Research article

Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design

Alessandro Fazio^{* 1,2} , Michael C Jewett^{* 1,4} , Pascale Daran-Lapujade³ , Roberta Mustacchi¹ , Renata Usaite¹ , Jack T Pronk³ , Christopher T Workman² and Jens Nielsen^1,5

¹Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, Building 223, DK-2800, Kgs. Lyngby, Denmark

²Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Building 208, DK-2800 Kgs. Lyngby, Denmark

³Kluyver Centre for Genomics of Industrial Fermentation and Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands

⁴Department of Genetics, Harvard Medical School, Boston, MA 02115, USA

⁵Department of Chemical and Biological Engineering, Chalmers University of Technology, SE- 412 96, Gothenburg, Sweden

author email corresponding author email* Contributed equally

BMC Genomics 2008, 9:341doi:10.1186/1471-2164-9-341

Published:	18 July 2008

Abstract

Background

Characterization of cellular growth is central to understanding living systems. Here, we applied a three-factor design to study the relationship between specific growth rate and genome-wide gene expression in 36 steady-state chemostat cultures of Saccharomyces cerevisiae. The three factors we considered were specific growth rate, nutrient limitation, and oxygen availability.

Results

We identified 268 growth rate dependent genes, independent of nutrient limitation and oxygen availability. The transcriptional response was used to identify key areas in metabolism around which mRNA expression changes are significantly associated. Among key metabolic pathways, this analysis revealed de novo synthesis of pyrimidine ribonucleotides and ATP producing and consuming reactions at fast cellular growth. By scoring the significance of overlap between growth rate dependent genes and known transcription factor target sets, transcription factors that coordinate balanced growth were also identified. Our analysis shows that Fhl1, Rap1, and Sfp1, regulating protein biosynthesis, have significantly enriched target sets for genes up-regulated with increasing growth rate. Cell cycle regulators, such as Ace2 and Swi6, and stress response regulators, such as Yap1, were also shown to have significantly enriched target sets.

Conclusion

Our work, which is the first genome-wide gene expression study to investigate specific growth rate and consider the impact of oxygen availability, provides a more conservative estimate of growth rate dependent genes than previously reported. We also provide a global view of how a small set of transcription factors, 13 in total, contribute to control of cellular growth rate. We anticipate that multi-factorial designs will play an increasing role in elucidating cellular regulation.