TITLE

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

AUTHOR(S)
Chang-Yi Wu; Bird, Amanda J.; Chung, Lisa M.; Newton, Michael A.; Winge, Dennis R.; Eide, David J.
PUB. DATE
January 2008
SOURCE
BMC Genomics;2008, Vol. 9, Special section p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
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. Conclusion: 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.
ACCESSION #
38122965

 

Related Articles

  • Inferring yeast cell cycle regulators and interactions using transcription factor activities. Young-Lyeol Yang; Suen, Jason; Brynildsen, Mark P; Galbraith, Simon J; Liao, James C // BMC Genomics;2005, Vol. 6, p90 

    Background: Since transcription factors are often regulated at the post-transcriptional level, their activities, rather than expression levels may provide valuable information for investigating functions and their interactions. The recently developed Network Component Analysis (NCA) and its...

  • Co-expression networks: graph properties and topological comparisons. Xulvi-Brunet, Ramon; Hongzhe Li // Bioinformatics;Jan2010, Vol. 26 Issue 2, p205 

    Motivation: Microarray-based gene expression data have been generated widely to study different biological processes and systems. Gene co-expression networks are often used to extract information about groups of genes that are ‘functionally’ related or co-regulated. However, the...

  • Degradation of the Saccharomyces cerevisiae Mating-Type Regulator α1: Genetic Dissection of Cis-determinants and Trans-acting Pathways. Nixon, Christina E.; Wilcox, Alexander J.; Laney, Jeffrey D. // Genetics;Jun2010, Vol. 185 Issue 2, p497 

    Mating phenotype in the yeast Saccharomyces cerevisiae is a dynamic trait, and efficient transitions between alternate haploid cell types allow the organism to access the advantageous diploid form. Mating identity is determined by cell type-specific transcriptional regulators, but these factors...

  • Rapid GAL Gene Switch of Saccharomyces cerevisiae Depends on Nuclear Gal3, Not Nucleocytoplasmic Trafficking of Gal3 and Gal80. Egriboz, Onur; Jiang, Fenglei; Hopper, James E. // Genetics;Nov2011, Vol. 189 Issue 3, p825 

    The yeast transcriptional activator Gal4 localizes to UASGAL sites even in the absence of galactose but cannot activate transcription due to an association with the Gal80 protein. By 4 min after galactose addition, Gal4-activated gene transcription ensues. It is well established that this rapid...

  • Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes. Bordel, Sergio; Agren, Rasmus; Nielsen, Jens // PLoS Computational Biology;Jul2010, Vol. 6 Issue 7, p1 

    Genome-scale metabolic models are available for an increasing number of organisms and can be used to define the region of feasible metabolic flux distributions. In this work we use as constraints a small set of experimental metabolic fluxes, which reduces the region of feasible metabolic states....

  • Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae. Hyunsoo Kim; Hu, William; Kluger, Yuval // BMC Bioinformatics;2006, Vol. 7, p1 

    Background: Gene expression and transcription factor (TF) binding data have been used to reveal gene transcriptional regulatory networks. Existing knowledge of gene regulation can be presented using gene connectivity networks. However, these composite connectivity networks do not specify the...

  • RNA world: Making sense of antisense. Flintoft, Louisa // Nature Reviews Genetics;Jan2008, Vol. 9 Issue 1, p6 

    The article evaluates a research paper entitled "Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae," by J. Camblong and colleagues. In their research of the Saccharomyces cerevisiae PHO84 gene, researchers found reduced levels of its...

  • Gene Expression From Random Libraries of Yeast Promoters. Ligr, Martin; Siddharthan, Rahul; Cross, Fredrick R.; Siggia, Eric D. // Genetics;Apr2006, Vol. 172 Issue 4, p2113 

    Genomewide techniques to assay gene expression and transcription factor binding are in widespread use, but are far from providing predictive rules for the function of regulatory DNA. To investigate more intensively the grammar rules for active regulatory sequence, we made libraries from random...

  • Signal-dependent dynamics of transcription factor translocation controls gene expression. Hao, Nan; O'Shea, Erin K // Nature Structural & Molecular Biology;Jan2012, Vol. 19 Issue 1, p31 

    Information about environmental stimuli is often transmitted using common signaling molecules, but the mechanisms that ensure signaling specificity are not entirely known. Here we show that the identities and intensities of different stresses are transmitted by modulation of the amplitude,...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics