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Gering HE, Li X, Tang H, Swartz PD, Chang WC, Makris TM. A Ferric-Superoxide Intermediate Initiates P450-Catalyzed Cyclic Dipeptide Dimerization. J Am Chem Soc 2023; 145:19256-19264. [PMID: 37611404 DOI: 10.1021/jacs.3c04542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
The cytochrome P450 (CYP) AspB is involved in the biosynthesis of the diketopiperazine (DKP) aspergilazine A. Tryptophan-linked dimeric DKP alkaloids are a large family of natural products that are found in numerous species and exhibit broad and often potent bioactivity. The proposed mechanisms for C-N bond formation by AspB, and similar C-C bond formations by related CYPs, have invoked the use of a ferryl-intermediate as an oxidant to promote substrate dimerization. Here, the parallel application of steady-state and transient kinetic approaches reveals a very different mechanism that involves a ferric-superoxide species as a primary oxidant to initiate DKP-assembly. Single turnover kinetic isotope effects and a substrate analog suggest the probable nature and site for abstraction. The direct observation of CYP-superoxide reactivity rationalizes the atypical outcome of AspB and reveals a new reaction manifold in heme enzymes.
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Affiliation(s)
- Hannah E Gering
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Xiaojun Li
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Haoyu Tang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Paul D Swartz
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Thomas M Makris
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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2
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Deletti G, Green SD, Weber C, Patterson KN, Joshi SS, Khopade TM, Coban M, Veek-Wilson J, Caulfield TR, Viswanathan R, Lane AL. Unveiling an indole alkaloid diketopiperazine biosynthetic pathway that features a unique stereoisomerase and multifunctional methyltransferase. Nat Commun 2023; 14:2558. [PMID: 37137876 PMCID: PMC10156859 DOI: 10.1038/s41467-023-38168-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 04/19/2023] [Indexed: 05/05/2023] Open
Abstract
The 2,5-diketopiperazines are a prominent class of bioactive molecules. The nocardioazines are actinomycete natural products that feature a pyrroloindoline diketopiperazine scaffold composed of two D-tryptophan residues functionalized by N- and C-methylation, prenylation, and diannulation. Here we identify and characterize the nocardioazine B biosynthetic pathway from marine Nocardiopsis sp. CMB-M0232 by using heterologous biotransformations, in vitro biochemical assays, and macromolecular modeling. Assembly of the cyclo-L-Trp-L-Trp diketopiperazine precursor is catalyzed by a cyclodipeptide synthase. A separate genomic locus encodes tailoring of this precursor and includes an aspartate/glutamate racemase homolog as an unusual D/L isomerase acting upon diketopiperazine substrates, a phytoene synthase-like prenyltransferase as the catalyst of indole alkaloid diketopiperazine prenylation, and a rare dual function methyltransferase as the catalyst of both N- and C-methylation as the final steps of nocardioazine B biosynthesis. The biosynthetic paradigms revealed herein showcase Nature's molecular ingenuity and lay the foundation for diketopiperazine diversification via biocatalytic approaches.
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Affiliation(s)
- Garrett Deletti
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Sajan D Green
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Caleb Weber
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Kristen N Patterson
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Swapnil S Joshi
- Departments of Chemistry & Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
| | - Tushar M Khopade
- Departments of Chemistry & Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
| | - Mathew Coban
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - James Veek-Wilson
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA
| | - Thomas R Caulfield
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, 32224, USA
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Rajesh Viswanathan
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA.
- Departments of Chemistry & Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India.
| | - Amy L Lane
- Department of Chemistry & Biochemistry, University of North Florida, Jacksonville, FL, 32224, USA.
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3
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Khopade TM, Ajayan K, Vincent DM, Lane AL, Viswanathan R. Biomimetic Total Synthesis of (+)-Nocardioazine B and Analogs. J Org Chem 2022; 87:11519-11533. [PMID: 35960860 DOI: 10.1021/acs.joc.2c01120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nocardioazines A and B are prenylated, bioactive pyrroloindoline natural products, isolated from Nocardiopsis, with a desymmetrized cyclo-d-Trp-d-Trp DKP core. Based on our deeper biosynthetic understanding, a biomimetic total synthesis of (+)-nocardioazine B is accomplished in merely seven steps and 23.2% overall yield. This pathway accesses regio- and stereoselectively C3-isoprenylated analogs of (+)-nocardioazine B, using the same number of steps and in similar efficiency. The successful strategy mandated that the biomimetic C3-prenylation step be executed early. The use of an unprotected carboxylic acid of Trp led to high diastereoselectivity toward formation of key intermediates exo-12a, exo-12b, and exo-12c (>19:1). Evidence shows that N1-methylation causes the prenylation reaction to bifurcate away to result in a C2-normal-prenylated isomer. Nocardioazine A, possessing an isoprenoidal-epoxide bridge, inhibits P-glycoprotein (P-gp)-mediated membrane efflux, in multidrug-resistant mammalian colon cancer cells. As several P-gp inhibitors have failed due to their toxicity effects, endogenous amino-acid-derived noncytotoxic inhibitors (from the nocardioazine core) are worthy leads toward a rejuvenated strategy against resistant carcinomas. This total synthesis provides direct access to Trp-derived isoprenylated DKP natural products and their derivatives.
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Affiliation(s)
- Tushar M Khopade
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh 517507, India
| | - Kalyani Ajayan
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh 517507, India
| | - Dona Mariya Vincent
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh 517507, India
| | - Amy L Lane
- Department of Chemistry, University of North Florida, Jacksonville, Florida 32224, United States
| | - Rajesh Viswanathan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh 517507, India.,Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh 517507, India
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4
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Chen BS, Zhang D, de Souza FZR, Liu L. Recent Advances in the Synthesis of Marine-Derived Alkaloids via Enzymatic Reactions. Mar Drugs 2022; 20:md20060368. [PMID: 35736171 PMCID: PMC9229328 DOI: 10.3390/md20060368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
Alkaloids are a large and structurally diverse group of marine-derived natural products. Most marine-derived alkaloids are biologically active and show promising applications in modern (agro)chemical, pharmaceutical, and fine chemical industries. Different approaches have been established to access these marine-derived alkaloids. Among these employed methods, biotechnological approaches, namely, (chemo)enzymatic synthesis, have significant potential for playing a central role in alkaloid production on an industrial scale. In this review, we discuss research progress on marine-derived alkaloid synthesis via enzymatic reactions and note the advantages and disadvantages of their applications for industrial production, as well as green chemistry for marine natural product research.
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Affiliation(s)
- Bi-Shuang Chen
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; (B.-S.C.); (D.Z.); (L.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Di Zhang
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; (B.-S.C.); (D.Z.); (L.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
| | - Fayene Zeferino Ribeiro de Souza
- Centro Universitário Planalto do Distrito Federal, Universidade Virtual do Estado de São Paulo (UNIPLAN), Campus Bauru 17014-350, Brazil
- Correspondence: ; Tel.: +55-014-32452580
| | - Lan Liu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China; (B.-S.C.); (D.Z.); (L.L.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
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5
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Gao B, Yang B, Feng X, Li C. Recent advances in the biosynthesis strategies of nitrogen heterocyclic natural products. Nat Prod Rep 2021; 39:139-162. [PMID: 34374396 DOI: 10.1039/d1np00017a] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Covering: 2015 to 2020Nitrogen heterocyclic natural products (NHNPs) are primary or secondary metabolites containing nitrogen heterocyclic (N-heterocyclic) skeletons. Due to the existence of the N-heterocyclic structure, NHNPs exhibit various bioactivities such as anticancer and antibacterial, which makes them widely used in medicines, pesticides, and food additives. However, the low content of these NHNPs in native organisms severely restricts their commercial application. Although a variety of NHNPs have been produced through extraction or chemical synthesis strategies, these methods suffer from several problems. The development of biotechnology provides new options for the production of NHNPs. This review introduces the recent progress of two strategies for the biosynthesis of NHNPs: enzymatic biosynthesis and microbial cell factory. In the enzymatic biosynthesis part, the recent progress in the mining of enzymes that synthesize N-heterocyclic skeletons (e.g., pyrrole, piperidine, diketopiperazine, and isoquinoline), the engineering of tailoring enzymes, and enzyme cascades constructed to synthesize NHNPs are discussed. In the microbial cell factory part, with tropane alkaloids (TAs) and tetrahydroisoquinoline (THIQ) alkaloids as the representative compounds, the strategies of unraveling unknown natural biosynthesis pathways of NHNPs in plants are summarized, and various metabolic engineering strategies to enhance their production in microbes are introduced. Ultimately, future perspectives for accelerating the biosynthesis of NHNPs are discussed.
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Affiliation(s)
- Bo Gao
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.
| | - Bo Yang
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xudong Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China. and SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China and Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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6
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Areal A, Domínguez M, Vendrig P, Alvarez S, Álvarez R, de Lera ÁR. Total Synthesis of Homo- and Heterodimeric Bispyrrolidinoindoline Dioxopiperazine Natural Products. JOURNAL OF NATURAL PRODUCTS 2021; 84:1725-1737. [PMID: 34019401 DOI: 10.1021/acs.jnatprod.0c01273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Total synthesis and structural confirmation of homo- and heterodimeric bispyrrolidinoindoline dioxopiperazine alkaloids isolated from fungi and bacteria, namely, ditryptoleucine A, ditryptoleucine B (11), the N,N'-bis-demethylated analogue (+)-12, (-)-dibrevianamide F (13), (-)-SF-5280-451 (14), tetratryptomycin A (15), (-)-tryprophenaline (17), and (-)-SF-5280-415 (18), has been carried out starting from the corresponding bispyrrolidinoindolines derived from tryptophan. Our efforts to synthesize all possible diastereomers of the natural ditryptoleucine isolates uncovered structural factors that determine the rate and efficiency of dioxopiperazine ring formation, leading in some cases to mixtures of diastereomers by concomitant epimerization, to the formation of their putative monomeric dioxopiperazine dipeptide biogenetic precursors, and to the alternative formation of a dimer with a fused 1,3,5-triazepan-6-one heterocycle.
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Affiliation(s)
- Andrea Areal
- Departamento de Química Orgánica, CINBIO, and Instituto de Investigacións Biomédicas de Vigo (IBIV), Universidade de Vigo, As Lagoas-Marcosende, 36310 Vigo, Spain
| | - Marta Domínguez
- Departamento de Química Orgánica, CINBIO, and Instituto de Investigacións Biomédicas de Vigo (IBIV), Universidade de Vigo, As Lagoas-Marcosende, 36310 Vigo, Spain
| | - Pim Vendrig
- Departamento de Química Orgánica, CINBIO, and Instituto de Investigacións Biomédicas de Vigo (IBIV), Universidade de Vigo, As Lagoas-Marcosende, 36310 Vigo, Spain
| | - Susana Alvarez
- Departamento de Química Orgánica, CINBIO, and Instituto de Investigacións Biomédicas de Vigo (IBIV), Universidade de Vigo, As Lagoas-Marcosende, 36310 Vigo, Spain
| | - Rosana Álvarez
- Departamento de Química Orgánica, CINBIO, and Instituto de Investigacións Biomédicas de Vigo (IBIV), Universidade de Vigo, As Lagoas-Marcosende, 36310 Vigo, Spain
| | - Ángel R de Lera
- Departamento de Química Orgánica, CINBIO, and Instituto de Investigacións Biomédicas de Vigo (IBIV), Universidade de Vigo, As Lagoas-Marcosende, 36310 Vigo, Spain
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7
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Khopade T, Ajayan K, Joshi SS, Lane AL, Viswanathan R. Bioinspired Brønsted Acid-Promoted Regioselective Tryptophan Isoprenylations. ACS OMEGA 2021; 6:10840-10858. [PMID: 34056238 PMCID: PMC8153798 DOI: 10.1021/acsomega.1c00515] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/16/2021] [Indexed: 05/16/2023]
Abstract
Tryptophan-containing isoprenoid indole alkaloid natural products are well known for their intricate structural architectures and significant biological activities. Nature employs dimethylallyl tryptophan synthases (DMATSs) or aromatic indole prenyltransferases (iPTs) to catalyze regio- and stereoselective prenylation of l-Trp. Regioselective synthetic routes that isoprenylate cyclo-Trp-Trp in a 2,5-diketopiperazine (DKP) core, in a desymmetrizing manner, are nonexistent and are highly desirable. Herein, we present an elaborate report on Brønsted acid-promoted regioselective tryptophan isoprenylation strategy, applicable to both the monomeric amino acid and its dimeric l-Trp DKP. This report outlines a method that regio- and stereoselectively increases sp3 centers of a privileged bioactive core. We report on conditions involving screening of Brønsted acids, their conjugate base as salt, solvent, temperature, and various substrates with diverse side chains. Furthermore, we extensively delineate effects on regio- and stereoselection of isoprenylation and their stereochemical confirmation via NMR experiments. Regioselectively, the C3-position undergoes normal-isoprenylation or benzylation and forms exo-ring-fused pyrroloindolines selectively. Through appropriate prenyl group migrations, we report access to the bioactive tryprostatin alkaloids, and by C3-normal-farnesylation, we access anticancer drimentines as direct targets of this method. The optimized strategy affords iso-tryprostatin B-type products and predrimentine C with 58 and 55% yields, respectively. The current work has several similarities to biosynthesis, such as-reactions can be performed on unprotected substrates, conditions that enable Brønsted acid promotion, and they are easy to perform under ambient conditions, without the need for stoichiometric levels of any transition metal or expensive ligands.
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Affiliation(s)
- Tushar
M. Khopade
- Departments
of Chemistry & Biology, Indian Institute
of Science Education and Research, Tirupati 517507, Andhra
Pradesh India
| | - Kalyani Ajayan
- Departments
of Chemistry & Biology, Indian Institute
of Science Education and Research, Tirupati 517507, Andhra
Pradesh India
| | - Swapnil S. Joshi
- Departments
of Chemistry & Biology, Indian Institute
of Science Education and Research, Tirupati 517507, Andhra
Pradesh India
| | - Amy L. Lane
- Department
of Chemistry, University of North Florida, Jacksonville 32224, Florida, United States
| | - Rajesh Viswanathan
- Departments
of Chemistry & Biology, Indian Institute
of Science Education and Research, Tirupati 517507, Andhra
Pradesh India
- Department
of Chemistry, University of North Florida, Jacksonville 32224, Florida, United States
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8
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Liu J, Xie X, Li SM. Increasing cytochrome P450 enzyme diversity by identification of two distinct cyclodipeptide dimerases. Chem Commun (Camb) 2021; 56:11042-11045. [PMID: 32808942 DOI: 10.1039/d0cc04772d] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Genome mining revealed the presence of two cdps-p450 operons in Saccharopolyspora antimicrobica. Heterologous expression, biochemical characterisation and structure elucidation proved that the two P450 enzymes catalyse distinct regio- and stereospecific dimerizations of cyclo-(l-Trp-l-Trp), which significantly expands the repertoire of diketopiperazine-tailoring enzymes. TtpB1 connects the monomers via C3-C3', both from the opposite side of H-11/H-11', while TtpB2 is characterised as the first P450 to mainly catalyse the unusual linkage between N1' and C3 from the H-11 side.
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Affiliation(s)
- Jing Liu
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany.
| | - Xiulan Xie
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, Marburg 35032, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany.
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9
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Le Chevalier F, Correia I, Matheron L, Babin M, Moutiez M, Canu N, Gondry M, Lequin O, Belin P. In vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in Escherichia coli. Microb Cell Fact 2020; 19:178. [PMID: 32894164 PMCID: PMC7487605 DOI: 10.1186/s12934-020-01432-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 08/27/2020] [Indexed: 11/23/2022] Open
Abstract
Background Cyclodipeptide oxidases (CDOs) are enzymes involved in the biosynthesis of 2,5-diketopiperazines, a class of naturally occurring compounds with a large range of pharmaceutical activities. CDOs belong to cyclodipeptide synthase (CDPS)-dependent pathways, in which they play an early role in the chemical diversification of cyclodipeptides by introducing Cα-Cβ dehydrogenations. Although the activities of more than 100 CDPSs have been determined, the activities of only a few CDOs have been characterized. Furthermore, the assessment of the CDO activities on chemically-synthesized cyclodipeptides has shown these enzymes to be relatively promiscuous, making them interesting tools for cyclodipeptide chemical diversification. The purpose of this study is to provide the first completely microbial toolkit for the efficient bioproduction of a variety of dehydrogenated 2,5-diketopiperazines. Results We mined genomes for CDOs encoded in biosynthetic gene clusters of CDPS-dependent pathways and selected several for characterization. We co-expressed each with their associated CDPS in the pathway using Escherichia coli as a chassis and showed that the cyclodipeptides and the dehydrogenated derivatives were produced in the culture supernatants. We determined the biological activities of the six novel CDOs by solving the chemical structures of the biologically produced dehydrogenated cyclodipeptides. Then, we assessed the six novel CDOs plus two previously characterized CDOs in combinatorial engineering experiments in E. coli. We co-expressed each of the eight CDOs with each of 18 CDPSs selected for the diversity of cyclodipeptides they synthesize. We detected more than 50 dehydrogenated cyclodipeptides and determined the best CDPS/CDO combinations to optimize the production of 23. Conclusions Our study establishes the usefulness of CDPS and CDO for the bioproduction of dehydrogenated cyclodipeptides. It constitutes the first step toward the bioproduction of more complex and diverse 2,5-diketopiperazines.
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Affiliation(s)
- Fabien Le Chevalier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Isabelle Correia
- Laboratoire des Biomolécules (LBM), Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, 75005, Paris, France
| | - Lucrèce Matheron
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), FRE3631, 75005, Paris, France
| | - Morgan Babin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Mireille Moutiez
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Nicolas Canu
- 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
| | - Olivier Lequin
- Laboratoire des Biomolécules (LBM), Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, 75005, Paris, France
| | - Pascal Belin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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10
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Ding Y, Zhu X, Hao L, Zhao M, Hua Q, An F. Bioactive Indolyl Diketopiperazines from the Marine Derived Endophytic Aspergillus versicolor DY180635. Mar Drugs 2020; 18:E338. [PMID: 32605149 PMCID: PMC7401283 DOI: 10.3390/md18070338] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 01/25/2023] Open
Abstract
Four new indolyl diketopiperazines, aspamides A-E (1-4) and two new diketopiperazines, aspamides F-G (5-6), along with 11 known diketopiperazines and intermediates were isolated from the solid culture of Aspergillus versicolor, which is an endophyte with the sea crab (Chiromantes haematocheir). Further chiral high-performance liquid chromatography resolution gave enantiomers (+)- and (-)-4, respectively. The structures and absolute configurations of compounds 1-6 were determined by the comprehensive analyses of nuclear magnetic resonance (NMR), high-resolution mass spectrometry (HR-MS), and electronic circular dichroism (ECD) calculation. All isolated compounds were selected for the virtual screening on the coronavirus 3-chymoretpsin-like protease (Mpro) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), and the docking scores of compounds 1-2, 5, 6, 8 and 17 were top among all screened molecules, may be helpful in fighting with Corona Virus Disease-19 (COVID-19) after further studies.
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Affiliation(s)
| | | | | | | | | | - Faliang An
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai 200237, China; (Y.D.); (X.Z.); (L.H.); (M.Z.); (Q.H.)
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11
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Highly efficient production of chitooligosaccharides by enzymes mined directly from the marine metagenome. Carbohydr Polym 2020; 234:115909. [DOI: 10.1016/j.carbpol.2020.115909] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 12/12/2022]
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12
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Chevrette MG, Gutiérrez-García K, Selem-Mojica N, Aguilar-Martínez C, Yañez-Olvera A, Ramos-Aboites HE, Hoskisson PA, Barona-Gómez F. Evolutionary dynamics of natural product biosynthesis in bacteria. Nat Prod Rep 2019; 37:566-599. [PMID: 31822877 DOI: 10.1039/c9np00048h] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2008 up to 2019The forces of biochemical adaptive evolution operate at the level of genes, manifesting in complex phenotypes and the global biodiversity of proteins and metabolites. While evolutionary histories have been deciphered for some other complex traits, the origins of natural product biosynthesis largely remain a mystery. This fundamental knowledge gap is surprising given the many decades of research probing the genetic, chemical, and biophysical mechanisms of bacterial natural product biosynthesis. Recently, evolutionary thinking has begun to permeate this otherwise mechanistically dominated field. Natural products are now sometimes referred to as 'specialized' rather than 'secondary' metabolites, reinforcing the importance of their biological and ecological functions. Here, we review known evolutionary mechanisms underlying the overwhelming chemical diversity of bacterial secondary metabolism, focusing on enzyme promiscuity and the evolution of enzymatic domains that enable metabolic traits. We discuss the mechanisms that drive the assembly of natural product biosynthetic gene clusters and propose formal definitions for 'specialized' and 'secondary' metabolism. We further explore how biosynthetic gene clusters evolve to synthesize related molecular species, and in turn how the biological and ecological roles that emerge from metabolic diversity are acted on by selection. Finally, we reconcile chemical, functional, and genetic data into an evolutionary model, the dynamic chemical matrix evolutionary hypothesis, in which the relationships between chemical distance, biomolecular activity, and relative fitness shape adaptive landscapes.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
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13
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Dubois P, Correia I, Le Chevalier F, Dubois S, Jacques I, Canu N, Moutiez M, Thai R, Gondry M, Lequin O, Belin P. Reprogramming Escherichia coli for the production of prenylated indole diketopiperazine alkaloids. Sci Rep 2019; 9:9208. [PMID: 31239480 PMCID: PMC6592928 DOI: 10.1038/s41598-019-45519-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/05/2019] [Indexed: 11/09/2022] Open
Abstract
Prenylated indole diketopiperazine (DKP) alkaloids are important bioactive molecules or their precursors. In the context of synthetic biology, efficient means for their biological production would increase their chemical diversification and the discovery of novel bioactive compounds. Here, we prove the suitability of the Escherichia coli chassis for the production of prenylated indole DKP alkaloids. We used enzyme combinations not found in nature by co-expressing bacterial cyclodipeptide synthases (CDPSs) that assemble the DKP ring and fungal prenyltransferases (PTs) that transfer the allylic moiety from the dimethylallyl diphosphate (DMAPP) to the indole ring of tryptophanyl-containing cyclodipeptides. Of the 11 tested combinations, seven resulted in the production of eight different prenylated indole DKP alkaloids as determined by LC-MS/MS and NMR characterization. Two were previously undescribed. Engineering E. coli by introducing a hybrid mevalonate pathway for increasing intracellular DMAPP levels improved prenylated indole DKP alkaloid production. Purified product yields of 2–26 mg/L per culture were obtained from culture supernatants. Our study paves the way for the bioproduction of novel prenylated indole DKP alkaloids in a tractable chassis that can exploit the cyclodipeptide diversity achievable with CDPSs and the numerous described PT activities.
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Affiliation(s)
- Pavlina Dubois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France
| | - Isabelle Correia
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 75005, Paris, France
| | - Fabien Le Chevalier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France
| | | | - Isabelle Jacques
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France.,Isabelle B. Jacques, APTEEUS, Institut Pasteur de Lille, Lille, France
| | - Nicolas Canu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France
| | - Mireille Moutiez
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France
| | - Robert Thai
- SIMOPRO, CEA, 91198, Gif-sur-Yvette, cedex, France
| | - Muriel Gondry
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France
| | - Olivier Lequin
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 75005, Paris, France.
| | - Pascal Belin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, cedex, France.
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14
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Borgman P, Lopez RD, Lane AL. The expanding spectrum of diketopiperazine natural product biosynthetic pathways containing cyclodipeptide synthases. Org Biomol Chem 2019; 17:2305-2314. [PMID: 30688950 DOI: 10.1039/c8ob03063d] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microorganisms are remarkable chemists, with enzymes as their tools for executing multi-step syntheses to yield myriad natural products. Microbial synthetic aptitudes are illustrated by the structurally diverse 2,5-diketopiperazine (DKP) family of bioactive nonribosomal peptide natural products. Nonribosomal peptide synthetases (NRPSs) have long been recognized as catalysts for formation of DKP scaffolds from two amino acid substrates. Cyclodipeptide synthases (CDPSs) are more recently recognized catalysts of DKP assembly, employing two aminoacyl-tRNAs (aa-tRNAs) as substrates. CDPS-encoding genes are typically found in genomic neighbourhoods with genes encoding additional biosynthetic enzymes. These include oxidoreductases, cytochrome P450s, prenyltransferases, methyltransferases, and cyclases, which equip the DKP scaffold with groups that diversify chemical structures and confer biological activity. These tailoring enzymes have been characterized from nine CDPS-containing biosynthetic pathways to date, including four during the last year. In this review, we highlight these nine DKP pathways, emphasizing recently characterized tailoring reactions and connecting new developments to earlier findings. Featured pathways encompass a broad spectrum of chemistry, including the formation of challenging C-C and C-O bonds, regioselective methylation, a unique indole alkaloid DKP prenylation strategy, and unprecedented peptide-nucleobase bond formation. These CDPS-containing pathways also provide intriguing models of metabolic pathway evolution across related and divergent microorganisms, and open doors to synthetic biology approaches for generation of DKP combinatorial libraries. Further, bioinformatics analyses support that much unique genetically encoded DKP tailoring potential remains unexplored, suggesting opportunities for further expansion of Nature's biosynthetic spectrum. Together, recent studies of DKP pathways demonstrate the chemical ingenuity of microorganisms, highlight the wealth of unique enzymology provided by bacterial biosynthetic pathways, and suggest an abundance of untapped biosynthetic potential for future exploration.
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Affiliation(s)
- Paul Borgman
- Department of Chemistry, University of North Florida, 1 UNF Dr, Jacksonville, FL 32224, USA.
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15
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Jiang G, Zuo R, Zhang Y, Powell MM, Zhang P, Hylton SM, Loria R, Ding Y. One-Pot Biocombinatorial Synthesis of Herbicidal Thaxtomins. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03317] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Guangde Jiang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Ran Zuo
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Yi Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Magan M. Powell
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Peilan Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Sarah M. Hylton
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Rosemary Loria
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
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16
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Discovery and Biosynthesis of the Antibiotic Bicyclomycin in Distantly Related Bacterial Classes. Appl Environ Microbiol 2018; 84:AEM.02828-17. [PMID: 29500259 PMCID: PMC5930311 DOI: 10.1128/aem.02828-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/21/2018] [Indexed: 01/23/2023] Open
Abstract
Bicyclomycin (BCM) is a clinically promising antibiotic that is biosynthesized by Streptomyces cinnamoneus DSM 41675. BCM is structurally characterized by a core cyclo(l-Ile-l-Leu) 2,5-diketopiperazine (DKP) that is extensively oxidized. Here, we identify the BCM biosynthetic gene cluster, which shows that the core of BCM is biosynthesized by a cyclodipeptide synthase, and the oxidative modifications are introduced by five 2-oxoglutarate-dependent dioxygenases and one cytochrome P450 monooxygenase. The discovery of the gene cluster enabled the identification of BCM pathways encoded by the genomes of hundreds of Pseudomonas aeruginosa isolates distributed globally, and heterologous expression of the pathway from P. aeruginosa SCV20265 demonstrated that the product is chemically identical to BCM produced by S. cinnamoneus. Overall, putative BCM gene clusters have been found in at least seven genera spanning Actinobacteria and Proteobacteria (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria). This represents a rare example of horizontal gene transfer of an intact biosynthetic gene cluster across such distantly related bacteria, and we show that these gene clusters are almost always associated with mobile genetic elements. IMPORTANCE Bicyclomycin is the only natural product antibiotic that selectively inhibits the transcription termination factor Rho. This mechanism of action, combined with its proven biological safety and its activity against clinically relevant Gram-negative bacterial pathogens, makes it a very promising antibiotic candidate. Here, we report the identification of the bicyclomycin biosynthetic gene cluster in the known bicyclomycin-producing organism Streptomyces cinnamoneus, which will enable the engineered production of new bicyclomycin derivatives. The identification of this gene cluster also led to the discovery of hundreds of bicyclomycin pathways encoded in highly diverse bacteria, including in the opportunistic pathogen Pseudomonas aeruginosa. This wide distribution of a complex biosynthetic pathway is very unusual and provides an insight into how a pathway for an antibiotic can be transferred between diverse bacteria.
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17
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Liu J, Yu H, Li SM. Expanding tryptophan-containing cyclodipeptide synthase spectrum by identification of nine members from Streptomyces strains. Appl Microbiol Biotechnol 2018; 102:4435-4444. [PMID: 29574613 DOI: 10.1007/s00253-018-8908-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 02/28/2018] [Indexed: 02/05/2023]
Abstract
Cyclodipeptide synthases (CDPSs) comprise normally 200-300 amino acid residues and are mainly found in bacteria. They hijack aminoacyl-tRNAs from the ribosomal machinery for cyclodipeptide formation. In this study, nine new CDPS genes from eight Streptomyces strains were cloned into pET28a vector and expressed in Escherichia coli. Structural elucidation of the isolated products led to the identification of one cyclo-L-Trp-L-Leu, two cyclo-L-Trp-L-Pro, and three cyclo-L-Trp-L-Trp synthases. Other three CDPSs produce cyclo-L-Trp-L-Ala or cyclo-L-Trp-L-Tyr as the major cyclodipeptide. Total product yields of 46 to 211 mg/L E. coli culture were obtained. Our findings represent rare examples of CDPS family derived from actinobacteria that form various tryptophan-containing cyclodipeptides. Furthermore, this study highlights the potential of the microbial machinery for tryptophan-containing cyclodipeptide biosynthesis and provides valid experimental basis for further combination of these CDPS genes with other modification genes in synthetic biology.
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Affiliation(s)
- Jing Liu
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany
| | - Huili Yu
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037, Marburg, Germany.
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18
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Gondry M, Jacques IB, Thai R, Babin M, Canu N, Seguin J, Belin P, Pernodet JL, Moutiez M. A Comprehensive Overview of the Cyclodipeptide Synthase Family Enriched with the Characterization of 32 New Enzymes. Front Microbiol 2018; 9:46. [PMID: 29483897 PMCID: PMC5816076 DOI: 10.3389/fmicb.2018.00046] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/09/2018] [Indexed: 11/13/2022] Open
Abstract
Cyclodipeptide synthases (CDPSs) use as substrates two amino acids activated as aminoacyl-tRNAs to synthesize cyclodipeptides in secondary metabolites biosynthetic pathways. Since the first description of a CDPS in 2002, the number of putative CDPSs in databases has increased exponentially, reaching around 800 in June 2017. They are likely to be involved in numerous biosynthetic pathways but the diversity of their products is still under-explored. Here, we describe the activity of 32 new CDPSs, bringing the number of experimentally characterized CDPSs to about 100. We detect 16 new cyclodipeptides, one of which containing an arginine which has never been observed previously. This brings to 75 the number of cyclodipeptides formed by CDPSs out of the possible 210 natural ones. We also identify several consensus sequences related to the synthesis of a specific cyclodipeptide, improving the predictive model of CDPS specificity. The improved prediction method enables to propose the main product synthesized for about 80% of the CDPS sequences available in databases and opens the way for the deciphering of CDPS-dependent pathways. Analysis of phylum distribution and predicted activity for all CDPSs identified in databases shows that the experimentally characterized set is representative of the whole family. Our work also demonstrates that some cyclodipeptides, precursors of diketopiperazines with interesting pharmacological properties and previously described as being synthesized by fungal non-ribosomal peptide synthetases, can also be produced by CDPSs in bacteria.
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Affiliation(s)
- Muriel Gondry
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Isabelle B Jacques
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Robert Thai
- SIMOPRO, Institut Frédéric Joliot, CEA-Saclay, Gif-sur-Yvette, France
| | - Morgan Babin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nicolas Canu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jérôme Seguin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pascal Belin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Luc Pernodet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mireille Moutiez
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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19
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Convenient synthetic approach for tri- and tetraprenylated cyclodipeptides by consecutive enzymatic prenylations. Appl Microbiol Biotechnol 2018; 102:2671-2681. [PMID: 29372298 DOI: 10.1007/s00253-018-8761-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/02/2018] [Accepted: 01/04/2018] [Indexed: 12/16/2022]
Abstract
The prenyltransferases EchPT1 and EchPT2 from Aspergillus ruber are responsible for the consecutive prenylations of cyclo-L-Trp-L-Ala, leading to the formation of the triprenylated echinulin as the predominant product. In this study, we demonstrate that EchPT1 also accepts all stereoisomers of cyclo-Trp-Ala and cyclo-Trp-Pro and catalyses regiospecific reverse C2-prenylation at the indole nucleus. EchPT1 products were well accepted by EchPT2 for multiple consecutive prenylations, with conversion yields of 84 to 98% for six of the eight substrates. C2-, C5- and C7-triprenylated derivatives are identified as major enzyme products, with product yields of 40 to 86% in seven cases. High product yields of 25-36%, i.e. approximate 30% of the total enzyme products, were observed for tetraprenylated derivatives in the four reaction mixtures with one D- and one L-configured amino acid residues. To the best of our knowledge, enzymatic preparation of tetraprenylated cyclodipeptides with such high efficacy has not been reported prior to this study.
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20
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Brockmeyer K, Li SM. Mutations of Residues in Pocket P1 of a Cyclodipeptide Synthase Strongly Increase Product Formation. JOURNAL OF NATURAL PRODUCTS 2017; 80:2917-2922. [PMID: 29064250 DOI: 10.1021/acs.jnatprod.7b00430] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Expression of a cyclodipeptide synthase gene from Nocardiopsis prasina (CDPS-Np) in Escherichia coli resulted in the formation of cyclo-(l-Tyr-l-Tyr) (1) as the minor and cyclo-(l-Tyr-l-Phe) (2) as the major products. Site-directed mutagenesis revealed a strong influence on product accumulation of the amino acid residues in pocket P1. An 8-fold increase in product formation for 1 and 10-fold for 2 were detected in the double mutant T82V_Y196F compared with the wild type.
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Affiliation(s)
- Kirsten Brockmeyer
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg , Robert-Koch-Straße 4, 35037 Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg , Robert-Koch-Straße 4, 35037 Marburg, Germany
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21
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González O, Ortíz-Castro R, Díaz-Pérez C, Díaz-Pérez AL, Magaña-Dueñas V, López-Bucio J, Campos-García J. Non-ribosomal Peptide Synthases from Pseudomonas aeruginosa Play a Role in Cyclodipeptide Biosynthesis, Quorum-Sensing Regulation, and Root Development in a Plant Host. MICROBIAL ECOLOGY 2017; 73:616-629. [PMID: 27900439 DOI: 10.1007/s00248-016-0896-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 11/06/2016] [Indexed: 06/06/2023]
Abstract
Diverse molecules mediate cross-kingdom communication between bacteria and their eukaryotic partners and determine pathogenic or symbiotic relationships. N-acyl-L-homoserine lactone-dependent quorum-sensing signaling represses the biosynthesis of bacterial cyclodipeptides (CDPs) that act as auxin signal mimics in the host plant Arabidopsis thaliana. In this work, we performed bioinformatics, biochemical, and plant growth analyses to identify non-ribosomal peptide synthase (NRPS) proteins of Pseudomonas aeruginosa, which are involved in CDP synthesis. A reverse genetics strategy allowed the identification of the genes encoding putative multi-modular-NRPS (MM-NRPS). Mutations in these genes affected the synthesis of the CDPs cyclo(L-Pro-L-Val), cyclo(L-Pro-L-Leu), and cyclo(L-Pro-L-Tyr), while showing wild-type-like levels of virulence factors, such as violacein, elastase, and pyocyanin. When analyzing the bioactivity of purified, naturally produced CDPs, it was found that cyclo(L-Pro-L-Tyr) and cyclo(L-Pro-L-Val) were capable of antagonizing quorum-sensing-LasR (QS-LasR)-dependent signaling in a contrasting manner in the cell-free supernatants of the selected NRPS mutants, which showed QS induction. Using a bacteria-plant interaction system, we further show that the pvdJ, ambB, and pchE P. aeruginosa mutants failed to repress primary root growth, but improved root branching in A. thaliana seedlings. These results indicated that the CDP production in P. aeruginosa depended on the functional MM-NRPS, which influences quorum-sensing of bacteria and plays a role in root architecture remodeling.
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Affiliation(s)
- Omar González
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. B-3, Ciudad Universitaria, 58030, Morelia, Michoacán, México
| | - Randy Ortíz-Castro
- Laboratorio de Biología del Desarrollo Vegetal, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. A1´, Ciudad Universitaria, 58030, Morelia, Michoacán, México
- Instituto de Ecología A.C., Xalapa, Ver., México
| | - César Díaz-Pérez
- Depto. Ingeniería Agroindustrial, División de Ciencias de la Salud e Ingenierías, Universidad de Guanajuato, Salvatierra, Gto., México
| | - Alma L Díaz-Pérez
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. B-3, Ciudad Universitaria, 58030, Morelia, Michoacán, México
| | - Viridiana Magaña-Dueñas
- Laboratorio de Biología del Desarrollo Vegetal, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. A1´, Ciudad Universitaria, 58030, Morelia, Michoacán, México
| | - José López-Bucio
- Laboratorio de Biología del Desarrollo Vegetal, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. A1´, Ciudad Universitaria, 58030, Morelia, Michoacán, México
| | - Jesús Campos-García
- Laboratorio de Biotecnología Microbiana, Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Edif. B-3, Ciudad Universitaria, 58030, Morelia, Michoacán, México.
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22
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Moutiez M, Belin P, Gondry M. Aminoacyl-tRNA-Utilizing Enzymes in Natural Product Biosynthesis. Chem Rev 2017; 117:5578-5618. [DOI: 10.1021/acs.chemrev.6b00523] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Mireille Moutiez
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Pascal Belin
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
| | - Muriel Gondry
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France
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23
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Ulrich EC, van der Donk WA. Cameo appearances of aminoacyl-tRNA in natural product biosynthesis. Curr Opin Chem Biol 2016; 35:29-36. [PMID: 27599269 PMCID: PMC5161580 DOI: 10.1016/j.cbpa.2016.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/22/2016] [Indexed: 11/19/2022]
Abstract
The breadth of unprecedented enzymatic reactions performed during the formation of microbial natural products has continued to expand as new biosynthetic gene clusters are unearthed by genome mining. Enzymes that use aminoacyl-tRNA (aa-tRNA) outside of the translation machinery have been known for decades, and accounts of their use in natural product biosynthesis are just beginning to accumulate. This review will highlight the recent discoveries and advances in our mechanistic understanding of aa-tRNA-dependent enzymes that play key roles in the biosynthesis of a growing number of microbial natural products.
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Affiliation(s)
- Emily C Ulrich
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- Department of Chemistry and the Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA.
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