Limits...
Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.

Boer VM, Crutchfield CA, Bradley PH, Botstein D, Rabinowitz JD - Mol. Biol. Cell (2009)

Bottom Line: Nitrogen (ammonium) and carbon (glucose) limitation were characterized by low intracellular amino acid and high nucleotide levels, whereas phosphorus (phosphate) limitation resulted in the converse.Low adenylate energy charge was found selectively in phosphorus limitation, suggesting the energy charge may actually measure phosphorus availability.A simple but physically realistic model involving the availability of these metabolites was adequate to account for cellular growth rate.

View Article: PubMed Central - PubMed

Affiliation: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.

ABSTRACT
Microbes tailor their growth rate to nutrient availability. Here, we measured, using liquid chromatography-mass spectrometry, >100 intracellular metabolites in steady-state cultures of Saccharomyces cerevisiae growing at five different rates and in each of five different limiting nutrients. In contrast to gene transcripts, where approximately 25% correlated with growth rate irrespective of the nature of the limiting nutrient, metabolite concentrations were highly sensitive to the limiting nutrient's identity. Nitrogen (ammonium) and carbon (glucose) limitation were characterized by low intracellular amino acid and high nucleotide levels, whereas phosphorus (phosphate) limitation resulted in the converse. Low adenylate energy charge was found selectively in phosphorus limitation, suggesting the energy charge may actually measure phosphorus availability. Particularly strong concentration responses occurred in metabolites closely linked to the limiting nutrient, e.g., glutamine in nitrogen limitation, ATP in phosphorus limitation, and pyruvate in carbon limitation. A simple but physically realistic model involving the availability of these metabolites was adequate to account for cellular growth rate. The complete data can be accessed at the interactive website http://growthrate.princeton.edu/metabolome.

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Metabolites with consistent growth rate responses across conditions. Conventions are as per Figure 2: limiting nutrients are C, limitation for the carbon source, glucose; N, limitation for the nitrogen source, ammonium; P, limitation for the phosphorus source, phosphate; L, limitation for leucine in a leucine auxotroph; and U, limitation for uracil in a uracil auxotroph. Within each condition, steady-state growth rate increases from left to right from 0.05 to 0.3 h−1. Metabolites were fit to the single-parameter model in Eq. 6, with mall representing the overall growth rate slope. The r values indicate goodness of fit. Note that orotate concentrations consistently increase with faster growth except under uracil limitation, where the knockout of URA3 causes the buildup of orotate.
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Figure 7: Metabolites with consistent growth rate responses across conditions. Conventions are as per Figure 2: limiting nutrients are C, limitation for the carbon source, glucose; N, limitation for the nitrogen source, ammonium; P, limitation for the phosphorus source, phosphate; L, limitation for leucine in a leucine auxotroph; and U, limitation for uracil in a uracil auxotroph. Within each condition, steady-state growth rate increases from left to right from 0.05 to 0.3 h−1. Metabolites were fit to the single-parameter model in Eq. 6, with mall representing the overall growth rate slope. The r values indicate goodness of fit. Note that orotate concentrations consistently increase with faster growth except under uracil limitation, where the knockout of URA3 causes the buildup of orotate.

Mentions: Although the concentrations of most metabolites were highly dependent on the limiting nutrient, some metabolites did show a general trend to increase or decrease with growth rate (Figure 7 and Table 2). Metabolites whose abundance was strongly correlated with growth rate, irrespective of nutrient limitation, were identified on the basis of their goodness-of-fit (r) to an analogue of Eq. 2 with all nutrient-specific terms removed: Metabolites showing a statistically significant positive growth rate slope across all nutrient conditions (Bonferroni–Holm corrected p value <0.05, which corresponded to r > 0.64) included the lower glycolytic intermediates dihydroxyacetone-phosphate and bisphosphoglycerate and the nucleotide precursor ribose phosphate. When we considered only natural limitation conditions, taking the same goodness-of-fit cut-off, we found that two pyrimidine intermediates (orotate and dihydroorotate) and the arginine biosynthetic intermediate argininosuccinate also increased significantly with growth rate.


Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.

Boer VM, Crutchfield CA, Bradley PH, Botstein D, Rabinowitz JD - Mol. Biol. Cell (2009)

Metabolites with consistent growth rate responses across conditions. Conventions are as per Figure 2: limiting nutrients are C, limitation for the carbon source, glucose; N, limitation for the nitrogen source, ammonium; P, limitation for the phosphorus source, phosphate; L, limitation for leucine in a leucine auxotroph; and U, limitation for uracil in a uracil auxotroph. Within each condition, steady-state growth rate increases from left to right from 0.05 to 0.3 h−1. Metabolites were fit to the single-parameter model in Eq. 6, with mall representing the overall growth rate slope. The r values indicate goodness of fit. Note that orotate concentrations consistently increase with faster growth except under uracil limitation, where the knockout of URA3 causes the buildup of orotate.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2801714&req=5

Figure 7: Metabolites with consistent growth rate responses across conditions. Conventions are as per Figure 2: limiting nutrients are C, limitation for the carbon source, glucose; N, limitation for the nitrogen source, ammonium; P, limitation for the phosphorus source, phosphate; L, limitation for leucine in a leucine auxotroph; and U, limitation for uracil in a uracil auxotroph. Within each condition, steady-state growth rate increases from left to right from 0.05 to 0.3 h−1. Metabolites were fit to the single-parameter model in Eq. 6, with mall representing the overall growth rate slope. The r values indicate goodness of fit. Note that orotate concentrations consistently increase with faster growth except under uracil limitation, where the knockout of URA3 causes the buildup of orotate.
Mentions: Although the concentrations of most metabolites were highly dependent on the limiting nutrient, some metabolites did show a general trend to increase or decrease with growth rate (Figure 7 and Table 2). Metabolites whose abundance was strongly correlated with growth rate, irrespective of nutrient limitation, were identified on the basis of their goodness-of-fit (r) to an analogue of Eq. 2 with all nutrient-specific terms removed: Metabolites showing a statistically significant positive growth rate slope across all nutrient conditions (Bonferroni–Holm corrected p value <0.05, which corresponded to r > 0.64) included the lower glycolytic intermediates dihydroxyacetone-phosphate and bisphosphoglycerate and the nucleotide precursor ribose phosphate. When we considered only natural limitation conditions, taking the same goodness-of-fit cut-off, we found that two pyrimidine intermediates (orotate and dihydroorotate) and the arginine biosynthetic intermediate argininosuccinate also increased significantly with growth rate.

Bottom Line: Nitrogen (ammonium) and carbon (glucose) limitation were characterized by low intracellular amino acid and high nucleotide levels, whereas phosphorus (phosphate) limitation resulted in the converse.Low adenylate energy charge was found selectively in phosphorus limitation, suggesting the energy charge may actually measure phosphorus availability.A simple but physically realistic model involving the availability of these metabolites was adequate to account for cellular growth rate.

View Article: PubMed Central - PubMed

Affiliation: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.

ABSTRACT
Microbes tailor their growth rate to nutrient availability. Here, we measured, using liquid chromatography-mass spectrometry, >100 intracellular metabolites in steady-state cultures of Saccharomyces cerevisiae growing at five different rates and in each of five different limiting nutrients. In contrast to gene transcripts, where approximately 25% correlated with growth rate irrespective of the nature of the limiting nutrient, metabolite concentrations were highly sensitive to the limiting nutrient's identity. Nitrogen (ammonium) and carbon (glucose) limitation were characterized by low intracellular amino acid and high nucleotide levels, whereas phosphorus (phosphate) limitation resulted in the converse. Low adenylate energy charge was found selectively in phosphorus limitation, suggesting the energy charge may actually measure phosphorus availability. Particularly strong concentration responses occurred in metabolites closely linked to the limiting nutrient, e.g., glutamine in nitrogen limitation, ATP in phosphorus limitation, and pyruvate in carbon limitation. A simple but physically realistic model involving the availability of these metabolites was adequate to account for cellular growth rate. The complete data can be accessed at the interactive website http://growthrate.princeton.edu/metabolome.

Show MeSH