1
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Kim M, Kim J, Lee GS, Olinares PDB, Airan Y, Chow JL, Park J, Jeong Y, Park J, Chait BT, Herzon SB, Kim CS, Kang JY. Structural study on human microbiome-derived polyketide synthases that assemble genotoxic colibactin. Structure 2025:S0969-2126(25)00173-X. [PMID: 40381618 DOI: 10.1016/j.str.2025.04.017] [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: 01/13/2025] [Revised: 03/14/2025] [Accepted: 04/22/2025] [Indexed: 05/20/2025]
Abstract
Colibactin, a human microbiome-derived genotoxin, promotes colorectal cancer by damaging the host gut epithelial genomes. While colibactin is synthesized via a hybrid non-ribosomal peptide synthetase (NRPS)-polyketide synthase (PKS) pathway, known as pks or clb, the structural details of its biosynthetic enzymes remain limited, hindering our understanding of its biosynthesis and clinical application. In this study, we report the cryo-EM structures of two colibactin-producing PKS enzymes, ClbC and ClbI, captured in different reaction states using a substrate-mimic crosslinker. Our structural analysis revealed the binding sites of carrier protein (CP) domains of the ClbC and ClbI on their ketosynthase (KS) domains. Further, we identified a novel NRPS-PKS docking interaction between ClbI and its upstream enzyme, ClbH, mediated by the C-terminal peptide ClbH and the dimeric interface of ClbI, establishing a 1:2 stoichiometry. These findings advance our understanding of colibactin assembly line and provide broader insights into NRPS-PKS natural product biosynthesis mechanisms.
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Affiliation(s)
- Minjae Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jinwoo Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Gyu Sung Lee
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, Republic of Korea
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Yougant Airan
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Jasmine L Chow
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Jongseok Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Yujin Jeong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jiho Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Department of Pharmacology and Therapeutic Radiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Chung Sub Kim
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea.
| | - Jin Young Kang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
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2
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Zhang T, He Y, Li C, Yao H, Zhang M, Li Y. Intelligent decoding platform for peptide sequences: SERS detection via high affinity self-assembled silver nanoparticles and machine learning analysis. Anal Chim Acta 2025; 1347:343797. [PMID: 40024661 DOI: 10.1016/j.aca.2025.343797] [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: 12/18/2024] [Revised: 01/26/2025] [Accepted: 02/12/2025] [Indexed: 03/04/2025]
Abstract
BACKGROUND Peptides are compounds formed by the dehydration-condensation reaction of two or more amino acids which play an important role in the life functions of the organism. Changes in the structure of amino acids and peptides are vital for elucidating the process of disease development. However, the existing methods make it difficult to accurately recognize slight variations in peptide sequences, which becomes a difficult detection task. Therefore, the necessity of novel, accurate, comprehensive and deep strategies for peptide sequence identification is imperative. RESULTS Here, an intelligent decoding system was developed, which synthesized a substrate (Ag/BDHA) with high affinity and self-assembly capabilities by double reduction method and utilized surface-enhanced Raman scattering (SERS) to achieve label-free, high-affinity and accurate capturing of peptide sequences. The platform can recognize peptide chains with the same molecular weight but different amino acid sequences, filling the loopholes of mass spectroscopy. Interestingly, it can also distinguish peptide chains with different amino acid lengths, different amino acid positions and different amino acid mutations. And further combined with machine learning methods to simplify the output of detection results, including thermogram, confusion matrix, principal component analysis and hierarchical cluster analysis, which was more suitable for practical applications. More importantly, to explore the potential for application, real influenza A viruses were selected and analyzed and successfully identifying mutations and subtypes of viruses. SIGNIFICANCE In sum, the original, versatile and intelligent detection system based on surface-enhanced Raman scattering we proposed provides a promising method and strategy for the precise and valid analysis of different variations of peptide sequences, which is of great significance for explaining life processes, exploring disease pathogenesis, and developing innovative drugs.
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Affiliation(s)
- Ting Zhang
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD), College of Pharmacy, Harbin Medical University, Heilongjiang, 150081, PR China; Department of Inorganic Chemistry and Physical Chemistry, College of Pharmacy, Harbin Medical University, Heilongjiang, 150081, PR China
| | - Yingying He
- Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, Heilongjiang, 150081, PR China
| | - Chengming Li
- Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, Heilongjiang, 150081, PR China
| | - Huan Yao
- Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, Heilongjiang, 150081, PR China
| | - Mingxu Zhang
- Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, Heilongjiang, 150081, PR China
| | - Yang Li
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD), College of Pharmacy, Harbin Medical University, Heilongjiang, 150081, PR China; Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, Heilongjiang, 150081, PR China; Research Unit of Health Sciences and Technology (HST), Faculty of Medicine University of Oulu, Finland.
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3
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Scat S, Weissman KJ, Chagot B. Insights into docking in megasynthases from the investigation of the toblerol trans-AT polyketide synthase: many α-helical means to an end. RSC Chem Biol 2024; 5:669-683. [PMID: 38966669 PMCID: PMC11221535 DOI: 10.1039/d4cb00075g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
The fidelity of biosynthesis by modular polyketide synthases (PKSs) depends on specific moderate affinity interactions between successive polypeptide subunits mediated by docking domains (DDs). These sequence elements are notably portable, allowing their transplantation into alternative biosynthetic and metabolic contexts. Herein, we use integrative structural biology to characterize a pair of DDs from the toblerol trans-AT PKS. Both are intrinsically disordered regions (IDRs) that fold into a 3 α-helix docking complex of unprecedented topology. The C-terminal docking domain (CDD) resembles the 4 α-helix type (4HB) CDDs, which shows that the same type of DD can be redeployed to form complexes of distinct geometry. By carefully re-examining known DD structures, we further extend this observation to type 2 docking domains, establishing previously unsuspected structural relations between DD types. Taken together, these data illustrate the plasticity of α-helical DDs, which allow the formation of a diverse topological spectrum of docked complexes. The newly identified DDs should also find utility in modular PKS genetic engineering.
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Affiliation(s)
- Serge Scat
- Université de Lorraine, CNRS, IMoPA F-54000 Nancy France
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4
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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: 3] [Impact Index Per Article: 3.0] [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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5
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Zhang K, Kries H. Biomimetic engineering of nonribosomal peptide synthesis. Biochem Soc Trans 2023; 51:1521-1532. [PMID: 37409512 DOI: 10.1042/bst20221264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/07/2023]
Abstract
Nonribosomal peptides (NRPs) have gained attention due to their diverse biological activities and potential applications in medicine and agriculture. The natural diversity of NRPs is a result of evolutionary processes that have occurred over millions of years. Recent studies have shed light on the mechanisms by which nonribosomal peptide synthetases (NRPSs) evolve, including gene duplication, recombination, and horizontal transfer. Mimicking natural evolution could be a useful strategy for engineering NRPSs to produce novel compounds with desired properties. Furthermore, the emergence of antibiotic-resistant bacteria has highlighted the urgent need for new drugs, and NRPs represent a promising avenue for drug discovery. This review discusses the engineering potential of NRPSs in light of their evolutionary history.
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Affiliation(s)
- Kexin Zhang
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena), 07745 Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI Jena), 07745 Jena, Germany
- Organic Chemistry I, University of Bayreuth, 95440 Bayreuth, Germany
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6
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Abbood N, Effert J, Bozhueyuek KAJ, Bode HB. Guidelines for Optimizing Type S Nonribosomal Peptide Synthetases. ACS Synth Biol 2023; 12:2432-2443. [PMID: 37523786 PMCID: PMC10443035 DOI: 10.1021/acssynbio.3c00295] [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: 05/08/2023] [Indexed: 08/02/2023]
Abstract
Bacterial biosynthetic assembly lines, such as nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), play a crucial role in the synthesis of natural products that have significant therapeutic potential. The ability to engineer these biosynthetic assembly lines offers opportunities to produce artificial nonribosomal peptides, polyketides, and their hybrids with improved properties. In this study, we introduced a synthetic NRPS variant, termed type S NRPS, which simplifies the engineering process and enables biocombinatorial approaches for generating nonribosomal peptide libraries in a parallelized high-throughput manner. However, initial generations of type S NRPSs exhibited a bottleneck that led to significantly reduced production yields. To address this challenge, we employed two optimization strategies. First, we truncated SYNZIPs from the N- and/or C-terminus of the NRPS. SYNZIPs comprise a large set of well-characterized synthetic protein interaction reagents. Second, we incorporated a structurally flexible glycine-serine linker between the NRPS protein and the attached SYNZIP, aiming to improve dynamic domain-domain interactions. Through an iterative optimization process, we achieved remarkable improvements in production yields, with titer increases of up to 55-fold compared to the nonoptimized counterparts. These optimizations successfully restored production levels of type S NRPSs to those observed in wild-type NRPSs and even surpassed them. Overall, our findings demonstrate the potential of engineering bacterial biosynthetic assembly lines for the production of artificial nonribosomal peptides. In addition, optimizing the SYNZIP toolbox can have valuable implications for diverse applications in synthetic biology, such as metabolic engineering, cell signaling studies, or engineering of other multienzyme complexes, such as PKSs.
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Affiliation(s)
- Nadya Abbood
- Max-Planck-Institute
for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular
Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Juliana Effert
- Max-Planck-Institute
for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
| | - Kenan A. J. Bozhueyuek
- Max-Planck-Institute
for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular
Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Myria
Biosciences AG, Mattenstrasse
26, 4058 Basel, Switzerland
| | - Helge B. Bode
- Max-Planck-Institute
for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular
Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Chemical
Biology, Department of Chemistry, Philipps-University
Marburg, 35043 Marburg, Germany
- Senckenberg
Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
- Center for
Synthetic Microbiology (SYNMIKRO), Phillips
University Marburg, 35043 Marburg, Germany
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7
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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: 6] [Impact Index Per Article: 3.0] [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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8
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Kudo F, Chikuma T, Nambu M, Chisuga T, Sumimoto S, Iwasaki A, Suenaga K, Miyanaga A, Eguchi T. Unique Initiation and Termination Mechanisms Involved in the Biosynthesis of a Hybrid Polyketide-Nonribosomal Peptide Lyngbyapeptin B Produced by the Marine Cyanobacterium Moorena bouillonii. ACS Chem Biol 2023; 18:875-883. [PMID: 36921345 PMCID: PMC10127204 DOI: 10.1021/acschembio.3c00011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Lyngbyapeptin B is a hybrid polyketide-nonribosomal peptide isolated from particular marine cyanobacteria. In this report, we carried out genome sequence analysis of a producer cyanobacterium Moorena bouillonii to understand the biosynthetic mechanisms that generate the unique structural features of lyngbyapeptin B, including the (E)-3-methoxy-2-butenoyl starter unit and the C-terminal thiazole moiety. We identified a putative lyngbyapeptin B biosynthetic (lynB) gene cluster comprising nine open reading frames that include two polyketide synthases (PKSs: LynB1 and LynB2), four nonribosomal peptide synthetases (NRPSs: LynB3, LynB4, LynB5, and LynB6), a putative nonheme diiron oxygenase (LynB7), a type II thioesterase (LynB8), and a hypothetical protein (LynB9). In vitro enzymatic analysis of LynB2 with methyltransferase (MT) and acyl carrier protein (ACP) domains revealed that the LynB2 MT domain (LynB2-MT) catalyzes O-methylation of the acetoacetyl-LynB2 ACP domain (LynB2-ACP) to yield (E)-3-methoxy-2-butenoyl-LynB2-ACP. In addition, in vitro enzymatic analysis of LynB7 revealed that LynB7 catalyzes the oxidative decarboxylation of (4R)-2-methyl-2-thiazoline-4-carboxylic acid to yield 2-methylthiazole in the presence of Fe2+ and molecular oxygen. This result indicates that LynB7 is responsible for the last post-NRPS modification to give the C-terminal thiazole moiety in lyngbyapeptin B biosynthesis. Overall, we identified and characterized a new marine cyanobacterial hybrid PKS-NRPS biosynthetic gene cluster for lyngbyapeptin B production, revealing two unique enzymatic logics.
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Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Tokyo 152-8551, Japan
| | - Takuji Chikuma
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Tokyo 152-8551, Japan
| | - Mizuki Nambu
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Tokyo 152-8551, Japan
| | - Taichi Chisuga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Tokyo 152-8551, Japan
| | - Shimpei Sumimoto
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Arihiro Iwasaki
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Kiyotake Suenaga
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 O-okayama, Tokyo 152-8551, Japan
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9
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Cai X, Zhao L, Bode HB. Engineering of Specific Single-Module Nonribosomal Peptide Synthetases of the RXP Type for the Production of Defined Peptides. ACS Synth Biol 2022; 12:203-212. [PMID: 36535068 PMCID: PMC9872161 DOI: 10.1021/acssynbio.2c00472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Rhabdopeptide/xenortide-like peptide (RXP) nonribosomal peptide synthetases (NRPSs) derived from entomophathogenic Xenorhabdus and Photorhabdus bacteria often produce libraries of different peptides varying in amino acid composition, number and degree of methylation, which mainly is a result of promiscuous docking domains (DDs) mediating protein-protein interactions between the different NRPS subunits. In this study, we present two specific RXP-NRPS systems with rather specific DDs that were used as platforms to generate a series of defined RXPs via the exchange of adenylation/methyltransferase (A-MT) domains in the systems followed by heterologous expression in Escherichia coli. Additionally, these results suggest that NRPS subunit interaction is not only exclusively dependent on DDs but at least partially also on A domains.
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Affiliation(s)
- Xiaofeng Cai
- School
of Pharmacy, Tongji Medical College, Huazhong
University of Science and Technology, 430030 Wuhan, China,Molecular
Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany,
| | - Lei Zhao
- Molecular
Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany,State
Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai
Institute of Organic Chemistry, Chinese
Academy of Sciences, 200032 Shanghai, China
| | - Helge B. Bode
- Molecular
Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany,Department
of Natural Products in Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, 35043 Marburg, Germany,Chemical
Biology, Department of Chemistry, Philipps
University Marburg, 35037 Marburg, Germany,Senckenberg
Gesellschaft für Naturforschung, 60325 Frankfurt, Germany,
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10
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Abd-Elgawad MMM. Xenorhabdus spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes. Life (Basel) 2022; 12:1360. [PMID: 36143397 PMCID: PMC9503066 DOI: 10.3390/life12091360] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 12/17/2022] Open
Abstract
Mounting concern over the misuse of chemical pesticides has sparked broad interest for safe and effective alternatives to control plant pests and pathogens. Xenorhabdus bacteria, as pesticidal symbionts of the entomopathogenic nematodes Steinernema species, can contribute to this solution with a treasure trove of insecticidal compounds and an ability to suppress a variety of plant pathogens. As many challenges face sound exploitation of plant-phytonematode interactions, a full useful spectrum of such interactions should address nematicidal activity of Xenorhabdus. Steinernema-Xenorhabdus complex or Xenorhabdus individually should be involved in mechanisms underlying the favorable side of plant-nematode interactions in emerging cropping systems. Using Xenorhabdus bacteria should earnestly be harnessed to control not only phytonematodes, but also other plant pests and pathogens within integrated pest management plans. This review highlights the significance of fitting Xenorhabdus-obtained insecticidal, nematicidal, fungicidal, acaricidal, pharmaceutical, antimicrobial, and toxic compounds into existing, or arising, holistic strategies, for controlling many pests/pathogens. The widespread utilization of Xenorhabdus bacteria, however, has been slow-going, due to costs and some issues with their commercial processing. Yet, advances have been ongoing via further mastering of genome sequencing, discovering more of the beneficial Xenorhabdus species/strains, and their successful experimentations for pest control. Their documented pathogenicity to a broad range of arthropods and pathogens and versatility bode well for useful industrial products. The numerous beneficial traits of Xenorhabdus bacteria can facilitate their integration with other tactics for better pest/disease management programs.
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Affiliation(s)
- Mahfouz M M Abd-Elgawad
- Plant Pathology Department, Agricultural and Biological Research Division, National Research Centre, El-Behooth St., Dokki, Giza 12622, Egypt
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11
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Booth TJ, Bozhüyük KAJ, Liston JD, Batey SFD, Lacey E, Wilkinson B. Bifurcation drives the evolution of assembly-line biosynthesis. Nat Commun 2022; 13:3498. [PMID: 35715397 PMCID: PMC9205934 DOI: 10.1038/s41467-022-30950-z] [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] [Received: 06/06/2021] [Accepted: 05/18/2022] [Indexed: 11/09/2022] Open
Abstract
Reprogramming biosynthetic assembly-lines is a topic of intense interest. This is unsurprising as the scaffolds of most antibiotics in current clinical use are produced by such pathways. The modular nature of assembly-lines provides a direct relationship between the sequence of enzymatic domains and the chemical structure of the product, but rational reprogramming efforts have been met with limited success. To gain greater insight into the design process, we wanted to examine how Nature creates assembly-lines and searched for biosynthetic pathways that might represent evolutionary transitions. By examining the biosynthesis of the anti-tubercular wollamides, we uncover how whole gene duplication and neofunctionalization can result in pathway bifurcation. We show that, in the case of the wollamide biosynthesis, neofunctionalization is initiated by intragenomic recombination. This pathway bifurcation leads to redundancy, providing the genetic robustness required to enable large structural changes during the evolution of antibiotic structures. Should the new product be non-functional, gene loss can restore the original genotype. However, if the new product confers an advantage, depreciation and eventual loss of the original gene creates a new linear pathway. This provides the blind watchmaker equivalent to the design, build, test cycle of synthetic biology.
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Affiliation(s)
- Thomas J Booth
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
- School of Molecular Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Kenan A J Bozhüyük
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
| | - Jonathon D Liston
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Sibyl F D Batey
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
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12
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Kinner A, Nerke P, Siedentop R, Steinmetz T, Classen T, Rosenthal K, Nett M, Pietruszka J, Lütz S. Recent Advances in Biocatalysis for Drug Synthesis. Biomedicines 2022; 10:964. [PMID: 35625702 PMCID: PMC9138302 DOI: 10.3390/biomedicines10050964] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/16/2022] [Accepted: 04/17/2022] [Indexed: 02/01/2023] Open
Abstract
Biocatalysis is constantly providing novel options for the synthesis of active pharmaceutical ingredients (APIs). In addition to drug development and manufacturing, biocatalysis also plays a role in drug discovery and can support many active ingredient syntheses at an early stage to build up entire scaffolds in a targeted and preparative manner. Recent progress in recruiting new enzymes by genome mining and screening or adapting their substrate, as well as product scope, by protein engineering has made biocatalysts a competitive tool applied in academic and industrial spheres. This is especially true for the advances in the field of nonribosomal peptide synthesis and enzyme cascades that are expanding the capabilities for the discovery and synthesis of new bioactive compounds via biotransformation. Here we highlight some of the most recent developments to add to the portfolio of biocatalysis with special relevance for the synthesis and late-stage functionalization of APIs, in order to bypass pure chemical processes.
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Affiliation(s)
- Alina Kinner
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
| | - Philipp Nerke
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
| | - Regine Siedentop
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
| | - Till Steinmetz
- Laboratory for Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (T.S.); (M.N.)
| | - Thomas Classen
- Institute of Bio- and Geosciences: Biotechnology (IBG-1), Forschungszentrum Jülich, 52428 Jülich, Germany; (T.C.); (J.P.)
| | - Katrin Rosenthal
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
| | - Markus Nett
- Laboratory for Technical Biology, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (T.S.); (M.N.)
| | - Jörg Pietruszka
- Institute of Bio- and Geosciences: Biotechnology (IBG-1), Forschungszentrum Jülich, 52428 Jülich, Germany; (T.C.); (J.P.)
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf Located at Forschungszentrum Jülich, 52426 Jülich, Germany
| | - Stephan Lütz
- Chair for Bioprocess Engineering, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany; (A.K.); (P.N.); (R.S.); (K.R.)
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13
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Wenski SL, Thiengmag S, Helfrich EJ. Complex peptide natural products: Biosynthetic principles, challenges and opportunities for pathway engineering. Synth Syst Biotechnol 2022; 7:631-647. [PMID: 35224231 PMCID: PMC8842026 DOI: 10.1016/j.synbio.2022.01.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/03/2023] Open
Abstract
Complex peptide natural products exhibit diverse biological functions and a wide range of physico-chemical properties. As a result, many peptides have entered the clinics for various applications. Two main routes for the biosynthesis of complex peptides have evolved in nature: ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic pathways and non-ribosomal peptide synthetases (NRPSs). Insights into both bioorthogonal peptide biosynthetic strategies led to the establishment of universal principles for each of the two routes. These universal rules can be leveraged for the targeted identification of novel peptide biosynthetic blueprints in genome sequences and used for the rational engineering of biosynthetic pathways to produce non-natural peptides. In this review, we contrast the key principles of both biosynthetic routes and compare the different biochemical strategies to install the most frequently encountered peptide modifications. In addition, the influence of the fundamentally different biosynthetic principles on past, current and future engineering approaches is illustrated. Despite the different biosynthetic principles of both peptide biosynthetic routes, the arsenal of characterized peptide modifications encountered in RiPP and NRPS systems is largely overlapping. The continuous expansion of the biocatalytic toolbox of peptide modifying enzymes for both routes paves the way towards the production of complex tailor-made peptides and opens up the possibility to produce NRPS-derived peptides using the ribosomal route and vice versa.
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Affiliation(s)
- Sebastian L. Wenski
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
| | - Sirinthra Thiengmag
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
| | - Eric J.N. Helfrich
- Institute for Molecular Bio Science, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), 60325, Frankfurt am Main, Germany
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14
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Microbial Lipopeptide-Producing Strains and Their Metabolic Roles under Anaerobic Conditions. Microorganisms 2021; 9:microorganisms9102030. [PMID: 34683351 PMCID: PMC8540375 DOI: 10.3390/microorganisms9102030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 01/17/2023] Open
Abstract
The lipopeptide produced by microorganisms is one of the representative biosurfactants and is characterized as a series of structural analogues of different families. Thirty-four families covering about 300 lipopeptide compounds have been reported in the last decades, and most of the reported lipopeptides produced by microorganisms were under aerobic conditions. The lipopeptide-producing strains under anaerobic conditions have attracted much attention from both the academic and industrial communities, due to the needs and the challenge of their applications in anaerobic environments, such as in oil reservoirs and in microbial enhanced oil recovery (MEOR). In this review, the fifty-eight reported bacterial strains, mostly isolated from oil reservoirs and dominated by the species Bacillus subtilis, producing lipopeptide biosurfactants, and the species Pseudomonas aeruginosa, producing glycolipid biosurfactants under anaerobic conditions were summarized. The metabolic pathway and the non-ribosomal peptide synthetases (NRPSs) of the strain Bacillus subtilis under anaerobic conditions were analyzed, which is expected to better understand the key mechanisms of the growth and production of lipopeptide biosurfactants of such kind of bacteria under anaerobic conditions, and to expand the industrial application of anaerobic biosurfactant-producing bacteria.
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15
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Fage CD, Kosol S, Jenner M, Öster C, Gallo A, Kaniusaite M, Steinbach R, Staniforth M, Stavros VG, Marahiel MA, Cryle MJ, Lewandowski JR. Communication Breakdown: Dissecting the COM Interfaces between the Subunits of Nonribosomal Peptide Synthetases. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02113] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Christopher D. Fage
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Simone Kosol
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, U.K
| | - Carl Öster
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Angelo Gallo
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - 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
| | - Roman Steinbach
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Michael Staniforth
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Vasilios G. Stavros
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
| | - Mohamed A. Marahiel
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Max J. Cryle
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
| | - Józef R. Lewandowski
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7AL, U.K
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16
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Bozhueyuek KAJ, Watzel J, Abbood N, Bode HB. Synthetic Zippers as an Enabling Tool for Engineering of Non-Ribosomal Peptide Synthetases*. Angew Chem Int Ed Engl 2021; 60:17531-17538. [PMID: 34015175 PMCID: PMC8362031 DOI: 10.1002/anie.202102859] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/31/2021] [Indexed: 12/29/2022]
Abstract
Non‐ribosomal peptide synthetases (NRPSs) are the origin of a wide range of natural products, including many clinically used drugs. Efficient engineering of these often giant biosynthetic machineries to produce novel non‐ribosomal peptides (NRPs) is an ongoing challenge. Here we describe a cloning and co‐expression strategy to functionally combine NRPS fragments of Gram‐negative and ‐positive origin, synthesising novel peptides at titres up to 220 mg L−1. Extending from the recently introduced definition of eXchange Units (XUs), we inserted synthetic zippers (SZs) to split single protein NRPSs into independently expressed and translated polypeptide chains. These synthetic type of NRPS (type S) enables easier access to engineering, overcomes cloning limitations, and provides a simple and rapid approach to building peptide libraries via the combination of different NRPS subunits.
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Affiliation(s)
- Kenan A J Bozhueyuek
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jonas Watzel
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Nadya Abbood
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
| | - Helge B Bode
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany.,Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main, Germany
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17
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Iacovelli R, Bovenberg RAL, Driessen AJM. Nonribosomal peptide synthetases and their biotechnological potential in Penicillium rubens. J Ind Microbiol Biotechnol 2021; 48:6324005. [PMID: 34279620 PMCID: PMC8788816 DOI: 10.1093/jimb/kuab045] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/12/2021] [Indexed: 01/23/2023]
Abstract
Nonribosomal peptide synthetases (NRPS) are large multimodular enzymes that synthesize a diverse variety of peptides. Many of these are currently used as pharmaceuticals, thanks to their activity as antimicrobials (penicillin, vancomycin, daptomycin, echinocandin), immunosuppressant (cyclosporin) and anticancer compounds (bleomycin). Because of their biotechnological potential, NRPSs have been extensively studied in the past decades. In this review, we provide an overview of the main structural and functional features of these enzymes, and we consider the challenges and prospects of engineering NRPSs for the synthesis of novel compounds. Furthermore, we discuss secondary metabolism and NRP synthesis in the filamentous fungus Penicillium rubens and examine its potential for the production of novel and modified β-lactam antibiotics.
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Affiliation(s)
- Riccardo Iacovelli
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Roel A L Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands.,DSM Biotechnology Centre, 2613 AX Delft, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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18
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Bozhueyuek KAJ, Watzel J, Abbood N, Bode HB. Synthetic Zippers as an Enabling Tool for Engineering of Non‐Ribosomal Peptide Synthetases**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Kenan A. J. Bozhueyuek
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Jonas Watzel
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
| | - Nadya Abbood
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
| | - Helge B. Bode
- Molecular Biotechnology Institute of Molecular Biosciences Goethe University Frankfurt 60438 Frankfurt am Main Germany
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
- Senckenberg Gesellschaft für Naturforschung 60325 Frankfurt am Main Germany
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19
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Watzel J, Duchardt-Ferner E, Sarawi S, Bode HB, Wöhnert J. Cooperation between a T Domain and a Minimal C-Terminal Docking Domain to Enable Specific Assembly in a Multiprotein NRPS. Angew Chem Int Ed Engl 2021; 60:14171-14178. [PMID: 33876501 PMCID: PMC8251938 DOI: 10.1002/anie.202103498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 01/27/2023]
Abstract
Non-ribosomal peptide synthetases (NRPS) produce natural products from amino acid building blocks. They often consist of multiple polypeptide chains which assemble in a specific linear order via specialized N- and C-terminal docking domains (N/C DDs). Typically, docking domains function independently from other domains in NRPS assembly. Thus, docking domain replacements enable the assembly of "designer" NRPS from proteins that normally do not interact. The multiprotein "peptide-antimicrobial-Xenorhabdus" (PAX) peptide-producing PaxS NRPS is assembled from the three proteins PaxA, PaxB and PaxC. Herein, we show that the small C DD of PaxA cooperates with its preceding thiolation (T1 ) domain to bind the N DD of PaxB with very high affinity, establishing a structural and thermodynamical basis for this unprecedented docking interaction, and we test its functional importance in vivo in a truncated PaxS assembly line. Similar docking interactions are apparently present in other NRPS systems.
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Affiliation(s)
- Jonas Watzel
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Sepas Sarawi
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany.,Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt am Main, Germany.,Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
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20
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Watzel J, Duchardt‐Ferner E, Sarawi S, Bode HB, Wöhnert J. Kooperation zwischen T‐Domäne und minimaler C‐terminaler Docking‐Domäne für funktionelle Proteininteraktionen in Multiprotein‐NRPS. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jonas Watzel
- Molekulare Biotechnologie Institut für Molekulare Biowissenschaften Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Elke Duchardt‐Ferner
- Institut für Molekulare Biowissenschaften und Biomolekulares Magnetresonanz Zentrum (BMRZ) Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Sepas Sarawi
- Institut für Molekulare Biowissenschaften und Biomolekulares Magnetresonanz Zentrum (BMRZ) Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
- Molekulare Biotechnologie Institut für Molekulare Biowissenschaften Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Helge B. Bode
- Abteilung Naturstoffe in organismischen Interaktionen Max-Planck-Institut für terrestrische Mikrobiologie 35043 Marburg Deutschland
- Senckenberg Gesellschaft für Naturforschung 60325 Frankfurt am Main Deutschland
- Molekulare Biotechnologie Institut für Molekulare Biowissenschaften Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften und Biomolekulares Magnetresonanz Zentrum (BMRZ) Goethe-Universität Frankfurt 60438 Frankfurt am Main Deutschland
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21
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Booysen E, Dicks LMT. Does the Future of Antibiotics Lie in Secondary Metabolites Produced by Xenorhabdus spp.? A Review. Probiotics Antimicrob Proteins 2021; 12:1310-1320. [PMID: 32844362 DOI: 10.1007/s12602-020-09688-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The over-prescription of antibiotics for treatment of infections is primarily to blame for the increase in bacterial resistance. Added to the problem is the slow rate at which novel antibiotics are discovered and the many processes that need to be followed to classify antimicrobials safe for medical use. Xenorhabdus spp. of the family Enterobacteriaceae, mutualistically associated with entomopathogenic nematodes of the genus Steinernema, produce a variety of antibacterial peptides, including bacteriocins, depsipeptides, xenocoumacins and PAX (peptide antimicrobial-Xenorhabdus) peptides, plus additional secondary metabolites with antibacterial and antifungal activity. The secondary metabolites of some strains are active against protozoa and a few have anti-carcinogenic properties. It is thus not surprising that nematodes invaded by a single strain of a Xenorhabdus species are not infected by other microorganisms. In this review, the antimicrobial compounds produced by Xenorhabdus spp. are listed and the gene clusters involved in synthesis of these secondary metabolites are discussed. We also review growth conditions required for increased production of antimicrobial compounds.
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Affiliation(s)
- E Booysen
- Department of Microbiology, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - L M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch, 7600, South Africa.
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22
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Behsaz B, Bode E, Gurevich A, Shi YN, Grundmann F, Acharya D, Caraballo-Rodríguez AM, Bouslimani A, Panitchpakdi M, Linck A, Guan C, Oh J, Dorrestein PC, Bode HB, Pevzner PA, Mohimani H. Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. Nat Commun 2021; 12:3225. [PMID: 34050176 PMCID: PMC8163882 DOI: 10.1038/s41467-021-23502-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs.
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Affiliation(s)
- Bahar Behsaz
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Edna Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St Petersburg, Russia
| | - Yan-Ni Shi
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Florian Grundmann
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Deepa Acharya
- Tiny Earth Chemistry Hub, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Annabell Linck
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Changhui Guan
- The Jackson Laboratory of Medical Genomics, Farmington, CT, USA
| | - Julia Oh
- The Jackson Laboratory of Medical Genomics, Farmington, CT, USA
| | - Pieter C Dorrestein
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt & Senckenberg Research Institute, Frankfurt am Main, Germany.
- Max-Planck-Institute for Terrestrial Microbiology, Department for Natural Products in Organismic Interactions, Marburg, Germany.
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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23
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Liu D, Rubin GM, Dhakal D, Chen M, Ding Y. Biocatalytic synthesis of peptidic natural products and related analogues. iScience 2021; 24:102512. [PMID: 34041453 PMCID: PMC8141463 DOI: 10.1016/j.isci.2021.102512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Peptidic natural products (PNPs) represent a rich source of lead compounds for the discovery and development of therapeutic agents for the treatment of a variety of diseases. However, the chemical synthesis of PNPs with diverse modifications for drug research is often faced with significant challenges, including the unavailability of constituent nonproteinogenic amino acids, inefficient cyclization protocols, and poor compatibility with other functional groups. Advances in the understanding of PNP biosynthesis and biocatalysis provide a promising, sustainable alternative for the synthesis of these compounds and their analogues. Here we discuss current progress in using native and engineered biosynthetic enzymes for the production of both ribosomally and nonribosomally synthesized peptides. In addition, we highlight new in vitro and in vivo approaches for the generation and screening of PNP libraries.
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Affiliation(s)
- Dake Liu
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Garret M. Rubin
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, Gainesville, FL 32610, USA
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Watzel J, Sarawi S, Duchardt-Ferner E, Bode HB, Wöhnert J. NMR resonance assignments for a docking domain pair with an attached thiolation domain from the PAX peptide-producing NRPS from Xenorhabdus cabanillasii. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:229-234. [PMID: 33675014 PMCID: PMC7973640 DOI: 10.1007/s12104-021-10010-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/16/2021] [Indexed: 05/09/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are large multienzyme machineries. They synthesize numerous important natural products starting from amino acids. For peptide synthesis functionally specialized NRPS modules interact in a defined manner. Individual modules are either located on a single or on multiple different polypeptide chains. The "peptide-antimicrobial-Xenorhabdus" (PAX) peptide producing NRPS PaxS from Xenorhabdus bacteria consists of the three proteins PaxA, PaxB and PaxC. Different docking domains (DDs) located at the N-termini of PaxB and PaxC and at the C-termini of PaxA and BaxB mediate specific non-covalent interactions between them. The N-terminal docking domains precede condensation domains while the C-terminal docking domains follow thiolation domains. The binding specificity of individual DDs is important for the correct assembly of multi-protein NRPS systems. In many multi-protein NRPS systems the docking domains are sufficient to mediate the necessary interactions between individual protein chains. However, it remains unclear if this is a general feature for all types of structurally different docking domains or if the neighboring domains in some cases support the function of the docking domains. Here, we report the 1H, 13C and 15 N NMR resonance assignments for a C-terminal di-domain construct containing a thiolation (T) domain followed by a C-terminal docking domain (CDD) from PaxA and for its binding partner - the N-terminal docking domain (NDD) from PaxB from the Gram-negative entomopathogenic bacterium Xenorhabdus cabanillasii JM26 in their free states and for a 1:1 complex formed by the two proteins. These NMR resonance assignments will facilitate further structural and dynamic studies of this protein complex.
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Affiliation(s)
- Jonas Watzel
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Sepas Sarawi
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Senckenberg Gesellschaft Für Naturforschung, 60325, Frankfurt am Main, Germany
- Department of Natural Products in Organismic Interactions, Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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25
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Booysen E, Rautenbach M, Stander MA, Dicks LMT. Profiling the Production of Antimicrobial Secondary Metabolites by Xenorhabdus khoisanae J194 Under Different Culturing Conditions. Front Chem 2021; 9:626653. [PMID: 33859975 PMCID: PMC8042232 DOI: 10.3389/fchem.2021.626653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Species from the genus Xenorhabdus, endosymbiotic bacteria of Steinernema nematodes, produce several antibacterial and antifungal compounds, some of which are anti-parasitic. In this study, we report on the effect growth conditions have on the production of antimicrobial compounds produced by Xenorhabdus khoisanae J194. The strain was cultured in aerated and non-aerated broth, respectively, and on solid media. Production of antimicrobial compounds was detected after 24 h of growth in liquid media, with highest levels recorded after 96 h. Highest antimicrobial activity was obtained from cells cultured on solid media. By using ultraperformance liquid chromatography linked to mass spectrometry and HPLC, a plethora of known Xenorhabdus compounds were identified. These compounds are the PAX lipopeptides (PAX 1', PAX 3', PAX 5, and PAX 7E), xenocoumacins and xenoamicins. Differences observed in the MS-MS fractionation patterns collected in this study, when compared to previous studies indicated that this strain produces novel xenoamicins. Three novel antimicrobial compounds, khoicin, xenopep and rhabdin, were identified and structurally characterized based on MS-MS fractionation patterns, amino acid analysis and whole genome analysis. The various compounds produced under the three different conditions indicates that the secondary metabolism of X. khoisanae J194 may be regulated by oxygen, water activity or both. Based on these findings X. khoisanae J194 produce a variety of antimicrobial compounds that may have application in disease control.
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Affiliation(s)
- Elzaan Booysen
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| | - Marina Rautenbach
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Marietjie A Stander
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa.,LCMS Central Analytical Facility, Stellenbosch University, Stellenbosch, South Africa
| | - Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
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Smith HG, Beech MJ, Lewandowski JR, Challis GL, Jenner M. Docking domain-mediated subunit interactions in natural product megasynth(et)ases. J Ind Microbiol Biotechnol 2021; 48:6152290. [PMID: 33640957 PMCID: PMC9113145 DOI: 10.1093/jimb/kuab018] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/24/2021] [Indexed: 12/19/2022]
Abstract
Polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) multienzymes produce numerous high value metabolites. The protein subunits which constitute these megasynth(et)ases must undergo ordered self-assembly to ensure correct organisation of catalytic domains for the biosynthesis of a given natural product. Short amino acid regions at the N- and C-termini of each subunit, termed docking domains (DDs), often occur in complementary pairs, which interact to facilitate substrate transfer and maintain pathway fidelity. This review details all structurally characterised examples of NRPS and PKS DDs to date and summarises efforts to utilise DDs for the engineering of biosynthetic pathways.
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Affiliation(s)
- Helen G Smith
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Matthew J Beech
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | | | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Monash University, Clayton, VIC 3800, Australia
| | - Matthew Jenner
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
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28
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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: 2.6] [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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29
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Alonzo DA, Schmeing TM. Biosynthesis of depsipeptides, or Depsi: The peptides with varied generations. Protein Sci 2020; 29:2316-2347. [PMID: 33073901 DOI: 10.1002/pro.3979] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022]
Abstract
Depsipeptides are compounds that contain both ester bonds and amide bonds. Important natural product depsipeptides include the piscicide antimycin, the K+ ionophores cereulide and valinomycin, the anticancer agent cryptophycin, and the antimicrobial kutzneride. Furthermore, database searches return hundreds of uncharacterized systems likely to produce novel depsipeptides. These compounds are made by specialized nonribosomal peptide synthetases (NRPSs). NRPSs are biosynthetic megaenzymes that use a module architecture and multi-step catalytic cycle to assemble monomer substrates into peptides, or in the case of specialized depsipeptide synthetases, depsipeptides. Two NRPS domains, the condensation domain and the thioesterase domain, catalyze ester bond formation, and ester bonds are introduced into depsipeptides in several different ways. The two most common occur during cyclization, in a reaction between a hydroxy-containing side chain and the C-terminal amino acid residue in a peptide intermediate, and during incorporation into the growing peptide chain of an α-hydroxy acyl moiety, recruited either by direct selection of an α-hydroxy acid substrate or by selection of an α-keto acid substrate that is reduced in situ. In this article, we discuss how and when these esters are introduced during depsipeptide synthesis, survey notable depsipeptide synthetases, and review insight into bacterial depsipeptide synthetases recently gained from structural studies.
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Affiliation(s)
- Diego A Alonzo
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
| | - T Martin Schmeing
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, Quebec, Canada
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30
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Risser F, Collin S, Dos Santos-Morais R, Gruez A, Chagot B, Weissman KJ. Towards improved understanding of intersubunit interactions in modular polyketide biosynthesis: Docking in the enacyloxin IIa polyketide synthase. J Struct Biol 2020; 212:107581. [DOI: 10.1016/j.jsb.2020.107581] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 12/26/2022]
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31
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Siebels I, Nowak S, Heil CS, Tufar P, Cortina NS, Bode HB, Grininger M. Cell-Free Synthesis of Natural Compounds from Genomic DNA of Biosynthetic Gene Clusters. ACS Synth Biol 2020; 9:2418-2426. [PMID: 32818377 DOI: 10.1021/acssynbio.0c00186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A variety of chemicals can be produced in a living host cell via optimized and engineered biosynthetic pathways. Despite the successes, pathway engineering remains demanding because of the lack of specific functions or substrates in the host cell, the cell's sensitivity in vital physiological processes to the heterologous components, or constrained mass transfer across the membrane. In this study, we show that complex multidomain proteins involved in natural compound biosynthesis can be produced from encoding DNA in vitro in a minimal complex PURE system to directly run multistep reactions. Specifically, we synthesize indigoidine and rhabdopeptides with the in vitro produced multidomain nonribosomal peptide synthetases BpsA and KJ12ABC from the organisms Streptomyces lavendulae and Xenorhabdus KJ12.1, respectively. These in vitro produced proteins are analyzed in yield, post-translational modification and in their ability to synthesize the natural compounds, and compared to recombinantly produced proteins. Our study highlights cell-free PURE system as suitable setting for the characterization of biosynthetic gene clusters that can potentially be harnessed for the rapid engineering of biosynthetic pathways.
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Affiliation(s)
- Ilka Siebels
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
| | - Sarah Nowak
- Fachbereich Biowissenschaften, Molecular Biotechnology, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
| | - Christina S. Heil
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
| | - Peter Tufar
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
| | - Niña S. Cortina
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
| | - Helge B. Bode
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Fachbereich Biowissenschaften, Molecular Biotechnology, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, 60325, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, 60438, Germany
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32
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Fidor A, Grabski M, Gawor J, Gromadka R, Węgrzyn G, Mazur-Marzec H. Nostoc edaphicum CCNP1411 from the Baltic Sea-A New Producer of Nostocyclopeptides. Mar Drugs 2020; 18:E442. [PMID: 32858999 PMCID: PMC7551626 DOI: 10.3390/md18090442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022] Open
Abstract
Nostocyclopeptides (Ncps) constitute a small class of nonribosomal peptides, exclusively produced by cyanobacteria of the genus Nostoc. The peptides inhibit the organic anion transporters, OATP1B3 and OATP1B1, and prevent the transport of the toxic microcystins and nodularin into hepatocytes. So far, only three structural analogues, Ncp-A1, Ncp-A2 and Ncp-M1, and their linear forms were identified in Nostoc strains as naturally produced cyanometabolites. In the current work, the whole genome sequence of the new Ncps producer, N. edaphicum CCNP1411 from the Baltic Sea, has been determined. The genome consists of the circular chromosome (7,733,505 bps) and five circular plasmids (from 44.5 kb to 264.8 kb). The nostocyclopeptide biosynthetic gene cluster (located between positions 7,609,981-7,643,289 bps of the chromosome) has been identified and characterized in silico. The LC-MS/MS analyzes of N. edaphicum CCNP1411 cell extracts prepared in aqueous methanol revealed several products of the genes. Besides the known peptides, Ncp-A1 and Ncp-A2, six other compounds putatively characterized as new noctocyclopeptide analogues were detected. This includes Ncp-E1 and E2 and their linear forms (Ncp-E1-L and E2-L), a cyclic Ncp-E3 and a linear Ncp-E4-L. Regardless of the extraction conditions, the cell contents of the linear nostocyclopeptides were found to be higher than the cyclic ones, suggesting a slow rate of the macrocyclization process.
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Affiliation(s)
- Anna Fidor
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Piłsudskiego 46, PL-81378 Gdynia, Poland;
| | - Michał Grabski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (G.W.)
| | - Jan Gawor
- DNA Sequencing and Oligonucleotide Synthesis Laboratory, Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Robert Gromadka
- DNA Sequencing and Oligonucleotide Synthesis Laboratory, Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (G.W.)
| | - Hanna Mazur-Marzec
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Piłsudskiego 46, PL-81378 Gdynia, Poland;
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Dehling E, Rüschenbaum J, Diecker J, Dörner W, Mootz HD. Photo-crosslink analysis in nonribosomal peptide synthetases reveals aberrant gel migration of branched crosslink isomers and spatial proximity between non-neighboring domains. Chem Sci 2020; 11:8945-8954. [PMID: 34123148 PMCID: PMC8163358 DOI: 10.1039/d0sc01969k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are large, multi-modular enzyme templates for the biosynthesis of important peptide natural products. Modules are composed of a set of semi-autonomous domains that facilitate the individual reaction steps. Only little is known about the existence and relevance of a higher-order architecture in these mega-enzymes, for which contacts between non-neighboring domains in three-dimensional space would be characteristic. Similarly poorly understood is the structure of communication-mediating (COM) domains that facilitate NRPS subunit docking at the boundaries between epimerization and condensation domains. We investigated a COM domain pair in a minimal two module NRPS using genetically encoded photo-crosslinking moieties in the N-terminal acceptor COM domain. Crosslinks into the C-terminal donor COM domain of the partner module resulted in protein products with the expected migration behavior on SDS-PAGE gels corresponding to the added molecular weight of the proteins. Additionally, an unexpected apparent high-molecular weight crosslink product was revealed by mass spectrometric analysis to represent a T-form isomer with branched connectivity of the two polypeptide chains. Synthesis of the linear L-form and branched T-form isomers by click chemistry confirmed this designation. Our data revealed a surprising spatial proximity between the acceptor COM domain and the functionally unrelated small subdomain of the preceding adenylation domain. These findings provide an insight into three-dimensional domain arrangements in NRPSs in solution and suggest the described photo-crosslinking approach as a promising tool for the systematic investigation of their higher-order architecture. Photo-crosslink analysis reveals unexpected insights into the higher-order architecture of NRPS and the nature of crosslink isomers.![]()
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Affiliation(s)
- Eva Dehling
- Institute of Biochemistry, Department of Chemistry and Pharmacy, University of Muenster D-48149 Münster Germany
| | - Jennifer Rüschenbaum
- Institute of Biochemistry, Department of Chemistry and Pharmacy, University of Muenster D-48149 Münster Germany
| | - Julia Diecker
- Institute of Biochemistry, Department of Chemistry and Pharmacy, University of Muenster D-48149 Münster Germany
| | - Wolfgang Dörner
- Institute of Biochemistry, Department of Chemistry and Pharmacy, University of Muenster D-48149 Münster Germany
| | - Henning D Mootz
- Institute of Biochemistry, Department of Chemistry and Pharmacy, University of Muenster D-48149 Münster Germany
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34
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Kegler C, Bode HB. Artificial Splitting of a Non-Ribosomal Peptide Synthetase by Inserting Natural Docking Domains. Angew Chem Int Ed Engl 2020; 59:13463-13467. [PMID: 32329545 PMCID: PMC7496407 DOI: 10.1002/anie.201915989] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/18/2020] [Indexed: 12/13/2022]
Abstract
The interaction in multisubunit non‐ribosomal peptide synthetases (NRPSs) is mediated by docking domains that ensure the correct subunit‐to‐subunit interaction. We introduced natural docking domains into the three‐module xefoampeptide synthetase (XfpS) to create two to three artificial NRPS XfpS subunits. The enzymatic performance of the split biosynthesis was measured by absolute quantification of the products by HPLC‐ESI‐MS. The connecting role of the docking domains was probed by deleting integral parts of them. The peptide production data was compared to soluble protein amounts of the NRPS using SDS‐PAGE. Reduced peptide synthesis was not a result of reduced soluble NRPS concentration but a consequence of the deletion of vital docking domain parts. Splitting the xefoampeptide biosynthesis polypeptide by introducing docking domains was feasible and resulted in higher amounts of product in one of the two tested split‐module cases compared to the full‐length wild‐type enzyme.
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Affiliation(s)
- Carsten Kegler
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Helge B Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, 60438, Frankfurt, Germany.,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt, Germany
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35
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Kegler C, Bode HB. Artificial Splitting of a Non‐Ribosomal Peptide Synthetase by Inserting Natural Docking Domains. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201915989] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Carsten Kegler
- Molekulare Biotechnologie, Fachbereich Biowissenschaften Goethe Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt am Main Germany
| | - Helge B. Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften Goethe Universität Frankfurt Max-von-Laue-Straße 9 60438 Frankfurt am Main Germany
- Buchmann Institute for Molecular Life Sciences (BMLS) Goethe-Universität Frankfurt 60438 Frankfurt Germany
- Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25 60325 Frankfurt Germany
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36
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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: 91] [Impact Index Per Article: 18.2] [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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37
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Watzel J, Hacker C, Duchardt-Ferner E, Bode HB, Wöhnert J. A New Docking Domain Type in the Peptide-Antimicrobial-Xenorhabdus Peptide Producing Nonribosomal Peptide Synthetase from Xenorhabdus bovienii. ACS Chem Biol 2020; 15:982-989. [DOI: 10.1021/acschembio.9b01022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jonas Watzel
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Carolin Hacker
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Helge B. Bode
- Molecular Biotechnology, Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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38
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Heterogeneity in Bacterial Specialized Metabolism. J Mol Biol 2019; 431:4589-4598. [DOI: 10.1016/j.jmb.2019.04.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 11/17/2022]
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Kosol S, Gallo A, Griffiths D, Valentic TR, Masschelein J, Jenner M, de Los Santos ELC, Manzi L, Sydor PK, Rea D, Zhou S, Fülöp V, Oldham NJ, Tsai SC, Challis GL, Lewandowski JR. Structural basis for chain release from the enacyloxin polyketide synthase. Nat Chem 2019; 11:913-923. [PMID: 31548674 PMCID: PMC6783305 DOI: 10.1038/s41557-019-0335-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/19/2019] [Indexed: 02/06/2023]
Abstract
Modular polyketide synthases and non-ribosomal peptide synthetases are molecular assembly lines that consist of several multienzyme subunits that undergo dynamic self-assembly to form a functional megacomplex. N- and C-terminal docking domains are usually responsible for mediating the interactions between subunits. Here we show that communication between two non-ribosomal peptide synthetase subunits responsible for chain release from the enacyloxin polyketide synthase, which assembles an antibiotic with promising activity against Acinetobacter baumannii, is mediated by an intrinsically disordered short linear motif and a β-hairpin docking domain. The structures, interactions and dynamics of these subunits were characterized using several complementary biophysical techniques to provide extensive insights into binding and catalysis. Bioinformatics analyses reveal that short linear motif/β-hairpin docking domain pairs mediate subunit interactions in numerous non-ribosomal peptide and hybrid polyketide-non-ribosomal peptide synthetases, including those responsible for assembling several important drugs. Short linear motifs and β-hairpin docking domains from heterologous systems are shown to interact productively, highlighting the potential of such interfaces as tools for biosynthetic engineering.
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Affiliation(s)
- Simone Kosol
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Angelo Gallo
- Department of Chemistry, University of Warwick, Coventry, UK
| | | | - Timothy R Valentic
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
- Department of Chemistry, University of California, Irvine, CA, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | | | - Matthew Jenner
- Department of Chemistry, University of Warwick, Coventry, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
| | | | - Lucio Manzi
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - Paulina K Sydor
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Dean Rea
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Shanshan Zhou
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Vilmos Fülöp
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Neil J Oldham
- School of Chemistry, University of Nottingham, Nottingham, UK
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Gregory L Challis
- Department of Chemistry, University of Warwick, Coventry, UK.
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.
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Zhao L, Bode HB. Production of a photohexapeptide library from entomopathogenic Photorhabdus asymbiotica PB68.1. Org Biomol Chem 2019; 17:7858-7862. [PMID: 31403156 DOI: 10.1039/c9ob01489f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new natural product compound library, photohexapeptide library, was identified from entomopathogenic Photorhabdus asymbiotica PB68.1 after the NRPS-encoding gene phpS was activated via promoter exchange. Peptide structures, including the absolute configurations of amino acids, were determined by using a combination of bioinformatics analysis and isotopic labelling experiments followed by detailed HPLC-MS analysis. Additionally, their structures were confirmed by chemical synthesis and NMR after preparative isolation. The chemical diversity of the photohexapeptides results from promiscuous adenylation domain specificity being an excellent example of how to create libraries in nature.
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Affiliation(s)
- Lei Zhao
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany.
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41
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Alanjary M, Cano-Prieto C, Gross H, Medema MH. Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines. Nat Prod Rep 2019; 36:1249-1261. [PMID: 31259995 DOI: 10.1039/c9np00021f] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2014 to 2019Nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) have been the subject of engineering efforts for multiple decades. Their modular assembly line architecture potentially allows unlocking vast chemical space for biosynthesis. However, attempts thus far are often met with mixed success, due to limited molecular compatibility of the parts used for engineering. Now, new engineering strategies, increases in genomic data, and improved computational tools provide more opportunities for major progress. In this review we highlight some of the challenges and progressive strategies for the re-design of NRPSs & type I PKSs and survey useful computational tools and approaches to attain the ultimate goal of semi-automated and design-based engineering of novel peptide and polyketide products.
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Affiliation(s)
- Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
| | - Carolina Cano-Prieto
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - Harald Gross
- Department of Pharmaceutical Biology, Pharmaceutical Institute, Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
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42
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Moss NA, Seiler G, Leão TF, Castro-Falcón G, Gerwick L, Hughes CC, Gerwick WH. Nature's Combinatorial Biosynthesis Produces Vatiamides A-F. Angew Chem Int Ed Engl 2019; 58:9027-9031. [PMID: 31071229 DOI: 10.1002/anie.201902571] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/18/2019] [Indexed: 12/11/2022]
Abstract
Hybrid type I PKS/NRPS biosynthetic pathways typically proceed in a collinear manner wherein one molecular building block is enzymatically incorporated in a sequence that corresponds to gene arrangement. In this work, genome mining combined with the use of a fluorogenic azide-based click probe led to the discovery and characterization of vatiamides A-F, three structurally diverse alkynylated lipopeptides, and their brominated analogues, from the cyanobacterium Moorea producens ASI16Jul14-2. These derive from a unique combinatorial non-collinear PKS/NRPS system encoded by a 90 kb gene cluster in which an upstream PKS cassette interacts with three separate cognate NRPS partners. This is facilitated by a series of promiscuous intermodule PKS-NRPS docking motifs possessing identical amino acid sequences. This interaction confers a new type of combinatorial capacity for creating molecular diversity in microbial systems.
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Affiliation(s)
- Nathan A Moss
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Grant Seiler
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Tiago F Leão
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Gabriel Castro-Falcón
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Chambers C Hughes
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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Moss NA, Seiler G, Leão TF, Castro‐Falcón G, Gerwick L, Hughes CC, Gerwick WH. Nature's Combinatorial Biosynthesis Produces Vatiamides A–F. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902571] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nathan A. Moss
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Grant Seiler
- Department of Chemistry and BiochemistryUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Tiago F. Leão
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Gabriel Castro‐Falcón
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Lena Gerwick
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Chambers C. Hughes
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - William H. Gerwick
- Center for Marine Biotechnology and BiomedicineScripps Institution of OceanographyUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
- Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
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Cai X, Zhao L, Bode HB. Reprogramming Promiscuous Nonribosomal Peptide Synthetases for Production of Specific Peptides. Org Lett 2019; 21:2116-2120. [DOI: 10.1021/acs.orglett.9b00395] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xiaofeng Cai
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China
| | - Lei Zhao
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Helge B. Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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