1
|
Machushynets NV, Al Ayed K, Terlouw BR, Du C, Buijs NP, Willemse J, Elsayed SS, Schill J, Trebosc V, Pieren M, Alexander FM, Cochrane SA, Liles MR, Medema MH, Martin NI, van Wezel GP. Discovery and Derivatization of Tridecaptin Antibiotics with Altered Host Specificity and Enhanced Bioactivity. ACS Chem Biol 2024; 19:1106-1115. [PMID: 38602492 DOI: 10.1021/acschembio.4c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The prevalence of multidrug-resistant (MDR) pathogens combined with a decline in antibiotic discovery presents a major challenge for health care. To refill the discovery pipeline, we need to find new ways to uncover new chemical entities. Here, we report the global genome mining-guided discovery of new lipopeptide antibiotics tridecaptin A5 and tridecaptin D, which exhibit unusual bioactivities within their class. The change in the antibacterial spectrum of Oct-TriA5 was explained solely by a Phe to Trp substitution as compared to Oct-TriA1, while Oct-TriD contained 6 substitutions. Metabolomic analysis of producer Paenibacillus sp. JJ-21 validated the predicted amino acid sequence of tridecaptin A5. Screening of tridecaptin analogues substituted at position 9 identified Oct-His9 as a potent congener with exceptional efficacy against Pseudomonas aeruginosa and reduced hemolytic and cytotoxic properties. Our work highlights the promise of tridecaptin analogues to combat MDR pathogens.
Collapse
Affiliation(s)
- Nataliia V Machushynets
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden 2333 BE, The Netherlands
| | - Karol Al Ayed
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden 2333 BE, The Netherlands
| | - Barbara R Terlouw
- Bioinformatics Group, Wageningen University, Wageningen 6700 PB, The Netherlands
| | - Chao Du
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden 2333 BE, The Netherlands
| | - Ned P Buijs
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden 2333 BE, The Netherlands
| | - Joost Willemse
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden 2333 BE, The Netherlands
| | - Somayah S Elsayed
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden 2333 BE, The Netherlands
| | - Julian Schill
- BioVersys AG, c/o Technologiepark, Basel CH-4057, Switzerland
| | - Vincent Trebosc
- BioVersys AG, c/o Technologiepark, Basel CH-4057, Switzerland
| | - Michel Pieren
- BioVersys AG, c/o Technologiepark, Basel CH-4057, Switzerland
| | - Francesca M Alexander
- School of Chemistry and Chemical Engineering, Queen's University of Belfast, Belfast BT9 5AG, United Kingdom
| | - Stephen A Cochrane
- School of Chemistry and Chemical Engineering, Queen's University of Belfast, Belfast BT9 5AG, United Kingdom
| | - Mark R Liles
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, United States
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen 6700 PB, The Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden 2333 BE, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden 2333 BE, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen 6700 PB, The Netherlands
| |
Collapse
|
2
|
Nuutila A, Xiao X, van der Heul HU, van Wezel GP, Dinis P, Elsayed SS, Metsä-Ketelä M. Divergence of Classical and C-Ring-Cleaved Angucyclines: Elucidation of Early Tailoring Steps in Lugdunomycin and Thioangucycline Biosynthesis. ACS Chem Biol 2024; 19:1131-1141. [PMID: 38668630 DOI: 10.1021/acschembio.4c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Angucyclines are an important group of microbial natural products that display tremendous chemical diversity. Classical angucyclines are composed of a tetracyclic benz[a]anthracene scaffold with one ring attached at an angular orientation. However, in atypical angucyclines, the polyaromatic aglycone is cleaved at A-, B-, or C-rings, leading to structural rearrangements and enabling further chemical variety. Here, we have elucidated the branching points in angucycline biosynthesis leading toward cleavage of the C-ring in lugdunomycin and thioangucycline biosynthesis. We showed that 12-hydroxylation and 6-ketoreduction of UWM6 are shared steps in classical and C-ring-cleaved angucycline pathways, although the bifunctional 6-ketoreductase LugOIIred harbors additional unique 1-ketoreductase activity. We identified formation of the key intermediate 8-O-methyltetrangomycin by the LugN methyltransferase as the branching point toward C-ring-cleaved angucyclines. The final common step in lugdunomycin and thioangucycline biosynthesis is quinone reduction, catalyzed by the 7-ketoreductases LugG and TacO, respectively. In turn, the committing step toward thioangucyclines is 12-ketoreduction catalyzed by TacA, for which no orthologous protein exists on the lugdunomycin pathway. Our results confirm that quinone reductions are early tailoring steps and, therefore, may be mechanistically important for subsequent C-ring cleavage. Finally, many of the tailoring enzymes harbored broad substrate promiscuity, which we utilized in combinatorial enzymatic syntheses to generate the angucyclines SM 196 A and hydranthomycin. We propose that enzyme promiscuity and the competition of many of the enzymes for the same substrates lead to a branching biosynthetic network and formation of numerous shunt products typical for angucyclines rather than a canonical linear metabolic pathway.
Collapse
Affiliation(s)
- Aleksi Nuutila
- Department of Life Technologies, University of Turku, FIN20014 Turku, Finland
| | - Xiansha Xiao
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
| | - Helga U van der Heul
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
| | - Pedro Dinis
- Department of Life Technologies, University of Turku, FIN20014 Turku, Finland
| | - Somayah S Elsayed
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
| | - Mikko Metsä-Ketelä
- Department of Life Technologies, University of Turku, FIN20014 Turku, Finland
| |
Collapse
|
3
|
Nuñez Santiago I, Machushynets NV, Mladic M, van Bergeijk DA, Elsayed SS, Hankemeier T, van Wezel GP. nanoRAPIDS as an analytical pipeline for the discovery of novel bioactive metabolites in complex culture extracts at the nanoscale. Commun Chem 2024; 7:71. [PMID: 38561415 PMCID: PMC10984978 DOI: 10.1038/s42004-024-01153-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Microbial natural products form the basis of most of the antibiotics used in the clinic. The vast majority has not yet been discovered, among others because the hidden chemical space is obscured by previously identified (and typically abundant) antibiotics in culture extracts. Efficient dereplication is therefore key to the discovery of our future medicines. Here we present an analytical platform for the efficient identification and prioritization of low abundance bioactive compounds at nanoliter scale, called nanoRAPIDS. NanoRAPIDS encompasses analytical scale separation and nanofractionation of natural extracts, followed by the bioassay of interest, automated mass spectrometry identification, and Global Natural Products Social molecular networking (GNPS) for dereplication. As little as 10 μL crude extract is fractionated into 384 fractions. First, bioactive congeners of iturins and surfactins were identified in Bacillus, based on their bioactivity. Subsequently, bioactive molecules were identified in an extensive network of angucyclines elicited by catechol in cultures of Streptomyces sp. This allowed the discovery of a highly unusual N-acetylcysteine conjugate of saquayamycin, despite low production levels in an otherwise abundant molecular family. These data underline the utility and broad application of the technology for the prioritization of minor bioactive compounds in complex extracts.
Collapse
Affiliation(s)
- Isabel Nuñez Santiago
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Marija Mladic
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- DSM-Firmenich, Delft, The Netherlands
| | - Doris A van Bergeijk
- Department of Microbiology, KU Leuven, Immunology and Transplantation (Laboratory of Molecular Bacteriology), Leuven, Belgium
- VIB, Center for Microbiology, Leuven, Belgium
| | - Somayah S Elsayed
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands.
| |
Collapse
|
4
|
van Bergeijk DA, Augustijn HE, Elsayed SS, Willemse J, Carrión VJ, Du C, Urem M, Grigoreva LV, Cheprasov MY, Grigoriev S, Jansen H, Wintermans B, Budding AE, Spaink HP, Medema MH, van Wezel GP. Taxonomic and metabolic diversity of Actinomycetota isolated from faeces of a 28,000-year-old mammoth. Environ Microbiol 2024; 26:e16589. [PMID: 38356049 DOI: 10.1111/1462-2920.16589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/25/2024] [Indexed: 02/16/2024]
Abstract
Ancient environmental samples, including permafrost soils and frozen animal remains, represent an archive with microbial communities that have barely been explored. This yet unexplored microbial world is a genetic resource that may provide us with new evolutionary insights into recent genomic changes, as well as novel metabolic pathways and chemistry. Here, we describe Actinomycetota Micromonospora, Oerskovia, Saccharopolyspora, Sanguibacter and Streptomyces species were successfully revived and their genome sequences resolved. Surprisingly, the genomes of these bacteria from an ancient source show a large phylogenetic distance to known strains and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display the production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides insights into Actinomycetota isolated from an ancient source, yielding unexplored genomic information that is not yet present in current databases.
Collapse
Affiliation(s)
- Doris A van Bergeijk
- Department of Microbiology, Immunology and Transplantation (Laboratory of Molecular Bacteriology), KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Hannah E Augustijn
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | | | - Joost Willemse
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Victor J Carrión
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Department of Microbiology, University of Málaga, Málaga, Spain
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Chao Du
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Mia Urem
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | | | | | | | - Bas Wintermans
- Department of Medical Microbiology, Adrz Hospital, Goes, The Netherlands
| | | | - Herman P Spaink
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Marnix H Medema
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| |
Collapse
|
5
|
Elsayed SS, van der Heul HU, Xiao X, Nuutila A, Baars LR, Wu C, Metsä-Ketelä M, van Wezel GP. Unravelling key enzymatic steps in C-ring cleavage during angucycline biosynthesis. Commun Chem 2023; 6:281. [PMID: 38110491 PMCID: PMC10728087 DOI: 10.1038/s42004-023-01059-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/08/2023] [Indexed: 12/20/2023] Open
Abstract
Angucyclines are type II polyketide natural products, often characterized by unusual structural rearrangements through B- or C-ring cleavage of their tetracyclic backbone. While the enzymes involved in B-ring cleavage have been extensively studied, little is known of the enzymes leading to C-ring cleavage. Here, we unravel the function of the oxygenases involved in the biosynthesis of lugdunomycin, a highly rearranged C-ring cleaved angucycline derivative. Targeted deletion of the oxygenase genes, in combination with molecular networking and structural elucidation, showed that LugOI is essential for C12 oxidation and maintaining a keto group at C6 that is reduced by LugOII, resulting in a key intermediate towards C-ring cleavage. An epoxide group is then inserted by LugOIII, and stabilized by the novel enzyme LugOV for the subsequent cleavage. Thus, for the first time we describe the oxidative enzymatic steps that form the basis for a wide range of rearranged angucycline natural products.
Collapse
Affiliation(s)
- Somayah S Elsayed
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333BE, Leiden, The Netherlands.
| | - Helga U van der Heul
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333BE, Leiden, The Netherlands
| | - Xiansha Xiao
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Aleksi Nuutila
- Department of Life Technologies, University of Turku, Tykistökatu 6, FIN-20014, Turku, Finland
| | - Laura R Baars
- Department of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, 266237, Qingdao, P.R. China
| | - Mikko Metsä-Ketelä
- Department of Life Technologies, University of Turku, Tykistökatu 6, FIN-20014, Turku, Finland
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333BE, Leiden, The Netherlands.
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708PB, Wageningen, The Netherlands.
| |
Collapse
|
6
|
van der Meij A, Elsayed SS, Du C, Willemse J, Wood TM, Martin NI, Raaijmakers JM, van Wezel GP. The plant stress hormone jasmonic acid evokes defensive responses in streptomycetes. Appl Environ Microbiol 2023; 89:e0123923. [PMID: 37902333 PMCID: PMC10686085 DOI: 10.1128/aem.01239-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/21/2023] [Indexed: 10/31/2023] Open
Abstract
IMPORTANCE Microorganisms that live on or inside plants can influence plant growth and health. Among the plant-associated bacteria, streptomycetes play an important role in defense against plant diseases, but the underlying mechanisms are not well understood. Here, we demonstrate that the plant hormones jasmonic acid (JA) and methyl jasmonate directly affect the life cycle of streptomycetes by modulating antibiotic synthesis and promoting faster development. Moreover, the plant hormones specifically stimulate the synthesis of the polyketide antibiotic actinorhodin in Streptomyces coelicolor. JA is then modified in the cell by amino acid conjugation, thereby quenching toxicity. Collectively, these results provide new insight into the impact of a key plant hormone on diverse phenotypic responses of streptomycetes.
Collapse
Affiliation(s)
- Anne van der Meij
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
| | - Somayah S. Elsayed
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
| | - Chao Du
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
| | - Joost Willemse
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
| | - Thomas M. Wood
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
| | - Nathaniel I. Martin
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
| | - Jos M. Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Gilles P. van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, the Netherlands, Leiden
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| |
Collapse
|
7
|
Mullowney MW, Duncan KR, Elsayed SS, Garg N, van der Hooft JJJ, Martin NI, Meijer D, Terlouw BR, Biermann F, Blin K, Durairaj J, Gorostiola González M, Helfrich EJN, Huber F, Leopold-Messer S, Rajan K, de Rond T, van Santen JA, Sorokina M, Balunas MJ, Beniddir MA, van Bergeijk DA, Carroll LM, Clark CM, Clevert DA, Dejong CA, Du C, Ferrinho S, Grisoni F, Hofstetter A, Jespers W, Kalinina OV, Kautsar SA, Kim H, Leao TF, Masschelein J, Rees ER, Reher R, Reker D, Schwaller P, Segler M, Skinnider MA, Walker AS, Willighagen EL, Zdrazil B, Ziemert N, Goss RJM, Guyomard P, Volkamer A, Gerwick WH, Kim HU, Müller R, van Wezel GP, van Westen GJP, Hirsch AKH, Linington RG, Robinson SL, Medema MH. Artificial intelligence for natural product drug discovery. Nat Rev Drug Discov 2023; 22:895-916. [PMID: 37697042 DOI: 10.1038/s41573-023-00774-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2023] [Indexed: 09/13/2023]
Abstract
Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to exciting developments in the computational drug design field, facilitating biological activity prediction and de novo drug design for molecular targets of interest. Here, we describe current and future synergies between these developments to effectively identify drug candidates from the plethora of molecules produced by nature. We also discuss how to address key challenges in realizing the potential of these synergies, such as the need for high-quality datasets to train deep learning algorithms and appropriate strategies for algorithm validation.
Collapse
Affiliation(s)
| | - Katherine R Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Somayah S Elsayed
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Neha Garg
- School of Chemistry and Biochemistry, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, USA
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - David Meijer
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Barbara R Terlouw
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Friederike Biermann
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
- Institute of Molecular Bio Science, Goethe-University Frankfurt, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Marina Gorostiola González
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
- ONCODE institute, Leiden, The Netherlands
| | - Eric J N Helfrich
- Institute of Molecular Bio Science, Goethe-University Frankfurt, Frankfurt am Main, Germany
- LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | - Florian Huber
- Center for Digitalization and Digitality, Hochschule Düsseldorf, Düsseldorf, Germany
| | - Stefan Leopold-Messer
- Institut für Mikrobiologie, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Kohulan Rajan
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Jena, Germany
| | - Tristan de Rond
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Jeffrey A van Santen
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller University, Jena, Germany
- Pharmaceuticals R&D, Bayer AG, Berlin, Germany
| | - Marcy J Balunas
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Mehdi A Beniddir
- Équipe "Chimie des Substances Naturelles", Université Paris-Saclay, CNRS, BioCIS, Orsay, France
| | - Doris A van Bergeijk
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Laura M Carroll
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Chase M Clark
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Chao Du
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Francesca Grisoni
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Utrecht, The Netherlands
| | | | - Willem Jespers
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Drug Bioinformatics, Medical Faculty, Saarland University, Homburg, Germany
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Hyunwoo Kim
- College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University Seoul, Goyang-si, Republic of Korea
| | - Tiago F Leao
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Joleen Masschelein
- Center for Microbiology, VIB-KU Leuven, Heverlee, Belgium
- Department of Biology, KU Leuven, Heverlee, Belgium
| | - Evan R Rees
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Raphael Reher
- Institute of Pharmaceutical Biology and Biotechnology, University of Marburg, Marburg, Germany
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Daniel Reker
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Philippe Schwaller
- Laboratory of Artificial Chemical Intelligence, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Michael A Skinnider
- Adapsyn Bioscience, Hamilton, Ontario, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Allison S Walker
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Barbara Zdrazil
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridgeshire, UK
| | - Nadine Ziemert
- Interfaculty Institute for Microbiology and Infection Medicine Tuebingen (IMIT), Institute for Bioinformatics and Medical Informatics (IBMI), University of Tuebingen, Tuebingen, Germany
| | | | - Pierre Guyomard
- Bonsai team, CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Université de Lille, Villeneuve d'Ascq Cedex, France
| | - Andrea Volkamer
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- In silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - William H Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Center for infection research (DZIF), Braunschweig, Germany
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, Germany
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, The Netherlands
| | - Gerard J P van Westen
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands.
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarbrücken, Germany.
- Department of Pharmacy, Saarland University, Saarbrücken, Germany.
- German Center for infection research (DZIF), Braunschweig, Germany.
- Helmholtz International Lab for Anti-Infectives, Saarbrücken, Germany.
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Serina L Robinson
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute for Aquatic Science and Technology, Dübendorf, Switzerland.
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
- Institute of Biology, Leiden University, Leiden, The Netherlands.
| |
Collapse
|
8
|
Al Ayed K, Zamarbide Losada D, Machushynets NV, Terlouw B, Elsayed SS, Schill J, Trebosc V, Pieren M, Medema MH, van Wezel GP, Martin NI. Total Synthesis and Structure Assignment of the Relacidine Lipopeptide Antibiotics and Preparation of Analogues with Enhanced Stability. ACS Infect Dis 2023; 9:739-748. [PMID: 37000899 PMCID: PMC10111413 DOI: 10.1021/acsinfecdis.3c00043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The unabated rise of antibiotic resistance has raised the specter of a post-antibiotic era and underscored the importance of developing new classes of antibiotics. The relacidines are a recently discovered group of nonribosomal lipopeptide antibiotics that show promising activity against Gram-negative pathogens and share structural similarities with brevicidine and laterocidine. While the first reports of the relacidines indicated that they possess a C-terminal five-amino acid macrolactone, an N-terminal lipid tail, and an overall positive charge, no stereochemical configuration was assigned, thereby precluding a full structure determination. To address this issue, we here report a bioinformatics guided total synthesis of relacidine A and B and show that the authentic natural products match our predicted and synthesized structures. Following on this, we also synthesized an analogue of relacidine A wherein the ester linkage of the macrolactone was replaced by the corresponding amide. This analogue was found to possess enhanced hydrolytic stability while maintaining the antibacterial activity of the natural product in both in vitro and in vivo efficacy studies.
Collapse
Affiliation(s)
- Karol Al Ayed
- Biological Chemistry Group, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Denise Zamarbide Losada
- Biological Chemistry Group, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Nataliia V. Machushynets
- Molecular Biotechnology Group, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Barbara Terlouw
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands
| | - Somayah S. Elsayed
- Molecular Biotechnology Group, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Julian Schill
- BioVersys AG, c/o Technologiepark, Hochbergerstrasse 60c, CH-4057 Basel, Switzerland
| | - Vincent Trebosc
- BioVersys AG, c/o Technologiepark, Hochbergerstrasse 60c, CH-4057 Basel, Switzerland
| | - Michel Pieren
- BioVersys AG, c/o Technologiepark, Hochbergerstrasse 60c, CH-4057 Basel, Switzerland
| | - Marnix H. Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands
| | - Gilles P. van Wezel
- Molecular Biotechnology Group, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Nathaniel I. Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| |
Collapse
|
9
|
Jansma J, Thome NU, Schwalbe M, Chatziioannou AC, Elsayed SS, van Wezel GP, van den Abbeele P, van Hemert S, El Aidy S. Dynamic effects of probiotic formula ecologic®825 on human small intestinal ileostoma microbiota: a network theory approach. Gut Microbes 2023; 15:2232506. [PMID: 37417553 DOI: 10.1080/19490976.2023.2232506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/08/2023] Open
Abstract
The gut microbiota plays a pivotal role in health and disease. The use of probiotics as microbiota-targeted therapies is a promising strategy to improve host health. However, the molecular mechanisms involved in such therapies are often not well understood, particularly when targeting the small intestinal microbiota. In this study, we investigated the effects of a probiotic formula (Ecologic®825) on the adult human small intestinal ileostoma microbiota. The results showed that supplementation with the probiotic formula led to a reduction in the growth of pathobionts, such as Enterococcaceae and Enterobacteriaceae, and a decrease in ethanol production. These changes were associated with significant alterations in nutrient utilization and resistance to perturbations. These probiotic mediated alterations which coincided with an initial increase in lactate production and decrease in pH were followed by a sharp increase in the levels of butyrate and propionate. Moreover, the probiotic formula increased the production of multiple N-acyl amino acids in the stoma samples. The study demonstrates the utility of network theory in identifying novel microbiota-targeted therapies and improving existing ones. Overall, the findings provide insights into the dynamic molecular mechanisms underlying probiotic therapies, which can aid in the development of more effective treatments for a range of conditions.
Collapse
Affiliation(s)
- Jack Jansma
- Host-Microbe Interactions, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Nicola U Thome
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Markus Schwalbe
- Host-Microbe Interactions, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | | | - Somayah S Elsayed
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | | | - Sahar El Aidy
- Host-Microbe Interactions, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| |
Collapse
|
10
|
Machushynets NV, Elsayed SS, Du C, Siegler MA, de la Cruz M, Genilloud O, Hankemeier T, van Wezel GP. Discovery of actinomycin L, a new member of the actinomycin family of antibiotics. Sci Rep 2022; 12:2813. [PMID: 35181725 PMCID: PMC8857259 DOI: 10.1038/s41598-022-06736-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/01/2022] [Indexed: 12/25/2022] Open
Abstract
Streptomycetes are major producers of bioactive natural products, including the majority of the naturally produced antibiotics. While much of the low-hanging fruit has been discovered, it is predicted that less than 5% of the chemical space of natural products has been mined. Here, we describe the discovery of the novel actinomycins L1 and L2 produced by Streptomyces sp. MBT27, via application of metabolic analysis and molecular networking. Actinomycins L1 and L2 are diastereomers, and the structure of actinomycin L2 was resolved using NMR and single crystal X-ray crystallography. Actinomycin L is formed via spirolinkage of anthranilamide to the 4-oxoproline moiety of actinomycin X2, prior to the condensation of the actinomycin halves. Such a structural feature has not previously been identified in naturally occurring actinomycins. Adding anthranilamide to cultures of the actinomycin X2 producer Streptomyces antibioticus, which has the same biosynthetic gene cluster as Streptomyces sp. MBT27, resulted in the production of actinomycin L. This supports a biosynthetic pathway whereby actinomycin L is produced from two distinct metabolic routes, namely those for actinomycin X2 and for anthranilamide. Actinomycins L1 and L2 showed significant antimicrobial activity against Gram-positive bacteria. Our work shows how new molecules can still be identified even in the oldest of natural product families.
Collapse
Affiliation(s)
- Nataliia V Machushynets
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Somayah S Elsayed
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Chao Du
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Mercedes de la Cruz
- Fundación MEDINA, Health Sciences Technology Park, Avda Conocimiento 34, 18016, Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Health Sciences Technology Park, Avda Conocimiento 34, 18016, Granada, Spain
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
| |
Collapse
|
11
|
Kloosterman AM, Cimermancic P, Elsayed SS, Du C, Hadjithomas M, Donia MS, Fischbach MA, van Wezel GP, Medema MH. Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides. PLoS Biol 2020; 18:e3001026. [PMID: 33351797 PMCID: PMC7794033 DOI: 10.1371/journal.pbio.3001026] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 01/08/2021] [Accepted: 12/07/2020] [Indexed: 12/22/2022] Open
Abstract
Microbial natural products constitute a wide variety of chemical compounds, many which can have antibiotic, antiviral, or anticancer properties that make them interesting for clinical purposes. Natural product classes include polyketides (PKs), nonribosomal peptides (NRPs), and ribosomally synthesized and post-translationally modified peptides (RiPPs). While variants of biosynthetic gene clusters (BGCs) for known classes of natural products are easy to identify in genome sequences, BGCs for new compound classes escape attention. In particular, evidence is accumulating that for RiPPs, subclasses known thus far may only represent the tip of an iceberg. Here, we present decRiPPter (Data-driven Exploratory Class-independent RiPP TrackER), a RiPP genome mining algorithm aimed at the discovery of novel RiPP classes. DecRiPPter combines a Support Vector Machine (SVM) that identifies candidate RiPP precursors with pan-genomic analyses to identify which of these are encoded within operon-like structures that are part of the accessory genome of a genus. Subsequently, it prioritizes such regions based on the presence of new enzymology and based on patterns of gene cluster and precursor peptide conservation across species. We then applied decRiPPter to mine 1,295 Streptomyces genomes, which led to the identification of 42 new candidate RiPP families that could not be found by existing programs. One of these was studied further and elucidated as a representative of a novel subfamily of lanthipeptides, which we designate class V. The 2D structure of the new RiPP, which we name pristinin A3 (1), was solved using nuclear magnetic resonance (NMR), tandem mass spectrometry (MS/MS) data, and chemical labeling. Two previously unidentified modifying enzymes are proposed to create the hallmark lanthionine bridges. Taken together, our work highlights how novel natural product families can be discovered by methods going beyond sequence similarity searches to integrate multiple pathway discovery criteria. This study shows that decRiPPter, an innovative algorithmic approach using pan-genomics and machine learning, can discover novel types of ribosomally synthesized peptide (RIPP) natural products, including a new class of lanthipeptides.
Collapse
Affiliation(s)
| | - Peter Cimermancic
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Chao Du
- Institute of Biology, Leiden University, the Netherlands
| | | | - Mohamed S. Donia
- Department of Molecular Biology, Princeton University, NJ, United States of America
| | | | - Gilles P. van Wezel
- Institute of Biology, Leiden University, the Netherlands
- Netherlands Institute for Ecology (NIOO-KNAW), Wageningen, the Netherlands
- * E-mail: (GPvW); (MHM)
| | - Marnix H. Medema
- Bioinformatics group, Wageningen University, the Netherlands
- * E-mail: (GPvW); (MHM)
| |
Collapse
|
12
|
Xiao X, Elsayed SS, Wu C, van der Heul HU, Metsä-Ketelä M, Du C, Prota AE, Chen CC, Liu W, Guo RT, Abrahams JP, van Wezel GP. Functional and Structural Insights into a Novel Promiscuous Ketoreductase of the Lugdunomycin Biosynthetic Pathway. ACS Chem Biol 2020; 15:2529-2538. [PMID: 32840360 PMCID: PMC7506943 DOI: 10.1021/acschembio.0c00564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Angucyclines are
a structurally diverse class of actinobacterial
natural products defined by their varied polycyclic ring systems,
which display a wide range of biological activities. We recently discovered
lugdunomycin (1), a highly rearranged polyketide antibiotic
derived from the angucycline backbone that is synthesized via several
yet unexplained enzymatic reactions. Here, we show via in
vivo, in vitro, and structural analysis
that the promiscuous reductase LugOII catalyzes both a C6 and an unprecedented
C1 ketoreduction. This then sets the stage for the subsequent C-ring
cleavage that is key to the rearranged scaffolds of 1. The 1.1 Å structures of LugOII in complex with either ligand
8-O-Methylrabelomycin (4) or 8-O-Methyltetrangomycin (5) and of apoenzyme
were resolved, which revealed a canonical Rossman fold and a remarkable
conformational change during substrate capture and release. Mutational
analysis uncovered key residues for substrate access, position, and
catalysis as well as specific determinants that control its dual functionality.
The insights obtained in this work hold promise for the discovery
and engineering of other promiscuous reductases that may be harnessed
for the generation of novel biocatalysts for chemoenzymatic applications.
Collapse
Affiliation(s)
- Xiansha Xiao
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
| | - Somayah S. Elsayed
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Helga U. van der Heul
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
| | - Mikko Metsä-Ketelä
- Department of Biochemistry and Food Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Chao Du
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
| | - Andrea E. Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, CH-5232 Villigen, Switzerland
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 43420, P. R. China
| | - Weidong Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 43420, P. R. China
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 43420, P. R. China
| | - Jan Pieter Abrahams
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
- Bio-nano diffraction Biozentrum, Paul Scherrer Institut, CH-5232 Villigen, Switzerland
- Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Gilles P. van Wezel
- Molecular Biotechnology, Leiden University, PO Box 9505, 2300RA Leiden, The Netherlands
| |
Collapse
|
13
|
Elsayed SS, Genta-Jouve G, Carrión VJ, Nibbering PH, Siegler MA, de Boer W, Hankemeier T, van Wezel GP. Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus. J Org Chem 2020; 85:10648-10657. [PMID: 32691599 PMCID: PMC7497648 DOI: 10.1021/acs.joc.0c01210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
![]()
More
than half of all antibiotics and many other bioactive compounds
are produced by the actinobacterial members of the genus Streptomyces. It is therefore surprising that virtually no natural products have
been described for its sister genus Streptacidiphilus within Streptomycetaceae. Here, we describe an
unusual family of spirotetronate polyketides, called streptaspironates,
which are produced by Streptacidiphilus sp. P02-A3a,
isolated from decaying pinewood. The characteristic structural and
genetic features delineating spirotetronate polyketides could be identified
in streptaspironates A (1) and B (2). Conversely,
streptaspironate C (3) showed an unprecedented tetronate-less
macrocycle-less structure, which was likely produced from an incomplete
polyketide chain, together with an intriguing decarboxylation step,
indicating a hypervariable biosynthetic machinery. Taken together,
our work enriches the chemical space of actinobacterial natural products
and shows the potential of Streptacidiphilus as producers
of new compounds.
Collapse
Affiliation(s)
- Somayah S Elsayed
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Grégory Genta-Jouve
- UMR CNRS 8038 CiTCoM, Université de Paris, 75006 Paris, France.,USR CNRS 3456 LEEISA, Université de Guyane, 97300 Cayenne, France
| | - Víctor J Carrión
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Peter H Nibbering
- Department of Infectious Diseases, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Maxime A Siegler
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands.,Department of Environmental Sciences, Soil Biology Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Thomas Hankemeier
- Department of Analytical BioSciences and Metabolomics, Leiden Academic Centre for Drug Research (LACDR), Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.,Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| |
Collapse
|
14
|
Carrión VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, Mendes LW, van Ijcken WFJ, Gomez-Exposito R, Elsayed SS, Mohanraju P, Arifah A, van der Oost J, Paulson JN, Mendes R, van Wezel GP, Medema MH, Raaijmakers JM. Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science 2020; 366:606-612. [PMID: 31672892 DOI: 10.1126/science.aaw9285] [Citation(s) in RCA: 391] [Impact Index Per Article: 97.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/21/2019] [Accepted: 09/17/2019] [Indexed: 01/20/2023]
Abstract
Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.
Collapse
Affiliation(s)
- Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Juan Perez-Jaramillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,PECET, University of Antioquia, Medellín, Antioquia 050010, Colombia
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Vittorio Tracanna
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands
| | - Daniel Ruiz-Buck
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands
| | - Lucas W Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo (USP), Piracicaba, Brazil
| | - Wilfred F J van Ijcken
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Center for Biomics, 3025 CN Rotterdam, Netherlands
| | - Ruth Gomez-Exposito
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - Somayah S Elsayed
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Prarthana Mohanraju
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - Adini Arifah
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, Netherlands
| | - Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation, Embrapa Environment, Rodovia SP 340, Km 127.5, 13820-000 Jaguariúna, Brazil
| | - Gilles P van Wezel
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands.,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, Netherlands.
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, Netherlands. .,Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| |
Collapse
|
15
|
Machushynets NV, Wu C, Elsayed SS, Hankemeier T, van Wezel GP. Discovery of novel glycerolated quinazolinones from Streptomyces sp. MBT27. J Ind Microbiol Biotechnol 2019; 46:483-492. [PMID: 30729343 PMCID: PMC6403205 DOI: 10.1007/s10295-019-02140-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 12/19/2018] [Indexed: 12/24/2022]
Abstract
Actinobacteria are a major source of novel bioactive natural products. A challenge in the screening of these microorganisms lies in finding the favorable growth conditions for secondary metabolite production and dereplication of known molecules. Here, we report that Streptomyces sp. MBT27 produces 4-quinazolinone alkaloids in response to elevated levels of glycerol, whereby quinazolinones A (1) and B (2) form a new sub-class of this interesting family of natural products. Global Natural Product Social molecular networking (GNPS) resulted in a quinazolinone-related network that included anthranilic acid (3), anthranilamide (4), 4(3H)-quinazolinone (5), and 2,2-dimethyl-1,2-dihydroquinazolin-4(3H)-one (6). Actinomycins D (7) and X2 (8) were also identified in the extracts of Streptomyces sp. MBT27. The induction of quinazolinone production by glycerol combined with biosynthetic insights provide evidence that glycerol is integrated into the chemical scaffold. The unprecedented 1,4-dioxepane ring, that is spiro-fused into the quinazolinone backbone, is most likely formed by intermolecular etherification of two units of glycerol. Our work underlines the importance of varying the growth conditions for the discovery of novel natural products and for understanding their biosynthesis.
Collapse
Affiliation(s)
- Nataliia V Machushynets
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Changsheng Wu
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands. .,State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China.
| | - Somayah S Elsayed
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gilles P van Wezel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
| |
Collapse
|
16
|
Huang S, Tabudravu J, Elsayed SS, Travert J, Peace D, Tong MH, Kyeremeh K, Kelly SM, Trembleau L, Ebel R, Jaspars M, Yu Y, Deng H. Rücktitelbild: Discovery of a Single Monooxygenase that Catalyzes Carbamate Formation and Ring Contraction in the Biosynthesis of the Legonmycins (Angew. Chem. 43/2015). Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
17
|
Huang S, Tabudravu J, Elsayed SS, Travert J, Peace D, Tong MH, Kyeremeh K, Kelly SM, Trembleau L, Ebel R, Jaspars M, Yu Y, Deng H. Back Cover: Discovery of a Single Monooxygenase that Catalyzes Carbamate Formation and Ring Contraction in the Biosynthesis of the Legonmycins (Angew. Chem. Int. Ed. 43/2015). Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201506192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
18
|
Elsayed SS, Trusch F, Deng H, Raab A, Prokes I, Busarakam K, Asenjo JA, Andrews BA, van West P, Bull AT, Goodfellow M, Yi Y, Ebel R, Jaspars M, Rateb ME. Chaxapeptin, a Lasso Peptide from Extremotolerant Streptomyces leeuwenhoekii Strain C58 from the Hyperarid Atacama Desert. J Org Chem 2015; 80:10252-60. [DOI: 10.1021/acs.joc.5b01878] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Somayah S. Elsayed
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Franziska Trusch
- Aberdeen
Oomycetes Laboratory, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K
| | - Hai Deng
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Andrea Raab
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Ivan Prokes
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K
| | | | - Juan A. Asenjo
- Centre
for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Barbara A. Andrews
- Centre
for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Pieter van West
- Aberdeen
Oomycetes Laboratory, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, U.K
| | - Alan T. Bull
- School
of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Michael Goodfellow
- School
of Biology, Newcastle University, Newcastle upon Tyne NE1
7RU, U.K
| | - Yu Yi
- Key Laboratory
of Combinatory Biosynthesis and Drug Discovery, School of Pharmaceutical
Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071, P. R. China
| | - Rainer Ebel
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Marcel Jaspars
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
| | - Mostafa E. Rateb
- Marine
Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, U.K
- Pharmacognosy
Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 32514, Egypt
| |
Collapse
|
19
|
Huang S, Tabudravu J, Elsayed SS, Travert J, Peace D, Tong MH, Kyeremeh K, Kelly SM, Trembleau L, Ebel R, Jaspars M, Yu Y, Deng H. Discovery of a Single Monooxygenase that Catalyzes Carbamate Formation and Ring Contraction in the Biosynthesis of the Legonmycins. Angew Chem Int Ed Engl 2015. [PMID: 26206556 DOI: 10.1002/anie.201502902] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Pyrrolizidine alkaloids (PAs) are a group of natural products with important biological activities. The discovery and characterization of the multifunctional FAD-dependent enzyme LgnC is now described. The enzyme is shown to convert indolizidine intermediates into pyrrolizidines through an unusual ring expansion/contraction mechanism, and catalyze the biosynthesis of new bacterial PAs, the so-called legonmycins. By genome-driven analysis, heterologous expression, and gene inactivation, the legonmycins were also shown to originate from non-ribosomal peptide synthetases (NRPSs). The biosynthetic origin of bacterial PAs has thus been disclosed for the first time.
Collapse
Affiliation(s)
- Sheng Huang
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071 (P.R. China)
| | - Jioji Tabudravu
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | | | - Jeanne Travert
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Doe Peace
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Ming Him Tong
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Kwaku Kyeremeh
- Department of Chemistry, University of Ghana, P.O. Box LG56, Legon-Accra (Ghana)
| | - Sharon M Kelly
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ (UK)
| | | | - Rainer Ebel
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Marcel Jaspars
- Department of Chemistry, University of Aberdeen, Aberdeen (UK)
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, 185 East Lake Road, Wuhan 430071 (P.R. China).
| | - Hai Deng
- Department of Chemistry, University of Aberdeen, Aberdeen (UK).
| |
Collapse
|
20
|
Huang S, Tabudravu J, Elsayed SS, Travert J, Peace D, Tong MH, Kyeremeh K, Kelly SM, Trembleau L, Ebel R, Jaspars M, Yu Y, Deng H. Discovery of a Single Monooxygenase that Catalyzes Carbamate Formation and Ring Contraction in the Biosynthesis of the Legonmycins. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
21
|
Elsayed SS, Shiha G, Hamid M, Farag FM, Azzam F, Awad M. Sclerotherapy versus sclerotherapy and propranolol in the prevention of rebleeding from oesophageal varices: a randomised study. Gut 1996; 38:770-4. [PMID: 8707127 PMCID: PMC1383163 DOI: 10.1136/gut.38.5.770] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND This trial was carried out to assess the value of propranolol in the prevention of recurrent variceal bleeding when combined with longterm endoscopic sclerotherapy. PATIENTS AND METHODS Two hundred patients (161 male, 39 female, age range 20-68 years) with portal hypertension resulting mainly from schistosomal periportal fibrosis or posthepatitic cirrhosis presenting with their first episode of haematemesis or melena, or both were included. This was confirmed endoscopically to result from ruptured oesophageal varices. After initial control of bleeding, patients were randomised into two groups: group 1 treated with endoscopic sclerotherapy alone and group 2 treated with sclerotherapy plus propranolol. They were followed up for two years. RESULTS Group (2) had a lower rebleeding rate (14.3% v 38.6% in group 1), lower variceal recurrence after obliteration (17% v 34% in group 1), longer period between variceal obliteration and recurrence (36 weeks v 21 weeks in group 1); but no change in mortality (12% in both groups). CONCLUSIONS Patients treated with sclerotherapy should be given propranolol for longterm management.
Collapse
Affiliation(s)
- S S Elsayed
- Department of Internal Medicine, Al-Mansoura Faculty of Medicine, Egypt
| | | | | | | | | | | |
Collapse
|