ABSTRACT
Genome-wide location analysis was used to determine how the yeast cell cycle gene expression program is regulated by each of the nine known cell cycle transcriptional activators. We found that cell cycle transcriptional activators that function during one stage of the cell cycle regulate transcriptional activators that function during the next stage. This serial regulation of transcriptional activators forms a connected regulatory network that is itself a cycle. Our results also reveal how the nine transcriptional regulators coordinately regulate global gene expression and diverse stage-specific functions to produce a continuous cycle of cellular events. This information forms the foundation for a complete map of the transcriptional regulatory network that controls the cell cycle.
Subject(s)
Cell Cycle/genetics , Gene Expression Regulation, Fungal , Saccharomyces cerevisiae/cytology , Saccharomyces cerevisiae/genetics , Trans-Activators/metabolism , Transcription Factors/metabolism , Cyclin-Dependent Kinases/genetics , Cyclins/genetics , Genome, FungalABSTRACT
Understanding how DNA binding proteins control global gene expression and chromosomal maintenance requires knowledge of the chromosomal locations at which these proteins function in vivo. We developed a microarray method that reveals the genome-wide location of DNA-bound proteins and used this method to monitor binding of gene-specific transcription activators in yeast. A combination of location and expression profiles was used to identify genes whose expression is directly controlled by Gal4 and Ste12 as cells respond to changes in carbon source and mating pheromone, respectively. The results identify pathways that are coordinately regulated by each of the two activators and reveal previously unknown functions for Gal4 and Ste12. Genome-wide location analysis will facilitate investigation of gene regulatory networks, gene function, and genome maintenance.
Subject(s)
DNA-Binding Proteins/metabolism , Fungal Proteins/metabolism , Gene Expression Profiling , Gene Expression Regulation, Fungal , Genome, Fungal , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae/genetics , Transcription Factors/metabolism , Binding Sites , Cell Cycle , DNA, Fungal/genetics , DNA, Fungal/metabolism , Galactose/metabolism , Genes, Fungal , Mating Factor , Oligonucleotide Array Sequence Analysis , Peptides/pharmacology , Promoter Regions, Genetic , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae/physiology , Transcriptional ActivationABSTRACT
The Escherichia coli export chaperone SecB binds nascent precursors of certain periplasmic and outer membrane proteins and prevents them from folding or aggregating in the cytoplasm. In this study, we demonstrate that the C-terminal 13 residues of SecB were highly mobile using (1)H NMR spectroscopy. A protein lacking the C-terminal 13 amino acids of wild-type SecB was found to retain the ability to bind unfolded maltose-binding protein (MBP) in vitro but to interfere with the normal kinetics of pre-MBP export when overexpressed in vivo. The defect in export was reversed by overproduction of the peripheral membrane ATPase SecA. Therefore, deletion of the mobile region of SecB may alter the interactions of SecB with SecA.
