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

Barbara R. Terlouw; Kai Blin; Jorge C. Navarro-Muñoz; Nicole E. Avalon; Marc G. Chevrette; Susan Egbert; Sanghoon Lee; David Meijer; Michael J.J. Recchia; Zachary L. Reitz; Jeffrey A. van Santen; Nelly Selem-Mojica; Thomas Tørring; Liana Zaroubi; Mohammad Alanjary; Gajender Aleti; César Aguilar; Suhad A.A. Al-Salihi; Hannah E. Augustijn; J. Abraham Avelar-Rivas; Luis A. Avitia-Domínguez; Francisco Barona-Gómez; Jordan Bernaldo-Agüero; Vincent A. Bielinski; Friederike Biermann; Thomas J. Booth; Victor J. Carrion Bravo; Raquel Castelo-Branco; Fernanda O. Chagas; Pablo Cruz-Morales; Chao Du; Katherine R. Duncan; Athina Gavriilidou; Damien Gayrard; Karina Gutiérrez-García; Kristina Haslinger; Eric J.N. Helfrich; Justin J.J. van der Hooft; Afif P. Jati; Edward Kalkreuter; Nikolaos Kalyvas; Kyo B. Kang; Satria Kautsar; Wonyong Kim; Aditya M. Kunjapur; Yong-Xin Li; Geng-Min Lin; Catarina Loureiro; Joris J.R. Louwen; Nico L.L. Louwen; George Lund; Jonathan Parra; Benjamin Philmus; Bita Pourmohsenin; Lotte J.U. Pronk; Adriana Rego; Devasahayam Arokia Balaya Rex; Serina Robinson; L. Rodrigo Rosas-Becerra; Eve T. Roxborough; Michelle A. Schorn; Darren J. Scobie; Kumar Saurabh Singh; Nika Sokolova; Xiaoyu Tang; Daniel Udwary; Aruna Vigneshwari; Kristiina Vind; Sophie P.J.M. Vromans; Valentin Waschulin; Sam E. Williams; Jaclyn M. Winter; Thomas E. Witte; Huali Xie; Dong Yang; Jingwei Yu; Mitja Zdouc; Zheng Zhong; Jérôme Collemare; Roger G. Linington; Tilmann Weber; Marnix H. Medema

doi:10.1093/nar/gkac1049

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

Barbara R. Terlouw, Kai Blin, Jorge C. Navarro-Muñoz, Nicole E. Avalon, Marc G. Chevrette, Susan Egbert, Sanghoon Lee, David Meijer, Michael J.J. Recchia, Zachary L. Reitz, Jeffrey A. van Santen, Nelly Selem-Mojica, Thomas Tørring, Liana Zaroubi, Mohammad Alanjary, Gajender Aleti, César Aguilar, Suhad A.A. Al-Salihi, Hannah E. Augustijn, J. Abraham Avelar-RivasLuis A. Avitia-Domínguez, Francisco Barona-Gómez, Jordan Bernaldo-Agüero, Vincent A. Bielinski, Friederike Biermann, Thomas J. Booth, Victor J. Carrion Bravo, Raquel Castelo-Branco, Fernanda O. Chagas, Pablo Cruz-Morales, Chao Du, Katherine R. Duncan, Athina Gavriilidou, Damien Gayrard, Karina Gutiérrez-García, Kristina Haslinger, Eric J.N. Helfrich, Justin J.J. van der Hooft, Afif P. Jati, Edward Kalkreuter, Nikolaos Kalyvas, Kyo B. Kang, Satria Kautsar, Wonyong Kim, Aditya M. Kunjapur, Yong-Xin Li, Geng-Min Lin, Catarina Loureiro, Joris J.R. Louwen, Nico L.L. Louwen, George Lund, Jonathan Parra, Benjamin Philmus, Bita Pourmohsenin, Lotte J.U. Pronk, Adriana Rego, Devasahayam Arokia Balaya Rex, Serina Robinson, L. Rodrigo Rosas-Becerra, Eve T. Roxborough, Michelle A. Schorn, Darren J. Scobie, Kumar Saurabh Singh, Nika Sokolova, Xiaoyu Tang, Daniel Udwary, Aruna Vigneshwari, Kristiina Vind, Sophie P.J.M. Vromans, Valentin Waschulin, Sam E. Williams, Jaclyn M. Winter, Thomas E. Witte, Huali Xie, Dong Yang, Jingwei Yu, Mitja Zdouc, Zheng Zhong, Jérôme Collemare, Roger G. Linington, Tilmann Weber^* (Corresponding author), Marnix H. Medema^* (Corresponding author)

^*Corresponding author for this work

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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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/

Original language	English
Pages (from-to)	D603-D610
Journal	Nucleic Acids Research
Volume	51
Issue number	D1
Early online date	2022
DOIs	https://doi.org/10.1093/nar/gkac1049
Publication status	Published - 2023

Keywords

RS400-RS431
Multigene Family
Genomics
Biosynthetic Pathways/genetics
Genome

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10.1093/nar/gkac1049Licence: CC BY

544095177.pdfFinal published version, 2.17 MBLicence: CC BY

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Terlouw, B. R., Blin, K., Navarro-Muñoz, J. C., Avalon, N. E., Chevrette, M. G., Egbert, S., Lee, S., Meijer, D., Recchia, M. J. J., Reitz, Z. L., van Santen, J. A., Selem-Mojica, N., Tørring, T., Zaroubi, L., Alanjary, M., Aleti, G., Aguilar, C., Al-Salihi, S. A. A., Augustijn, H. E., ... Medema, M. H. (2023). MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters. Nucleic Acids Research, 51(D1), D603-D610. https://doi.org/10.1093/nar/gkac1049

@article{4e99309a68404150801f070cfa20d40c,

title = "MIBiG 3.0:: a community-driven effort to annotate experimentally validated biosynthetic gene clusters",

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/",

keywords = "RS400-RS431, Multigene Family, Genomics, Biosynthetic Pathways/genetics, Genome",

author = "Terlouw, {Barbara R.} and Kai Blin and Navarro-Mu{\~n}oz, {Jorge C.} and Avalon, {Nicole E.} and Chevrette, {Marc G.} and Susan Egbert and Sanghoon Lee and David Meijer and Recchia, {Michael J.J.} and Reitz, {Zachary L.} and {van Santen}, {Jeffrey A.} and Nelly Selem-Mojica and Thomas T{\o}rring and Liana Zaroubi and Mohammad Alanjary and Gajender Aleti and C{\'e}sar Aguilar and Al-Salihi, {Suhad A.A.} and Augustijn, {Hannah E.} and Avelar-Rivas, {J. Abraham} and Avitia-Dom{\'i}nguez, {Luis A.} and Francisco Barona-G{\'o}mez and Jordan Bernaldo-Ag{\"u}ero and Bielinski, {Vincent A.} and Friederike Biermann and Booth, {Thomas J.} and {Carrion Bravo}, {Victor J.} and Raquel Castelo-Branco and Chagas, {Fernanda O.} and Pablo Cruz-Morales and Chao Du and Duncan, {Katherine R.} and Athina Gavriilidou and Damien Gayrard and Karina Guti{\'e}rrez-Garc{\'i}a and Kristina Haslinger and Helfrich, {Eric J.N.} and {van der Hooft}, {Justin J.J.} and Jati, {Afif P.} and Edward Kalkreuter and Nikolaos Kalyvas and Kang, {Kyo B.} and Satria Kautsar and Wonyong Kim and Kunjapur, {Aditya M.} and Yong-Xin Li and Geng-Min Lin and Catarina Loureiro and Louwen, {Joris J.R.} and Louwen, {Nico L.L.} and George Lund and Jonathan Parra and Benjamin Philmus and Bita Pourmohsenin and Pronk, {Lotte J.U.} and Adriana Rego and {Balaya Rex}, {Devasahayam Arokia} and Serina Robinson and Rosas-Becerra, {L. Rodrigo} and Roxborough, {Eve T.} and Schorn, {Michelle A.} and Scobie, {Darren J.} and Singh, {Kumar Saurabh} and Nika Sokolova and Xiaoyu Tang and Daniel Udwary and Aruna Vigneshwari and Kristiina Vind and Vromans, {Sophie P.J.M.} and Valentin Waschulin and Williams, {Sam E.} and Winter, {Jaclyn M.} and Witte, {Thomas E.} and Huali Xie and Dong Yang and Jingwei Yu and Mitja Zdouc and Zheng Zhong and J{\'e}r{\^o}me Collemare and Linington, {Roger G.} and Tilmann Weber and Medema, {Marnix H.}",

note = "Data archiving: no NIOO data",

year = "2023",

doi = "10.1093/nar/gkac1049",

language = "English",

volume = "51",

pages = "D603--D610",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "D1",

}

Terlouw, BR, Blin, K, Navarro-Muñoz, JC, Avalon, NE, Chevrette, MG, Egbert, S, Lee, S, Meijer, D, Recchia, MJJ, Reitz, ZL, van Santen, JA, Selem-Mojica, N, Tørring, T, Zaroubi, L, Alanjary, M, Aleti, G, Aguilar, C, Al-Salihi, SAA, Augustijn, HE, Avelar-Rivas, JA, Avitia-Domínguez, LA, Barona-Gómez, F, Bernaldo-Agüero, J, Bielinski, VA, Biermann, F, Booth, TJ, Carrion Bravo, VJ, Castelo-Branco, R, Chagas, FO, Cruz-Morales, P, Du, C, Duncan, KR, Gavriilidou, A, Gayrard, D, Gutiérrez-García, K, Haslinger, K, Helfrich, EJN, van der Hooft, JJJ, Jati, AP, Kalkreuter, E, Kalyvas, N, Kang, KB, Kautsar, S, Kim, W, Kunjapur, AM, Li, Y-X, Lin, G-M, Loureiro, C, Louwen, JJR, Louwen, NLL, Lund, G, Parra, J, Philmus, B, Pourmohsenin, B, Pronk, LJU, Rego, A, Balaya Rex, DA, Robinson, S, Rosas-Becerra, LR, Roxborough, ET, Schorn, MA, Scobie, DJ, Singh, KS, Sokolova, N, Tang, X, Udwary, D, Vigneshwari, A, Vind, K, Vromans, SPJM, Waschulin, V, Williams, SE, Winter, JM, Witte, TE, Xie, H, Yang, D, Yu, J, Zdouc, M, Zhong, Z, Collemare, J, Linington, RG, Weber, T & Medema, MH 2023, 'MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters', Nucleic Acids Research, vol. 51, no. D1, pp. D603-D610. https://doi.org/10.1093/nar/gkac1049

TY - JOUR

T1 - MIBiG 3.0:

T2 - a community-driven effort to annotate experimentally validated biosynthetic gene clusters

AU - Terlouw, Barbara R.

AU - Blin, Kai

AU - Navarro-Muñoz, Jorge C.

AU - Avalon, Nicole E.

AU - Chevrette, Marc G.

AU - Egbert, Susan

AU - Lee, Sanghoon

AU - Meijer, David

AU - Recchia, Michael J.J.

AU - Reitz, Zachary L.

AU - van Santen, Jeffrey A.

AU - Selem-Mojica, Nelly

AU - Tørring, Thomas

AU - Zaroubi, Liana

AU - Alanjary, Mohammad

AU - Aleti, Gajender

AU - Aguilar, César

AU - Al-Salihi, Suhad A.A.

AU - Augustijn, Hannah E.

AU - Avelar-Rivas, J. Abraham

AU - Avitia-Domínguez, Luis A.

AU - Barona-Gómez, Francisco

AU - Bernaldo-Agüero, Jordan

AU - Bielinski, Vincent A.

AU - Biermann, Friederike

AU - Booth, Thomas J.

AU - Carrion Bravo, Victor J.

AU - Castelo-Branco, Raquel

AU - Chagas, Fernanda O.

AU - Cruz-Morales, Pablo

AU - Du, Chao

AU - Duncan, Katherine R.

AU - Gavriilidou, Athina

AU - Gayrard, Damien

AU - Gutiérrez-García, Karina

AU - Haslinger, Kristina

AU - Helfrich, Eric J.N.

AU - van der Hooft, Justin J.J.

AU - Jati, Afif P.

AU - Kalkreuter, Edward

AU - Kalyvas, Nikolaos

AU - Kang, Kyo B.

AU - Kautsar, Satria

AU - Kim, Wonyong

AU - Kunjapur, Aditya M.

AU - Li, Yong-Xin

AU - Lin, Geng-Min

AU - Loureiro, Catarina

AU - Louwen, Joris J.R.

AU - Louwen, Nico L.L.

AU - Lund, George

AU - Parra, Jonathan

AU - Philmus, Benjamin

AU - Pourmohsenin, Bita

AU - Pronk, Lotte J.U.

AU - Rego, Adriana

AU - Balaya Rex, Devasahayam Arokia

AU - Robinson, Serina

AU - Rosas-Becerra, L. Rodrigo

AU - Roxborough, Eve T.

AU - Schorn, Michelle A.

AU - Scobie, Darren J.

AU - Singh, Kumar Saurabh

AU - Sokolova, Nika

AU - Tang, Xiaoyu

AU - Udwary, Daniel

AU - Vigneshwari, Aruna

AU - Vind, Kristiina

AU - Vromans, Sophie P.J.M.

AU - Waschulin, Valentin

AU - Williams, Sam E.

AU - Winter, Jaclyn M.

AU - Witte, Thomas E.

AU - Xie, Huali

AU - Yang, Dong

AU - Yu, Jingwei

AU - Zdouc, Mitja

AU - Zhong, Zheng

AU - Collemare, Jérôme

AU - Linington, Roger G.

AU - Weber, Tilmann

AU - Medema, Marnix H.

N1 - Data archiving: no NIOO data

PY - 2023

Y1 - 2023

N2 - 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/

AB - 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/

KW - RS400-RS431

KW - Multigene Family

KW - Genomics

KW - Biosynthetic Pathways/genetics

KW - Genome

U2 - 10.1093/nar/gkac1049

DO - 10.1093/nar/gkac1049

M3 - Article

C2 - 36399496

SN - 0305-1048

VL - 51

SP - D603-D610

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

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

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Keywords

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