revised 9-27-04 JM
Genomic analysis of stationary phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes
M. Juanita Martinez1, Sushmita Roy2, Amanda B. Archuletta1, Peter D. Wentzell3, Sonia Santa Anna-Arriola1, Angelina L. Rodriguez1, Anthony D. Aragon1, Gabriel A. Quiñones1, Chris Allen1, and Margaret Werner-Washburne(1,4)
1 Department of Biology, University of New Mexico
2 Department of Computer Science, University of New Mexico
3 Department of Chemistry; Dalhousie University; Halifax, Nova Scotia, Canada
4 To whom correspondence should be addressed: Department of Biology, University of New Mexico, Albuquerque, NM 87131, maggieww@unm.edu, Phone: (505) 277-9338, Fax: (505) 277-9338Download manuscript (pdf) <---manuscript not available, under review
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 minutes of re-feeding. 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 over-representation
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 37ºC. Analysis of these genes
suggests that mitochondrial function is critical for entry into stationary
phase and that post-translational 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 homologs and of these, many have human
homologs that are disease-related, demonstrate that yeast is a bona
fide model system for studying the quiescent state of eukaryotic
cells.
- Figure 1. Dynamics of Gene expression during exit
- Figure 2. Time Course 1 Microarray data
- Table I. Cluster information for Time Course 1
- Figure 3. Time Course 2 data
Figure 6. Evolutionary distribution