Research article

Transcriptome analysis of a respiratory Saccharomyces cerevisiae strain suggests the expression of its phenotype is glucose insensitive and predominantly controlled by Hap4, Cat8 and Mig1

Nicklas Bonander¹ , Cecilia Ferndahl² , Petter Mostad³ , Martin DB Wilks⁴ , Celia Chang⁵ , Louise Showe⁵ , Lena Gustafsson² , Christer Larsson² and Roslyn M Bill¹

¹  School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK

²  Department of Chemical and Biological Engineering/Molecular Biotechnology, Chalmers University of Technology, Box 462, 405 30, Göteborg, Sweden

³  Mathematical Sciences, Chalmers University of Technology and Göteborg University, SE-412 96, Göteborg, Sweden

⁴  Cameron International Ltd., Queen Street, Stourton, Leeds, LS10 1SB, UK

⁵  The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania, 19104, USA

author email corresponding author email

BMC Genomics 2008, 9:365doi:10.1186/1471-2164-9-365

Published:	31 July 2008

Abstract

Background

We previously described the first respiratory Saccharomyces cerevisiae strain, KOY.TM6*P, by integrating the gene encoding a chimeric hexose transporter, Tm6*, into the genome of an hxt null yeast. Subsequently we transferred this respiratory phenotype in the presence of up to 50 g/L glucose to a yeast strain, V5 hxt1-7Δ, in which only HXT1-7 had been deleted. In this study, we compared the transcriptome of the resultant strain, V5.TM6*P, with that of its wild-type parent, V5, at different glucose concentrations.

Results

cDNA array analyses revealed that alterations in gene expression that occur when transitioning from a respiro-fermentative (V5) to a respiratory (V5.TM6*P) strain, are very similar to those in cells undergoing a diauxic shift. We also undertook an analysis of transcription factor binding sites in our dataset by examining previously-published biological data for Hap4 (in complex with Hap2, 3, 5), Cat8 and Mig1, and used this in combination with verified binding consensus sequences to identify genes likely to be regulated by one or more of these. Of the induced genes in our dataset, 77% had binding sites for the Hap complex, with 72% having at least two. In addition, 13% were found to have a binding site for Cat8 and 21% had a binding site for Mig1. Unexpectedly, both the up- and down-regulation of many of the genes in our dataset had a clear glucose dependence in the parent V5 strain that was not present in V5.TM6*P. This indicates that the relief of glucose repression is already operable at much higher glucose concentrations than is widely accepted and suggests that glucose sensing might occur inside the cell.

Conclusion

Our dataset gives a remarkably complete view of the involvement of genes in the TCA cycle, glyoxylate cycle and respiratory chain in the expression of the phenotype of V5.TM6*P. Furthermore, 88% of the transcriptional response of the induced genes in our dataset can be related to the potential activities of just three proteins: Hap4, Cat8 and Mig1. Overall, our data support genetic remodelling in V5.TM6*P consistent with a respiratory metabolism which is insensitive to external glucose concentrations.