1
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Reed KB, Brooks SM, Wells J, Blake KJ, Zhao M, Placido K, d'Oelsnitz S, Trivedi A, Gadhiyar S, Alper HS. A modular and synthetic biosynthesis platform for de novo production of diverse halogenated tryptophan-derived molecules. Nat Commun 2024; 15:3188. [PMID: 38609402 PMCID: PMC11015028 DOI: 10.1038/s41467-024-47387-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 03/31/2024] [Indexed: 04/14/2024] Open
Abstract
Halogen-containing molecules are ubiquitous in modern society and present unique chemical possibilities. As a whole, de novo fermentation and synthetic pathway construction for these molecules remain relatively underexplored and could unlock molecules with exciting new applications in industries ranging from textiles to agrochemicals to pharmaceuticals. Here, we report a mix-and-match co-culture platform to de novo generate a large array of halogenated tryptophan derivatives in Escherichia coli from glucose. First, we engineer E. coli to produce between 300 and 700 mg/L of six different halogenated tryptophan precursors. Second, we harness the native promiscuity of multiple downstream enzymes to access unexplored regions of metabolism. Finally, through modular co-culture fermentations, we demonstrate a plug-and-play bioproduction platform, culminating in the generation of 26 distinct halogenated molecules produced de novo including precursors to prodrugs 4-chloro- and 4-bromo-kynurenine and new-to-nature halogenated beta carbolines.
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Affiliation(s)
- Kevin B Reed
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Sierra M Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Jordan Wells
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Kristin J Blake
- Mass Spectrometry Facility, Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Austin, TX, USA
| | - Minye Zhao
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Kira Placido
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Simon d'Oelsnitz
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, USA
| | - Adit Trivedi
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Shruti Gadhiyar
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, USA.
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2
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Li W, Liu S. A biomimetic approach to lycogarubin C, lynamicin D and related analogues. Org Biomol Chem 2024; 22:2558-2561. [PMID: 38450726 DOI: 10.1039/d4ob00033a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
An efficient and biomimetic synthetic approach to 3,4-diindolylpyrrole-2,5-dicarboxylate derivatives, including lycogarubin C, lynamicin D and related analogues, was discovered. The crucial transformation included the one-pot formation of two C-N bonds and one C-C bond to construct characteristic pyrrole rings.
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Affiliation(s)
- Wenxue Li
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China.
| | - Sheng Liu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang 550014, China.
- Natural Products Research Center of Guizhou Province, Guiyang, China
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3
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Dashti Y, Errington J. Chemistry and biology of specialized metabolites produced by Actinomadura. Nat Prod Rep 2024; 41:370-401. [PMID: 38099919 PMCID: PMC10951976 DOI: 10.1039/d3np00047h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Indexed: 03/21/2024]
Abstract
Covering: up to the end of 2022In recent years rare Actinobacteria have become increasingly recognised as a rich source of novel bioactive metabolites. Actinomadura are Gram-positive bacteria that occupy a wide range of ecological niches. This review highlights about 230 secondary metabolites produced by Actinomadura spp., reported until the end of 2022, including their bioactivities and selected biosynthetic pathways. Notably, the bioactive compounds produced by Actinomadura spp. demonstrate a wide range of activities, including antimicrobial, antitumor and anticoccidial effects, highlighting their potential in various fields.
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Affiliation(s)
- Yousef Dashti
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2015, Australia.
| | - Jeff Errington
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2015, Australia.
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4
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Bitzenhofer NL, Classen T, Jaeger KE, Loeschcke A. Biotransformation Of l-Tryptophan To Produce Arcyriaflavin A With Pseudomonas putida KT2440. Chembiochem 2023; 24:e202300576. [PMID: 37743253 DOI: 10.1002/cbic.202300576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 09/26/2023]
Abstract
Natural products such as indolocarbazoles are a valuable source of highly bioactive compounds with numerous potential applications in the pharmaceutical industry. Arcyriaflavin A, isolated from marine invertebrates and slime molds, is one representative of this group and acts as a cyclin D1-cyclin-dependent kinase 4 inhibitor. To date, access to this compound has mostly relied on multi-step total synthesis. In this study, biosynthetic access to arcyriaflavin A was explored using recombinant Pseudomonas putida KT2440 based on a previously generated producer strain. We used a Design of Experiment approach to analyze four key parameters, which led to the optimization of the bioprocess. By engineering the formation of outer membrane vesicles and using an adsorbent in the culture broth, we succeeded to increase the yield of arcyriaflavin A in the cell-free supernatant, resulting in a nearly eight-fold increase in the overall production titers. Finally, we managed to scale up the bioprocess leading to a final yield of 4.7 mg arcyriaflavin A product isolated from 1 L of bacterial culture. Thus, this study showcases an integrative approach to improve biotransformation and moreover also provides starting points for further optimization of indolocarbazole production in P. putida.
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Affiliation(s)
- Nora Lisa Bitzenhofer
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich, Stetternicher Forst, Building 15.8, 52426, Jülich, Germany
| | - Thomas Classen
- Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, Stetternicher Forst, Building 15.8, 52426, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich, Stetternicher Forst, Building 15.8, 52426, Jülich, Germany
- Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, Stetternicher Forst, Building 15.8, 52426, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich, Stetternicher Forst, Building 15.8, 52426, Jülich, Germany
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5
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Abstract
The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M Snodgrass
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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6
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Weihmann R, Kubicki S, Bitzenhofer NL, Domröse A, Bator I, Kirschen LM, Kofler F, Funk A, Tiso T, Blank LM, Jaeger KE, Drepper T, Thies S, Loeschcke A. The modular pYT vector series employed for chromosomal gene integration and expression to produce carbazoles and glycolipids in P. putida. FEMS MICROBES 2022; 4:xtac030. [PMID: 37333445 PMCID: PMC10117823 DOI: 10.1093/femsmc/xtac030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/03/2022] [Accepted: 12/16/2022] [Indexed: 10/22/2023] Open
Abstract
The expression of biosynthetic genes in bacterial hosts can enable access to high-value compounds, for which appropriate molecular genetic tools are essential. Therefore, we developed a toolbox of modular vectors, which facilitate chromosomal gene integration and expression in Pseudomonas putida KT2440. To this end, we designed an integrative sequence, allowing customisation regarding the modes of integration (random, at attTn7, or into the 16S rRNA gene), promoters, antibiotic resistance markers as well as fluorescent proteins and enzymes as transcription reporters. We thus established a toolbox of vectors carrying integrative sequences, designated as pYT series, of which we present 27 ready-to-use variants along with a set of strains equipped with unique 'landing pads' for directing a pYT interposon into one specific copy of the 16S rRNA gene. We used genes of the well-described violacein biosynthesis as reporter to showcase random Tn5-based chromosomal integration leading to constitutive expression and production of violacein and deoxyviolacein. Deoxyviolacein was likewise produced after gene integration into the 16S rRNA gene of rrn operons. Integration in the attTn7 site was used to characterise the suitability of different inducible promoters and successive strain development for the metabolically challenging production of mono-rhamnolipids. Finally, to establish arcyriaflavin A production in P. putida for the first time, we compared different integration and expression modes, revealing integration at attTn7 and expression with NagR/PnagAa to be most suitable. In summary, the new toolbox can be utilised for the rapid generation of various types of P. putida expression and production strains.
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Affiliation(s)
- Robin Weihmann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Sonja Kubicki
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Nora Lisa Bitzenhofer
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Andreas Domröse
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Isabel Bator
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Lisa-Marie Kirschen
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Franziska Kofler
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Aileen Funk
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Till Tiso
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Lars M Blank
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Bio-and Geosciences IBG 1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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7
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López-Francés A, del Corte X, Serna-Burgos Z, Martínez de Marigorta E, Palacios F, Vicario J. Exploring the Synthetic Potential of γ-Lactam Derivatives Obtained from a Multicomponent Reaction. Applications as Antiproliferative Agents. Molecules 2022; 27:molecules27113624. [PMID: 35684563 PMCID: PMC9182551 DOI: 10.3390/molecules27113624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 12/04/2022] Open
Abstract
A study on the reactivity of 3-amino α,β-unsaturated γ-lactam derivatives obtained from a multicomponent reaction is presented. Key features of the substrates are the presence of an endocyclic α,β-unsaturated amide moiety and an enamine functionality. Following different synthetic protocols, the functionalization at three different positions of the lactam core is achieved. In the presence of a soft base, under thermodynamic conditions, the functionalization at C-4 takes place where the substrates behave as enamines, while the use of a strong base, under kinetic conditions, leads to the formation of C-5-functionalized γ-lactams, in the presence of ethyl glyoxalate, through a highly diastereoselective vinylogous aldol reaction. Moreover, the nucleophilic addition of organometallic species allows the functionalization at C-3, through the imine tautomer, affording γ-lactams bearing tetrasubstituted stereocenters, where the substrates act as imine electrophiles. Taking into account the advantage of the presence of a chiral stereocenter in C-5 substituted γ-lactams, further diastereoselective transformations are also explored, leading to novel bicyclic substrates holding a fused γ and δ-lactam skeleton. Remarkably, an example of a highly stereoselective formal [3+3] cycloaddition reaction of chiral γ-lactam substrates is reported for the synthesis of 1,4-dihidropyridines, where a non-covalent attractive interaction of a carbonyl group with an electron-deficient arene seems to drive the stereoselectivity of the reaction to the exclusive formation of the cis isomer. In order to unambiguously determine the substitution pattern resulting from the diverse reactions, an extensive characterization of the substrates is detailed through 2D NMR and/or X-ray experiments. Likewise, applications of the substrates as antiproliferative agents against lung and ovarian cancer cells are also described.
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Affiliation(s)
| | | | | | | | - Francisco Palacios
- Correspondence: (F.P.); (J.V.); Tel.: +34-945013103 (F.P.); +34-945013087 (J.V.)
| | - Javier Vicario
- Correspondence: (F.P.); (J.V.); Tel.: +34-945013103 (F.P.); +34-945013087 (J.V.)
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8
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del Corte X, López-Francés A, Villate-Beitia I, Sainz-Ramos M, Martínez de Marigorta E, Palacios F, Alonso C, de los Santos JM, Pedraz JL, Vicario J. Multicomponent Synthesis of Unsaturated γ-Lactam Derivatives. Applications as Antiproliferative Agents through the Bioisosterism Approach: Carbonyl vs. Phosphoryl Group. Pharmaceuticals (Basel) 2022; 15:ph15050511. [PMID: 35631337 PMCID: PMC9144317 DOI: 10.3390/ph15050511] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 12/16/2022] Open
Abstract
We report efficient synthetic methodologies for the preparation of 3-amino and 3-hydroxy 3-pyrrolin-2-ones (unsaturated γ-lactams) through a multicomponent reaction of amines, aldehydes and acetylene or pyruvate derivatives. The densely substituted γ-lactam substrates show in vitro cytotoxicity, inhibiting the growth of the carcinoma human tumor cell lines RKO (human colon epithelial carcinoma), SKOV3 (human ovarian carcinoma) and A549 (carcinomic human alveolar basal epithelial cell). In view of the possibilities for the diversity of the substituents that offer a multicomponent, synthetic methodology, an extensive structure–activity profile is presented. In addition, the bioisosteric replacement of the flat ester group by a tetrahedral phosphonate or phosphine oxide moiety in γ-lactam substrates leads to increased growth inhibition activity. Cell morphology analysis and flow cytometry assays indicate that the main pathway by which our compounds induce cytotoxicity is based on the activation of the intracellular apoptotic mechanism.
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Affiliation(s)
- Xabier del Corte
- Department of Organic Chemistry I, Faculty of Pharmacy, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (X.d.C.); (A.L.-F.); (E.M.d.M.); (F.P.); (C.A.); (J.M.d.l.S.)
| | - Adrián López-Francés
- Department of Organic Chemistry I, Faculty of Pharmacy, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (X.d.C.); (A.L.-F.); (E.M.d.M.); (F.P.); (C.A.); (J.M.d.l.S.)
| | - Ilia Villate-Beitia
- NanoBioCel Group, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (I.V.-B.); (M.S.-R.)
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Research Group, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
| | - Myriam Sainz-Ramos
- NanoBioCel Group, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (I.V.-B.); (M.S.-R.)
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Research Group, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
| | - Edorta Martínez de Marigorta
- Department of Organic Chemistry I, Faculty of Pharmacy, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (X.d.C.); (A.L.-F.); (E.M.d.M.); (F.P.); (C.A.); (J.M.d.l.S.)
| | - Francisco Palacios
- Department of Organic Chemistry I, Faculty of Pharmacy, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (X.d.C.); (A.L.-F.); (E.M.d.M.); (F.P.); (C.A.); (J.M.d.l.S.)
| | - Concepción Alonso
- Department of Organic Chemistry I, Faculty of Pharmacy, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (X.d.C.); (A.L.-F.); (E.M.d.M.); (F.P.); (C.A.); (J.M.d.l.S.)
| | - Jesús M. de los Santos
- Department of Organic Chemistry I, Faculty of Pharmacy, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (X.d.C.); (A.L.-F.); (E.M.d.M.); (F.P.); (C.A.); (J.M.d.l.S.)
| | - José Luis Pedraz
- NanoBioCel Group, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain; (I.V.-B.); (M.S.-R.)
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
- Bioaraba, NanoBioCel Research Group, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), 01006 Vitoria-Gasteiz, Spain
- Correspondence: (J.L.P.); (J.V.)
| | - Javier Vicario
- Department of Organic Chemistry I, Faculty of Pharmacy, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (X.d.C.); (A.L.-F.); (E.M.d.M.); (F.P.); (C.A.); (J.M.d.l.S.)
- Correspondence: (J.L.P.); (J.V.)
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9
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Cros A, Alfaro-Espinoza G, De Maria A, Wirth NT, Nikel PI. Synthetic metabolism for biohalogenation. Curr Opin Biotechnol 2021; 74:180-193. [PMID: 34954625 DOI: 10.1016/j.copbio.2021.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 12/19/2022]
Abstract
The pressing need for novel bioproduction approaches faces a limitation in the number and type of molecules accessed through synthetic biology. Halogenation is widely used for tuning physicochemical properties of molecules and polymers, but traditional halogenation chemistry often lacks specificity and generates harmful by-products. Here, we pose that deploying synthetic metabolism tailored for biohalogenation represents an unique opportunity towards economically attractive and environmentally friendly organohalide production. On this background, we discuss growth-coupled selection of functional metabolic modules that harness the rich repertoire of biosynthetic and biodegradation capabilities of environmental bacteria for in vivo biohalogenation. By rationally combining these approaches, the chemical landscape of living cells can accommodate bioproduction of added-value organohalides which, as of today, are obtained by traditional chemistry.
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Affiliation(s)
- Antonin Cros
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Gabriela Alfaro-Espinoza
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; Division Biodeterioration and Reference Organisms, Federal Institute for Materials Research and Testing (BAM), 12205 Berlin, Germany
| | - Alberto De Maria
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
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10
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Lai HE, Obled AMC, Chee SM, Morgan RM, Lynch R, Sharma SV, Moore SJ, Polizzi KM, Goss RJM, Freemont PS. GenoChemetic Strategy for Derivatization of the Violacein Natural Product Scaffold. ACS Chem Biol 2021; 16:2116-2123. [PMID: 34648268 PMCID: PMC8609527 DOI: 10.1021/acschembio.1c00483] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Natural products and their analogues are often challenging to synthesize due to their complex scaffolds and embedded functional groups. Solely relying on engineering the biosynthesis of natural products may lead to limited compound diversity. Integrating synthetic biology with synthetic chemistry allows rapid access to much more diverse portfolios of xenobiotic compounds, which may accelerate the discovery of new therapeutics. As a proof-of-concept, by supplementing an Escherichia coli strain expressing the violacein biosynthesis pathway with 5-bromo-tryptophan in vitro or tryptophan 7-halogenase RebH in vivo, six halogenated analogues of violacein or deoxyviolacein were generated, demonstrating the promiscuity of the violacein biosynthesis pathway. Furthermore, 20 new derivatives were generated from 5-brominated violacein analogues via the Suzuki-Miyaura cross-coupling reaction directly using the crude extract without prior purification. Herein we demonstrate a flexible and rapid approach to access a diverse chemical space that can be applied to a wide range of natural product scaffolds.
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Affiliation(s)
- Hung-En Lai
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
| | - Alan M. C. Obled
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Soo Mei Chee
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
- London Biofoundry, Imperial College Translation & Innovation Hub, London W12 0BZ, U.K
| | - Rhodri M. Morgan
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Rosemary Lynch
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Sunil V. Sharma
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Simon J. Moore
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
| | - Karen M. Polizzi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Rebecca J. M. Goss
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, U.K
| | - Paul S. Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, U.K
- London Biofoundry, Imperial College Translation & Innovation Hub, London W12 0BZ, U.K
- UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, U.K
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11
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Corte X, López‐Francés A, Marigorta EM, Palacios F, Vicario J. Stereo‐ and Regioselective [3+3] Annulation Reaction Catalyzed by Ytterbium: Synthesis of Bicyclic 1,4‐Dihydropyridines. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202100785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xabier Corte
- Departamento de Química Orgánica I Centro de Investigación y Estudios Avanzados “Lucio Lascaray” Facultad de Farmacia Universidad del País Vasco, UPV/EHU Paseo de la Universidad 7 01006 Vitoria-Gasteiz Spain
| | - Adrián López‐Francés
- Departamento de Química Orgánica I Centro de Investigación y Estudios Avanzados “Lucio Lascaray” Facultad de Farmacia Universidad del País Vasco, UPV/EHU Paseo de la Universidad 7 01006 Vitoria-Gasteiz Spain
| | - Edorta Martínez Marigorta
- Departamento de Química Orgánica I Centro de Investigación y Estudios Avanzados “Lucio Lascaray” Facultad de Farmacia Universidad del País Vasco, UPV/EHU Paseo de la Universidad 7 01006 Vitoria-Gasteiz Spain
| | - Francisco Palacios
- Departamento de Química Orgánica I Centro de Investigación y Estudios Avanzados “Lucio Lascaray” Facultad de Farmacia Universidad del País Vasco, UPV/EHU Paseo de la Universidad 7 01006 Vitoria-Gasteiz Spain
| | - Javier Vicario
- Departamento de Química Orgánica I Centro de Investigación y Estudios Avanzados “Lucio Lascaray” Facultad de Farmacia Universidad del País Vasco, UPV/EHU Paseo de la Universidad 7 01006 Vitoria-Gasteiz Spain
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12
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Crowe C, Molyneux S, Sharma SV, Zhang Y, Gkotsi DS, Connaris H, Goss RJM. Halogenases: a palette of emerging opportunities for synthetic biology-synthetic chemistry and C-H functionalisation. Chem Soc Rev 2021; 50:9443-9481. [PMID: 34368824 PMCID: PMC8407142 DOI: 10.1039/d0cs01551b] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Indexed: 12/14/2022]
Abstract
The enzymatic generation of carbon-halogen bonds is a powerful strategy used by both nature and synthetic chemists to tune the bioactivity, bioavailability and reactivity of compounds, opening up the opportunity for selective C-H functionalisation. Genes encoding halogenase enzymes have recently been shown to transcend all kingdoms of life. These enzymes install halogen atoms into aromatic and less activated aliphatic substrates, achieving selectivities that are often challenging to accomplish using synthetic methodologies. Significant advances in both halogenase discovery and engineering have provided a toolbox of enzymes, enabling the ready use of these catalysts in biotransformations, synthetic biology, and in combination with chemical catalysis to enable late stage C-H functionalisation. With a focus on substrate scope, this review outlines the mechanisms employed by the major classes of halogenases, while in parallel, it highlights key advances in the utilisation of the combination of enzymatic halogenation and chemical catalysis for C-H activation and diversification.
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Affiliation(s)
- Charlotte Crowe
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Samuel Molyneux
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Sunil V. Sharma
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Ying Zhang
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Danai S. Gkotsi
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Helen Connaris
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
| | - Rebecca J. M. Goss
- School of Chemistry, and BSRC, University of St Andrews, North HaughSt Andrews KY16 9STUK
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13
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A Multicomponent Protocol for the Synthesis of Highly Functionalized γ-Lactam Derivatives and Their Applications as Antiproliferative Agents. Pharmaceuticals (Basel) 2021; 14:ph14080782. [PMID: 34451879 PMCID: PMC8400033 DOI: 10.3390/ph14080782] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/30/2021] [Accepted: 08/05/2021] [Indexed: 01/13/2023] Open
Abstract
An efficient synthetic methodology for the preparation of 3-amino 1,5-dihydro-2H-pyrrol-2-ones through a multicomponent reaction of amines, aldehydes, and pyruvate derivatives is reported. In addition, the densely substituted lactam substrates show in vitro cytotoxicity, inhibiting the growth of carcinoma human tumor cell lines HEK293 (human embryonic kidney), MCF7 (human breast adenocarcinoma), HTB81 (human prostate carcinoma), HeLa (human epithelioid cervix carcinoma), RKO (human colon epithelial carcinoma), SKOV3 (human ovarian carcinoma), and A549 (carcinomic human alveolar basal epithelial cell). Given the possibilities in the diversity of the substituents that offer the multicomponent synthetic methodology, an extensive structure-activity profile is presented. In addition, both enantiomers of phosphonate-derived γ-lactam have been synthesized and isolated and a study of the cytotoxic activity of the racemic substrate vs. its two enantiomers is also presented. Cell morphology analysis and flow cytometry assays indicate that the main pathway by which our compounds induce cytotoxicity is based on the activation of the intracellular apoptotic mechanism.
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14
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Song X, Lv J, Cao Z, Huang H, Chen G, Awakawa T, Hu D, Gao H, Abe I, Yao X. Extensive expansion of the chemical diversity of fusidane-type antibiotics using a stochastic combinational strategy. Acta Pharm Sin B 2021; 11:1676-1685. [PMID: 34221876 PMCID: PMC8245791 DOI: 10.1016/j.apsb.2020.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/11/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022] Open
Abstract
Fusidane-type antibiotics, represented by helvolic acid, fusidic acid and cephalosporin P1, are fungi-derived antimicrobials with little cross-resistance to commonly used antibiotics. Generation of new fusidane-type derivatives is therefore of great value, but this is hindered by available approaches. Here, we developed a stochastic combinational strategy by random assembly of all the post-tailoring genes derived from helvolic acid, fusidic acid, and cephalosporin P1 biosynthetic pathways in a strain that produces their common intermediate. Among a total of 27 gene combinations, 24 combinations produce expected products and afford 58 fusidane-type analogues, of which 54 are new compounds. Moreover, random gene combination can induce unexpected activity of some post-tailoring enzymes, leading to a further increase in chemical diversity. These newly generated derivatives provide new insights into the structure‒activity relationship of fusidane-type antibiotics. The stochastic combinational strategy established in this study proves to be a powerful approach for expanding structural diversity of natural products.
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15
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Goel B, Tripathi N, Mukherjee D, Jain SK. Glycorandomization: A promising diversification strategy for the drug development. Eur J Med Chem 2021; 213:113156. [PMID: 33460832 DOI: 10.1016/j.ejmech.2021.113156] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/04/2021] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
Glycorandomization is a natural product derivatization strategy in which different sugar moieties are linked to the aglycone part of the naturally existing glycosides to create glycorandomized libraries. Sugars attached to the natural products are responsible for affecting their solubility, mechanism of action, target recognition, and toxicity and thus, by changing the sugar part, these properties could be modified. Glycorandomization can be done via two approaches (i) a synthetic approach known as neoglycorandomization, and (ii) chemoenzymatic approach including in-vitro and in-vivo glycorandomization. Glycorandomization can be a promising technology for the drug discovery that has proved its potential to improve pharmacokinetic (solubility) and pharmacodynamic profile (mechanism of action, toxicity, and target recognition) of the parent compounds. The substrate flexibility of glycosyltransferases and other enzymes towards sugars and/or aglycone substrates has made this technique versatile. Further, the enzymes can be altered by genetic engineering to generate glycorandomized libraries of diverse natural product scaffolds. This technique has the potential to produce new compounds that can be helpful to the mankind by treating the threatening disease states. This review covers the different strategies for glycorandomization as a tool in drug discovery and development. The fundamentals of glycorandomization, different types, and further development of differentially glycorandomized libraries of natural products and small molecule based drugs have been discussed.
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Affiliation(s)
- Bharat Goel
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, Uttar Pradesh, India
| | - Nancy Tripathi
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, Uttar Pradesh, India
| | - Debaraj Mukherjee
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180001, India
| | - Shreyans K Jain
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, Uttar Pradesh, India.
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16
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Menon BRK, Richmond D, Menon N. Halogenases for biosynthetic pathway engineering: Toward new routes to naturals and non-naturals. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2020. [DOI: 10.1080/01614940.2020.1823788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Binuraj R. K. Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Daniel Richmond
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
| | - Navya Menon
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, UK
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17
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Flavin Adenine Dinucleotide-Dependent Halogenase XanH and Engineering of Multifunctional Fusion Halogenases. Appl Environ Microbiol 2020; 86:AEM.01225-20. [PMID: 32651204 DOI: 10.1128/aem.01225-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022] Open
Abstract
Xantholipin (compound 1), a polycyclic xanthone antibiotic, exhibited strong antibacterial activities and showed potent cytotoxicity. The biosynthetic gene cluster of compound 1 has been identified in our previous work, and the construction of xanthone nucleus has been well demonstrated. However, limited information of the halogenation involved in compound 1 biosynthesis is available. In this study, based on the genetic manipulation and biochemical assay, we characterized XanH as an indispensable flavin adenine dinucleotide (FAD)-dependent halogenase (FDH) for the biosynthesis of compound 1. XanH was found to be a bifunctional protein capable of flavin reduction and chlorination and exclusively used the NADH. However, the reduced flavin could not be fully and effectively utilized, and the presence of an extra flavin reductase (FDR) and chemical-reducing agent could promote the halogenation. XanH accepted its natural free-standing substrate with angular fused polycyclic aromatic systems. Meanwhile, it exhibited moderate halogenation activity and possessed high substrate specificity. The requirement of extra FDR for higher halogenation activity is tedious for future engineering. To facilitate efforts in engineering XanH derivative proteins, we constructed the self-sufficient FDR-XanH fusion proteins. The fusion protein E1 with comparable activities to that of XanH could be used as a good alternative for future protein engineering. Taken together, these findings reported here not only improve the understanding of polycyclic xanthones biosynthesis but also expand the substrate scope of FDH and pave the way for future engineering of biocatalysts for new active substance synthesis.IMPORTANCE Halogenation is important in medicinal chemistry and plays an essential role in the biosynthesis of active secondary metabolites. Halogenases have evolved to catalyze reactions with high efficiency and selectivity, and engineering efforts have been made to engage the selective reactivity in natural product biosynthesis. The enzymatic halogenations are an environmentally friendly approach with high regio- and stereoselectivity, which make it a potential complement to organic synthesis. FDHs constitute one of the most extensively elucidated class of halogenases; however, the inventory awaits to be expanded for biotechnology applications and for the generation of halogenated natural product analogues. In this study, XanH was found to reduce flavin and halogenated the freely diffusing natural substrate with an angular fused hexacyclic scaffold, findings which were different from those for the exclusively studied FDHs. Moreover, the FDR-XanH fusion protein E1 with comparable reactivity to that of XanH serves as a successful example of genetic fusions and sets an important stage for future protein engineering.
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18
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Chilczuk T, Schäberle TF, Vahdati S, Mettal U, El Omari M, Enke H, Wiese M, König GM, Niedermeyer THJ. Halogenation-Guided Chemical Screening Provides Insight into Tjipanazole Biosynthesis by the Cyanobacterium Fischerella ambigua. Chembiochem 2020; 21:2170-2177. [PMID: 32182403 PMCID: PMC7497240 DOI: 10.1002/cbic.202000025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/21/2020] [Indexed: 12/19/2022]
Abstract
Halogenated natural products (HNPs) show a wide range of interesting biological activities. Chemistry-guided screening with a software tool dedicated to identifying halogenated compounds in HPLC-MS data indicated the presence of several uncharacterised HNPs in an extract of the cyanobacterium Fischerella ambigua (Näg.) Gomont 108b. Three new natural products, tjipanazoles K, L, and M, were isolated from this strain together with the known tjipanazoles D and I. Taking into account the structures of all tjipanazole derivatives detected in this strain, reanalysis of the tjipanazole biosynthetic gene cluster allowed us to propose a biosynthetic pathway for the tjipanazoles. As the isolated tjipanazoles show structural similarity to arcyriaflavin A, an inhibitor of the clinically relevant multidrug-transporter ABCG2 overexpressed by different cancer cell lines, the isolated compounds were tested for ABCG2 inhibitory activity. Only tjipanazole K showed appreciable transporter inhibition, whereas the compounds lacking the pyrrolo[3,4-c] ring or featuring additional chloro substituents were found to be much less active.
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Affiliation(s)
- Tomasz Chilczuk
- Department of Pharmaceutical Biology/Pharmacognosy Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Till F Schäberle
- Institute for Insect Biotechnology, Justus-Liebig-University Gießen, Heinrich-Buff-Ring 26-32, 35392, Gießen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Winchesterstrasse 2, 35394, Gießen, Germany
| | - Sahel Vahdati
- Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Ute Mettal
- Institute for Insect Biotechnology, Justus-Liebig-University Gießen, Heinrich-Buff-Ring 26-32, 35392, Gießen, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Winchesterstrasse 2, 35394, Gießen, Germany
| | - Mustafa El Omari
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Heike Enke
- Cyano Biotech GmbH, Magnusstraße 11, 12489, Berlin, Germany
| | - Michael Wiese
- Department of Pharmaceutical and Cell Biological Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Gabriele M König
- Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Timo H J Niedermeyer
- Department of Pharmaceutical Biology/Pharmacognosy Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany
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19
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Zenkov RG, Ektova LV, Vlasova OА, Belitskiy GА, Yakubovskaya MG, Kirsanov KI. Indolo[2,3-a]carbazoles: diversity, biological properties, application in antitumor therapy. Chem Heterocycl Compd (N Y) 2020. [DOI: 10.1007/s10593-020-02714-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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20
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Yang CL, Zhang B, Xue WW, Li W, Xu ZF, Shi J, Shen Y, Jiao RH, Tan RX, Ge HM. Discovery, Biosynthesis, and Heterologous Production of Loonamycin, a Potent Anticancer Indolocarbazole Alkaloid. Org Lett 2020; 22:4665-4669. [DOI: 10.1021/acs.orglett.0c01456] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Cheng Long Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Bo Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wen Wen Xue
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wu Li
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zi Fei Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jing Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yan Shen
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Rui Hua Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ren Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Hui Ming Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Life Sciences, Nanjing University, Nanjing 210023, China
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21
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A Co-Culturing Approach Enables Discovery and Biosynthesis of a Bioactive Indole Alkaloid Metabolite. Molecules 2020; 25:molecules25020256. [PMID: 31936318 PMCID: PMC7024260 DOI: 10.3390/molecules25020256] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/26/2019] [Accepted: 01/03/2020] [Indexed: 12/19/2022] Open
Abstract
Whole-genome sequence data of the genus Streptomyces have shown a far greater chemical diversity of metabolites than what have been discovered under typical laboratory fermentation conditions. In our previous natural product discovery efforts on Streptomyces sp. MA37, a bacterium isolated from the rhizosphere soil sample in Legon, Ghana, we discovered a handful of specialised metabolites from this talented strain. However, analysis of the draft genome of MA37 suggested that most of the encoded biosynthetic gene clusters (BGCs) remained cryptic or silent, and only a small fraction of BGCs for the production of specialised metabolites were expressed when cultured in our laboratory conditions. In order to induce the expression of the seemingly silent BGCs, we have carried out a co-culture experiment by growing the MA37 strain with the Gram-negative bacterium Pseudomonas sp. in a co-culture chamber that allows co-fermentation of two microorganisms with no direct contact but allows exchange of nutrients, metabolites, and other chemical cues. This co-culture approach led to the upregulation of several metabolites that were not previously observed in the monocultures of each strain. Moreover, the co-culture induced the expression of the cryptic indole alkaloid BGC in MA37 and led to the characterization of the known indolocarbazole alkaloid, BE-13793C 1. Neither bacterium produced compound 1 when cultured alone. The structure of 1 was elucidated by Nuclear Magnetic Resonance (NMR), mass spectrometry analyses and comparison of experimental with literature data. A putative biosynthetic pathway of 1 was proposed. Furthermore, BE-13793C 1 showed strong anti-proliferative activity against HT-29 (ATCC HTB-38) cells but no toxic effect to normal lung (ATCC CCL-171) cells. To the best of our knowledge, this is the first report for the activity of 1 against HT-29. No significant antimicrobial and anti-trypanosomal activities for 1 were observed. This research provides a solid foundation for the fact that a co-culture approach paves the way for increasing the chemical diversity of strain MA37. Further characterization of other upregulated metabolites in this strain is currently ongoing in our laboratory.
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22
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Fisher B, Snodgrass HM, Jones KA, Andorfer MC, Lewis JC. Site-Selective C-H Halogenation Using Flavin-Dependent Halogenases Identified via Family-Wide Activity Profiling. ACS CENTRAL SCIENCE 2019; 5:1844-1856. [PMID: 31807686 PMCID: PMC6891866 DOI: 10.1021/acscentsci.9b00835] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Indexed: 05/19/2023]
Abstract
Enzymes are powerful catalysts for site-selective C-H bond functionalization. Identifying suitable enzymes for this task and for biocatalysis in general remains challenging, however, due to the fundamental difficulty of predicting catalytic activity from sequence information. In this study, family-wide activity profiling was used to obtain sequence-function information on flavin-dependent halogenases (FDHs). This broad survey provided a number of insights into FDH activity, including halide specificity and substrate preference, that were not apparent from the more focused studies reported to date. Regions of FDH sequence space that are most likely to contain enzymes suitable for halogenating small-molecule substrates were also identified. FDHs with novel substrate scope and complementary regioselectivity on large, three-dimensionally complex compounds were characterized and used for preparative-scale late-stage C-H functionalization. In many cases, these enzymes provide activities that required several rounds of directed evolution to accomplish in previous efforts, highlighting that this approach can achieve significant time savings for biocatalyst identification and provide advanced starting points for further evolution.
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Affiliation(s)
- Brian
F. Fisher
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M. Snodgrass
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krysten A. Jones
- Department
of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Mary C. Andorfer
- Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jared C. Lewis
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- E-mail:
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23
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Cartuche L, Reyes-Batlle M, Sifaoui I, Arberas-Jiménez I, Piñero JE, Fernández JJ, Lorenzo-Morales J, Díaz-Marrero AR. Antiamoebic Activities of Indolocarbazole Metabolites Isolated from Streptomyces sanyensis Cultures. Mar Drugs 2019; 17:md17100588. [PMID: 31627366 PMCID: PMC6836125 DOI: 10.3390/md17100588] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 12/19/2022] Open
Abstract
Indolocarbazoles are a family of natural alkaloids characterized by their potent protein kinase and topoisomerase I inhibitory activity. Among them, staurosporine (1) has exhibited promising inhibitory activity against parasites. Based on new insights on the activity and mechanism of action of STS in Acanthamoeba parasites, this work reports the isolation, identification, and the anti-Acanthamoeba activity of the minor metabolites 7-oxostaurosporine (2), 4′-demethylamino-4′-oxostaurosporine (3), and streptocarbazole B (4), isolated from cultures of the mangrove strain Streptomyces sanyensis. A clear correlation between the antiparasitic activities and the structural elements and conformations of the indolocarbazoles 1–4 was observed. Also, the study reveals that 7-oxostaurosporine (2) affects membrane permeability and causes mitochondrial damages on trophozoites of A. castellanii Neff.
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Affiliation(s)
- Luis Cartuche
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Tenerife, Spain.
- Departamento de Química y Ciencias Exactas, Sección Química Básica y Aplicada, Universidad Técnica Particular de Loja (UTPL), San Cayetano alto s/n, A.P. 1101608 Loja, Ecuador.
| | - María Reyes-Batlle
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Islas Canarias, Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain.
| | - Ines Sifaoui
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Islas Canarias, Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain.
| | - Iñigo Arberas-Jiménez
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Islas Canarias, Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain.
| | - José E Piñero
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Islas Canarias, Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain.
| | - José J Fernández
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Tenerife, Spain.
- Departamento de Química Orgánica, Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez, 2, 38206 La Laguna, Tenerife, Spain.
| | - Jacob Lorenzo-Morales
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Islas Canarias, Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38206 La Laguna, Tenerife, Spain.
| | - Ana R Díaz-Marrero
- Instituto Universitario de Bio-Orgánica Antonio González (IUBO AG), Centro de Investigaciones Biomédicas de Canarias (CIBICAN), Universidad de La Laguna (ULL), Avda. Astrofísico F. Sánchez 2, 38206 La Laguna, Tenerife, Spain.
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Myronovskyi M, Luzhetskyy A. Heterologous production of small molecules in the optimized Streptomyces hosts. Nat Prod Rep 2019; 36:1281-1294. [PMID: 31453623 DOI: 10.1039/c9np00023b] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Time span of literature covered: 2010-2018The genome mining of streptomycetes has revealed their great biosynthetic potential to produce novel natural products. One of the most promising exploitation routes of this biosynthetic potential is the refactoring and heterologous expression of corresponding biosynthetic gene clusters in a panel of specifically selected and optimized chassis strains. This article will review selected recent reports on heterologous production of natural products in streptomycetes. In the first part, the importance of heterologous production for drug discovery will be discussed. In the second part, the review will discuss recently developed genetic control elements (such as promoters, ribosome binding sites, terminators) and their application to achieve successful heterologous expression of biosynthetic gene clusters. Finally, the most widely used Streptomyces hosts for heterologous expression of biosynthetic gene clusters will be compared in detail. The article will be of interest to natural product chemists, molecular biologists, pharmacists and all individuals working in the natural products drug discovery field.
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Affiliation(s)
| | - Andriy Luzhetskyy
- Saarland University, Department Pharmacy, Saarbrücken, Germany and Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany.
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25
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Pommerehne K, Walisko J, Ebersbach A, Krull R. The antitumor antibiotic rebeccamycin-challenges and advanced approaches in production processes. Appl Microbiol Biotechnol 2019; 103:3627-3636. [PMID: 30888461 DOI: 10.1007/s00253-019-09741-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 10/27/2022]
Abstract
Rebeccamycin is an antibiotic and antitumor substance isolated from the filamentous bacterium Lentzea aerocolonigenes. After its discovery, investigations of rebeccamycin focused on elucidating its structure, biological activity, and biosynthetic pathway. For potential medical application, a sufficient drug supply has to be ensured, meaning that the production process of rebeccamycin plays a major role. In addition to the natural production of rebeccamycin in L. aerocolonigenes, where the complex cell morphology is an important factor for a sufficient production, rebeccamycin can also be heterologously produced or chemically synthesized. Each of these production processes has its own challenges, and first approaches to production often lead to low final product concentrations, which is why process optimizations are performed. This review provides an overview of the production of rebeccamycin and the different approaches used for rebeccamycin formation including process optimizations.
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Affiliation(s)
- Kathrin Pommerehne
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany.,Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Franz-Liszt-Straße 35a, 38106, Braunschweig, Germany
| | - Jana Walisko
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Anna Ebersbach
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany
| | - Rainer Krull
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Rebenring 56, 38106, Braunschweig, Germany. .,Center of Pharmaceutical Engineering, Technische Universität Braunschweig, Franz-Liszt-Straße 35a, 38106, Braunschweig, Germany.
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26
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Nepal KK, Wang G. Streptomycetes: Surrogate hosts for the genetic manipulation of biosynthetic gene clusters and production of natural products. Biotechnol Adv 2019; 37:1-20. [PMID: 30312648 PMCID: PMC6343487 DOI: 10.1016/j.biotechadv.2018.10.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/04/2018] [Accepted: 10/05/2018] [Indexed: 12/23/2022]
Abstract
Due to the worldwide prevalence of multidrug-resistant pathogens and high incidence of diseases such as cancer, there is an urgent need for the discovery and development of new drugs. Nearly half of the FDA-approved drugs are derived from natural products that are produced by living organisms, mainly bacteria, fungi, and plants. Commercial development is often limited by the low yield of the desired compounds expressed by the native producers. In addition, recent advances in whole genome sequencing and bioinformatics have revealed an abundance of cryptic biosynthetic gene clusters within microbial genomes. Genetic manipulation of clusters in the native host is commonly used to awaken poorly expressed or silent gene clusters, however, the lack of feasible genetic manipulation systems in many strains often hinders our ability to engineer the native producers. The transfer of gene clusters into heterologous hosts for expression of partial or entire biosynthetic pathways is an approach that can be used to overcome this limitation. Heterologous expression also facilitates the chimeric fusion of different biosynthetic pathways, leading to the generation of "unnatural" natural products. The genus Streptomyces is especially known to be a prolific source of drugs/antibiotics, its members are often used as heterologous expression hosts. In this review, we summarize recent applications of Streptomyces species, S. coelicolor, S. lividans, S. albus, S. venezuelae and S. avermitilis, as heterologous expression systems.
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Affiliation(s)
- Keshav K Nepal
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 U.S. 1 North, Fort Pierce, FL 34946, USA
| | - Guojun Wang
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 U.S. 1 North, Fort Pierce, FL 34946, USA.
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27
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Janosik T, Rannug A, Rannug U, Wahlström N, Slätt J, Bergman J. Chemistry and Properties of Indolocarbazoles. Chem Rev 2018; 118:9058-9128. [PMID: 30191712 DOI: 10.1021/acs.chemrev.8b00186] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The indolocarbazoles are an important class of nitrogen heterocycles which has evolved significantly in recent years, with numerous studies focusing on their diverse biological effects, or targeting new materials with potential applications in organic electronics. This review aims at providing a broad survey of the chemistry and properties of indolocarbazoles from an interdisciplinary point of view, with particular emphasis on practical synthetic aspects, as well as certain topics which have not been previously accounted for in detail, such as the occurrence, formation, biological activities, and metabolism of indolo[3,2- b]carbazoles. The literature of the past decade forms the basis of the text, which is further supplemented with older key references.
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Affiliation(s)
- Tomasz Janosik
- Research Institutes of Sweden , Bioscience and Materials, RISE Surface, Process and Formulation , SE-151 36 Södertälje , Sweden
| | - Agneta Rannug
- Institute of Environmental Medicine , Karolinska Institutet , SE-171 77 Stockholm , Sweden
| | - Ulf Rannug
- Department of Molecular Biosciences, The Wenner-Gren Institute , Stockholm University , SE-106 91 Stockholm , Sweden
| | | | - Johnny Slätt
- Department of Chemistry, Applied Physical Chemistry , KTH Royal Institute of Technology , SE-100 44 Stockholm , Sweden
| | - Jan Bergman
- Karolinska Institutet , Department of Biosciences and Nutrition , SE-141 83 Huddinge , Sweden
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28
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Xiao F, Li H, Xu M, Li T, Wang J, Sun C, Hong K, Li W. Staurosporine Derivatives Generated by Pathway Engineering in a Heterologous Host and Their Cytotoxic Selectivity. JOURNAL OF NATURAL PRODUCTS 2018; 81:1745-1751. [PMID: 30106291 DOI: 10.1021/acs.jnatprod.8b00103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Two new staurosporine derivatives, staurosporines M1 and M2 (4 and 5), in addition to five previously reported metabolites (1-3, 6, and 7), were generated by the heterologous expression of engineered spc gene clusters in Streptomyces coelicolor M1146. The structures of these derivatives were determined by a combination of spectroscopic methods and CD measurement. Compounds 1, 2, 4, and 5 showed effective activities against three tumor cell lines (HCT-116, K562, and Huh 7.5), and 3 was active against HCT-116 and K562 cells. In addition, compounds 3 and 5 showed undetectable toxicity up to 100 μM toward the normal hepatic cell line LO2. Based on the IC50 values, their structure and activity relationships are discussed.
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Affiliation(s)
- Fei Xiao
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , People's Republic of China
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , People's Republic of China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology , Qingdao 266000 , People's Republic of China
| | - Mingyuan Xu
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , People's Republic of China
| | - Tong Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , People's Republic of China
| | - Ju Wang
- Key Laboratory of Experimental Marine Biology , Institute of Oceanology, Chinese Academy of Sciences , Qingdao 266071 , People's Republic of China
| | - Chaomin Sun
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology , Qingdao 266000 , People's Republic of China
- Key Laboratory of Experimental Marine Biology , Institute of Oceanology, Chinese Academy of Sciences , Qingdao 266071 , People's Republic of China
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education of China, School of Pharmaceutical Sciences , Wuhan University , Wuhan 430071 , People's Republic of China
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education of China, School of Medicine and Pharmacy , Ocean University of China , Qingdao 266003 , People's Republic of China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology , Qingdao 266000 , People's Republic of China
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29
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Heine T, van Berkel WJH, Gassner G, van Pée KH, Tischler D. Two-Component FAD-Dependent Monooxygenases: Current Knowledge and Biotechnological Opportunities. BIOLOGY 2018; 7:biology7030042. [PMID: 30072664 PMCID: PMC6165268 DOI: 10.3390/biology7030042] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 12/11/2022]
Abstract
Flavoprotein monooxygenases create valuable compounds that are of high interest for the chemical, pharmaceutical, and agrochemical industries, among others. Monooxygenases that use flavin as cofactor are either single- or two-component systems. Here we summarize the current knowledge about two-component flavin adenine dinucleotide (FAD)-dependent monooxygenases and describe their biotechnological relevance. Two-component FAD-dependent monooxygenases catalyze hydroxylation, epoxidation, and halogenation reactions and are physiologically involved in amino acid metabolism, mineralization of aromatic compounds, and biosynthesis of secondary metabolites. The monooxygenase component of these enzymes is strictly dependent on reduced FAD, which is supplied by the reductase component. More and more representatives of two-component FAD-dependent monooxygenases have been discovered and characterized in recent years, which has resulted in the identification of novel physiological roles, functional properties, and a variety of biocatalytic opportunities.
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Affiliation(s)
- Thomas Heine
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
| | - Willem J H van Berkel
- Laboratory of Biochemistry, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| | - George Gassner
- Department of Chemistry and Biochemistry, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 94132, USA.
| | - Karl-Heinz van Pée
- Allgemeine Biochemie, Technische Universität Dresden, 01062 Dresden, Germany.
| | - Dirk Tischler
- Institute of Biosciences, Environmental Microbiology, TU Bergakademie Freiberg, Leipziger Str. 29, 09599 Freiberg, Germany.
- Microbial Biotechnology, Ruhr University Bochum, Universitätsstr. 150, 44780 Bochum, Germany.
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30
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Xie L, Zhang L, Wang C, Wang X, Xu YM, Yu H, Wu P, Li S, Han L, Gunatilaka AAL, Wei X, Lin M, Molnár I, Xu Y. Methylglucosylation of aromatic amino and phenolic moieties of drug-like biosynthons by combinatorial biosynthesis. Proc Natl Acad Sci U S A 2018; 115:E4980-E4989. [PMID: 29760061 PMCID: PMC5984488 DOI: 10.1073/pnas.1716046115] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Glycosylation is a prominent strategy to optimize the pharmacokinetic and pharmacodynamic properties of drug-like small-molecule scaffolds by modulating their solubility, stability, bioavailability, and bioactivity. Glycosyltransferases applicable for "sugarcoating" various small-molecule acceptors have been isolated and characterized from plants and bacteria, but remained cryptic from filamentous fungi until recently, despite the frequent use of some fungi for whole-cell biocatalytic glycosylations. Here, we use bioinformatic and genomic tools combined with heterologous expression to identify a glycosyltransferase-methyltransferase (GT-MT) gene pair that encodes a methylglucosylation functional module in the ascomycetous fungus Beauveria bassiana The GT is the founding member of a family nonorthologous to characterized fungal enzymes. Using combinatorial biosynthetic and biocatalytic platforms, we reveal that this GT is a promiscuous enzyme that efficiently modifies a broad range of drug-like substrates, including polyketides, anthraquinones, flavonoids, and naphthalenes. It yields both O- and N-glucosides with remarkable regio- and stereospecificity, a spectrum not demonstrated for other characterized fungal enzymes. These glucosides are faithfully processed by the dedicated MT to afford 4-O-methylglucosides. The resulting "unnatural products" show increased solubility, while representative polyketide methylglucosides also display increased stability against glycoside hydrolysis. Upon methylglucosidation, specific polyketides were found to attain cancer cell line-specific antiproliferative or matrix attachment inhibitory activities. These findings will guide genome mining for fungal GTs with novel substrate and product specificities, and empower the efficient combinatorial biosynthesis of a broad range of natural and unnatural glycosides in total biosynthetic or biocatalytic formats.
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Affiliation(s)
- Linan Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China
| | - Liwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China
| | - Chen Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China
- Natural Products Center, University of Arizona, Tucson, AZ 85706
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, People's Republic of China
| | - Xiaojing Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China
- Natural Products Center, University of Arizona, Tucson, AZ 85706
| | - Ya-Ming Xu
- Natural Products Center, University of Arizona, Tucson, AZ 85706
| | - Hefen Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Capital Medical University, 100069 Beijing, People's Republic of China
| | - Ping Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, People's Republic of China
| | - Shenglan Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Capital Medical University, 100069 Beijing, People's Republic of China
| | - Lida Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China
| | | | - Xiaoyi Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, People's Republic of China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China;
| | - István Molnár
- Natural Products Center, University of Arizona, Tucson, AZ 85706;
| | - Yuquan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081 Beijing, People's Republic of China;
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31
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Gkotsi DS, Dhaliwal J, McLachlan MMW, Mulholand KR, Goss RJM. Halogenases: powerful tools for biocatalysis (mechanisms applications and scope). Curr Opin Chem Biol 2018; 43:119-126. [DOI: 10.1016/j.cbpa.2018.01.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/04/2018] [Indexed: 10/24/2022]
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32
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Andorfer MC, Lewis JC. Understanding and Improving the Activity of Flavin-Dependent Halogenases via Random and Targeted Mutagenesis. Annu Rev Biochem 2018; 87:159-185. [PMID: 29589959 DOI: 10.1146/annurev-biochem-062917-012042] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Flavin-dependent halogenases (FDHs) catalyze the halogenation of organic substrates by coordinating reactions of reduced flavin, molecular oxygen, and chloride. Targeted and random mutagenesis of these enzymes have been used to both understand and alter their reactivity. These studies have led to insights into residues essential for catalysis and FDH variants with improved stability, expanded substrate scope, and altered site selectivity. Mutations throughout FDH structures have contributed to all of these advances. More recent studies have sought to rationalize the impact of these mutations on FDH function and to identify new FDHs to deepen our understanding of this enzyme class and to expand their utility for biocatalytic applications.
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Affiliation(s)
- Mary C Andorfer
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Jared C Lewis
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA;
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Fräbel S, Wagner B, Krischke M, Schmidts V, Thiele CM, Staniek A, Warzecha H. Engineering of new-to-nature halogenated indigo precursors in plants. Metab Eng 2018; 46:20-27. [PMID: 29466700 DOI: 10.1016/j.ymben.2018.02.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/14/2017] [Accepted: 02/13/2018] [Indexed: 11/16/2022]
Abstract
Plants are versatile chemists producing a tremendous variety of specialized compounds. Here, we describe the engineering of entirely novel metabolic pathways in planta enabling generation of halogenated indigo precursors as non-natural plant products. Indican (indolyl-β-D-glucopyranoside) is a secondary metabolite characteristic of a number of dyers plants. Its deglucosylation and subsequent oxidative dimerization leads to the blue dye, indigo. Halogenated indican derivatives are commonly used as detection reagents in histochemical and molecular biology applications; their production, however, relies largely on chemical synthesis. To attain the de novo biosynthesis in a plant-based system devoid of indican, we employed a sequence of enzymes from diverse sources, including three microbial tryptophan halogenases substituting the amino acid at either C5, C6, or C7 of the indole moiety. Subsequent processing of the halotryptophan by bacterial tryptophanase TnaA in concert with a mutant of the human cytochrome P450 monooxygenase 2A6 and glycosylation of the resulting indoxyl derivatives by an endogenous tobacco glucosyltransferase yielded corresponding haloindican variants in transiently transformed Nicotiana benthamiana plants. Accumulation levels were highest when the 5-halogenase PyrH was utilized, reaching 0.93 ± 0.089 mg/g dry weight of 5-chloroindican. The identity of the latter was unambiguously confirmed by NMR analysis. Moreover, our combinatorial approach, facilitated by the modular assembly capabilities of the GoldenBraid cloning system and inspired by the unique compartmentation of plant cells, afforded testing a number of alternative subcellular localizations for pathway design. In consequence, chloroplasts were validated as functional biosynthetic venues for haloindican, with the requisite reducing augmentation of the halogenases as well as the cytochrome P450 monooxygenase fulfilled by catalytic systems native to the organelle. Thus, our study puts forward a viable alternative production platform for halogenated fine chemicals, eschewing reliance on fossil fuel resources and toxic chemicals. We further contend that in planta generation of halogenated indigoid precursors previously unknown to nature offers an extended view on and, indeed, pushes forward the established frontiers of biosynthetic capacity of plants.
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Affiliation(s)
- Sabine Fräbel
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Schnittspahnstraße 4, 64287 Darmstadt, Germany
| | - Bastian Wagner
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Schnittspahnstraße 4, 64287 Darmstadt, Germany
| | - Markus Krischke
- Lehrstuhl für Pharmazeutische Biologie, Julius-von-Sachs-Institut der Universität Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, 64287 Darmstadt, Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Str. 4, 64287 Darmstadt, Germany
| | - Agata Staniek
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Schnittspahnstraße 4, 64287 Darmstadt, Germany
| | - Heribert Warzecha
- Plant Biotechnology and Metabolic Engineering, Technische Universität Darmstadt, Schnittspahnstraße 4, 64287 Darmstadt, Germany.
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34
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Reed KB, Alper HS. Expanding beyond canonical metabolism: Interfacing alternative elements, synthetic biology, and metabolic engineering. Synth Syst Biotechnol 2018; 3:20-33. [PMID: 29911196 PMCID: PMC5884228 DOI: 10.1016/j.synbio.2017.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/08/2017] [Accepted: 12/09/2017] [Indexed: 12/15/2022] Open
Abstract
Metabolic engineering offers an exquisite capacity to produce new molecules in a renewable manner. However, most industrial applications have focused on only a small subset of elements from the periodic table, centered around carbon biochemistry. This review aims to illustrate the expanse of chemical elements that can currently (and potentially) be integrated into useful products using cellular systems. Specifically, we describe recent advances in expanding the cellular scope to include the halogens, selenium and the metalloids, and a variety of metal incorporations. These examples range from small molecules, heteroatom-linked uncommon elements, and natural products to biomining and nanotechnology applications. Collectively, this review covers the promise of an expanded range of elemental incorporations and the future impacts it may have on biotechnology.
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Affiliation(s)
- Kevin B. Reed
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA
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35
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Casini A, Chang FY, Eluere R, King AM, Young EM, Dudley QM, Karim A, Pratt K, Bristol C, Forget A, Ghodasara A, Warden-Rothman R, Gan R, Cristofaro A, Borujeni AE, Ryu MH, Li J, Kwon YC, Wang H, Tatsis E, Rodriguez-Lopez C, O’Connor S, Medema MH, Fischbach MA, Jewett MC, Voigt C, Gordon DB. A Pressure Test to Make 10 Molecules in 90 Days: External Evaluation of Methods to Engineer Biology. J Am Chem Soc 2018; 140:4302-4316. [DOI: 10.1021/jacs.7b13292] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Arturo Casini
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Fang-Yuan Chang
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Raissa Eluere
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Andrew M. King
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Eric M. Young
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Quentin M. Dudley
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty Karim
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Katelin Pratt
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Cassandra Bristol
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Anthony Forget
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Amar Ghodasara
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Robert Warden-Rothman
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Rui Gan
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexander Cristofaro
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Amin Espah Borujeni
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Min-Hyung Ryu
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - Jian Li
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Yong-Chan Kwon
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - He Wang
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Evangelos Tatsis
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | | | - Sarah O’Connor
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - Michael A. Fischbach
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Bioengineering and Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, California 94305, United States
| | - Michael C. Jewett
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Christopher Voigt
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
| | - D. Benjamin Gordon
- The Foundry, 75 Ames Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States,
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36
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Payne JT, Butkovich PH, Gu Y, Kunze KN, Park HJ, Wang DS, Lewis JC. Enantioselective Desymmetrization of Methylenedianilines via Enzyme-Catalyzed Remote Halogenation. J Am Chem Soc 2018; 140:546-549. [PMID: 29294291 PMCID: PMC5898188 DOI: 10.1021/jacs.7b09573] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extensive effort has been devoted to engineering flavin-dependent halogenases (FDHs) with improved stability, expanded substrate scope, and altered regioselectivity. Here, we show that variants of rebeccamycin halogenase (RebH) catalyze enantioselective desymmetrization of methylenedianilines via halogenation of these substrates distal to their pro-stereogenic center. Structure-guided engineering was used to increase the conversion and selectivity of these reactions, and the synthetic utility of the halogenated products was shown via conversion of to a chiral α-substituted indole. These results constitute the first reported examples of asymmetric catalysis by FDHs.
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Affiliation(s)
| | - Paul H. Butkovich
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637
| | - Yifan Gu
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637
| | | | - Hyun June Park
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637
| | | | - Jared C. Lewis
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, Chicago, IL 60637
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37
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Saha M, Das AR. Access of Diverse 2-Pyrrolidinone, 3,4,5-Substituted Furanone and 2-Oxo-dihydropyrroles Applying Graphene Oxide Nanosheet: Unraveling of Solvent Selectivity. ChemistrySelect 2017. [DOI: 10.1002/slct.201701989] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Moumita Saha
- Department of Chemistry; University of Calcutta; Kolkata-700009, India
| | - Asish R. Das
- Department of Chemistry; University of Calcutta; Kolkata-700009, India
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38
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Andorfer MC, Belsare KD, Girlich AM, Lewis JC. Aromatic Halogenation by Using Bifunctional Flavin Reductase-Halogenase Fusion Enzymes. Chembiochem 2017; 18:2099-2103. [PMID: 28879681 PMCID: PMC5898195 DOI: 10.1002/cbic.201700391] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Indexed: 11/11/2022]
Abstract
The remarkable site selectivity and broad substrate scope of flavin-dependent halogenases (FDHs) has led to much interest in their potential as biocatalysts. Multiple engineering efforts have demonstrated that FDHs can be tuned for non-native substrate scope and site selectivity. FDHs have also proven useful as in vivo biocatalysts and have been successfully incorporated into biosynthetic pathways to build new chlorinated aromatic compounds in several heterologous organisms. In both cases, reduced flavin cofactor, usually supplied by a separate flavin reductase (FR), is required. Herein, we report functional synthetic, fused FDH-FR proteins containing various FDHs and FRs joined by different linkers. We show that FDH-FR fusion proteins can increase product titers compared to the individual components for in vivo biocatalysis in Escherichia coli.
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Affiliation(s)
- Mary C Andorfer
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, SCL 302, Chicago, IL, 60637, USA
| | - Ketaki D Belsare
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, SCL 302, Chicago, IL, 60637, USA
| | - Anna M Girlich
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, SCL 302, Chicago, IL, 60637, USA
| | - Jared C Lewis
- Department of Chemistry, University of Chicago, 5735 South Ellis Avenue, SCL 302, Chicago, IL, 60637, USA
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39
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Sharma SV, Tong X, Pubill-Ulldemolins C, Cartmell C, Bogosyan EJA, Rackham EJ, Marelli E, Hamed RB, Goss RJM. Living GenoChemetics by hyphenating synthetic biology and synthetic chemistry in vivo. Nat Commun 2017; 8:229. [PMID: 28794415 PMCID: PMC5550429 DOI: 10.1038/s41467-017-00194-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/07/2017] [Indexed: 01/21/2023] Open
Abstract
Marrying synthetic biology with synthetic chemistry provides a powerful approach toward natural product diversification, combining the best of both worlds: expediency and synthetic capability of biogenic pathways and chemical diversity enabled by organic synthesis. Biosynthetic pathway engineering can be employed to insert a chemically orthogonal tag into a complex natural scaffold affording the possibility of site-selective modification without employing protecting group strategies. Here we show that, by installing a sufficiently reactive handle (e.g., a C–Br bond) and developing compatible mild aqueous chemistries, synchronous biosynthesis of the tagged metabolite and its subsequent chemical modification in living culture can be achieved. This approach can potentially enable many new applications: for example, assay of directed evolution of enzymes catalyzing halo-metabolite biosynthesis in living cells or generating and following the fate of tagged metabolites and biomolecules in living systems. We report synthetic biological access to new-to-nature bromo-metabolites and the concomitant biorthogonal cross-coupling of halo-metabolites in living cultures. Coupling synthetic biology and chemical reactions in cells is a challenging task. The authors engineer bacteria capable of generating bromo-metabolites, develop a mild Suzuki-Miyaura cross-coupling reaction compatible with cell growth and carry out the cross-coupling chemistry in live cell cultures.
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Affiliation(s)
- Sunil V Sharma
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Xiaoxue Tong
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Cristina Pubill-Ulldemolins
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Christopher Cartmell
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Emma J A Bogosyan
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,Analytical Development, GSK, Cobden Street, Montrose, Angus, DD10 8EA, UK
| | - Emma J Rackham
- School of Chemistry, University of East, Norwich, NR4 7TJ, UK.,School of Medicine, University of East Anglia, Bob Champion Research and Education Building, James Watson Road, Norwich, NR4 7UQ, UK
| | - Enrico Marelli
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Refaat B Hamed
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Rebecca J M Goss
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK. .,BSRC, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.
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40
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Ma L, Zhang W, Zhu Y, Zhang G, Zhang H, Zhang Q, Zhang L, Yuan C, Zhang C. Identification and characterization of a biosynthetic gene cluster for tryptophan dimers in deep sea-derived Streptomyces sp. SCSIO 03032. Appl Microbiol Biotechnol 2017; 101:6123-6136. [PMID: 28620687 DOI: 10.1007/s00253-017-8375-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/23/2017] [Accepted: 06/01/2017] [Indexed: 01/12/2023]
Abstract
Tryptophan dimers (TDs) are an important class of natural products with diverse bioactivities and share conserved biosynthetic pathways. We report the identification of a partial gene cluster (spm) responsible for the biosynthesis of a class of unusual TDs with non-planar skeletons including spiroindimicins (SPMs), indimicins (IDMs), and lynamicins (LNMs) from the deep-sea derived Streptomyces sp. SCSIO 03032. Bioinformatics analysis, targeted gene disruptions, and heterologous expression studies confirmed the involvement of the spm gene cluster in the biosynthesis of SPM/IDM/LNMs, and revealed the indispensable roles for the halogenase/reductase pair SpmHF, the amino acid oxidase SpmO, and the chromopyrrolic acid (CPA) synthase SpmD, as well as the positive regulator SpmR and the putative transporter SpmA. However, the spm gene cluster was unable to confer a heterologous host the ability to produce SPM/IDM/LNMs. In addition, the P450 enzyme SpmP and the monooxygenase SpmX2 were found to be non-relevant to the biosynthesis of SPM/IDM/LNMs. Sequence alignment and structure modeling suggested the lack of key conserved amino acid residues in the substrate-binding pocket of SpmP. Furthermore, feeding experiments in the non-producing ΔspmO mutant revealed several biosynthetic precursors en route to SPMs, indicating that key enzymes responsible for the biosynthesis of SPMs should be encoded by genes outside of the identified spm gene cluster. Finally, the biosynthetic pathways of SPM/IDM/LNMs are proposed to lay a basis for further insights into their intriguing biosynthetic machinery.
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Affiliation(s)
- Liang Ma
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjun Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Yiguang Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Guangtao Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Haibo Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Qingbo Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Liping Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Chengshan Yuan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Changsheng Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.
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41
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Schnepel C, Sewald N. Enzymatic Halogenation: A Timely Strategy for Regioselective C−H Activation. Chemistry 2017; 23:12064-12086. [DOI: 10.1002/chem.201701209] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Christian Schnepel
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
| | - Norbert Sewald
- Organische und Bioorganische Chemie; Fakultät für Chemie; Universität Bielefeld; Universitätsstraße 25 33615 Bielefeld Germany
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42
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Woodruff LBA, Gorochowski TE, Roehner N, Mikkelsen TS, Densmore D, Gordon DB, Nicol R, Voigt CA. Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration. Nucleic Acids Res 2017; 45:1553-1565. [PMID: 28007941 PMCID: PMC5388403 DOI: 10.1093/nar/gkw1226] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 11/22/2016] [Indexed: 11/14/2022] Open
Abstract
Genetic designs can consist of dozens of genes and hundreds of genetic parts. After evaluating a design, it is desirable to implement changes without the cost and burden of starting the construction process from scratch. Here, we report a two-step process where a large design space is divided into deep pools of composite parts, from which individuals are retrieved and assembled to build a final construct. The pools are built via multiplexed assembly and sequenced using next-generation sequencing. Each pool consists of ∼20 Mb of up to 5000 unique and sequence-verified composite parts that are barcoded for retrieval by PCR. This approach is applied to a 16-gene nitrogen fixation pathway, which is broken into pools containing a total of 55 848 composite parts (71.0 Mb). The pools encompass an enormous design space (1043 possible 23 kb constructs), from which an algorithm-guided 192-member 4.5 Mb library is built. Next, all 1030 possible genetic circuits based on 10 repressors (NOR/NOT gates) are encoded in pools where each repressor is fused to all permutations of input promoters. These demonstrate that multiplexing can be applied to encompass entire design spaces from which individuals can be accessed and evaluated.
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Affiliation(s)
- Lauren B A Woodruff
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas E Gorochowski
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas Roehner
- Biological Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Tarjei S Mikkelsen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Douglas Densmore
- Biological Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - D Benjamin Gordon
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert Nicol
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Christopher A Voigt
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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43
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Asamizu S. Biosynthesis of nitrogen-containing natural products, C7N aminocyclitols and bis-indoles, from actinomycetes. Biosci Biotechnol Biochem 2017; 81:871-881. [DOI: 10.1080/09168451.2017.1281726] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Abstract
Actinomycetes are a major source of bioactive natural products with important pharmaceutical properties. Understanding the natural enzymatic assembly of complex small molecules is important for rational metabolic pathway design to produce “artificial” natural products in bacterial cells. This review will highlight current research on the biosynthetic mechanisms of two classes of nitrogen-containing natural products, C7N aminocyclitols and bis-indoles. Validamycin A is a member of C7N aminocyclitol natural products from Streptomyces hygroscopicus. Here, two important biosynthetic steps, pseudoglycosyltranferase-catalyzed C–N bond formation, and C7-sugar phosphate cyclase-catalyzed divergent carbasugar formation, will be reviewed. In addition, the bis-indolic natural products indolocarbazole, staurosporine from Streptomyces sp. TP-A0274, and rearranged bis-indole violacein from Chromobacterium violaceum are reviewed including the oxidative course of the assembly pathway for the bis-indolic scaffold. The identified biosynthesis mechanisms will be useful to generating new biocatalytic tools and bioactive compounds.
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Affiliation(s)
- Shumpei Asamizu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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44
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Latham J, Brandenburger E, Shepherd SA, Menon BRK, Micklefield J. Development of Halogenase Enzymes for Use in Synthesis. Chem Rev 2017; 118:232-269. [PMID: 28466644 DOI: 10.1021/acs.chemrev.7b00032] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature has evolved halogenase enzymes to regioselectively halogenate a diverse range of biosynthetic precursors, with the halogens introduced often having a profound effect on the biological activity of the resulting natural products. Synthetic endeavors to create non-natural bioactive small molecules for pharmaceutical and agrochemical applications have also arrived at a similar conclusion: halogens can dramatically improve the properties of organic molecules for selective modulation of biological targets in vivo. Consequently, a high proportion of pharmaceuticals and agrochemicals on the market today possess halogens. Halogenated organic compounds are also common intermediates in synthesis and are particularly valuable in metal-catalyzed cross-coupling reactions. Despite the potential utility of organohalogens, traditional nonenzymatic halogenation chemistry utilizes deleterious reagents and often lacks regiocontrol. Reliable, facile, and cleaner methods for the regioselective halogenation of organic compounds are therefore essential in the development of economical and environmentally friendly industrial processes. A potential avenue toward such methods is the use of halogenase enzymes, responsible for the biosynthesis of halogenated natural products, as biocatalysts. This Review will discuss advances in developing halogenases for biocatalysis, potential untapped sources of such biocatalysts and how further optimization of these enzymes is required to achieve the goal of industrial scale biohalogenation.
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Affiliation(s)
- Jonathan Latham
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Eileen Brandenburger
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sarah A Shepherd
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Binuraj R K Menon
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jason Micklefield
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
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45
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Cloning, expression, purification and biophysical analysis of two putative halogenases from the glycopeptide A47,934 gene cluster of Streptomyces toyocaensis. Protein Expr Purif 2017; 132:9-18. [DOI: 10.1016/j.pep.2017.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/22/2016] [Accepted: 01/04/2017] [Indexed: 10/20/2022]
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46
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47
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Salcedo RG, Olano C, Fernández R, Braña AF, Méndez C, de la Calle F, Salas JA. Elucidation of the glycosylation steps during biosynthesis of antitumor macrolides PM100117 and PM100118 and engineering for novel derivatives. Microb Cell Fact 2016; 15:187. [PMID: 27829451 PMCID: PMC5103430 DOI: 10.1186/s12934-016-0591-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/03/2016] [Indexed: 03/14/2023] Open
Abstract
BACKGROUND Antitumor compounds PM100117 and PM100118 are glycosylated polyketides derived from the marine actinobacteria Streptomyces caniferus GUA-06-05-006A. The organization and characterization of the PM100117/18 biosynthesis gene cluster has been recently reported. RESULTS Based on the preceding information and new genetic engineering data, we have outlined the pathway by which PM100117/18 are glycosylated. Furthermore, these genetic engineering experiments have allowed the generation of novel PM100117/18 analogues. Deletion of putative glycosyltranferase genes and additional genes presumably involved in late biosynthesis steps of the three 2,6-dideoxysugars appended to the PM100117/18 polyketide skeleton, resulted in the generation of a series of intermediates and novel derivatives. CONCLUSIONS Isolation and identification of the novel compounds constitutes an important contribution to our knowledge on PM100117/18 glycosylation, and set the basis for further characterization of specific enzymatic reactions, additional genetic engineering and combinatorial biosynthesis approaches.
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Affiliation(s)
- Raúl García Salcedo
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Asturias, 33006, Oviedo, Spain
| | - Carlos Olano
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Asturias, 33006, Oviedo, Spain
| | - Rogelio Fernández
- Drug Discovery Area, PharmaMar S.A., Avda. de los Reyes, Colmenar Viejo, 128770, Madrid, Spain
| | - Alfredo F Braña
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Asturias, 33006, Oviedo, Spain
| | - Carmen Méndez
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Asturias, 33006, Oviedo, Spain
| | - Fernando de la Calle
- Drug Discovery Area, PharmaMar S.A., Avda. de los Reyes, Colmenar Viejo, 128770, Madrid, Spain
| | - José A Salas
- Departamento de Biología Funcional e Instituto Universitario de Oncología del Principado de Asturias (I.U.O.P.A), Universidad de Oviedo, Asturias, 33006, Oviedo, Spain.
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48
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Abstract
Bacterial genomes encode the biosynthetic potential to produce hundreds of thousands of complex molecules with diverse applications, from medicine to agriculture and materials. Accessing these natural products promises to reinvigorate drug discovery pipelines and provide novel routes to synthesize complex chemicals. The pathways leading to the production of these molecules often comprise dozens of genes spanning large areas of the genome and are controlled by complex regulatory networks with some of the most interesting molecules being produced by non-model organisms. In this Review, we discuss how advances in synthetic biology--including novel DNA construction technologies, the use of genetic parts for the precise control of expression and for synthetic regulatory circuits--and multiplexed genome engineering can be used to optimize the design and synthesis of pathways that produce natural products.
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49
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An influence of the copy number of biosynthetic gene clusters on the production level of antibiotics in a heterologous host. J Biotechnol 2016; 232:110-7. [PMID: 27264245 DOI: 10.1016/j.jbiotec.2016.05.038] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 11/24/2022]
Abstract
Streptomyces albus J1074 is a well-known host for heterologous expression of secondary metabolites. To further increase its potential and to study the influence of cluster multiplication, additional φC31-attachment site was integrated into its genome using a system for transposon mutagenesis. Four secondary metabolite clusters were expressed in strains with different numbers of attachment sites, ranging from one to three copies of the site. Secondary metabolite production was examined and a new compound could be detected, purified and its structure was elucidated.
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50
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Liao L, Chen R, Jiang M, Tian X, Liu H, Yu Y, Fan C, Chen B. Bioprospecting potential of halogenases from Arctic marine actinomycetes. BMC Microbiol 2016; 16:34. [PMID: 26964536 PMCID: PMC4785625 DOI: 10.1186/s12866-016-0662-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/05/2016] [Indexed: 11/14/2022] Open
Abstract
Background Halometabolites, an important group of natural products, generally require halogenases for their biosynthesis. Actinomycetes from the Arctic Ocean have rarely been investigated for halogenases and their gene clusters associated, albeit great potential of halometabolite production has been predicted. Therefore, we initiated this research on the screening of halogenases from Arctic marine actinomycetes isolates to explore their genetic potential of halometabolite biosynthesis. Results Nine halogenase genes were discovered from sixty Arctic marine actinomycetes using in-house designed or previously reported PCR primers. Four representative genotypes were further cloned to obtain full coding regions through genome walking. The resulting halogenases were predicted to be involved in halogenation of indole groups, antitumor agent ansamitocin-like substrates, or unknown peptide-like compounds. Genome sequencing revealed a potential gene cluster containing the halogenase predicted to catalyze peptide-like compounds. However, the gene cluster was probably silent under the current conditions. Conclusions PCR-based screening of halogenase genes is a powerful and efficient tool to conduct bioprospecting of halometabolite-producing actinomycetes from the Arctic. Genome sequencing can also identify cryptic gene clusters potentially producing new halometabolites, which might be easily missed by traditional isolation and chemical characterization. In addition, our study indicates that great genetic potential of new halometabolites can be expected from mostly untapped actinomycetes from the polar regions. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0662-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li Liao
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China
| | - Ruiqin Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China.,College of Bioengineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ming Jiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20030, China
| | - Xiaoqing Tian
- Key Laboratory of East China Sea & Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
| | - Huan Liu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China.,College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Yong Yu
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China
| | - Chenqi Fan
- Key Laboratory of East China Sea & Oceanic Fishery Resources Exploitation and Utilization, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, 451 Jinqiao Road, Shanghai, 200136, China.
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