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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Model-based determination of the nutrient mean effect and growth rate slope, using arginine as an example metabolite. Arginine concentration data (plotted using the same conventions as in Figure 2) were fit to Eq. 2; bn is the nutrient mean effect and mn is the growth rate slope. Units of the nutrient mean effect are log2(fold-change) and of the growth rate slope are log2(fold-change)/(growth rate). For example, a nutrient mean effect of −2 (as found for arginine in glucose limitation) implies that the average arginine concentration in glucose limitation is one-quarter (i.e., 2−2) the overall average. Once growth rate slope and nutrient mean effects are calculated, they can be plotted against each other (bottom right). Candidate growth-limiting metabolites have a negative nutrient mean effect and a positive growth rate slope, and accordingly fall in the top left quadrant. Overflow metabolites have a positive nutrient mean effect and negative growth rate slope, and accordingly fall in the bottom right quadrant. Compound-nutrient pairs are plotted when the nutrient mean effect and growth rate slope are both significant at FDR <0.1. For arginine, this occurred in nitrogen limitation and in carbon limitation but not in the other nutrient conditions. In both nitrogen limitation and carbon limitation, arginine showed a growth-limiting pattern.
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Figure 3: Model-based determination of the nutrient mean effect and growth rate slope, using arginine as an example metabolite. Arginine concentration data (plotted using the same conventions as in Figure 2) were fit to Eq. 2; bn is the nutrient mean effect and mn is the growth rate slope. Units of the nutrient mean effect are log2(fold-change) and of the growth rate slope are log2(fold-change)/(growth rate). For example, a nutrient mean effect of −2 (as found for arginine in glucose limitation) implies that the average arginine concentration in glucose limitation is one-quarter (i.e., 2−2) the overall average. Once growth rate slope and nutrient mean effects are calculated, they can be plotted against each other (bottom right). Candidate growth-limiting metabolites have a negative nutrient mean effect and a positive growth rate slope, and accordingly fall in the top left quadrant. Overflow metabolites have a positive nutrient mean effect and negative growth rate slope, and accordingly fall in the bottom right quadrant. Compound-nutrient pairs are plotted when the nutrient mean effect and growth rate slope are both significant at FDR <0.1. For arginine, this occurred in nitrogen limitation and in carbon limitation but not in the other nutrient conditions. In both nitrogen limitation and carbon limitation, arginine showed a growth-limiting pattern.

Mentions: Examples of metabolites that are potentially limiting growth under glucose limitation, ammonium limitation, phosphate limitation, and uracil limitation (from top to bottom). Metabolite concentrations are plotted on a log2 scale and mean-centered as per Figure 1. Values represent the median (black circles) and interquartile range (bars) of N = 4 independent samples from each chemostat. For a given limiting nutrient, steady-state growth rate increases from left to right from 0.05 to 0.3 h−1. Limiting nutrients are as per Figure 1: 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; U, limitation for uracil in a uracil auxotroph. Trend lines are a fit to the linear model described in Figure 3.


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)

Model-based determination of the nutrient mean effect and growth rate slope, using arginine as an example metabolite. Arginine concentration data (plotted using the same conventions as in Figure 2) were fit to Eq. 2; bn is the nutrient mean effect and mn is the growth rate slope. Units of the nutrient mean effect are log2(fold-change) and of the growth rate slope are log2(fold-change)/(growth rate). For example, a nutrient mean effect of −2 (as found for arginine in glucose limitation) implies that the average arginine concentration in glucose limitation is one-quarter (i.e., 2−2) the overall average. Once growth rate slope and nutrient mean effects are calculated, they can be plotted against each other (bottom right). Candidate growth-limiting metabolites have a negative nutrient mean effect and a positive growth rate slope, and accordingly fall in the top left quadrant. Overflow metabolites have a positive nutrient mean effect and negative growth rate slope, and accordingly fall in the bottom right quadrant. Compound-nutrient pairs are plotted when the nutrient mean effect and growth rate slope are both significant at FDR <0.1. For arginine, this occurred in nitrogen limitation and in carbon limitation but not in the other nutrient conditions. In both nitrogen limitation and carbon limitation, arginine showed a growth-limiting pattern.
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Related In: Results  -  Collection

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Figure 3: Model-based determination of the nutrient mean effect and growth rate slope, using arginine as an example metabolite. Arginine concentration data (plotted using the same conventions as in Figure 2) were fit to Eq. 2; bn is the nutrient mean effect and mn is the growth rate slope. Units of the nutrient mean effect are log2(fold-change) and of the growth rate slope are log2(fold-change)/(growth rate). For example, a nutrient mean effect of −2 (as found for arginine in glucose limitation) implies that the average arginine concentration in glucose limitation is one-quarter (i.e., 2−2) the overall average. Once growth rate slope and nutrient mean effects are calculated, they can be plotted against each other (bottom right). Candidate growth-limiting metabolites have a negative nutrient mean effect and a positive growth rate slope, and accordingly fall in the top left quadrant. Overflow metabolites have a positive nutrient mean effect and negative growth rate slope, and accordingly fall in the bottom right quadrant. Compound-nutrient pairs are plotted when the nutrient mean effect and growth rate slope are both significant at FDR <0.1. For arginine, this occurred in nitrogen limitation and in carbon limitation but not in the other nutrient conditions. In both nitrogen limitation and carbon limitation, arginine showed a growth-limiting pattern.
Mentions: Examples of metabolites that are potentially limiting growth under glucose limitation, ammonium limitation, phosphate limitation, and uracil limitation (from top to bottom). Metabolite concentrations are plotted on a log2 scale and mean-centered as per Figure 1. Values represent the median (black circles) and interquartile range (bars) of N = 4 independent samples from each chemostat. For a given limiting nutrient, steady-state growth rate increases from left to right from 0.05 to 0.3 h−1. Limiting nutrients are as per Figure 1: 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; U, limitation for uracil in a uracil auxotroph. Trend lines are a fit to the linear model described in Figure 3.

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