Next Generation Sequencing Facilitates Quantitative Analysis of wild typeHDAC1 and HDAC1_S434A Transcriptomes with or without PKA inhibitor H89 treatment

Cells need to reprogram their metabolism to adapt to extracellular nutrient changes. The histone acetyltransferase SAGA (Spt-Ada-Gcn5-acetyltransferase) complex has been reported to acetylate its subunit Ada3 and form homo-dimers to enhance its ability to acetylate nucleosomes and facilitate metabolic gene transcription. How cells transduce extracellular nutrient changes to SAGA structure and function changes remains unclear. Here, we found that SAGA is deacetylated by Rpd3L complex and uncovered how its deacetylase activity is repressed by nutrient sensor protein kinase A (PKA). When sucrose is used as the sole carbon source, PKA catalytic subunit Tpk2 is activated, which phosphorylates Rpd3L catalytic subunit Rpd3 at serine 50 and serine 354 to inhibit its ability to deacetylate Ada3. Moreover, Tpk2 phosphorylates Rpd3L subunit Ash1 at serine 149 and serine 388, which specifically reduces the interaction between Rpd3L and SAGA. By phosphorylating both Rpd3 and Ash1, Tpk2 inhibits Rpd3L-mediated Ada3 deacetylation, which promotes SAGA dimerization, nucleosome acetylation and transcription of genes involved in sucrose utilization and tricarboxylate (TCA) cycle, resulting in metabolic shift from glycolysis to TCA cycle. Most importantly, PKA phosphorylates HDAC1, the Rpd3 homolog in mammals to repress its deacetylase activity and promote TCA cycle gene transcription. Blocking PKA-catalyzed HDAC1 phosphorylation reduced TCA cycle and impaired cell growth. Our work hence reveals a conserved role of PKA in regulating Rpd3/HDAC1 and metabolism adaptation and provides a potential target for future cancer treatment.