Clustering and Expression Patterns for the annotated AAC3 Gene and the Unannotated YDL246C Gene.

 

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

 

 

 

            Using the microarray-oriented site Expression Connection, I will investigate the same two genes as were investigated by other means in the previous assignment.  These genes are the ATP/ADP inner mitochondrial membrane co-transporter AAC3 gene, and the unannotated YDL246C gene (which previously showed homology with a mouse dehydrogenase gene.  Each of the microarrays shown below represents a different set of experimental conditions.  Many of the arrays show expression changes over time, however, the dependent variable in some is concentration of the experimental condition. There is a large amount of data shown below. To completely analyze all of it could take years, and possibly effect the addition of several letters to my name (PhD for instance). Thus, I will seek to understand the functions of each gene by either comparing it to the most similar expression pathways shown, or comparing it to another gene that is consistently expressed throughout a large number of the microarrays in a similar manner.

 

 

Scale : (fold repression/induction)
 

 

 

 

AAC3 Gene:

 

Expression at different alpha-factor concentrations  (Rosetta Inpharmatics).

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR085W

 

AAC3

 

 

ATP/ADP exchange

 

ATP/ADP antiporter

 

mitochondrial inner membrane

YIL009W

 

FAA3

 

 

not yet annotated

 

long-chain-fatty-acid-CoA-ligase

 

not yet annotated

YMR083W

 

ADH3

 

 

not yet annotated

 

acylglycerone-phosphate reductase

 

not yet annotated

YJL200C

 

 

 

 

not yet annotated

 

aconitate hydratase

 

not yet annotated

YBR072W

 

HSP26

 

 

stress response*

 

heat shock protein

 

nucleus*

YPL012W

 

RRP12

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPR062W

 

FCY1

 

 

not yet annotated

 

cytosine deaminase

 

not yet annotated

YJR148W

 

BAT2

 

 

not yet annotated

 

branched-chain amino acid aminotransferase

 

not yet annotated

YGR155W

 

CYS4

 

 

not yet annotated

 

cystathione beta-synthase

 

not yet annotated

YJL186W

 

MNN5

 

 

protein amino acid glycosylation

 

not yet annotated

 

not yet annotated

YJL111W

 

CCT7

 

 

protein folding*

 

chaperone

 

cytoplasm*

 

http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl

 The above experiment shows mild amounts of repression in the AAC3 gene at high doses of the alpha-factor phermone. The gene clusters with several genes that help to explain its function in this experiment. One of these genes is the FAA3 gene which codes for acyl-CoA synthase. Acyl-CoA synthase is an important protein in the activation of endogenous fatty acids. Both of these genes are important in anaerobic metabolism, one in the movement of ATP and ADP across the inner mitochondrial membrane under anaerobic conditions, and the other in the manipulation of fatty acids (which are an important energy source under anaerobic conditions) and, this clustering pattern makes sense.

http://genome-www.stanford.edu/cgi-bin/SGD/functionJunction?locus=FAA3

 

Expression in response to alpha-factor  (Rosetta Inpharmatics).

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR085W

 

AAC3

 

 

ATP/ADP exchange

 

ATP/ADP antiporter

 

mitochondrial inner membrane

YJL064W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YLR219W

 

MSC3

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR033W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR436W

 

PPZ2

 

 

sodium ion homeostasis

 

protein serine/threonine phosphatase

 

cellular_component unknown

YOL131W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHL012W

 

 

 

 

not yet annotated

 

UTP--glucose-1-phosphate uridylyltransferase

 

not yet annotated

YIR019C

 

MUC1

 

 

not yet annotated

 

glucan 1,4-alpha-glucosidase

 

not yet annotated

YGL176C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJL127C

 

SPT10

 

 

chromatin modeling*

 

molecular_function unknown

 

nucleus

YFR019W

 

FAB1

 

 

vacuole organization and biogenesis

 

1-phosphatidylinositol-3-phosphate 5-kinase

 

vacuolar membrane

YPL278C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL184W

 

SPE1

 

 

not yet annotated

 

ornithine decarboxylase

 

not yet annotated

 In the above array, the AAC3 gene clusters with several other genes (MUC1 and YGL176C) that are involved in metabolism in the mitochondria. It also clusters with an unknown ORF called YBR033W that is located on the same chromosome (II). This could be due to an aneuploidy causing mutation that has caused part of chromosome II to be duplicated in the experimental strain yet not in the control strain.

 

  http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl

Expression during the cell cycle  (Stanford University).

 

Name

Score

Peak

AAC3

0.25

 

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 AAC3 (YBR085W)

http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl  

 

No other genes have a high enough score to cluster with the AAC3 gene in the microarray above.  This may be because other genes that are expressed in a similar fashion have not yet been annotated, or because the data above does not represent expression ratios during the cell cycle under anaerobic conditions when the AAC3 gene is actually expressed.

 

Expression in response to histone depletion  (The Whitehead Institute).

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YBR085W

 

AAC3

 

 

ATP/ADP exchange

 

ATP/ADP antiporter

 

mitochondrial inner membrane

YJL130C

 

URA2

 

 

not yet annotated

 

aspartate carbamoyltransferase

 

not yet annotated

YDR315C

 

IPK1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YPR201W

 

ARR3

 

 

not yet annotated

 

arsenite transporter

 

not yet annotated

YDR426C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YDR007W

 

TRP1

 

 

amino acid metabolism

 

phosphoribosylanthranilate isomerase

 

cytoplasm

YCL030C

 

HIS4

 

 

histidine biosynthesis

 

histidinol dehydrogenase*

 

cell

YHR109W

 

CTM1

 

 

protein modification

 

[cytochrome c]-lysine N-methyltransferase

 

cytosol

YIR017C

 

MET28

 

 

transcription regulation, from Pol II promoter*

 

specific RNA polymerase II transcription factor

 

nucleus

YMR247C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YFR054C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBL034C

 

STU1

 

 

microtubule nucleation

 

structural protein of cytoskeleton

 

spindle pole body

YLR393W

 

ATP10

 

 

protein complex assembly

 

molecular_function unknown

 

mitochondrial membrane

YJR008W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YIL025C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPR200C

 

ARR2

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

  http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl

 In the above histone depletion microarray, the AAC3 gene can be seen to cluster with TRP1 and ARR3. The TRP1 gene is involved in amino acid metabolism. The ARR3 gene has a similar function to the AAC3 gene. It is a transporter that moves specific molecules across a membrane. Perhaps it also shares a similar promoter, thus explaining its similar expression profile.

Evolution of expression during glucose limitation  (Stanford University).

Name

 

Process

 

Function

AAC3

 

ATP/ADP exchange

 

ATP/ADP antiporter

RPC19

 

transcription, from Pol I promoter*

 

DNA-directed RNA polymerase III*

YFR041C

 

biological_process unknown

 

molecular_function unknown

PBI2

 

biological_process unknown

 

not yet annotated

YBR262C

 

biological_process unknown

 

molecular_function unknown

YNL193W

 

biological_process unknown

 

molecular_function unknown

ATX1

 

oxidative stress response

 

molecular_function unknown

CUP1-2

 

not yet annotated

 

not yet annotated

RFA2

 

nucleotide-excision repair*

 

DNA replication factor

PSD1

 

not yet annotated

 

phosphatidylserine decarboxylase

FOL1

 

not yet annotated

 

dihydropteroate synthase

YLR294C

 

biological_process unknown

 

molecular_function unknown

SDH4

 

tricarboxylic acid cycle*

 

succinate dehydrogenase

KES1

 

sterol metabolism

 

molecular_function unknown

HHT1

 

not yet annotated

 

not yet annotated

AAD4

 

biological_process unknown

 

molecular_function unknown

QCR6

 

not yet annotated

 

ubiquinol-cytochrome-c reductase

TOM22

 

mitochondrial translocation

 

protein transporter

IDP1

 

glutamate biosynthesis*

 

isocitrate dehydrogenase (NADP+)

HOM2

 

not yet annotated

 

aspartate-semialdehyde dehydrogenase

END3

 

cytokinesis*

 

cytoskeletal adaptor

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl

This microarray shows AAC3 clustering with , among others, genes that are involved in the tricarboxylic acid cycle, mitochondrial translocation, and a cytochrome-c reductase (part of the electron transport chain.. All of these proteins would be expected to be located in the mitochondria. Perhaps the productivity of the mitochondria in the evolved strains was increased through a stronger promoter, or even selective aneuploidy of the gene. This would lead to the induction in so many different mitochondrial genes that is seen in the above data.

 

Conclusion:

The AAC3 gene shows a large amount of expression similarity with both other genes that may be expressed anaerobically and other mitochondrial genes. This upholds the annotations made with respect to its function and location, however the reason that it shares similarity with certain other genes is not always clear. For instance, the QCR6, cytochrome c gene is a part of the electron transport chain in oxidative phosphorylation, a process that requires oxygen. The AAC3 gene requires anaerobic conditions in order to be transcribed.

 

Expression during the diauxic shift  (Stanford University).

 

 The unannotated YDL246C ORF:

 

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YDL246C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YJR159W

 

SOR1

 

 

not yet annotated

 

L-iditol 2-dehydrogenase

 

not yet annotated

YJR108W

 

ABM1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YER101C

 

AST2

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YKL110C

 

KTI12

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl

As was shown in the previous webpage assignment, my ORF functions in a manner imilar to that of a dehydrogenase. In this particular microarray, the YDL246C ORF has clustered with a L-iditol 2-dehydrogenase.

 

Expression during sporulation  (Stanford University).

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YDL246C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YOR142W

 

LSC1

 

 

tricarboxylic acid cycle*

 

succinate--CoA ligase (ADP-forming)

 

mitochondrial matrix

YJR159W

 

SOR1

 

 

not yet annotated

 

L-iditol 2-dehydrogenase

 

not yet annotated

YBL051C

 

PIN4

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YHL033C

 

RPL8A

 

 

protein biosynthesis

 

structural protein of ribosome

 

cytosolic large ribosomal (60S) subunit

YNL229C

 

URE2

 

 

nitrogen utilization regulation

 

transcription co-repressor

 

soluble fraction

YHR003C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR024W

 

SCO2

 

 

copper ion transport

 

molecular_function unknown

 

mitochondrial membrane

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl

Interestingly, here, the ORF has clustered close to the same L-iditol 2-dehydrogenase gene.

Expression in response to histone depletion  (The Whitehead Institute).

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YDL246C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR298C

 

MAL31

 

 

transport

 

maltose permease

 

not yet annotated

YDR518W

 

EUG1

 

 

not yet annotated

 

protein disulfide isomerase

 

not yet annotated

YNR065C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YCL020W

 

 

 

 

 

 

 

 

 

YJR160C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBL101W-A

 

 

 

 

 

 

 

 

 

YPR047W

 

MSF1

 

 

protein biosynthesis

 

phenylalanine--tRNA ligase

 

mitochondrion

YPL110C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YIL159W

 

BNR1

 

 

osmotic response*

 

molecular_function unknown

 

cytokinetic ring (sensu Saccharomyces)

YDL139C

 

SCM3

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YJR159W

 

SOR1

 

 

not yet annotated

 

L-iditol 2-dehydrogenase

 

not yet annotated

YBL059W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGR289C

 

MAL11

 

 

alpha-glucoside transport

 

general alpha-glucoside:hydrogen symporter

 

membrane fraction

YML042W

 

CAT2

 

 

amino acid metabolism*

 

carnitine O-acetyltransferase

 

mitochondrion*

YOR023C

 

AHC1

 

 

nucleosome disassembly

 

molecular_function unknown

 

Ada2/Gcn5/Ada3 transcription activator complex

YDR523C

 

SPS1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YDR543C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKR049C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YPL154C

 

PEP4

 

 

not yet annotated

 

saccharopepsin

 

not yet annotated

YMR096W

 

SNZ1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

 

 

 

 

 

 

 

 

 

 

 

 

 As the histones are depleted, and time passes, in this experiment, the YDL246C gene begins to be increasingly expressed. Yet again, the L-iditol 2-dehydrogenase genes shows up with a very similar expression pattern.

 

Expression in response to alpha-factor  (Rosetta Inpharmatics).

 

 

Orf

 

Gene

 

 

Process

 

Function

 

Component

YDL246C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YIL056W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YKL026C

 

GPX1

 

 

not yet annotated

 

glutathione peroxidase

 

not yet annotated

YPL020C

 

ULP1

 

 

G2/M transition of mitotic cell cycle

 

cysteine-type peptidase

 

nuclear membrane

YDR416W

 

SYF1

 

 

mRNA splicing*

 

molecular_function unknown

 

not yet annotated

YBL075C

 

SSA3

 

 

stress response*

 

heat shock protein

 

cytoplasm

YOR008C-A

 

KIM1

 

 

not yet annotated

 

molecular_function unknown

 

not yet annotated

YGL039W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YBR212W

 

NGR1

 

 

biological_process unknown

 

not yet annotated

 

not yet annotated

YOL019W

 

TOS7

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YOR135C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

cellular_component unknown

YER168C

 

CCA1

 

 

protein synthesis elongation*

 

tRNA adenylyltransferase

 

nucleus*

YDL086W

 

 

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YJL149W

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YAL058W

 

CNE1

 

 

not yet annotated

 

not yet annotated

 

not yet annotated

YGR156W

 

PTI1

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

YGL188C

 

 

 

 

biological_process unknown

 

molecular_function unknown

 

not yet annotated

  http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl

 

 

Conclusion:

Because this gene shows so much similarity to the L-iditol 2-dehydrogenase it is likely that they belong to a similar pathway. The L-iditol 2-dehydrogenase protein is a sorbitol induced sorbitol dehydrogenase. This pathway is probagbly the best place to start in order to illuminate the function of the YDL246C genes function.

http://genome-www.stanford.edu/cgi-bin/SGD/functionJunction?locus=FAA3

References:

SGD database. 2001. http://genome-www.stanford.edu/cgi-bin/SGD/functionJunction

SGD database. 2001. http://genome-www4.stanford.edu/cgi-bin/SGD/expression/expressionConnection.pl


YPD database. 2001. Proteome, Inc. http://www.proteome.com/databases/YPD/reports/YJU3.html

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