The goal of the study was to compare the response to Protien Kinase A (PKA) inhibition between Saccharomyces cerevisiae and Kluyveromyces lactis. The ancestor of K. lactis did not undergo the Whole Genome Duplication (or Whole Genome Hybridization) event that S. cerevisiae experienced. We found that many paralog pairs in S. cerevisiae were differentially induced in response to PKA inhibition, and that the shared ortholog for these paralog paris in K. lactis was typically not induced. To inhibit PKA, strains containing point mutations rendering PKA sensitive to inhibition by the ATP analog 1-NM-PP1 were generated. The transcription factors Msn2/4 and Rph1/Gis1 in S. cerevisiae and their shared orthologs in K. lactis were deleted in both species to quantify and compare the effect of those transcription factors on the response to PKA inhibition in each species.
Overall design: Experiments were conducted in S. cerevisiae and K. lactis yeast. 3uM 1-NM-PP1 and DMSO control samples were collected at 50min. Strains contained either no deleted genes, deletions of Msn2 and Msn4 or their shared ortholog in K. lactis, deletions of Rph1 and Gis1 or their shared ortholog in K. lactis, or deletions of all four genes (or both genes in K. lactis). In S. cerevisiae all experiments were performed in strains containing either the PKA analog sensitive mutations or WT PKA. In K. lactis, all experiments were performed in strains containing the PKA analog sensitive strains, except the strain containing no transcription factor deletions, which was performed in both PKA Analog Sensitive and WT PKA strains. There were 3-4 biological replicates for each species, transcription factor mutation, PKA background, treatment combination, and a few technical replicates were included to assess batch effects of library preparation.
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