MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis
Abstract
Secondary or specialized metabolites show extraordinary structural diversity and potent biological activities relevant for clinical and industrial applications. The biosynthesis of these metabolites usually starts with the assembly of a core “scaffold”, which is subsequently modified by tailoring enzymes to define the molecule’s final structure and, in turn, its biological activity profile. Knowledge about reaction and substrate specificity of tailoring enzymes is essential for understanding and computationally predicting metabolite biosynthesis, but this information is usually scattered in the literature. Here, we present MITE, the Minimum Information about a Tailoring Enzyme database. MITE employs a comprehensive set of parameters to annotate tailoring enzymes, defining substrate and reaction specificity by the expressive reaction SMARTS chemical pattern language. Both human- and machine-readable, MITE can be used as a knowledgebase, for in silico biosynthesis, or to train machine learning applications, and tightly integrates with existing resources. Designed as a community-driven and open resource, MITE employs a rolling release model of data curation and expert review. MITE is freely accessible at https://mite.bioinformatics.nl/.
Authors 46
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ETH Zurich · Institute for Molecular Systems Biology
Affiliation as printed
Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
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Affiliation as printed
Industrial Genomics Laboratory, Centro de Biotecnología FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Av. Eugenio Garza Sada 2501 sur, Nuevo Leon, 64700, México
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Universidade Estadual de Campinas (UNICAMP)
Affiliation as printed
Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Rua Monteiro Lobato 270, Campinas, São Paulo, 13.083-862, Brazil
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Affiliation as printed
School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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Leiden University · Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, the Netherlands
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Scripps Institution of Oceanography · University of California, Irvine · University of California San Diego
Affiliation as printed
Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0212, USA
Department of Pharmaceutical Sciences, University of California, Irvine, 856 Health Sciences Road, Irvine, California, USA 92697
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Helmholtz Centre for Infection Research · Helmholtz Institute for Pharmaceutical Research Saarland · Saarland University
Affiliation as printed
Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
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Universidade Estadual de Campinas (UNICAMP)
Affiliation as printed
Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Rua Monteiro Lobato 270, Campinas, São Paulo, 13.083-862, Brazil
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Goethe University Frankfurt · LOEWE Centre for Translational Biodiversity Genomics · Wageningen University & Research
Affiliation as printed
Institute of Molecular Bio Science, Goethe-University Frankfurt, Frankfurt am Main, Germany
LOEWE Center for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
Wageningen University & Research
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SIB Swiss Institute of Bioinformatics
Affiliation as printed
SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, CH-1211, Geneva, Switzerland
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Helmholtz Centre for Infection Research · Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
Department of Microbial Drugs, Helmholtz Centre for Infection Research (HZI), Inhoffenstr. 7, 38124 Braunschweig, Germany
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Affiliation as printed
Institute for Organic Chemistry and BMWZ, Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany
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Goethe University Frankfurt · University of Bonn
Affiliation as printed
Institute for Pharmaceutical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
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Helmholtz Centre for Infection Research · Helmholtz Institute for Pharmaceutical Research Saarland
Affiliation as printed
Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
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SIB Swiss Institute of Bioinformatics
Affiliation as printed
SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel Servet, CH-1211, Geneva, Switzerland
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Affiliation as printed
Institute for Organic Chemistry, Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany
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University of Arizona · Carnegie Institution for Science
Affiliation as printed
Biosphere Sciences and Engineering Division, Carnegie Institution for Science, 3520 San Martin Dr, Baltimore, MD, 21218, USA
Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell St., Tucson, AZ 85721, USA
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Affiliation as printed
Department of Biotechnology and Nanomedicine, SINTEF Industry, P.O. Box 4760 Torgard, N-7465, Trondheim, Norway
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VTT Technical Research Centre of Finland
Affiliation as printed
Production Host Engineering Team, VTT Technical Research Centre of Finland Ltd, Maarintie 3, 02150 Espoo, Finland
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Universidade Estadual de Campinas (UNICAMP)
Affiliation as printed
Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Rua Monteiro Lobato 270, Campinas, São Paulo, 13.083-862, Brazil
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Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. - Hans-Knöll-Institut (HKI)
Affiliation as printed
Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Beutenbergstr. 11a, 07745 Jena, Germany
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Affiliation as printed
Institute for Organic Chemistry and BMWZ, Leibniz Universität Hannover, Schneiderberg 38, 30167 Hannover, Germany
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Affiliation as printed
Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Germany
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Affiliation as printed
Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Auf der Morgenstelle 24, 72076 Tübingen, Germany
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Korea Advanced Institute of Science and Technology
Affiliation as printed
Institute of Applied Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
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Regional Centre for Biotechnology · BRIC-National Agri-Food and Biomanufacturing Institute
Affiliation as printed
Computational Biology Lab, National Agri-Food and Biomanufacturing Institute (NABI), Sector 81, S.A.S. Nagar, Mohali, Punjab 140306, India
Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad - 121001 Haryana (NCR Delhi), India
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
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Affiliation as printed
Department of Biotechnology and Nanomedicine, SINTEF Industry, P.O. Box 4760 Torgard, N-7465, Trondheim, Norway
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BRIC-National Agri-Food and Biomanufacturing Institute
Affiliation as printed
Computational Biology Lab, National Agri-Food and Biomanufacturing Institute (NABI), Sector 81, S.A.S. Nagar, Mohali, Punjab 140306, India
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Regional Centre for Biotechnology · BRIC-National Agri-Food and Biomanufacturing Institute
Affiliation as printed
Computational Biology Lab, National Agri-Food and Biomanufacturing Institute (NABI), Sector 81, S.A.S. Nagar, Mohali, Punjab 140306, India
Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad - 121001 Haryana (NCR Delhi), India
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Affiliation as printed
Department of Chemistry, University of Zurich,Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Affiliation as printed
Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
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Affiliation as printed
Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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Novo Nordisk Foundation · Technical University of Denmark
Affiliation as printed
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
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Affiliation as printed
Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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Affiliation as printed
Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
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Southern University of Science and Technology
Affiliation as printed
Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, P.R. China
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Affiliation as printed
Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen, Germany
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Novo Nordisk Foundation · Technical University of Denmark
Affiliation as printed
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
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Novo Nordisk Foundation · Technical University of Denmark
Affiliation as printed
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
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University of Johannesburg · Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
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Wageningen University & Research
Affiliation as printed
Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
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