Abstract
BackgroundTo elucidate the biological processes affected by changes in growth rate and nutrient availability, we have performed a comprehensive analysis of the transcriptome, proteome and metabolome responses of chemostat cultures of the yeast, Saccharomyces cerevisiae, growing at a range of growth rates and in four different nutrient-limiting conditions.ResultsWe find significant changes in expression for many genes in each of the four nutrient-limited conditions tested. We also observe several processes that respond differently to changes in growth rate and are specific to each nutrient-limiting condition. These include carbohydrate storage, mitochondrial function, ribosome synthesis, and phosphate transport. Integrating transcriptome data with proteome measurements allows us to identify previously unrecognized examples of post-transcriptional regulation in response to both nutrient and growth-rate signals.ConclusionsOur results emphasize the unique properties of carbon metabolism and the carbon substrate, the limitation of which induces significant changes in gene regulation at the transcriptional and post-transcriptional level, as well as altering how many genes respond to growth rate. By comparison, the responses to growth limitation by other nutrients involve a smaller set of genes that participate in specific pathways.See associated commentary http://www.biomedcentral.com/1741-7007/8/62
Highlights
To elucidate the biological processes affected by changes in growth rate and nutrient availability, we have performed a comprehensive analysis of the transcriptome, proteome and metabolome responses of chemostat cultures of the yeast, Saccharomyces cerevisiae, growing at a range of growth rates and in four different nutrient-limiting conditions
Saccharomyces cerevisiae was grown under four different nutrient limitations at three different dilution rates (D = μ = 0.07 h-1, 0.1 h-1, and 0.2 h-1)
In the course of this analysis, we have shown that the mRNA and protein levels of many S. cerevisiae genes are under the control of a combination of these nutrient-specific sensing mechanisms and growth rate
Summary
To elucidate the biological processes affected by changes in growth rate and nutrient availability, we have performed a comprehensive analysis of the transcriptome, proteome and metabolome responses of chemostat cultures of the yeast, Saccharomyces cerevisiae, growing at a range of growth rates and in four different nutrient-limiting conditions. The importance of regulation at the proteome and metabolome levels means that integrative studies incorporating multiple types of data are necessary [7,19,20,21,22,23]. Another important feature of many studies is the use of defined controlled conditions, of which chemostat fermentors are an example [24,25,26,27], to ensure time-course and steadystate measurements are taken under rigorously defined conditions, making comparisons between experiments more robust [28,29]
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