Advertisement

Lysine Acetylation of Proteins and Its Characterization in Human Systems

  • David K. OrrenEmail author
  • Amrita Machwe
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1983)

Abstract

Posttranslational acetylation modifications of proteins have important consequences for cell biology, including effects on protein trafficking and cellular localization as well as on the interactions of acetylated proteins with other proteins and macromolecules such as DNA. Experiments to uncover and characterize protein acetylation events have historically been more challenging than investigating another common posttranslational modification, protein phosphorylation. More recently, high-quality antibodies that recognize acetylated lysine residues present in acetylated proteins and improved proteomic methodologies have facilitated the discovery that acetylation occurs on numerous cellular proteins and allowed characterization of the dynamics and functional effects of many acetylation events. This article summarizes some established biochemical information about how protein acetylation takes place and is regulated, in order to lay the foundation for subsequent descriptions of strategies used by our lab and others either to directly study acetylation of an individual factor or to identify groups of proteins targeted for acetylation that can then be examined in isolation.

Keywords

Posttranslational modifications Acetyltransferases Histone deacetylases Sirtuins Immunodetection Proteomics Bromodomain 

Notes

Acknowledgment

This work was supported by NIH grants R01 AG027258 and R01 AG026534 as well as by the Department of Toxicology and Cancer Biology of the University of Kentucky College of Medicine.

References

  1. 1.
    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 325:834–840CrossRefGoogle Scholar
  2. 2.
    Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q, Xiong Y, Guan KL (2010) Regulation of cellular metabolism by protein lysine acetylation. Science 327:1000–1004CrossRefGoogle Scholar
  3. 3.
    Kim GW, Yang XJ (2011) Comprehensive lysine acetylomes emerging from bacteria to humans. Trends Biochem Sci 36:211–220CrossRefGoogle Scholar
  4. 4.
    Dancy BM, Cole PA (2015) Protein lysine acetylation by p300/CBP. Chem Rev 115:2419–2432CrossRefGoogle Scholar
  5. 5.
    Sadoul K, Boyault C, Pabion M, Khochbin S (2008) Regulation of protein turnover by acetyltransferases and deacetylases. Biochimie 90:306–312CrossRefGoogle Scholar
  6. 6.
    Li K, Wang R, Lozada E, Fan W, Orren DK, Luo J (2010) Acetylation of WRN regulates it stability by inhibiting ubiquitination. PLoS One 5:e10341CrossRefGoogle Scholar
  7. 7.
    Blander G, Zalle N, Daniely Y, Taplick J, Gray MD, Oren M (2002) DNA damage-induced translocation of the Werner helicase is regulated by acetylation. J Biol Chem 277:50934–50940CrossRefGoogle Scholar
  8. 8.
    Karmakar P, Bohr VA (2005) Cellular dynamics and modulation of WRN protein is DNA damage specific. Mech Ageing Dev 126:1146–1158CrossRefGoogle Scholar
  9. 9.
    Li K, Casta A, Wang R, Lozada E, Fan W, Kane S, Ge Q, Orren D, Luo J (2008) Regulation of WRN protein cellular localization and enzymatic activities by SIRT1-mediated deacetylation. J Biol Chem 283:7590–7598CrossRefGoogle Scholar
  10. 10.
    Yang XJ, Seto E (2007) HATs and HDACs: from structure, function and regulation to novel strategies for therapy and prevention. Oncogene 26:5310–5318CrossRefGoogle Scholar
  11. 11.
    Drazic A, Myklebust LM, Ree R, Arnesen T (2016) The world of protein acetylation. Biochim Biophys Acta 1864:1372–1401CrossRefGoogle Scholar
  12. 12.
    Allis CD, Berger SL, Cote J, Dent S, Jenuwein T, Kouzarides T, Pillus L, Reinberg D, Shi Y, Shiekhattar R, Shilatifard A, Workman J, Zhang Y (2007) New nomenclature for chromatin-modifying enzymes. Cell 131:633–636CrossRefGoogle Scholar
  13. 13.
    Gong F, Miller KM (2013) Mammalian DNA repair: HATs and HDACs make their mark through histone acetylation. Mutat Res 750:23–30CrossRefGoogle Scholar
  14. 14.
    Yang XJ (2015) MOZ and MORF acetyltransferases: molecular interaction, animal development and human disease. Biochim Biophys Acta 1853:1818–1826CrossRefGoogle Scholar
  15. 15.
    Lee KK, Workman JL (2007) Histone acetyltransferase complexes: one size doesn’t fit all. Nat Rev Mol Cell Biol 8:284–295CrossRefGoogle Scholar
  16. 16.
    Liu N, Li S, Wu N, Cho KS (2017) Acetylation and deacetylation in cancer stem-like cells. Oncotarget 8:89315–89325PubMedPubMedCentralGoogle Scholar
  17. 17.
    Kalkhoven E (2004) CBP and p300: HATs for different occasions. Biochem Pharmacol 68:1145–1155CrossRefGoogle Scholar
  18. 18.
    Goodman RH, Smolik S (2000) CBP/p300 in cell growth, transformation, and development. Genes Dev 14:1553–1577PubMedGoogle Scholar
  19. 19.
    Vo N, Goodman RH (2001) CREB-binding protein and p300 in transcriptional regulation. J Biol Chem 276:13505–13508CrossRefGoogle Scholar
  20. 20.
    Yao TP, Oh SP, Fuchs M, Zhou ND, Chang LE, Newsome D et al (1998) Gene dosage-dependent embryonic development and proliferation defects in mice lacking the transcriptional integrator p300. Cell 93:361–372CrossRefGoogle Scholar
  21. 21.
    Rebel VI, Kung AL, Tanner EA, Yang H, Bronson RT, Livingston DM (2002) Distinct roles for CREB-binding protein and p300 in hematopoietic stem cell self-renewal. Proc Natl Acad Sci U S A 99:14789–14794CrossRefGoogle Scholar
  22. 22.
    Shikama N, Lutz W, Kretzschmar R, Sauter N, Roth JF, Marino S et al (2003) Essential function of p300 acetyltransferase activity in heart, lung and small intestine formation. EMBO J 22:5175–5185CrossRefGoogle Scholar
  23. 23.
    Eckschlager T, Pich J, Stiborova M, Hrabeta J (2017) Histone deacetylase inhibitors as cancer drugs. Int J Mol Sci 18:1414CrossRefGoogle Scholar
  24. 24.
    Phillips DM (1963) The presence of acetyl groups of histones. Biochem J 87:258–263CrossRefGoogle Scholar
  25. 25.
    Allfrey VG, Faulkner R, Mirsky AE (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci U S A 51:786–794CrossRefGoogle Scholar
  26. 26.
    Paik WK, Pearson D, Lee H, Kim S (1970) Nonenzymatic acetylation of histones with acetyl-CoA. Biochim Biophys Acta 213:513–522CrossRefGoogle Scholar
  27. 27.
    Horuichi K, Fujimoto D (1975) Use of phosphor-cellulose paper disks for the assay of histone acetyltransferase. Anal Biochem 69:491–496CrossRefGoogle Scholar
  28. 28.
    Brownell JE, Allis CD (1995) An activity gel assay detects a single, catalytically active histone acetyltransferase subunit in Tetrahymena macronuclei. Proc Natl Acad Sci U S A 92:6364–6368CrossRefGoogle Scholar
  29. 29.
    Sletten EM, Bertozzi CR (2009) Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Ed Engl 48:6974–6998CrossRefGoogle Scholar
  30. 30.
    Yang YY, Ascano JM, Hang HC (2010) Bioorthogonal chemical reporters for monitoring protein acetylation. J Am Chem Soc 132:3640–3641CrossRefGoogle Scholar
  31. 31.
    Wang L, Jin Q, Lee J-E, Su IH, Ge K (2010) Histone H3K27 methyltransferase Ezh2 represses Wnt genes to facilitate adipogenesis. Proc Natl Acad Sci 107:7317–7373CrossRefGoogle Scholar
  32. 32.
    Jin Q, Yu LR, Wang L, Zhang Z, Kasper LH, Lee JE, Wang C, Brindle PK, Dent SYR, Ge K (2011) Distinct roles of GCN5/PCAF-mediated H3K9ac and CPB/p300-mediated H3K18/27ac in nuclear receptor activation. EMBO J 30:249–262CrossRefGoogle Scholar
  33. 33.
    Lozada E, Yi J, Luo J, Orren DK (2014) Acetylation of Werner syndrome protein (WRN): relationships with DNA damage, DNA replication and DNA metabolic activities. Biogerontology 15:347–366CrossRefGoogle Scholar
  34. 34.
    Iwabata H, Yoshida M, Komatsu Y (2005) Proteomic analysis of organ-specific posttranslational lysine-acetylation and -methylation in mice by use of anti-acetyllysine and -methyllysine mouse monoclonal antibodies. Proteomics 5:4653–4664CrossRefGoogle Scholar
  35. 35.
    Kim SC, Sprung R, Chen Y, Xu Y, Ball H, Pei J, Cheng T, Kho Y, Xiao H, Xiao L, Grishin NV, White M, Yang XJ, Zhao Y (2006) Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell 23:607–618CrossRefGoogle Scholar
  36. 36.
    Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q, Xiong Y, Guan KL (2010) Regulation of cellular metabolism by protein lysine acetylation. Science 327:1000–1004CrossRefGoogle Scholar
  37. 37.
    Li T, Kon N, Jiang L, Tan M, Ludwig T, Zhao Y, Baer R, Gu W (2006) Tumor suppression in the absence of p53-mediated cell-cycle arrest, apoptosis, and senescence. Cell 149:1269–1283CrossRefGoogle Scholar
  38. 38.
    Sasaki K, Ito T, Nishino N, Khochbin S, Yoshida M (2009) Real-time imaging of histone H$ hyperacetylation in living cells. Proc Natl Acad Sci U S A 106:16257–16262CrossRefGoogle Scholar
  39. 39.
    Ito T, Umehara T, Sasaki K, Nakamura Y, Nishino N, Terada T, Shirouzu M, Padmanabhan B, Yokoyama S, Ito A, Yoshida M (2011) Real-time imaging of histone H4K12-specific acetylation determines the modes of action of histone deacetylase and bromodomain inhibitors. Chem Biol 18:495–507CrossRefGoogle Scholar
  40. 40.
    West AC, Johnstone RW (2014) New and emerging HDAC inhibitors for cancer treatment. J Clin Invest 124:30–39CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Toxicology and Cancer Biology and Markey Cancer CenterUniversity of Kentucky College of MedicineLexingtonUSA

Personalised recommendations