501
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Hacker C, Cai X, Kegler C, Zhao L, Weickhmann AK, Wurm JP, Bode HB, Wöhnert J. Structure-based redesign of docking domain interactions modulates the product spectrum of a rhabdopeptide-synthesizing NRPS. Nat Commun 2018; 9:4366. [PMID: 30341296 PMCID: PMC6195595 DOI: 10.1038/s41467-018-06712-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 09/21/2018] [Indexed: 12/18/2022] Open
Abstract
Several peptides in clinical use are derived from non-ribosomal peptide synthetases (NRPS). In these systems multiple NRPS subunits interact with each other in a specific linear order mediated by specific docking domains (DDs), whose structures are not known yet, to synthesize well-defined peptide products. In contrast to classical NRPSs, single-module NRPS subunits responsible for the generation of rhabdopeptide/xenortide-like peptides (RXPs) can act in different order depending on subunit stoichiometry thereby producing peptide libraries. To define the basis for their unusual interaction patterns, we determine the structures of all N-terminal DDs (NDDs) as well as of an NDD-CDD complex and characterize all putative DD interactions thermodynamically for such a system. Key amino acid residues for DD interactions are identified that upon their exchange change the DD affinity and result in predictable changes in peptide production. Recognition rules for DD interactions are identified that also operate in other megasynthase complexes. Rhabdopeptides are synthesized by non-ribosomal peptide synthetases (NRPSs) and the multiple NRPS subunits interact through docking domains (DD). Here the authors provide insights into DD interaction patterns and present the structures of three N-terminal docking domains (NDD) and a NDD-CDD complex and derive a set of recognition rules for DD interactions.
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Affiliation(s)
- Carolin Hacker
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Xiaofeng Cai
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Carsten Kegler
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Lei Zhao
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - A Katharina Weickhmann
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Jan Philip Wurm
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93053, Regensburg, Germany
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany. .,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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502
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Jiang G, Zuo R, Zhang Y, Powell MM, Zhang P, Hylton SM, Loria R, Ding Y. One-Pot Biocombinatorial Synthesis of Herbicidal Thaxtomins. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03317] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Guangde Jiang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Ran Zuo
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Yi Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Magan M. Powell
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Peilan Zhang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Sarah M. Hylton
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Rosemary Loria
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
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503
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Guo H, Schmidt A, Stephan P, Raguž L, Braga D, Kaiser M, Dahse HM, Weigel C, Lackner G, Beemelmanns C. Precursor-Directed Diversification of Cyclic Tetrapeptidic Pseudoxylallemycins. Chembiochem 2018; 19:2307-2311. [DOI: 10.1002/cbic.201800503] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Alexander Schmidt
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Philipp Stephan
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Luka Raguž
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Daniel Braga
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
- Friedrich-Schiller-Universität Jena; Junior Research Group Synthetic Microbiology at the Hans-Knöll-Institute; Adolf-Reichwein-Strasse 23 07745 Jena Germany
| | - Marcel Kaiser
- Parasite Chemotherapy Unit; Swiss Tropical and Public Health Institute; Socinstrasse 57 4002 Basel Switzerland
- Parasite Chemotherapy; University of Basel; Petersplatz 1 4003 Basel Switzerland
| | - Hans-Martin Dahse
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Christiane Weigel
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
| | - Gerald Lackner
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
- Friedrich-Schiller-Universität Jena; Junior Research Group Synthetic Microbiology at the Hans-Knöll-Institute; Adolf-Reichwein-Strasse 23 07745 Jena Germany
| | - Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology; Hans Knöll Institute; Beutenbergstraße 11a 07745 Jena Germany
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504
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Refining the Natural Product Repertoire in Entomopathogenic Bacteria. Trends Microbiol 2018; 26:833-840. [DOI: 10.1016/j.tim.2018.04.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/22/2018] [Accepted: 04/27/2018] [Indexed: 01/21/2023]
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505
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Tsunematsu Y, Maeda N, Yokoyama M, Chankhamjon P, Watanabe K, Scherlach K, Hertweck C. Enzymatic Amide Tailoring Promotes Retro-Aldol Amino Acid Conversion To Form the Antifungal Agent Aspirochlorine. Angew Chem Int Ed Engl 2018; 57:14051-14054. [DOI: 10.1002/anie.201806740] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Yuta Tsunematsu
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
- Department of Pharmaceutical Sciences; University of Shizuoka; Shizuoka 422-8526 Japan
| | - Naoya Maeda
- Department of Pharmaceutical Sciences; University of Shizuoka; Shizuoka 422-8526 Japan
| | - Mamoru Yokoyama
- Department of Pharmaceutical Sciences; University of Shizuoka; Shizuoka 422-8526 Japan
| | - Pranatchareeya Chankhamjon
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences; University of Shizuoka; Shizuoka 422-8526 Japan
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry; Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI); Beutenbergstr. 11a 07745 Jena Germany
- Friedrich Schiller University Jena; 07743 Jena Germany
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506
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Geudens N, Martins JC. Cyclic Lipodepsipeptides From Pseudomonas spp. - Biological Swiss-Army Knives. Front Microbiol 2018; 9:1867. [PMID: 30158910 PMCID: PMC6104475 DOI: 10.3389/fmicb.2018.01867] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/25/2018] [Indexed: 12/20/2022] Open
Abstract
Cyclic lipodepsipeptides produced by Pseudomonas spp. (Ps-CLPs) are biosurfactants that constitute a diverse class of versatile bioactive natural compounds with promising application potential. While chemically diverse, they obey a common structural blue-print, allowing the definition of 14 distinct groups with multiple structurally homologous members. In addition to antibacterial and antifungal properties the reported activity profile of Ps-CLPs includes their effect on bacterial motility, biofilm formation, induced defense responses in plants, their insecticidal activity and anti-proliferation effects on human cancer cell-lines. To further validate their status of potential bioactive substances, we assessed the results of 775 biological tests on 51 Ps-CLPs available from literature. From this, a fragmented view emerges. Taken as a group, Ps-CLPs present a broad activity profile. However, reports on individual Ps-CLPs are often much more limited in the scope of organisms that are challenged or activities that are explored. As a result, our analysis shows that the available data is currently too sparse to allow biological function to be correlated to a particular group of Ps-CLPs. Consequently, certain generalizations that appear in literature with respect to the biological activities of Ps-CLPs should be nuanced. This notwithstanding, the data for the two most extensively studied Ps-CLPs does indicate they can display activities against various biological targets. As the discovery of novel Ps-CLPs accelerates, current challenges to complete and maintain a useful overview of biological activity are discussed.
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Affiliation(s)
- Niels Geudens
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - José C Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
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507
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Molecular insights into antibiotic resistance - how a binding protein traps albicidin. Nat Commun 2018; 9:3095. [PMID: 30082794 PMCID: PMC6078987 DOI: 10.1038/s41467-018-05551-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 07/13/2018] [Indexed: 11/08/2022] Open
Abstract
The worldwide emergence of antibiotic resistance poses a serious threat to human health. A molecular understanding of resistance strategies employed by bacteria is obligatory to generate less-susceptible antibiotics. Albicidin is a highly potent antibacterial compound synthesized by the plant-pathogenic bacterium Xanthomonas albilineans. The drug-binding protein AlbA confers albicidin resistance to Klebsiella oxytoca. Here we show that AlbA binds albicidin with low nanomolar affinity resulting in full inhibition of its antibacterial activity. We report on the crystal structure of the drug-binding domain of AlbA (AlbAS) in complex with albicidin. Both α-helical repeat domains of AlbAS are required to cooperatively clamp albicidin, which is unusual for drug-binding proteins of the MerR family. Structure-guided NMR binding studies employing synthetic albicidin derivatives give valuable information about ligand promiscuity of AlbAS. Our findings thus expand the general understanding of antibiotic resistance mechanisms and support current drug-design efforts directed at more effective albicidin analogs.
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508
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Junk L, Kazmaier U. Total Synthesis of Keramamides A and L from a Common Precursor by Late-Stage Indole Synthesis and Configurational Revision. Angew Chem Int Ed Engl 2018; 57:11432-11435. [PMID: 30019808 DOI: 10.1002/anie.201806657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Indexed: 01/27/2023]
Abstract
The marine natural products keramamide A and L, members of the class of anabaenopeptin-type peptides, were synthesized for the first time by a convergent and flexible route. The installation of the substituted tryptophan moieties was accomplished at the very end of the synthesis on the cyclic peptides, and thus enabled the synthesis of both natural products from one common precursor. The preparation of several epimers clearly indicates that the originally proposed relative configurations of both Keramamides A and L were not correct.
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Affiliation(s)
- Lukas Junk
- Institut für Organische Chemie, Universität des Saarlandes, Campus C4.2, 66123, Saarbrücken, Germany
| | - Uli Kazmaier
- Institut für Organische Chemie, Universität des Saarlandes, Campus C4.2, 66123, Saarbrücken, Germany
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509
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Preparation of new halogenated diphenyl pyrazine analogs in Escherichia coli by a mono-module fungal nonribosomal peptide synthetase from Penicillium herquei. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.06.065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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510
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Junk L, Kazmaier U. Totalsynthese der Keramamide A und L aus einer gemeinsamen Vorstufe durch späte Indolsynthese und Revision ihrer Konfiguration. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lukas Junk
- Institut für Organische Chemie; Universität des Saarlandes; Campus C4.2 66123 Saarbrücken Deutschland
| | - Uli Kazmaier
- Institut für Organische Chemie; Universität des Saarlandes; Campus C4.2 66123 Saarbrücken Deutschland
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511
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Kodani S, Komaki H, Hemmi H, Miyake Y, Kaweewan I, Dohra H. Streptopeptolin, a Cyanopeptolin-Type Peptide from Streptomyces olivochromogenes. ACS OMEGA 2018; 3:8104-8110. [PMID: 30087936 PMCID: PMC6072256 DOI: 10.1021/acsomega.8b01042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
Cyanopeptolin-type peptides are cyclic depsipeptides that commonly have 3-amino-6-hydroxy-2-piperidone (Ahp) unit in the molecules. So far, cyanopeptolin-type peptides have been isolated as protease inhibitors from a wide variety of cyanobacteria. In the course of screening for new peptides, a new peptide streptopeptolin, which had the similar structure to cyanopeptolin, was isolated from the extract of Streptomyces olivochromogenes NBRC 3561. Streptopeptolin is the first cyanopeptolin-type peptide isolated from actinobacteria. The structure of streptopeptolin was determined by the analysis of electrospray ionization mass spectrometry and NMR to be cyclic depsipeptide containing unusual amino acids, Ahp, and N-methyl tyrosine. As a result of protease inhibition test, streptopeptolin showed inhibitory activity against chymotrypsin. The whole genome sequence data of S. olivochromogenes revealed the biosynthetic gene cluster for streptopeptolin, which encoded a nonribosomal peptide synthetase. We proposed a biosynthetic pathway of streptopeptolin based on bioinformatics analysis.
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Affiliation(s)
- Shinya Kodani
- Academic
Institute, Graduate School of Integrated Science and Technology, Graduate School of
Science and Technology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
| | - Hisayuki Komaki
- Biological
Resource Center, National Institute of Technology
and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hikaru Hemmi
- Food
Research
Institute, National Agriculture and Food
Research Organization (NARO), 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Yuto Miyake
- Academic
Institute, Graduate School of Integrated Science and Technology, Graduate School of
Science and Technology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
| | - Issara Kaweewan
- Academic
Institute, Graduate School of Integrated Science and Technology, Graduate School of
Science and Technology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
| | - Hideo Dohra
- Academic
Institute, Graduate School of Integrated Science and Technology, Graduate School of
Science and Technology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, Shizuoka 422-8529, Japan
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512
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Reher R, Kühl T, Annala S, Benkel T, Kaufmann D, Nubbemeyer B, Odhiambo JP, Heimer P, Bäuml CA, Kehraus S, Crüsemann M, Kostenis E, Tietze D, König GM, Imhof D. Deciphering Specificity Determinants for FR900359-Derived Gqα Inhibitors Based on Computational and Structure-Activity Studies. ChemMedChem 2018; 13:1634-1643. [DOI: 10.1002/cmdc.201800304] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Raphael Reher
- Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Toni Kühl
- Pharmaceutical Biochemistry and Bioanalytics; Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Suvi Annala
- Molecular, Cellular and Pharmacobiology Section; Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Tobias Benkel
- Molecular, Cellular and Pharmacobiology Section; Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Desireé Kaufmann
- Eduard Zintl Institute for Inorganic and Physical Chemistry; Technische Universität Darmstadt; Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Britta Nubbemeyer
- Pharmaceutical Biochemistry and Bioanalytics; Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Justin Patrick Odhiambo
- Pharmaceutical Biochemistry and Bioanalytics; Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Pascal Heimer
- Pharmaceutical Biochemistry and Bioanalytics; Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Charlotte Anneke Bäuml
- Pharmaceutical Biochemistry and Bioanalytics; Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
| | - Stefan Kehraus
- Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Max Crüsemann
- Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Evi Kostenis
- Molecular, Cellular and Pharmacobiology Section; Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Daniel Tietze
- Eduard Zintl Institute for Inorganic and Physical Chemistry; Technische Universität Darmstadt; Alarich-Weiss-Str. 4 64287 Darmstadt Germany
| | - Gabriele M. König
- Institute of Pharmaceutical Biology; University of Bonn; Nussallee 6 53115 Bonn Germany
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics; Pharmaceutical Institute; University of Bonn; An der Immenburg 4 53121 Bonn Germany
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513
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Katz L, Chen YY, Gonzalez R, Peterson TC, Zhao H, Baltz RH. Synthetic biology advances and applications in the biotechnology industry: a perspective. ACTA ACUST UNITED AC 2018; 45:449-461. [DOI: 10.1007/s10295-018-2056-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/06/2018] [Indexed: 12/22/2022]
Abstract
Abstract
Synthetic biology is a logical extension of what has been called recombinant DNA (rDNA) technology or genetic engineering since the 1970s. As rDNA technology has been the driver for the development of a thriving biotechnology industry today, starting with the commercialization of biosynthetic human insulin in the early 1980s, synthetic biology has the potential to take the industry to new heights in the coming years. Synthetic biology advances have been driven by dramatic cost reductions in DNA sequencing and DNA synthesis; by the development of sophisticated tools for genome editing, such as CRISPR/Cas9; and by advances in informatics, computational tools, and infrastructure to facilitate and scale analysis and design. Synthetic biology approaches have already been applied to the metabolic engineering of microorganisms for the production of industrially important chemicals and for the engineering of human cells to treat medical disorders. It also shows great promise to accelerate the discovery and development of novel secondary metabolites from microorganisms through traditional, engineered, and combinatorial biosynthesis. We anticipate that synthetic biology will continue to have broadening impacts on the biotechnology industry to address ongoing issues of human health, world food supply, renewable energy, and industrial chemicals and enzymes.
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Affiliation(s)
- Leonard Katz
- 0000 0001 2181 7878 grid.47840.3f QB3 Institute University of California-Berkeley 5885 Hollis St., 4th Floor 94608 Emeryville CA USA
| | - Yvonne Y Chen
- 0000 0000 9632 6718 grid.19006.3e Department of Chemical and Biomolecular Engineering University of California-Los Angeles 420 Westwood Plaza, Boelter Hall 5531 90095 Los Angeles CA USA
| | - Ramon Gonzalez
- 0000 0004 1936 8278 grid.21940.3e Departments of Chemical and Biomolecular Engineering and Bioengineering Rice University 6100 Main Street 77005 Houston TX USA
| | - Todd C Peterson
- grid.427368.c Synthetic Genomics, Inc. 11149 North Torrey Pines Road 92037 La Jolla CA USA
| | - Huimin Zhao
- 0000 0004 1936 9991 grid.35403.31 Department of Chemical and Biomolecular Engineering University of Illinois 600 South Mathews Avenue 61801 Urbana IL USA
| | - Richard H Baltz
- CognoGen Biotechnology Consulting 7636 Andora Drive 34238 Sarasota FL USA
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514
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Wiebach V, Mainz A, Siegert MAJ, Jungmann NA, Lesquame G, Tirat S, Dreux-Zigha A, Aszodi J, Le Beller D, Süssmuth RD. The anti-staphylococcal lipolanthines are ribosomally synthesized lipopeptides. Nat Chem Biol 2018; 14:652-654. [PMID: 29915235 DOI: 10.1038/s41589-018-0068-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/03/2018] [Indexed: 11/09/2022]
Abstract
The potent antibacterial lanthipeptide microvionin, isolated from a culture of Microbacterium arborescens, exhibits a new triamino-dicarboxylic acid moiety, termed avionin, and an unprecedented N-terminal guanidino fatty acid. We identified the corresponding biosynthetic gene cluster and reconstituted central steps of avionin biosynthesis in vitro. Genome mining and isolation of nocavionin from Nocardia terpenica revealed a widespread distribution of this lanthipeptide class, termed lipolanthines, which may be useful as future antimicrobial drugs.
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Affiliation(s)
- Vincent Wiebach
- Faculty II - Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Andi Mainz
- Faculty II - Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Mary-Ann J Siegert
- Faculty II - Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Natalia A Jungmann
- Faculty II - Department of Chemistry, Technische Universität Berlin, Berlin, Germany
| | | | - Sophie Tirat
- ICV-Institute Charles Viollette, Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, Lille, France
| | | | | | | | - Roderich D Süssmuth
- Faculty II - Department of Chemistry, Technische Universität Berlin, Berlin, Germany.
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515
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Woiwode U, Reischl RJ, Buckenmaier S, Lindner W, Lämmerhofer M. Imaging Peptide and Protein Chirality via Amino Acid Analysis by Chiral × Chiral Two-Dimensional Correlation Liquid Chromatography. Anal Chem 2018; 90:7963-7971. [DOI: 10.1021/acs.analchem.8b00676] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ulrich Woiwode
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Roland Johann Reischl
- University of Salzburg, Department of Biosciences, Bioanalytical Research Laboratories, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Stephan Buckenmaier
- Agilent Technologies, Research and Development, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Wolfgang Lindner
- Lindner
Consulting
GmbH, Ziegelofengasse 37, 3400 Klosterneuburg, Austria
- Institute of Analytical Chemistry, University of Vienna, Waehringerstrasse 38, 1090 Vienna, Austria
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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516
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Thongkongkaew T, Ding W, Bratovanov E, Oueis E, Garcı́a-Altares M, Zaburannyi N, Harmrolfs K, Zhang Y, Scherlach K, Müller R, Hertweck C. Two Types of Threonine-Tagged Lipopeptides Synergize in Host Colonization by Pathogenic Burkholderia Species. ACS Chem Biol 2018; 13:1370-1379. [PMID: 29669203 DOI: 10.1021/acschembio.8b00221] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacterial infections of agriculturally important mushrooms and plants pose a major threat to human food sources worldwide. However, structures of chemical mediators required by the pathogen for host colonization and infection remain elusive in most cases. Here, we report two types of threonine-tagged lipopeptides conserved among mushroom and rice pathogenic Burkholderia species that facilitate bacterial infection of hosts. Genome mining, metabolic profiling of infected mushrooms, and heterologous expression of orphan gene clusters allowed the discovery of these unprecedented metabolites in the mushroom pathogen Burkholderia gladioli (haereogladin, burriogladin) and the plant pathogen Burkholderia glumae (haereoglumin and burrioglumin). Through targeted gene deletions, the molecular basis of lipopeptide biosynthesis by nonribosomal peptide synthetases was revealed. Surprisingly, both types of lipopeptides feature unusual threonine tags, which yield longer peptide backbones than one would expect based on the canonical colinearity of the NRPS assembly lines. Both peptides play an indirect role in host infection as biosurfactants that enable host colonization by mediating swarming and biofilm formation abilities. Moreover, MALDI imaging mass spectrometry was applied to investigate the biological role of the lipopeptides. Our results shed light on conserved mechanisms that mushroom and plant pathogenic bacteria utilize for host infection and expand current knowledge on bacterial virulence factors that may represent a new starting point for the targeted development of crop protection measures in the future.
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Affiliation(s)
- Tawatchai Thongkongkaew
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Wei Ding
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Evgeni Bratovanov
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Emilia Oueis
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Marı́a Garcı́a-Altares
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Nestor Zaburannyi
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Kirsten Harmrolfs
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Youming Zhang
- Shandong University−Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People’s Republic of China
| | - Kirstin Scherlach
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
- Chair for Natural Product Chemistry, Friedrich Schiller University, 07743 Jena, Germany
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517
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Watters DJ. Ascidian Toxins with Potential for Drug Development. Mar Drugs 2018; 16:E162. [PMID: 29757250 PMCID: PMC5983293 DOI: 10.3390/md16050162] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 05/05/2018] [Accepted: 05/10/2018] [Indexed: 12/17/2022] Open
Abstract
Ascidians (tunicates) are invertebrate chordates, and prolific producers of a wide variety of biologically active secondary metabolites from cyclic peptides to aromatic alkaloids. Several of these compounds have properties which make them candidates for potential new drugs to treat diseases such as cancer. Many of these natural products are not produced by the ascidians themselves, rather by their associated symbionts. This review will focus mainly on the mechanism of action of important classes of cytotoxic molecules isolated from ascidians. These toxins affect DNA transcription, protein translation, drug efflux pumps, signaling pathways and the cytoskeleton. Two ascidian compounds have already found applications in the treatment of cancer and others are being investigated for their potential in cancer, neurodegenerative and other diseases.
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Affiliation(s)
- Dianne J Watters
- School of Environment and Science, Griffith University, Brisbane, Queensland 4111, Australia.
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518
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Schoppet M, Tailhades J, Kulkarni K, Cryle MJ. Precursor Manipulation in Glycopeptide Antibiotic Biosynthesis: Are β-Amino Acids Compatible with the Oxidative Cyclization Cascade? J Org Chem 2018; 83:7206-7214. [DOI: 10.1021/acs.joc.8b00418] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Melanie Schoppet
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | | | | | - Max J. Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
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519
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Klapper M, Braga D, Lackner G, Herbst R, Stallforth P. Bacterial Alkaloid Biosynthesis: Structural Diversity via a Minimalistic Nonribosomal Peptide Synthetase. Cell Chem Biol 2018; 25:659-665.e9. [PMID: 29606578 DOI: 10.1016/j.chembiol.2018.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/26/2018] [Accepted: 02/22/2018] [Indexed: 11/30/2022]
Abstract
Chemical and biochemical analyses of one of the most basic nonribosomal peptide synthetases (NRPS) from a Pseudomonas fluorescens strain revealed its striking plasticity. Determination of the potential substrate scope enabled us to anticipate novel secondary metabolites that could subsequently be isolated and tested for their bioactivities. Detailed analyses of the monomodular pyreudione synthetase showed that the biosynthesis of the bacterial pyreudione alkaloids does not require additional biosynthetic enzymes. Heterologous expression of a similar and functional, yet cryptic, NRPS of Pseudomonas entomophila was successful and allowed us to perform a phylogenetic analysis of their thioesterase domains.
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Affiliation(s)
- Martin Klapper
- Junior Research Group Chemistry of Microbial Communication, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Daniel Braga
- Junior Research Group Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Gerald Lackner
- Junior Research Group Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Rosa Herbst
- Junior Research Group Chemistry of Microbial Communication, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Pierre Stallforth
- Junior Research Group Chemistry of Microbial Communication, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstrasse 11a, 07745 Jena, Germany.
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520
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Synergistic activity of cosecreted natural products from amoebae-associated bacteria. Proc Natl Acad Sci U S A 2018; 115:3758-3763. [PMID: 29592954 DOI: 10.1073/pnas.1721790115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Investigating microbial interactions from an ecological perspective is a particularly fruitful approach to unveil both new chemistry and bioactivity. Microbial predator-prey interactions in particular rely on natural products as signal or defense molecules. In this context, we identified a grazing-resistant Pseudomonas strain, isolated from the bacterivorous amoeba Dictyostelium discoideum. Genome analysis of this bacterium revealed the presence of two biosynthetic gene clusters that were found adjacent to each other on a contiguous stretch of the bacterial genome. Although one cluster codes for the polyketide synthase producing the known antibiotic mupirocin, the other cluster encodes a nonribosomal peptide synthetase leading to the unreported cyclic lipopeptide jessenipeptin. We describe its complete structure elucidation, as well as its synergistic activity against methicillin-resistant Staphylococcus aureus, when in combination with mupirocin. Both biosynthetic gene clusters are regulated by quorum-sensing systems, with 3-oxo-decanoyl homoserine lactone (3-oxo-C10-AHL) and hexanoyl homoserine lactone (C6-AHL) being the respective signal molecules. This study highlights the regulation, richness, and complex interplay of bacterial natural products that emerge in the context of microbial competition.
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521
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Miley GP, Rote JC, Silverman RB, Kelleher NL, Thomson RJ. Total Synthesis of Tambromycin Enabled by Indole C-H Functionalization. Org Lett 2018; 20:2369-2373. [PMID: 29584440 DOI: 10.1021/acs.orglett.8b00700] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The total synthesis of tambromycin (1), a recently isolated tetrapeptide, is reported. This unusual natural product possesses a highly modified tryptophan-derived indole fragment fused to an α-methylserine-derived oxazoline ring, and a unique noncanonical amino acid residue named tambroline (11). A convergent synthesis of tambromycin was achieved by a 13-step route that leveraged recent developments in the field of C-H functionalization to prepare the complex indole fragment, as well as an efficient synthesis of tambroline that featured a diastereoselective amination of homoproline.
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522
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Vander Wood DA, Keatinge-Clay AT. The modules of trans-acyltransferase assembly lines redefined with a central acyl carrier protein. Proteins 2018. [PMID: 29524261 DOI: 10.1002/prot.25493] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Here, the term "module" is redefined for trans-acyltransferase (trans-AT) assembly lines to agree with how its domains cooperate and evolutionarily co-migrate. The key domain in both the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) modules of assembly lines is the acyl carrier protein (ACP). ACPs not only relay growing acyl chains through the assembly line but also collaborate with enzymes in modules, both in cis and in trans, to add a specific chemical moiety. A ketosynthase (KS) downstream of ACP often plays the role of gatekeeper, ensuring that only a single intermediate generated by the enzymes of a module is passed downstream. Bioinformatic analysis of 526 ACPs from 33 characterized trans-AT assembly lines reveals ACPs from the same module type generally clade together, reflective of the co-evolution of these domains with their cognate enzymes. While KSs downstream of ACPs from the same module type generally also clade together, KSs upstream of ACPs do not-in disagreement with the traditional definition of a module. Beyond nomenclature, the presented analysis impacts our understanding of module function, the evolution of assembly lines, pathway prediction, and assembly line engineering.
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Affiliation(s)
- Drew A Vander Wood
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Adrian T Keatinge-Clay
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
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523
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Boecker S, Grätz S, Kerwat D, Adam L, Schirmer D, Richter L, Schütze T, Petras D, Süssmuth RD, Meyer V. Aspergillus niger is a superior expression host for the production of bioactive fungal cyclodepsipeptides. Fungal Biol Biotechnol 2018; 5:4. [PMID: 29507740 PMCID: PMC5833056 DOI: 10.1186/s40694-018-0048-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/03/2018] [Indexed: 02/06/2023] Open
Abstract
Background Fungal cyclodepsipeptides (CDPs) are non-ribosomally synthesized peptides produced by a variety of filamentous fungi and are of interest to the pharmaceutical industry due to their anticancer, antimicrobial and anthelmintic bioactivities. However, both chemical synthesis and isolation of CDPs from their natural producers are limited due to high costs and comparatively low yields. These challenges might be overcome by heterologous expression of the respective CDP-synthesizing genes in a suitable fungal host. The well-established industrial fungus Aspergillus niger was recently genetically reprogrammed to overproduce the cyclodepsipeptide enniatin B in g/L scale, suggesting that it can generally serve as a high production strain for natural products such as CDPs. In this study, we thus aimed to determine whether other CDPs such as beauvericin and bassianolide can be produced with high titres in A. niger, and whether the generated expression strains can be used to synthesize new-to-nature CDP derivatives. Results The beauvericin and bassianolide synthetases were expressed under control of the tuneable Tet-on promoter, and titres of about 350–600 mg/L for bassianolide and beauvericin were achieved when using optimized feeding conditions, respectively. These are the highest concentrations ever reported for both compounds, whether isolated from natural or heterologous expression systems. We also show that the newly established Tet-on based expression strains can be used to produce new-to-nature beauvericin derivatives by precursor directed biosynthesis, including the compounds 12-hydroxyvalerate-beauvericin and bromo-beauvericin. By feeding deuterated variants of one of the necessary precursors (d-hydroxyisovalerate), we were able to purify deuterated analogues of beauvericin and bassianolide from the respective A. niger expression strains. These deuterated compounds could potentially be used as internal standards in stable isotope dilution analyses to evaluate and quantify fungal spoilage of food and feed products. Conclusion In this study, we show that the product portfolio of A. niger can be expanded from enniatin to other CDPs such as beauvericin and bassianolide, as well as derivatives thereof. This illustrates the capability of A. niger to produce a range of different peptide natural products in titres high enough to become industrially relevant. Electronic supplementary material The online version of this article (10.1186/s40694-018-0048-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simon Boecker
- 1Department Biological Chemistry, Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany.,2Department Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Stefan Grätz
- 1Department Biological Chemistry, Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Dennis Kerwat
- 1Department Biological Chemistry, Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Lutz Adam
- 1Department Biological Chemistry, Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - David Schirmer
- 1Department Biological Chemistry, Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Lennart Richter
- 1Department Biological Chemistry, Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Tabea Schütze
- 2Department Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Daniel Petras
- 1Department Biological Chemistry, Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Roderich D Süssmuth
- 1Department Biological Chemistry, Institute of Chemistry, Technische Universität Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany
| | - Vera Meyer
- 2Department Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
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524
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Cyclic lipodepsipeptides: time for a concerted action to unlock their application potential? Future Med Chem 2018; 10:479-481. [DOI: 10.4155/fmc-2017-0315] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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525
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Peschke M, Brieke C, Heimes M, Cryle MJ. The Thioesterase Domain in Glycopeptide Antibiotic Biosynthesis Is Selective for Cross-Linked Aglycones. ACS Chem Biol 2018; 13:110-120. [PMID: 29192758 DOI: 10.1021/acschembio.7b00943] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The biosynthesis of the glycopeptide antibiotics (GPAs)-which include teicoplanin and vancomycin-is a complex enzymatic process relying on the interplay of nonribosomal peptide synthesis and a cytochrome P450-mediated cyclization cascade. This unique cyclization cascade generates the highly cross-linked state of these nonribosomal peptides, which is crucial for their antimicrobial activity. Given that these essential oxidative transformations occur while the peptide remains bound to the terminal module of the nonribosomal peptide synthetase (NRPS) machinery, it is important to assess the selectivity of the terminal thioesterase (TE) domain and how this domain contributes to the maintenance of an efficient biosynthetic pathway while at the same time ensuring GPA maturation is completed. In this study, we report the in vitro characterization of the thioesterase domain from teicoplanin biosynthesis, the first GPA thioesterase to be characterized. Our results show that the activity of this TE domain relies on the presence of an unusual extended N-terminal linker region that appears to be unique to the NRPS machineries found in GPA biosynthesis. In addition, we show that the activity of this domain against carrier protein bound substrates is dramatically enhanced for mature GPA aglycones as opposed to linear peptides and partially cyclized intermediates. These results demonstrate how the interplay between NRPS and P450s during late stage GPA biosynthesis is not only maintained but also leads to the efficient production of mature GPA aglycones. Thus, GPA TE domains represent another impressive example of the ability of TE domains to act as logic gates during NRPS biosynthesis, ensuring that essential late-stage peptide modifications are completed before catalyzing the release of the mature, bioactive peptide product.
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Affiliation(s)
- Madeleine Peschke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Clara Brieke
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Michael Heimes
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Max J. Cryle
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
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526
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Production of α-keto carboxylic acid dimers in yeast by overexpression of NRPS-like genes from Aspergillus terreus. Appl Microbiol Biotechnol 2018; 102:1663-1672. [PMID: 29305695 DOI: 10.1007/s00253-017-8719-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 01/08/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are key enzymes in microorganisms for the assembly of peptide backbones of biologically and pharmacologically active natural products. The monomodular NRPS-like enzymes comprise often an adenylation (A), a thiolation (T), and a thioesterase (TE) domain. In contrast to the NRPSs, they do not contain any condensation domain and usually catalyze a dimerization of α-keto carboxylic acids and thereby provide diverse scaffolds for further modifications. In this study, we established an expression system for NRPS-like genes in Saccharomyces cerevisiae. By expression of four known genes from Aspergillus terreus, their predicted function was confirmed and product yields of up to 35 mg per liter culture were achieved. Furthermore, expression of ATEG_03090 from the same fungus, encoding for the last uncharacterized NRPS-like enzyme with an A-T-TE domain structure, led to the formation of the benzoquinone derivative atromentin. All the accumulated products were isolated and their structures were elucidated by NMR and MS analyses. This study provides a convenient system for proof of gene function as well as a basis for synthetic biology, since additional genes encoding modification enzymes can be introduced.
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527
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Miyanaga A, Kudo F, Eguchi T. Protein–protein interactions in polyketide synthase–nonribosomal peptide synthetase hybrid assembly lines. Nat Prod Rep 2018; 35:1185-1209. [DOI: 10.1039/c8np00022k] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The protein–protein interactions in polyketide synthase–nonribosomal peptide synthetase hybrids are summarized and discussed.
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Affiliation(s)
- Akimasa Miyanaga
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Fumitaka Kudo
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
| | - Tadashi Eguchi
- Department of Chemistry
- Tokyo Institute of Technology
- Tokyo 152-8551
- Japan
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528
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Tailhades J, Schoppet M, Greule A, Peschke M, Brieke C, Cryle MJ. A route to diastereomerically pure phenylglycine thioester peptides: crucial intermediates for investigating glycopeptide antibiotic biosynthesis. Chem Commun (Camb) 2018; 54:2146-2149. [DOI: 10.1039/c7cc09409d] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Non-ribosomal peptides contain an array of amino acid building blocks that can present challenges for the synthesis of important intermediates. Here we report a route to incorporate phenylglycine residues in peptide thioesters without significant racemisation.
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Affiliation(s)
- Julien Tailhades
- EMBL Australia, Monash University
- Clayton
- Australia
- The Monash Biomedicine Discovery Institute
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging
| | - Melanie Schoppet
- EMBL Australia, Monash University
- Clayton
- Australia
- The Monash Biomedicine Discovery Institute
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging
| | - Anja Greule
- EMBL Australia, Monash University
- Clayton
- Australia
- The Monash Biomedicine Discovery Institute
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging
| | - Madeleine Peschke
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- Jahnstrasse 29
- Germany
| | - Clara Brieke
- Department of Biomolecular Mechanisms
- Max Planck Institute for Medical Research
- Jahnstrasse 29
- Germany
| | - Max J. Cryle
- EMBL Australia, Monash University
- Clayton
- Australia
- The Monash Biomedicine Discovery Institute
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging
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529
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Baltz RH. Synthetic biology, genome mining, and combinatorial biosynthesis of NRPS-derived antibiotics: a perspective. J Ind Microbiol Biotechnol 2017; 45:635-649. [PMID: 29288438 DOI: 10.1007/s10295-017-1999-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/18/2017] [Indexed: 11/28/2022]
Abstract
Combinatorial biosynthesis of novel secondary metabolites derived from nonribosomal peptide synthetases (NRPSs) has been in slow development for about a quarter of a century. Progress has been hampered by the complexity of the giant multimodular multienzymes. More recently, advances have been made on understanding the chemical and structural biology of these complex megaenzymes, and on learning the design rules for engineering functional hybrid enzymes. In this perspective, I address what has been learned about successful engineering of complex lipopeptides related to daptomycin, and discuss how synthetic biology and microbial genome mining can converge to broaden the scope and enhance the speed and robustness of combinatorial biosynthesis of NRPS-derived natural products for drug discovery.
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Affiliation(s)
- Richard H Baltz
- CognoGen Biotechnology Consulting, 7636 Andora Drive, Sarasota, FL, 34238, USA.
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530
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Zhang S, Zhu J, Zechel DL, Jessen-Trefzer C, Eastman RT, Paululat T, Bechthold A. New WS9326A Derivatives and One New Annimycin Derivative with Antimalarial Activity are Produced by Streptomyces asterosporus DSM 41452 and Its Mutant. Chembiochem 2017; 19:272-279. [PMID: 29148157 DOI: 10.1002/cbic.201700428] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Indexed: 11/10/2022]
Abstract
In this study, we report that Streptomyces asterosporus DSM 41452 is a producer of new molecules related to the nonribosomal cyclodepsipeptide WS9326A and the polyketide annimycin. S. asterosporus DSM 41452 is shown to produce six cyclodepsipeptides and peptides, WS9326A to G. Notably, the compounds WS9326F and WS9326G have not been described before. The genome of S. asterosporus DSM 41452 was sequenced, and a putative WS9326A gene cluster was identified. Gene-deletion experiments confirmed that this cluster was responsible for the biosynthesis of WS9326A to G. Additionally, a gene-deletion experiment demonstrated that sas16 encoding a cytochrome P450 monooxygenase was involved in the synthesis of the novel (E)-2,3-dehydrotyrosine residue found in WS9326A and its derivatives. An insertion mutation within the putative annimycin gene cluster led to the production of a new annimycin derivative, annimycin B, which exhibited modest inhibitory activity against Plasmodium falciparum.
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Affiliation(s)
- Songya Zhang
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
| | - Jing Zhu
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
| | - David L Zechel
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario, K7L 3N6, Canada
| | - Claudia Jessen-Trefzer
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
| | - Richard T Eastman
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences/NIH, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Thomas Paululat
- Department of Chemistry and Biology, Universität Siegen, Adolf-Reichwein-Strasse 2, 57068, Siegen, Germany
| | - Andreas Bechthold
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Strasse 19 VF, 79104, Freiburg im Breisgau, Germany
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531
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Guo C, Mandalapu D, Ji X, Gao J, Zhang Q. Chemistry and Biology of Teixobactin. Chemistry 2017; 24:5406-5422. [PMID: 28991382 DOI: 10.1002/chem.201704167] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Indexed: 11/06/2022]
Abstract
Bacterial resistance to existing drugs is becoming a serious public health issue, urging extensive search for new antibiotics. Teixobactin, a cyclic depsipeptide discovered in a screen of uncultured bacteria, shows potent activity against all the tested Gram-positive bacteria. Remarkably, no teixobactin-resistant bacterial strain has been obtained despite extensive efforts, highlighting the great potential of teixobactin as a lead compound in the fight against antimicrobial resistance (AMR). This review summarizes recent progresses in the understanding of many aspects of teixobactin, including chemical structure, biological activity, biosynthetic pathway, and mode of action. We also discuss the different synthetic strategies in producing teixobactin and its analogues, and the structure-activity relationship (SAR) studies.
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Affiliation(s)
- Chuchu Guo
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | | | - Xinjian Ji
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
| | - Jiangtao Gao
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, P. R. China
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532
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Kittilä T, Cryle MJ. An enhanced chemoenzymatic method for loading substrates onto carrier protein domains. Biochem Cell Biol 2017; 96:372-379. [PMID: 29172027 DOI: 10.1139/bcb-2017-0275] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Non-ribosomal peptide synthetase (NRPS) machineries produce many medically relevant peptides that cannot be easily accessed by chemical synthesis. Thus, understanding NRPS mechanism is of crucial importance to allow efficient redesign of these machineries to produce new compounds. During NRPS-mediated synthesis, substrates are covalently attached to peptidyl carrier proteins (PCPs), and studies of NRPSs are impeded by difficulties in producing PCPs loaded with substrates. Different approaches to load substrates onto PCP domains have been described, but all suffer from difficulties in either the complexity of chemical synthesis or low enzymatic efficiency. Here, we describe an enhanced chemoenzymatic loading method that combines 2 approaches into a single, highly efficient one-pot loading reaction. First, d-pantetheine and ATP are converted into dephospho-coenzyme A via the actions of 2 enzymes from coenzyme A (CoA) biosynthesis. Next, phosphoadenylates are dephosphorylated using alkaline phosphatase to allow linker attachment to PCP domain by Sfp mutant R4-4, which is inhibited by phosphoadenylates. This route does not depend on activity of the commonly problematic dephospho-CoA kinase and, therefore, offers an improved method for substrate loading onto PCP domains.
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Affiliation(s)
- Tiia Kittilä
- a Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Max J Cryle
- a Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,b The Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,c EMBL Australia, Monash University, Clayton, Victoria 3800, Australia
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533
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Nonribosomal biosynthesis of backbone-modified peptides. Nat Chem 2017; 10:282-287. [DOI: 10.1038/nchem.2891] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 10/06/2017] [Indexed: 01/01/2023]
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534
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Meyer S, Mainz A, Kehr JC, Süssmuth RD, Dittmann E. Prerequisites of Isopeptide Bond Formation in Microcystin Biosynthesis. Chembiochem 2017; 18:2376-2379. [PMID: 29024253 DOI: 10.1002/cbic.201700389] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Indexed: 11/11/2022]
Abstract
The biosynthesis of the potent cyanobacterial hepatotoxin microcystin involves isopeptide bond formation through the carboxylic acid side chains of d-glutamate and β-methyl d-aspartate. Analysis of the in vitro activation profiles of the two corresponding adenylation domains, McyE-A and McyB-A2 , either in a didomain or a tridomain context with the cognate thiolation domain and the upstream condensation domain revealed that substrate activation of both domains strictly depended on the presence of the condensation domains. We further identified two key amino acids in the binding pockets of both adenylation domains that could serve as a bioinformatic signature of isopeptide bond-forming modules incorporating d-glutamate or d-aspartate. Our findings further contribute to the understanding of the multifaceted role of condensation domains in nonribosomal peptide synthetase assembly lines.
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Affiliation(s)
- Sabine Meyer
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Strasse 24/25, 14476, Potsdam-Golm, Germany
| | - Andi Mainz
- Technical University Berlin, Department of Organic Chemistry, Strasse des 17. Juni 124/ TC2, 10626, Berlin, Germany
| | - Jan-Christoph Kehr
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Strasse 24/25, 14476, Potsdam-Golm, Germany
| | - Roderich D Süssmuth
- Technical University Berlin, Department of Organic Chemistry, Strasse des 17. Juni 124/ TC2, 10626, Berlin, Germany
| | - Elke Dittmann
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Strasse 24/25, 14476, Potsdam-Golm, Germany
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535
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Aldemir H, Gulder TAM. Erweiterung des Strukturraums ribosomaler Peptide: autokatalytische N-Methylierung in der Omphalotin-Biosynthese. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hülya Aldemir
- Fakultät für Chemie; Technische Universität München (TUM); Lichtenbergstraße 4 85748 Garching Deutschland
| | - Tobias A. M. Gulder
- Fakultät für Chemie; Technische Universität München (TUM); Lichtenbergstraße 4 85748 Garching Deutschland
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536
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Kaweewan I, Komaki H, Hemmi H, Kodani S. Isolation and Structure Determination of New Antibacterial Peptide Curacomycin Based on Genome Mining. ASIAN J ORG CHEM 2017. [DOI: 10.1002/ajoc.201700433] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Issara Kaweewan
- Graduate School of Integrated Science and Technology; Shizuoka University; 836 Ohya Suruga-ku Shizuoka 422-8529 Japan
| | - Hisayuki Komaki
- Biological Resource Center; National Institute of Technology and Evaluation (NBRC); 2-5-8 Kazusakamatari Kisarazu Chiba 292-0818 Japan
| | - Hikaru Hemmi
- Food Research Institute; National Agriculture and Food Research Organization (NARO); 2-1-12 Kannondai Tsukuba Ibaraki 305-8642 Japan
| | - Shinya Kodani
- Graduate School of Integrated Science and Technology; Shizuoka University; 836 Ohya Suruga-ku Shizuoka 422-8529 Japan
- Academic Institute; Shizuoka University; 836 Ohya Suruga-ku Shizuoka 422-8529 Japan
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537
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Aldemir H, Gulder TAM. Expanding the Structural Space of Ribosomal Peptides: Autocatalytic N-Methylation in Omphalotin Biosynthesis. Angew Chem Int Ed Engl 2017; 56:13570-13572. [PMID: 28949431 DOI: 10.1002/anie.201708456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Indexed: 11/11/2022]
Abstract
Tail-Me: The N-methylation of backbone amide bonds in peptide natural products was thought to be exclusive to non-ribosomal peptides. A newly discovered methylation mechanism now brings this structural feature into the world of ribosomal peptides, thereby significantly expanding the structural diversity of ribosomally synthesized and post-translationally modified peptides (RiPPs).
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Affiliation(s)
- Hülya Aldemir
- Biosystems Chemistry, Department of Chemistry and Center for Integrated Protein Science Munich (CiPSM), Technical University of Munich (TUM), Lichtenbergstraße 4, 85748, Garching, Germany
| | - Tobias A M Gulder
- Biosystems Chemistry, Department of Chemistry and Center for Integrated Protein Science Munich (CiPSM), Technical University of Munich (TUM), Lichtenbergstraße 4, 85748, Garching, Germany
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538
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Steiniger C, Hoffmann S, Mainz A, Kaiser M, Voigt K, Meyer V, Süssmuth RD. Harnessing fungal nonribosomal cyclodepsipeptide synthetases for mechanistic insights and tailored engineering. Chem Sci 2017; 8:7834-7843. [PMID: 29163920 PMCID: PMC5674221 DOI: 10.1039/c7sc03093b] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/25/2017] [Indexed: 11/21/2022] Open
Abstract
Hybrid fungal CDP synthetases are constructed from three different origins to produce highly active cyclodepsipeptides up to g L–1 scale.
Nonribosomal peptide synthetases represent potential platforms for the design and engineering of structurally complex peptides. While previous focus has been centred mainly on bacterial systems, fungal synthetases assembling drugs like the antifungal echinocandins, the antibacterial cephalosporins or the anthelmintic cyclodepsipeptide (CDP) PF1022 await in-depth exploitation. As various mechanistic features of fungal CDP biosynthesis are only partly understood, effective engineering of NRPSs has been severely hampered. By combining protein truncation, in trans expression and combinatorial swapping, we assigned important functional segments of fungal CDP synthetases and assessed their in vivo biosynthetic capabilities. Hence, artificial assembly line components comprising of up to three different synthetases were generated. Using Aspergillus niger as a heterologous expression host, we obtained new-to-nature octa-enniatin (4 mg L–1) and octa-beauvericin (10.8 mg L–1), as well as high titers of the hybrid CDP hexa-bassianolide (1.3 g L–1) with an engineered ring size. The hybrid compounds showed up to 12-fold enhanced antiparasitic activity against Leishmania donovani and Trypanosoma cruzi compared to the reference drugs miltefosine and benznidazole, respectively. Our findings thus contribute to a rational engineering of iterative nonribosomal assembly lines.
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Affiliation(s)
- Charlotte Steiniger
- Fachgebiet Biologische Chemie , Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany .
| | - Sylvester Hoffmann
- Fachgebiet Biologische Chemie , Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany .
| | - Andi Mainz
- Fachgebiet Biologische Chemie , Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany .
| | - Marcel Kaiser
- Parasite Chemotherapy , Medical Parasitology & Infection Biology , Swiss Tropical and Public Health Institute , Socinstrasse 57 , 4051 Basel , Switzerland.,University of Basel , Petersplatz 1 , 4003 Basel , Switzerland
| | - Kerstin Voigt
- Jena Microbial Resource Collection (JMRC) , Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie , Hans-Knöll-Institut , Adolf-Reichwein-Straße 23 , 07745 Jena , Germany
| | - Vera Meyer
- Fachgebiet Angewandte und Molekulare Mikrobiologie , Institut für Biotechnologie , Technische Universität Berlin , Gustav-Meyer-Allee 25 , 13355 Berlin , Germany
| | - Roderich D Süssmuth
- Fachgebiet Biologische Chemie , Institut für Chemie , Technische Universität Berlin , Strasse des 17. Juni 124 , 10623 Berlin , Germany .
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539
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Kittilä T, Kittel C, Tailhades J, Butz D, Schoppet M, Büttner A, Goode RJA, Schittenhelm RB, van Pee KH, Süssmuth RD, Wohlleben W, Cryle MJ, Stegmann E. Halogenation of glycopeptide antibiotics occurs at the amino acid level during non-ribosomal peptide synthesis. Chem Sci 2017; 8:5992-6004. [PMID: 28989629 PMCID: PMC5620994 DOI: 10.1039/c7sc00460e] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 06/20/2017] [Indexed: 12/30/2022] Open
Abstract
Halogenation plays a significant role in the activity of the glycopeptide antibiotics (GPAs), although up until now the timing and therefore exact substrate involved was unclear. Here, we present results combined from in vivo and in vitro studies that reveal the substrates for the halogenase enzymes from GPA biosynthesis as amino acid residues bound to peptidyl carrier protein (PCP)-domains from the non-ribosomal peptide synthetase machinery: no activity was detected upon either free amino acids or PCP-bound peptides. Furthermore, we show that the selectivity of GPA halogenase enzymes depends upon both the structure of the bound amino acid and the PCP domain, rather than being driven solely via the PCP domain. These studies provide the first detailed understanding of how halogenation is performed during GPA biosynthesis and highlight the importance and versatility of trans-acting enzymes that operate during peptide assembly by non-ribosomal peptide synthetases.
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Affiliation(s)
- Tiia Kittilä
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany
| | - Claudia Kittel
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen , Microbiology/Biotechnology , University of Tuebingen , Auf der Morgenstelle 28 , 72076 Tuebingen , Germany .
| | - Julien Tailhades
- EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
| | - Diane Butz
- Institut für Chemie , Technische Universität Berlin , 10623 Berlin , Germany
| | - Melanie Schoppet
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany
- EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
| | - Anita Büttner
- Allgemeine Biochemie , TU Dresden , 01062 Dresden , Germany
| | - Rob J A Goode
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
- Monash Biomedical Proteomics Facility , Monash University , Clayton , Victoria 3800 , Australia
| | - Ralf B Schittenhelm
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
- Monash Biomedical Proteomics Facility , Monash University , Clayton , Victoria 3800 , Australia
| | - Karl-Heinz van Pee
- Institut für Chemie , Technische Universität Berlin , 10623 Berlin , Germany
| | | | - Wolfgang Wohlleben
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen , Microbiology/Biotechnology , University of Tuebingen , Auf der Morgenstelle 28 , 72076 Tuebingen , Germany .
- German Centre for Infection Research (DZIF) , Partner Site Tuebingen , Tuebingen , Germany
| | - Max J Cryle
- Department of Biomolecular Mechanisms , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany
- EMBL Australia , Monash University , Clayton , Victoria 3800 , Australia .
- The Monash Biomedicine Discovery Institute , Department of Biochemistry and Molecular Biology , Monash University , Clayton , Victoria 3800 , Australia
- ARC Centre of Excellence in Advanced Molecular Imaging , Monash University , Clayton , Victoria 3800 , Australia
| | - Evi Stegmann
- Interfaculty Institute of Microbiology and Infection Medicine Tuebingen , Microbiology/Biotechnology , University of Tuebingen , Auf der Morgenstelle 28 , 72076 Tuebingen , Germany .
- German Centre for Infection Research (DZIF) , Partner Site Tuebingen , Tuebingen , Germany
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540
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Abstract
Covering: up to 2017.Natural products are important secondary metabolites produced by bacterial and fungal species that play important roles in cellular growth and signaling, nutrient acquisition, intra- and interspecies communication, and virulence. A subset of natural products is produced by nonribosomal peptide synthetases (NRPSs), a family of large, modular enzymes that function in an assembly line fashion. Because of the pharmaceutical activity of many NRPS products, much effort has gone into the exploration of their biosynthetic pathways and the diverse products they make. Many interesting NRPS pathways have been identified and characterized from both terrestrial and marine bacterial sources. Recently, several NRPS pathways in human commensal bacterial species have been identified that produce molecules with antibiotic activity, suggesting another source of interesting NRPS pathways may be the commensal and pathogenic bacteria that live on the human body. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) have been identified as a significant cause of human bacterial infections that are frequently multidrug resistant. The emerging resistance profile of these organisms has prompted calls from multiple international agencies to identify novel antibacterial targets and develop new approaches to treat infections from ESKAPE pathogens. Each of these species contains several NRPS biosynthetic gene clusters. While some have been well characterized and produce known natural products with important biological roles in microbial physiology, others have yet to be investigated. This review catalogs the NRPS pathways of ESKAPE pathogens. The exploration of novel NRPS products may lead to a better understanding of the chemical communication used by human pathogens and potentially to the discovery of novel therapeutic approaches.
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Affiliation(s)
- Andrew M Gulick
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
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541
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Ramm S, Krawczyk B, Mühlenweg A, Poch A, Mösker E, Süssmuth RD. A Self‐Sacrificing
N
‐Methyltransferase Is the Precursor of the Fungal Natural Product Omphalotin. Angew Chem Int Ed Engl 2017; 56:9994-9997. [DOI: 10.1002/anie.201703488] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/16/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Sascha Ramm
- Institut für Chemie Strasse des 17. Juni 124 10623 Berlin Germany
| | | | - Agnes Mühlenweg
- Institut für Chemie Strasse des 17. Juni 124 10623 Berlin Germany
| | - Annette Poch
- Institut für Chemie Strasse des 17. Juni 124 10623 Berlin Germany
| | - Eva Mösker
- Institut für Chemie Strasse des 17. Juni 124 10623 Berlin Germany
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542
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Abstract
The need for new drugs for the treatment of various diseases is enormous. From the previous century until the present, numerous peptide and peptide-derived natural products have been isolated from bacteria and fungi. Hence, microorganisms play a pivotal role as sources for novel drugs with an emphasis on anti-infective agents. Various disciplines from biology, chemistry, and medicine are involved in early stages of the search for peptide natural products including taxonomy, microbiology, bioanalytics, bioinformatics, and medicinal chemistry. Under biochemical aspects, small peptide drugs are basically either ribosomally synthesized and post-translationally modified (RiPPs) or synthesized by multimodular nonribosomal peptide synthetases (NRPSs). Within the context of current developments on bioactive peptide natural products, this Account predominantly highlights recent discoveries, approaches, and research from our laboratory on RiPPs and NRPSs from bacteria and fungi. In our search for peptides showing bioactivities of interest, different approaches were applied: classical screening, in silico prediction, in vitro reconstitution, site-directed mutagenesis, chemoenzymatics, heterologous expression, and total synthesis including structure-activity relationship (SAR) studies in the research on the labyrinthopeptins, albicidin, and the cyclodepsipeptides (CDPs). The ribosomally synthesized labyrinthopeptins, class III lanthipeptides, which have been discovered in a classical screening campaign, display highly attractive antiallodynic (against neuropathic pain caused by dysfunction of the nervous system) and antiviral activities. Therefore, the biosynthetic assembly was investigated by extensive enzymatic studies of the modifying enzymes, and site-directed mutagenesis was performed for the generation of analogs. By genome mining, other class III lanthipeptides have been uncovered, while synthetic access proved to be an unmet challenge for the labyrinthopeptins. In contrast, for the gyrase inhibitor albicidin, the establishment of a chemical synthesis followed by medicinal chemistry studies was the only viable option to gain access to derivatives. Albicidin, which has been discovered investigating plant host-pathogen interactions, has a strong activity against Gram-negative bacteria, for example, Escherichia coli and Pseudomonas aeruginosa, and a future synthetic derivative may become a lead structure for development of an anti-Gram-negative drug. The compound class of the cyclodepsipeptides contributes already two marketed drugs, enniatin (fusafungine) and emodepside. Cyclodepsipeptides show general antibacterial and antifungal effects, whereas specific insecticidal and anthelmintic activities provide lead structures for drug development. Hence, exploiting the chances of reprogramming NRPSs, the generation of chimeric or otherwise designed synthetases could render a new untapped structural space and thus novel bioactivities. While current developments in the fields of genomics, bioinformatics, and molecular biology facilitate the search for new natural products and the design of new peptide structures, the next decade will show which compounds have been carried on further applications and whether current developments have led to an increase in drug candidates.
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Affiliation(s)
- Tam Dang
- Technische Universität Berlin, Institut für Chemie, Fachgebiet Biologische
Chemie, Strasse des 17.
Juni 124, 10623 Berlin, Germany
| | - Roderich D. Süssmuth
- Technische Universität Berlin, Institut für Chemie, Fachgebiet Biologische
Chemie, Strasse des 17.
Juni 124, 10623 Berlin, Germany
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543
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Ramm S, Krawczyk B, Mühlenweg A, Poch A, Mösker E, Süssmuth RD. Eine sich selbst opfernde
N
‐Methyltransferase ist die Vorstufe des pilzlichen Sekundärmetaboliten Omphalotin. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sascha Ramm
- Institut für Chemie Straße des 17. Juni 124 10623 Berlin Deutschland
| | | | - Agnes Mühlenweg
- Institut für Chemie Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Annette Poch
- Institut für Chemie Straße des 17. Juni 124 10623 Berlin Deutschland
| | - Eva Mösker
- Institut für Chemie Straße des 17. Juni 124 10623 Berlin Deutschland
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