Transcriptomics,Genomics

Dataset Information

26

Transcriptome data - Respiratory S. cerevisiae Strain Phenotype is Glucose Insensitive and vital TFs are Hap4 Cat8 Mig1


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 demonstrated the transferability of this respiratory phenotype in the presence of up to 100 g/L glucose to a yeast strain in which only HXT1-7 had been deleted. In this study, we wanted to examine the basis of the respiratory phenotype of the resultant strain, V5.TM6*P, by comparing its transcriptome with that of its 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. Highly complete collections of known genes of the TCA cycle, glyoxylate cycle and respiratory chain were identified, consistent with a respiratory metabolism. We also undertook an analysis of transcription factor binding sites in our dataset by examining previously-published biological data for Hap4, Cat8 and Mig1, and using this in combination with verified binding consensus sequences, to identify genes likely to be regulated by one or more of these transcription factors. Of the induced genes of our dataset, 77 % had binding sites for Hap2/3/5 (Hap4 is an activator of this complex), with 72 % having at least two (the latter set being more induced than the former). This is relevant since Hap4 is known to be involved in the transcriptional activation of respiratory genes and other mitochondrial functions. In addition, 13 % of genes were found to have a binding site for Cat8, which together with its complexes with Sip4 have previously been identified as mediating de-repression of a number of genes during the diauxic shift. Finally, 21 % of genes had a binding site for Mig1 which is a transcriptional repressor involved in glucose repression. 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 important result 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. Conclusions 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 transcription factors; Hap2/3/5, 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. Overall design: Compare a wild type Saccaromyces cerevisise strain V5 strain (=V), with a mutant strain where glucose transport has been reduced by at least 30% in the strain V5.TM6*P (=T), mutant is devoided of 7 hexose transporters HXT1, HXT2, HXT3, HXT4, HXT5, HXT6, HXT7, the plasma membrane contains a HXT1-HXT7 fusion protein. This construct is a combination of a low and high affinity glucose transporter. The glucose concentration in the culture media of each array is the parameter that can be how the arrays are sorted. Accession Strain Glucose [g/L] GSM298426 V5.TM6*P 36.5 GSM298477 V5.TM6*P 36.5 GSM298478 V5.TM6*P 34.8 GSM298480 V5.TM6*P 34.8 GSM298483 V5.TM6*P 26.3 GSM298484 V5.TM6*P 26.3 GSM298485 V5.TM6*P 25.1 GSM298487 V5.TM6*P 25.1 GSM298489 V5.TM6*P 13.5 GSM298491 V5.TM6*P 13.5 GSM298492 V5.TM6*P 5.6 GSM298494 V5.TM6*P 5.6 GSM298496 V5-wild type 38.4 GSM298497 V5-wild type 38.4 GSM298500 V5-wild type 35 GSM298501 V5-wild type 35 GSM298502 V5-wild type 25.5 GSM298503 V5-wild type 25.5 GSM298504 V5-wild type 24.4 GSM298505 V5-wild type 24.4 GSM298506 V5-wild type 10.5 GSM298508 V5-wild type 10.5 GSM298509 V5-wild type 7.4 GSM298510 V5-wild type 7.4

INSTRUMENT(S): Wistar Yeast YA04 array

SUBMITTER: Nicklas Bonander  

PROVIDER: GSE11799 | GEO | 2008-06-20

SECONDARY ACCESSION(S): PRJNA105887

REPOSITORIES: GEO

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Publications

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.

Bonander Nicklas N   Ferndahl Cecilia C   Mostad Petter P   Wilks Martin D B MD   Chang Celia C   Showe Louise L   Gustafsson Lena L   Larsson Christer C   Bill Roslyn M RM  

BMC genomics 20080731


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 hxt1-7Delta, 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 g  ...[more]

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