title: Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae.
abstract: BACKGROUND
  The 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.
  
  
  RESULTS
  With 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.
  
  
  CONCLUSIONS
  We 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.
authors.affiliation: Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA. cywu@nutrisci.wisc.edu
authors.forename: Chang-Yi
authors.initials: CY
authors.lastname: Wu
authors.forename: Amanda J
authors.initials: AJ
authors.lastname: Bird
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Chung
authors.forename: Michael A
authors.initials: MA
authors.lastname: Newton
authors.forename: Dennis R
authors.initials: DR
authors.lastname: Winge
authors.forename: David J
authors.initials: DJ
authors.lastname: Eide
mesh_terms: D001483:Base Sequence; D004271:DNA, Fungal / Q000235:genetics; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D023281:Genomics / Q000379:methods; D006706:Homeostasis; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism*; D015534:Trans-Activators / Q000235:genetics* / Q000378:metabolism*; D014157:Transcription Factors; D015032:Zinc / Q000378:metabolism*
chemical_list: D004271:DNA, Fungal; D029701:Saccharomyces cerevisiae Proteins; D015534:Trans-Activators; D014157:Transcription Factors; C103264:ZAP1 protein, S cerevisiae; D015032:Zinc