Cellular ubiquitin pool dynamics and homeostasis

BMB Reports

Volumn 47, Issue 9, 2014, Pages 475-482

  Park, Chul Woo ^a   Ryu, Kwon Yul ^a  

^a University of Seoul   (South Korea)

Author keywords

Dynamics; Free ubiquitin; Homeostasis; Polyubiquitin gene; Ubiquitin; Ubiquitin conjugates

Indexed keywords

DEUBIQUITINASE; UBIQUITIN; UBIQUITIN CONJUGATING ENZYME; UBIQUITIN PROTEIN LIGASE;

ANIMAL; DEFICIENCY; GENETICS; HUMAN; METABOLISM; PROTEOMICS; UBIQUITINATION;

ANIMALS; HUMANS; PROTEOMICS; UBIQUITIN; UBIQUITIN-ACTIVATING ENZYMES; UBIQUITIN-CONJUGATING ENZYMES; UBIQUITIN-PROTEIN LIGASES; UBIQUITIN-SPECIFIC PROTEASES; UBIQUITINATION;

EID: 84907430840     PISSN: 19766696     EISSN: 1976670X     Source Type: Journal    
DOI: 10.5483/BMBRep.2014.47.9.128     Document Type: Short Survey

References (57)

1. Hershko, A. and Ciechanover, A. (1998) The ubiquitin system. Annu. Rev. Biochem. 67, 425-479.
2. Hicke, L. (2001) Protein regulation by monoubiquitin. Nat. Rev. Mol. Cell Biol. 2, 195-201.
3. Pickart, C. M. and Fushman, D. (2004) Polyubiquitin chains: polymeric protein signals. Curr. Opin. Chem. Biol. 8, 610-616.
4. Amerik, A. Y. and Hochstrasser, M. (2004) Mechanism and function of deubiquitinating enzymes. Biochim. Biophys. Acta 1695, 189-207.
5. Komander, D., Clague, M. J. and Urbe, S. (2009) Breaking the chains: structure and function of the deubiquitinases. Nat. Rev. Mol. Cell Biol. 10, 550-563.
6. Wiborg, O., Pedersen, M. S., Wind, A., Berglund, L. E., Marcker, K. A. and Vuust, J. (1985) The human ubiquitin multigene family: some genes contain multiple directly repeated ubiquitin coding sequences. EMBO J. 4, 755-759.
7. Baker, R. T. and Board, P. G. (1991) The human ubiquitin- 52 amino acid fusion protein gene shares several structural features with mammalian ribosomal protein genes. Nucleic Acids Res. 19, 1035-1040.
8. Redman, K. L. and Rechsteiner, M. (1989) Identification of the long ubiquitin extension as ribosomal protein S27a. Nature 338, 438-440.
9. Ohtani-Kaneko, R., Asahara, M., Takada, K., Kanda, T., Iigo, M., Hara, M., Yokosawa, H., Ohkawa, K. and Hirata, K. (1996) Nerve growth factor (NGF) induces increase in multi-ubiquitin chains and concomitant decrease in free ubiquitin in nuclei of PC12h. Neurosci. Res. 26, 349-355.
10. Ryu, K. Y., Baker, R. T. and Kopito, R. R. (2006) Ubiquitin-specific protease 2 as a tool for quantification of total ubiquitin levels in biological specimens. Anal. Biochem. 353, 153-155.
11. Fornace, A. J., Jr., Alamo, I., Jr., Hollander, M. C. and Lamoreaux, E. (1989) Ubiquitin mRNA is a major stress-induced transcript in mammalian cells. Nucleic Acids Res. 17, 1215-1230.
12. Bond, U. and Schlesinger, M. J. (1986) The chicken ubiquitin gene contains a heat shock promoter and expresses an unstable mRNA in heat-shocked cells. Mol. Cell. Biol. 6, 4602-4610.
13. Reyes-Turcu, F. E., Ventii, K. H. and Wilkinson, K. D. (2009) Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes. Annu. Rev. Biochem. 78, 363-397.
14. Yao, T. and Cohen, R. E. (2002) A cryptic protease couples deubiquitination and degradation by the proteasome. Nature 419, 403-407.
15. Verma, R., Aravind, L., Oania, R., McDonald, W. H., Yates, J. R., 3rd, Koonin, E. V. and Deshaies, R. J. (2002) Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science 298, 611-615.
16. Swaminathan, S., Amerik, A. Y. and Hochstrasser, M. (1999) The Doa4 deubiquitinating enzyme is required for ubiquitin homeostasis in yeast. Mol. Biol. Cell 10, 2583-2594.
17. Kimura, Y., Yashiroda, H., Kudo, T., Koitabashi, S., Murata, S., Kakizuka, A. and Tanaka, K. (2009) An inhibitor of a deubiquitinating enzyme regulates ubiquitin homeostasis. Cell 137, 549-559.
18. Vijay-Kumar, S., Bugg, C. E. and Cook, W. J. (1987) Structure of ubiquitin refined at 1.8 A resolution. J. Mol. Biol. 194, 531-544.
19. Weissman, A. M., Shabek, N. and Ciechanover, A. (2011) The predator becomes the prey: regulating the ubiquitin system by ubiquitylation and degradation. Nat. Rev. Mol. Cell Biol. 12, 605-620.
20. Anderson, C., Crimmins, S., Wilson, J. A., Korbel, G. A., Ploegh, H. L. and Wilson, S. M. (2005) Loss of Usp14 results in reduced levels of ubiquitin in ataxia mice. J. Neurochem. 95, 724-731.
21. Leggett, D. S., Hanna, J., Borodovsky, A., Crosas, B., Schmidt, M., Baker, R. T., Walz, T., Ploegh, H. and Finley, D. (2002) Multiple associated proteins regulate proteasome structure and function. Mol. Cell 10, 495-507.
22. Lee, M. J., Lee, B. H., Hanna, J., King, R. W. and Finley, D. (2011) Trimming of ubiquitin chains by proteasome- associated deubiquitinating enzymes. Mol. Cell. Proteomics 10, R110 003871.
23. Hanna, J., Meides, A., Zhang, D. P. and Finley, D. (2007) A ubiquitin stress response induces altered proteasome composition. Cell 129, 747-759.
24. Carlson, N., Rogers, S. and Rechsteiner, M. (1987) Microinjection of ubiquitin: changes in protein degradation in HeLa cells subjected to heat-shock. J. Cell Biol. 104, 547-555.
25. Dantuma, N. P., Groothuis, T. A., Salomons, F. A. and Neefjes, J. (2006) A dynamic ubiquitin equilibrium couples proteasomal activity to chromatin remodeling. J. Cell Biol. 173, 19-26.
26. Peng, J., Schwartz, D., Elias, J. E., Thoreen, C. C., Cheng, D., Marsischky, G., Roelofs, J., Finley, D. and Gygi, S. P. (2003) A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol. 21, 921-926.
27. Kirkpatrick, D. S., Denison, C. and Gygi, S. P. (2005) Weighing in on ubiquitin: the expanding role of mass-spectrometry-based proteomics. Nat. Cell Biol. 7, 750-757.
28. Kirkpatrick, D. S., Gerber, S. A. and Gygi, S. P. (2005) The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 35, 265-273.
29. Bennett, E. J., Shaler, T. A., Woodman, B., Ryu, K. Y., Zaitseva, T. S., Becker, C. H., Bates, G. P., Schulman, H. and Kopito, R. R. (2007) Global changes to the ubiquitin system in Huntington's disease. Nature 448, 704-708.
30. Kim, W., Bennett, E. J., Huttlin, E. L., Guo, A., Li, J., Possemato, A., Sowa, M. E., Rad, R., Rush, J., Comb, M. J., Harper, J. W. and Gygi, S. P. (2011) Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol. Cell 44, 325-340.
31. Udeshi, N. D., Mani, D. R., Eisenhaure, T., Mertins, P., Jaffe, J. D., Clauser, K. R., Hacohen, N. and Carr, S. A. (2012) Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition. Mol. Cell. Proteomics 11, 148-159.
32. Kaiser, S. E., Riley, B. E., Shaler, T. A., Trevino, R. S., Becker, C. H., Schulman, H. and Kopito, R. R. (2011) Protein standard absolute quantification (PSAQ) method for the measurement of cellular ubiquitin pools. Nat. Methods 8, 691-696.
33. Newton, K., Matsumoto, M. L., Wertz, I. E., Kirkpatrick, D. S., Lill, J. R., Tan, J., Dugger, D., Gordon, N., Sidhu, S. S., Fellouse, F. A., Komuves, L., French, D. M., Ferrando, R. E., Lam, C., Compaan, D., Yu, C., Bosanac, I., Hymowitz, S. G., Kelley, R. F. and Dixit, V. M. (2008) Ubiquitin chain editing revealed by polyubiquitin linkage- specific antibodies. Cell 134, 668-678.
34. Komander, D. (2009) The emerging complexity of protein ubiquitination. Biochem. Soc. Trans. 37, 937-953.
35. Ye, Y. and Rape, M. (2009) Building ubiquitin chains: E2 enzymes at work. Nat. Rev. Mol. Cell Biol. 10, 755-764.
36. Husnjak, K. and Dikic, I. (2012) Ubiquitin-binding proteins: decoders of ubiquitin-mediated cellular functions. Annu. Rev. Biochem. 81, 291-322.
37. Xu, P., Duong, D. M., Seyfried, N. T., Cheng, D., Xie, Y., Robert, J., Rush, J., Hochstrasser, M., Finley, D. and Peng, J. (2009) Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell 137, 133-145.
38. Finley, D., Ozkaynak, E. and Varshavsky, A. (1987) The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation, and other stresses. Cell 48, 1035-1046.
39. Hanna, J., Leggett, D. S. and Finley, D. (2003) Ubiquitin depletion as a key mediator of toxicity by translational inhibitors. Mol. Cell. Biol. 23, 9251-9261.
40. Ryu, K. Y., Maehr, R., Gilchrist, C. A., Long, M. A., Bouley, D. M., Mueller, B., Ploegh, H. L. and Kopito, R. R. (2007) The mouse polyubiquitin gene UbC is essential for fetal liver development, cell-cycle progression and stress tolerance. EMBO J. 26, 2693-2706.
41. Park, H., Yoon, M. S. and Ryu, K. Y. (2013) Disruption of polyubiquitin gene Ubc leads to defective proliferation of hepatocytes and bipotent fetal liver epithelial progenitor cells. Biochem. Biophys. Res. Commun. 435, 434-440.
42. Ryu, K. Y., Fujiki, N., Kazantzis, M., Garza, J. C., Bouley, D. M., Stahl, A., Lu, X. Y., Nishino, S. and Kopito, R. R. (2010) Loss of polyubiquitin gene Ubb leads to metabolic and sleep abnormalities in mice. Neuropathol. Appl. Neurobiol. 36, 285-299.
43. Ryu, K. Y., Garza, J. C., Lu, X. Y., Barsh, G. S. and Kopito, R. R. (2008) Hypothalamic neurodegeneration and adult-onset obesity in mice lacking the Ubb polyubiquitin gene. Proc. Natl. Acad. Sci. U.S.A. 105, 4016-4021.
44. Ryu, K. Y., Sinnar, S. A., Reinholdt, L. G., Vaccari, S., Hall, S., Garcia, M. A., Zaitseva, T. S., Bouley, D. M., Boekelheide, K., Handel, M. A., Conti, M. and Kopito, R. R. (2008) The mouse polyubiquitin gene Ubb is essential for meiotic progression. Mol. Cell. Biol. 28, 1136-1146.
45. Park, C. W., Ryu, H. W. and Ryu, K. Y. (2012) Locus coeruleus neurons are resistant to dysfunction and degeneration by maintaining free ubiquitin levels although total ubiquitin levels decrease upon disruption of polyubiquitin gene Ubb. Biochem. Biophys. Res. Commun. 418, 541-546.
46. Oh, C., Park, S., Lee, E. K. and Yoo, Y. J. (2013) Downregulation of ubiquitin level via knockdown of polyubiquitin gene Ubb as potential cancer therapeutic intervention. Sci. Rep. 3, 2623.
47. Wilkinson, K. D., Lee, K. M., Deshpande, S., Duerksen-Hughes, P., Boss, J. M. and Pohl, J. (1989) The neuron-specific protein PGP 9.5 is a ubiquitin carboxyl- terminal hydrolase. Science 246, 670-673.
48. Liu, Y., Fallon, L., Lashuel, H. A., Liu, Z. and Lansbury, P. T., Jr. (2002) The UCH-L1 gene encodes two opposing enzymatic activities that affect alpha-synuclein degradation and Parkinson's disease susceptibility. Cell 111, 209-218.
49. Saigoh, K., Wang, Y. L., Suh, J. G., Yamanishi, T., Sakai, Y., Kiyosawa, H., Harada, T., Ichihara, N., Wakana, S., Kikuchi, T. and Wada, K. (1999) Intragenic deletion in the gene encoding ubiquitin carboxy-terminal hydrolase in gad mice. Nat. Genet. 23, 47-51.
50. Gong, B., Cao, Z., Zheng, P., Vitolo, O. V., Liu, S., Staniszewski, A., Moolman, D., Zhang, H., Shelanski, M. and Arancio, O. (2006) Ubiquitin hydrolase Uch-L1 rescues beta-amyloid-induced decreases in synaptic function and contextual memory. Cell 126, 775-788.
51. Osaka, H., Wang, Y. L., Takada, K., Takizawa, S., Setsuie, R., Li, H., Sato, Y., Nishikawa, K., Sun, Y. J., Sakurai, M., Harada, T., Hara, Y., Kimura, I., Chiba, S., Namikawa, K., Kiyama, H., Noda, M., Aoki, S. and Wada, K. (2003) Ubiquitin carboxy-terminal hydrolase L1 binds to and stabilizes monoubiquitin in neuron. Hum. Mol. Genet. 12, 1945-1958.
52. Wilson, S. M., Bhattacharyya, B., Rachel, R. A., Coppola, V., Tessarollo, L., Householder, D. B., Fletcher, C. F., Miller, R. J., Copeland, N. G. and Jenkins, N. A. (2002) Synaptic defects in ataxia mice result from a mutation in Usp14, encoding a ubiquitin-specific protease. Nat. Genet. 32, 420-425.
53. Chen, P. C., Qin, L. N., Li, X. M., Walters, B. J., Wilson, J. A., Mei, L. and Wilson, S. M. (2009) The proteasome- associated deubiquitinating enzyme Usp14 is essential for the maintenance of synaptic ubiquitin levels and the development of neuromuscular junctions. J. Neurosci. 29, 10909-10919.
54. Crimmins, S., Jin, Y., Wheeler, C., Huffman, A. K., Chapman, C., Dobrunz, L. E., Levey, A., Roth, K. A., Wilson, J. A. and Wilson, S. M. (2006) Transgenic rescue of ataxia mice with neuronal-specific expression of ubiquitin- specific protease 14. J. Neurosci. 26, 11423-11431.
55. Bizzi, A., Schaetzle, B., Patton, A., Gambetti, P. and Autilio-Gambetti, L. (1991) Axonal transport of two major components of the ubiquitin system: free ubiquitin and ubiquitin carboxyl-terminal hydrolase PGP 9.5. Brain Res. 548, 292-299.
56. Chen, P. C., Bhattacharyya, B. J., Hanna, J., Minkel, H., Wilson, J. A., Finley, D., Miller, R. J. and Wilson, S. M. (2011) Ubiquitin homeostasis is critical for synaptic development and function. J. Neurosci. 31, 17505-17513.
57. Walters, B. J., Campbell, S. L., Chen, P. C., Taylor, A. P., Schroeder, D. G., Dobrunz, L. E., Artavanis-Tsakonas, K., Ploegh, H. L., Wilson, J. A., Cox, G. A. and Wilson, S. M. (2008) Differential effects of Usp14 and Uch-L1 on the ubiquitin proteasome system and synaptic activity. Mol. Cell. Neurosci. 39, 539-548.