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Open Access Research article

Genomic phenotyping of the essential and non-essential yeast genome detects novel pathways for alkylation resistance

J Peter Svensson13, Laia QuirĂ³s Pesudo1, Rebecca C Fry14, Yeyejide A Adeleye2, Paul Carmichael2 and Leona D Samson1*

Author Affiliations

1 Biological Engineering Department, Center for Environmental Health Sciences, Biology Department, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, U.S.A

2 Safety & Environmental Assurance Centre (SEAC), Unilever, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK

3 Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden

4 Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, Chapel Hill, NC 27599, U.S.A

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BMC Systems Biology 2011, 5:157  doi:10.1186/1752-0509-5-157

Published: 6 October 2011

Abstract

Background

A myriad of new chemicals has been introduced into our environment and exposure to these agents can damage cells and induce cytotoxicity through different mechanisms, including damaging DNA directly. Analysis of global transcriptional and phenotypic responses in the yeast S. cerevisiae provides means to identify pathways of damage recovery upon toxic exposure.

Results

Here we present a phenotypic screen of S. cerevisiae in liquid culture in a microtiter format. Detailed growth measurements were analyzed to reveal effects on ~5,500 different haploid strains that have either non-essential genes deleted or essential genes modified to generate unstable transcripts. The pattern of yeast mutants that are growth-inhibited (compared to WT cells) reveals the mechanisms ordinarily used to recover after damage. In addition to identifying previously-described DNA repair and cell cycle checkpoint deficient strains, we also identified new functional groups that profoundly affect MMS sensitivity, including RNA processing and telomere maintenance.

Conclusions

We present here a data-driven method to reveal modes of toxicity of different agents that impair cellular growth. The results from this study complement previous genomic phenotyping studies as we have expanded the data to include essential genes and to provide detailed mutant growth analysis for each individual strain. This eukaryotic testing system could potentially be used to screen compounds for toxicity, to identify mechanisms of toxicity, and to reduce the need for animal testing.