Phosphorylation of Jhd2 by the Ras-cAMP-PKA(Tpk2) pathway regulates histone modifications and autophagy

Abstract

Cells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. How cells transduce nutrient availability to appropriate gene expression remains poorly understood. Here we show that glycolysis regulates histone modifications and gene expression by activating protein kinase A (PKA) via the Ras-cyclic AMP pathway. The catalytic subunit of PKA, Tpk2 antagonizes Jhd2-catalyzed H3K4 demethylation by phosphorylating Jhd2 at Ser321 and Ser340 in response to glucose availability. Tpk2-catalyzed Jhd2 phosphorylation impairs its nuclear localization, reduces its binding to chromatin, and promotes its polyubiquitination and degradation by the proteasome. Tpk2-catalyzed Jhd2 phosphorylation also maintains H3K14 acetylation by preventing the binding of histone deacetylase Rpd3 to chromatin. By phosphorylating Jhd2, Tpk2 regulates gene expression, maintains normal chronological life span and promotes autophagy. These results provide a direct connection between metabolism and histone modifications and shed lights on how cells rewire their biological responses to nutrient signals.

Regulation of telomere silencing by the core histones–autophagy–Sir2 axis

“…Set1-catalyzed H3K4me3 has been reported to be required to maintain telomere silencing ( Nislow et al, 1997 ; Corda et al, 1999 ; Fingerman et al, 2005 ). Loss of H3K4me3 leads to reduced chronological life span ( Mei et al, 2019 ; Yu et al, 2022 ). In this study, we show that Set1-catalyzed H3K4me3 maintains telomere silencing via the core histones–autophagy–Sir2 axis.…”

The TORC1 activates Rpd3L complex to deacetylate Ino80 and H2A.Z and repress autophagy

“…Immunoblot analysis was performed following procedures previously described in ( 60 ). In brief, cells were grown in 5 ml of YPD or indicated medium until OD 600 of 0.7 to 1.0.…”

SESAME-catalyzed H3T11 phosphorylation inhibits Dot1-catalyzed H3K79me3 to regulate autophagy and telomere silencing

“…The peptide pull-down assays were performed in accordance with the protocol described 67 . In brief, 1.0 µg of biotinylated histone peptides were incubated with 1 μg of protein or 0.5 ml whole cell extract in binding buffer (50 mM Tris-HCl, pH 7.5, 250 mM NaCl, 0.1% NP-40, 1 mM PMSF, protease inhibitors) overnight at 4 °C.…”

“…The immunoprecipitated proteins were digested with sequencing-grade trypsin (Promega) at 37 °C overnight and the supernatant was then desalted using C18 columns (Thermo Fisher) and lyophilized. The dried peptides were reconstituted in 0.1% formic acid (FA) and loaded onto an Acclaim PepMap 100 C18 LC column (Thermo Fisher) utilizing a Thermo Easy nLC 1000 LC system (Thermo Fisher) connected to Q Exactive HF mass spectrometer (Thermo Fisher) 67 . The peptides were eluted with a 5–20% gradient of acetonitrile with 0.1% formic acid over 70 min.…”

“…The peptide pull-down assays were performed in accordance with the protocol described 67 . In brief, 1.0 µg of biotinylated histone peptides were incubated with 1 μg of protein or 0.5 ml whole cell extract in…”