Transcript A Chemostat-based Transcriptome Analysis

Acclimation of Saccharomyces cerevisiae
to Low Temperature: A Chemostat-based
Transcriptome Analysis
Tai LT, Daran-Lapujade P, Walsh MC,
Pronk JT, Daran JM
(2007) American Society for Cell Biology 18: 5100-5112
Alex George
Bobek Seddighzadeh
Journal Club Presentation
BIOL 398-01/S10: Bioinformatics Lab
April 13, 2010
Outline
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DNA microarrays determine gene expression
Chemostat cultures foster constant growth rates
Suboptimal temperatures influence cellular processes
Investigate steady state acclimatized growth of
suboptimal temperature growth of S. cerevisiae.
• In-depth analysis of the tables and result presented
in the study
• Discussion on temperature and growth rate changes
that illicit a transcriptional response
DNA microarrays are used to
determine gene expression levels
• Each spot contains a probe
that correlates to a gene
• Labeled sample is washed
over chip to form
complementary bonds
• Strength of fluorescent
signal indicates more
binding
• Our experiment: Only one
sample hybridized at a timerelative abundance
Chemostat cultures maintain a
constant specific growth rate
• Batch culture- limited supply
of nutrients provided
• Chemostat culture- nutrients
are continuously provided in
order to control specific
growth rate
• Specific growth rate has
been shown to impact
transcript profiles
Suboptimal Temperatures Affect
Various Cellular
Processes/Characteristics
• Optimum growth range for S Cerevisiae:
– 25-35 C⁰
• Below this temperature Enzyme Kinetics slow
• Cellular processes/characteristics affected:
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Growth Phase
Respiration
Membrane lipid composition
Trehalose content
Time Exposure is Important to Low-Temp
Parameters on Microbial Physiology
• Cold shock: sudden exposure to environmental
changes
• The response to cold shock triggers adaptation
• Prolonged exposures leads to acclimation
• Acclimation: a permanently adapted physiological
state in response to environment
Limitations From Previous Studies Led
to Further Investigations by Tai et al.
• Major discrepancies exist amongst lowtemperature transcriptome data published
• Batch cultures do not allow for control of specific
growth rate and culture variables
• The differences between adaptation and
acclimation have not been thoroughly investigated
• The goal of this study:
– Investigate Steady state acclimatized growth of
suboptimal temperature growth of S. cerevisiae.
– Grow S. cerevisiae in anaerobic chemostat cultures at
fixed specific growth grate of 0.03 h ⁻1
Growth efficiency and fermentation rates were
not severely affected by growth temperature
The number of significantly different and similar genes
between 12º and 30ºC cultures for both N and C limitations
Heat Map representing the level of expression of a total of
1065 genes in Nitrogen- and Carbon-Limiting Cultures
N-limiting: Up
(202 genes)
C & N-Limiting:Up
(96 genes)
C-Limiting: Up
(123 genes)
C-lim. 30ºC
C-lim 12ºC
N-lim 30ºC
N-lim 12ºC
C & N-Limiting: Down
(139 genes)
N-Limiting: Down
(369 genes)
C-Limiting: Down
(136 genes)
Trehalose and glycogen levels were not
affected by increased gene expression
Few Genes Showed Consistent
Responses in Acclimation and
Adaption
Only 91 genes were consistently up regulated
More Stress Response Elements
are Upstream of genes that Were
Reduced
Once cells become adapted to cold temp, the stress response and
up-regulation of carbohydrate storage recedes
Of 29 Genes, only 11 Genes
Showed Consistent Patterns of
Regulation
The only genes that were defined as commonly regulated on low
temperature adaptations were involved in lipid metabolism
Negligible Overlap with Growth-rate–
responsive Genes was Observed
25% of down-regulated genes and 10% of up-regulated are likely
to be only related to specific growth rate.
A Significant Overlap Between Regulated
Genes in Batch Cultures Exist
Environmental factors make
isolating one variable difficult
• In study, changing the temperature resulted
in a higher residual glucose concentration
in 12° C cultures
• By combining two variables, such as
nutrients and temperature, a core set of
genes can be identified because the
responses are content-independent
Change in specific growth rate may illicit
response, not temperature
• Previous studies indicated increase in
synthesis of storage carbohydrates and
regulation of carbohydrate storage
genes as temperature decreases
• Chemostat study shows no correlation
indicating role of specific growth rate
Slow temperature change elicits different
transcriptional response than cold-shock
• 235 genes responded to low
temperature regardless of limiting
nutrient
• Only one gene was in common with
batch culture studies
• Indicates transcription regulation for
acclimation is different than that for
acclimitization