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Combining CRISPRi and metabolomics for functional annotation of compound libraries

Anglada-Girotto, Miquel and Handschin, Gabriel and Ortmayr, Karin and Campos, Adrian I. and Gillet, Ludovic and Manfredi, Pablo and Mulholland, Claire V. and Berney, Michael and Jenal, Urs and Picotti, Paola and Zampieri, Mattia. (2022) Combining CRISPRi and metabolomics for functional annotation of compound libraries. Nature Chemical Biology, 18 (5). pp. 482-491.

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Official URL: https://edoc.unibas.ch/90015/

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Abstract

Molecular profiling of small molecules offers invaluable insights into the function of compounds and allows for hypothesis generation about small-molecule direct targets and secondary effects. However, current profiling methods are limited in either the number of measurable parameters or throughput. Here we developed a multiplexed, unbiased framework that, by linking genetic to drug-induced changes in nearly a thousand metabolites, allows for high-throughput functional annotation of compound libraries in Escherichia coli. First, we generated a reference map of metabolic changes from CRISPR interference (CRISPRi) with 352 genes in all major essential biological processes. Next, on the basis of the comparison of genetic changes with 1,342 drug-induced metabolic changes, we made de novo predictions of compound functionality and revealed antibacterials with unconventional modes of action (MoAs). We show that our framework, combining dynamic gene silencing with metabolomics, can be adapted as a general strategy for comprehensive high-throughput analysis of compound functionality from bacteria to human cell lines.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Infection Biology > Molecular Microbiology (Jenal)
05 Faculty of Science > Departement Biozentrum > Growth & Development > Molecular Microbiology (Jenal)
UniBasel Contributors:Jenal, Urs and Manfredi, Pablo
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Nature Publishing Group
ISSN:1552-4450
e-ISSN:1552-4469
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
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Last Modified:10 Oct 2022 10:00
Deposited On:10 Oct 2022 10:00

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