1
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Peng YJ, Chen Y, Zhou CZ, Miao W, Jiang YL, Zeng X, Zhang CC. Modular catalytic activity of nonribosomal peptide synthetases depends on the dynamic interaction between adenylation and condensation domains. Structure 2024; 32:440-452.e4. [PMID: 38340732 DOI: 10.1016/j.str.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024]
Abstract
Nonribosomal peptide synthetases (NRPSs) are large multidomain enzymes for the synthesis of a variety of bioactive peptides in a modular and pipelined fashion. Here, we investigated how the condensation (C) domain and the adenylation (A) domain cooperate with each other for the efficient catalytic activity in microcystin NRPS modules. We solved two crystal structures of the microcystin NRPS modules, representing two different conformations in the NRPS catalytic cycle. Our data reveal that the dynamic interaction between the C and the A domains in these modules is mediated by the conserved "RXGR" motif, and this interaction is important for the adenylation activity. Furthermore, the "RXGR" motif-mediated dynamic interaction and its functional regulation are prevalent in different NRPSs modules possessing both the A and the C domains. This study provides new insights into the catalytic mechanism of NRPSs and their engineering strategy for synthetic peptides with different structures and properties.
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Affiliation(s)
- Ye-Jun Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuxing Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Cong-Zhao Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Wei Miao
- Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China; Hubei Hongshan Laboratory, Wuhan 430070, People's Republic of China
| | - Yong-Liang Jiang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, People's Republic of China.
| | - Xiaoli Zeng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.
| | - Cheng-Cai Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; Key Laboratory of Lake and Watershed Science for Water Security, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China; Hubei Hongshan Laboratory, Wuhan 430070, People's Republic of China.
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2
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Bozhüyük KAJ, Präve L, Kegler C, Schenk L, Kaiser S, Schelhas C, Shi YN, Kuttenlochner W, Schreiber M, Kandler J, Alanjary M, Mohiuddin TM, Groll M, Hochberg GKA, Bode HB. Evolution-inspired engineering of nonribosomal peptide synthetases. Science 2024; 383:eadg4320. [PMID: 38513038 DOI: 10.1126/science.adg4320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/09/2024] [Indexed: 03/23/2024]
Abstract
Many clinically used drugs are derived from or inspired by bacterial natural products that often are produced through nonribosomal peptide synthetases (NRPSs), megasynthetases that activate and join individual amino acids in an assembly line fashion. In this work, we describe a detailed phylogenetic analysis of several bacterial NRPSs that led to the identification of yet undescribed recombination sites within the thiolation (T) domain that can be used for NRPS engineering. We then developed an evolution-inspired "eXchange Unit between T domains" (XUT) approach, which allows the assembly of NRPS fragments over a broad range of GC contents, protein similarities, and extender unit specificities, as demonstrated for the specific production of a proteasome inhibitor designed and assembled from five different NRPS fragments.
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Affiliation(s)
- Kenan A J Bozhüyük
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Myria Biosciences AG, Tech Park Basel, Hochbergstrasse 60C, 4057 Basel, Switzerland
| | - Leonard Präve
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Carsten Kegler
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Leonie Schenk
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Sebastian Kaiser
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Christian Schelhas
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
| | - Yan-Ni Shi
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Wolfgang Kuttenlochner
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Max Schreiber
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Joshua Kandler
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - T M Mohiuddin
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
| | - Helge B Bode
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) & Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt, Germany
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3
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Sun X, Alfermann J, Li H, Watkins MB, Chen YT, Morrell TE, Mayerthaler F, Wang CY, Komatsuzaki T, Chu JW, Ando N, Mootz HD, Yang H. Subdomain dynamics enable chemical chain reactions in non-ribosomal peptide synthetases. Nat Chem 2024; 16:259-268. [PMID: 38049653 DOI: 10.1038/s41557-023-01361-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/03/2023] [Indexed: 12/06/2023]
Abstract
Many peptide-derived natural products are produced by non-ribosomal peptide synthetases (NRPSs) in an assembly-line fashion. Each amino acid is coupled to a designated peptidyl carrier protein (PCP) through two distinct reactions catalysed sequentially by the single active site of the adenylation domain (A-domain). Accumulating evidence suggests that large-amplitude structural changes occur in different NRPS states; yet how these molecular machines orchestrate such biochemical sequences has remained elusive. Here, using single-molecule Förster resonance energy transfer, we show that the A-domain of gramicidin S synthetase I adopts structurally extended and functionally obligatory conformations for alternating between adenylation and thioester-formation structures during enzymatic cycles. Complementary biochemical, computational and small-angle X-ray scattering studies reveal interconversion among these three conformations as intrinsic and hierarchical where intra-A-domain organizations propagate to remodel inter-A-PCP didomain configurations during catalysis. The tight kinetic coupling between structural transitions and enzymatic transformations is quantified, and how the gramicidin S synthetase I A-domain utilizes its inherent conformational dynamics to drive directional biosynthesis with a flexibly linked PCP domain is revealed.
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Affiliation(s)
- Xun Sun
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonas Alfermann
- Institute of Biochemistry, University of Münster, Münster, Germany
| | - Hao Li
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Maxwell B Watkins
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology; Institute of Molecular Medicine and Bioengineering; Department of Biological Science and Technology; Centre for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Thomas E Morrell
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | | | - Chia-Ying Wang
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tamiki Komatsuzaki
- Research Centre of Mathematics for Social Creativity, Research Institute for Electronic Science; The Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Japan
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology; Institute of Molecular Medicine and Bioengineering; Department of Biological Science and Technology; Centre for Intelligent Drug Systems and Smart Bio-devices (IDS²B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Nozomi Ando
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Henning D Mootz
- Institute of Biochemistry, University of Münster, Münster, Germany.
| | - Haw Yang
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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4
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Platt AJ, Padrick S, Ma AT, Beld J. A dissected non-ribosomal peptide synthetase maintains activity. Biochim Biophys Acta Proteins Proteom 2024; 1872:140972. [PMID: 37951518 DOI: 10.1016/j.bbapap.2023.140972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) generate chemically complex compounds and their modular architecture suggests that changing their domain organization can predictably alter their products. Ebony, a small three-domain NRPS, catalyzes the formation of β-alanine containing amides from biogenic amines. To examine the necessity of interdomain interactions, we modeled and docked domains of Ebony to reveal potential interfaces between them. Testing the same domain combinations in vitro showed that 8 % of activity was preserved after Ebony was dissected into a di-domain and a detached C-terminal domain, suggesting that sufficient interaction was maintained after dissection. Our work creates a model to identify domain interfaces necessary for catalysis, an important step toward utilizing Ebony as a combinatorial engineering platform for novel amides.
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Affiliation(s)
- Amanda J Platt
- Department of Microbiology and Immunology, Institute of Molecular Medicine and Infectious Disease, Center for Advanced Microbial Processing, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Shae Padrick
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15(th) Street, Philadelphia, PA 19102, USA
| | - Amy T Ma
- Department of Microbiology and Immunology, Institute of Molecular Medicine and Infectious Disease, Center for Advanced Microbial Processing, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Joris Beld
- Department of Microbiology and Immunology, Institute of Molecular Medicine and Infectious Disease, Center for Advanced Microbial Processing, Drexel University College of Medicine, Philadelphia, PA, USA.
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5
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Becker R, Pederick JL, Dawes EG, Bruning JB, Abell AD. Structure-guided design and synthesis of ATP-competitive N-acyl-substituted sulfamide d-alanine-d-alanine ligase inhibitors. Bioorg Med Chem 2023; 96:117509. [PMID: 37948922 DOI: 10.1016/j.bmc.2023.117509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/10/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023]
Abstract
d-Alanine-d-alanine ligase (Ddl) catalyses the ATP-dependent formation of d-Ala-d-Ala, a critical component in bacterial cell wall biosynthesis and is a validated target for new antimicrobial agents. Here, we describe the structure-guided design, synthesis, and evaluation of ATP-competitive N-acyl-substituted sulfamides 27-36, 42, 46, 47 as inhibitors of Staphylococcus aureus Ddl (SaDdl). A crystal structure of SaDdl complexed with ATP and d-Ala-d-Ala (PDB: 7U9K) identified ATP-mimetic 8 as an initial scaffold for further inhibitor design. Evaluation of 8 in SaDdl enzyme inhibition assays revealed the ability to reduce enzyme activity to 72 ± 8 % (IC50 = 1.6 mM). The sulfamide linker of 8 was extended with 2-(4-methoxyphenyl)ethanol to give 29, to investigate further interactions with the d-Ala pocket of SaDdl, as predicted by molecular docking. This compound reduced enzyme activity to 89 ± 1 %, with replacement of the 4-methoxyphenyl group in 29 with alternative phenyl substituents (27, 28, 31-33, 35, 36) failing to significantly improve on this (80-89 % remaining enzyme activity). Exchanging these phenyl substituents with selected heterocycles (42, 46, 47) did improve activity, with the most active compound (42) reducing SaDdl activity to 70 ± 1 % (IC50 = 1.7 mM), which compares favourably to the FDA-approved inhibitor d-cycloserine (DCS) (IC50 = 0.1 mM). To the best of our knowledge, this is the first reported study of bisubstrate SaDdl inhibitors.
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Affiliation(s)
- Rouven Becker
- Department of Chemistry, School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jordan L Pederick
- Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Edward G Dawes
- Department of Chemistry, School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D Abell
- Department of Chemistry, School of Physics, Chemistry and Earth Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia; Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; Centre for Nanoscale BioPhotonics (CNBP), University of Adelaide, Adelaide, South Australia 5005, Australia.
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6
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Rambaher MH, Zdovc I, Glavač NK, Gobec S, Frlan R. Mur ligase F as a new target for the flavonoids quercitrin, myricetin, and (-)-epicatechin. J Comput Aided Mol Des 2023; 37:721-733. [PMID: 37796382 PMCID: PMC10618370 DOI: 10.1007/s10822-023-00535-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023]
Abstract
MurC, D, E, and F are ATP-dependent ligases involved in the stepwise assembly of the tetrapeptide stem of forming peptidoglycan. As highly conserved targets found exclusively in bacterial cells, they are of significant interest for antibacterial drug discovery. In this study, we employed a computer-aided molecular design approach to identify potential inhibitors of MurF. A biochemical inhibition assay was conducted, screening twenty-four flavonoids and related compounds against MurC-F, resulting in the identification of quercitrin, myricetin, and (-)-epicatechin as MurF inhibitors with IC50 values of 143 µM, 139 µM, and 92 µM, respectively. Notably, (-)-epicatechin demonstrated mixed type inhibition with ATP and uncompetitive inhibition with D-Ala-D-Ala dipeptide and UM3DAP substrates. Furthermore, in silico analysis using Sitemap and subsequent docking analysis using Glide revealed two plausible binding sites for (-)-epicatechin. The study also investigated the crucial structural features required for activity, with a particular focus on the substitution pattern and hydroxyl group positions, which were found to be important for the activity. The study highlights the significance of computational approaches in targeting essential enzymes involved in bacterial peptidoglycan synthesis.
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Affiliation(s)
- Martina Hrast Rambaher
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Irena Zdovc
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Gerbičeva ul. 60, Ljubljana, Slovenia
| | - Nina Kočevar Glavač
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Stanislav Gobec
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.
| | - Rok Frlan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.
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7
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Pederick JL, Woolman JC, Bruning JB. Comparative functional and structural analysis of Pseudomonas aeruginosa d-alanine-d-alanine ligase isoforms as prospective antibiotic targets. FEBS J 2023; 290:5536-5553. [PMID: 37581574 DOI: 10.1111/febs.16932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/02/2023] [Accepted: 08/14/2023] [Indexed: 08/16/2023]
Abstract
Pseudomonas aeruginosa is a major human pathogen in the healthcare setting. The emergence of multi-drug-resistant and extensive drug-resistant P. aeruginosa is of great concern, and clearly indicates that new alternatives to current first-line antibiotics are required in the future. Inhibition of d-alanine-d-alanine production presents as a promising avenue as it is a key component in the essential process of cell wall biosynthesis. In P. aeruginosa, d-alanine-d-alanine production is facilitated by two isoforms, d-alanine-d-alanine ligase A (PaDdlA) and d-alanine-d-alanine ligase B (PaDdlA), but neither enzyme has been individually characterised to date. Here, we present the functional and structural characterisation of PaDdlA and PaDdlB, and assess their potential as antibiotic targets. This was achieved using a combination of in vitro enzyme-activity assays and X-ray crystallography. The former revealed that both isoforms effectively catalyse d-alanine-d-alanine production with near identical efficiency, and that this is effectively disrupted by the model d-alanine-d-alanine ligase inhibitor, d-cycloserine. Next, each isoform was co-crystallised with ATP and either d-alanine-d-alanine or d-cycloserine, allowing direct comparison of the key structural features. Both isoforms possess the same structural architecture and share a high level of conservation within the active site. Although residues forming the d-alanine pocket are completely conserved, the ATP-binding pocket possesses several amino acid substitutions resulting in a differing chemical environment around the ATP adenine base. Together, these findings support that the discovery of dual PaDdlA/PaDdlB competitive inhibitors is a viable approach for developing new antibiotics against P. aeruginosa.
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Affiliation(s)
- Jordan L Pederick
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, SA, Australia
| | - Jessica C Woolman
- School of Biological Sciences, The University of Adelaide, SA, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, SA, Australia
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8
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Ishikawa F, Tsukumo N, Morishita E, Asamizu S, Kusuhara S, Marumoto S, Takashima K, Onaka H, Tanabe G. Biosynthetic diversification of non-ribosomal peptides through activity-based protein profiling of adenylation domains. Chem Commun (Camb) 2023; 59:9473-9476. [PMID: 37477345 DOI: 10.1039/d3cc02633g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
We describe activity-based protein profiling for analyzing the adenylation domains of non-ribosomal peptide synthetases (ABPP-NRPS) in bacterial proteomes. Using a range of non-proteoinogenic amino acid sulfamoyladenosines, the competitive format of ABPP-NRPS provided substrate tolerance toward non-proteinogenic amino acids. When coupled with precursor-directed biosynthesis, a non-proteinogenic amino acid (O-allyl-L-serine) was successfully incorporated into gramicidin S.
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Affiliation(s)
- Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka 577-8502, Japan.
| | - Natsumi Tsukumo
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka 577-8502, Japan.
| | - Erika Morishita
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka 577-8502, Japan.
| | - Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Saaya Kusuhara
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka 577-8502, Japan.
| | - Shinsuke Marumoto
- Joint Research Center, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka 577-8502, Japan
| | - Katsuki Takashima
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka 577-8502, Japan.
| | - Hiroyasu Onaka
- Graduate School of Agricultural and Life Sciences and Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka 577-8502, Japan.
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11
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Ishikawa F, Konno S, Uchiyama Y, Kakeya H, Tanabe G. Exploring a chemical scaffold for rapid and selective photoaffinity labelling of non-ribosomal peptide synthetases in living bacterial cells. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220026. [PMID: 36633280 PMCID: PMC9835605 DOI: 10.1098/rstb.2022.0026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/19/2022] [Indexed: 01/13/2023] Open
Abstract
Non-ribosomal peptide synthetases (NRPSs) biosynthesize many pharmaceuticals and virulence factors. The biosynthesis of these natural peptide products from biosynthetic gene clusters depends on complex regulations in bacteria. However, our current knowledge of NRPSs is based on enzymological studies using full NRPS systems and/or a single NRPS domain in heterologous hosts. Chemical and/or biochemical strategies to capture the endogenous activities of NRPSs facilitate studies on NRPS cell biology in bacterial cells. Here, we describe a chemical scaffold for the rapid and selective photoaffinity labelling of NRPSs in purified systems, crude biological samples and living bacterial cells. We synthesized photoaffinity labelling probes coupled with 5'-O-N-(phenylalanyl)sulfamoyladenosine with clickable alkyl diazirine or trifluoromethyl phenyl diazirine. We found that a trifluoromethyl phenyl diazirine-based probe cross-linked the Phe-activating domain of a GrsA-NRPS with high selectivity and sensitivity at shorter ultraviolet (UV) irradiation times (less than 5 min) relative to a prototypical benzophenone-based probe. Our results demonstrated that this quick labelling protocol can prevent damage to proteins and cells caused by long UV irradiation times, providing a mild photoaffinity labelling method for biological samples. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Sho Konno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuko Uchiyama
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Hideaki Kakeya
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
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12
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Lu Z, Liu XH, Yuan X, Liu F, Wang T. Engineered Biosynthesis through the Adenylation Domains from Nonribosomal Peptide Synthetases. Curr Top Med Chem 2023; 23:1973-1984. [PMID: 37264622 DOI: 10.2174/1568026623666230601142757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 06/03/2023]
Abstract
Nonribosomal peptide synthetases, consisted of multiple catalytic domains, are involved in the biosynthesis of an important family of bioactive natural products in a coordinated manner. Among the functional domains, adenylation domains are specifically responsible for recognizing carboxylic acid building blocks and synthesizing aminoacyl adenylates. Given their critical roles in the biosynthesis of the growing peptide, A-domains are also referred to as the "gatekeeper". In this review, very recent developments on the A-domains from NRPSs are reviewed to expand the fundamental knowledge of the A domain, including knowledge on the structures, functions, and molecular interactions. Several recent examples were also discussed to highlight the great potential of A-domain engineering. This study should provide a framework for the combinatorial biosynthesis or synthetic biology-driven microbial production of novel nonribosomal peptides.
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Affiliation(s)
- Zhenhua Lu
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310000, Zhejiang, China
| | - Xiao-Huan Liu
- School of Biological Science, Jining Medical University, Jining, China
| | - Xinsong Yuan
- Department of Chemical and Chemical Engineering, Hefei Normal University, Hefei, 230000, Anhui, China
| | - Fei Liu
- School of Biological Science, Jining Medical University, Jining, China
| | - Tao Wang
- School of Biological Science, Jining Medical University, Jining, China
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13
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Abstract
Assembly line enzymes, including polyketide synthases and nonribosomal peptide synthetases, play central roles in the construction of complex natural products. Due to the sequential biochemistry processed in each domain, the domain architecture of the assembly line enzymes strictly correlates with the product molecule. This colinearity makes assembly line enzymes an ideal target for rational reprogramming. Although many of the past engineering attempts suffered from decreased product yield, recent advancements in the bioinformatic analysis and engineering design now provide new opportunity to work on these modular megaenzymes. This chapter describes the methods for analyzing and engineering the assembly line enzymes, including module and domain analysis needed for designing the engineering of assembly line biosynthesis, and the expression vector construction with an example of two-vector heterologous expression system in Streptomyces.
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Affiliation(s)
- Lihan Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, Hangzhou, Zhejiang Province, China.
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.
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14
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Zheng X, Zheng T, Liao Y, Luo L. Identification of Potential Inhibitors of MurD Enzyme of Staphylococcus aureus from a Marine Natural Product Library. Molecules 2021; 26:molecules26216426. [PMID: 34770835 PMCID: PMC8587310 DOI: 10.3390/molecules26216426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen that can cause fatal bacterial infections. MurD catalyzes the formation of peptide bond between UDP-N-acetylehyl-l-alanine and d-glutamic acid, which plays an important role in the synthesis of peptidoglycan and the formation of cell wall by S. aureus. Because S. aureus is resistant to most existing antibiotics, it is necessary to develop new inhibitors. In this study, Schrodinger 11.5 Prime homology modeling was selected to prepare the protein model of MurD enzyme, and its structure was optimized. We used a virtual screening program and similarity screening to screen 47163 compounds from three marine natural product libraries to explore new inhibitors of S. aureus. ADME provides analysis of the physicochemical properties of the best performing compounds during the screening process. To determine the stability of the docking effect, a 100 ns molecular dynamics was performed to verify how tightly the compound was bound to the protein. By docking analysis and molecular dynamics analysis, both 46604 and 46608 have strong interaction with the docking pocket, have good pharmacological properties, and maintain stable conformation with the target protein, so they have a chance to become drugs for S. aureus. Through virtual screening, similarity screening, ADME study and molecular dynamics simulation, 46604 and 46608 were selected as potential drug candidates for S. aureus.
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Affiliation(s)
- Xiaoqi Zheng
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (X.Z.); (T.Z.); (Y.L.)
| | - Tongyu Zheng
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (X.Z.); (T.Z.); (Y.L.)
| | - Yinglin Liao
- The First Clinical College, Guangdong Medical University, Zhanjiang 524023, China; (X.Z.); (T.Z.); (Y.L.)
| | - Lianxiang Luo
- The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang 524023, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang 524023, China
- The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang 524023, China
- Correspondence:
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15
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Kancherla AK, Marincin KA, Mishra SH, Frueh DP. Minimizing Pervasive Artifacts in 4D Covariance Maps for Protein Side Chain NMR Assignments. J Phys Chem A 2021; 125:8313-8323. [PMID: 34510900 PMCID: PMC8480538 DOI: 10.1021/acs.jpca.1c05507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/24/2021] [Indexed: 01/23/2023]
Abstract
Nuclear magnetic resonance (NMR) is a mainstay of biophysical studies that provides atomic level readouts to formulate molecular mechanisms. Side chains are particularly important to derive mechanisms involving proteins as they carry functional groups, but NMR studies of side chains are often limited by challenges in assigning their signals. Here, we designed a novel computational method that combines spectral derivatives and matrix square-rooting to produce reliable 4D covariance maps from routinely acquired 3D spectra and facilitates side chain resonance assignments. Thus, we generate two 4D maps from 3D-HcccoNH and 3D-HCcH-TOCSY spectra that each help overcome signal overlap or sensitivity losses. These 4D maps feature HC-HSQCs of individual side chains that can be paired to assigned backbone amide resonances of individual aliphatic signals, and both are obtained from a single modified covariance calculation. Further, we present 4D maps produced using conventional triple resonance experiments to easily assign asparagine side chain amide resonances. The 4D covariance maps encapsulate the lengthy manual pattern recognition used in traditional assignment methods and distill the information as correlations that can be easily visualized. We showcase the utility of the 4D covariance maps with a 10 kDa peptidyl carrier protein and a 52 kDa cyclization domain from a nonribosomal peptide synthetase.
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Affiliation(s)
- Aswani K. Kancherla
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Room 701 Hunterian, Baltimore, Maryland 21205, United States
| | - Kenneth A. Marincin
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Room 701 Hunterian, Baltimore, Maryland 21205, United States
| | - Subrata H. Mishra
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Room 701 Hunterian, Baltimore, Maryland 21205, United States
| | - Dominique P. Frueh
- Department
of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Room 701 Hunterian, Baltimore, Maryland 21205, United States
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16
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York A, Lloyd AJ, Del Genio CI, Shearer J, Hinxman KJ, Fritz K, Fulop V, Dowson CG, Khalid S, Roper DI. Structure-based modeling and dynamics of MurM, a Streptococcus pneumoniae penicillin resistance determinant present at the cytoplasmic membrane. Structure 2021; 29:731-742.e6. [PMID: 33740396 PMCID: PMC8280954 DOI: 10.1016/j.str.2021.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 01/13/2021] [Accepted: 03/01/2021] [Indexed: 11/28/2022]
Abstract
Branched Lipid II, required for the formation of indirectly crosslinked peptidoglycan, is generated by MurM, a protein essential for high-level penicillin resistance in the human pathogen Streptococcus pneumoniae. We have solved the X-ray crystal structure of Staphylococcus aureus FemX, an isofunctional homolog, and have used this as a template to generate a MurM homology model. Using this model, we perform molecular docking and molecular dynamics to examine the interaction of MurM with the phospholipid bilayer and the membrane-embedded Lipid II substrate. Our model suggests that MurM is associated with the major membrane phospholipid cardiolipin, and experimental evidence confirms that the activity of MurM is enhanced by this phospholipid and inhibited by its direct precursor phosphatidylglycerol. The spatial association of pneumococcal membrane phospholipids and their impact on MurM activity may therefore be critical to the final architecture of peptidoglycan and the expression of clinically relevant penicillin resistance in this pathogen.
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Affiliation(s)
- Anna York
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Adrian J Lloyd
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Charo I Del Genio
- Centre for Fluid and Complex Systems, School of Computing, Electronics and Mathematics, University of Coventry, West Midlands CV1 5FB, UK
| | - Jonathan Shearer
- School of Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | - Karen J Hinxman
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Konstantin Fritz
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Vilmos Fulop
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Christopher G Dowson
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, UK.
| | - David I Roper
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK; Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
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17
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Izoré T, Candace Ho YT, Kaczmarski JA, Gavriilidou A, Chow KH, Steer DL, Goode RJA, Schittenhelm RB, Tailhades J, Tosin M, Challis GL, Krenske EH, Ziemert N, Jackson CJ, Cryle MJ. Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity. Nat Commun 2021; 12:2511. [PMID: 33947858 PMCID: PMC8097023 DOI: 10.1038/s41467-021-22623-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/23/2021] [Indexed: 02/08/2023] Open
Abstract
Non-ribosomal peptide synthetases are important enzymes for the assembly of complex peptide natural products. Within these multi-modular assembly lines, condensation domains perform the central function of chain assembly, typically by forming a peptide bond between two peptidyl carrier protein (PCP)-bound substrates. In this work, we report structural snapshots of a condensation domain in complex with an aminoacyl-PCP acceptor substrate. These structures allow the identification of a mechanism that controls access of acceptor substrates to the active site in condensation domains. The structures of this complex also allow us to demonstrate that condensation domain active sites do not contain a distinct pocket to select the side chain of the acceptor substrate during peptide assembly but that residues within the active site motif can instead serve to tune the selectivity of these central biosynthetic domains.
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Affiliation(s)
- Thierry Izoré
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- EMBL Australia, Monash University, Clayton, VIC, Australia.
| | - Y T Candace Ho
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Joe A Kaczmarski
- Research School of Chemistry, The Australian National University, Acton, ACT, Australia
| | - Athina Gavriilidou
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Microbiology/Biotechnology, University of Tübingen, Tübingen, Germany
| | - Ka Ho Chow
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - David L Steer
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, VIC, Australia
| | - Robert J A Goode
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, VIC, Australia
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Monash Proteomics and Metabolomics Facility, Monash University, Clayton, VIC, Australia
| | - Julien Tailhades
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- EMBL Australia, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
| | - Manuela Tosin
- Department of Chemistry, University of Warwick, Coventry, UK
| | - Gregory L Challis
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
- Department of Chemistry, University of Warwick, Coventry, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry, UK
| | - Elizabeth H Krenske
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Nadine Ziemert
- German Centre for Infection Research (DZIF), Partnersite Tübingen, Tübingen, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Colin J Jackson
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia
- Research School of Chemistry, The Australian National University, Acton, ACT, Australia
| | - Max J Cryle
- Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
- EMBL Australia, Monash University, Clayton, VIC, Australia.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Clayton, VIC, Australia.
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18
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Naudin EA, McEwen AG, Tan SK, Poussin-Courmontagne P, Schmitt JL, Birck C, DeGrado WF, Torbeev V. Acyl Transfer Catalytic Activity in De Novo Designed Protein with N-Terminus of α-Helix As Oxyanion-Binding Site. J Am Chem Soc 2021; 143:3330-3339. [PMID: 33635059 PMCID: PMC8012002 DOI: 10.1021/jacs.0c10053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The design of catalytic proteins with functional sites capable of specific chemistry is gaining momentum and a number of artificial enzymes have recently been reported, including hydrolases, oxidoreductases, retro-aldolases, and others. Our goal is to develop a peptide ligase for robust catalysis of amide bond formation that possesses no stringent restrictions to the amino acid composition at the ligation junction. We report here the successful completion of the first step in this long-term project by building a completely de novo protein with predefined acyl transfer catalytic activity. We applied a minimalist approach to rationally design an oxyanion hole within a small cavity that contains an adjacent thiol nucleophile. The N-terminus of the α-helix with unpaired hydrogen-bond donors was exploited as a structural motif to stabilize negatively charged tetrahedral intermediates in nucleophilic addition-elimination reactions at the acyl group. Cysteine acting as a principal catalytic residue was introduced at the second residue position of the α-helix N-terminus in a designed three-α-helix protein based on structural informatics prediction. We showed that this minimal set of functional elements is sufficient for the emergence of catalytic activity in a de novo protein. Using peptide-αthioesters as acyl-donors, we demonstrated their catalyzed amidation concomitant with hydrolysis and proved that the environment at the catalytic site critically influences the reaction outcome. These results represent a promising starting point for the development of efficient catalysts for protein labeling, conjugation, and peptide ligation.
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Affiliation(s)
- Elise A Naudin
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
| | - Alastair G McEwen
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - Sophia K Tan
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158-9001, United States
| | - Pierre Poussin-Courmontagne
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - Jean-Louis Schmitt
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
| | - Catherine Birck
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - William F DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158-9001, United States
| | - Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
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19
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Kirchner N, Cano-Prieto C, Schulz-Fincke AC, Gütschow M, Ortlieb N, Moschny J, Niedermeyer THJ, Horak J, Lämmerhofer M, van der Voort M, Raaijmakers JM, Gross H. Discovery of Thanafactin A, a Linear, Proline-Containing Octalipopeptide from Pseudomonas sp. SH-C52, Motivated by Genome Mining. J Nat Prod 2021; 84:101-109. [PMID: 33382250 DOI: 10.1021/acs.jnatprod.0c01174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Genome mining of the bacterial strains Pseudomonas sp. SH-C52 and Pseudomonas fluorescens DSM 11579 showed that both strains contained a highly similar gene cluster encoding an octamodular nonribosomal peptide synthetase (NRPS) system which was not associated with a known secondary metabolite. Insertional mutagenesis of an NRPS component followed by comparative profiling led to the discovery of the corresponding novel linear octalipopeptide thanafactin A, which was subsequently isolated and its structure determined by two-dimensional NMR and further spectroscopic and chromatographic methods. In bioassays, thanafactin A exhibited weak protease inhibitory activity and was found to modulate swarming motility in a strain-specific manner.
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Affiliation(s)
- Norbert Kirchner
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
| | - Carolina Cano-Prieto
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
| | | | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, 53121 Bonn, Germany
| | - Nico Ortlieb
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Julia Moschny
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Timo H J Niedermeyer
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
| | - Jeannie Horak
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen, 72076 Tübingen, Germany
- Dr. von Hauner Children's Hospital, Department of Metabolic and Nutritional Medicine, University of Munich Medical Center, Campus Innenstadt, 80337 Muenchen, Germany
| | - Michael Lämmerhofer
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis, University of Tübingen, 72076 Tübingen, Germany
| | - Menno van der Voort
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, 72076 Tübingen, Germany
- German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
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20
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Bourgeois G, Seguin J, Babin M, Gondry M, Mechulam Y, Schmitt E. Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates. RNA 2020; 26:1589-1602. [PMID: 32680846 PMCID: PMC7566563 DOI: 10.1261/rna.075184.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Cyclodipeptide synthases (CDPSs) catalyze the synthesis of various cyclodipeptides by using two aminoacyl-tRNA (aa-tRNA) substrates in a sequential mechanism. Here, we studied binding of phenylalanyl-tRNAPhe to the CDPS from Candidatus Glomeribacter gigasporarum (Cglo-CDPS) by gel filtration and electrophoretic mobility shift assay. We determined the crystal structure of the Cglo-CDPS:Phe-tRNAPhe complex to 5 Å resolution and further studied it in solution using small-angle X-ray scattering (SAXS). The data show that the major groove of the acceptor stem of the aa-tRNA interacts with the enzyme through the basic β2 and β7 strands of CDPSs belonging to the XYP subfamily. A bending of the CCA extremity enables the amino acid moiety to be positioned in the P1 pocket while the terminal A76 adenosine occupies the P2 pocket. Such a positioning indicates that the present structure illustrates the binding of the first aa-tRNA. In cells, CDPSs and the elongation factor EF-Tu share aminoacylated tRNAs as substrates. The present study shows that CDPSs and EF-Tu interact with opposite sides of tRNA. This may explain how CDPSs hijack aa-tRNAs from canonical ribosomal protein synthesis.
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Affiliation(s)
- Gabrielle Bourgeois
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Jérôme Seguin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Morgan Babin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Muriel Gondry
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France
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21
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Isa MA. Comparative modeling and dynamic simulation of UDP-N-acetylmuramoyl-alanine ligase (MurC) from Mycobacterium tuberculosis through virtual screening and toxicity analysis. Life Sci 2020; 262:118466. [PMID: 32961233 DOI: 10.1016/j.lfs.2020.118466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/04/2020] [Accepted: 09/14/2020] [Indexed: 11/18/2022]
Abstract
INTRODUCTION UDP-N-acetylmuramic-alanine ligase (MurC) is an enzyme catalyzing the addition of L-alanine to UDP-acetylmuramoyl nucleotide precursor in Mycobacterium tuberculosis (M. tuberculosis). This enzyme is a prerequisite for the biosynthesis of the peptidoglycans in M. tuberculosis. AIM This study aimed to identify the novel inhibitors of MurC using in silico approach. MATERIALS AND METHODS The three dimensional (3D) structure of MurC was determined using comparative modeling and based on the template obtained from Haemophilus influenza (1P31). The structural analysis of the model structure shown that three residues (Lys126, Glu170, and Glu358) are critical for in the catalytic activity of the enzyme, and their inhibition will block the function of the enzyme. Ten thousand and ninety-five (10095) compounds obtained through virtual screening against Zinc and PubChem databases based on their ability to bind to MurC with minimum binding energies. These ligands screened for the physicochemical properties, molecular docking, and pharmacokinetic analyses. FINDING Six compounds had desirable physicochemical and pharmacokinetic properties with excellent binding energy ranged between -12.27 and -10.09 kcal/mol. These compounds subjected to Molecular Dynamic (MD) Simulation and Molecular Mechanics Generalized Born Surface Area (MM-GBSA) analyses. The outcome of the analysis revealed that four ligands (PubChem1548994, ZINC11882115, ZINC22241774, and ZINC12330603) formed a stable conformation in the substrate-binding site of the protein during the 50 ns MD simulation. CONCLUSION Therefore, the ligands mentioned above might regard as novel inhibitors of M. tuberculosis which requires further in vitro and in vivo validation.
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Affiliation(s)
- Mustafa Alhaji Isa
- Department of Microbiology, Faculty of Sciences, University of Maiduguri, P.M.B. 1069, Nigeria.
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22
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Yuan Y, Xu QM, Yu SC, Sun HZ, Cheng JS, Yuan YJ. Control of the polymyxin analog ratio by domain swapping in the nonribosomal peptide synthetase of Paenibacillus polymyxa. J Ind Microbiol Biotechnol 2020; 47:551-562. [PMID: 32495197 DOI: 10.1007/s10295-020-02275-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 04/15/2020] [Indexed: 11/26/2022]
Abstract
Polymyxins are used as the last-line therapy against multidrug-resistant bacteria. However, their further clinical development needs to solve problems related to the presence of heterogeneous analogs, but there is still no platform or methods that can regulate the biosynthesis of polymyxin analogs. In this study, we present an approach to swap domains in the polymyxin gene cluster to regulate the production of different analogs. Following adenylation domain swapping, the proportion of polymyxin B1 increased from 41.36 to 52.90%, while that of B1-1 decreased from 18.25 to 3.09%. The ratio of polymyxin B1 and B3 following starter condensation domain swapping changed from 41.36 and 16.99 to 55.03 and 6.39%, respectively. The two domain-swapping strains produced 62.96% of polymyxin B1, 6.70% of B3 and 3.32% of B1-1. This study also revealed the presence of overflow fluxes between acetoin, 2,3-butanediol and polymyxin. To our best knowledge, this is the first report of engineering the polymyxin synthetase gene cluster in situ to regulate the relative proportions of polymyxin analogs. This research paves a way for regulating lipopeptide analogs and will facilitate the development of novel lipopeptide derivatives.
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Affiliation(s)
- Ye Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
| | - Qiu-Man Xu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Binshuixi Road 393, Xiqing District, Tianjin, 300387, People's Republic of China.
| | - Si-Cen Yu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
| | - Hui-Zhong Sun
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
| | - Jing-Sheng Cheng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China.
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, People's Republic of China
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23
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Iacovelli R, Zwahlen RD, Bovenberg RAL, Driessen AJM. Biochemical characterization of the Nocardia lactamdurans ACV synthetase. PLoS One 2020; 15:e0231290. [PMID: 32275728 PMCID: PMC7147772 DOI: 10.1371/journal.pone.0231290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/19/2020] [Indexed: 01/19/2023] Open
Abstract
The L-δ-(α-aminoadipoyl)-L-cysteinyl-D-valine synthetase (ACVS) is a nonribosomal peptide synthetase (NRPS) that fulfills a crucial role in the synthesis of β-lactams. Although some of the enzymological aspects of this enzyme have been elucidated, its large size, at over 400 kDa, has hampered heterologous expression and stable purification attempts. Here we have successfully overexpressed the Nocardia lactamdurans ACVS in E. coli HM0079. The protein was purified to homogeneity and characterized for tripeptide formation with a focus on the substrate specificity of the three modules. The first L-α-aminoadipic acid-activating module is highly specific, whereas the modules for L-cysteine and L-valine are more promiscuous. Engineering of the first module of ACVS confirmed the strict specificity observed towards its substrate, which can be understood in terms of the non-canonical peptide bond position.
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Affiliation(s)
- Riccardo Iacovelli
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Reto D. Zwahlen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Roel A. L. Bovenberg
- Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- DSM Biotechnology Centre, Delft, The Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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24
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Abstract
The class of fungal indole alkaloids containing the bicyclo[2.2.2]diazaoctane ring is comprised of diverse molecules that display a range of biological activities. While much interest has been garnered due to their therapeutic potential, this class of molecules also displays unique chemical functionality, making them intriguing synthetic targets. Many elegant and intricate total syntheses have been developed to generate these alkaloids, but the selectivity required to produce them in high yield presents great barriers. Alternatively, if we can understand the molecular mechanisms behind how fungi make these complex molecules, we can leverage the power of nature to perform these chemical transformations. Here, we describe the various studies regarding the evolutionary development of enzymes involved in fungal indole alkaloid biosynthesis.
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Affiliation(s)
- Amy E. Fraley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, United States
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25
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Jaremko MJ, Davis TD, Corpuz JC, Burkart MD. Type II non-ribosomal peptide synthetase proteins: structure, mechanism, and protein-protein interactions. Nat Prod Rep 2020; 37:355-379. [PMID: 31593192 PMCID: PMC7101270 DOI: 10.1039/c9np00047j] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: 1990 to 2019 Many medicinally-relevant compounds are derived from non-ribosomal peptide synthetase (NRPS) products. Type I NRPSs are organized into large modular complexes, while type II NRPS systems contain standalone or minimal domains that often encompass specialized tailoring enzymes that produce bioactive metabolites. Protein-protein interactions and communication between the type II biosynthetic machinery and various downstream pathways are critical for efficient metabolite production. Importantly, the architecture of type II NRPS proteins makes them ideal targets for combinatorial biosynthesis and metabolic engineering. Future investigations exploring the molecular basis or protein-protein recognition in type II NRPS pathways will guide these engineering efforts. In this review, we consolidate the broad range of NRPS systems containing type II proteins and focus on structural investigations, enzymatic mechanisms, and protein-protein interactions important to unraveling pathways that produce unique metabolites, including dehydrogenated prolines, substituted benzoic acids, substituted amino acids, and cyclopropanes.
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Affiliation(s)
- Matt J Jaremko
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Joshua C Corpuz
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, La Jolla, San Diego, California 92093-0358, USA.
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26
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Chen H, Zhou H, Sun T, Xu J, Tu Q, Yang J, Zhang Y, Bian X. Identification of Holrhizins E-Q Reveals the Diversity of Nonribosomal Lipopeptides in Paraburkholderia rhizoxinica. J Nat Prod 2020; 83:537-541. [PMID: 32031805 DOI: 10.1021/acs.jnatprod.9b00927] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The products of a nonribosomal peptide synthetase gene, holA, from Paraburkholderia rhizoxinica were investigated using our recently established recombineering technique. Fifteen products, including 13 new linear lipopeptides, holrhizins E-Q (2-8, 10-15), together with the two known holrhizins A and B (1, 9), were detected in the activated mutant, and their structures were identified using HRESIMS, NMR spectroscopy, Marfey's analysis, and feeding experiments with labeled amino acids. The lipohexapeptides 1-3 and 7-14 differ in three amino acid residues and the N-terminal fatty acid chains. The diversity of the holrhizins originates from the substrate flexibility of the A4, A5, and A6 domains as well as the starter C domain in the biosynthetic pathway.
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Affiliation(s)
- Hanna Chen
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
| | - Haibo Zhou
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
| | - Tao Sun
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
| | - Jiaying Xu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science , Hunan Normal University , Changsha , 410081 , People's Republic of China
| | - Qiang Tu
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
| | - Jie Yang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
- Jiangsu Marine Resources Development Research Institute , Lianyungang , 222005 , People's Republic of China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology , Shandong University , Qingdao , Shandong 266237 , People's Republic of China
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27
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Zhou W, Liang H, Qin X, Cao D, Zhu X, Ju J, Shen B, Duan Y, Huang Y. The Isolation of Pyrroloformamide Congeners and Characterization of Their Biosynthetic Gene Cluster. J Nat Prod 2020; 83:202-209. [PMID: 32049520 PMCID: PMC7577424 DOI: 10.1021/acs.jnatprod.9b00321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Dithiolopyrrolones are microbial natural products containing a disulfide or thiosulfonate bridge embedded in a unique bicyclic structure. By interfering with zinc ion homeostasis in living cells, they show strong antibacterial activity against a variety of bacterial pathogens, as well as potent cytotoxicity against human cancer cells. In the current study, two new dithiolopyrrolones, pyrroloformamide C (3) and pyrroloformamide D (4), were isolated from Streptomyces sp. CB02980, together with the known pyrroloformamides 1 and 2. The biosynthetic gene cluster for pyrroloformamides was identified from Streptomyces sp. CB02980, which shared high sequence similarity with those of dithiolopyrrolones, including holomycin and thiolutin. Gene replacement of pyfE, which encodes a nonribosomal peptide synthetase (NRPS), abolished the production of 1-4. Overexpression of pyfN, a type II thioesterase gene, increased the production of 1 and 2. Genome neighborhood network analysis of the characterized and orphan gene clusters of dithiolopyrrolones revealed a unified mechanism for their biosynthesis, involving an iterative-acting NRPS and a set of conserved tailoring enzymes for the bicyclic core formation.
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Affiliation(s)
- Wenqing Zhou
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, People’s Republic of China
| | - Haoyu Liang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, People’s Republic of China
| | - Xiangjing Qin
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People’s Republic of China
| | - Danfeng Cao
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, People’s Republic of China
| | - Xiangcheng Zhu
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, People’s Republic of China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discover, Changsha, Hunan 410011, People’s Republic of China
| | - Jianhua Ju
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, People’s Republic of China
| | - Ben Shen
- Departments of Chemistry, Jupiter, Florida 33458, United States
- Molecular Medicine, Jupiter, Florida 33458, United States
- Natural Products Library Initiative, Jupiter, Florida 33458, United States
| | - Yanwen Duan
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, People’s Republic of China
- Hunan Engineering Research Center of Combinatorial Biosynthesis and Natural Product Drug Discover, Changsha, Hunan 410011, People’s Republic of China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan 410011, People’s Republic of China
| | - Yong Huang
- Xiangya International Academy of Translational Medicine at Central South University, Changsha, Hunan 410013, People’s Republic of China
- National Engineering Research Center of Combinatorial Biosynthesis for Drug Discovery, Changsha, Hunan 410011, People’s Republic of China
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28
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Tang S, Zhang W, Li Z, Li H, Geng C, Huang X, Lu X. Discovery and Characterization of a PKS-NRPS Hybrid in Aspergillus terreus by Genome Mining. J Nat Prod 2020; 83:473-480. [PMID: 32077283 DOI: 10.1021/acs.jnatprod.9b01140] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fungal polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) hybrids have been characterized to produce polyketide-amino acid compounds with striking structural features and biological activities. In this study, a PKS-NRPS hybrid enzyme was found in Aspergillus terreus by genome mining. By activating the cluster-specific transcriptional regulator, this cryptic PKS-NRPS gene cluster was successfully activated and ten products (1-10) were identified as pyranterreones. Using functional genetics, bioinformatics, and isotope-labeling feeding analysis, the biosynthetic pathway was revealed. This is the second PKS-NRPS hybrid identified in A. terreus.
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Affiliation(s)
- Shen Tang
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources , Jiangxi Agricultural University , Nanchang 330045 , People's Republic of China
- Shandong Provincial Key Laboratory of Synthetic Biology , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , No. 189 Songling Road , Qingdao 266101 , People's Republic of China
| | - Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , No. 189 Songling Road , Qingdao 266101 , People's Republic of China
| | - Zhimin Li
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources , Jiangxi Agricultural University , Nanchang 330045 , People's Republic of China
| | - Hongcheng Li
- College of Bioscience and Bioengineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources , Jiangxi Agricultural University , Nanchang 330045 , People's Republic of China
- Shandong Provincial Key Laboratory of Synthetic Biology , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , No. 189 Songling Road , Qingdao 266101 , People's Republic of China
| | - Ce Geng
- Shandong Provincial Key Laboratory of Synthetic Biology , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , No. 189 Songling Road , Qingdao 266101 , People's Republic of China
| | - Xuenian Huang
- Shandong Provincial Key Laboratory of Synthetic Biology , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , No. 189 Songling Road , Qingdao 266101 , People's Republic of China
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , No. 189 Songling Road , Qingdao 266101 , People's Republic of China
- Key Laboratory of Biofuels , Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , No. 189 Songling Road , Qingdao 266101 , People's Republic of China
- Marine Biology and Biotechnology Laboratory , Qingdao National Laboratory for Marine Science and Technology , Wenhai Rd 1, Aoshanwei , Qingdao 266237 , People's Republic of China
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29
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Henager SH, Henriquez S, Dempsey DR, Cole PA. Analysis of Site-Specific Phosphorylation of PTEN by Using Enzyme-Catalyzed Expressed Protein Ligation. Chembiochem 2020; 21:64-68. [PMID: 31206229 PMCID: PMC7012368 DOI: 10.1002/cbic.201900316] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Indexed: 01/05/2023]
Abstract
The activity and localization of PTEN, a tumor suppressor lipid phosphatase that converts the phospholipid PIP3 to PIP2, is governed in part by phosphorylation on a cluster of four Ser and Thr residues near the C terminus. Prior enzymatic characterization of the four monophosphorylated (1p) PTENs by using classical expressed protein ligation (EPL) was complicated by the inclusion of a non-native Cys at the ligation junction (aa379), which may alter the properties of the semisynthetic protein. Here, we apply subtiligase-mediated EPL to create wt 1p-PTENs. These PTENs are more autoinhibited than previously appreciated, consistent with the role of Tyr379 in driving autoinhibition. Alkaline phosphatase sensitivity analysis revealed that these autoinhibited 1p conformations are kinetically labile. In contrast to the Cys mutant 1p-PTENs, which are poorly recognized by an anti-phospho-PTEN antibody, three of the four wt 1p-PTENs are recognized by a commonly used anti-phospho-PTEN antibody.
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Affiliation(s)
- Samuel H Henager
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Stephanie Henriquez
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205, USA
| | - Daniel R Dempsey
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Philip A Cole
- Division of Genetics, Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, 25 Shattuck Street, Boston, MA, 02115, USA
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30
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Berry D, Mace W, Grage K, Wesche F, Gore S, Schardl CL, Young CA, Dijkwel PP, Leuchtmann A, Bode HB, Scott B. Efficient nonenzymatic cyclization and domain shuffling drive pyrrolopyrazine diversity from truncated variants of a fungal NRPS. Proc Natl Acad Sci U S A 2019; 116:25614-25623. [PMID: 31801877 PMCID: PMC6926027 DOI: 10.1073/pnas.1913080116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) generate the core peptide scaffolds of many natural products. These include small cyclic dipeptides such as the insect feeding deterrent peramine, which is a pyrrolopyrazine (PPZ) produced by grass-endophytic Epichloë fungi. Biosynthesis of peramine is catalyzed by the 2-module NRPS, PpzA-1, which has a C-terminal reductase (R) domain that is required for reductive release and cyclization of the NRPS-tethered dipeptidyl-thioester intermediate. However, some PpzA variants lack this R domain due to insertion of a transposable element into the 3' end of ppzA We demonstrate here that these truncated PpzA variants utilize nonenzymatic cyclization of the dipeptidyl thioester to a 2,5-diketopiperazine (DKP) to synthesize a range of novel PPZ products. Truncation of the R domain is sufficient to subfunctionalize PpzA-1 into a dedicated DKP synthetase, exemplified by the truncated variant, PpzA-2, which has also evolved altered substrate specificity and reduced N-methyltransferase activity relative to PpzA-1. Further allelic diversity has been generated by recombination-mediated domain shuffling between ppzA-1 and ppzA-2, resulting in the ppzA-3 and ppzA-4 alleles, each of which encodes synthesis of a unique PPZ metabolite. This research establishes that efficient NRPS-catalyzed DKP biosynthesis can occur in vivo through nonenzymatic dipeptidyl cyclization and presents a remarkably clean example of NRPS evolution through recombinant exchange of functionally divergent domains. This work highlights that allelic variants of a single NRPS can result in a surprising level of secondary metabolite diversity comparable to that observed for some gene clusters.
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Affiliation(s)
- Daniel Berry
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- Bioprotection Research Centre, Massey University, Palmerston North 4442, New Zealand
| | - Wade Mace
- Grasslands Research Centre, AgResearch Ltd., Palmerston North 4442, New Zealand
| | - Katrin Grage
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Frank Wesche
- Fachbereich Biowissenschaften, Molekulare Biotechnologie, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany
| | - Sagar Gore
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | | | | | - Paul P Dijkwel
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- Bioprotection Research Centre, Massey University, Palmerston North 4442, New Zealand
| | - Adrian Leuchtmann
- Institute of Integrative Biology, ETH Zürich, CH-8092 Zürich, Switzerland
| | - Helge B Bode
- Fachbereich Biowissenschaften, Molekulare Biotechnologie, Goethe Universität Frankfurt, 60438 Frankfurt am Main, Germany;
- Buchmann Institute for Molecular Life Sciences, Goethe-Universität, 60438 Frankfurt am Main, Germany
- Landes-Offensive zur Entwicklung Wissenschaftlich-Ökonomischer Exzellenz (LOEWE) Centre for Translational Biodiversity Genomics, 60325 Frankfurt am Main, Germany
| | - Barry Scott
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand;
- Bioprotection Research Centre, Massey University, Palmerston North 4442, New Zealand
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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: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Thomas SE, Collins P, James RH, Mendes V, Charoensutthivarakul S, Radoux C, Abell C, Coyne AG, Floto RA, von Delft F, Blundell TL. Structure-guided fragment-based drug discovery at the synchrotron: screening binding sites and correlations with hotspot mapping. Philos Trans A Math Phys Eng Sci 2019; 377:20180422. [PMID: 31030650 PMCID: PMC6501894 DOI: 10.1098/rsta.2018.0422] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Structure-guided drug discovery emerged in the 1970s and 1980s, stimulated by the three-dimensional structures of protein targets that became available, mainly through X-ray crystal structure analysis, assisted by the development of synchrotron radiation sources. Structures of known drugs or inhibitors were used to guide the development of leads. The growth of high-throughput screening during the late 1980s and the early 1990s in the pharmaceutical industry of chemical libraries of hundreds of thousands of compounds of molecular weight of approximately 500 Da was impressive but still explored only a tiny fraction of the chemical space of the predicted 1040 drug-like compounds. The use of fragments with molecular weights less than 300 Da in drug discovery not only decreased the chemical space needing exploration but also increased promiscuity in binding targets. Here we discuss advances in X-ray fragment screening and the challenge of identifying sites where fragments not only bind but can be chemically elaborated while retaining their positions and binding modes. We first describe the analysis of fragment binding using conventional X-ray difference Fourier techniques, with Mycobacterium abscessus SAICAR synthetase (PurC) as an example. We observe that all fragments occupy positions predicted by computational hotspot mapping. We compare this with fragment screening at Diamond Synchrotron Light Source XChem facility using PanDDA software, which identifies many more fragment hits, only some of which bind to the predicted hotspots. Many low occupancy sites identified may not support elaboration to give adequate ligand affinity, although they will likely be useful in drug discovery as 'warm spots' for guiding elaboration of fragments bound at hotspots. We discuss implications of these observations for fragment screening at the synchrotron sources. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.
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Affiliation(s)
- Sherine E. Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Patrick Collins
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Rory Hennell James
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | | | - Chris Radoux
- The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Anthony G. Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - R. Andres Floto
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC-Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Frank von Delft
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
- e-mail:
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Schaub AJ, Moreno GO, Zhao S, Truong HV, Luo R, Tsai SC. Computational structural enzymology methodologies for the study and engineering of fatty acid synthases, polyketide synthases and nonribosomal peptide synthetases. Methods Enzymol 2019; 622:375-409. [PMID: 31155062 PMCID: PMC7197764 DOI: 10.1016/bs.mie.2019.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Various computational methodologies can be applied to enzymological studies on enzymes in the fatty acid, polyketide, and non-ribosomal peptide biosynthetic pathways. These multi-domain complexes are called fatty acid synthases, polyketide synthases, and non-ribosomal peptide synthetases. These mega-synthases biosynthesize chemically diverse and complex bioactive molecules, with the intermediates being chauffeured between catalytic partners via a carrier protein. Recent efforts have been made to engineer these systems to expand their product diversity. A major stumbling block is our poor understanding of the transient protein-protein and protein-substrate interactions between the carrier protein and its many catalytic partner domains and product intermediates. The innate reactivity of pathway intermediates in two major classes of polyketide synthases has frustrated our mechanistic understanding of these interactions during the biosynthesis of these natural products, ultimately impeding the engineering of these systems for the generation of engineered natural products. Computational techniques described in this chapter can aid data interpretation or used to generate testable models of these experimentally intractable transient interactions, thereby providing insight into key interactions that are difficult to capture otherwise, with the potential to expand the diversity in these systems.
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Affiliation(s)
- Andrew J Schaub
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Gabriel O Moreno
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Shiji Zhao
- Mathematical, Computational and Systems Biology Program, Center for Complex Biological Systems, University of California, Irvine, CA, United States
| | - Hau V Truong
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, CA, United States.
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, Chemistry, Pharmaceutical Sciences, University of California, Irvine, CA, United States.
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Abstract
Non-ribosomal peptide synthetases (NRPSs) are large, modular enzymes that produce bioactive peptides of tremendous structural and chemical diversity, due to the incorporation, alongside the canonical 20 amino acids, of non-proteinogenic amino acids, fatty acids, sugars and heterocyclic rings. For linear NRPSs, the size and composition of the peptide product is dictated by the number, order and specificity of the individual modules, each made of several domains. Given the size and complexity of NRPSs, most in vitro studies have focused on individual domains, di-domains or single modules extracted from the full-length proteins. However, intermodular interactions could play a critical role and regulate the activity of the domains and modules in unpredictable ways. Here we investigate in vitro substrate activation by three A domains of the tyrocidine synthetase TycC enzyme, systematically comparing their activity when alone (with the respective PCP domain), in pairs (di-modular constructs) or all together (tri-modular construct). Furthermore, we study the impact of mutations in the A or PCP domains in these various constructs. Our results suggest that substrate adenylation and effects of mutations largely depend on the context in which the domains/modules are. Therefore, generalizing properties observed for domains or modules in isolation should be done with caution.
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Affiliation(s)
- Anna Degen
- German Cancer Research Center DKFZ and Faculty of Biosciences, University of Heidelberg, 69120, Heidelberg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Florian Mayerthaler
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, 48149, Münster, Germany
| | - Henning D Mootz
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, 48149, Münster, Germany
| | - Barbara Di Ventura
- Institute of Biology II, University of Freiburg, 79104, Freiburg, Germany.
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany.
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Azam MA, Jupudi S, Saha N, Paul RK. Combining molecular docking and molecular dynamics studies for modelling Staphylococcus aureus MurD inhibitory activity. SAR QSAR Environ Res 2019; 30:1-20. [PMID: 30406684 DOI: 10.1080/1062936x.2018.1539034] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Indexed: 06/08/2023]
Abstract
The ATP-dependent bacterial MurD enzyme catalyses the formation of the peptide bond between cytoplasmic intermediate UDP-N-acetylmuramoyl-L-alanine and D-glutamic acid. This is essential for bacterial cell wall peptidoglycan synthesis in both Gram-positive and Gram-negative bacteria. MurD is recognized as an important target for the development of new antibacterial agents. In the present study we prepared the 3D-stucture of the catalytic pocket of the Staphylococcus aureus MurD enzyme by homology modelling. Extra-precision docking, binding free energy calculation by the MM-GBSA approach and a 40 ns molecular dynamics (MD) simulation of 2-thioxothiazolidin-4-one based inhibitor $1 was carried out to elucidate its inhibition potential for the S. aureus MurD enzyme. Molecular docking results showed that Lys19, Gly147, Tyr148, Lys328, Thr330 and Phe431 residues are responsible for the inhibitor-protein complex stabilization. Binding free energy calculation revealed electrostatic solvation and van der Waals energy components as major contributors for the inhibitor binding. The inhibitor-modelled S. aureus protein complex had a stable conformation in response to the atomic flexibility and interaction, when subjected to MD simulation at 40 ns in aqueous solution. We designed some molecules as potent inhibitors of S. aureus MurD, and to validate the stability of the designed molecule D1-modelled protein complex we performed a 20 ns MD simulation. Results obtained from this study can be utilized for the design of potent S. aureus MurD inhibitors.
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Affiliation(s)
- M A Azam
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy, Tamil Nadu (A Constituent College of JSS Academy of Higher Education and Research, Mysuru) , India
| | - S Jupudi
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy, Tamil Nadu (A Constituent College of JSS Academy of Higher Education and Research, Mysuru) , India
| | - N Saha
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy, Tamil Nadu (A Constituent College of JSS Academy of Higher Education and Research, Mysuru) , India
| | - R K Paul
- a Department of Pharmaceutical Chemistry , JSS College of Pharmacy, Tamil Nadu (A Constituent College of JSS Academy of Higher Education and Research, Mysuru) , India
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Tripathi A, Park SR, Sikkema AP, Cho HJ, Wu J, Lee B, Xi C, Smith JL, Sherman DH. A Defined and Flexible Pocket Explains Aryl Substrate Promiscuity of the Cahuitamycin Starter Unit-Activating Enzyme CahJ. Chembiochem 2018; 19:1595-1600. [PMID: 29742306 PMCID: PMC6105470 DOI: 10.1002/cbic.201800233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Indexed: 01/02/2023]
Abstract
Cahuitamycins are biofilm inhibitors assembled by a convergent nonribosomal peptide synthetase pathway. Previous genetic analysis indicated that a discrete enzyme, CahJ, serves as a gatekeeper for cahuitamycin structural diversification. Here, the CahJ protein was probed structurally and functionally to guide the formation of new analogues by mutasynthetic studies. This analysis enabled the in vivo production of a new cahuitamycin congener through targeted precursor incorporation.
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Affiliation(s)
- Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sung Ryeol Park
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
- Baruch S. Blumberg Institute, Natural Products Discovery Institute, 3805 Old Easton Road, Doylestown, PA, 18902, USA
| | - Andrew P Sikkema
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Hyo Je Cho
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jianfeng Wu
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, 48109, USA
| | - Brian Lee
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
| | - Chuanwu Xi
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, 48109, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI, 48109-2216, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
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Abstract
Covering: up to 2017 The participation of non-heme dinuclear iron cluster-containing monooxygenases in natural product biosynthetic pathways has been recognized only recently. At present, two families have been discovered. The archetypal member of the first family, CmlA, catalyzes β-hydroxylation of l-p-aminophenylalanine (l-PAPA) covalently linked to the nonribosomal peptide synthetase (NRPS) CmlP, thereby effecting the first step in the biosynthesis of chloramphenicol by Streptomyces venezuelae. CmlA houses the diiron cluster in a metallo-β-lactamase protein fold instead of the 4-helix bundle fold of nearly every other diiron monooxygenase. CmlA couples O2 activation and substrate hydroxylation via a structural change caused by formation of the l-PAPA-loaded CmlP:CmlA complex. The other new diiron family is typified by two enzymes, AurF and CmlI, which catalyze conversion of aryl-amine substrates to aryl-nitro products with incorporation of oxygen from O2. AurF from Streptomyces thioluteus catalyzes the formation of p-nitrobenzoate from p-aminobenzoate as a precursor to the biostatic compound aureothin, whereas CmlI from S. venezuelae catalyzes the ultimate aryl-amine to aryl-nitro step in chloramphenicol biosynthesis. Both enzymes stabilize a novel type of peroxo-intermediate as the reactive species. The rare 6-electron N-oxygenation reactions of CmlI and AurF involve two progressively oxidized pathway intermediates. The enzymes optimize efficiency by utilizing one of the reaction pathway intermediates as an in situ reductant for the diiron cluster, while simultaneously generating the next pathway intermediate. For CmlI, this reduction allows mid-pathway regeneration of the peroxo intermediate required to complete the biosynthesis. CmlI ensures specificity by carrying out the multistep aryl-amine oxygenation without dissociating intermediate products.
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Affiliation(s)
- Anna J Komor
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
| | - Andrew J Jasniewski
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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Kimura Y, Tsutsumi K, Konno A, Ikegami K, Hameed S, Kaneko T, Kaplan OI, Teramoto T, Fujiwara M, Ishihara T, Blacque OE, Setou M. Environmental responsiveness of tubulin glutamylation in sensory cilia is regulated by the p38 MAPK pathway. Sci Rep 2018; 8:8392. [PMID: 29849065 PMCID: PMC5976657 DOI: 10.1038/s41598-018-26694-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/16/2018] [Indexed: 01/09/2023] Open
Abstract
Glutamylation is a post-translational modification found on tubulin that can alter the interaction between microtubules (MTs) and associated proteins. The molecular mechanisms regulating tubulin glutamylation in response to the environment are not well understood. Here, we show that in the sensory cilia of Caenorhabditis elegans, tubulin glutamylation is upregulated in response to various signals such as temperature, osmolality, and dietary conditions. Similarly, tubulin glutamylation is modified in mammalian photoreceptor cells following light adaptation. A tubulin glutamate ligase gene ttll-4, which is essential for tubulin glutamylation of axonemal MTs in sensory cilia, is activated by p38 MAPK. Amino acid substitution of TTLL-4 has revealed that a Thr residue (a putative MAPK-phosphorylation site) is required for enhancement of tubulin glutamylation. Intraflagellar transport (IFT), a bidirectional trafficking system specifically observed along axonemal MTs, is required for the formation, maintenance, and function of sensory cilia. Measurement of the velocity of IFT particles revealed that starvation accelerates IFT, which was also dependent on the Thr residue of TTLL-4. Similarly, starvation-induced attenuation of avoidance behaviour from high osmolality conditions was also dependent on ttll-4. Our data suggest that a novel evolutionarily conserved regulatory system exists for tubulin glutamylation in sensory cilia in response to the environment.
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Affiliation(s)
- Yoshishige Kimura
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka, 431-3192, Japan
- Department of Liberal Arts and Sciences, Kanagawa University of Human Services, 1-10-1 Heisei-cho, Yokosuka, Kanagawa, 238-8522, Japan
| | - Koji Tsutsumi
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka, 431-3192, Japan
- Division of Cell Biology, Department of Biosciences, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Alu Konno
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Koji Ikegami
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka, 431-3192, Japan
- Department of Anatomy and Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, Hiroshima, 734-8553, Japan
| | - Saira Hameed
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Tomomi Kaneko
- Department of Liberal Arts and Sciences, Kanagawa University of Human Services, 1-10-1 Heisei-cho, Yokosuka, Kanagawa, 238-8522, Japan
| | - Oktay Ismail Kaplan
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, 4, Ireland
- Abdullah Gul Universitesi, Doga Bilimleri Fakultesi, Sumer Kampusu, 38090, Kocasinan, Kayseri, Turkey
| | - Takayuki Teramoto
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Manabi Fujiwara
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takeshi Ishihara
- Department of Biology, Faculty of Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Mitsutoshi Setou
- Department of Cellular & Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka, 431-3192, Japan.
- Department of Systems Molecular Anatomy, Institute for Medical Photonics Research, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka, 431-3192, Japan.
- The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
- Department of Anatomy, The University of Hong Kong, Hong Kong, China.
- Division of Neural Systematics, National Institute for Physiological Sciences, 38 Nishigonaka Myodaiji, Okazaki, Aichi, 444-8585, Japan.
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Komaki H, Sakurai K, Hosoyama A, Kimura A, Igarashi Y, Tamura T. Diversity of nonribosomal peptide synthetase and polyketide synthase gene clusters among taxonomically close Streptomyces strains. Sci Rep 2018; 8:6888. [PMID: 29720592 PMCID: PMC5932044 DOI: 10.1038/s41598-018-24921-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/26/2018] [Indexed: 11/23/2022] Open
Abstract
To identify the species of butyrolactol-producing Streptomyces strain TP-A0882, whole genome-sequencing of three type strains in a close taxonomic relationship was performed. In silico DNA-DNA hybridization using the genome sequences suggested that Streptomyces sp. TP-A0882 is classified as Streptomyces diastaticus subsp. ardesiacus. Strain TP-A0882, S. diastaticus subsp. ardesiacus NBRC 15402T, Streptomyces coelicoflavus NBRC 15399T, and Streptomyces rubrogriseus NBRC 15455T harbor at least 14, 14, 10, and 12 biosynthetic gene clusters (BGCs), respectively, coding for nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). All 14 gene clusters were shared by S. diastaticus subsp. ardesiacus strains TP-A0882 and NBRC 15402T, while only four gene clusters were shared by the three distinct species. Although BGCs for bacteriocin, ectoine, indole, melanine, siderophores such as deferrioxamine, terpenes such as albaflavenone, hopene, carotenoid and geosmin are shared by the three species, many BGCs for secondary metabolites such as butyrolactone, lantipeptides, oligosaccharide, some terpenes are species-specific. These results indicate the possibility that strains belonging to the same species possess the same set of secondary metabolite-biosynthetic pathways, whereas strains belonging to distinct species have species-specific pathways, in addition to some common pathways, even if the strains are taxonomically close.
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Affiliation(s)
- Hisayuki Komaki
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba, 292-0818, Japan.
| | | | | | | | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Toyama, 939-0398, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), Chiba, 292-0818, Japan
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40
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Yang X, Lennard KR, He C, Walker MC, Ball AT, Doigneaux C, Tavassoli A, van der Donk WA. A lanthipeptide library used to identify a protein-protein interaction inhibitor. Nat Chem Biol 2018; 14:375-380. [PMID: 29507389 PMCID: PMC5866752 DOI: 10.1038/s41589-018-0008-5] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/14/2017] [Indexed: 02/08/2023]
Abstract
In this article we describe the production and screening of a genetically encoded library of 106 lanthipeptides in Escherichia coli using the substrate-tolerant lanthipeptide synthetase ProcM. This plasmid-encoded library was combined with a bacterial reverse two-hybrid system for the interaction of the HIV p6 protein with the UEV domain of the human TSG101 protein, which is a critical protein-protein interaction for HIV budding from infected cells. Using this approach, we identified an inhibitor of this interaction from the lanthipeptide library, whose activity was verified in vitro and in cell-based virus-like particle-budding assays. Given the variety of lanthipeptide backbone scaffolds that may be produced with ProcM, this method may be used for the generation of genetically encoded libraries of natural product-like lanthipeptides containing substantial structural diversity. Such libraries may be combined with any cell-based assay to identify lanthipeptides with new biological activities.
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Affiliation(s)
- Xiao Yang
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Katherine R Lennard
- Department of Chemistry and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Chang He
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mark C Walker
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrew T Ball
- Department of Chemistry and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Cyrielle Doigneaux
- Department of Chemistry and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Ali Tavassoli
- Department of Chemistry and Institute for Life Sciences, University of Southampton, Southampton, UK.
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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41
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Abstract
The structural diversity and complexity of marine natural products have made them a rich and productive source of new bioactive molecules for drug development. The identification of these new compounds has led to extensive study of the protein constituents of the biosynthetic pathways from the producing microbes. Essential processes in the dissection of biosynthesis have been the elucidation of catalytic functions and the determination of 3D structures for enzymes of the polyketide synthases and nonribosomal peptide synthetases that carry out individual reactions. The size and complexity of these proteins present numerous difficulties in the process of going from gene to structure. Here, we review the problems that may be encountered at the various steps of this process and discuss some of the solutions devised in our and other labs for the cloning, production, purification, and structure solution of complex proteins using Escherichia coli as a heterologous host.
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Affiliation(s)
| | | | - Qingyun Dan
- University of Michigan, Ann Arbor, MI, United States
| | - Amy E Fraley
- University of Michigan, Ann Arbor, MI, United States
| | | | - Janet L Smith
- University of Michigan, Ann Arbor, MI, United States.
| | - W Clay Brown
- University of Michigan, Ann Arbor, MI, United States.
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42
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Suzuki S, Hara R, Kino K. Production of aminoacyl prolines using the adenylation domain of nonribosomal peptide synthetase with class III polyphosphate kinase 2-mediated ATP regeneration. J Biosci Bioeng 2018; 125:644-648. [PMID: 29366718 DOI: 10.1016/j.jbiosc.2017.12.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 12/25/2017] [Accepted: 12/26/2017] [Indexed: 11/19/2022]
Abstract
An ATP regeneration system is advantageous for industrial processes that are coupled with ATP-dependent enzymes. For ATP regeneration from AMP, a few methods have been reported; however, these methods employ multiple enzymes. To establish an ATP regeneration system using a single enzyme, we focused on class III polyphosphate kinase 2 (class III PPK2) that can synthesize ATP from AMP and polyphosphate. We constructed an ATP regeneration system from AMP using Deipr_1912, a class III PPK2 from Deinococcus proteolyticus NBRC 101906T, coupled with aminoacyl proline (Xaa-Pro) synthesis catalyzed by the adenylation domain of tyrocidine synthetase A (TycA-A). Using this system, 0.87 mM of l-Trp-l-Pro was successfully synthesized from AMP after 72 h. Farther, addition of inorganic pyrophosphatase from Escherichia coli to the coupling reaction increased the reaction rate by 14-fold to yield 6.2 mM l-Trp-l-Pro. When the coupling reaction was applied to whole-cell reactions in E. coli BL21(DE3) pepQ-putA-, ATP was successfully regenerated from AMP by Deipr_1912, and 6.7 mM of l-Trp-l-Pro was produced after 24 h with the supplementation of 10 mM AMP. In addition, by altering the substrate amino acid of TycA-A, not only l-Trp-l-Pro, but also various other l-Xaa-l-Pro (Xaa = Val, Leu, Met, or Tyr) were produced using the whole-cell reaction incorporating ATP regeneration. Therefore, a production method for Xaa-Pro employing the adenylation domain of a nonribosomal peptide synthetase was established by introducing an ATP regeneration system that utilizes class III PPK2 with pyrophosphatase.
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Affiliation(s)
- Shin Suzuki
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Ryotaro Hara
- Research Institute for Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Kuniki Kino
- Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan; Research Institute for Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan.
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43
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Paul S, Ishida H, Nguyen LT, Liu Z, Vogel HJ. Structural and dynamic characterization of a freestanding acyl carrier protein involved in the biosynthesis of cyclic lipopeptide antibiotics. Protein Sci 2017; 26:946-959. [PMID: 28187530 PMCID: PMC5405426 DOI: 10.1002/pro.3138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/31/2017] [Accepted: 02/03/2017] [Indexed: 11/08/2022]
Abstract
Friulimicin is a cyclic lipodecapeptide antibiotic that is produced by Actinoplanes friuliensis. Similar to the related lipopeptide drug daptomycin, the peptide skeleton of friulimicin is synthesized by a large multienzyme nonribosomal peptide synthetase (NRPS) system. The LipD protein plays a major role in the acylation reaction of friulimicin. The attachment of the fatty acid group promotes its antibiotic activity. Phylogenetic analysis reveals that LipD is most closely related to other freestanding acyl carrier proteins (ACPs), for which the genes are located near to NRPS gene clusters. Here, we report that the solution NMR structure of apo-LipD is very similar to other four-helix bundle forming ACPs from fatty acid synthase (FAS), polyketide synthase, and NRPS systems. By recording NMR dynamics data, we found that the backbone motions in holo-LipD are more restricted than in apo-LipD due to the attachment of phosphopantetheine moiety. This enhanced stability of holo-LipD was also observed in differential scanning calorimetry experiments. Furthermore, we demonstrate that, unlike several other ACPs, the folding of LipD does not depend on the presence of divalent cations, although the presence of Mg2+ or Ca2+ can increase the protein stability. We propose that small structural rearrangements in the tertiary structure of holo-LipD which lead to the enhanced stability are important for the cognate enzyme recognition for the acylation reaction. Our results also highlight the different surface charges of LipD and FAS-ACP from A. friuliensis that would allow the acyl-CoA ligase to interact preferentially with the LipD instead of binding to the FAS-ACP.
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Affiliation(s)
- Subrata Paul
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Hiroaki Ishida
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Leonard T. Nguyen
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Zhihong Liu
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
| | - Hans J. Vogel
- Biochemistry Research GroupDepartment of Biological Sciences, University of CalgaryCalgaryAlbertaCanada
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44
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Qadri M, Nalli Y, Jain SK, Chaubey A, Ali A, Strobel GA, Vishwakarma RA, Riyaz-Ul-Hassan S. An Insight into the Secondary Metabolism of Muscodor yucatanensis: Small-Molecule Epigenetic Modifiers Induce Expression of Secondary Metabolism-Related Genes and Production of New Metabolites in the Endophyte. Microb Ecol 2017; 73:954-965. [PMID: 27924400 DOI: 10.1007/s00248-016-0901-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/13/2016] [Indexed: 05/02/2023]
Abstract
Muscodor spp. are proficient producers of bioactive volatile organic compounds (VOCs) with many potential applications. However, all members of this genus produce varying amounts and types of VOCs which suggests the involvement of epigenetics as a possible explanation. The members of this genus are poorly explored for the production of soluble compounds (extrolites). In this study, the polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) genes from an endophyte, Muscodor yucatanensis Ni30, were cloned and sequenced. The PKS genes belonged to reduced, partially reduced, non-reduced, and highly reduced subtypes. Strains over-expressing PKS genes were developed through the use of small-molecule epigenetic modifiers (suberoylanilide hydroxamic acid (SAHA) and 5-azacytidine). The putative epigenetic variants of this organism differed considerably from the wild type in morphological features and cultural characteristics as well as metabolites that were produced. Each variant produced a different set of VOCs distinct from the wild type, and several VOCs including methyl 3-(3,5-di-tert-butyl-4-hydroxyphenyl)hexane-2,4-diol and 2-carboxymethyl-3-n-hexylmaleic appeared in the variant strains, the production of which could be attributed to the activity of otherwise silent PKS genes. The bioactive extrolite brefeldin A was isolated and characterized from the wild type. However, this metabolite was not detected in EV-1, but instead, two other products were isolated and characterized as ergosterol and xylaguaianol C. Hence, M. yucatanensis has the genetic potential to produce several previously undetectable VOCs and organic solvent soluble products. It is also the case that small-molecule epigenetic modifiers can be used to produce stable variant strains of fungi with the potential to produce new molecules. Finally, this work hints to the prospect that the epigenetics of an endophytic microorganism can be influenced by any number of environmental and chemical factors associated with its host plant which may help to explain the enormous chemical diversity of secondary metabolic products found in Muscodor spp.
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Affiliation(s)
- Masroor Qadri
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Yedukondalu Nalli
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Shreyans K Jain
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Asha Chaubey
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Fermentation Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Asif Ali
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Gary A Strobel
- Department of Plant Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Ram A Vishwakarma
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Syed Riyaz-Ul-Hassan
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.
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45
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Abstract
Nonribosomal peptide synthetases (NRPSs) employ multiple domains separated by linker regions to incorporate substrates into natural products. During synthesis, substrates are covalently tethered to carrier proteins that translocate between catalytic partner domains. The molecular parameters that govern translocation and associated linker remodeling remain unknown. Here, we used NMR to characterize the structure, dynamics, and invisible states of a peptidyl carrier protein flanked by its linkers. We showed that the N-terminal linker stabilizes and interacts with the protein core while modulating dynamics at specific sites involved in post-translational modifications and/or domain interactions. The results detail the molecular communication between peptidyl carrier proteins and their linkers and could guide efforts in engineering NRPSs to obtain new pharmaceuticals.
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Affiliation(s)
- Bradley J. Harden
- Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205
| | - Dominique P. Frueh
- Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD, 21205
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46
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Jasniewski AJ, Knoot CJ, Lipscomb JD, Que L. A Carboxylate Shift Regulates Dioxygen Activation by the Diiron Nonheme β-Hydroxylase CmlA upon Binding of a Substrate-Loaded Nonribosomal Peptide Synthetase. Biochemistry 2016; 55:5818-5831. [PMID: 27668828 PMCID: PMC5258830 DOI: 10.1021/acs.biochem.6b00834] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The first step in the nonribosomal peptide synthetase (NRPS)-based biosynthesis of chloramphenicol is the β-hydroxylation of the precursor l-p-aminophenylalanine (l-PAPA) catalyzed by the monooxygenase CmlA. The active site of CmlA contains a dinuclear iron cluster that is reduced to the diferrous state (WTR) to initiate O2 activation. However, rapid O2 activation occurs only when WTR is bound to CmlP, the NRPS to which l-PAPA is covalently attached. Here the X-ray crystal structure of WTR is reported, which is very similar to that of the as-isolated diferric enzyme in which the irons are coordinately saturated. X-ray absorption spectroscopy is used to investigate the WTR cluster ligand structure as well as the structures of WTR in complex with a functional CmlP variant (CmlPAT) with and without l-PAPA attached. It is found that formation of the active WTR:CmlPAT-l-PAPA complex converts at least one iron of the cluster from six- to five-coordinate by changing a bidentately bound amino acid carboxylate to monodentate on Fe1. The only bidentate carboxylate in the structure of WTR is E377. The crystal structure of the CmlA variant E377D shows only monodentate carboxylate coordination. Reduced E377D reacts rapidly with O2 in the presence or absence of CmlPAT-l-PAPA, showing loss of regulation. However, this variant fails to catalyze hydroxylation, suggesting that E377 has the dual role of coupling regulation of O2 reactivity with juxtaposition of the substrate and the reactive oxygen species. The carboxylate shift in response to substrate binding represents a novel regulatory strategy for oxygen activation in diiron oxygenases.
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Affiliation(s)
- Andrew J. Jasniewski
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - Cory J. Knoot
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - John D. Lipscomb
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455
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47
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Peschke M, Brieke C, Cryle MJ. F-O-G Ring Formation in Glycopeptide Antibiotic Biosynthesis is Catalysed by OxyE. Sci Rep 2016; 6:35584. [PMID: 27752135 PMCID: PMC5067714 DOI: 10.1038/srep35584] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/04/2016] [Indexed: 12/19/2022] Open
Abstract
The glycopeptide antibiotics are peptide-based natural products with impressive antibiotic function that derives from their unique three-dimensional structure. Biosynthesis of the glycopeptide antibiotics centres of the combination of peptide synthesis, mediated by a non-ribosomal peptide synthetase, and the crosslinking of aromatic side chains of the peptide, mediated by the action of a cascade of Cytochrome P450s. Here, we report the first example of in vitro activity of OxyE, which catalyses the F-O-G ring formation reaction in teicoplanin biosynthesis. OxyE was found to only act after an initial C-O-D crosslink is installed by OxyB and to require an interaction with the unique NRPS domain from glycopeptide antibiotic - the X-domain - in order to display catalytic activity. We could demonstrate that OxyE displays limited stereoselectivity for the peptide, which mirrors the results from OxyB-catalysed turnover and is in sharp contrast to OxyA. Furthermore, we show that activity of a three-enzyme cascade (OxyB/OxyA/OxyE) in generating tricyclic glycopeptide antibiotic peptides depends upon the order of addition of the OxyA and OxyE enzymes to the reaction. This work demonstrates that complex enzymatic cascades from glycopeptide antibiotic biosynthesis can be reconstituted in vitro and provides new insights into the biosynthesis of these important antibiotics.
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Affiliation(s)
- Madeleine Peschke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Clara Brieke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Max J. Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
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48
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Šink R, Kotnik M, Zega A, Barreteau H, Gobec S, Blanot D, Dessen A, Contreras-Martel C. Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited. PLoS One 2016; 11:e0152075. [PMID: 27031227 PMCID: PMC4816537 DOI: 10.1371/journal.pone.0152075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 03/08/2016] [Indexed: 11/30/2022] Open
Abstract
The biosynthetic pathway of peptidoglycan, an essential component of bacterial cell wall, is a well-recognized target for antibiotic development. Peptidoglycan precursors are synthesized in the bacterial cytosol by various enzymes including the ATP-hydrolyzing Mur ligases, which catalyze the stepwise addition of amino acids to a UDP-MurNAc precursor to yield UDP-MurNAc-pentapeptide. MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala in the presence of ATP; structural and biochemical studies have suggested the binding of the substrates with an ordered kinetic mechanism in which ligand binding inevitably closes the active site. In this work, we challenge this assumption by reporting the crystal structures of intermediate forms of MurD either in the absence of ligands or in the presence of small molecules. A detailed analysis provides insight into the events that lead to the closure of MurD and reveals that minor structural modifications contribute to major overall conformation alterations. These novel insights will be instrumental in the development of new potential antibiotics designed to target the peptidoglycan biosynthetic pathway.
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Affiliation(s)
- Roman Šink
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia
| | - Miha Kotnik
- Lek Pharmaceuticals d. d., Verovškova 57, Ljubljana, Slovenia
| | - Anamarija Zega
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia
| | - Hélène Barreteau
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, Ljubljana, Slovenia
| | - Didier Blanot
- Laboratoire des Enveloppes Bactériennes et Antibiotiques, Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Andréa Dessen
- Univ. Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- Brazilian National Laboratory for Biosciences (LNBio), CNPEM, Campinas, São Paulo, Brazil
| | - Carlos Contreras-Martel
- Univ. Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- * E-mail:
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49
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Castellano I, Migliaccio O, D’Aniello S, Merlino A, Napolitano A, Palumbo A. Shedding light on ovothiol biosynthesis in marine metazoans. Sci Rep 2016; 6:21506. [PMID: 26916575 PMCID: PMC4768315 DOI: 10.1038/srep21506] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/26/2016] [Indexed: 01/23/2023] Open
Abstract
Ovothiol, isolated from marine invertebrate eggs, is considered one of the most powerful antioxidant with potential for drug development. However, its biological functions in marine organisms still represent a matter of debate. In sea urchins, the most accepted view is that ovothiol protects the eggs by the high oxidative burst at fertilization. In this work we address the role of ovothiol during sea urchin development to give new insights on ovothiol biosynthesis in metazoans. The gene involved in ovothiol biosynthesis OvoA was identified in Paracentrotus lividus genome (PlOvoA). PlOvoA embryo expression significantly increased at the pluteus stage and was up-regulated by metals at concentrations mimicking polluted sea-water and by cyclic toxic algal blooms, leading to ovothiol biosynthesis. In silico analyses of the PlOvoA upstream region revealed metal and stress responsive elements. Structural protein models highlighted conserved active site residues likely responsible for ovothiol biosynthesis. Phylogenetic analyses indicated that OvoA evolved in most marine metazoans and was lost in bony vertebrates during the transition from the aquatic to terrestrial environment. These results highlight the crucial role of OvoA in protecting embryos released in seawater from environmental cues, thus allowing the survival under different conditions.
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Affiliation(s)
- Immacolata Castellano
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Oriana Migliaccio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Salvatore D’Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples “Federico II”, Italy
| | | | - Anna Palumbo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
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50
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Ishikawa F, Kakeya H. Affinity Purification Method for the Identification of Nonribosomal Peptide Biosynthetic Enzymes Using a Synthetic Probe for Adenylation Domains. Methods Mol Biol 2016; 1401:63-76. [PMID: 26831701 DOI: 10.1007/978-1-4939-3375-4_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A series of inhibitors have been designed based on 5'-O-sulfamoyl adenosine (AMS) that display tight binding characteristics towards the inhibition of adenylation (A) domains in nonribosomal peptide synthetases (NRPSs). We recently developed an affinity probe for A domains that could be used to facilitate the specific isolation and identification of NRPS modules. Our synthetic probe, which is a biotinylated variant of L-Phe-AMS (L-Phe-AMS-biotin), selectively targets the A domains in NRPS modules that recognize and convert L-Phe to an aminoacyl adenylate in whole proteomes. In this chapter, we describe the design and synthesis of L-Phe-AMS-biotin and provide a summary of our work towards the development of a series of protocols for the specific enrichment of NRPS modules using this probe.
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Affiliation(s)
- Fumihiro Ishikawa
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Science, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hideaki Kakeya
- Department of System Chemotherapy and Molecular Sciences, Division of Bioinformatics and Chemical Genomics, Graduate School of Pharmaceutical Science, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
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