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Open Access Research article

Combining chemical genomics screens in yeast to reveal spectrum of effects of chemical inhibition of sphingolipid biosynthesis

Danielle Kemmer1, Lianne M McHardy1, Shawn Hoon2, Delphine Rebérioux1, Guri Giaever345, Corey Nislow456, Calvin D Roskelley7 and Michel Roberge1*

Author Affiliations

1 Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada

2 Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA

3 Department of Pharmaceutical Sciences, University of Toronto, Toronto, Canada

4 Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada

5 Department of Molecular Genetics, University of Toronto, Toronto, Canada

6 Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada

7 Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada

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BMC Microbiology 2009, 9:9  doi:10.1186/1471-2180-9-9

Published: 14 January 2009

Abstract

Background

Single genome-wide screens for the effect of altered gene dosage on drug sensitivity in the model organism Saccharomyces cerevisiae provide only a partial picture of the mechanism of action of a drug.

Results

Using the example of the tumor cell invasion inhibitor dihydromotuporamine C, we show that a more complete picture of drug action can be obtained by combining different chemical genomics approaches – analysis of the sensitivity of ρ0 cells lacking mitochondrial DNA, drug-induced haploinsufficiency, suppression of drug sensitivity by gene overexpression and chemical-genetic synthetic lethality screening using strains deleted of nonessential genes. Killing of yeast by this chemical requires a functional mitochondrial electron-transport chain and cytochrome c heme lyase function. However, we find that it does not require genes associated with programmed cell death in yeast. The chemical also inhibits endocytosis and intracellular vesicle trafficking and interferes with vacuolar acidification in yeast and in human cancer cells. These effects can all be ascribed to inhibition of sphingolipid biosynthesis by dihydromotuporamine C.

Conclusion

Despite their similar conceptual basis, namely altering drug sensitivity by modifying gene dosage, each of the screening approaches provided a distinct set of information that, when integrated, revealed a more complete picture of the mechanism of action of a drug on cells.