Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae

Chang-Yi Wu,Dennis R Winge,David J Eide,Lisa M Chung,Amanda J Bird,Michael A Newton

doi:10.1186/1471-2164-9-370

Chang-Yi Wu, Dennis R Winge + Show 4 more

Open Access

https://doi.org/10.1186/1471-2164-9-370

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Abstract

BackgroundThe Zap1 transcription factor is a central player in the response of yeast to changes in zinc status. We previously used transcriptome profiling with DNA microarrays to identify 46 potential Zap1 target genes in the yeast genome. In this new study, we used complementary methods to identify additional Zap1 target genes.ResultsWith alternative growth conditions for the microarray experiments and a more sensitive motif identification algorithm, we identified 31 new potential targets of Zap1 activation. Moreover, an analysis of the response of Zap1 target genes to a range of zinc concentrations and to zinc withdrawal over time demonstrated that these genes respond differently to zinc deficiency. Some genes are induced under mild zinc deficiency and act as a first line of defense against this stress. First-line defense genes serve to maintain zinc homeostasis by increasing zinc uptake, and by mobilizing and conserving intracellular zinc pools. Other genes respond only to severe zinc limitation and act as a second line of defense. These second-line defense genes allow cells to adapt to conditions of zinc deficiency and include genes involved in maintaining secretory pathway and cell wall function, and stress responses.ConclusionWe have identified several new targets of Zap1-mediated regulation. Furthermore, our results indicate that through the differential regulation of its target genes, Zap1 prioritizes mechanisms of zinc homeostasis and adaptive responses to zinc deficiency.

Highlights

The Zap1 transcription factor is a central player in the response of yeast to changes in zinc status
We first compared gene expression in wild type cells grown in low and high zinc and identified 458 genes expressed more highly in low zinc in duplicate microarrays. We refer to this as "Experiment 1" or "E1." We compared gene expression in wild type and zap1Δ mutant cells grown in low zinc and identified 214 genes that were expressed at a higher level in wild type cells in duplicate arrays
We refer to this condition as "Experiment 2" or "E2." A set of 111 genes showed increased expression in both E1 and E2

Summary

Introduction

The Zap transcription factor is a central player in the response of yeast to changes in zinc status. We previously used transcriptome profiling with DNA microarrays to identify 46 potential Zap target genes in the yeast genome. In this new study, we used complementary methods to identify additional Zap target genes. Recent studies have begun to probe the cellular responses to the stress of zinc deficiency. Zinc is a critical cofactor for many proteins and plays important roles in myriad biological processes. Cells may alter their metabolic processes to adapt to growth under conditions where certain zinc-dependent proteins are less active. We are examining the cellular responses to zinc deficiency in the yeast Saccharomyces cerevisiae

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