This webpage
was produced as an assignment for an undergraduate course at Davidson College.
EXPLORING GENE EXPRESSION OF MY
FAVORITE YEAST ORFs, CDC28 and YBR161W, WITH DNA MIRCOARRAYS
CDC28.
I saw previously
that CDC28 is a cyclin-dependent kinase essential to the proliferation of Saccharomyces
cerevisiae cells; this protein controls the essential process of yeast
cells ‘deciding’ to replicate their DNA and enter mitosis. I explored the expression patterns of CDC28
under different experimental conditions using the public database SGD Expression
Connection (SGD, 2001; http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl).
I
found microarray data for the following conditions:
- expression at different
alpha-factor conditions
- expresssion in response to
alpha-factor
- expression in response to
DNA-damaging agents
- expression during the cell cycle
- expression during the diauxic
shift
- evolution of expression during
glucose limitation
- expression during sporulation
- expression in response to
environmental changes
- and expression in response to
histone depletion.
While
there was a great deal of information to be found in the database results, I
decided to focus my analysis on the experiments that pertained to the function
of my gene.
I. Expression at Different Alpha-Factor
Concentrations.
Alpha-factor
is a pheromone that arrests yeast’s cell cycle in the G1 phase and induces
genes necessary for mating (Zymo Research, 2001; http://www.zymor.com/y1001-frame.html). In the life cycle of yeast, cells
alternately undergo sexual and asexual reproduction; i.e., they alternate
beteween meiosis and mitosis depending on environmental factors and subsequent
gene expression.
Figure 1. The life cycle of yeast. Yeast cells alternate between budding and
mating, as well as mitosis and meiosis.
(With permission from Tom Manney, http://www.phys.ksu.edu/gene/Mating4.html).
If
CDC28 is indeed responsible for controlling mitosis in budding yeast, it makes
sense that this protein would be repressed as higher concentrations of alpha pheromone trigger cells to arrest G1
phase and any subsequent mitotic division, and undergo meiosis. The DNA microarray data supports this:
Scale : (fold repression/induction)
Click on a color strip to see data for that gene.
Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene
|
Orf |
|
Gene |
|
|
|
Process |
|
Function |
|
Component |
|
|
CDC28 |
|
|
|
protein amino acid
phosphorylation* |
|
cyclin-dependent protein
kinase |
|
cytoplasm |
|
|
|
NDD1 |
|
|
|
not yet annotated |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
ADE17 |
|
|
|
`de novo` IMP biosynthesis |
|
IMP cyclohydrolase* |
|
cytosol |
|
|
|
BBP1 |
|
|
|
microtubule nucleation |
|
structural protein of
cytoskeleton |
|
spindle pole body |
|
|
|
SCO1 |
|
|
|
protein complex assembly* |
|
molecular_function unknown |
|
mitochondrial inner
membrane |
|
|
|
NUD1 |
|
|
|
microtubule nucleation |
|
structural protein of
cytoskeleton |
|
spindle pole body |
|
|
|
HHF2 |
|
|
|
not yet annotated |
|
not yet annotated |
|
nucleosome |
|
|
|
HTB2 |
|
|
|
not yet annotated |
|
not yet annotated |
|
nucleosome |
|
|
|
HHT1 |
|
|
|
not yet annotated |
|
not yet annotated |
|
nucleosome |
|
|
|
HPR5 |
|
|
|
DNA repair |
|
DNA helicase |
|
nucleus |
|
|
|
CBF2 |
|
|
|
mitosis |
|
not yet annotated |
|
not yet annotated |
|
|
|
SPC34 |
|
|
|
microtubule nucleation |
|
structural protein of
cytoskeleton |
|
spindle pole body |
|
|
|
EST1 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
GAS1 |
|
|
|
biological_process unknown |
|
not yet annotated |
|
not yet annotated |
|
|
|
HTA2 |
|
|
|
not yet annotated |
|
not yet annotated |
|
nucleosome |
|
|
|
HTA1 |
|
|
|
not yet annotated |
|
not yet annotated |
|
nucleosome |
|
|
|
HHF1 |
|
|
|
not yet annotated |
|
not yet annotated |
|
nucleosome |
|
|
|
HTB1 |
|
|
|
chromatin
assembly/disassembly |
|
DNA binding |
|
nucleosome |
|
|
|
HHT2 |
|
|
|
not yet annotated |
|
not yet annotated |
|
nucleosome |
|
|
|
REM50 |
|
|
|
not yet annotated |
|
molecular_function unknown |
|
not yet annotated |
* : indicates that more than one annotation exists for the gene.
Figure 2. Clustered data for expression at
different alpha-factor concentrations. (SGD, 2001).
Figure 3. Expression
changes in CDC28 at different alpha-factor concentrations. CDC28 is repressed to a nearly constant
value relative to the control (SGD, 2001).
While CDC28 does not follow a linear
pattern, it is repressed at different alpha-factor concentrations. It is clustered with other genes that are
highly repressed as alpha-factor concentration increases. Many of these genes are non-annotated, but a
few are structural proteins in the cytoskeleton. This makes intuitive sense in that as the cells arrest mitosis
and begin sexual reproduction, they do not need to form new cytoskeletons, and
these structural genes should be repressed.
Interestingly, while CDC28 is a cytoplasmic protein, many of the genes
that are co-regulated with it reside in various locations within the cell, such
as the mitochondrial inner membrane and the nucleosome. CDC28 is repressed to a nearly constant
value and does not change with increasing concentrations of alpha-factor; once
the signal is turned off, it stays off and does not fluctuate with increasing
signal.
II.
Expression in
Response to Alpha-Factor.
In this experimental condition, CDC28 is exposed to alpha-factor and its response is monitored over time.
Scale : (fold repression/induction)
Click on a color strip to see data for that gene.
Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to the query gene
|
Orf |
|
Gene |
|
|
|
Process |
|
Function |
|
Component |
|
|
CDC28 |
|
|
|
protein amino acid
phosphorylation* |
|
cyclin-dependent protein
kinase |
|
cytoplasm |
|
|
|
BMH1 |
|
|
|
pseudohyphal growth* |
|
not yet annotated |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
KIC1 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
YRF1-1 |
|
|
|
biological_process unknown |
|
not yet annotated |
|
not yet annotated |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
CYC8 |
|
|
|
transcription |
|
not yet annotated |
|
not yet annotated |
|
|
|
USV1 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
YRF1-5 |
|
|
|
biological_process unknown |
|
not yet annotated |
|
not yet annotated |
|
|
|
CDC39 |
|
|
|
cell cycle control* |
|
molecular_function unknown |
|
nucleus |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
not yet annotated |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
HEF3 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
CDD1 |
|
|
|
cytidine catabolism* |
|
cytidine deaminase |
|
cellular_component unknown |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
EHT1 |
|
|
|
lipid metabolism |
|
molecular_function unknown |
|
lipid particle |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
* : indicates that more than one annotation exists for the gene.
Figure 4. Clustered
data for CDC28 expression when exposed to alpha-factor over time (SGD,
2001).
Figure 5. CDC28
expression changes when exposed to alpha-factor over time (SGD, 2001).
The microarray data indicate that
initially, CDC28 is repressed and then at the end of the time points taken, it
is induced. The genes CDC28 are
clustered with exhibit similar expression profiles. Most of these genes have unknown functions and are not yet
annotated. The genes that are
annotated, however, play roles in essential cell cycling functions such as transcription
and lipid metabolism. These expression
changes may be indicative of the trend that when initially exposed to
alpha-factor, CDC28 is repressed for reasons explained above. As time passes however, the cell may have
completed meiosis and is ready to enter the cell cycle of mitosis and interphase
again, and consequently CDC28 is induced.
III.
Expression During
the Cell Cycle.
This
experiment attempted to catalog the different genes associated with the cell
cycle. The authors analyzed yeast cells
under three different conditions: alpha-factor arrest, elutriation, and arrest
of a CDC15 temperature-sensitive mutant.
They found 800 genes with significantly altered transcription levels
over the course of the cell cycle. More
than half of these 800 genes responded to one or both of two important cyclins,
CLN3 and CLB2, which are known to interact with CDC28 (Spellman et al.,
1998; http://www.molbiolcell.org/cgi/content/full/9/12/3273).
The authors picked reference genes
representative of each of the phases of the cell cycle: G1, S, G2 and
mitosis. These genes show a diagonal
clustering; that is, they alternate with each other through each phase of the
cell cycle, so the red and green stripes are diagonals leaning to the right
across the page:
|
Name |
Score |
Peak |
|
|
0.66 |
|
|
|
|
Reference Genes |
|
||
|
10.9 |
G1 |
|
|
|
10.68 |
S |
|
|
|
3.08 |
G2 |
|
|
|
6.726 |
M |
|
|
|
11.8 |
M/G1 |
|
|
|
|
|
|
|
|
Plot of CDC28 (YBR160W) |
|
||
Figure 6. Comparison of CDC28 expression to that
of reference genes from each phase of the cell cycle. Peaks and valleys in the graph indicate individual cycles of the
cell (SGD, 2001).
By reading across each row and
comparing how each of the reference genes is expressed with how CDC28 is
expressed, CDC28 expresses similarly to CLN2 and HTA1; these genes are co-regulated
so they each induce and repress at the same time. CDC28 is expressed inversely to ASH1; when CDC28 is induced, ASH1
is repressed and vice versa. CLB4 and
SWI5 don’t seem to co-regulate with CDC28; the colors were too close to black,
i.e. with ratios too close to 1, to make out appreciable differences.
These
statements are approximations; CDC28 was not largely induced or repressed for
any of these experimental conditions.
This may be due to the fact that since CDC28 is such an important
protein in the signaling process of cell cycling, only slight changes in its
induction and repression cause significant changes in many other proteins in a
complex cascade. Hence, it is not
necessary for CDC28 to be largely induced or repressed when so many other
proteins depend on it for activation and deactivation.
IV.
Expression During Sporulation.
This experiment measured gene expression during
sporulation. Given that yeast produce
spores by undergoing meiotic division, we would expect the data to be similar
to that of II above.
Scale : (fold repression/induction)
Click on a color strip to see data for that gene.
Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to
the query gene
|
Orf |
|
Gene |
|
|
|
Process |
|
Function |
|
Component |
|
|
CDC28 |
|
|
|
protein amino acid
phosphorylation* |
|
cyclin-dependent protein
kinase |
|
cytoplasm |
|
|
|
RPA43 |
|
|
|
transcription, from Pol I
promoter |
|
DNA-directed RNA polymerase
I |
|
DNA-directed RNA polymerase
I |
|
|
|
KHA1 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
APE2 |
|
|
|
peptide metabolism |
|
leucyl aminopeptidase |
|
cytoplasm* |
|
|
|
ATR1 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
RPS13 |
|
|
|
protein biosynthesis |
|
structural protein of
ribosome |
|
cytosolic small ribosomal
(40S) subunit |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
BUD28 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
cellular_component unknown |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
RPL15B |
|
|
|
protein biosynthesis |
|
structural protein of
ribosome* |
|
cytosolic large ribosomal
(60S) subunit |
|
|
|
SMP1 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
RPL22A |
|
|
|
protein biosynthesis |
|
structural protein of
ribosome |
|
cytosolic large ribosomal
(60S) subunit |
|
|
|
DBP10 |
|
|
|
35S primary transcript
processing* |
|
ATP dependent RNA helicase |
|
nucleolus |
|
|
|
FKS1 |
|
|
|
cell wall organization and
biogenesis* |
|
1,3-beta-glucan synthase |
|
actin cap (sensu
Saccharomyces)* |
|
|
|
RPS29B |
|
|
|
protein biosynthesis |
|
structural protein of
ribosome |
|
cytosolic small ribosomal
(40S) subunit |
|
|
|
MRPL49 |
|
|
|
protein biosynthesis |
|
structural protein of
ribosome |
|
mitochondrial large
ribosomal subunit |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
* : indicates that more than one annotation exists for the gene.
Figure 7. Microarray data for sporulation over
time. Notice similarities to data from
exposure to alpha-factor over time above.
Figure 8. Response of CDC28 to sporulation over
time. Note similarity to Figure 5 (SGD,
2001).
This experiment was similar to a
previous experiment monitoring gene response to alpha-factor over time in that
above, alpha-factor was signaling cells to mate, where here, sporulation
entails the yeast cells forming spores necessary for mating. While CDC28 is regulated similarly as seen
in Figure 8, it was interesting to find how many more annotated genes clustered
with CDC28 in Figure 7. Many of these
genes are involved with such processes as RNA transcription, peptide metabolism
and biosynthesis, as well as cell wall biogenesis. It appears that many more proteins are worked out in this
signaling pathway relative to previous ones.
Conclusions.
For many of the non-annotated genes, because they exhibit
similar expression profiles, they may have similar functions to CDC28. While many were more intensely induced or
repressed than my gene, this is expected given that a cell should have very few
critical proteins for complex signaling like CDC28.
YBR161W.
Previously, I
found that YBR161W is an ORF located in close proximity to CDC28 on chromosome
II. Based on sequence similarity, it
may be a functional homolog to the yeast gene Sur1, which has been found to
play a key role in cell wall formation.
Again, I searched SGD’s Expression
Connection Database, and yielded a great deal of information on the expression
profiles of my non-annotated gene. I
focused my analysis on the experiments that gave the most insight into
potential functions and processes associated with YBR161W.
I.
Expression
at Different Alpha-Factor Concentrations.
Scale : (fold repression/induction)
Click on a color strip to see data for that gene.
Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to
the query gene
|
Orf |
|
Gene |
|
|
|
Process |
|
Function |
|
Component |
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
ERP5 |
|
|
|
not yet annotated |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
SDT1 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
MCD4 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
GCV3 |
|
|
|
glycine metabolism |
|
not yet annotated |
|
not yet annotated |
|
|
|
SHE1 |
|
|
|
biological_process unknown |
|
not yet annotated |
|
not yet annotated |
|
|
|
CLB6 |
|
|
|
G1/S transition of mitotic
cell cycle* |
|
cyclin |
|
cellular_component unknown |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
MMS4 |
|
|
|
DNA repair |
|
transcription co-activator |
|
nucleus |
|
|
|
RFA1 |
|
|
|
nucleotide-excision repair* |
|
RNA binding* |
|
DNA replication factor A
complex |
|
|
|
ECO1 |
|
|
|
not yet annotated |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
MSH2 |
|
|
|
DNA repair |
|
not yet annotated |
|
not yet annotated |
|
|
|
PEA2 |
|
|
|
establishment of cell
polarity (sensu Saccharomyces)* |
|
cytoskeletal regulatory
protein binding |
|
actin cap (sensu
Saccharomyces)* |
|
|
|
ATM1 |
|
|
|
iron homeostasis |
|
ATP-binding cassette (ABC)
transporter |
|
mitochondrial inner
membrane |
* : indicates that more than one annotation exists for the gene.
Figure 9. Clustering data for YBR161W when
exposed to increasing concentrations of alpha-factor (SGD, 2001).
Figure 10. Response
of YBR161W to increasing alpha-factor concentrations (SGD, 2001).
Interestingly, YBR161W is regulated similarly to CDC28 under this experimental condition. Also of note, YBR161W clustered with one of the 9 essential cyclins, CLB6, that CDC28 is known to activate and deactivate. CLB6 is one of the key genes responsible for signaling the end of G1 and the beginning of S phase. If YBR161W is also involved in the cell’s ‘decision’ to undergo DNA replication, it makes sense that these other genes involved in DNA repair and establishment of cell polarity should be clustered here as well.
II.
Expression in Response to Alpha-Factor.
Scale : (fold repression/induction)
Click on a color strip to see data for that gene.
Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to
the query gene
|
Orf |
|
Gene |
|
|
|
Process |
|
Function |
|
Component |
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
EUG1 |
|
|
|
not yet annotated |
|
protein disulfide isomerase |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
DNA helicase |
|
cellular_component unknown |
|
|
|
BET3 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
SLY1 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
IRR1 |
|
|
|
mitotic sister chromatid
cohesion* |
|
molecular_function unknown |
|
cohesin |
|
|
|
ERG11 |
|
|
|
ergosterol biosynthesis |
|
lanosterol
14-alpha-demethylase |
|
endoplasmic reticulum |
|
|
|
LEU1 |
|
|
|
not yet annotated |
|
3-isopropylmalate
dehydratase |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
ISW2 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
ERV25 |
|
|
|
not yet annotated |
|
not yet annotated |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
NUP116 |
|
|
|
mRNA-nucleus export* |
|
structural protein |
|
nuclear pore |
|
|
|
ACC1 |
|
|
|
fatty acid biosynthesis* |
|
acetyl-CoA carboxylase* |
|
cytosol* |
|
|
|
SWD1 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
CHO1 |
|
|
|
phosphatidylserine biosynthesis |
|
CDP-diacylglycerol-serine
O-phosphatidyltransferase |
|
endoplasmic reticulum |
|
|
|
CDC2 |
|
|
|
nucleotide-excision repair* |
|
delta DNA polymerase |
|
delta DNA polymerase |
|
|
|
TFC7 |
|
|
|
transcription initiation,
from Pol III promoter |
|
RNA polymerase III
transcription factor |
|
transcription factor TFIIIC |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
cellular_component unknown |
* : indicates that more than one annotation exists for the gene.
Figure 11.
Clustering data for
YBR161W when exposed to alpha-factor over time (SGD, 2001).
Figure 12. Response of YBR161W to alpha-factor over time (SGD, 2001).
Interestingly, here my favorite non-annotated gene is clustering with other genes involved in DNA replication, but intead of repair functions, these genes are involved in a variety of functions such as cohesion of sister chromatids, ergosterol biosynthesis, mRNA-nucleus export, fatty acid biosynthesis, transcription initiation, as well as one gene involved in necleotide-excision repair. This is not the same gene involved in nucleotide-excision repair from above; that gene was involved in RNA binding, where this gene is a DNA polymerase. There don’t appear to be significant correlations between these 2 experiments except to say that YBR161W has something to do with DNA replication.
III.
Expression During the Cell Cycle.
|
Name |
Score |
Peak |
|
|
1.851 |
G1 |
|
|
|
Reference Genes |
|
||
|
10.9 |
G1 |
|
|
|
10.68 |
S |
|
|
|
3.08 |
G2 |
|
|
|
6.726 |
M |
|
|
|
11.8 |
M/G1 |
|
|
|
|
|
|
|
|
Plot of YBR161W |
|
||
Figure 13. Comparison of YBR161W to reference genes from each phase of the cell cycle. Peaks and valleys of the graph indicate a full cycle for the cell.
Interestingly, the reference genes follow a diagonal pattern as before, indicating induction and repression as the cell cycles through the 4 phases of G1, DNA replication, G2 and mitosis. Readingly across as above, it appears that YBR161W is co-regulated with CLN2 and HTA1. There is too much black in the strip for YBR161W to determine which of these 2 genes, and hence which phase, it is more closely imitating. YBR161W co-regulates with CLB4 in some of the mutant conditions but not all. YBR161W is oppositely regulated with SWI5 and ASH1; that is, when SWI5 and ASH1 are induced, YBR161W is repressed and vice versa, though these correlations are not precise across each row.
As before, these generalizations are approximate; YBR161W was not strongly induced or repressed for many of the time points or mutants, therefore, strict correlations are difficult to extract.
IV.
Expression During the Diauxic Shift.
This experiment measured gene expression responses to changes in available glucose. We saw in class that when yeast cells were placed under this environmental stress, they responded by consuming as much glucose as possible and reproducing as quickly as possible to safeguard against possible starvation.
Scale : (fold repression/induction)
Click on a color strip to see data for that gene.
Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to
the query gene
|
Orf |
|
Gene |
|
|
|
Process |
|
Function |
|
Component |
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
IPL1 |
|
|
|
not yet annotated |
|
protein kinase |
|
not yet annotated |
|
|
|
AAR2 |
|
|
|
mRNA splicing |
|
molecular_function unknown |
|
cellular_component unknown |
|
|
|
ITC1 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
nucleus |
|
|
|
DIG2 |
|
|
|
invasive growth |
|
not yet annotated |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
UPC2 |
|
|
|
steroid metabolism |
|
RNA polymerase II
transcription factor |
|
cellular_component unknown |
|
|
|
RIM101 |
|
|
|
meiosis |
|
transcription factor |
|
not yet annotated |
|
|
|
MAK10 |
|
|
|
not yet annotated |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
TYR1 |
|
|
|
not yet annotated |
|
prephenate dehydrogenase
(NADP+) |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
YJU2 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
AGE1 |
|
|
|
ER to Golgi transport* |
|
ARF GTPase activator |
|
cellular_component unknown |
|
|
|
HIS2 |
|
|
|
histidine biosynthesis |
|
histidinol-phosphatase |
|
cell |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
BUD9 |
|
|
|
polar budding |
|
molecular_function unknown |
|
cell |
* : indicates that more than one annotation exists for the gene.
Figure 14. Clustering data for YBR161W when exposed to limited glucose (SGD, 2001).
Figure 15. Time response of YBR161W to diauxic shift (SGD, 2001).
Here, YBR161W clustered with genes involved in meiosis, mRNA splicing, polar budding and RNA polymerase transcription factor. Again, these clustering data indicate that YBR161W probably serves some function in the DNA replication process.
V.
Expression During Sporulation.
Scale : (fold repression/induction)
Click on a color strip to see data for that gene.
Up to 20 similar genes are shown, with a Pearson correlation of > 0.8 to
the query gene
|
Orf |
|
Gene |
|
|
|
Process |
|
Function |
|
Component |
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
EGD1 |
|
|
|
nascent polypeptide
association |
|
chaperone |
|
nascent
polypeptide-associated complex |
|
|
|
ADE6 |
|
|
|
not yet annotated |
|
phosphoribosylformylglycinamidine
synthase |
|
not yet annotated |
|
|
|
GPA2 |
|
|
|
pseudohyphal growth* |
|
heterotrimeric G-protein
GTPase |
|
cellular_component unknown |
|
|
|
VAN1 |
|
|
|
not yet annotated |
|
mannosyltransferase |
|
not yet annotated |
|
|
|
NVJ1 |
|
|
|
not yet annotated |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
SPT20 |
|
|
|
not yet annotated |
|
not yet annotated |
|
SAGA complex |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
CPR1 |
|
|
|
biological_process unknown |
|
peptidylprolyl isomerase |
|
cytoplasm |
|
|
|
FYV6 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
cellular_component unknown |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
HIS7 |
|
|
|
histidine biosynthesis |
|
imidazoleglycerol-phosphate
synthase |
|
cell |
|
|
|
RPL7B |
|
|
|
protein biosynthesis |
|
structural protein of
ribosome |
|
cytosolic large ribosomal
(60S) subunit |
|
|
|
STM1 |
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
|
|
|
RPS8B |
|
|
|
protein biosynthesis |
|
structural protein of
ribosome |
|
cytosolic small ribosomal
(40S) subunit |
|
|
|
OPI1 |
|
|
|
phospholipid metabolism |
|
not yet annotated |
|
not yet annotated |
|
|
|
RAS2 |
|
|
|
pseudohyphal growth* |
|
RAS small monomeric GTPase |
|
plasma membrane |
|
|
|
EFT2 |
|
|
|
protein synthesis elongation |
|
translation elongation
factor |
|
ribosome |
|
|
|
|
|
|
|
biological_process unknown |
|
molecular_function unknown |
|
not yet annotated |
* : indicates that more than one annotation exists for the gene.
Figure 16. Clustering data for YBR161W during sporulation (SGD, 2001).
Figure 17. Expression response of YBR161W to sporulation over time (SGD, 2001).
Again, the annotated genes YBR161W clustered with all seem to pertain to DNA replication, for example, protein biosynthesis, protein synthesis elongation and translation elongation, as well as nascent polypeptide formation. Also, for the first time, YBR161W has clustered with genes involved in cell wall production, i.e. phospholipid metabolism. Recall that previous BLAST searches suggested YBR161W was a functional homolog to Sur1, a gene involved in the production of phospholipids in the cellular membrane.
Conclusions.
While YBR161W consistently clustered with annotated genes involved in DNA replication for each experimental condition, it did not cluster with the same gene several times, nor with different genes but the same specific function. While it may have coding similarities to the gene Sur1, it never clustered with that gene, indicating that they may not be regulated similarly. To conclude with confidence that YBR161W is a functional homolog of any of these genes, more experimental evidence will be necessary. Though it may be reasonable to assume that YBR161W plays a role in DNA replication, what that specific role may be has yet to be determined.
References.
1. SGD, Expression Connection. 2001. < http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl> Accessed 2001 Oct 16.
2. Spellman P, Sherlock G, Zhang M, Vishwanath R, Anders K, Eisen M, Brown P, Botstein D, Futcher B. 1998. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9(12). <http://www.molbiolcell.org/cgi/content/full/9/12/3273> Accessed 2001 Oct 16.
3. Zymo Research. 2001. Alpha-factor mating pheromone. <http://www.zymor.com/y1001-frame.html>. Accessed 2001 Oct 16.
Department of Biology,
Davidson College, Davidson, NC 28036
Send comments,
questions, and suggestions to: emoldham@davidson.edu