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MBC in Press, published online ahead of print September 29, 2004
Mol. Biol. Cell 10.1091/mbc.E03-11-0856

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Submitted on November 28, 2003
Revised on September 8, 2004
Accepted on September 16, 2004

Genomic Analysis of Stationary Phase and Exit in Saccharomyces cerevisiae: Gene Expression and Identification of Novel Essential Genes

M. Juanita Martinez,* Sushmita Roy,{dagger} Amanda B. Archuletta,* Peter D. Wentzell,{ddagger} Sonia Santa Anna-Arriola,* Angelina L. Rodriguez,* Anthony D. Aragon,* Gabriel A. Quiñones,* Chris Allen,* and Margaret Werner-Washburne*{sect}

Departments of *Biology and {dagger}Computer Science, University of New Mexico, Albuquerque, NM 87131; and {ddagger}Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada

Monitoring Editor: Thomas Fox

Most cells on earth exist in a quiescent state. In yeast, quiescence is induced by carbon starvation and exit occurs when a carbon source becomes available. To understand how cells survive in, and exit from this state, mRNA abundance was examined using oligonucleotide-based microarrays and qRT-PCR. Cells in stationary-phase cultures exhibited a coordinated response within 5-10 min of refeeding. Levels of >1800 mRNAs increased dramatically (≥64-fold) and a smaller group of stationary-phase mRNAs decreased in abundance. Motif analysis of sequences upstream of genes clustered by VxInsight identified an overrepresentation of Rap1p and BUF (RPA) binding sites in genes whose mRNA levels rapidly increased during exit. Examination of 95 strains carrying deletions in stationary-phase genes induced identified thirty-two genes essential for survival in stationary phase at 37°C. Analysis of these genes suggests that mitochondrial function is critical for entry into stationary phase and that posttranslational modifications and protection from oxidative stress become important later. The phylogenetic conservation of stationary-phase genes, and our findings that two-thirds of the essential stationary-phase genes have human homologues and of these, many have human homologues that are disease-related, demonstrate that yeast is a bona fide model system for studying the quiescent state of eukaryotic cells.

{sect}Corresponding author. E-mail: maggieww{at}unm.edu




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