MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis

Nucleic Acids Research, vol. 54, pp. D635–D642

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 (Simplified Molecular Input Line Entry System Arbitrary Target Specification) chemical pattern language. Both human and machine readable, MITE can be used as a knowledge base, 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 47

1. Adriano Rutz

   ETH Zurich · Institute for Molecular Systems Biology

   Affiliation as printed

   Institute for Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3 , Zürich 8093 ,

2. Daniel Probst

   Wageningen University & Research

   Affiliation as printed

   Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1 , Wageningen 6708PB ,

3. César Aguilar

   Tecnológico de Monterrey

   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 ,

4. Daniel Yuri Akiyama

   Universidade Estadual de Campinas (UNICAMP)

   Affiliation as printed

   Institute of Chemistry, University of Campinas (UNICAMP), Rua Monteiro Lobato 270, Campinas Department of Organic Chemistry, , São Paulo 13.083-862 ,

5. Fabrizio Alberti

   University of Warwick

   Affiliation as printed

   School of Life Sciences, University of Warwick , Gibbet Hill Road , Coventry CV4 7AL ,

6. Hannah E. Augustijn Aachen Institute of Biology, Leiden University

   Leiden University · Wageningen University & Research

   Affiliation as printed

   Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1 , Wageningen 6708PB ,

   Institute of Biology, Leiden University , Sylviusweg 72 , Leiden 2333BE ,

7. Nicole E. Avalon

   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 ,

   University of California Department of Pharmaceutical Sciences, , 856 Health Sciences Road , Irvine, CA 92697 ,

8. Christine Beemelmanns

   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 , Saarbrücken 66123 ,

   Saarland University, Campus E8.1 Department Anti-infectives from Microbiota, , Saarbrücken 66123 ,

9. Hellen Bertoletti Barbieri

   Universidade Estadual de Campinas (UNICAMP)

   Affiliation as printed

   Institute of Chemistry, University of Campinas (UNICAMP), Rua Monteiro Lobato 270, Campinas Department of Organic Chemistry, , São Paulo 13.083-862 ,

10. Friederike Biermann

    Goethe University Frankfurt · LOEWE Centre for Translational Biodiversity Genomics · Wageningen University & Research

    Affiliation as printed

    Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1 , Wageningen 6708PB ,

    Institute for Molecular Biosciences, Goethe University Frankfurt , Max-von-Laue-Straße 9 , Frankfurt am Main 60438 ,

    LOEWE Center for Translational Biodiversity Genomics (TBG) , Senckenberganlage 25 , Frankfurt am Main 60325 ,

11. Alan James Bridge

    SIB Swiss Institute of Bioinformatics

    Affiliation as printed

    SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire , 1 rue Michel Servet, 1211 Geneva 4 ,

12. Esteban Charria Girón

    Helmholtz Centre for Infection Research · Wageningen University & Research

    Affiliation as printed

    Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1 , Wageningen 6708PB ,

    Helmholtz Centre for Infection Research (HZI) Department of Microbial Drugs, , Inhoffenstraße 7, Braunschweig 38124 ,

13. Russell John Cox

    Leibniz University Hannover

    Affiliation as printed

    Institute for Organic Chemistry and BMWZ, Leibniz Universität Hannover , Schneiderberg 38 , Hannover 30167 ,

14. Max Crüsemann

    Goethe University Frankfurt · University of Bonn

    Affiliation as printed

    Institute for Pharmaceutical Biology, Goethe University Frankfurt , Max-von-Laue-Straße 9, Frankfurt am Main 60438 ,

    Institute of Pharmaceutical Biology, University of Bonn , Nussallee 6 , Bonn 53115 ,

15. Paul Michael D'Agostino

    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 , Saarbrücken 66123 ,

16. Marc Feuermann

    SIB Swiss Institute of Bioinformatics

    Affiliation as printed

    SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire , 1 rue Michel Servet, 1211 Geneva 4 ,

17. Jennifer Gerke

    Leibniz University Hannover

    Affiliation as printed

    Institute for Organic Chemistry, Leibniz Universität Hannover , Schneiderberg 38 , Hannover 30167 ,

18. Karina Gutiérrez-García

    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 ,

    University of Arizona Department of Ecology and Evolutionary Biology, , 1041 E. Lowell St. , Tucson, AZ 85721 ,

19. Jonathan E Holme

    SINTEF · SINTEF Industry

    Affiliation as printed

    Department of Biotechnology and Nanomedicine , SINTEF Industry, P.O. Box 4760 Torgard, Trondheim N-7465 ,

20. Ji-Yeon Hwang

    National Cancer Institute · Center for Cancer Research

    Affiliation as printed

    Molecular Targets Program, Center for Cancer Research, National Cancer Institute , Frederick, MD 21702-1201 ,

21. Riccardo Iacovelli

    VTT Technical Research Centre of Finland

    Affiliation as printed

    Production Host Engineering Team, VTT Technical Research Centre of Finland Ltd , Maarintie 3 , Espoo 02150 ,

22. Júlio César Jeronimo Barbosa

    Universidade Estadual de Campinas (UNICAMP)

    Affiliation as printed

    Institute of Chemistry, University of Campinas (UNICAMP), Rua Monteiro Lobato 270, Campinas Department of Organic Chemistry, , São Paulo 13.083-862 ,

23. Martin Klapper

    Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. - Hans-Knöll-Institut (HKI)

    Affiliation as printed

    Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute Department of Paleobiotechnology, , Beutenbergstraße 11A , Jena 07745 ,

24. Anna M. Köhler

    Leibniz University Hannover

    Affiliation as printed

    Institute for Organic Chemistry and BMWZ, Leibniz Universität Hannover , Schneiderberg 38 , Hannover 30167 ,

25. Aleksandra E. Korenskaia

    University of Tübingen

    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 , Tübingen 72076 ,

26. Noel Kubach

    University of Tübingen

    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 , Tübingen 72076 ,

27. Byung Tae Lee

    Korea Advanced Institute of Science and Technology

    Affiliation as printed

    Institute of Applied Sciences, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141 ,

28. Catarina Loureiro

    Wageningen University & Research

    Affiliation as printed

    Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1 , Wageningen 6708PB ,

29. Shrikant Subhash Mantri

    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 ,

    Regional Centre for Biotechnology, NCR Biotech Science Cluster , 3rd Milestone, Faridabad–Gurugram Expressway, Faridabad, Haryana (NCR Delhi) 121001 ,

30. David Meijer

    Wageningen University & Research

    Affiliation as printed

    Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1 , Wageningen 6708PB ,

31. Jorge Carlos Navarro-Muñoz

    Wageningen University & Research

    Affiliation as printed

    Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1 , Wageningen 6708PB ,

32. Giang‐Son Nguyen

    SINTEF · SINTEF Industry

    Affiliation as printed

    Department of Biotechnology and Nanomedicine , SINTEF Industry, P.O. Box 4760 Torgard, Trondheim N-7465 ,

33. Sunaina Paliyal

    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 ,

34. Mohit Panghal

    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 ,

    Regional Centre for Biotechnology, NCR Biotech Science Cluster , 3rd Milestone, Faridabad–Gurugram Expressway, Faridabad, Haryana (NCR Delhi) 121001 ,

35. Simon Sieber

    University of Zurich

    Affiliation as printed

    University of Zurich Department of Chemistry, , Winterthurerstrasse 190 , Zurich 8057 ,

36. Nika Sokolova

    University of Groningen

    Affiliation as printed

    University of Groningen Department of Chemical and Pharmaceutical Biology, , Antonius Deusinglaan 1, Groningen 9713AV ,

37. Sven T. Sowa

    University of Basel

    Affiliation as printed

    University of Basel Department of Pharmaceutical Sciences, , Klingelbergstrasse 50 , Basel 4056 ,

38. Judit Szenei

    Novo Nordisk Foundation · Technical University of Denmark

    Affiliation as printed

    The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Building 220, Søltofts Plads , Kongens Lyngby 2800 ,

39. Barbara R. Terlouw

    Wageningen University & Research

    Affiliation as printed

    Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1 , Wageningen 6708PB ,

40. Heiner G Weddeling

    University of Basel

    Affiliation as printed

    University of Basel Department of Pharmaceutical Sciences, , Klingelbergstrasse 50 , Basel 4056 ,

41. Jingwei Yu

    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 ,

42. Nadine Ziemert

    German Center for Infection Research · University of Tübingen

    Affiliation as printed

    German Center for Infection Research (DZIF), Partner Site Tübingen ,  72076 Tübingen ,

    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 , Tübingen 72076 ,

43. Tilmann Weber

    Novo Nordisk Foundation · Technical University of Denmark

    Affiliation as printed

    The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Building 220, Søltofts Plads , Kongens Lyngby 2800 ,

44. Kai Blin

    Novo Nordisk Foundation · Technical University of Denmark

    Affiliation as printed

    The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Building 220, Søltofts Plads , Kongens Lyngby 2800 ,

45. Justin J. J. van der Hooft

    University of Johannesburg · Wageningen University & Research

    Affiliation as printed

    Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1 , Wageningen 6708PB ,

    University of Johannesburg Department of Biochemistry, , C2 Lab Building 224, Kingsway Campus, Cnr University & Kingsway Road, Auckland Park , Johannesburg 2006 ,

46. Marnix H. Medema corresponding

    Wageningen University & Research

    Affiliation as printed

    Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1 , Wageningen 6708PB ,

47. Mitja M. Zdouc corresponding

    Wageningen University & Research

    Affiliation as printed

    Bioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1 , Wageningen 6708PB ,