Genomic analysis of stationary-phase and exit in Saccharomyces cerevisiae: Gene expression and identification of novel essential genes
Date
2004-12
Authors
Martinez, MJ
Roy, S.
Archuletta, AB
Wentzell, PD
Santa Anna-Arriola, S.
Rodriguez, AL
Aragon, AD
Quinones, GA
Allen, C.
Werner-Washburne, M.
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Abstract
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 quantitative reverse transcription-polymerase chain reaction. Cells in stationary-phase cultures
exhibited a coordinated response within 5-10 min of refeeding. Levels of > 1800 mRNAs increased
dramatically (greater than or equal to 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 32 genes essential for survival in stationary-phase at 37degreesC. 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.
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Citation
Martinez, MJ, S. Roy, AB Archuletta, PD Wentzell, et al. 2004. "Genomic analysis of stationary-phase and exit in Saccharomyces cerevisiae: Gene expression and
identification of novel essential genes." Molecular biology of the cell 15(12): 5295-5305.
doi:10.1091/mbc.E03-11-0856