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Deep mutational scanning of essential bacterial proteins can guide antibiotic development

Author

Listed:
  • Liselot Dewachter

    (Centre of Microbial and Plant Genetics, KU Leuven
    VIB-KU Leuven Center for Microbiology)

  • Aaron N. Brooks

    (Inscripta, Inc)

  • Katherine Noon

    (Inscripta, Inc)

  • Charlotte Cialek

    (Inscripta, Inc)

  • Alia Clark-ElSayed

    (Inscripta, Inc)

  • Thomas Schalck

    (Centre of Microbial and Plant Genetics, KU Leuven
    VIB-KU Leuven Center for Microbiology)

  • Nandini Krishnamurthy

    (Inscripta, Inc)

  • Wim Versées

    (Vrije Universiteit Brussel
    VIB-VUB Center for Structural Biology)

  • Wim Vranken

    (Vrije Universiteit Brussel
    VIB-VUB Center for Structural Biology
    Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB)

  • Jan Michiels

    (Centre of Microbial and Plant Genetics, KU Leuven
    VIB-KU Leuven Center for Microbiology)

Abstract

Deep mutational scanning is a powerful approach to investigate a wide variety of research questions including protein function and stability. Here, we perform deep mutational scanning on three essential E. coli proteins (FabZ, LpxC and MurA) involved in cell envelope synthesis using high-throughput CRISPR genome editing, and study the effect of the mutations in their original genomic context. We use more than 17,000 variants of the proteins to interrogate protein function and the importance of individual amino acids in supporting viability. Additionally, we exploit these libraries to study resistance development against antimicrobial compounds that target the selected proteins. Among the three proteins studied, MurA seems to be the superior antimicrobial target due to its low mutational flexibility, which decreases the chance of acquiring resistance-conferring mutations that simultaneously preserve MurA function. Additionally, we rank anti-LpxC lead compounds for further development, guided by the number of resistance-conferring mutations against each compound. Our results show that deep mutational scanning studies can be used to guide drug development, which we hope will contribute towards the development of novel antimicrobial therapies.

Suggested Citation

  • Liselot Dewachter & Aaron N. Brooks & Katherine Noon & Charlotte Cialek & Alia Clark-ElSayed & Thomas Schalck & Nandini Krishnamurthy & Wim Versées & Wim Vranken & Jan Michiels, 2023. "Deep mutational scanning of essential bacterial proteins can guide antibiotic development," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-35940-3
    DOI: 10.1038/s41467-023-35940-3
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    References listed on IDEAS

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    1. Gregory M. Findlay & Riza M. Daza & Beth Martin & Melissa D. Zhang & Anh P. Leith & Molly Gasperini & Joseph D. Janizek & Xingfan Huang & Lea M. Starita & Jay Shendure, 2018. "Accurate classification of BRCA1 variants with saturation genome editing," Nature, Nature, vol. 562(7726), pages 217-222, October.
    2. Toon Swings & David C. Marciano & Benu Atri & Rachel E. Bosserman & Chen Wang & Marlies Leysen & Camille Bonte & Thomas Schalck & Ian Furey & Bram Van den Bergh & Natalie Verstraeten & Peter J. Christ, 2018. "CRISPR-FRT targets shared sites in a knock-out collection for off-the-shelf genome editing," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
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    1. Takahiro Nemoto & Tommaso Ocari & Arthur Planul & Muge Tekinsoy & Emilia A. Zin & Deniz Dalkara & Ulisse Ferrari, 2023. "ACIDES: on-line monitoring of forward genetic screens for protein engineering," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    2. Liselot Dewachter & Babette Deckers & Israel Mares-Mejía & Elen Louwagie & Silke Vercauteren & Paul Matthay & Simon Brückner & Anna-Maria Möller & Franz Narberhaus & Sibylle C. Vonesch & Wim Versées &, 2024. "The role of the essential GTPase ObgE in regulating lipopolysaccharide synthesis in Escherichia coli," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

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