed in these studies provide new tools for studying the molecular details of E domains, as well as the potential to study C domains. In particular, they would elucidate key information for how these domains function and interact with their substrates in nature, further enhancing the knowledge needed to assist combinatorial biosynthetic efforts of NRPS systems to produce novel compounds.
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Affiliation(s)
- Woojoo E Kim
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University 3-4-1 Kowakae Higashi-osaka Osaka 577-8502 Japan
| | - Rebecca N Re
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Kyoto University Sakyo Kyoto 606-8501 Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University 3-4-1 Kowakae Higashi-osaka Osaka 577-8502 Japan
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
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Therapeutic peptides: current applications and future directions. Signal Transduct Target Ther 2022; 7:48. [PMID: 35165272 PMCID: PMC8844085 DOI: 10.1038/s41392-022-00904-4] [Citation(s) in RCA: 437] [Impact Index Per Article: 218.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Peptide drug development has made great progress in the last decade thanks to new production, modification, and analytic technologies. Peptides have been produced and modified using both chemical and biological methods, together with novel design and delivery strategies, which have helped to overcome the inherent drawbacks of peptides and have allowed the continued advancement of this field. A wide variety of natural and modified peptides have been obtained and studied, covering multiple therapeutic areas. This review summarizes the efforts and achievements in peptide drug discovery, production, and modification, and their current applications. We also discuss the value and challenges associated with future developments in therapeutic peptides.
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Aminoacyl chain translocation catalysed by a type II thioesterase domain in an unusual non-ribosomal peptide synthetase. Nat Commun 2022; 13:62. [PMID: 35013184 PMCID: PMC8748450 DOI: 10.1038/s41467-021-27512-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 11/18/2021] [Indexed: 01/11/2023] Open
Abstract
Non-Ribosomal Peptide Synthetases (NRPSs) assemble a diverse range of natural products with important applications in both medicine and agriculture. They consist of several multienzyme subunits that must interact with each other in a highly controlled manner to facilitate efficient chain transfer, thus ensuring biosynthetic fidelity. Several mechanisms for chain transfer are known for NRPSs, promoting structural diversity. Herein, we report the first biochemically characterized example of a type II thioesterase (TEII) domain capable of catalysing aminoacyl chain transfer between thiolation (T) domains on two separate NRPS subunits responsible for installation of a dehydrobutyrine moiety. Biochemical dissection of this process reveals the central role of the TEII-catalysed chain translocation event and expands the enzymatic scope of TEII domains beyond canonical (amino)acyl chain hydrolysis. The apparent co-evolution of the TEII domain with the NRPS subunits highlights a unique feature of this enzymatic cassette, which will undoubtedly find utility in biosynthetic engineering efforts. Non-Ribosomal Peptide Synthetases (NRPSs) are responsible for the construction of many types of natural products. Here the authors characterize a key type II thioesterase domain that sheds light on the chain translocation processes of legonmycin NRPSs.
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27
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Wurlitzer JM, Stanišić A, Ziethe S, Jordan PM, Günther K, Werz O, Kries H, Gressler M. Macrophage-targeting oligopeptides from Mortierella alpina. Chem Sci 2022; 13:9091-9101. [PMID: 36091214 PMCID: PMC9365243 DOI: 10.1039/d2sc00860b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/15/2022] [Indexed: 12/27/2022] Open
Abstract
The realm of natural products of early diverging fungi such as Mortierella species is largely unexplored. Herein, the nonribosomal peptide synthetase (NRPS) MalA catalysing the biosynthesis of the surface-active biosurfactants, malpinins, has been identified and biochemically characterised. The investigation of the substrate specificity of respective adenylation (A) domains indicated a substrate-tolerant enzyme with an unusual, inactive C-terminal NRPS module. Specificity-based precursor-directed biosynthesis yielded 20 new congeners produced by a single enzyme. Moreover, MalA incorporates artificial, click-functionalised amino acids which allowed postbiosynthetic coupling to a fluorophore. The fluorescent malpinin conjugate penetrates mammalian cell membranes via an phagocytosis-mediated mechanism, suggesting Mortierella oligopeptides as carrier peptides for directed cell targeting. The current study demonstrates substrate-specificity testing as a powerful tool to identify flexible NRPS modules and highlights basal fungi as reservoir for chemically tractable compounds in pharmaceutical applications. Specificity profiling of a nonribosomal peptide synthetase of an early diverging fungus revealed high substrate flexibility. Feeding studies with click-functionalised amino acids enabled the production of fluorescent peptides targeting macrophages.![]()
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Affiliation(s)
- Jacob M. Wurlitzer
- Department Pharmaceutical Microbiology at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Friedrich-Schiller-University, Winzerlaer Strasse 2, Jena 07745, Germany
| | - Aleksa Stanišić
- Junior Group Biosynthetic Design of Natural Products at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Sebastian Ziethe
- Department Pharmaceutical Microbiology at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Friedrich-Schiller-University, Winzerlaer Strasse 2, Jena 07745, Germany
| | - Paul M. Jordan
- Department Pharmaceutical/Medicinal Chemistry at the Friedrich-Schiller-University, Philosophenweg 14, Jena 07743, Germany
| | - Kerstin Günther
- Department Pharmaceutical/Medicinal Chemistry at the Friedrich-Schiller-University, Philosophenweg 14, Jena 07743, Germany
| | - Oliver Werz
- Department Pharmaceutical/Medicinal Chemistry at the Friedrich-Schiller-University, Philosophenweg 14, Jena 07743, Germany
| | - Hajo Kries
- Junior Group Biosynthetic Design of Natural Products at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Beutenbergstrasse 11a, Jena 07745, Germany
| | - Markus Gressler
- Department Pharmaceutical Microbiology at the Leibniz Institute for Natural Product Research and Infection Biology (Hans-Knöll-Institute), Friedrich-Schiller-University, Winzerlaer Strasse 2, Jena 07745, Germany
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28
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Dell M, Dunbar KL, Hertweck C. Ribosome-independent peptide biosynthesis: the challenge of a unifying nomenclature. Nat Prod Rep 2021; 39:453-459. [PMID: 34586117 DOI: 10.1039/d1np00019e] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The first machineries for non-ribosomal peptide (NRP) biosynthesis were uncovered over 50 years ago, and the dissection of these megasynthetases set the stage for the nomenclature system that has been used ever since. Although the number of exceptions to the canonical biosynthetic pathways has surged in the intervening years, the NRP synthetase (NRPS) classification system has remained relatively unchanged. This has led to the exclusion of many biosynthetic pathways whose biosynthetic machineries violate the classical rules for NRP assembly, and ultimately to a rupture in the field of NRP biosynthesis. In an attempt to unify the classification of NRP pathways and to facilitate the communication within the research field, we propose a revised framework for grouping ribosome-independent peptide biosynthetic pathways based on recognizable commonalities in their biosynthetic logic. Importantly, the framework can be further refined as needed.
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Affiliation(s)
- Maria Dell
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.
| | - Kyle L Dunbar
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutenbergstr. 11a, 07745, Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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Stanišić A, Hüsken A, Stephan P, Niquille DL, Reinstein J, Kries H. Engineered Nonribosomal Peptide Synthetase Shows Opposite Amino Acid Loading and Condensation Specificity. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01270] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Aleksa Stanišić
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - Annika Hüsken
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - David L. Niquille
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square NE47-140, Cambridge, Massachusetts 02139, United States
| | - Jochen Reinstein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
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30
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Bonhomme S, Dessen A, Macheboeuf P. The inherent flexibility of type I non-ribosomal peptide synthetase multienzymes drives their catalytic activities. Open Biol 2021; 11:200386. [PMID: 34034506 PMCID: PMC8150014 DOI: 10.1098/rsob.200386] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Non-ribosomal peptide synthetases (NRPSs) are multienzymes that produce complex natural metabolites with many applications in medicine and agriculture. They are composed of numerous catalytic domains that elongate and chemically modify amino acid substrates or derivatives and of non-catalytic carrier protein domains that can tether and shuttle the growing products to the different catalytic domains. The intrinsic flexibility of NRPSs permits conformational rearrangements that are required to allow interactions between catalytic and carrier protein domains. Their large size coupled to this flexibility renders these multi-domain proteins very challenging for structural characterization. Here, we summarize recent studies that offer structural views of multi-domain NRPSs in various catalytically relevant conformations, thus providing an increased comprehension of their catalytic cycle. A better structural understanding of these multienzymes provides novel perspectives for their re-engineering to synthesize new bioactive metabolites.
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Affiliation(s)
- Sarah Bonhomme
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Andréa Dessen
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France.,Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, São Paulo, Brazil
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31
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Pang B, Liao R, Tang Z, Guo S, Wu Z, Liu W. Caerulomycin and collismycin antibiotics share a trans-acting flavoprotein-dependent assembly line for 2,2'-bipyridine formation. Nat Commun 2021; 12:3124. [PMID: 34035275 PMCID: PMC8149447 DOI: 10.1038/s41467-021-23475-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 04/28/2021] [Indexed: 11/09/2022] Open
Abstract
Linear nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) template the modular biosynthesis of numerous nonribosomal peptides, polyketides and their hybrids through assembly line chemistry. This chemistry can be complex and highly varied, and thus challenges our understanding in NRPS and PKS-programmed, diverse biosynthetic processes using amino acid and carboxylate building blocks. Here, we report that caerulomycin and collismycin peptide-polyketide hybrid antibiotics share an assembly line that involves unusual NRPS activity to engage a trans-acting flavoprotein in C-C bond formation and heterocyclization during 2,2'-bipyridine formation. Simultaneously, this assembly line provides dethiolated and thiolated 2,2'-bipyridine intermediates through differential treatment of the sulfhydryl group arising from L-cysteine incorporation. Subsequent L-leucine extension, which does not contribute any atoms to either caerulomycins or collismycins, plays a key role in sulfur fate determination by selectively advancing one of the two 2,2'-bipyridine intermediates down a path to the final products with or without sulfur decoration. These findings further the appreciation of assembly line chemistry and will facilitate the development of related molecules using synthetic biology approaches.
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Affiliation(s)
- Bo Pang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Rijing Liao
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Shengjie Guo
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Zhuhua Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai, China. .,Huzhou Center of Bio-Synthetic Innovation, Huzhou, China.
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32
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Schalk F, Fricke J, Um S, Conlon BH, Maus H, Jäger N, Heinzel T, Schirmeister T, Poulsen M, Beemelmanns C. GNPS-guided discovery of xylacremolide C and D, evaluation of their putative biosynthetic origin and bioactivity studies of xylacremolide A and B. RSC Adv 2021; 11:18748-18756. [PMID: 34046176 PMCID: PMC8142242 DOI: 10.1039/d1ra00997d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/10/2021] [Indexed: 01/26/2023] Open
Abstract
Targeted HRMS2-GNPS-based metabolomic analysis of Pseudoxylaria sp. X187, a fungal antagonist of the fungus-growing termite symbiosis, resulted in the identification of two lipopeptidic congeners of xylacremolides, named xylacremolide C and D, which are built from d-phenylalanine, l-proline and an acetyl-CoA starter unit elongated by four malonyl-CoA derived ketide units. The putative xya gene cluster was identified from a draft genome generated by Illumina and PacBio sequencing and RNAseq studies. Biological activities of xylacremolide A and B were evaluated and revealed weak histone deacetylase inhibitory (HDACi) and antifungal activities, as well as moderate protease inhibition activity across a panel of nine human, viral and bacterial proteases.
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Affiliation(s)
- Felix Schalk
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
| | - Janis Fricke
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
| | - Soohyun Um
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
| | - Benjamin H Conlon
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen Universitetsparken 15 2100 Copenhagen East Denmark
| | - Hannah Maus
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Nils Jäger
- Institute of Biochemistry and Biophysics at Center for Molecular Biomedicine (CMB), Department of Biochemistry, Friedrich Schiller University Jena Hans-Knöll-Straße 2 07745 Jena Germany
| | - Thorsten Heinzel
- Institute of Biochemistry and Biophysics at Center for Molecular Biomedicine (CMB), Department of Biochemistry, Friedrich Schiller University Jena Hans-Knöll-Straße 2 07745 Jena Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz Staudingerweg 5 55128 Mainz Germany
| | - Michael Poulsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen Universitetsparken 15 2100 Copenhagen East Denmark
| | - Christine Beemelmanns
- Chemical Biology of Microbe-Host Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI) Beutenbergstraße 11a 07745 Jena Germany
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33
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Baunach M, Chowdhury S, Stallforth P, Dittmann E. The Landscape of Recombination Events That Create Nonribosomal Peptide Diversity. Mol Biol Evol 2021; 38:2116-2130. [PMID: 33480992 PMCID: PMC8097286 DOI: 10.1093/molbev/msab015] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nonribosomal peptides (NRP) are crucial molecular mediators in microbial ecology and provide indispensable drugs. Nevertheless, the evolution of the flexible biosynthetic machineries that correlates with the stunning structural diversity of NRPs is poorly understood. Here, we show that recombination is a key driver in the evolution of bacterial NRP synthetase (NRPS) genes across distant bacterial phyla, which has guided structural diversification in a plethora of NRP families by extensive mixing and matching of biosynthesis genes. The systematic dissection of a large number of individual recombination events did not only unveil a striking plurality in the nature and origin of the exchange units but allowed the deduction of overarching principles that enable the efficient exchange of adenylation (A) domain substrates while keeping the functionality of the dynamic multienzyme complexes. In the majority of cases, recombination events have targeted variable portions of the Acore domains, yet domain interfaces and the flexible Asub domain remained untapped. Our results strongly contradict the widespread assumption that adenylation and condensation (C) domains coevolve and significantly challenge the attributed role of C domains as stringent selectivity filter during NRP synthesis. Moreover, they teach valuable lessons on the choice of natural exchange units in the evolution of NRPS diversity, which may guide future engineering approaches.
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Affiliation(s)
- Martin Baunach
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Somak Chowdhury
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Jena, Germany
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), Jena, Germany
| | - Elke Dittmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
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34
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Combinatorial biosynthesis for the generation of new-to-nature peptide antimicrobials. Biochem Soc Trans 2021; 49:203-215. [PMID: 33439248 DOI: 10.1042/bst20200425] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
Abstract
Natural peptide products are a valuable source of important therapeutic agents, including antibiotics, antivirals and crop protection agents. Aided by an increased understanding of structure-activity relationships of these complex molecules and the biosynthetic machineries that produce them, it has become possible to re-engineer complete machineries and biosynthetic pathways to create novel products with improved pharmacological properties or modified structures to combat antimicrobial resistance. In this review, we will address the progress that has been made using non-ribosomally produced peptides and ribosomally synthesized and post-translationally modified peptides as scaffolds for designed biosynthetic pathways or combinatorial synthesis for the creation of novel peptide antimicrobials.
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35
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Dekimpe S, Masschelein J. Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis. Nat Prod Rep 2021; 38:1910-1937. [DOI: 10.1039/d0np00098a] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.
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Affiliation(s)
- Sofie Dekimpe
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery & Engineering
- Department of Biology
- KU Leuven
- Leuven
- Belgium
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36
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Théatre A, Hoste ACR, Rigolet A, Benneceur I, Bechet M, Ongena M, Deleu M, Jacques P. Bacillus sp.: A Remarkable Source of Bioactive Lipopeptides. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2021; 181:123-179. [DOI: 10.1007/10_2021_182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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37
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Huang HM, Stephan P, Kries H. Engineering DNA-Templated Nonribosomal Peptide Synthesis. Cell Chem Biol 2020; 28:221-227.e7. [PMID: 33238159 DOI: 10.1016/j.chembiol.2020.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/16/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022]
Abstract
Diffusive escape of intermediates limits the rate enhancement that nanocontainers or macromolecular scaffolds can provide for artificial biocatalytic cascades. Nonribosomal peptide synthetases (NRPSs) naturally form gigantic assembly lines and prevent escape by covalently tethering intermediates. Here, we have built DNA-templated NRPS (DT-NRPS) by adding zinc-finger tags to split NRPS modules. The zinc fingers direct the NRPS modules to 9-bp binding sites on a DNA strand, where they form a catalytically active enzyme cascade. Geometric constraints of the DT-NRPSs were investigated using the template DNA as a molecular ruler. Up to four DT-NRPS modules were assembled on DNA to synthesize peptides. DT-NRPSs outperform previously reported DNA-templated enzyme cascades in terms of DNA acceleration, which demonstrates that covalent intermediate channeling is possible along the DNA template. Attachment of assembly line enzymes to a DNA scaffold is a promising catalytic strategy for the sequence-controlled biosynthesis of nonribosomal peptides and other polymers.
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Affiliation(s)
- Hsin-Mei Huang
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany.
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38
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Romanowski S, Eustáquio AS. Synthetic biology for natural product drug production and engineering. Curr Opin Chem Biol 2020; 58:137-145. [DOI: 10.1016/j.cbpa.2020.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 09/09/2020] [Accepted: 09/21/2020] [Indexed: 12/23/2022]
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39
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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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40
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Calcott MJ, Owen JG, Ackerley DF. Efficient rational modification of non-ribosomal peptides by adenylation domain substitution. Nat Commun 2020; 11:4554. [PMID: 32917865 PMCID: PMC7486941 DOI: 10.1038/s41467-020-18365-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/19/2020] [Indexed: 12/22/2022] Open
Abstract
Non-ribosomal peptide synthetase (NRPS) enzymes form modular assembly-lines, wherein each module governs the incorporation of a specific monomer into a short peptide product. Modules are comprised of one or more key domains, including adenylation (A) domains, which recognise and activate the monomer substrate; condensation (C) domains, which catalyse amide bond formation; and thiolation (T) domains, which shuttle reaction intermediates between catalytic domains. This arrangement offers prospects for rational peptide modification via substitution of substrate-specifying domains. For over 20 years, it has been considered that C domains play key roles in proof-reading the substrate; a presumption that has greatly complicated rational NRPS redesign. Here we present evidence from both directed and natural evolution studies that any substrate-specifying role for C domains is likely to be the exception rather than the rule, and that novel non-ribosomal peptides can be generated by substitution of A domains alone. We identify permissive A domain recombination boundaries and show that these allow us to efficiently generate modified pyoverdine peptides at high yields. We further demonstrate the transferability of our approach in the PheATE-ProCAT model system originally used to infer C domain substrate specificity, generating modified dipeptide products at yields that are inconsistent with the prevailing dogma.
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Affiliation(s)
- Mark J Calcott
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Centre for Biodiscovery and Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - Jeremy G Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- Centre for Biodiscovery and Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
- Centre for Biodiscovery and Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
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41
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Bekiesch P, Zehl M, Domingo-Contreras E, Martín J, Pérez-Victoria I, Reyes F, Kaplan A, Rückert C, Busche T, Kalinowski J, Zotchev SB. Viennamycins: Lipopeptides Produced by a Streptomyces sp. JOURNAL OF NATURAL PRODUCTS 2020; 83:2381-2389. [PMID: 32786880 PMCID: PMC7460545 DOI: 10.1021/acs.jnatprod.0c00152] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Indexed: 06/11/2023]
Abstract
Extracts from Streptomyces sp. S4.7 isolated from the rhizosphere of edelweiss, an alpine medicinal plant, exhibited activity against Gram-positive bacteria. LC-HRMS analyses of the extracts resulted in the detection of two unknown, structurally related lipopeptides that were assumed to be responsible for the antibiotic activity. LC-MS guided isolation and structure elucidation of viennamycins A and B (1 and 2) by HR-MS/MS, 1D and 2D NMR, and Marfey's analyses revealed them to be novel compounds, with viennamycin A containing cysteic acid, a unique feature for lipopeptides. Tests for antibacterial, antifungal, and cytotoxic activities of purified viennamycins, both with and without divalent cations, did not reveal any bioactivity, suggesting that their biological function, which could not be determined in the tests used, is atypical for lipopeptides. The genome of Streptomyces sp. S4.7 was sequenced and analyzed, revealing the viennamycin biosynthetic gene cluster. Detailed bioinformatics-based analysis of the viennamycin gene cluster allowed elucidation of the biosynthetic pathway for these lipopeptides.
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Affiliation(s)
- Paulina Bekiesch
- Department
of Pharmacognosy, University of Vienna, 1090 Vienna, Austria
| | - Martin Zehl
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Elizabeth Domingo-Contreras
- Fundación
Medina, Centro de Excelencia
en Investigación de Medicamentos Innovadores en Andalucía, 18016, Armilla, Granada, Spain
| | - Jesús Martín
- Fundación
Medina, Centro de Excelencia
en Investigación de Medicamentos Innovadores en Andalucía, 18016, Armilla, Granada, Spain
| | - Ignacio Pérez-Victoria
- Fundación
Medina, Centro de Excelencia
en Investigación de Medicamentos Innovadores en Andalucía, 18016, Armilla, Granada, Spain
| | - Fernando Reyes
- Fundación
Medina, Centro de Excelencia
en Investigación de Medicamentos Innovadores en Andalucía, 18016, Armilla, Granada, Spain
| | - Arthur Kaplan
- Department
of Pharmacognosy, University of Vienna, 1090 Vienna, Austria
| | - Christian Rückert
- Center
for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Tobias Busche
- Center
for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Center
for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Sergey B. Zotchev
- Department
of Pharmacognosy, University of Vienna, 1090 Vienna, Austria
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42
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Tietze A, Shi YN, Kronenwerth M, Bode HB. Nonribosomal Peptides Produced by Minimal and Engineered Synthetases with Terminal Reductase Domains. Chembiochem 2020; 21:2750-2754. [PMID: 32378773 PMCID: PMC7586950 DOI: 10.1002/cbic.202000176] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/06/2020] [Indexed: 12/11/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) use terminal reductase domains for 2‐electron reduction of the enzyme‐bound thioester releasing the generated peptides as C‐terminal aldehydes. Herein, we reveal the biosynthesis of a pyrazine that originates from an aldehyde‐generating minimal NRPS termed ATRed in entomopathogenic Xenorhabdus indica. Reductase domains were also investigated in terms of NRPS engineering and, although no general applicable approach was deduced, we show that they can indeed be used for the production of similar natural and unnatural pyrazinones.
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Affiliation(s)
- Andreas Tietze
- Fachbereich Biowissenschaften, Molekulare Biotechnologie, Goethe-Universität Frankfurt, 60438, Frankfurt am Main, Germany
| | - Yan-Ni Shi
- Fachbereich Biowissenschaften, Molekulare Biotechnologie, Goethe-Universität Frankfurt, 60438, Frankfurt am Main, Germany
| | - Max Kronenwerth
- Fachbereich Biowissenschaften, Molekulare Biotechnologie, Goethe-Universität Frankfurt, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Fachbereich Biowissenschaften, Molekulare Biotechnologie, Goethe-Universität Frankfurt, 60438, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, 60438, Frankfurt am Main, Germany.,Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt, Germany
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43
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Hwang S, Lee N, Cho S, Palsson B, Cho BK. Repurposing Modular Polyketide Synthases and Non-ribosomal Peptide Synthetases for Novel Chemical Biosynthesis. Front Mol Biosci 2020; 7:87. [PMID: 32500080 PMCID: PMC7242659 DOI: 10.3389/fmolb.2020.00087] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/16/2020] [Indexed: 12/16/2022] Open
Abstract
In nature, various enzymes govern diverse biochemical reactions through their specific three-dimensional structures, which have been harnessed to produce many useful bioactive compounds including clinical agents and commodity chemicals. Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are particularly unique multifunctional enzymes that display modular organization. Individual modules incorporate their own specific substrates and collaborate to assemble complex polyketides or non-ribosomal polypeptides in a linear fashion. Due to the modular properties of PKSs and NRPSs, they have been attractive rational engineering targets for novel chemical production through the predictable modification of each moiety of the complex chemical through engineering of the cognate module. Thus, individual reactions of each module could be separated as a retro-biosynthetic biopart and repurposed to new biosynthetic pathways for the production of biofuels or commodity chemicals. Despite these potentials, repurposing attempts have often failed owing to impaired catalytic activity or the production of unintended products due to incompatible protein–protein interactions between the modules and structural perturbation of the enzyme. Recent advances in the structural, computational, and synthetic tools provide more opportunities for successful repurposing. In this review, we focused on the representative strategies and examples for the repurposing of modular PKSs and NRPSs, along with their advantages and current limitations. Thereafter, synthetic biology tools and perspectives were suggested for potential further advancement, including the rational and large-scale high-throughput approaches. Ultimately, the potential diverse reactions from modular PKSs and NRPSs would be leveraged to expand the reservoir of useful chemicals.
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Affiliation(s)
- Soonkyu Hwang
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Namil Lee
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Suhyung Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Byung-Kwan Cho
- Systems and Synthetic Biology Laboratory, Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,Intelligent Synthetic Biology Center, Daejeon, South Korea
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44
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Reimer JM, Eivaskhani M, Harb I, Guarné A, Weigt M, Schmeing TM. Structures of a dimodular nonribosomal peptide synthetase reveal conformational flexibility. Science 2020; 366:366/6466/eaaw4388. [PMID: 31699907 DOI: 10.1126/science.aaw4388] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 06/04/2019] [Accepted: 10/10/2019] [Indexed: 01/01/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are biosynthetic enzymes that synthesize natural product therapeutics using a modular synthetic logic, whereby each module adds one aminoacyl substrate to the nascent peptide. We have determined five x-ray crystal structures of large constructs of the NRPS linear gramicidin synthetase, including a structure of a full core dimodule in conformations organized for the condensation reaction and intermodular peptidyl substrate delivery. The structures reveal differences in the relative positions of adjacent modules, which are not strictly coupled to the catalytic cycle and are consistent with small-angle x-ray scattering data. The structures and covariation analysis of homologs allowed us to create mutants that improve the yield of a peptide from a module-swapped dimodular NRPS.
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Affiliation(s)
- Janice M Reimer
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Maximilian Eivaskhani
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Ingrid Harb
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Alba Guarné
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada
| | - Martin Weigt
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005 Paris, France
| | - T Martin Schmeing
- Department of Biochemistry and Center de Recherche en Biologie Structurale, McGill University, Montréal, QC H3G 0B1, Canada.
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45
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Jaremko MJ, Davis TD, Corpuz JC, Burkart MD. Type II non-ribosomal peptide synthetase proteins: structure, mechanism, and protein-protein interactions. Nat Prod Rep 2020; 37:355-379. [PMID: 31593192 PMCID: PMC7101270 DOI: 10.1039/c9np00047j] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: 1990 to 2019 Many medicinally-relevant compounds are derived from non-ribosomal peptide synthetase (NRPS) products. Type I NRPSs are organized into large modular complexes, while type II NRPS systems contain standalone or minimal domains that often encompass specialized tailoring enzymes that produce bioactive metabolites. Protein-protein interactions and communication between the type II biosynthetic machinery and various downstream pathways are critical for efficient metabolite production. Importantly, the architecture of type II NRPS proteins makes them ideal targets for combinatorial biosynthesis and metabolic engineering. Future investigations exploring the molecular basis or protein-protein recognition in type II NRPS pathways will guide these engineering efforts. In this review, we consolidate the broad range of NRPS systems containing type II proteins and focus on structural investigations, enzymatic mechanisms, and protein-protein interactions important to unraveling pathways that produce unique metabolites, including dehydrogenated prolines, substituted benzoic acids, substituted amino acids, and cyclopropanes.
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Affiliation(s)
- Matt J Jaremko
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Joshua C Corpuz
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
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46
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D’Ambrosio HK, Derbyshire ER. Investigating the Role of Class I Adenylate-Forming Enzymes in Natural Product Biosynthesis. ACS Chem Biol 2020; 15:17-27. [PMID: 31815417 DOI: 10.1021/acschembio.9b00865] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Adenylate-forming enzymes represent one of the most important enzyme classes in biology, responsible for the activation of carboxylate substrates for biosynthetic modifications. The byproduct of the adenylate-forming enzyme acetyl-CoA synthetase, acetyl-CoA, is incorporated into virtually every primary and secondary metabolic pathway. Modification of acetyl-CoA by an array of other adenylate-forming enzymes produces complex classes of natural products including nonribosomal peptides, polyketides, phenylpropanoids, lipopeptides, and terpenes. Adenylation domains possess a variety of unique structural and functional features that provide for such diversification in their resulting metabolites. As the number of organisms with sequenced genomes increases, more adenylate-forming enzymes are being identified, each with roles in metabolite production that have yet to be characterized. In this Review, we explore the broad role of class I adenylate-forming enzymes in the context of natural product biosynthesis and how they contribute to primary and secondary metabolism by focusing on important work conducted in the field. We highlight features of subclasses from this family that facilitate the production of structurally diverse metabolites, including those from noncanonical adenylation domains, and additionally discuss when biological roles for these compounds are known.
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Affiliation(s)
- Hannah K. D’Ambrosio
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Emily R. Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, North Carolina 27710, United States
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47
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In cellulo FRET-FLIM and single molecule tracking reveal the supra-molecular organization of the pyoverdine bio-synthetic enzymes in Pseudomonas aeruginosa. Q Rev Biophys 2020; 53:e1. [PMID: 31915092 DOI: 10.1017/s0033583519000155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The bio-synthesis of pyoverdine (PVD) in Pseudomonas aeruginosa involves multiple enzymatic steps including the action of non-ribosomal peptide synthetases (NRPSs). One hallmark of NRPS is their ability to make usage of non-proteinogenic amino-acids synthesized by co-expressed accessory enzymes. It is generally proposed that different enzymes of a secondary metabolic pathway assemble into large supra-molecular complexes. However, evidence for the assembly of sequential enzymes in the cellular context is sparse. Here, we used in cellulo single-molecule tracking and Förster resonance energy transfer measured by fluorescence lifetime microscopy (FRET-FLIM) to explore the spatial partitioning of the ornithine hydroxylase PvdA and its interactions with NRPS. We found PvdA was mostly diffusing bound to large complexes in the cytoplasm with a small exchangeable trapped fraction. FRET-FLIM clearly showed that PvdA is physically interacting with PvdJ, PvdI, PvdL, and PvdD, the four NRPS involved in the PVD pathway in Pseudomonas aeruginosa PAO1. The binding modes of PvdA were strikingly different according to the NRPS it is interacting with, suggesting that PvdA binding sites have co-evolved with the enzymatic active sites of NRPS. Our data provide evidence for strongly organized multi-enzymatic complexes responsible for the bio-synthesis of PVD and illustrate how binding sites have evolved to finely control the co-localization of sequential enzymes and promote metabolic pathway efficiency.
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48
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Götze S, Stallforth P. Structure, properties, and biological functions of nonribosomal lipopeptides from pseudomonads. Nat Prod Rep 2020; 37:29-54. [DOI: 10.1039/c9np00022d] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacteria of the genusPseudomonasdisplay a fascinating metabolic diversity. In this review, we focus our attention on the natural product class of nonribosomal lipopeptides, which help pseudomonads to colonize a wide range of ecological niches.
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Affiliation(s)
- Sebastian Götze
- Faculty 7: Natural and Environmental Sciences
- Institute for Environmental Sciences
- University Koblenz Landau
- 76829 Landau
- Germany
| | - Pierre Stallforth
- Junior Research Group Chemistry of Microbial Communication
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
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49
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Götze S, Arp J, Lackner G, Zhang S, Kries H, Klapper M, García-Altares M, Willing K, Günther M, Stallforth P. Structure elucidation of the syringafactin lipopeptides provides insight in the evolution of nonribosomal peptide synthetases. Chem Sci 2019; 10:10979-10990. [PMID: 32953002 PMCID: PMC7472662 DOI: 10.1039/c9sc03633d] [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: 07/23/2019] [Accepted: 11/08/2019] [Indexed: 11/21/2022] Open
Abstract
Modular biosynthetic machineries such as polyketide synthases (PKSs) or nonribosomal peptide synthetases (NRPSs) give rise to a vast structural diversity of bioactive metabolites indispensable in the treatment of cancer or infectious diseases. Here, we provide evidence for different evolutionary processes leading to the diversification of modular NRPSs and thus, their respective products. Discovery of a novel lipo-octapeptide family from Pseudomonas, the virginiafactins, and detailed structure elucidation of closely related peptides, the cichofactins and syringafactins, allowed retracing recombinational diversification of the respective NRPS genes. Bioinformatics analyses allowed us to spot an evolutionary snapshot of these processes, where recombination occurred both within the same and between different biosynthetic gene clusters. Our systems feature a recent diversification process, which may represent a typical paradigm to variations in modular biosynthetic machineries.
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Affiliation(s)
- Sebastian Götze
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - Johannes Arp
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - Gerald Lackner
- Independent Junior Research Group Synthetic Microbiology , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany
| | - Shuaibing Zhang
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - Hajo Kries
- Independent Junior Research Group Biosynthetic Design of Natural Products , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany
| | - Martin Klapper
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - María García-Altares
- Department Biomolecular Chemistry , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany
| | - Karsten Willing
- Department Bio Pilot Plant , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany
| | - Markus Günther
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
| | - Pierre Stallforth
- Independent Junior Research Group Chemistry of Microbial Communication , Leibniz Institute for Natural Product Research and Infection Biology , Hans Knöll Institute (HKI) , Beutenbergstrasse 11a , 07745 Jena , Germany .
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50
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Fan W, Liu H, Liu P, Deng X, Chen H, Liu Q, Feng Y. Characterization of protein interaction surface on fatty acyl selectivity of starter condensation domain in lipopeptide biosynthesis. Appl Microbiol Biotechnol 2019; 104:653-660. [DOI: 10.1007/s00253-019-10251-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 10/22/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022]
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