This is an assignment for an undergradutate course at Davidson College

 

Expression of sec18 changes in reponse to changing cellular environments.  Below are listed microarrays that clustered sec18 expression with various cellular environments.  Explanations for such expression follow the microarrays.

 

Expression of Sec18 and its cluster at different concentrations of alpha factor

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR080C

 

SEC18

 

 

ER to Golgi transport*

 

adenosinetriphosphatase

 

cytoplasm*

YDL164C

 

CDC9

 

 

nucleotide-excision repair*

 

DNA ligase (ATP)

 

replication fork

YGL188C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YER142C

 

MAG1

 

 

not yet annotated

 

DNA-3-methyladenine glycosidase II

 

not yet annotated

YPL065W

 

VPS28

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YPR072W

 

NOT5

 

 

transcription

 

not yet annotated

 

not yet annotated

YDR205W

 

MSC2

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJR042W

 

NUP85

 

 

mRNA-nucleus export*

 

structural protein

 

nuclear pore

YER056C-A

 

RPL34A

 

 

protein biosynthesis

 

structural protein of ribosome

 

cytosolic large ribosomal (60S) subunit

YBR144C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGR182C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR039C

 

RIC1

 

 

transcription regulation, from Pol II promoter*

 

molecular_function unknown

 

nucleus

YLR038C

 

COX12

 

 

not yet annotated

 

cytochrome-c oxidase

 

not yet annotated

YOR275C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJL102W

 

MEF2

 

 

protein synthesis elongation

 

translation elongation factor

 

mitochondrion

YMR184W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YAL067C

 

SEO1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YPR151C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL161C

 

 

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YKL006C-A

 

SFT1

 

 

intra Golgi transport

 

v-SNARE

 

Golgi membrane

YMR230W

 

RPS10B

 

 

protein biosynthesis

 

structural protein of ribosome

 

cytosolic small ribosomal (40S) subunit

 

 

 

 

As can be seen here the expression of sec 18 goes up very little in the presence of increasing alpha factor.  One would expect that since sec18 is involved in fusion between vesicles of the ER and golgi it would follow that sec18 expression would go up in response to increasing alpha factor.  It is known that the receptor for alpha factor is upregulated in response to increasing alpha factor.  The alpha-receptor is a tranmembrane protein that must go through the ER and golgo to approach the plasma membrane.  Figures were obtained from: <http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl>

 

 

 

Timed response of sec18 to alpha factor

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR080C

 

SEC18

 

 

ER to Golgi transport*

 

adenosinetriphosphatase

 

cytoplasm*

YDL087C

 

LUC7

 

 

mRNA splice site selection

 

small nuclear ribonucleoprotein

 

cellular_component unknown

YCL042W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YML131W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR046C

 

ZTA1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YML058C-A

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGL180W

 

APG1

 

 

autophagy

 

protein serine/threonine kinase

 

cytosol

YBL064C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHR079BC

 

 

 

 

 

 

 

 

 

YMR097C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR442W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJR078W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR368W

 

YPR1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YOR177C

 

MPC54

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR297W

 

PRC1

 

 

not yet annotated

 

carboxypeptidase C

 

not yet annotated

YJL021C

 

 

 

 

 

 

 

 

 

YOL098C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGR243W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL039W

 

PTM1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJL082W

 

IML2

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YLR225C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

 

See the Summary of the Gene Ontology annotations for this gene group

 

Expression in response to alpha-factor for SEC18/YBR080C

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Browse clustered data

 

 

 

 

 

 

 

Although the table here would indicate that sec18 expression increases over time in response to alpha factor, as is expected, the microarray data are ambiguous.  Induction is not evident because the color change is not dramatic.  The figres here were obtained from :<http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl>

 

 

Response of sec18 and its cluster to DNA damaging agents

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR080C

 

SEC18

 

 

ER to Golgi transport*

 

adenosinetriphosphatase

 

cytoplasm*

YNR034W

 

SOL1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YCL057W

 

PRD1

 

 

not yet annotated

 

saccharolysin

 

not yet annotated

YJR059W

 

PTK2

 

 

polyamine transport

 

not yet annotated

 

not yet annotated

YBR260C

 

RGD1

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YGL190C

 

CDC55

 

 

protein biosynthesis*

 

protein phosphatase type 2A

 

protein phosphatase type 2A

 

The response of sec18 to DNA damaging agents here is not dramatic.  Although it would be expected that protein and RNA expression would change in response to a DNA damaging agents, this does not necessarily mean that protein expression would require more traffic between the ER and the golgi.  If protein expression changed in favor of cytosolic proteins, there would be no need for a change in sec18 expression.  The figres here were obtained from < http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl>

 

 

 

Expression of Sec18 during the cell cycle

Name

Score

Peak

SEC18

0.471

 

Reference Genes

 

CLN2

10.9

G1

HTA1

10.68

S

CLB4

3.08

G2

SWI5

6.726

M

ASH1

11.8

M/G1

 

 

 

 

Plot of SEC18 (YBR080C)

 

 

The data here do not correlate nicely with the literature on sec18 in my opinion.  Sec18 is responsible for vacuolar fusion in the yeast daughter cell.  One would therefore expect sec18 expression to increase significantly in at lease one phase of cell division so as to mediate vacuolar fusion in the budding yeast daughter.  Sec18 is not increased significantly here however.  The only explanation for this would be that the quantity of sec18 stays relatively constant at an amount that can sufficiently mediate vacuolar fusion when the time is necessary.  Another question that remains is why sec18 would be downregulated during the cell cycle.  One possible reason for this would be that there comes a time when vesicular fusion could adversely affect the cell.  If all vacuoles fused together at any one time, then one daughter cell would not get the appropriate share of this organelle.  The figures here were obtained from this website: < http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl>

 

 

Expression of sec18 during the diauxic shift

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR080C

 

SEC18

 

 

ER to Golgi transport*

 

adenosinetriphosphatase

 

cytoplasm*

YML046W

 

PRP39

 

 

mRNA splicing

 

not yet annotated

 

not yet annotated

YGR229C

 

SMI1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YHR027C

 

RPN1

 

 

ubiquitin-dependent protein degradation

 

multicatalytic endopeptidase

 

19S proteasome regulatory particle

YMR130W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR020W

 

FMS1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YBR198C

 

TAF90

 

 

transcription initiation, from Pol II promoter*

 

general RNA polymerase II transcription factor

 

TFIID complex*

YER160C

 

 

 

 

 

 

 

 

 

YLR386W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YML069W

 

POB3

 

 

chromatin modeling*

 

molecular_function unknown

 

nucleus

YDR381W

 

YRA1

 

 

mRNA processing

 

not yet annotated

 

not yet annotated

YLR052W

 

IES3

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPR129W

 

SCD6

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YBR082C

 

UBC4

 

 

stress response*

 

ubiquitin conjugating enzyme

 

cellular_component unknown

YGR261C

 

APL6

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YMR285C

 

NGL2

 

 

biological_process unknown

 

molecular_function unknown

 

cellular_component unknown

YER122C

 

GLO3

 

 

ER to Golgi transport*

 

ARF GTPase activator

 

ER-Golgi intermediate compartment

YNR076W

 

PAU6

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YCR027C

 

RSG1

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YPR118W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJL197W

 

UBP12

 

 

deubiquitylation

 

ubiquitin-specific protease

 

cellular_component unknown



Visit the Website
Browse clustered data

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

The data here indicate that sec18 expression does not appreciably change during the diauxic shift.  This figure was obtained from <http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl>

 

Expression of sec18 during sporulation

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR080C

 

SEC18

 

 

ER to Golgi transport*

 

adenosinetriphosphatase

 

cytoplasm*

YGR223C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR032W

 

HOF1

 

 

cytokinesis

 

cytoskeletal protein binding protein

 

cytokinetic ring (sensu Saccharomyces)

YOL095C

 

HMI1

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YPL206C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGL024W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YMR179W

 

SPT21

 

 

transcription

 

not yet annotated

 

not yet annotated

YKL132C

 

RMA1

 

 

not yet annotated

 

folylpolyglutamate synthase

 

not yet annotated



 

Expression during sporulation for SEC18/YBR080C

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The data here indicate that sec18 expression is not changed that much during yeast sporulation.  However, a slight induction in the first two hors would seem to be appropriate in that vesicular aggregation and fusion would have to occur to make sure the haploid daughters received their complement of vacuoles and other organelles.  The figure here was obtained from <http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl>

 

 

Expression of sec18 in response to environmental changes

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR080C

 

SEC18

 

 

ER to Golgi transport*

 

adenosinetriphosphatase

 

cytoplasm*



The data here do not represent the full figure from < http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl>.  A more complete picture of this information would show that sec18 is variably induced and repressed in response to different environmental conditions.  One reason why sec18 would be repressed in response to a changing environmental condition is that proteins in the ER change shape in response to varying conditions.  In response to heat, for example, proteins can be unfolded and must reside in the ER so they can refold in their proper confomration (Simola et al., 2000).  When this occurs, sec18 is downregulated so that ER vesicles cannot fuse with the golgi.  Conversely, sec18 may be upregulated to send proteins to the plasma membrane in cases where transmembrane proteins are denatured as a result of the environmental conditions.  The proteins transported to the plasma membrane with the help of sec18 may replace their misfolded counterparts or aid the recovery of those proteins that are misfolded.

 

 

 

 

 

 

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR080C

 

SEC18

 

 

ER to Golgi transport*

 

adenosinetriphosphatase

 

cytoplasm*

YBR069C

 

TAT1

 

 

transport

 

amino acid permease

 

not yet annotated

YDR158W

 

HOM2

 

 

not yet annotated

 

aspartate-semialdehyde dehydrogenase

 

not yet annotated

YGR230W

 

BNS1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YCR082W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGR105W

 

VMA21

 

 

vacuolar acidification

 

not yet annotated

 

not yet annotated

YML027W

 

YOX1

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YBL002W

 

HTB2

 

 

not yet annotated

 

not yet annotated

 

nucleosome

YDR133C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBL030C

 

PET9

 

 

ATP/ADP exchange

 

ATP/ADP antiporter

 

mitochondrial inner membrane

YGR181W

 

TIM13

 

 

mitochondrial translocation

 

protein transporter

 

mitochondrial intermembrane space

YJL208C

 

NUC1

 

 

DNA recombination

 

endodeoxyribonuclease*

 

mitochondrial inner membrane

YCR004C

 

YCP4

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHR208W

 

BAT1

 

 

not yet annotated

 

branched-chain amino acid aminotransferase

 

not yet annotated

YNL056W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR297W

 

SUR2

 

 

sphingolipid metabolism

 

sphingosine hydroxylase

 

endoplasmic reticulum

YDR381W

 

YRA1

 

 

mRNA processing

 

not yet annotated

 

not yet annotated

YNL231C

 

PDR16

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YBR068C

 

BAP2

 

 

transport

 

not yet annotated

 

not yet annotated

YML119W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPL190C

 

NAB3

 

 

mRNA splicing

 

not yet annotated

 

not yet annotated

Expression of sec18 in response to histone depletions

 

Expression in response to histone depletion for SEC18/YBR080C

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Browse clustered data

 

 

The data here indicate that sec18 is eventually downregulated in response to histone depletion.  This makes intuitive sense since histones maintain the integrity of DNA.  When the structure of DNA risks being disrupted by the loss of histones, protein synthesis should shut down since translated products may contain amino acid irregularities.  So as to stop protein traffic, sec18 would naturally be downregulated so that altered proteins made by mistake do not localize to other parts of the cell.  The figures here were obtained from < http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl>

 

References Cited

1)      Saccharomyces Genome Database [online database]. Available from: http://genome-www.stanford.edu/Saccharomyces/ Accessed 2001 Oct 17

2)      Simola et al. (2000).  Trehalose is required for heat-denatured proteins in the yeast ER but not for membrane traffic functions after severe heat stress.  Molecular Microbiology; 37 (1); 42-53

 

Click here to email me at seburke@davidson.edu

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