Using functional proteome microarrays to study protein lysine acetylation

Methods in Molecular Biology

Volumn 981, Issue , 2013, Pages 151-165

  Lu, Jin Ying ^a   Lin, Yu Yi ^a   Boeke, Jef D ^b   Zhu, Heng ^b  

^a NATIONAL TAIWAN UNIVERSITY HOSPITAL   (Taiwan)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Aging; Functional proteome microarray; Longevity; Lysine acetylation; Posttranslational modification; Protein chip

Indexed keywords

HISTONE ACETYLTRANSFERASE; LYSINE; PROTEOME; FUNGAL PROTEIN;

ACETYLATION; ARTICLE; CELL METABOLISM; CONTROLLED STUDY; FUNGAL CELL CULTURE; IN VITRO STUDY; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN MICROARRAY; PROTEIN PROCESSING; PROTEIN PURIFICATION; CHEMISTRY; ENZYMOLOGY; GENETICS; METABOLISM; METHODOLOGY; YEAST;

ACETYLATION; FUNGAL PROTEINS; HISTONE ACETYLTRANSFERASES; LYSINE; PROTEIN ARRAY ANALYSIS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; YEASTS;

MLCS; MLOWN;

EID: 84880251478     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-305-3_12     Document Type: Article

References (29)

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
2. Chen C, Zhu H (2006) Protein microarrays. Biotechniques 40:432-439
3. Tao SC, Chen CS, Zhu H (2007) Applications of protein microarray technology. Comb Chem High Throughput Screen 10:706-718
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
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
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
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
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
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
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
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
12. Ptacek J, Devgan G, Michaud G, Zhu H et al (2005) Global analysis of protein phosphorylation in yeast. Nature 438:679-684
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
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
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
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
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
18. Thao S, Chen CS, Zhu H, Escalante-Semerena JC (2010) Ne-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity. PLoS One 5(12):15123
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
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
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
22. Sterner DE, Berger SL (2000) Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev 64:435
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
24. Li Y, Yokota T, Gama V, Yoshida T, Gomez JA, Ishikawa K, Sasaguri H, Cohen HY, Sinclair DA, Mizusawa H, Matsuyama S (2007) Baxinhibiting peptide protects cells from polyglutamine toxicity caused by Ku70 acetylation. Cell Death Differ 14:2058-2067
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
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
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
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
29. Vijg J, Campisi J (2008) Puzzles, promises and a cure for ageing. Nature 454(7208): 1065-1071