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Cited by 43CRISPR and Genetic EngineeringBacterial Genetics and BiotechnologyAntibiotic Resistance in Bacteria

Deep mutational scanning of essential bacterial proteins can guide antibiotic development

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Dewachter, Liselot, Brooks, Aaron N., Noon, Katherine, Cialek, Charlotte, Clark-ElSayed, Alia, Schalck, Thomas, Krishnamurthy, Nandini, Versées, Wim +2 more·2023·Nature Communications
DOI 10.1038/s41467-023-35940-3PMC PMC9842644

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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.

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  • MAVEs have been used extensively in bacterial models, often to interrogate mechanisms of antibiotic resistance.

    “MAVEs have also been used extensively in bacterial models, often to interrogate mechanisms of antibiotic resistance (64); however, it is eukaryotic cellular models that have the greatest relevance to endocrine scientists.”

    From Massively parallel functional genomic assays in endocrinology: from promise to delivery (2026) · cites this paper as [64]

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Authors
Dewachter, L., Brooks, A. N., Noon, K., Cialek, C., Clark-ElSayed, A., Schalck, T., Krishnamurthy, N., Versées, W., Vranken, W., & Michiels, J.
Affiliations
  • VIB-KU Leuven Center for Microbiology (BE)
  • Vrije Universiteit Brussel (BE)
  • Université Libre de Bruxelles (BE)
Corresponding author
  • Dewachter, Liselot
  • Michiels, Jan
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2023-01-16
Volume
14
Issue
1
Pages
241-241
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-023-35940-3
PMC
PMC9842644
OpenAlex
W4316500219
Cited by
43
References
2
Citations by year
2026: 11 · 2025: 7 · 2024: 16 · 2023: 9
FWCI
3.72
Type
journal article
Language
en
Update notices
correction (2023-02-06)
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Lirias (KU Leuven) (submittedVersion, cc-by)
  • Lirias (submittedVersion, cc-by)
  • VUBIR (Vrije Universiteit Brussel) (submittedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • Digital Access to Libraries (submittedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Fonds Wetenschappelijk Onderzoek (G0B0420N, G055517N, G0C4322N, G0I1522N)
  • Vrije Universiteit Brussel (SRP50)
  • KU Leuven (C16/17/006)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
Keywords
deep mutational scanning, Escherichia coli, FabZ, LpxC, MurA, cell envelope synthesis, antibiotic resistance, CRISPR mutagenesis, resistance-conferring mutations, drug development
MeSH terms
Anti-Bacterial Agents, Bacterial Proteins, Escherichia coli, Mutation, Escherichia coli Proteins

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