Chemical methods for the proteome-wide identification of posttranslationally modified proteins

Current Opinion in Chemical Biology

Volumn 24, Issue , 2015, Pages 27-37

  Chuh, Kelly N ^a   Pratt, Matthew R ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE; PROTEOME; ADENOSINE DIPHOSPHATE RIBOSE; LIPID; PROTEIN;

ACETYLATION; ADENOSINE DIPHOSPHATE RIBOSYLATION; GLYCOSYLATION; LIPOGENESIS; MASS SPECTROMETRY; METHYLATION; OXIDATION; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN PROCESSING; REVIEW; ANIMAL; CHEMISTRY; HUMAN; METABOLISM; PROCEDURES; PROTEOMICS;

ACETYLATION; ADENOSINE DIPHOSPHATE RIBOSE; ANIMALS; GLYCOSYLATION; HUMANS; LIPIDS; METHYLATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; PROTEOME; PROTEOMICS;

EID: 84949117047     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2014.10.020     Document Type: Review

References (64)

1. Grammel M., Hang H.C. Chemical reporters for biological discovery. Nat Chem Biol 2013, 9:475-484.
2. Patterson D.M., Nazarova L.A., Prescher J.A. Finding the right (bioorthogonal) chemistry. ACS Chem Biol 2014, 9:592-605.
3. Essentials of Glycobiology 2009, Cold Spring Harbor Laboratory Press. A. Varki, R.D. Cummings, J.D. Esko, H.H. Freeze, P. Stanley, C.R. Bertozzi, G.W. Hart, M.E. Etzler (Eds.).
4. Saxon E., Bertozzi C. Cell surface engineering by a modified Staudinger reaction. Science 2000, 287:2007-2010.
5. Laughlin S.T., Bertozzi C.R. Imaging the glycome. Proc Natl Acad Sci U S A 2009, 106:12-17.
6. Yang L., Nyalwidhe J.O., Guo S., Drake R.R., Semmes O.J. Targeted identification of metastasis-associated cell-surface sialoglycoproteins in prostate cancer. Mol Cell Proteomics 2011, 10:M110007294.
7. Hubbard S.C., Boyce M., McVaugh C.T., Peehl D.M., Bertozzi C.R. Cell surface glycoproteomic analysis of prostate cancer-derived PC-3 cells. Bioorg Med Chem Lett 2011, 21:4945-4950.
8. Slade P.G., Hajivandi M., Bartel C.M., Gorfien S.F. Identifying the CHO secretome using mucin-type O-linked glycosylation and click-chemistry. J Proteome Res 2012, 11:6175-6186.
9. Hart G.W., Slawson C., Ramirez-Correa G., Lagerlof O. Cross talk between O-GlcNAcylation and phosphorylation: roles in signaling. Transcription, and chronic disease. Annu Rev Biochem 2011, 80:825-858.
10. Vocadlo D., Hang H., Kim E., Hanover J., Bertozzi C. A chemical approach for identifying O-GlcNAc-modified proteins in cells. Proc Natl Acad Sci U S A 2003, 100:9116-9121.
11. Hahne H., Sobotzki N., Nyberg T., Helm D., Borodkin V.S., van Aalten D.M.F., Agnew B., Kuster B. Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry. J Proteome Res 2013, 12:927-936.
12. Zaro B.W., Yang Y.-Y., Hang H.C., Pratt M.R. Chemical reporters for fluorescent detection and identification of O-GlcNAc-modified proteins reveal glycosylation of the ubiquitin ligase NEDD4-1. Proc Natl Acad Sci U S A 2011, 108:8146-8151.
13. Gurel Z., Zaro B.W., Pratt M.R., Sheibani N. Identification of O-GlcNAc modification targets in mouse retinal pericytes. PLOS ONE 2014, 9:e95561.
14. Clark P.M., Dweck J.F., Mason D.E., Hart C.R., Buck S.B., Peters E.C., Agnew B.J., Hsieh-Wilson L.C. Direct in-gel fluorescence detection and cellular imaging of O-GlcNAc-modified proteins. J Am Chem Soc 2008, 130:11576-11577.
15. Alfaro J.F., Gong C.-X., Monroe M.E., Aldrich J.T., Clauss T.R.W., Purvine S.O., Wang Z., Camp D.G., Shabanowitz J., Stanley P., et al. Tandem mass spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets. Proc Natl Acad Sci U S A 2012, 109:7280-7285.
16. Boyce M., Carrico I.S., Ganguli A.S., Yu S.-H., Hangauer M.J., Hubbard S.C., Kohler J.J., Bertozzi C.R. Metabolic cross-talk allows labeling of O-linked {beta}-N-acetylglucosamine-modified proteins via the N-acetylgalactosamine salvage pathway. Proc Natl Acad Sci U S A 2011, 108:3141-3146.
17. Palaniappan K.K., Hangauer M.J., Smith T.J., Smart B.P., Pitcher A.A., Cheng E.H., Bertozzi C.R., Boyce M. A chemical glycoproteomics platform reveals O-GlcNAcylation of mitochondrial voltage-dependent anion channel 2. Cell Rep 2013, 5:546-552.
18. Chuh K.N., Zaro B.W., Piller F., Piller V., Pratt M.R. Changes in metabolic chemical reporter structure yield a selective probe of O-GlcNAc modification. J Am Chem Soc 2014, 136:12283-12295.
19. Hang H.C., Wilson J.P., Charron G. Bioorthogonal chemical reporters for analyzing protein lipidation and lipid trafficking. Acc Chem Res 2011, 44:699-708.
20. Resh M.D. Use of analogs and inhibitors to study the functional significance of protein palmitoylation. Methods 2006, 40:191-197.
21. Wright M.H., Clough B., Rackham M.D., Rangachari K., Brannigan J.A., Grainger M., Moss D.K., Bottrill A.R., Heal W.P., Broncel M., et al. Validation of N-myristoyltransferase as an antimalarial drug target using an integrated chemical biology approach. Nat Chem 2014, 6:112-121.
22. Yount J.S., Moltedo B., Yang Y.-Y., Charron G., Moran T.M., López C.B., Hang H.C. Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3. Nat Chem Biol 2010, 6:610-614.
23. Wilson J.P., Raghavan A.S., Yang Y.-Y., Charron G., Hang H.C. Proteomic analysis of fatty-acylated proteins in mammalian cells with chemical reporters reveals S-acylation of histone H3 variants. Mol Cell Proteomics 2011, 10:M110001198.
24. Martin B.R., Wang C., Adibekian A., Tully S.E., Cravatt B.F. Global profiling of dynamic protein palmitoylation. Nat Meth 2011, 9:84-89.
25. Drisdel R.C., Green W.N. Labeling and quantifying sites of protein palmitoylation. BioTechniques 2004, 36:276-285.
26. Roth A.F., Wan J., Bailey A.O., Sun B., Kuchar J.A., Green W.N., Phinney B.S., Yates J.R., Davis N.G. Global analysis of protein palmitoylation in yeast. Cell 2006, 125:1003-1013.
27. Kang R., Wan J., Arstikaitis P., Takahashi H., Huang K., Bailey A.O., Thompson J.X., Roth A.F., Drisdel R.C., Mastro R., et al. Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation. Nature 2008, 456:904-909.
28. Ivaldi C., Martin B.R., Kieffer-Jaquinod S., Chapel A., Levade T., Garin J., Journet A. Proteomic analysis of S-acylated proteins in human B cells reveals palmitoylation of the immune regulators CD20 and CD23. PLoS ONE 2012, 7:e37187.
29. Jones M.L., Collins M.O., Goulding D., Choudhary J.S., Rayner J.C. Analysis of protein palmitoylation reveals a pervasive role in Plasmodium development and pathogenesis. Cell Host Microbe 2012, 12:246-258.
30. Wan J., Savas J.N., Roth A.F., Sanders S.S., Singaraja R.R., Hayden M.R., Yates J.R., Davis N.G. Tracking brain palmitoylation change: predominance of glial change in a mouse model of Huntington's disease. Chem Biol 2013, 20:1421-1434.
31. Resh M.D. Trafficking and signaling by fatty-acylated and prenylated proteins. Nat Chem Biol 2006, 2:584-590.
32. DeGraw A.J., Palsuledesai C., Ochocki J.D., Dozier J.K., Lenevich S., Rashidian M., Distefano M.D. Evaluation of alkyne-modified isoprenoids as chemical reporters of protein prenylation. Chem Biol Drug Des 2010, 76:460-471.
33. Charron G., Tsou L.K., Maguire W., Yount J.S., Hang H.C. Alkynyl-farnesol reporters for detection of protein S-prenylation in cells. Mol Biosyst 2011, 7:67-73.
34. Charron G., Li M.M.H., MacDonald M.R., Hang H.C. Prenylome profiling reveals S-farnesylation is crucial for membrane targeting and antiviral activity of ZAP long-isoform. Proc Natl Acad Sci U S A 2013, 110:11085-11090.
35. Shahbazian M.D., Grunstein M. Functions of site-specific histone acetylation and deacetylation. Annu Rev Biochem 2007, 76:75-100.
36. Yang X.-J., Seto E. Lysine acetylation: codified crosstalk with other posttranslational modifications. Mol Cell 2008, 31:449-461.
37. Yang Y.-Y., Ascano J.M., Hang H.C. Bioorthogonal chemical reporters for monitoring protein acetylation. J Am Chem Soc 2010, 132:3640-3641.
38. Yu-Ying Y., Markus G., Howard H.C. Identification of lysine acetyltransferase p300 substrates using 4-pentynoyl-coenzyme A and bioorthogonal proteomics. Bioorg Med Chem Lett 2011, 21:4976-4979.
39. Lin H., Su X., He B. Protein lysine acylation and cysteine succination by intermediates of energy metabolism. ACS Chem Biol 2012, 7:947-960.
40. Bao X., Zhao Q., Yang T., Fung Y.M.E., Li X.D. A chemical probe for lysine malonylation. Angew Chem Int Ed 2013, 52:4883-4886.
41. Alfonso L.F., Srivenugopal K.S., Bhat G.J. Does aspirin acetylate multiple cellular proteins? (Review). Mol Med Rep 2009, 2:533-537.
42. Bateman L.A., Zaro B.W., Miller S.M., Pratt M.R. An alkyne-aspirin chemical reporter for the detection of aspirin-dependent protein modification in living cells. J Am Chem Soc 2013, 135:14568-14573.
43. Greer E.L., Shi Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nat Rev Genet 2012, 13:343-357.
44. Bedford M.T., Clarke S.G. Protein arginine methylation in mammals: who, what, and why. Mol Cell 2009, 33:1-13.
45. Peters W., Willnow S., Duisken M., Kleine H., Macherey T., Duncan K.E., Litchfield D.W., Lüscher B., Weinhold E. Enzymatic site-specific functionalization of protein methyltransferase substrates with alkynes for click labeling. Angew Chem Int Ed Engl 2010, 10.1002/anie.201001240.
46. Binda O., Boyce M., Rush J.S., Palaniappan K.K., Bertozzi C.R., Gozani O. A chemical method for labeling lysine methyltransferase substrates. ChemBioChem 2011, 12:330-334.
47. Luo M. Current chemical biology approaches to interrogate protein methyltransferases. ACS Chem Biol 2012, 7:443-463.
48. Islam K., Chen Y., Wu H., Bothwell I.R., Blum G.J., Zeng H., Dong A., Zheng W., Min J., Deng H., et al. Defining efficient enzyme-cofactor pairs for bioorthogonal profiling of protein methylation. Proc Natl Acad Sci U S A 2013, 110:16778-16783.
49. Wang R., Islam K., Liu Y., Zheng W., Tang H., Lailler N., Blum G., Deng H., Luo M. Profiling genome-wide chromatin methylation with engineered posttranslation apparatus within living cells. J Am Chem Soc 2013, 135:1048-1056.
50. Willnow S., Martin M., Lüscher B., Weinhold E. A selenium-based click AdoMet analogue for versatile substrate labeling with wild-type protein methyltransferases. ChemBioChem 2012, 13:1167-1173.
51. Bothwell I.R., Islam K., Chen Y., Zheng W., Blum G., Deng H., Luo M. Se-adenosyl-l-selenomethionine cofactor analogue as a reporter of protein methylation. J Am Chem Soc 2012, 134:14905-14912.
52. Gibson B.A., Kraus W.L. New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs. Nat Rev Mol Cell Biol 2012, 13:411-424.
53. Du J., Jiang H., Lin H. Investigating the ADP-ribosyltransferase activity of sirtuins with NAD analogues and 32P-NAD. Biochemistry 2009, 48:2878-2890.
54. Jiang H., Kim J.H., Frizzell K.M., Kraus W.L., Lin H. Clickable NAD analogues for labeling substrate proteins of poly(ADP-ribose) polymerases. J Am Chem Soc 2010, 132:9363-9372.
55. Carter-O'Connell I., Jin H., Morgan R.K., David L.L., Cohen M.S. Engineering the substrate specificity of ADP-ribosyltransferases for identifying direct protein targets. J Am Chem Soc 2014, 10.1021/ja412897.
56. Yarbrough M.L., Li Y., Kinch L.N., Grishin N.V., Ball H.L., Orth K. AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signaling. Science 2009, 323:269-272.
57. Grammel M., Luong P., Orth K., Hang H.C. A chemical reporter for protein AMPylation. J Am Chem Soc 2011, 133:17103-17105.
58. Antelmann H., Helmann J.D. Thiol-based redox switches and gene regulation. Antioxid Redox Signal 2011, 14:1049-1063.
59. Saurin A.T., Neubert H., Brennan J.P., Eaton P. Widespread sulfenic acid formation in tissues in response to hydrogen peroxide. Proc Natl Acad Sci U S A 2004, 101:17982-17987.
60. Tyther R., Ahmeda A., Johns E., McDonagh B., Sheehan D. Proteomic profiling of perturbed protein sulfenation in renal medulla of the spontaneously hypertensive rat. J Proteome Res 2010, 9:2678-2687.
61. Paulsen C.E., Truong T.H., Garcia F.J., Homann A., Gupta V., Leonard S.E., Carroll K.S. Peroxide-dependent sulfenylation of the EGFR catalytic site enhances kinase activity. Nat Chem Biol 2011, 8:57-64.
62. Jaffrey S.R., Erdjument-Bromage H., Ferris C.D., Tempst P., Snyder S.H. Protein S-nitrosylation: a physiological signal for neuronal nitric oxide. Nat Cell Biol 2001, 3:193-197.
63. Forrester M.T., Thompson J.W., Foster M.W., Nogueira L., Moseley M.A., Stamler J.S. Proteomic analysis of S-nitrosylation and denitrosylation by resin-assisted capture. Nat Biotechnol 2009, 27:557-559.
64. Zaro B.W., Chuh K.N., Pratt M.R. Chemical reporter for visualizing metabolic cross-talk between carbohydrate metabolism and protein modification. ACS Chem Biol 2014, 9:1991-1996.