Cited by 172Fungal and yeast genetics researchBioinformatics and Genomic NetworksMicrobial Metabolic Engineering and Bioproduction

High-resolution chemical dissection of a model eukaryote reveals targets, pathways and gene functions

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Hoepfner, Dominic, Helliwell, Stephen B., Sadlish, Heather, Schuierer, Sven, Filipuzzi, Ireos, Brachat, Sophie, Bhullar, Bhupinder, Plikat, Uwe +27 more·2014·Microbiological Research

Abstract

Due to evolutionary conservation of biology, experimental knowledge captured from genetic studies in eukaryotic model organisms provides insight into human cellular pathways and ultimately physiology. Yeast chemogenomic profiling is a powerful approach for annotating cellular responses to small molecules. Using an optimized platform, we provide the relative sensitivities of the heterozygous and homozygous deletion collections for nearly 1800 biologically active compounds. The data quality enables unique insights into pathways that are sensitive and resistant to a given perturbation, as demonstrated with both known and novel compounds. We present examples of novel compounds that inhibit the therapeutically relevant fatty acid synthase and desaturase (Fas1p and Ole1p), and demonstrate how the individual profiles facilitate hypothesis-driven experiments to delineate compound mechanism of action. Importantly, the scale and diversity of tested compounds yields a dataset where the number of modulated pathways approaches saturation. This resource can be used to map novel biological connections, and also identify functions for unannotated genes. We validated hypotheses generated by global two-way hierarchical clustering of profiles for (i) novel compounds with a similar mechanism of action acting upon microtubules or vacuolar ATPases, and (ii) an un-annotated ORF, YIL060w, that plays a role in respiration in the mitochondria. Finally, we identify and characterize background mutations in the widely used yeast deletion collection which should improve the interpretation of past and future screens throughout the community. This comprehensive resource of cellular responses enables the expansion of our understanding of eukaryotic pathway biology.

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  • The topology of genetic networks connecting genes within protein complexes by uniform sets of genetic interactions is conserved in higher eukaryotes.

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Authors
Hoepfner, D., Helliwell, S. B., Sadlish, H., Schuierer, S., Filipuzzi, I., Brachat, S., Bhullar, B., Plikat, U., Abraham, Y., Altorfer, M., Aust, T., Baeriswyl, L., Cerino, R., Chang, L., Estoppey, D., Eichenberger, J., Frederiksen, M., Hartmann, N., Hohendahl, A., Knapp, B., Krastel, P., Melin, N., Nigsch, F., Oakeley, E. J., Petitjean, V., Petersen, F., Riedl, R., Schmitt, E. K., Staedtler, F., Studer, C., Tallarico, J. A., Wetzel, S., Fishman, M. C., Porter, J. A., & Movva, N. R.
Affiliations
Novartis (Switzerland) (CH)
Corresponding author
Hoepfner, Dominic
Venue
Microbiological Research
Publisher
Elsevier BV
Published
2014-02
Volume
169
Issue
2-3
Pages
107-120
ISSN
0944-5013 (ISSN-L)
OpenAlex
W2013242034
Cited by
166
References
50
Citations by year
2026: 5 · 2025: 11 · 2024: 12 · 2023: 6 · 2022: 13 · 2021: 6 · 2020: 11 · 2019: 23 · 2018: 20 · 2017: 23 · 2016: 12 · 2015: 18 · 2014: 5 · 2013: 1
FWCI
5.38
Type
journal article
Language
en
Open access
Locations
  • Microbiological Research (publishedVersion)
  • PubMed (publishedVersion)
Funders
Novartis Institutes for BioMedical Research
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Keywords
chemogenomics, fatty acid synthase inhibition, microtubule inhibitors, mitochondrial respiration, background mutations, Saccharomyces cerevisiae
MeSH terms
Antifungal Agents, Molecular Sequence Data, Phylogeny, Saccharomyces cerevisiae, Gene Expression Regulation, Fungal, Drug Resistance, Fungal, Saccharomyces cerevisiae Proteins, Biosynthetic Pathways, High-Throughput Screening Assays

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