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Lysine Acetylation of Proteins and Its Characterization in Human Systems

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Protein Acetylation

Part of the book series: Methods in Molecular Biology ((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.

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References

  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 325:834–840

    Article  CAS  Google Scholar 

  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 327:1000–1004

    Article  Google Scholar 

  3. Kim GW, Yang XJ (2011) Comprehensive lysine acetylomes emerging from bacteria to humans. Trends Biochem Sci 36:211–220

    Article  CAS  Google Scholar 

  4. Dancy BM, Cole PA (2015) Protein lysine acetylation by p300/CBP. Chem Rev 115:2419–2432

    Article  CAS  Google Scholar 

  5. Sadoul K, Boyault C, Pabion M, Khochbin S (2008) Regulation of protein turnover by acetyltransferases and deacetylases. Biochimie 90:306–312

    Article  CAS  Google Scholar 

  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:e10341

    Article  Google Scholar 

  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 277:50934–50940

    Article  CAS  Google Scholar 

  8. Karmakar P, Bohr VA (2005) Cellular dynamics and modulation of WRN protein is DNA damage specific. Mech Ageing Dev 126:1146–1158

    Article  CAS  Google Scholar 

  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 283:7590–7598

    Article  CAS  Google Scholar 

  10. Yang XJ, Seto E (2007) HATs and HDACs: from structure, function and regulation to novel strategies for therapy and prevention. Oncogene 26:5310–5318

    Article  CAS  Google Scholar 

  11. Drazic A, Myklebust LM, Ree R, Arnesen T (2016) The world of protein acetylation. Biochim Biophys Acta 1864:1372–1401

    Article  CAS  Google Scholar 

  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 131:633–636

    Article  CAS  Google Scholar 

  13. Gong F, Miller KM (2013) Mammalian DNA repair: HATs and HDACs make their mark through histone acetylation. Mutat Res 750:23–30

    Article  CAS  Google Scholar 

  14. Yang XJ (2015) MOZ and MORF acetyltransferases: molecular interaction, animal development and human disease. Biochim Biophys Acta 1853:1818–1826

    Article  CAS  Google Scholar 

  15. Lee KK, Workman JL (2007) Histone acetyltransferase complexes: one size doesn’t fit all. Nat Rev Mol Cell Biol 8:284–295

    Article  CAS  Google Scholar 

  16. Liu N, Li S, Wu N, Cho KS (2017) Acetylation and deacetylation in cancer stem-like cells. Oncotarget 8:89315–89325

    PubMed  PubMed Central  Google Scholar 

  17. Kalkhoven E (2004) CBP and p300: HATs for different occasions. Biochem Pharmacol 68:1145–1155

    Article  CAS  Google Scholar 

  18. Goodman RH, Smolik S (2000) CBP/p300 in cell growth, transformation, and development. Genes Dev 14:1553–1577

    CAS  PubMed  Google Scholar 

  19. Vo N, Goodman RH (2001) CREB-binding protein and p300 in transcriptional regulation. J Biol Chem 276:13505–13508

    Article  CAS  Google Scholar 

  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 93:361–372

    Article  CAS  Google Scholar 

  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 99:14789–14794

    Article  CAS  Google Scholar 

  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 22:5175–5185

    Article  CAS  Google Scholar 

  23. Eckschlager T, Pich J, Stiborova M, Hrabeta J (2017) Histone deacetylase inhibitors as cancer drugs. Int J Mol Sci 18:1414

    Article  Google Scholar 

  24. Phillips DM (1963) The presence of acetyl groups of histones. Biochem J 87:258–263

    Article  CAS  Google Scholar 

  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 51:786–794

    Article  CAS  Google Scholar 

  26. Paik WK, Pearson D, Lee H, Kim S (1970) Nonenzymatic acetylation of histones with acetyl-CoA. Biochim Biophys Acta 213:513–522

    Article  CAS  Google Scholar 

  27. Horuichi K, Fujimoto D (1975) Use of phosphor-cellulose paper disks for the assay of histone acetyltransferase. Anal Biochem 69:491–496

    Article  Google Scholar 

  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 92:6364–6368

    Article  CAS  Google Scholar 

  29. Sletten EM, Bertozzi CR (2009) Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Ed Engl 48:6974–6998

    Article  CAS  Google Scholar 

  30. Yang YY, Ascano JM, Hang HC (2010) Bioorthogonal chemical reporters for monitoring protein acetylation. J Am Chem Soc 132:3640–3641

    Article  CAS  Google Scholar 

  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 107:7317–7373

    Article  CAS  Google Scholar 

  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 30:249–262

    Article  CAS  Google Scholar 

  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 15:347–366

    Article  CAS  Google Scholar 

  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 5:4653–4664

    Article  CAS  Google Scholar 

  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 23:607–618

    Article  CAS  Google Scholar 

  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 327:1000–1004

    Article  CAS  Google Scholar 

  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 149:1269–1283

    Article  Google Scholar 

  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 106:16257–16262

    Article  CAS  Google Scholar 

  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 18:495–507

    Article  CAS  Google Scholar 

  40. West AC, Johnstone RW (2014) New and emerging HDAC inhibitors for cancer treatment. J Clin Invest 124:30–39

    Article  CAS  Google Scholar 

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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.

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Correspondence to David K. Orren .

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Orren, D.K., Machwe, A. (2019). Lysine Acetylation of Proteins and Its Characterization in Human Systems. In: Brosh, Jr., R. (eds) Protein Acetylation. Methods in Molecular Biology, vol 1983. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9434-2_7

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  • DOI: https://doi.org/10.1007/978-1-4939-9434-2_7

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9433-5

  • Online ISBN: 978-1-4939-9434-2

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