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Open Access Research article

How yeast re-programmes its transcriptional profile in response to different nutrient impulses

Duygu Dikicioglu1, Erkan Karabekmez1, Bharat Rash2, Pınar Pir34, Betul Kirdar1 and Stephen G Oliver13*

Author affiliations

1 Department of Chemical Engineering, Bogazici University, Bebek 34342, Istanbul, Turkey

2 Faculty of Life Sciences, University of Manchester, M1 9PT, Manchester, UK

3 Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, CB2 1GA, Cambridge, UK

4 Novacta Biosystems Limited, BioPark Hertfordshire, Welwyn Garden City, AL7 3AX, Herts, UK

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Citation and License

BMC Systems Biology 2011, 5:148  doi:10.1186/1752-0509-5-148

Published: 25 September 2011

Abstract

Background

A microorganism is able to adapt to changes in its physicochemical or nutritional environment and this is crucial for its survival. The yeast, Saccharomyces cerevisiae, has developed mechanisms to respond to such environmental changes in a rapid and effective manner; such responses may demand a widespread re-programming of gene activity. The dynamics of the re-organization of the cellular activities of S. cerevisiae in response to the sudden and transient removal of either carbon or nitrogen limitation has been studied by following both the short- and long-term changes in yeast's transcriptomic profiles.

Results

The study, which spans timescales from seconds to hours, has revealed the hierarchy of metabolic and genetic regulatory switches that allow yeast to adapt to, and recover from, a pulse of a previously limiting nutrient. At the transcriptome level, a glucose impulse evoked significant changes in the expression of genes concerned with glycolysis, carboxylic acid metabolism, oxidative phosphorylation, and nucleic acid and sulphur metabolism. In ammonium-limited cultures, an ammonium impulse resulted in the significant changes in the expression of genes involved in nitrogen metabolism and ion transport. Although both perturbations evoked significant changes in the expression of genes involved in the machinery and process of protein synthesis, the transcriptomic response was delayed and less complex in the case of an ammonium impulse. Analysis of the regulatory events by two different system-level, network-based approaches provided further information about dynamic organization of yeast cells as a response to a nutritional change.

Conclusions

The study provided important information on the temporal organization of transcriptomic organization and underlying regulatory events as a response to both carbon and nitrogen impulse. It has also revealed the importance of a long-term dynamic analysis of the response to the relaxation of a nutritional limitation to understand the molecular basis of the cells' dynamic behaviour.