YMP: Comparison

2-D reference gel

Identified proteins

Comparison

1.	Proteins with changed expression during fermentative and respiratory growth
1.1.	2-D gel of the S. cerevisiae wildtype BJ1991 mitochondria characteristic for respiration
1.2.	Regions presenting proteins with changed expression during fermentation (glucose, G) and respiration (glycerol, GLY)
1.3.	Corresponding transcriptional data

2.	*Respiratory chain of S. cerevisiae* - comparison of fermentative and respiratory growth**
2.1.	Schematic overview about the mechanism of the respiratory chain according to Joseph-Horne et al., 2001 and the database CYGD (MIPS)
2.2.	Regions presenting proteins of the respiratory chain during fermentation (glucose, G) and respiration (glycerol, GLY)
2.3.	Corresponding transcriptional data

3.	*TCA cycle of S. cerevisiae* - comparison of fermentative and respiratory growth**
3.1.	Schematic overview about the mechanism of the TCA cycle according to Steinmetz et al., 2002 and Przybyla-Zawislak et al., 1999
3.2.	Regions presenting proteins of the TCA cycle during fermentation (glucose, G) and respiration (glycerol, GLY)
3.3.	Corresponding transcriptional data

1. Proteins with changed expression during fermentative and respiratory growth

1.1. 2-D gel of the S. cerevisiae wildtype BJ1991 mitochondria characteristic for respiration (Regions presenting proteins with changed expression are marked with a frame)

1.2. Regions presenting proteins with changed expression during fermentation (glucose, G) and respiration (glycerol, GLY)

Selected 2-D regions are shown enlarged, and overlapped protein spots are indicated.

TCA cycle		Respiratory chain

Respiratory chain		Respiratory metabolism

Respiratory metabolism		Peroxisomal proteins

Amino acid biosynthesis		Unknown function

1.3. Corresponding transcriptional data show the expression change after growth on glycerol

View the corresponding transcriptional change of all identified proteins here (pdf file, 972 kb)
View the transcriptional data of all yeast genes here (txt file, 1.0 Mb)

Protein	Protein induction/ decrease	Transcriptional induction/ decrease*	Function	Process
Ach1p	+	+8.5	Acetyl-CoA hydrolase	Acetate and acetyl-CoA metabolism
Adh2p	+	+8.0	Alcohol dehydrogenase II	Ethanol metabolism
Ald4p	+	+9.8	Potassium-acitvated aldehyde dehydrogenase	Ethanol metabolism
Cat2p	+	+21.0	Carnitine O-acetyl-transferase	Carnitine metabolism
Cox4p	+	+3.7	Subunit IV	Respiratory chain (complex IV)
Cyb2p	+	+68.6	Lactate dehydrogenase cytochrome b2	Electron transport
Fat2p	+	+2.3	Peroxisomal-CoA synthetase	Unknown
Fox1p	+	+oo**	Fatty-acyl coenzyme A oxidase	Fatty acid beta-oxidation
Fox2p	+	+22.6	Multifunctional enzyme type 2	Fatty acid beta-oxidation
Icl2p	+	+3.7	Non-functional isocitrate lyase	Propionate metabolism, Threonine catabolism
Ilv3p	-	-2.3	Dihydroxy-acid dehydratase	Branched chain family amino acid biosynthesis
Om45p	+	+14.9	45-kDa outer membrane protein	Unknown
Pdh1p	+	+11.3	Hypothetical protein (PrpD homolog)	Propionate metabolism
Qcr7p	+	+1.3	Subunit 7	Respiratory chain (complex III)
Sdh1p	+	+7.0	Flavoprotein subunit (Succinate dehydrogenase)	Tricaboxylic cycle, Oxidative phosphorylation
Sdh2p	+	+9.8	Iron-sulfur protein subunit (Succinate dehydrogenase)	Tricaboxylic cycle, Oxidative phosphorylation
Sdh4p	+	+4.6	Membrane anchor for Sdh2p (Succinate dehydrogenase)	Tricaboxylic cycle, Oxidative phosphorylation
Ybr230p	+	+9.2	Hypothetical protein	Unknown

* Expression: increased (+), decreased (-)
** For FOX1 no significant signal was obtained during fermentative growth.

2. Respiratory chain of S. cerevisiae - comparison of fermentative and respiratory growth

2.1. Schematic overview about the mechanism of the respiratory chain according to
Joseph-Horne et al., 2001 and the database CYGD (MIPS)

UBQ, ubiquinone:ubiquinol pool; Cyt c, cytochrome c; DHG, dehydrogenase; MA, matrix; IMS, intermembrane space;
MIM, inner membrane; MOM, outer membrane

2.2. Regions presenting proteins of the respiratory chain during fermentation
(glucose, G) and respiration (glycerol, GLY)

Selected 2-D regions are shown enlarged, and overlapped protein spots are indicated.

NADH dehydrogenase	Complex II (succinate dehydrogenase)	Complex III (Cytochrome bc1)

Complex III (Cytochrome bc1)		Complex IV (Cytochrome c oxidase)

Complex V (ATP synthase)

Additional functions		Unknown function


2.3. Corresponding transcriptional data show the expression change after growth on glycerol

View the corresponding transcriptional change of all identified proteins here (pdf file, 972 kb)
View the transcriptional data of all yeast genes here (txt file, 1.0 Mb)

Protein	Protein induction/ decrease	Transcriptional induction/ decrease*	Function
NADH dehydrogenase
Nde1p	=	+1.5	NADH dehydrogenase
Complex II (succinate dehydrogenase)
Sdh1p	+	+7.0	Flavoprotein subunit
Sdh2p	+	+9.8	Iron-sulfur protein subunit
Sdh4p	+	+4.6	Membrane anchor for Sdh2p
Complex III (cytochrome bc1)
Abc1p	=	-1.9	Assembly protein
Cor1p	=	+3.0	Core protein 1
Qcr2p	=	+4.3	Core protein 2
Qcr7p	+	+1.3	Subunit 7
Rip1p	=	+2.5	Iron-sulfur protein
Complex IV (cytochrome c oxidase)
Cox4p	+	+3.7	Subunit IV
Cox6p	=	+2.0	Subunit VI
Cox12p	=	+2.1	Subunit VIB
Cox13p	=	+2.8	Subunit VIA
Cox14p	=	+3.0	Assembly protein
Complex V (ATP synthase)
Atp1p	=	+1.6	F1 alpha subunit
Atp2p	=	+1.7	F1 beta subunit
Atp3p	=	+3.0	F1 gamma subunit
Atp4p	=	+2.1	F0 subunit B
Atp5p	=	+3.2	OSCP subunit
Atp7p	=	+4.3	F0 subunit D
Atp11p	=	+1.1	Assembly protein
Atp16p	=	+2.6	F1 delta subunit
Additional functions
Cyb2p	+	+68.6	Lactate dehydrogenase cytochrome b2
Mba1p	=	+1.5	Respiratory chain assembly protein
Mcr1p	=	+11.3	NADH-cytochrome b5 reductase
Sco1p	=	+1.3	Inner mitochondrial membrane protein
Unknown function
Ypr004p	=	+1.4	Hypothetical protein

* Expression: increased (+), decreased (-)

3. TCA cycle of S. cerevisiae - comparison of fermentative and respiratory growth

3.1. Schematic overview about the mechanism of the TCA cycle according to Steinmetz et al., 2002 and Przybyla-Zawislak et al., 1999

OAA, oxaloacetate; a-KG, a-ketoglutarate

3.2. Regions presenting proteins of the TCA cycle during fermentation (glucose, G) and respiration
(glycerol, GLY)

Selected 2-D regions are shown enlarged, and overlapped protein spots are indicated.

3.3. Corresponding transcriptional data show the expression change after growth on glycerol

View the corresponding transcriptional change of all identified proteins here (pdf file, 972 kb)
View the transcriptional data of all yeast genes here (txt file, 1.0 Mb)

Protein	Protein induction/ decrease	Transcriptional induction/ decrease*	Function

Cit1p	=	+1.9	Citrate synthase

Aco1p	=	+1.7	Aconitase
Yjl200p	=	-5.5	Hypothetical protein (similarity to aconitases)

Idh1p	=	-1.1	Subunit 1 (Isocitrate dehydrogenase, NAD+ )
Idh2p	=	-1.7	Subunit 2 (Isocitrate dehydrogenase, NAD+)

Kgd1p	=	+3.2	E1 component (2-oxo-glutarate dehydrogenase complex)
Kgd2p	=	+5.7	E2 component (2-oxo-glutarate dehydrogenase complex)
Lpd1p	=	-1.4	Dihydrolipoamide dehydrogenase

Lsc1p	=	+1.4	alpha subunit (succinyl-CoA ligase)
Lsc2p	=	+3.5	beta subunit (succinyl-CoA ligase)

Sdh1p	+	+7.0	Flavoprotein subunit
Sdh2p	+	+9.8	Iron-sulfur protein subunit
Sdh4p	+	+4.6	Membrane anchor for Sdh2p

Mdh1p	=	+2.3	Malate dehydrogenase

* Expression: increased (+), decreased (-)

Questions? Comments?
Contact Alexander J. Kastaniotis (transcriptional data), Steffen Ohlmeier (2-D gel analysis) or Ulrich Bergmann (protein identification by mass spectrometry)