Skip to main content
SpringerLink
Log in

Using Functional Proteome Microarrays to Study Protein Lysine Acetylation

  • Protocol
  • First Online:
Book cover Protein Acetylation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 981))

Abstract

Emergence of proteome microarray provides a versatile platform to globally explore biological functions of broad significance. In the past decade, researchers have successfully fabricated functional proteome microarrays by printing individually purified proteins at a high-throughput, proteome-wide scale on one single slide. These arrays have been used to profile protein posttranslational modifications, including phosphorylation, ubiquitylation, acetylation, and nitrosylation. In this chapter, we summarize our work of using the yeast proteome microarrays to connect protein lysine acetylation substrates to their upstream modifying enzyme, the nucleosome acetyltransferase of H4 (NuA4), which is the only essential acetyltransferase in yeast. We further prove that the reversible acetylation on critical cell metabolism-related enzymes controls life span in yeast. Our studies represent a paradigm shift for the functional dissection of a crucial acetylation enzyme affecting aging and longevity pathways.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Smith MG, Jona G, Ptacek J, Devgan G, Zhu H, Zhu X, Snyder M (2005) Global analysis of protein function using protein microarrays. Mech Ageing Dev 126:171–175

    Article  PubMed  CAS  Google Scholar 

  2. Chen C, Zhu H (2006) Protein microarrays. Biotechniques 40:432–439

    Article  Google Scholar 

  3. Tao SC, Chen CS, Zhu H (2007) Applications of protein microarray technology. Comb Chem High Throughput Screen 10:706–718

    Article  PubMed  CAS  Google Scholar 

  4. Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M (2001) Global analysis of protein activities using proteome chips. Science 293:2101–2105

    Article  PubMed  CAS  Google Scholar 

  5. Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M (2004) Regulation of gene expression by a metabolic enzyme. Science 306: 482–484

    Article  PubMed  CAS  Google Scholar 

  6. Ho SW, Jona G, Chen CT, Johnston M, Snyder M (2006) Linking DNA-binding proteins to their recognition sequences by using protein microarrays. Pro Natl Acad Sci USA 103(26): 9940–9945

    Article  CAS  Google Scholar 

  7. Hu S, Xie Z, Onishi A, Yu X, Jiang L, Lin J, Rho HS, Woodard C, Wang H, Jeong JS, Long S, He X, Wade H, Blackshaw S, Qian J, Zhu H (2009) Profiling the human protein–DNA interactome reveals ERK2 as a transcriptional repressor of interferon signalling. Cell 139(3):610–622

    Article  PubMed  CAS  Google Scholar 

  8. Zhu J, Gopinath K, Murali A, Yi G, Hayward SD, Zhu H, Kao C (2007) RNA binding proteins that inhibit RNA virus infection. Proc Natl Acad Sci USA 104:3129–3134

    Article  PubMed  CAS  Google Scholar 

  9. Huang J, Zhu H, Haggarty SJ, Spring DR, Hwang H, Jin F, Snyder M, Schreiber SL (2004) Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc Natl Acad Sci USA 101:16594–16599

    Article  PubMed  CAS  Google Scholar 

  10. Zhu H, Klemic JF, Chang S, Bertone P, Casamayor A, Klemic KG, Smith D, Gerstein M, Reed MA, Snyder M (2000) Analysis of yeast protein kinases using protein chips. Nat Genet 26:283–289

    Article  PubMed  CAS  Google Scholar 

  11. Kafadar KA, Zhu H, Snyder M, Cyert MS (2003) Negative regulation of calcineurin signaling by Hrr25p, a yeast homolog of casein kinase I. Genes Dev 17:2698–2708

    Article  PubMed  CAS  Google Scholar 

  12. Ptacek J, Devgan G, Michaud G, Zhu H et al (2005) Global analysis of protein phosphorylation in yeast. Nature 438:679–684

    Article  PubMed  CAS  Google Scholar 

  13. Tao SC, Li Y, Zhou J, Qian J, Schnaar RL, Zhang Y, Goldstein IJ, Zhu H, Schneck JP (2008) Lectin microarrays identify cell-specific and functionally significant cell surface glycan markers. Glycobiology 18:761–769

    Article  PubMed  CAS  Google Scholar 

  14. Zhu J, Liao G, Shan L, Zhang J, Chen MR, Hayward GS, Hayward SD, Desai P, Zhu H (2009) Protein array identification of substrates of the Epstein-Barr Virus protein kinase BGLF4. J Virol 83:5219–5231

    Article  PubMed  CAS  Google Scholar 

  15. Kung L, Tao SC, Qian J, Smith M, Snyder M, Zhu H (2009) Global analysis of the glycoproteome in S. cerevisiae reveals new roles for protein glycosylation. Mol Syst Biol 5:308

    Article  PubMed  Google Scholar 

  16. Lu JY, Lin YY, Tao SC, Zhu J, Pickart CM, Qian J, Zhu H (2008) Functional dissection of a HECT ubiquitin E3 ligase. Mol Cell Proteomics 7:35–45

    PubMed  CAS  Google Scholar 

  17. Lin YY, Lu JY, Zhang J, Walter W, Dang W, Wan J, Tao SC, Qian J, Zhao Y, Boeke JD, Berger SL, Zhu H (2009) Protein acetylation microarray reveals NuA4 controls key metabolic target regulating gluconeogenesis. Cell 136:1073–1084

    Article  PubMed  CAS  Google Scholar 

  18. Thao S, Chen CS, Zhu H, Escalante-Semerena JC (2010) Nε-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity. PLoS One 5(12):15123

    Article  Google Scholar 

  19. Lu JY, Lin YY, Sheu JC, Wu JT, Lee FJ, Chen Y, Lin MI, Chiang FT, Tai TY, Berger SL, Zhao Y, Tsai KS, Zhu H, Chuang LM, Boeke JD (2011) Acetylation of AMPK controls intrinsic aging independently of caloric restriction. Cell 146:969–979

    Article  PubMed  CAS  Google Scholar 

  20. Oh YH, Hong MY, Jin Z, Lee T, Han MK, Park S, Kim HS (2007) Chip-based analysis of SUMO (small ubiquitin-like modifier) conjugation to a target protein. Biosens Bioelectron 22(7):1260–1267

    Article  PubMed  CAS  Google Scholar 

  21. Del Rincón SV, Rogers J, Widschwendter M, Sun D, Sieburg HB, Spruck C (2010) Development and validation of a method for profiling post-translational modification activities using protein microarrays. PLoS One 5(6): e11332

    Article  PubMed  Google Scholar 

  22. Sterner DE, Berger SL (2000) Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev 64:435

    Article  PubMed  CAS  Google Scholar 

  23. Smith ER, Eisen A, Gu W, Sattah M, Pannuti A, Zhou J, Cook RG, Lucchesi JC, Allis CD (1998) ESA1 is a histone acetyltransferase that is essential for growth in yeast. Proc Natl Acad Sci USA 95:3561–3565

    Article  PubMed  CAS  Google Scholar 

  24. Li Y, Yokota T, Gama V, Yoshida T, Gomez JA, Ishikawa K, Sasaguri H, Cohen HY, Sinclair DA, Mizusawa H, Matsuyama S (2007) Bax-inhibiting peptide protects cells from polyglutamine toxicity caused by Ku70 acetylation. Cell Death Differ 14:2058–2067

    Article  PubMed  CAS  Google Scholar 

  25. Burlini N, Lamponi S, Radrizzani M, Monti E, Tortora P (1987) Identification of a phosphorylated form of phosphoenolpyruvate carboxykinase from the yeast Saccharomyces cerevisiae. Biochim Biophys Acta 930: 220–229

    Article  PubMed  CAS  Google Scholar 

  26. 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  PubMed  CAS  Google Scholar 

  27. 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(5942):834–840

    Article  PubMed  CAS  Google Scholar 

  28. 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(5968): 1000–1004

    Article  PubMed  CAS  Google Scholar 

  29. Vijg J, Campisi J (2008) Puzzles, promises and a cure for ageing. Nature 454(7208): 1065–1071

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

The work was supported by National Science Council (NSC 98-2314-B-002-031-MY3 to J.-Y.L.), National Taiwan University Hospital (099-001376 to J.-Y.L.), National Taiwan University (99C101-603 to J.-Y.L. and Y.-Y.L.), Liver Disease Prevention & Treatment Research Foundation (J.-Y.L. and Y.-Y.L.), Taiwan, and the NIH Common Fund Grant (U54-RR020839 to H.Z. and J.D.B.), USA.

Author information

Authors and Affiliations

  1. Department of Laboratory Medicine, National Taiwan University Hospital, Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan

    Jin-ying Lu

  2. Department of Oncology, National Taiwan University Hospital, Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan

    Yu-yi Lin

  3. Department of Molecular Biology and Genetics, The High Throughput Biology Center, John Hopkins University School of Medicine, Baltimore, MD, USA

    Jef D. Boeke

  4. Departments of Pharmacology, The High Throughput Biology Center, John Hopkins University School of Medicine, Baltimore, MD, USA

    Heng Zhu

  5. Department Molecular Sciences, The High Throughput Biology Center, John Hopkins University School of Medicine, Baltimore, MD, USA

    Heng Zhu

Authors
  1. Jin-ying Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yu-yi Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jef D. Boeke
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Heng Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Adolf-Butenandt-Institut, Department of Molecular Biology, Ludwig-Maximilians-Universität München, Schillerstr. 44, München, 80336, Germany

    Sandra B. Hake

  2. , Dep. of Cell & Developmental Biology, Biocenter University of Würzburg, Am Hubland, Würzburg, 97074, Germany

    Christian J. Janzen

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Lu, Jy., Lin, Yy., Boeke, J.D., Zhu, H. (2013). Using Functional Proteome Microarrays to Study Protein Lysine Acetylation. In: Hake, S., Janzen, C. (eds) Protein Acetylation. Methods in Molecular Biology, vol 981. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-305-3_12

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-305-3_12

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-304-6

  • Online ISBN: 978-1-62703-305-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation