Post-translational modification of proteins in toxicological research: Focus on lysine acylation

Toxicological Research

Volumn 29, Issue 2, 2013, Pages 81-86

  Lee, Sangkyu ^a  

^a Kyungpook National University   (South Korea)

Author keywords

Lysine acylation; Post translational modification; Toxicoproteomics

Indexed keywords

EID: 84886296491     PISSN: 19768257     EISSN: 22342753     Source Type: Journal    
DOI: 10.5487/TR.2013.29.2.081     Document Type: Article

References (49)

1. Walsh, C.T., Garneau-Tsodikova, S. and Gatto, G.J. Jr. (2005) Protein posttranslational modifications: the chemistry of proteome diversifications. Angew. Chem. Int. Ed. Engl., 44, 7342- 7372.
2. Mann, M. and Jensen, O.N. (2003) Proteomic analysis of post-translational modifications. Nat. Biotechnol., 21, 255-261.
3. Cantin, G.T. and Yates, J.R. 3rd. (2004) Strategies for shotgun identification of post-translational modifications by mass spectrometry. J. Chromatogr. A, 1053, 7-14.
4. Lu, Z., Cheng, Z., Zhao, Y. and Volchenboum, S.L. (2011c) Bioinformatic analysis and post-translational modification crosstalk prediction of lysine acetylation. PLoS One, 6, e28228.
5. Keck, J.M., Jones, M.H., Wong, C.C., Binkley, J., Chen, D., Jaspersen, S.L., Holinger, E.P., Xu, T., Niepel, M., Rout, M.P., Vogel, J., Sidow, A., Yates, J.R. 3rd. and Winey, M. (2011) A cell cycle phosphoproteome of the yeast centrosome. Science, 332, 1557-1561.
6. Hunter, T. (2000) Signaling-2000 and beyond. Cell, 100, 113-127.
7. Olsen, J.V., Vermeulen, M., Santamaria, A., Kumar, C., Miller, M.L., Jensen, L.J., Gnad, F., Cox, J., Jensen, T.S., Nigg, E.A., Brunak, S. and Mann, M. (2010) Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci. Signaling, 3, ra3.
8. Norris, K.L., Lee, J.Y. and Yao, T.P. (2009) Acetylation goes global: the emergence of acetylation biology. Sci. Signaling, 2, pe76.
9. Kim, S.C., Sprung, R., Chen, Y., Xu, Y., Ball, H., Pei, J., Cheng, T., Kho, Y., Xiao, H., Xiao, L., Grishin, N.V., White, M., Yang, X.J. and Zhao, Y. (2006) Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol. Cell., 23, 607-618.
10. Choudhary, C., Kumar, C., Gnad, F., Nielsen, M.L., Rehman, M., Walther, T.C., Olsen, J.V. and Mann, M. (2009) Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science, 325, 834-840.
11. Lin, H., Su, X. and He, B. (2012) Protein lysine acylation and cysteine succination by intermediates of energy metabolism. ACS Chem. Biol., 7, 947-960.
12. Lu, J.Y., Lin, Y.Y., Sheu, J.C., Wu, J.T., Lee, F.J., Chen, Y., Lin, M.I., Chiang, F.T., Tai, T.Y., Berger, S.L., Zhao, Y., Tsai, K.S., Zhu, H., Chuang, L.M. and Boeke, J.D. (2011a) Acetylation of yeast AMPK controls intrinsic aging independently of caloric restriction. Cell, 146, 969-979.
13. Chuang, C., Lin, S.H., Huang, F., Pan, J., Josic, D. and Yu-Lee, L.Y. (2010) Acetylation of RNA processing proteins and cell cycle proteins in mitosis. J. Proteome Res., 9, 4554-4564.
14. Carafa, V., Nebbioso, A. and Altucci, L. (2012) Sirtuins and disease: the road ahead. Front. Pharmacol., 3, 4.
15. Wang, Q., Zhang, Y., Yang, C., Xiong, H., Lin, Y., Yao, J., Li, H., Xie, L., Zhao, W., Yao, Y., Ning, Z.B., Zeng, R., Xiong, Y., Guan, K.L., Zhao, S. and Zhao, G.P. (2010) Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science, 327, 1004-1007.
16. 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, S.M., He, F., Qin, L., Chin, J., Yang, P., Chen, X., Lei, Q., Xiong, Y. and Guan, K.L. (2010) Regulation of cellular metabolism by protein lysine acetylation. Science, 327, 1000-1004.
17. Chen, Y., Sprung, R., Tang, Y., Ball, H., Sangras, B., Kim, S.C., Falck, J.R., Peng, J., Gu, W. and Zhao, Y. (2007) Lysine propionylation and butyrylation are novel post-translational modifications in histones. Mol. Cell. Proteomics, 6, 812-819.
18. Cronican, A.A., Fitz, N.F., Carter, A., Saleem, M., Shiva, S., Barchowsky, A., Koldamova, R., Schug, J. and Lefterov, I. (2013) Genome-wide alteration of histone H3K9 acetylation pattern in mouse offspring prenatally exposed to arsenic. PLoS One, 8, e53478.
19. Sebastián, C., Zwaans, B.M., Silberman, D.M., Gymrek, M., Goren, A., Zhong, L., Ram, O., Truelove, J., Guimaraes, A.R., Toiber, D., Cosentino, C., Greenson, J.K., MacDonald, A.I., McGlynn, L., Maxwell, F., Edwards, J., Giacosa, S., Guccione, E., Weissleder, R., Bernstein, B.E., Regev, A., Shiels, P.G., Lombard, D.B. and Mostoslavsky, R. (2012) The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell, 151, 1185-1199.
20. Lu, Z., Bourdi, M., Li, J.H., Aponte, A.M., Chen, Y., Lombard, D.B., Gucek, M., Pohl, L.R. and Sack, M.N. (2011b) SIRT3-dependent deacetylation exacerbates acetaminophen hepatotoxicity. EMBO Rep., 12, 840-846
21. Peserico, A and Simone, C. (2011) Physical and functional HAT/HDAC interplay regulates protein acetylation balance. J. Biomed. Biotechnol., 2011, 371832.
22. Yang, X.J. and Seto, E. (2008) Lysine acetylation: codified crosstalk with other posttranslational modifications. Mol. Cell., 31, 449-461. 23. Shepard, B.D. and Tuma, P.L. (2009) Alcohol-induced protein hyperacetylation: mechanisms and consequences. World J. Gastroenterol., 15, 1219-1230.
23. Shepard, B.D. and Tuma, P.L. (2009) Alcohol-induced protein hyperacetylation: mechanisms and consequences. World J. Gastroenterol., 15, 1219-1230.
24. Fritz, K.S., Galligan, J.J., Hirschey, M.D., Verdin, E. and Petersen, D.R. (2012) Mitochondrial acetylome analysis in a mouse model of alcohol-induced liver injury utilizing SIRT3 knockout mice. J. Proteome Res., 11, 1633-1643.
25. You, M., Liang, X., Ajmo, J.M. and Ness, G.C. (2008) Involvement of mammalian sirtuin 1 in the action of ethanol in the liver. Am. J. Physiol. Gastrointest. Liver Physiol., 294, G892-G898.
26. Shimazu, T., Hirschey, M.D., Hua, L., Dittenhafer-Reed, K.E., Schwer, B., Lombard, D.B., Li, Y., Bunkenborg, J., Alt, F.W., Denu, J.M., Jacobson, M.P. and Verdin, E. (2010) SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production. Cell Metab., 12, 654-661.
27. Qiu, X., Brown, K., Hirschey, M.D., Verdin, E. and Chen, D. (2010) Calorie restriction reduces oxidative stress by SIRT3-mediated SOD2 activation. Cell Metab., 12, 662-667.
28. Hirschey, M.D., Shimazu, T., Goetzman, E., Jing, E., Schwer, B., Lombard, D.B., Grueter, C.A., Harris, C., Biddinger, S., Ilkayeva, O.R., Stevens, R.D., Li, Y., Saha, A.K., Ruderman, N.B., Bain, J.R., Newgard, C.B., Farese, R.V. Jr., Alt, F.W., Kahn, C.R. and Verdin, E. (2010) SIRT3 regulates mitochondrial fatty-acid oxidation by reversible enzyme deacetylation. Nature, 464, 121-125.
29. Kendrick, A.A., Choudhury, M., Rahman, S.M., McCurdy, C.E., Friederich, M., Van Hove, J.L., Watson, P.A., Birdsey, N., Bao, J., Gius, D., Sack, M.N., Jing, E., Kahn, C.R., Friedman, J.E. and Jonscher, K.R. (2011) Fatty liver is associated with reduced SIRT3 activity and mitochondrial protein hyperacetylation. Biochem. J., 433, 505-514.
30. Jo, W.J., Ren, X., Chu, F., Aleshin, M., Wintz, H., Burlingame, A., Smith, M.T., Vulpe, C.D. and Zhang, L. (2009) Acetylated H4K16 by MYST1 protects UROtsa cells from arsenic toxicity and is decreased following chronic arsenic exposure. Toxicol. Appl. Pharmacol., 241, 294-302.
31. Wilkins, M.R., Gasteiger, E., Gooley, A.A., Herbert, B.R., Molloy, M.P., Binz, P.A., Ou, K., Sanchez, J.C., Bairoch, A., Williams, K.L. and Hochstrasser, D.F. (1999) High-throughput mass spectrometric discovery of protein post-translational modifications. J. Mol. Biol., 289, 645-657.
32. Osés-Prieto, J.A., Zhang, X. and Burlingame, A.L. (2007) Formation of epsilon-formyllysine on silver-stained proteins: implications for assignment of isobaric dimethylation sites by tandem mass spectrometry. Mol. Cell. Proteomics, 6, 181-192.
33. Wisniewski, J.R., Zougman, A. and Mann, M. (2008) Nepsilon-formylation of lysine is a widespread post-translational modification of nuclear proteins occurring at residues involved in regulation of chromatin function. Nucleic Acids Res., 36, 570-577.
34. Cai, H. and Guengerich, F.P. (2000) Acylation of protein lysines by trichloroethylene oxide. Chem. Res. Toxicol., 13, 327-335.
35. Jiang, T., Zhou, X., Taghizadeh, K., Dong, M. and Dedon, P.C. (2007) N-formylation of lysine in histone proteins as a secondary modification arising from oxidative DNA damage. Proc. Natl. Acad. Sci. U.S.A., 104, 60-65.
36. Eilstein, J., Giménez-Arnau, E., Duché, D., Rousset, F. and Lepoittevin, J.P. (2007) Mechanistic studies on the lysineinduced N-formylation of 2,5-dimethyl-p-benzoquinonediimine. Chem. Res. Toxicol., 20, 1155-1161.
37. Zhang, K., Chen, Y., Zhang, Z. and Zhao, Y. (2009) Identification and verification of lysine propionylation and butyrylation in yeast core histones using PTMap software. J. Proteome Res., 8, 900-906.
38. Cheng, Z., Tang, Y., Chen, Y., Kim, S., Liu, H., Li, S.S., Gu, W. and Zhao, Y. (2009) Molecular characterization of propionyllysines in non-histone proteins. Mol. Cell. Proteomics, 8, 45-52.
39. Liu, B., Lin, Y., Darwanto, A., Song, X., Xu, G. and Zhang, K. (2009) Identification and characterization of propionylation at histone H3 lysine 23 in mammalian cells. J. Biol. Chem., 284, 32288-32295.
40. Es-Haghi, A., Shariatizi, S., Ebrahim-Habibi, A. and Nemat-Gorgani, M. (2012) Amyloid fibrillation in native and chemically-modified forms of carbonic anhydrase II: role of surface hydrophobicity. Biochim. Biophys. Acta, 1824, 468-477.
41. Peng, C., Lu, Z., Xie, Z., Cheng, Z., Chen, Y., Tan, M., Luo, H., Zhang, Y., He, W., Yang, K., Zwaans, B.M., Tishkoff, D., Ho, L., Lombard, D., He, T.C., Dai, J., Verdin, E., Ye, Y. and Zhao, Y. (2011) The first identification of lysine malonylation substrates and its regulatory enzyme. Mol. Cell. Proteomics, 10, M111.012658.
42. Xie, Z., Dai, J., Dai, L., Tan, M., Cheng, Z., Wu, Y., Boeke, J.D. and Zhao, Y. (2012) Lysine succinylation and lysine malonylation in histones. Mol. Cell. Proteomics, 11, 100-107.
43. Newman, J.C., He, W. and Verdin, E. (2012) Mitochondrial protein acylation and intermediary metabolism: regulation by sirtuins and implications for metabolic disease. J. Biol. Chem., 287, 42436-42443.
44. Saggerson, D. (2008) Malonyl-CoA, a key signaling molecule in mammalian cells. Annu. Rev. Nutr., 28, 253-272.
45. Montellier, E., Rousseaux, S., Zhao, Y. and Khochbin, S. (2012) Histone crotonylation specifically marks the haploid male germ cell gene expression program: post-meiotic malespecific gene expression. BioEssays, 34, 187-193.
46. Tan, M., Luo, H., Lee, S., Jin, F., Yang, J.S., Montellier, E., Buchou, T., Cheng, Z., Rousseaux, S., Rajagopal, N., Lu, Z., Ye, Z., Zhu, Q., Wysocka, J., Ye, Y., Khochbin, S., Ren, B. and Zhao, Y. (2011) Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell, 146, 1016-1028.
47. George, J., Singh, R., Mahmood, Z. and Shukla, Y. (2010) Toxicoproteomics: new paradigms in toxicology research. Toxicol. Mech. Methods, 20, 415-423.
48. Wetmore, B.A. and Merrick, B.A. (2004) Toxicoproteomics: proteomics applied to toxicology and pathology. Toxicol. Pathol., 32, 619-642.
49. Beltrao, P., Albanèse, V., Kenner, L.R., Swaney, D.L., Burlingame, A., Villèn, J., Lim, W.A., Fraser, J.S., Frydman, J. and Krogan, N.J. (2012) Systematic functional prioritization of protein posttranslational modifications. Cell, 150, 413-425.