A fluorescence assay for elucidating the substrate specificities of deubiquitinating enzymes

Biochemical and Biophysical Research Communications

Volumn 416, Issue 1-2, 2011, Pages 76-79

  Yin, Si Tao ^a,b   Huang, Hao ^a,b   Zhang, Yu Hang ^a   Zhou, Zi Ren ^a   Song, Ai Xin ^a   Hong, Fa Shui ^b   Hu, Hong Yu ^a  

^a INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

^b MEDICAL COLLEGE OF SOOCHOW UNIVERSITY   (China)

Author keywords

Deubiquitinating enzyme; Fluorescence; Ni 2+ NTA affinity; Substrate specificity; Ubiquitin C terminal hydrolase

Indexed keywords

UBIQUITIN THIOLESTERASE; UBIQUITIN THIOLESTERASE 37; UBIQUITIN THIOLESTERASE L1; UBIQUITIN THIOLESTERASE L3; UBIQUITIN THIOLESTERASE L5; UNCLASSIFIED DRUG;

ARTICLE; ENZYME ACTIVITY; ENZYME SPECIFICITY; FLUORESCENCE; FUSION GENE; HYDROLYSIS; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS;

CARBOXYPEPTIDASES; CYSTEINE ENDOPEPTIDASES; HUMANS; SPECTROMETRY, FLUORESCENCE; SUBSTRATE SPECIFICITY; UBIQUITIN THIOLESTERASE;

EID: 83055186369     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2011.10.147     Document Type: Article

References (29)

1. Hershko A., Ciechanover A. The ubiquitin system. Annu. Rev. Biochem. 1998, 67:425-479.
2. Hochstrasser M. Protein degradation or regulation: Ub the judge. Cell 1996, 84:813-815.
3. Nijman S.M., Luna-Vargas M.P., Velds A., Brummelkamp T.R., Dirac A.M., Sixma T.K., Bernards R. A genomic and functional inventory of deubiquitinating enzymes. Cell 2005, 123:773-786.
4. Amerik A.Y., Hochstrasser M. Mechanism and function of deubiquitinating enzymes. Biochim. Biophys. Acta 2004, 1695:189-207.
5. D'Andrea A., Pellman D. Deubiquitinating enzymes: a new class of biological regulators. Crit. Rev. Biochem. Mol. Biol. 1998, 33:337-352.
6. Komander D., Clague M.J., Urbe S. Breaking the chains: structure and function of the deubiquitinases. Nat. Rev. Mol. Cell Biol. 2009, 10:550-563.
7. Reyes-Turcu F.E., Ventii K.H., Wilkinson K.D. Regulation and cellular roles of ubiquitin-specific deubiquitinating enzymes. Annu. Rev. Biochem. 2009, 78:363-397.
8. Layfield R., Franklin K., Landon M., Walker G., Wang P., Ramage R., Brown A., Love S., Urquhart K., Muir T., Baker R., Mayer R.J. Chemically synthesized ubiquitin extension proteins detect distinct catalytic capacities of deubiquitinating enzymes. Anal. Biochem. 1999, 274:40-49.
9. Drag M., Mikolajczyk J., Bekes M., Reyes-Turcu F.E., Ellman J.A., Wilkinson K.D., Salvesen G.S. Positional-scanning fluorigenic substrate libraries reveal unexpected specificity determinants of DUBs (deubiquitinating enzymes). Biochem. J. 2008, 415:367-375.
10. Hassiepen U., Eidhoff U., Meder G., Bulber J.F., Hein A., Bodendorf U., Lorthiois E., Martoglio B. A sensitive fluorescence intensity assay for deubiquitinating proteases using ubiquitin-rhodamine110-glycine as substrate. Anal. Biochem. 2007, 371:201-207.
11. Dang L.C., Melandri F.D., Stein R.L. Kinetic and mechanistic studies on the hydrolysis of ubiquitin C-terminal 7-amido-4-methylcoumarin by deubiquitinating enzymes. Biochemistry 1998, 37:1868-1879.
12. Nicholson B., Leach C.A., Goldenberg S.J., Francis D.M., Kodrasov M.P., Tian X., Shanks J., Sterner D.E., Bernal A., Mattern M.R., Wilkinson K.D., Butt T.R. Characterization of ubiquitin and ubiquitin-like-protein isopeptidase activities. Protein Sci. 2008, 17:1035-1043.
13. Pilon A., Yost P., Chase T.E., Lohnas G., Burkett T., Roberts S., Bentley W.E. Ubiquitin fusion technology: bioprocessing of peptides. Biotechnol. Prog. 1997, 13:374-379.
14. Horton R.A., Strachan E.A., Vogel K.W., Riddle S.M. A substrate for deubiquitinating enzymes based on time-resolved fluorescence resonance energy transfer between terbium and yellow fluorescent protein. Anal. Biochem. 2007, 360:138-143.
15. Martin S.F., Hattersley N., Samuel I.D., Hay R.T., Tatham M.H. A fluorescence-resonance-energy-transfer-based protease activity assay and its use to monitor paralog-specific small ubiquitin-like modifier processing. Anal. Biochem. 2007, 363:83-90.
16. Tirat A., Schilb A., Riou V., Leder L., Gerhartz B., Zimmermann J., Worpenberg S., Eidhoff U., Freuler F., Stettler T., Mayr L., Ottl J., Leuenberger B., Filipuzzi I. Synthesis and characterization of fluorescent ubiquitin derivatives as highly sensitive substrates for the deubiquitinating enzymes UCH-L3 and USP-2. Anal. Biochem. 2005, 343:244-255.
17. Mason D.E., Ek J., Peters E.C., Harris J.L. Substrate profiling of deubiquitin hydrolases with a positional scanning library and mass spectrometry. Biochemistry 2004, 43:6535-6544.
18. Larsen C.N., Krantz B.A., Wilkinson K.D. Substrate specificity of deubiquitinating enzymes: ubiquitin C-terminal hydrolases. Biochemistry 1998, 37:3358-3368.
19. Raasi S., Pickart C.M. Ubiquitin chain synthesis. Methods Mol. Biol. 2005, 301:47-55.
20. Song A.X., Zhou C.J., Peng Y., Gao X.C., Zhou Z.R., Fu Q.S., Hong J., Lin D.H., Hu H.Y. Structural transformation of the tandem ubiquitin-interacting motifs in ataxin-3 and their cooperative interactions with ubiquitin chains. PLoS One 2010, 5:e13202.
21. Zhou Z.R., Gao H.C., Zhou C.J., Chang Y.G., Hong J., Song A.X., Lin D.H., Hu H.Y. Differential ubiquitin binding of the UBA domains from human c-Cbl and Cbl-b: NMR structural and biochemical insights. Protein Sci. 2008, 17:1805-1814.
22. Khorasanizadeh S., Peters I.D., Butt T.R., Roder H. Folding and stability of a tryptophan-containing mutant of ubiquitin. Biochemistry 1993, 32:7054-7063.
23. Luchansky S.J., Lansbury P.T., Stein R.L. Substrate recognition and catalysis by UCH-L1. Biochemistry 2006, 45:14717-14725.
24. Qiu X.B., Ouyang S.Y., Li C.J., Miao S., Wang L., Goldberg A.L. HRpn13/ADRM1/GP110 is a novel proteasome subunit that binds the deubiquitinating enzyme, UCH37. EMBO J. 2006, 25:5742-5753.
25. Hamazaki J., Iemura S., Natsume T., Yashiroda H., Tanaka K., Murata S. A novel proteasome interacting protein recruits the deubiquitinating enzyme UCH37 to 26S proteasomes. EMBO J. 2006, 25:4524-4536.
26. Nishio K., Kim S.W., Kawai K., Mizushima T., Yamane T., Hamazaki J., Murata S., Tanaka K., Morimoto Y. Crystal structure of the de-ubiquitinating enzyme UCH37 (human UCH-L5) catalytic domain. Biochem. Biophys. Res. Commun. 2009, 390:855-860.
27. Yao T., Song L., Xu W., DeMartino G.N., Florens L., Swanson S.K., Washburn M.P., Conaway R.C., Conaway J.W., Cohen R.E. Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1. Nat. Cell Biol. 2006, 8:994-1002.
28. Z.R. Zhou, Zhang, Y. H., Liu, S., Song, A. X., Hu, H. Y., Length of the active-site crossover loop defines the substrate specificity of ubiquitin C-terminal hydrolases for ubiquitin chains. Biochemical J. (2011).
29. Kang S.H., Park J.J., Chung S.S., Bang O.S., Chung C.H. Strategies for assaying deubiquitinating enzymes. Methods Enzymol. 2005, 398:500-508.