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

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.

Figure 1

Characterization of the wild-type yeast ionome. (a) Wild-type BY4743 cells were grown in rich yeast extract-peptone-dextrose (YPD) + mineral supplements to post-diauxic-shift phase, harvested, digested with HNO₃, and then analyzed for the levels of the indicated elements. Mean values are shown and the error bars indicate 1 standard deviation (n = 40). (b) The element content of the supplemented growth medium was also assayed (n = 6). The ratio of cell concentration, calculated from the data in panel (a) and assuming homogeneous distribution in the cell, to medium concentration is plotted.

Figure 2

Overview of the effects of mutations on element content. (a) Number of mutants showing increases (open bars) and decreases (filled bars) for each element. (b) Number of mutants showing one or more changes in their ionome profiles.

Figure 3

Functional classes of genes identified by ionome profiling of their corresponding mutants. The number of genes identified in each functional class is represented. See Additional data file 3 for a complete list of the specific genes in each functional category.

Figure 4

Mutants within functional categories show similar ionome phenotypes. The effects of mutations altering (a) vacuolar or (b) mitochondrial function on the ionome profile are shown. Elements are listed along the horizontal axis and the genes affected are listed along the vertical axis. Increases greater than 2.5 standard deviations of the wild-type means are shown in red and decreases greater than 2.5 standard deviations are shown in green. The bars at the top represent the consensus for each group of genes. This figure was generated using TreeView software.

Figure 5

Biplot representation of the ionome results. The length of each eigenvector is proportional to the variance in the data for that element. The angle between eigenvectors represents correlations among different elements. Three groups of elements (circled, and denoted I, II, and III) show strong positive correlations.

Figure 6

Δydr065w mutants are defective for vacuolar acidification. Wild-type (BY4743) and BY4743 Δydr065w cells were harvested in exponential phase, incubated with LysoSensor Green DND-189, and then examined by differential interference contrast (DIC) (left panel) and fluorescence (right panel) microscopy. Failure to accumulate the fluorophore indicates defective vacuolar acidification. Intact vacuoles in the mutant cells are apparent in the DIC image.