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

Yu Yi Lin, Samara Kiihl, Yasir Suhail, Shang Yun Liu, Yi Hsuan Chou, Zheng Kuang, Jin Ying Lu, Chin Ni Khor, Chi Long Lin, Joel S. Bader, Rafael Irizarry, Jef D. Boeke

Research output: Contribution to journalArticle

Abstract

First identified as histone-modifying proteins, lysine acetyltransferases (KATs) and deacetylases (KDACs) antagonize each other through modification of the side chains of lysine residues in histone proteins. Acetylation of many non-histone proteins involved in chromatin, metabolism or cytoskeleton regulation were further identified in eukaryotic organisms, but the corresponding enzymes and substrate-specific functions of the modifications are unclear. Moreover, mechanisms underlying functional specificity of individual KDACs remain enigmatic, and the substrate spectra of each KDAC lack comprehensive definition. Here we dissect the functional specificity of 12 critical human KDACs using a genome-wide synthetic lethality screen 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 acetylation and deacetylation 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. Deacetylation of AMPK enhances physical interaction with the upstream kinase LKB1, leading to AMPK phosphorylation and activation, and resulting in lipid breakdown in human liver cells. These findings provide new insights into previously underappreciated metabolic 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.

Original languageEnglish (US)
Pages (from-to)251-255
Number of pages5
JournalNature
Volume482
Issue number7384
DOIs
StatePublished - Feb 9 2012

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Adenosine Monophosphate
Protein Kinases
Lysine
Dissection
Acetylation
Histones
Biological Phenomena
Proteins
Enzymes
Substrate Specificity
Cytoskeleton
Chromatin
Cultured Cells
Catalytic Domain
Cell Cycle
Phosphotransferases
Phosphorylation
Genome
Lipids
Food

ASJC Scopus subject areas

  • Medicine(all)
  • General

Cite this

Lin, Y. Y., Kiihl, S., Suhail, Y., Liu, S. Y., Chou, Y. H., Kuang, Z., ... Boeke, J. D. (2012). Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature, 482(7384), 251-255. https://doi.org/10.1038/nature10804

Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. / Lin, Yu Yi; Kiihl, Samara; Suhail, Yasir; Liu, Shang Yun; Chou, Yi Hsuan; Kuang, Zheng; Lu, Jin Ying; Khor, Chin Ni; Lin, Chi Long; Bader, Joel S.; Irizarry, Rafael; Boeke, Jef D.

In: Nature, Vol. 482, No. 7384, 09.02.2012, p. 251-255.

Research output: Contribution to journalArticle

Lin, YY, Kiihl, S, Suhail, Y, Liu, SY, Chou, YH, Kuang, Z, Lu, JY, Khor, CN, Lin, CL, Bader, JS, Irizarry, R & Boeke, JD 2012, 'Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK', Nature, vol. 482, no. 7384, pp. 251-255. https://doi.org/10.1038/nature10804
Lin YY, Kiihl S, Suhail Y, Liu SY, Chou YH, Kuang Z et al. Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature. 2012 Feb 9;482(7384):251-255. https://doi.org/10.1038/nature10804
Lin, Yu Yi ; Kiihl, Samara ; Suhail, Yasir ; Liu, Shang Yun ; Chou, Yi Hsuan ; Kuang, Zheng ; Lu, Jin Ying ; Khor, Chin Ni ; Lin, Chi Long ; Bader, Joel S. ; Irizarry, Rafael ; Boeke, Jef D. / Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. In: Nature. 2012 ; Vol. 482, No. 7384. pp. 251-255.
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