Nutrient control of eukaryote cell growth: a systems biology study in yeast.
BACKGROUND
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.


RESULTS
We 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.


CONCLUSIONS
Our 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.
Gutteridge
Alex
A
Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
Pir
Pinar
P
Castrillo
Juan I
JI
Charles
Philip D
PD
Lilley
Kathryn S
KS
Oliver
Stephen G
SG
D002244:Carbon / Q000378:metabolism; D049109:Cell Proliferation; D005057:Eukaryotic Cells / Q000502:physiology*; D020869:Gene Expression Profiling / Q000379:methods; D015966:Gene Expression Regulation, Fungal / Q000502:physiology*; D053858:Metabolic Networks and Pathways / Q000502:physiology; D009584:Nitrogen / Q000378:metabolism; D009747:Nutritional Physiological Phenomena / Q000502:physiology; D010758:Phosphorus / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000254:growth & development*; D013455:Sulfur / Q000378:metabolism; D049490:Systems Biology / Q000379:methods*
D010758:Phosphorus; D013455:Sulfur; D002244:Carbon; D009584:Nitrogen