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Open Access Research

Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae

David J Eide1*, Suzanne Clark1, T Murlidharan Nair2, Mathias Gehl3, Michael Gribskov2, Mary Lou Guerinot4 and Jeffrey F Harper3

Author Affiliations

1 Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA

2 San Diego Supercomputer Center, University of California-San Diego, La Jolla, CA 92903, USA

3 Biochemistry Department, University of Nevada, Reno, Nevada 89557, USA

4 Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA

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Genome Biology 2005, 6:R77  doi:10.1186/gb-2005-6-9-r77

Published: 30 August 2005

Abstract

Background

Nutrient minerals are essential yet potentially toxic, and homeostatic mechanisms are required to regulate their intracellular levels. We describe here a genome-wide screen for genes involved in the homeostasis of minerals in Saccharomyces cerevisiae. Using inductively coupled plasma-atomic emission spectroscopy (ICP-AES), we assayed 4,385 mutant strains for the accumulation of 13 elements (calcium, cobalt, copper, iron, potassium, magnesium, manganese, nickel, phosphorus, selenium, sodium, sulfur, and zinc). We refer to the resulting accumulation profile as the yeast 'ionome'.

Results

We identified 212 strains that showed altered ionome profiles when grown on a rich growth medium. Surprisingly few of these mutants (four strains) were affected for only one element. Rather, levels of multiple elements were altered in most mutants. It was also remarkable that only six genes previously shown to be involved in the uptake and utilization of minerals were identified here, indicating that homeostasis is robust under these replete conditions. Many mutants identified affected either mitochondrial or vacuolar function and these groups showed similar effects on the accumulation of many different elements. In addition, intriguing positive and negative correlations among different elements were observed. Finally, ionome profile data allowed us to correctly predict a function for a previously uncharacterized gene, YDR065W. We show that this gene is required for vacuolar acidification.

Conclusion

Our results indicate the power of ionomics to identify new aspects of mineral homeostasis and how these data can be used to develop hypotheses regarding the functions of previously uncharacterized genes.