This web page was produced as an assignment for an undergraduate course at Davidson College.

MICROARRAY DATA FOR ANNOTATED GENE BUD8

Microarray experiments allow investigators to compare the level of transcription of many genes at a time.  Here, I have clustered genes that have similar expression as BUD8.  I chose the most informative experiments for this webpage, and most of the figures have been altered from their original form.

Different Microarray experiments:

Expression when exposed to different alpha-factor concentrations

Expression response to alpha-factor

Expression in response to DNA-damaging agents

Expression during cell cycle

Expression in the diauxic shift

Evolution of expression when glucose is limited

Expression during sporulation

Expression response to environmental changes

Expression in response to histone depletion

 

Background review:

As stated in my second web assignment, the BUD8 gene is specifically involved in the bud initiation of bipolar budding.  It is localized to the distal pole of the growing daughter cell and the mother side of the mother-bud neck in both haploid and diploid yeast form cells.    It is also involved in the formation of pseudohyphal filaments during the budding process.

 

 

Scale : (fold repression/induction)

This scale is used for all microarray experiments presented on this page.

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

Experiment 1: BUD8 expression at different alpha-factor concentrations

 

Orf

Gene

Process

Function

Component

YLR353W

BUD8

pseudohyphal growth*

molecular_function unknown

cell

YLR442C

SIR3

chromatin silencing at HML and HMR (sensu Saccharomyces)*

not yet annotated

nucleolus*

YGR170W

PSD2

not yet annotated

phosphatidylserine decarboxylase

not yet annotated

YOR098C

NUP1

mRNA-nucleus export*

structural protein

nuclear pore

YGL205W

POX1

fatty acid beta-oxidation

acyl-CoA oxidase

peroxisomal matrix

 

This experiment was primarily profiling the genome wide transcription reponse to monitor signal transduction during the yeast response to pheromone.  In this case, BUD8 shows similar expression patterns as such genes as SIR3 and NUP1.  These genes don’t seem to share much of the same function as BUD8.  SIR3 is involved in cell aging and chromatin silencing at the telomere, and NUP1 is a structural protein.  However, it is interesting to note that SIR3 is also located on chromosome XII with BUD8. http://www.rii.com/tech/pubs/s287873.htm

 

 Experiment 2: Expression in response to damaging agents

 

 

Orf

Gene

Process

Function

Component

YLR353W

BUD8

pseudohyphal growth*

molecular_function unknown

cell

YBR202W

CDC47

DNA replication initiation*

chromatin binding*

cytoplasm*

YFR034C

PHO4

not yet annotated

transcription factor

not yet annotated

YOL130W

ALR1

di-, tri-valent inorganic cation transport

di-, tri-valent inorganic cation transporter

plasma membrane

YNL240C

NAR1

not yet annotated

molecular_function unknown

not yet annotated

YJR147W

HMS2

pseudohyphal growth

transcription factor

not yet annotated

YNL148C

ALF1

post-chaperonine tubulin folding pathway*

cochaperone

microtubule

YJL133W

MRS3

transport*

carrier

mitochondrion

When exposed to various damaging agents, BUD8 clusters with several different genes than in the alpha concentration experiments. 

Many of the functions and components are unknown at this time.  One gene to point out is HMS2, which is a transcription factor that is involved in pseudohyphal growth, as is BUD8.  HMS2 is located on the tenth chromosome and is a heat shock transcription factor homolog.  http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=YJR147W

The BUD8 expression seems most similar to the CDC47 gene, which is involved in DNA replication initiation.

 

 Expression 3:   BUD8 Expression during the cell cycle

BUD8 compared to reference genes during the cell cycle.

Name

Score

Peak

BUD8

4.286

M

Reference Genes

 

CLN2

10.9

G1

HTA1

10.68

S

CLB4

3.08

G2

SWI5

6.726

M

ASH1

11.8

M/G1

 

 

 

 

 

BUD8 compared to 20 different genes with similar expression during the cell cycle.

 

 

 

Name

Score

Peak

BUD8

4.286

M

SUR7

5.674

M

YML035C-A

1.5085

M

HST3

8.396

M

HOF1

10.97

M

WSC4

9.908

M

YIL158W

5.693

M

SRC1

7.306

M

ALK1

7.36

M

CDC5

9.901

M

SWI5

6.726

M

YLR190W

10.65

M

BUD4

4.456

M

YCL012W

5.242

M

BUD3

5.369

G2

YJL051W

6.092

M

YML033W

6.421

M

MYO1

5.613

M

TIR3

1.603

M

YCL063W

3.017

G2

APC1

1.721

M

 

During the cell cycle, BUD8 is repressed and induced in varying degrees with a peak in the mitosis phase of the cycle.  The four grouping represent the BUD8 expression to different pheromones.  The BUD8 gene appears to be consistently repressed at the beginning of each cycle with a gradual induction similar to the SWI5 transcriptional activator to which BUD8 was compared.  When clustered with 20 genes of similar expression, the BUD3 and BUD4 genes have the closest score to BUD8.  The BUD3 and BUD4 genes are also involved in bud site selection and they co-assemble at the bud sites.

 

 

Experiment 4: BUD8 Expression in response to environmental changes

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YLR353W

 

BUD8

 

 

 

 

 

 

 

 

In response to environmental changes, BUD8 did not show a similar expression pattern to any other genes.

 

 

 

Experiment 5: BUD8 Expression in response to histone depletion

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YLR353W

 

BUD8

 

 

pseudohyphal growth*

 

molecular_function unknown

 

cell

YHR038W

 

FIL1

 

 

protein biosynthesis

 

translation termination factor

 

mitochondrion

YPL118W

 

MRP51

 

 

protein biosynthesis*

 

structural protein of ribosome

 

mitochondrial small ribosomal subunit

YIL022W

 

TIM44

 

 

mitochondrial translocation

 

protein transporter

 

mitochondrial matrix

YBR251W

 

MRPS5

 

 

protein biosynthesis

 

structural protein of ribosome

 

mitochondrial small ribosomal subunit*

YBR185C

 

MBA1

 

 

respiration

 

not yet annotated

 

not yet annotated

YDR524C

 

AGE1

 

 

ER to Golgi transport*

 

ARF GTPase activator

 

cellular_component unknown

YJL101C

 

GSH1

 

 

not yet annotated

 

glutamate--cysteine ligase

 

not yet annotated

YER107C

 

GLE2

 

 

mRNA-nucleus export*

 

structural protein

 

nuclear pore

YKR092C

 

SRP40

 

 

nucleocytoplasmic transport

 

chaperone

 

nucleolus

YFR049W

 

YMR31

 

 

protein biosynthesis

 

structural protein of ribosome

 

mitochondrial small ribosomal subunit

YIL125W

 

KGD1

 

 

tricarboxylic acid cycle*

 

oxoglutarate dehydrogenase (lipoamide)

 

mitochondrial matrix

YIL124W

 

AYR1

 

 

phosphatidic acid biosynthesis

 

acylglycerone-phosphate reductase

 

endoplasmic reticulum*

Genes that show similar expression patterns as BUD8 when exposed to histone depletion.

SUMMARY:

BUD8 does not appear to have similar expression patterns with the same genes throughout the microarray experiments.  However this data does help characterize the expression pattern of BUD8 and it shows us that there are many complex processes occurring simultaneously in the life of a yeast.

 

REFERENCES:

http://www.rii.com/tech/pubs/s287873.htm, accessed October 17, 2001.

 

http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=YJR147W, accessed October 17, 2001.

 

http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl, accessed October 17, 2001.

 

 

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