Identification of novel transcriptional regulators of PKA subunits inSaccharomyces cerevisiaeby quantitative promoter–reporter screening

Abstract

The cAMP-dependent protein kinase (PKA) signaling is a broad pathway that plays important roles in the transduction of environmental signals triggering precise physiological responses. However, how PKA achieves the cAMP-signal transduction specificity is still in study. The regulation of expression of subunits of PKA should contribute to the signal specificity. Saccharomyces cerevisiae PKA holoenzyme contains two catalytic subunits encoded by TPK1, TPK2 and TPK3 genes, and two regulatory subunits encoded by BCY1 gene. We studied the activity of these gene promoters using a fluorescent reporter synthetic genetic array screen, with the goal of systematically identifying novel regulators of expression of PKA subunits. Gene ontology analysis of the identified modulators showed enrichment not only in the category of transcriptional regulators, but also in less expected categories such as lipid and phosphate metabolism. Inositol, choline and phosphate were identified as novel upstream signals that regulate transcription of PKA subunit genes. The results support the role of transcription regulation of PKA subunits in cAMP specificity signaling. Interestingly, known targets of PKA phosphorylation are associated with the identified pathways opening the possibility of a reciprocal regulation. PKA would be coordinating different metabolic pathways and these processes would in turn regulate expression of the kinase subunits.

Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning

“…Since the exact phosphorylation site of many PKA targets (Pautasso et al, 2016) is not known or at least recorded in the Biogrid database, we also tested if sites identified by our features were enriched in serine phosphorylation sites in general. Overall, Biogrid contains 14994 unique serine phosphorylation sites that occur in yeast IDRs.…”