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PMID: 19087243 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3.

BMC genomics ·Vol. 9 ·2008-12-16 ·Pages 601

Westholm JO, Nordberg N, Murén E, Ameur A, Komorowski J, Ronne H

Abstract

Expression of a large number of yeast genes is repressed by glucose. The zinc finger protein Mig1 is the main effector in glucose repression, but yeast also has two related proteins: Mig2 and Mig3. We have used microarrays to study global gene expression in all possible combinations of mig1, mig2 and mig3 deletion mutants. Mig1 and Mig2 repress a largely overlapping set of genes on 2% glucose. Genes that are upregulated in a mig1 mig2 double mutant were grouped according to the contribution of Mig2. Most of them show partially redundant repression, with Mig1 being the major repressor, but some genes show complete redundancy, and some are repressed only by Mig1. Several redundantly repressed genes are involved in phosphate metabolism. The promoters of these genes are enriched for Pho4 sites, a novel GGGAGG motif, and a variant Mig1 site which is absent from genes repressed only by Mig1. Genes repressed only by Mig1 on 2% glucose include the hexose transporter gene HXT4, but Mig2 contributes to HXT4 repression on 10% glucose. HXT6 is one of the few genes that are more strongly repressed by Mig2. Mig3 does not seem to overlap in function with Mig1 and Mig2. Instead, Mig3 downregulates the SIR2 gene encoding a histone deacetylase involved in gene silencing and the control of aging. Mig2 fine-tunes glucose repression by targeting a subset of the Mig1-repressed genes, and by responding to higher glucose concentrations. Mig3 does not target the same genes as Mig1 and Mig2, but instead downregulates the SIR2 gene.

MeSH Terms
Binding Sites DNA-Binding Proteins/genetics,metabolism Down-Regulation Gene Expression Regulation, Fungal Glucose/metabolism Histone Deacetylases/genetics,metabolism Monosaccharide Transport Proteins/genetics,metabolism Nucleosomes/metabolism Oligonucleotide Array Sequence Analysis Promoter Regions, Genetic Repressor Proteins/genetics,metabolism Saccharomyces cerevisiae/genetics,metabolism Saccharomyces cerevisiae Proteins/genetics,metabolism Silent Information Regulator Proteins, Saccharomyces cerevisiae/genetics,metabolism Sirtuin 2 Sirtuins/genetics,metabolism Transcription Factors/genetics,metabolism
Chemicals
DNA-Binding Proteins MIG1 protein, S cerevisiae Mig2 protein, S cerevisiae Mig3 protein, S cerevisiae Monosaccharide Transport Proteins Nucleosomes PHO4 protein, S cerevisiae Repressor Proteins Saccharomyces cerevisiae Proteins Silent Information Regulator Proteins, Saccharomyces cerevisiae Transcription Factors SIR2 protein, S cerevisiae Sirtuin 2 Sirtuins Histone Deacetylases Glucose
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Westholm Jakub Orzechowski
The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE-751 24 Uppsala, Sweden. Jakub.Orzechowski@lcb.uu.se
Nordberg Niklas
Murén Eva
Ameur Adam
Komorowski Jan
Ronne Hans
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Article Info
Journal
BMC genomics
Abbr.
BMC Genomics
ISSN
1471-2164
DOI
10.1186/1471-2164-9-601
Email
jakub.orzechowski@lcb.uu.se
Published
2008-12-16
Epub
2008-00-16
Pages
601
Language
English
Region
England
NLM ID
100965258
PMCID
PMC2631581
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2164-9-601 PMC Full Text View journal details
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