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Evolutionary Genome Mining for the Discovery and Engineering of Natural Product Biosynthesis

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Engineering Natural Product Biosynthesis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2489))

Abstract

Genome mining has become an invaluable tool in natural products research to quickly identify and characterize the biosynthetic pathways that assemble secondary or specialized metabolites. Recently, evolutionary principles have been incorporated into genome mining strategies in an effort to better assess and prioritize novelty and understand their chemical diversification for engineering purposes. Here, we provide an introduction to the principles underlying evolutionary genome mining, including bioinformatic strategies and natural product biosynthetic databases. We introduce workflows for traditional genome mining, focusing on the popular pipeline antiSMASH, and methods to predict enzyme substrate specificity from genomic information. We then provide an in-depth discussion of evolutionary genome mining workflows, including EvoMining, CORASON, ARTS, and others, as adopted by our group for the discovery and prioritization of natural products biosynthetic gene clusters and their products.

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Author information

Author notes

  1. Nelly Selem-Mojica

    Present address: Centro de Ciencias Matemáticas, UNAM, Morelia, Michoacán, Mexico

  2. César Aguilar

    Present address: Department of Chemistry, Purdue University, West Lafayette, IN, USA

  3. Marc G. Chevrette and Nelly Selem-Mojica contributed equally to this work.

Authors and Affiliations

  1. Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA

    Marc G. Chevrette & Jo Handelsman

  2. Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Guanajuato, Mexico

    Nelly Selem-Mojica, César Aguilar, Edder D. Bustos-Diaz & Francisco Barona-Gómez

  3. Department of Chemistry, Beloit College, Beloit, WI, USA

    Kristin Labby

Authors
  1. Marc G. Chevrette
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  2. Nelly Selem-Mojica
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  3. César Aguilar
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  4. Kristin Labby
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  5. Edder D. Bustos-Diaz
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  6. Jo Handelsman
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  7. Francisco Barona-Gómez
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Corresponding author

Correspondence to Francisco Barona-Gómez .

Editor information

Editors and Affiliations

  1. Department of Chemistry & BioDiscovery Institute, University of North Texas, Denton, USA

    Elizabeth Skellam

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Chevrette, M.G. et al. (2022). Evolutionary Genome Mining for the Discovery and Engineering of Natural Product Biosynthesis. In: Skellam, E. (eds) Engineering Natural Product Biosynthesis. Methods in Molecular Biology, vol 2489. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2273-5_8

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  • DOI: https://doi.org/10.1007/978-1-0716-2273-5_8

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2272-8

  • Online ISBN: 978-1-0716-2273-5

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