MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters-Reference-Cited by-同舟云学术

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

Published:2022-11-18 Issue:D1 Volume:51 Page:D603-D610
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Terlouw Barbara R¹^ORCID,Blin Kai²^ORCID,Navarro-Muñoz Jorge C¹³^ORCID,Avalon Nicole E⁴^ORCID,Chevrette Marc G⁵^ORCID,Egbert Susan⁶^ORCID,Lee Sanghoon⁷^ORCID,Meijer David¹^ORCID,Recchia Michael J J⁷^ORCID,Reitz Zachary L¹^ORCID,van Santen Jeffrey A⁷⁸^ORCID,Selem-Mojica Nelly⁹^ORCID,Tørring Thomas¹⁰^ORCID,Zaroubi Liana⁷^ORCID,Alanjary Mohammad¹^ORCID,Aleti Gajender¹¹^ORCID,Aguilar César¹²^ORCID,Al-Salihi Suhad A A¹³^ORCID,Augustijn Hannah E¹¹⁴^ORCID,Avelar-Rivas J Abraham¹⁵,Avitia-Domínguez Luis A¹⁴¹⁵^ORCID,Barona-Gómez Francisco¹⁴¹⁵^ORCID,Bernaldo-Agüero Jordan¹⁶^ORCID,Bielinski Vincent A¹⁷^ORCID,Biermann Friederike¹¹⁸¹⁹^ORCID,Booth Thomas J²²⁰^ORCID,Carrion Bravo Victor J¹⁴²¹²²^ORCID,Castelo-Branco Raquel²³²⁴,Chagas Fernanda O²⁵^ORCID,Cruz-Morales Pablo²^ORCID,Du Chao¹⁴^ORCID,Duncan Katherine R²⁶^ORCID,Gavriilidou Athina²⁷²⁸^ORCID,Gayrard Damien²⁹^ORCID,Gutiérrez-García Karina³⁰^ORCID,Haslinger Kristina³¹^ORCID,Helfrich Eric J N¹⁸¹⁹^ORCID,van der Hooft Justin J J¹³²^ORCID,Jati Afif P³³^ORCID,Kalkreuter Edward³⁴^ORCID,Kalyvas Nikolaos³^ORCID,Kang Kyo Bin³⁵^ORCID,Kautsar Satria³⁴^ORCID,Kim Wonyong³⁶^ORCID,Kunjapur Aditya M³⁷^ORCID,Li Yong-Xin³⁸^ORCID,Lin Geng-Min³⁹^ORCID,Loureiro Catarina⁴⁰^ORCID,Louwen Joris J R¹^ORCID,Louwen Nico L L¹^ORCID,Lund George⁴¹^ORCID,Parra Jonathan⁴²⁴³⁴⁴^ORCID,Philmus Benjamin⁴⁵^ORCID,Pourmohsenin Bita²⁷²⁸^ORCID,Pronk Lotte J U¹^ORCID,Rego Adriana²³⁴⁶^ORCID,Rex Devasahayam Arokia Balaya⁴⁷^ORCID,Robinson Serina⁴⁸^ORCID,Rosas-Becerra L Rodrigo¹⁴¹⁵^ORCID,Roxborough Eve T⁴⁹^ORCID,Schorn Michelle A⁴⁰^ORCID,Scobie Darren J²⁶^ORCID,Singh Kumar Saurabh¹^ORCID,Sokolova Nika³¹^ORCID,Tang Xiaoyu⁵⁰^ORCID,Udwary Daniel⁵¹^ORCID,Vigneshwari Aruna⁵²^ORCID,Vind Kristiina⁵³⁵⁴^ORCID,Vromans Sophie P J M¹^ORCID,Waschulin Valentin⁵⁵^ORCID,Williams Sam E⁵⁶^ORCID,Winter Jaclyn M⁵⁷^ORCID,Witte Thomas E⁵⁸^ORCID,Xie Huali¹⁵⁹^ORCID,Yang Dong⁶⁰^ORCID,Yu Jingwei⁶¹^ORCID,Zdouc Mitja¹^ORCID,Zhong Zheng⁴⁰^ORCID,Collemare Jérôme³^ORCID,Linington Roger G⁷^ORCID,Weber Tilmann²^ORCID,Medema Marnix H¹¹⁴^ORCID

Affiliation:

1. Bioinformatics Group, Wageningen University , Droevendaalsesteeg, 6708 PB Wageningen , The Netherlands

2. The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Kgs. Lyngby, Denmark

3. Westerdijk Fungal Biodiversity Institute , Uppsalalaan 8, 3584 CT Utrecht , The Netherlands

4. Scripps Institution of Oceanography, University of California San Diego , 9500 Gilman Drive, La Jolla , CA 92093-0212 , USA

5. Department of Microbiology and Cell Science, University of Florida , Gainesville , FL 32611, USA

6. Department of Chemistry, University of Manitoba , 66 Chancellors Cir, Winnipeg , MB R3T 2N2 , Canada

7. Department of Chemistry, Simon Fraser University, 8888 University Drive , Burnaby, British Columbia V5A 1S6 , Canada

8. Unnatural Products , 2161 Delaware Ave. Suite A, Santa Cruz , CA 95060 , USA

9. Centro de Ciencias Matemáticas UNAM , Morelia , México

10. Department of Biological and Chemical Engineering, Aarhus University , Denmark

11. Food and Animal Sciences, Department of Agricultural and Environmental Sciences, Tennessee State University , Nashville , TN 37209, USA

12. Department of Chemistry, Purdue University , West Lafayette , IN , USA

13. Department of Applied Sciences, University of Technology , Iraq

14. Institute of Biology, Leiden University , Sylviusweg 72, 2333BE Leiden, The Netherlands

15. Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada , Cinvestav. Km 9.6 Libramiento Norte Carretera Irapuato-León, CP 36824 Irapuato , Gto., México

16. Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México , Cuernavaca , Morelos , México

17. Synthetic Biology and Bioenergy Group, J. Craig Venter Institute , La Jolla , CA 92037 , USA

18. Institute of Molecular Bio Science, Goethe-University Frankfurt , D-60438 Frankfurt am Main, Germany

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

20. School of Molecular Sciences, University of Western Australia , Perth , Australia

21. Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga , Málaga, Spain

22. Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) , Wageningen , The Netherlands

23. Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto , Portugal

24. Faculty of Sciences, University of Porto , 4150 -179 Porto , Portugal

25. Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro , Rio de Janeiro , RJ , 21941-599, Brazil

26. University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences , 141 Cathedral Street, Glasgow , G4 ORE UK

27. Translational Genome Mining for Natural Products, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen , Tübingen, Germany

28. Interfaculty Institute for Biomedical Informatics (IBMI), University of Tübingen , Tübingen , Germany

29. Department of Molecular Microbiology , John Innes Centre, Norwich Research Park, Norwich , NR4 7UH, UK

30. Department of Embryology, Carnegie Institution for Science , 3520 San Martin Drive, Baltimore , MD 21218, USA

31. Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands

32. Department of Biochemistry, University of Johannesburg , Auckland Park, Johannesburg 2006 , South Africa

33. Indonesian Society of Bioinformatics And Biodiversity , Indonesia

34. Department of Chemistry, University of Florida Scripps Biomedical Research , 110 Scripps Way, Jupiter , FL 33458, USA

35. College of Pharmacy, Sookmyung Women's University , Seoul , South Korea

36. Korean Lichen Research Institute, Sunchon National Universtiy , Suncheon , South Korea

37. Department of Chemical & Biomolecular Engineering, University of Delaware , Newark , DE 19716 , USA

38. Department of Chemistry, The University of Hong Kong , Pokfulam Road, Hong Kong , P.R. China

39. Department of Biological Engineering, Massachusetts Institute of Technology , Cambridge , MA , USA

40. Laboratory of Microbiology, Wageningen University , Stippeneng 4, 6708WE, Wageningen , The Netherlands

41. Sustainable Soils and Crops, Rothamsted Research , Harpenden , Hertfordshire , UK

42. Instituto de Investigaciones Farmacéuticas (INIFAR), Facultad de Farmacia, Universidad de Costa Rica , San José , 11501-2060 , Costa Rica

43. Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica , San José , 11501-2060 , Costa Rica

44. Centro Nacional de Innovaciones Biotecnológicas (CENIBiot) , CeNAT-CONARE, 1174-1200, San José , Costa Rica

45. Department of Pharmaceutical Sciences, Oregon State University , USA

46. Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto , Portugal

47. Centre for Integrative Omics Data Science, Yenepoya (Deemed to be University) , Mangalore 575018 , India

48. Department of Environmental Microbiology, Eawag: Swiss Federal Institute for Aquatic Science and Technology , Überlandstrasse 133, CH-8600 Dübendorf , Switzerland

49. School of Chemistry, University of Nottingham, University Park , Nottingham NG7 2RD, UK

50. Institute of Chemical Biology, Shenzhen Bay Laboratory , Shenzhen 518132 , China

51. DOE Joint Genome Institute , Lawrence Berkeley National Lab, Berkeley, CA, USA

52. Department of Microbiology, University of Szeged , Hungary

53. Host-Microbe Interactomics Group, Wageningen University , 6708 WD Wageningen, The Netherlands

54. NAICONS Srl , 20139 Milan , Italy

55. School of Life Sciences, The University of Warwick , Coventry CV4 7AL, UK

56. School of Biochemistry, University of Bristol, University Walk , Bristol BS8 1TD, UK

57. Department of Medicinal Chemistry, University of Utah , Salt Lake City , UT 84112 , USA

58. Department of Chemistry and Biomolecular Sciences, University of Ottawa , Ottawa , Canada

59. Key laboratory of Detection for Biotoxins, Ministry of Agriculture and Rural Affairs and Oil Crops Research Institute, Chinese Academy of Agricultural Sciences , Wuhan 430061 , China

60. Department of Chemistry and Natural Products Discovery Center, UF Scripps Biomedical Research, University of Florida , Jupiter , FL 33458 , USA

61. SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology , Shenzhen , Guangdong 518055 , China

Abstract

Abstract With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.

Funder

ERC Starting

Novo Nordisk Foundation

Danish National Research Foundation

Natural Sciences and Engineering Council of Canada

Netherlands Organization for Scientific Research (NWO) Veni Science

CARTNET

SECRETed

MARBLES

Horizon 2020 Marie Skłodowska-Curie Actions

Horizon 2020 Marie Sklodowska-Curie Individual Fellowship

U.S. Department of Energy