Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK

Abstract

First identified as histone-modifying proteins, lysine acetyltranferases (KATs) and deacetylases (KDACs) antagonize each other through modification of the side chains of lysine residues in histone proteins1. (De)acetylation of many non-histone proteins involved in chromatin, metabolism or cytoskeleton regulation were further identified in eukaryotic organisms2–6, but the corresponding modifying enzymes and substrate-specific functions of the modification are unclear. Moreover, mechanisms underlying functional specificity of individual KDACs7 remain enigmatic, and the substrate spectra of each KDAC lack comprehensive definition. Here we dissect the functional specificity of twelve critical human KDACs using a genome-wide synthetic lethality screen8–13 in cultured human cells. The genetic interaction profiles revealed enzyme-substrate relationships between individual KDACs and many important substrates governing a wide array of biological processes including metabolism, development and cell cycle progression. We further confirmed that (de)acetylation of the catalytic subunit of the adenosine monophosphate-activated protein kinase (AMPK), a critical cellular energy-sensing protein kinase complex, is controlled by the opposing catalytic activities of HDAC1 and p300. Its deacetylation enhances physical interaction with the upstream kinase LKB1, in turn leading to AMPK phosphorylation and activation, resulting in lipid breakdown in human liver cells. These findings provide new insights into previously underappreciated metabolism-regulatory roles of HDAC1 in coordinating nutrient availability and cellular responses upstream of AMPK, and demonstrate the importance of high-throughput genetic interaction profiling to elucidate functional specificity and critical substrates of individual human KDACs potentially valuable for therapeutic applications.

Valproic Acid Is a Novel Activator of AMP-Activated Protein Kinase and Decreases Liver Mass, Hepatic Fat Accumulation, and Serum Glucose in Obese Mice

“…Since VPA is a known inhibitor of HDAC1 (Phiel et al, 2001), which has been previously shown to regulate AMPK phosphorylation/activation (Lin et al, 2012), our data demonstrating that treatment with VPA resulted in increased levels of phosphorylated AMPK were potentially in conflict with this finding. We found that although inhibition of deacetylase activity was observed following treatment of mouse nuclear extracts and human recombinant HDAC1with VPA, the acetylation of AMPK in primary mouse hepatocytes was unchanged following treatment with VPA as compared with vehicle treatment, indicating that any inhibition of HDAC1 activity that may have occurred as a result of VPA treatment did not impact the acetylation status of AMPK as compared with vehicle-treated control samples.…”

“…It has been previously demonstrated in yeast and HepG2 cells (a hepatocarcinoma cell line) that the activity of AMPK is regulated by HDAC1 (Lin et al, 2012). Deacetylation of AMPK by HDAC1 was shown to facilitate its interaction with upstream kinases, thereby stimulating the phosphorylation and activation of AMPK.…”

5′-AMP–Activated Protein Kinase–Activating Transcription Factor 1 Cascade Modulates Human Monocyte–Derived Macrophages to Atheroprotective Functions in Response to Heme or Metformin

“…13 AMPK may modify transcription via phosphorylation of a large and growing number of transcription factors and chromatin proteins. 12,[14][15][16][17][18][19][20] Critically, these include ATF1. 8 Purified AMPK phosphorylated recombinant purified ATF1 in an in vitro kinase assay in a cell-free system, in an article defining AMPK-mediated phosphorylation of CREB-family proteins in vivo in skeletal muscle during exercise.…”

Molecular Pathways: Old Drugs Define New Pathways: Non-Histone Acetylation at the Crossroads of the DNA Damage Response and Autophagy

“…In acute myelogenous leukemia, inhibition of mTOR signaling has been proposed to overcome HDAC inhibitor resistance (64) and, conversely in DLBCL cells, inhibition of HDACs to rescue mTOR inhibitor resistance (55). Even more recently, HDAC1 has been directly shown to regulate metabolism in mammalian cells through deacetylation of the AMPK kinase, thus leading to its interaction and activation by the upstream LKB1 kinase (65). In this way, HDAC1 can act as a direct energy sensor in the cells, hinting at complex regulatory links among metabolism, DDR, and autophagy.…”