Abstract
Lysine (K) acetylation refers to transfer of the acetyl moiety from acetyl-CoA to the ε-amino group of a lysine residue. This is posttranslational and reversible, with its level dynamically maintained by lysine acetyltransferases (KATs) and deacetylases (KDACs). Traditionally, eukaryotic KDACs have been referred to as HDACs (histone deacetylases). Recent proteomic studies have revealed that hundreds of bacterial proteins and thousands of eukaryotic proteins contain acetyl-lysine (AcK) residues, indicating that K-acetylomes are comparable to phosphoproteomes. The current challenges are to assign enzymes that execute specific acetylation events, to determine the impact of these events, and to relate this modification to other posttranslational modifications, cell signaling networks, and pathophysiology under different cellular and developmental contexts. In this chapter, we provide a brief overview about the acetylomes, KATs, HDACs, AcK-recognizing protein domains, and acetylation-modulating therapeutics, and emphasize the latest developments in related areas. The remaining chapters of the book focus on and cover various aspects of HDACs (both the Rpd3/Hda1 and sirtuin families), which shall provide novel insights into how to utilize these enzymes for developing a new generation of HDAC-related therapeutics.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Akella JS, Wloga D, Kim J, Starostina NG, Lyons-Abbott S, Morrissette NS, Dougan ST, Kipreos ET, Gaertig J (2010) MEC-17 is an alpha-tubulin acetyltransferase. Nature 467:218–222
Allis CD, Berger SL, Cote J, Dent S, Jenuwien T, Kouzarides T, Pillus L, Reinberg D, Shi Y, Shiekhattar R et al (2007) New nomenclature for chromatin-modifying enzymes. Cell 131:633–636
Arif M, Vedamurthy BM, Choudhari R, Ostwal YB, Mantelingu K, Kodaganur GS, Kundu TK (2010) Nitric oxide-mediated histone hyperacetylation in oral cancer: target for a water-soluble HAT inhibitor, CTK7A. Chem Biol 17:903–913
Avvakumov N, Côté J (2007) Histone acetyltransferases of the MYST family and their roles in cancer. Oncogene 26:5395–5407
Bannister AJ, Kouzarides T (1996) The CBP co-activator is a histone acetyltransferase. Nature 384:641–643
Barak R, Welch M, Yanovsky A, Oosawa K, Eisenbach M (1992) Acetyladenylate or its derivative acetylates the chemotaxis protein CheY in vitro and increases its activity at the flagellar switch. Biochemistry 31:10099–10107
Bowers EM, Yan G, Mukherjee C, Orry A, Wang L, Holbert MA, Crump NT, Hazzalin CA, Liszczak G, Yuan H et al (2010) Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. Chem Biol 17:471–482
Cai Y, Jin J, Swanson SK, Cole MD, Choi SH, Florens L, Washburn MP, Conaway JW, Conaway RC (2010) Subunit composition and substrate specificity of a MOF-containing histone acetyltransferase distinct from the male-specific lethal (MSL) complex. J Biol Chem 285:4268–4272
Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325:834–840
Chu CW, Hou F, Zhang J, Phu L, Loktev AV, Kirkpatrick DS, Jackson PK, Zhao Y, Zou H (2011) A novel acetylation of {beta}-tubulin by San modulates microtubule polymerization via down-regulating tubulin incorporation. Mol Biol Cell 22:448
Doyon Y, Cayrou C, Ullah M, Landry AJ, Cote V, Selleck W, Lane WS, Tan S, Yang XJ, Cote J (2006) ING tumor suppressors are critical regulators of chromatin acetylation required for genome expression and perpetuation. Mol Cell 21:51–64
Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith WB, Fedorov O, Morse EM, Keates T, Hickman TT, Felletar I et al (2010) Selective inhibition of BET bromodomains. Nature 468:1067–1073
Fischer A, Sananbenesi F, Mungenast A, Tsai LH (2010) Targeting the correct HDAC(s) to treat cognitive disorders. Trends Pharmacol Sci 31:605–617
Gershey EL, Vidali G, Allfrey VG (1968) Chemical studies of histone acetylation. The occurrence of epsilon-N-acetyllysine in the f2a1 histone. J Biol Chem 243:5018–5022
Goodman RH, Smolik S (2000) CBP/p300 in cell growth, transformation, and development. Genes Dev 14:1553–1577
Greenwood C, Selth LA, Dirac-Svejstrup AB, Svejstrup JQ (2009) An iron-sulfur cluster domain in Elp3 important for the structural integrity of elongator. J Biol Chem 284:141–149
Gregoretti IV, Lee YM, Goodson HV (2004) Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis. J Mol Biol 338:17–31
Grozinger CM, Schreiber SL (2002) Deacetylase enzymes: biological functions and the use of small-molecule inhibitors. Chem Biol 9:3–16
Guelman S, Kozuka K, Mao Y, Pham V, Solloway MJ, Wang J, Wu J, Lill JR, Zha J (2009) The double-histone-acetyltransferase complex ATAC is essential for mammalian development. Mol Cell Biol 29:1176–1188
Huangfu D, Maehr R, Guo W, Eijkelenboom A, Snitow M, Chen AE, Melton DA (2008a) Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds. Nat Biotechnol 26:795–797
Huangfu D, Osafune K, Maehr R, Guo W, Eijkelenboom A, Chen S, Muhlestein W, Melton DA (2008b) Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2. Nat Biotechnol 26:1269–1275
Hubbert C, Guardiola A, Shao R, Kawaguchi Y, Ito A, Nixon A, Yoshida M, Wang XF, Yao TP (2002) HDAC6 is a microtubule-associated deacetylase. Nature 417:455–458
Jaenisch R, Young R (2008) Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132:567–582
Kang SK, Cha SH, Jeon HG (2006) Curcumin-induced histone hypoacetylation enhances caspase-3-dependent glioma cell death and neurogenesis of neural progenitor cells. Stem Cells Dev 15:165–174
Khochbin S, Verdel A, Lemercier C, Seigneurin-Berny D (2001) Functional significance of histone deacetylase diversity. Curr Opin Genet Dev 11:162–166
Kim GW, Yang XJ (2011) Comprehensive lysine acetylomes emerging from bacteria to humans. Trends Biochem Sci 36(4):211–220
Kim SC, Sprung R, Chen Y, Xu Y, Ball H, Pei J, Cheng T, Kho Y, Xiao H, Xiao L et al (2006) Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell 23:607–618
Kouzarides T (2000) Acetylation: a regulatory modification to rival phosphorylation? EMBO J 19:1176–1179
Lafon A, Chang CS, Scott EM, Jacobson SJ, Pillus L (2007) MYST opportunities for growth control: yeast genes illuminate human cancer gene functions. Oncogene 26:5373–5384
Lee KK, Workman JL (2007) Histone acetyltransferase complexes: one size doesn’t fit all. Nat Rev Mol Cell Biol 8:284–295
Li X, Wu L, Corsa CA, Kunkel S, Dou Y (2009) Two mammalian MOF complexes regulate transcription activation by distinct mechanisms. Mol Cell 36:290–301
Lopes da Rosa J, Boyartchuk VL, Zhu LJ, Kaufman PD (2010) Histone acetyltransferase Rtt109 is required for Candida albicans pathogenesis. Proc Natl Acad Sci USA 107:1594–1599
Mali P, Chou BK, Yen J, Ye Z, Zou J, Dowey S, Brodsky RA, Ohm JE, Yu W, Baylin SB et al (2010) Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes. Stem Cells 28:713–720
Michishita E, Park JY, Burneskis JM, Barrett JC, Horikawa I (2005) Evolutionarily conserved and nonconserved cellular localizations and functions of human SIRT proteins. Mol Biol Cell 16:4623–4635
Moriniere J, Rousseaux S, Steuerwald U, Soler-Lopez M, Curtet S, Vitte AL, Govin J, Gaucher J, Sadoul K, Hart DJ et al (2009) Cooperative binding of two acetylation marks on a histone tail by a single bromodomain. Nature 461:664–668
Mottet D, Castronovo V (2008) Histone deacetylases: target enzymes for cancer therapy. Clin Exp Metastasis 25:183–189
Nicodeme E, Jeffrey KL, Schaefer U, Beinke S, Dewell S, Chung CW, Chandwani R, Marazzi I, Wilson P, Coste H et al (2010) Suppression of inflammation by a synthetic histone mimic. Nature 468:1119–1123
Norris KL, Lee JY, Yao TP (2009) Acetylation goes global: the emergence of acetylation biology. Sci Signal 2:pe76
Ogryzko VV, Schiltz RL, Russanova V, Howard BH, Nakatani Y (1996) The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 87:953–959
Orpinell M, Fournier M, Riss A, Nagy Z, Krebs AR, Frontini M, Tora L (2010) The ATAC acetyl transferase complex controls mitotic progression by targeting non-histone substrates. EMBO J 29:2381–2394
Piperno G, Fuller MT (1985) Monoclonal antibodies specific for an acetylated form of alpha-tubulin recognize the antigen in cilia and flagella from a variety of organisms. J Cell Biol 101:2085–2094
Prestel M, Feller C, Straub T, Mitlohner H, Becker PB (2010) The activation potential of MOF is constrained for dosage compensation. Mol Cell 38:815–826
Raja SJ, Charapitsa I, Conrad T, Vaquerizas JM, Gebhardt P, Holz H, Kadlec J, Fraterman S, Luscombe NM, Akhtar A (2010) The nonspecific lethal complex is a transcriptional regulator in Drosophila. Mol Cell 38:827–841
Ramakrishnan R, Schuster M, Bourret RB (1998) Acetylation at Lys-92 enhances signaling by the chemotaxis response regulator protein CheY. Proc Natl Acad Sci USA 95:4918–4923
Roth SY, Denu JM, Allis CD (2001) Histone acetyltransferases. Annu Rev Biochem 70:81–120
Sanchez R, Zhou MM (2009) The role of human bromodomains in chromatin biology and gene transcription. Curr Opin Drug Discov Devel 12:659–665
Sauve AA (2010) Sirtuin chemical mechanisms. Biochim Biophys Acta 1804:1565–1566
Scher MB, Vaquero A, Reinberg D (2007) SirT3 is a nuclear NAD+-dependent histone deacetylase that translocates to the mitochondria upon cellular stress. Genes Dev 21:920–928
Shi Y, Zhao Y, Deng H (2010) Powering reprogramming with vitamin C. Cell Stem Cell 6:1–2
Shida T, Cueva JG, Xu Z, Goodman MB, Nachury MV (2010) The major {alpha}-tubulin K40 acetyltransferase {alpha}TAT1 promotes rapid ciliogenesis and efficient mechanosensation. Proc Natl Acad Sci USA 107:21517–21522
Stadtfeld M, Hochedlinger K (2010) Induced pluripotency: history, mechanisms, and applications. Genes Dev 24:2239–2263
Starai VJ, Escalante-Semerena JC (2004) Identification of the protein acetyltransferase (Pat) enzyme that acetylates acetyl-CoA synthetase in Salmonella enterica. J Mol Biol 340:1005–1012
Sterner DE, Berger SL (2000) Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev 64:435–459
Sterner R, Vidali G, Allfrey VG (1979) Studies of acetylation and deacetylation in high mobility group proteins. Identification of the sites of acetylation in HMG-1. J Biol Chem 254:11577–11583
Suganuma T, Gutierrez JL, Li B, Florens L, Swanson SK, Washburn MP, Abmayr SM, Workman JL (2008) ATAC is a double histone acetyltransferase complex that stimulates nucleosome sliding. Nat Struct Mol Biol 15:364–372
Suganuma T, Mushegian A, Swanson SK, Abmayr SM, Florens L, Washburn MP, Workman JL (2010) The ATAC acetyltransferase complex coordinates MAP kinases to regulate JNK target genes. Cell 142:726–736
Takahashi K, Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126:663–676
Tang Y, Holbert MA, Wurtele H, Meeth K, Rocha W, Gharib M, Jiang E, Thibault P, Verreault A, Cole PA et al (2008) Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP. Nat Struct Mol Biol 15:738–745
Tsai WW, Wang Z, Yiu TT, Akdemir KC, Xia W, Winter S, Tsai CY, Shi X, Schwarzer D, Plunkett W et al (2010) TRIM24 links a non-canonical histone signature to breast cancer. Nature 468:927–932
Tursun B, Patel T, Kratsios P, Hobert O (2011) Direct conversion of C. elegans germ cells into specific neuron types. Science 331:304–308
Ullah M, Pelletier N, Xiao L, Zhao SP, Wang K, Degerny C, Tahmasebi S, Cayrou C, Doyon Y, Goh SL et al (2008) Molecular architecture of quartet MOZ/MORF histone acetyltransferase complexes. Mol Cell Biol 28:6828–6843
Verdin E, Hirschey MD, Finley LW, Haigis MC (2010) Sirtuin regulation of mitochondria: energy production, apoptosis, and signaling. Trends Biochem Sci 35:669–675
Wang YL, Faiola F, Xu M, Pan S, Martinez E (2008) Human ATAC Is a GCN5/PCAF-containing acetylase complex with a novel NC2-like histone fold module that interacts with the TATA-binding protein. J Biol Chem 283:33808–33815
Wang Q, Zhang Y, Yang C, Xiong H, Lin Y, Yao J, Li H, Xie L, Zhao W, Yao Y et al (2010) Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science 327:1004–1007
Wu H, Min J, Antoshenko T, Plotnikov AN (2009) Crystal structures of human CDY proteins reveal a crotonase-like fold. Proteins 76:1054–1061
Wurtele H, Tsao S, Lepine G, Mullick A, Tremblay J, Drogaris P, Lee EH, Thibault P, Verreault A, Raymond M (2010) Modulation of histone H3 lysine 56 acetylation as an antifungal therapeutic strategy. Nat Med 16:774–780
Yamanaka S, Blau HM (2010) Nuclear reprogramming to a pluripotent state by three approaches. Nature 465:704–712
Yang XJ, Seto E (2008a) Lysine acetylation: codified crosstalk with other posttranslational modifications. Mol Cell 31:449–461
Yang XJ, Seto E (2008b) The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat Rev Mol Cell Biol 9:206–218
Yoshida M, Kijima M, Akita M, Beppu T (1990) Potent and specific inhibition of mammalian histone deacetylase both in vivo and in vitro by trichostatin A. J Biol Chem 265:17174–17179
Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008) The diversity of lysine-acetylated proteins in Escherichia coli. J Microbiol Biotechnol 18:1529–1536
Zeng L, Zhang Q, Li S, Plotnikov AN, Walsh MJ, Zhou MM (2010) Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature 466:258–262
Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009) Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol Cell Proteomics 8:215–225
Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H et al (2010) Regulation of cellular metabolism by protein lysine acetylation. Science 327:1000–1004
Zhou H, Wu S, Joo JY, Zhu S, Han DW, Lin T, Trauger S, Bien G, Yao S, Zhu Y et al (2009) Generation of induced pluripotent stem cells using recombinant proteins. Cell Stem Cell 4:381–384
Acknowledgments
This work was supported by operating grants from MDEIE (Développement économique, innovation et exportation) Québec, Canadian Institutes of Health Research, and Canadian Cancer Society (to X.-J.Y.).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Aka, J.A., Kim, GW., Yang, XJ. (2011). K-Acetylation and Its Enzymes: Overview and New Developments. In: Yao, TP., Seto, E. (eds) Histone Deacetylases: the Biology and Clinical Implication. Handbook of Experimental Pharmacology, vol 206. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21631-2_1
Download citation
DOI: https://doi.org/10.1007/978-3-642-21631-2_1
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-21630-5
Online ISBN: 978-3-642-21631-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)