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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

E-mail me with questions or comments!

Function