Genome-wide Responses to

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Genome-wide Responses to Mitochondrial Dysfunction
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overview
Transcriptional changes due to disruption of
mitochondrial function

• Two different yeast strains
• S. cerevisiae lacking mtDNA (??).(petite).
• Respiratory deficient, obligatory fermentative
  metabolism.
• Wild-type S. cerevisiae (?).
• Respiratory competent, partially oxidative
  metabolism.

Compared genome-wide expression with microarrays.
Compared with previous microarray experiment
looking at genome-wide changes in expression in
yeast cells undergoing diauxic shift.
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yeast carbon metabolism
Aerobic metabolism (oxidative metabolism) Glycol
ysis ?TCA cycle ?oxidative phosphorylation
Anaerobic metabolism (fermentation) Glucose ?
Acetyl CoA ? Ethanol
Diauxic shift Metabolic change as fermentable
carbon source is used up from
Glucose Fermentative (Glycolysis ? Ethanol)
to
Oxidative Metabolism (Ethanol ? TCA cycle)
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(No Transcript)
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differential gene expression

• Clusters D and E
• intermediary metabolism
• small molecule
• transport pathways
• in ?? and diauxic shift
• Reflect metabolic changes
• to compensate for loss of
• respiration in petite cells.

• Clusters A and B
• Oxidative phosphorylation
• Apparatus
• in petite ??
• No attempt by cells to
• upregulate oxidative
• metabolism
• in diauxic shift
• Change to oxidative
• metabolism in shift

• Cluster C
• Cytoplasmic ribosomal
• Proteins
• in diauxic shift
• Shows slowing of growth
• rate upon change to
• oxidative metabolism

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metabolic remodelling
Metabolic pathways were altered in respiratory
deficient cells
Intermediates of TCA cycle needed for synthesis
of amino acids and nucleotides Oxaloacetate
(OAA) is not regenerated in petite (??)
cells TCA cycle, so must be replenished another
way.
Metabolic pathways altered
? OAA and Acetyl-CoA supply
? Acetyl-CoA hydrolase
? in enzymes involved in flux and conversion of
metabolites made by fatty acid oxidation to TCA
and glyoxylate cycle intermediates.
? in nutrient and metabolite transporters.
? in enzymes for reoxidation of NADH
?? petites reconfigure metabolism by recruiting
peroxisomal activities, small molecule transport
systems and lipid, sugar and amino acid turnover
to get more OAA and Acetyl-CoA.
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effect of mitochondrial inhibitors
Different transcriptional responses due to
different mitochondrial inhibitors.
Antimycin effects are similar to petite cells.
CCCP different response.
Oligomycin different response.
Petite expression profile shows effects of loss
of electron transport rather than loss of
mitochondrial ATP synthesis.
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peroxisome proliferation
In ?? petites, peroxisome biogenesis is
induced. peroxisome targeted GFP used to trace
peroxisomes in ?? cells.
Antimycin also induced peroxisome biogenesis.
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RTG genes
RTG genes important in retrograde
regulation. RTG1, 2 3 upregulate peroxisomal
citrate synthase in ?? petits. RTG genes increase
expression of TCA cycle enzymes in ?? petits.
Array profiling of ?? cells with mutations in
each RTG gene.
Cluster A Genes induced in ?? petits whose
induction is dependent on RTG signalling pathway.
Cluster B Genes requiring RTG genes for
expression in ?? petits.
Cluster C Genes showing enhanced expression in
?? petits without RTG genes.
Cluster D Genes showing enhanced expression in
?? petits independent of RTG genes, indicating
novel retrograde regulation pathways.