Skip to main content
Biochemical Journal logoLink to Biochemical Journal
. 2002 Oct 1;367(Pt 1):87–95. doi: 10.1042/BJ20011851

Structural and functional characterization of the USP11 deubiquitinating enzyme, which interacts with the RanGTP-associated protein RanBPM.

Haruko Ideguchi 1, Atsuhisa Ueda 1, Masatsugu Tanaka 1, Jun Yang 1, Takashi Tsuji 1, Shigeru Ohno 1, Eri Hagiwara 1, Akiko Aoki 1, Yoshiaki Ishigatsubo 1
PMCID: PMC1222860  PMID: 12084015

Abstract

RanBPM is a RanGTP-binding protein required for correct nucleation of microtubules. To characterize the mechanism, we searched for RanBPM-binding proteins by using a yeast two-hybrid method and isolated a cDNA encoding the ubiquitin-specific protease USP11. The full-length cDNA of USP11 was cloned from a Jurkat cell library. Sequencing revealed that USP11 possesses Cys box, His box, Asp and KRF domains, which are highly conserved in many ubiquitin-specific proteases. By immunoblotting using HeLa cells, we concluded that 921-residue version of USP11 was the predominant form, and USP11 may be a ubiquitous protein in various human tissues. By immunofluorescence assay, USP11 primarily was localized in the nucleus of non-dividing cells, suggesting an association between USP11 and RanBPM in the nucleus. Furthermore, the association between USP11 and RanBPM in vivo was confirmed not only by yeast two-hybrid assay but also by co-immunoprecipitation assays using exogenously expressed USP11 and RanBPM. We next revealed proteasome-dependent degradation of RanBPM by pulse-chase analysis using proteasome inhibitors. In fact, ubiquitinated RanBPM was detected by both in vivo and in vitro ubiquitination assays. Finally, ubiquitin conjugation to RanBPM was inhibited in a dose-dependent manner by the addition of recombinant USP11. We conclude that RanBPM was the enzymic substrate for USP11 and was deubiquitinated specifically.

Full Text

The Full Text of this article is available as a PDF (323.3 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Baek S. H., Choi K. S., Yoo Y. J., Cho J. M., Baker R. T., Tanaka K., Chung C. H. Molecular cloning of a novel ubiquitin-specific protease, UBP41, with isopeptidase activity in chick skeletal muscle. J Biol Chem. 1997 Oct 10;272(41):25560–25565. doi: 10.1074/jbc.272.41.25560. [DOI] [PubMed] [Google Scholar]
  2. Baker R. T., Tobias J. W., Varshavsky A. Ubiquitin-specific proteases of Saccharomyces cerevisiae. Cloning of UBP2 and UBP3, and functional analysis of the UBP gene family. J Biol Chem. 1992 Nov 15;267(32):23364–23375. [PubMed] [Google Scholar]
  3. Baker R. T., Wang X. W., Woollatt E., White J. A., Sutherland G. R. Identification, functional characterization, and chromosomal localization of USP15, a novel human ubiquitin-specific protease related to the UNP oncoprotein, and a systematic nomenclature for human ubiquitin-specific proteases. Genomics. 1999 Aug 1;59(3):264–274. doi: 10.1006/geno.1999.5879. [DOI] [PubMed] [Google Scholar]
  4. Brandau O., Nyakatura G., Jedele K. B., Platzer M., Achatz H., Ross M., Murken J., Rosenthal A., Meindl A. UHX1 and PCTK1: precise characterisation and localisation within a gene-rich region in Xp11.23 and evaluation as candidate genes for retinal diseases mapped to Xp21.1-p11.2. Eur J Hum Genet. 1998 Sep-Oct;6(5):459–466. doi: 10.1038/sj.ejhg.5200207. [DOI] [PubMed] [Google Scholar]
  5. Carazo-Salas R. E., Gruss O. J., Mattaj I. W., Karsenti E. Ran-GTP coordinates regulation of microtubule nucleation and dynamics during mitotic-spindle assembly. Nat Cell Biol. 2001 Mar;3(3):228–234. doi: 10.1038/35060009. [DOI] [PubMed] [Google Scholar]
  6. Carazo-Salas R. E., Guarguaglini G., Gruss O. J., Segref A., Karsenti E., Mattaj I. W. Generation of GTP-bound Ran by RCC1 is required for chromatin-induced mitotic spindle formation. Nature. 1999 Jul 8;400(6740):178–181. doi: 10.1038/22133. [DOI] [PubMed] [Google Scholar]
  7. Carrano A. C., Eytan E., Hershko A., Pagano M. SKP2 is required for ubiquitin-mediated degradation of the CDK inhibitor p27. Nat Cell Biol. 1999 Aug;1(4):193–199. doi: 10.1038/12013. [DOI] [PubMed] [Google Scholar]
  8. Carrano A. C., Pagano M. Role of the F-box protein Skp2 in adhesion-dependent cell cycle progression. J Cell Biol. 2001 Jun 25;153(7):1381–1390. doi: 10.1083/jcb.153.7.1381. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chung C. H., Baek S. H. Deubiquitinating enzymes: their diversity and emerging roles. Biochem Biophys Res Commun. 1999 Dec 29;266(3):633–640. doi: 10.1006/bbrc.1999.1880. [DOI] [PubMed] [Google Scholar]
  10. Ciechanover A. The ubiquitin-proteasome pathway: on protein death and cell life. EMBO J. 1998 Dec 15;17(24):7151–7160. doi: 10.1093/emboj/17.24.7151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Fujiwara T., Saito A., Suzuki M., Shinomiya H., Suzuki T., Takahashi E., Tanigami A., Ichiyama A., Chung C. H., Nakamura Y. Identification and chromosomal assignment of USP1, a novel gene encoding a human ubiquitin-specific protease. Genomics. 1998 Nov 15;54(1):155–158. doi: 10.1006/geno.1998.5554. [DOI] [PubMed] [Google Scholar]
  12. Gnesutta N., Ceriani M., Innocenti M., Mauri I., Zippel R., Sturani E., Borgonovo B., Berruti G., Martegani E. Cloning and characterization of mouse UBPy, a deubiquitinating enzyme that interacts with the ras guanine nucleotide exchange factor CDC25(Mm)/Ras-GRF1. J Biol Chem. 2001 Aug 10;276(42):39448–39454. doi: 10.1074/jbc.M103454200. [DOI] [PubMed] [Google Scholar]
  13. Gruss O. J., Carazo-Salas R. E., Schatz C. A., Guarguaglini G., Kast J., Wilm M., Le Bot N., Vernos I., Karsenti E., Mattaj I. W. Ran induces spindle assembly by reversing the inhibitory effect of importin alpha on TPX2 activity. Cell. 2001 Jan 12;104(1):83–93. doi: 10.1016/s0092-8674(01)00193-3. [DOI] [PubMed] [Google Scholar]
  14. Hershko A., Ciechanover A. The ubiquitin system for protein degradation. Annu Rev Biochem. 1992;61:761–807. doi: 10.1146/annurev.bi.61.070192.003553. [DOI] [PubMed] [Google Scholar]
  15. Hershko A., Ciechanover A. The ubiquitin system. Annu Rev Biochem. 1998;67:425–479. doi: 10.1146/annurev.biochem.67.1.425. [DOI] [PubMed] [Google Scholar]
  16. Hershko A., Rose I. A. Ubiquitin-aldehyde: a general inhibitor of ubiquitin-recycling processes. Proc Natl Acad Sci U S A. 1987 Apr;84(7):1829–1833. doi: 10.1073/pnas.84.7.1829. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hochstrasser M. Ubiquitin-dependent protein degradation. Annu Rev Genet. 1996;30:405–439. doi: 10.1146/annurev.genet.30.1.405. [DOI] [PubMed] [Google Scholar]
  18. Li S. J., Hochstrasser M. A new protease required for cell-cycle progression in yeast. Nature. 1999 Mar 18;398(6724):246–251. doi: 10.1038/18457. [DOI] [PubMed] [Google Scholar]
  19. Marti A., Wirbelauer C., Scheffner M., Krek W. Interaction between ubiquitin-protein ligase SCFSKP2 and E2F-1 underlies the regulation of E2F-1 degradation. Nat Cell Biol. 1999 May;1(1):14–19. doi: 10.1038/8984. [DOI] [PubMed] [Google Scholar]
  20. Nachury M. V., Maresca T. J., Salmon W. C., Waterman-Storer C. M., Heald R., Weis K. Importin beta is a mitotic target of the small GTPase Ran in spindle assembly. Cell. 2001 Jan 12;104(1):95–106. doi: 10.1016/s0092-8674(01)00194-5. [DOI] [PubMed] [Google Scholar]
  21. Nakamura M., Masuda H., Horii J., Kuma K. i., Yokoyama N., Ohba T., Nishitani H., Miyata T., Tanaka M., Nishimoto T. When overexpressed, a novel centrosomal protein, RanBPM, causes ectopic microtubule nucleation similar to gamma-tubulin. J Cell Biol. 1998 Nov 16;143(4):1041–1052. doi: 10.1083/jcb.143.4.1041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Nakayama K. I., Hatakeyama S., Nakayama K. Regulation of the cell cycle at the G1-S transition by proteolysis of cyclin E and p27Kip1. Biochem Biophys Res Commun. 2001 Apr 13;282(4):853–860. doi: 10.1006/bbrc.2001.4627. [DOI] [PubMed] [Google Scholar]
  23. Nishitani H., Hirose E., Uchimura Y., Nakamura M., Umeda M., Nishii K., Mori N., Nishimoto T. Full-sized RanBPM cDNA encodes a protein possessing a long stretch of proline and glutamine within the N-terminal region, comprising a large protein complex. Gene. 2001 Jul 11;272(1-2):25–33. doi: 10.1016/s0378-1119(01)00553-4. [DOI] [PubMed] [Google Scholar]
  24. Ohba T., Nakamura M., Nishitani H., Nishimoto T. Self-organization of microtubule asters induced in Xenopus egg extracts by GTP-bound Ran. Science. 1999 May 21;284(5418):1356–1358. doi: 10.1126/science.284.5418.1356. [DOI] [PubMed] [Google Scholar]
  25. Ostrowska H., Wojcik C., Omura S., Worowski K. Lactacystin, a specific inhibitor of the proteasome, inhibits human platelet lysosomal cathepsin A-like enzyme. Biochem Biophys Res Commun. 1997 May 29;234(3):729–732. doi: 10.1006/bbrc.1997.6434. [DOI] [PubMed] [Google Scholar]
  26. Ponting C., Schultz J., Bork P. SPRY domains in ryanodine receptors (Ca(2+)-release channels). Trends Biochem Sci. 1997 Jun;22(6):193–194. doi: 10.1016/s0968-0004(97)01049-9. [DOI] [PubMed] [Google Scholar]
  27. Shinohara K., Tomioka M., Nakano H., Toné S., Ito H., Kawashima S. Apoptosis induction resulting from proteasome inhibition. Biochem J. 1996 Jul 15;317(Pt 2):385–388. doi: 10.1042/bj3170385. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Shirane M., Harumiya Y., Ishida N., Hirai A., Miyamoto C., Hatakeyama S., Nakayama K., Kitagawa M. Down-regulation of p27(Kip1) by two mechanisms, ubiquitin-mediated degradation and proteolytic processing. J Biol Chem. 1999 May 14;274(20):13886–13893. doi: 10.1074/jbc.274.20.13886. [DOI] [PubMed] [Google Scholar]
  29. Sutterlüty H., Chatelain E., Marti A., Wirbelauer C., Senften M., Müller U., Krek W. p45SKP2 promotes p27Kip1 degradation and induces S phase in quiescent cells. Nat Cell Biol. 1999 Aug;1(4):207–214. doi: 10.1038/12027. [DOI] [PubMed] [Google Scholar]
  30. Swanson D. A., Freund C. L., Ploder L., McInnes R. R., Valle D. A ubiquitin C-terminal hydrolase gene on the proximal short arm of the X chromosome: implications for X-linked retinal disorders. Hum Mol Genet. 1996 Apr;5(4):533–538. doi: 10.1093/hmg/5.4.533. [DOI] [PubMed] [Google Scholar]
  31. Taya S., Yamamoto T., Kano K., Kawano Y., Iwamatsu A., Tsuchiya T., Tanaka K., Kanai-Azuma M., Wood S. A., Mattick J. S. The Ras target AF-6 is a substrate of the fam deubiquitinating enzyme. J Cell Biol. 1998 Aug 24;142(4):1053–1062. doi: 10.1083/jcb.142.4.1053. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Tsubuki S., Saito Y., Tomioka M., Ito H., Kawashima S. Differential inhibition of calpain and proteasome activities by peptidyl aldehydes of di-leucine and tri-leucine. J Biochem. 1996 Mar;119(3):572–576. doi: 10.1093/oxfordjournals.jbchem.a021280. [DOI] [PubMed] [Google Scholar]
  33. Wiese C., Wilde A., Moore M. S., Adam S. A., Merdes A., Zheng Y. Role of importin-beta in coupling Ran to downstream targets in microtubule assembly. Science. 2001 Jan 26;291(5504):653–656. doi: 10.1126/science.1057661. [DOI] [PubMed] [Google Scholar]
  34. Wilde A., Lizarraga S. B., Zhang L., Wiese C., Gliksman N. R., Walczak C. E., Zheng Y. Ran stimulates spindle assembly by altering microtubule dynamics and the balance of motor activities. Nat Cell Biol. 2001 Mar;3(3):221–227. doi: 10.1038/35060000. [DOI] [PubMed] [Google Scholar]
  35. Wilde A., Zheng Y. Stimulation of microtubule aster formation and spindle assembly by the small GTPase Ran. Science. 1999 May 21;284(5418):1359–1362. doi: 10.1126/science.284.5418.1359. [DOI] [PubMed] [Google Scholar]
  36. Wilkinson K. D. Regulation of ubiquitin-dependent processes by deubiquitinating enzymes. FASEB J. 1997 Dec;11(14):1245–1256. doi: 10.1096/fasebj.11.14.9409543. [DOI] [PubMed] [Google Scholar]
  37. Wilkinson K. D., Urban M. K., Haas A. L. Ubiquitin is the ATP-dependent proteolysis factor I of rabbit reticulocytes. J Biol Chem. 1980 Aug 25;255(16):7529–7532. [PubMed] [Google Scholar]

Articles from Biochemical Journal are provided here courtesy of The Biochemical Society

RESOURCES