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Gene profiling of TRA1 and tra1-L3733A

ABSTRACT: Tra1 is a component of the Saccharomyces cerevisiae SAGA and NuA4 complexes and a member of the phosphatidylinositol 3-kinase kinase family that contain a C-terminal PI3K domain followed by a 35-residue FATC domain. We analyzed alleles with single residue changes in the FATC domain. Of these tra1-L3733A had the most pronounced effects, resulting in phenotypes similar but not identical to those resulting from mutations in the PI3K domain or SAGA or NuA4 components. To analyze the transcriptional effects of the tra1-L3733A allele, we performed gene profiling of wild-type and tra1-L3733A strains. Expression of 11 genes was elevated ≥ 2-fold, 79 genes were decreased ≥ 2-fold. Of the 11 genes with elevated expression, four (HSP26, PIR3, DDR2 and GRE1) have roles in cellular stress response. The only gene ontology process significantly enriched in the genes with decreased expression greater than 2-fold was lysine biosynthesis (GO: 0009085). Broader analysis of gene ontology processes revealed expression of genes involved in cellular respiration (GO:0045333) and the overlapping process generation of precursor metabolites and energy (GO: 0006091) showed an average upward shift of ~10% relative to the total collection of genes. A similar trend of less magnitude was seen for vitamin metabolic processes (GO:0006766). A slight downward shift was seen for genes involved in translation (GO:0006412) and membrane organization (GO:0016044).

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE18591 | GEO | 2010/09/20

SECONDARY ACCESSION(S): PRJNA121329

REPOSITORIES: GEO

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Project description:Tra1 is a component of the Saccharomyces cerevisiae SAGA and NuA4 complexes and a member of the phosphatidylinositol 3-kinase (PI3K) related kinase family that contain a C- terminal PI3K domain followed by a ~ 35-residue FATC domain. We have characterized four alleles with single residue changes in the FATC domain. Of these tra1-L3733A had the most pronounced effects with phenotypes including temperature and cold sensitivity, and reduced growth in media containing ethanol, Calcofluor white, rapamycin, chloramphenicol and geneticin. Tra1-L3733A interacted at normal levels with components of the NuA4 and SAGA complexes, and did not significantly alter histone acetylation patterns. The tra1-L3733A allele resulted in two-fold or greater change in expression of approximately 11% of yeast genes in rich media. Of the 279 genes with increased expression, 175 were ribosomal subunits or involved in ribosomal function or biogenesis. Elevated levels of Pol I and Pol III transcripts were also observed. The phenotypes of the tra1-L3733A overlapped with but were not identical to strains containing deletions of SAGA or NuA4 components or with strains containing mutations in the PI3K domain. Our finding that the double mutant allele, tra1-SRR3413/L3733A with alterations in the PI3K and FATC domains, resulted in wild type growth, suggests a model whereby the FATC domain negatively regulates the activity of the PI3K domain. Expression of genes involved in ribosome biosynthesis, other than the ribosomal subunits themselves, returned to near normal levels in the double mutant strain. We also characterized tra1-G3745, which contains an additional glycine residue following the normal C-terminal phenylalanine. This allele did not support viability and showed severe dominant negative effects. In contrast to what was observed for tra1-L3733A, tra1-G4745 resulted in decreased expression of genes required for ribosome biogenesis and did not interact with Esa1 or Spt7. Three biological replicate experiments including one dye-swap were performed for yeast strains CY3003(TRA1::Tn10LUK with IB150(myc9-tra1_L3733A-YCplac111)) and CY3015(TRA1::Tn10LUK with IB157(myc9-tra1_SRR3413_L3733A-YCplac111)) with reference to CY2706(TRA1::Tn10LUK with 1980(myc9-TRA1-YCplac111)). Similarly, three biological replicate experiments including one dye-swap were performed for yeast strain CY3019(TRA1::Tn10LUK with 1259(myc-TRA1-YCplac111) and IB162(myc9-tra1_G3745-YCplac111)) with reference to CY3020(TRA1::Tn10LUK with 1259(myc-TRA1-YCplac111) and IB160(myc9-TRA1-YCplac111)).

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Gene profiling of TRA1 and tra1-L3733A

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