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Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast.

Slavov N, Botstein D - Mol. Biol. Cell (2011)

Bottom Line: All genes with universal GRR, which comprise 25% of the genome, are expressed periodically in the yeast metabolic cycle (YMC).This idea is supported by oxygen consumption data from metabolically synchronized cultures with doubling times ranging from 5 to 14 h.We found that the high oxygen consumption phase of the YMC can coincide exactly with the S phase of the cell division cycle, suggesting that oxidative metabolism and DNA replication are not incompatible.

View Article: PubMed Central - PubMed

Affiliation: Massachusetts Institute of Technology, Cambridge, MA 02139, USA. nslavov@alum.mit.edu

ABSTRACT
We studied the steady-state responses to changes in growth rate of yeast when ethanol is the sole source of carbon and energy. Analysis of these data, together with data from studies where glucose was the carbon source, allowed us to distinguish a "universal" growth rate response (GRR) common to all media studied from a GRR specific to the carbon source. Genes with positive universal GRR include ribosomal, translation, and mitochondrial genes, and those with negative GRR include autophagy, vacuolar, and stress response genes. The carbon source-specific GRR genes control mitochondrial function, peroxisomes, and synthesis of vitamins and cofactors, suggesting this response may reflect the intensity of oxidative metabolism. All genes with universal GRR, which comprise 25% of the genome, are expressed periodically in the yeast metabolic cycle (YMC). We propose that the universal GRR may be accounted for by changes in the relative durations of the YMC phases. This idea is supported by oxygen consumption data from metabolically synchronized cultures with doubling times ranging from 5 to 14 h. We found that the high oxygen consumption phase of the YMC can coincide exactly with the S phase of the cell division cycle, suggesting that oxidative metabolism and DNA replication are not incompatible.

Show MeSH
Enzymes participating in ethanol utilization and catabolism. Each row of panels shows the expression levels of a set of enzymes catalyzing a reaction from ethanol catabolism. The left panels show the log2 expression levels relative to the reference and the right panels show zero-transformed data to enhance the viability of growth rate trends.
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Figure 9: Enzymes participating in ethanol utilization and catabolism. Each row of panels shows the expression levels of a set of enzymes catalyzing a reaction from ethanol catabolism. The left panels show the log2 expression levels relative to the reference and the right panels show zero-transformed data to enhance the viability of growth rate trends.

Mentions: The first re­action in ethanol utilization is its oxidation to acetaldehyde. The expression levels of the six isoenzymes (Adh1p to Adh6p) that can catalyze this reaction are shown in the top panels of Figure 9. The isoenzyme showing strongest induction (∼30-fold) across all nutrient limitations when ethanol is the carbon source is Adh2p. Interestingly, ADH2 gene expression is induced equally strongly in the glucose-limited cultures, whereas it is repressed in phosphate- and ammonia-limited cultures using glucose as a carbon source. This expression pattern suggests that ADH2 expression is more likely repressed by glucose than induced by ethanol. ADH3 is also induced in ethanol carbon source (approximately two- to fourfold) with positive slopes in all nutrient limitations, which could reflect the shuttling of NADH from the mitochondria to the cytoplasm that increases with the growth rate.


Coupling among growth rate response, metabolic cycle, and cell division cycle in yeast.

Slavov N, Botstein D - Mol. Biol. Cell (2011)

Enzymes participating in ethanol utilization and catabolism. Each row of panels shows the expression levels of a set of enzymes catalyzing a reaction from ethanol catabolism. The left panels show the log2 expression levels relative to the reference and the right panels show zero-transformed data to enhance the viability of growth rate trends.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3113766&req=5

Figure 9: Enzymes participating in ethanol utilization and catabolism. Each row of panels shows the expression levels of a set of enzymes catalyzing a reaction from ethanol catabolism. The left panels show the log2 expression levels relative to the reference and the right panels show zero-transformed data to enhance the viability of growth rate trends.
Mentions: The first re­action in ethanol utilization is its oxidation to acetaldehyde. The expression levels of the six isoenzymes (Adh1p to Adh6p) that can catalyze this reaction are shown in the top panels of Figure 9. The isoenzyme showing strongest induction (∼30-fold) across all nutrient limitations when ethanol is the carbon source is Adh2p. Interestingly, ADH2 gene expression is induced equally strongly in the glucose-limited cultures, whereas it is repressed in phosphate- and ammonia-limited cultures using glucose as a carbon source. This expression pattern suggests that ADH2 expression is more likely repressed by glucose than induced by ethanol. ADH3 is also induced in ethanol carbon source (approximately two- to fourfold) with positive slopes in all nutrient limitations, which could reflect the shuttling of NADH from the mitochondria to the cytoplasm that increases with the growth rate.

Bottom Line: All genes with universal GRR, which comprise 25% of the genome, are expressed periodically in the yeast metabolic cycle (YMC).This idea is supported by oxygen consumption data from metabolically synchronized cultures with doubling times ranging from 5 to 14 h.We found that the high oxygen consumption phase of the YMC can coincide exactly with the S phase of the cell division cycle, suggesting that oxidative metabolism and DNA replication are not incompatible.

View Article: PubMed Central - PubMed

Affiliation: Massachusetts Institute of Technology, Cambridge, MA 02139, USA. nslavov@alum.mit.edu

ABSTRACT
We studied the steady-state responses to changes in growth rate of yeast when ethanol is the sole source of carbon and energy. Analysis of these data, together with data from studies where glucose was the carbon source, allowed us to distinguish a "universal" growth rate response (GRR) common to all media studied from a GRR specific to the carbon source. Genes with positive universal GRR include ribosomal, translation, and mitochondrial genes, and those with negative GRR include autophagy, vacuolar, and stress response genes. The carbon source-specific GRR genes control mitochondrial function, peroxisomes, and synthesis of vitamins and cofactors, suggesting this response may reflect the intensity of oxidative metabolism. All genes with universal GRR, which comprise 25% of the genome, are expressed periodically in the yeast metabolic cycle (YMC). We propose that the universal GRR may be accounted for by changes in the relative durations of the YMC phases. This idea is supported by oxygen consumption data from metabolically synchronized cultures with doubling times ranging from 5 to 14 h. We found that the high oxygen consumption phase of the YMC can coincide exactly with the S phase of the cell division cycle, suggesting that oxidative metabolism and DNA replication are not incompatible.

Show MeSH