Skip to main content

A method to identify p62’s UBA domain interacting proteins

Abstract

The UBA domain is a conserved sequence motif among polyubiquitin binding proteins. For the first time, we demonstrate a systematic, high throughput approach to identification of UBA domain-interacting proteins from a proteome-wide perspective. Using the rabbit reticulocyte lysatein vitro expression cloning system, we have successfully identified eleven proteins that interact with p62’s UBA domain, and the majority of the eleven proteins are associated with neurodegenerative disorders, such as Alzheimer’s disease. Therefore, p62 may play a novel regulatory role through its UBA domain. Our approach provides an easy route to the characterization of UBA domain interacting proteins and its application will unfold the important roles that the UBA domain plays.

References

  1. 1.

    Park I, Chung J, Walsh CT, Yun Y, Strominger JL, Shin J. Phosphotyrosine-independent binding of a 62-kDa protein to thesrc homology 2 (SH2) domain of p56lck and its regulation by phosphorylation of Ser-59 in thelck unique N-terminal region.Proc Natl Acad Sci 1995; 92:12338–12342.

    PubMed  Article  CAS  Google Scholar 

  2. 2.

    Joung I, Strominger JL, Shin J. Molecular cloning of a phosphotyrosine-independent ligand of the p56lck SH2 domain.Proc Natl Acad Sci 1996; 93:5991–5995.

    PubMed  Article  CAS  Google Scholar 

  3. 3.

    Cooper JA, Howell B. The when and how of Src regulation.Cell 1993; 73:1051–1054.

    PubMed  Article  CAS  Google Scholar 

  4. 4.

    Weiss A, Littman DR. Signal transduction by lymphocyte antigen receptors.Cell 1994; 76:263–274.

    PubMed  Article  CAS  Google Scholar 

  5. 5.

    Puls A, Schmidt S, Grawe F, Stabel S. Interaction of protein kinase C zeta with ZIP, a novel protein kinase C-binding protein.Proc Natl Acad Sci 1997; 94:6191–6196.

    PubMed  Article  CAS  Google Scholar 

  6. 6.

    Sanchez P, De Carcer G, Sandoval IV, Moscat J, Diaz-Meco MT. Localization of atypical protein kinase C isoforms into lysosome-targeted endosomes through interaction with p62.Mol Cel Biol 1998; 18:3069–3080.

    CAS  Google Scholar 

  7. 7.

    Vadlamundi RK, Joung I, Strominger JL, Shin J. p62, a phosphotyrosine-independent ligand of the SH2 domain of p56lck, belongs to a new class of ubiquitin-binding protein.J Biol Chem 1996; 271:20235–20237.

    Article  Google Scholar 

  8. 8.

    Bertolaet BL, Clarke DJ, Wolff M, Watson MH, Henze M, Divita G, Reed SI. UBA domains of DNA damage-inducible proteins interact with ubiquitin.Nat Struct Biol 2001; 8:417–422.

    PubMed  Article  CAS  Google Scholar 

  9. 9.

    Geetha T, Wooten MW. Structure and functional properties of the ubiquitin-binding protein p62.FEBS Lett 2001;512:19–24.

    Article  Google Scholar 

  10. 10.

    Weissman AM. Themes and variations on ubiquitylation.Nat Rev Mol Cell Bio 2001; 2:169–178.

    Article  CAS  Google Scholar 

  11. 11.

    Pickart CM. Ubiquitin enters the new millennium.Mol Cell 2001; 8:499–504.

    PubMed  Article  CAS  Google Scholar 

  12. 12.

    Hicke L. A new ticket for entry into budding vesicles-ubiquitin.Cell 2001; 106:527–530.

    PubMed  Article  CAS  Google Scholar 

  13. 13.

    Hofmann K, Bucher P. The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination pathway.TIBS 1996; 21:172–173.

    PubMed  CAS  Google Scholar 

  14. 14.

    Rao H, Sastry A. Recognition of specific ubiquitin conjugates is important for the proteolytic functions of the ubiquitin-associated domain proteins Dsk2 and Rad23.J Biol Chem 2002; 277:11691–11695.

    PubMed  Article  CAS  Google Scholar 

  15. 15.

    Hicke L, Riezman H. Ubiquitination of a yeast plasma membrane receptor signals its ligand-stimulated endocytosis.Cell 1996; 84:277–287.

    PubMed  Article  CAS  Google Scholar 

  16. 16.

    Hicke L. Ubiquitin-dependent internalization and down-regulation of plasma membrane proteins.FASEB J 1997; 11:1215–1226.

    PubMed  Google Scholar 

  17. 17.

    Shin J. p62 and the sequestosome, a novel mechanism for protein metabolism.Arch Pharm Res 1998; 21:829–833.

    Google Scholar 

  18. 18.

    Lee YH, Ko J, Joung I, Kim JH, Shin J. Immediate early response of the p62 gene encoding a non-proteasomal multiubiquitin chain binding protein.FEBS Lett 1998;438:297–300.

    PubMed  Article  CAS  Google Scholar 

  19. 19.

    Sato S, Ward CL, Kopito RR. Cotranslational ubiquitination of cystic fibrosis transmembrane conductance regulatorin vitro.J Biol Chem 1998; 273:7189–7192.

    PubMed  Article  CAS  Google Scholar 

  20. 20.

    Tibbles KW, Brierley I, Cavanagh D, Brown TD. A region of the coronavirus infectious bronchitis virus a1 polyprotein encoding the 3C-like protease domain is subject to rapid turnover when expressed in rabbit reticulocyte lysate.J Gen Virol 1995; 76:3059–3070.

    PubMed  Article  CAS  Google Scholar 

  21. 21.

    Roher AE, Weiss N, Kokjohn TA, Kuo Y, Kalback W, Anthony J, Watson D, Leuhers DC, Walker D, Emmerling M, Goux W, Beach T. Increased Aβ peptide and reduced cholesterol and myelin proteins characterize white matter degeneration in Alzheimer’s Disease.Biochemistry 2002;41:11080–11090.

    PubMed  Article  CAS  Google Scholar 

  22. 22.

    Kang J, Lemaire HG, Unterbeck A, Salbaum JM, Masters CL, Grzeschik KH, Multhaup G, Beyreuther K, Muller-Hill B. The precursor of Alzheimer’s disease amyloid A4 protein resembles a cell-surface receptor.Nature 1987; 325:733–736.

    PubMed  Article  CAS  Google Scholar 

  23. 23.

    Layfield R, Fergusson J, Aitken A, Lowe J, Landon M, Mayer RJ. Neurofibrillary tangles of Alzheimer’s disease brains contain 14-3-3 proteins.Neurosci Lett 1996; 209:57–60.

    PubMed  Article  CAS  Google Scholar 

  24. 24.

    Ho CS, Marinescu V, Steinhilb ML, Gaut JR, Turner RS, Stuenkel EL. Synergistic effects of Munc18a and X11 proteins on amyloid precursor protein metabolism.J Biol Chem 2002; 277:27021–27028.

    PubMed  Article  CAS  Google Scholar 

  25. 25.

    Blass JP, Sheu KF, Cooper AJ, Jung EH, Gibson GE. Thiamin and Alzheimer’s disease.J Nutr Sci Vitaminol 1992; Spec No:401–404.

  26. 26.

    Yoo BC, Seidl R, Cairns N, Lubec G. Heat-shock protein 70 levels in brain of patients with Down syndrome and Alzheimer’s disease.J Neural Transm 1999; 57:315–322.

    CAS  Google Scholar 

  27. 27.

    Renkawek K, Bosman GJ, Gaestel M. Increased expression of heat-shock protein 27KDa in Alzheimer disease: a preliminary study.Neuroreport 1993; 5:14–16.

    PubMed  Article  CAS  Google Scholar 

  28. 28.

    Mao JJ, Katayama S, Watanabe C, Harada Y, Noda K, Yamamura Y, Nakamura S. The relationship between alphacrystallin and neurofibrillary tangles in Alzheimer’s disease.Neuropath Appl Neuro 2001; 27:180–188.

    Article  CAS  Google Scholar 

  29. 29.

    Beffert U, Morfini G, Bock HH, Reyna H, Brady ST, Herz J. Reelin-mediated signaling locally regulates protein kinase B/Akt and glycogen synthase kinase 3β.J Biol Chem 2002;277:49958–49964.

    PubMed  Article  CAS  Google Scholar 

  30. 30.

    Ohkubo N, Lee YD, Morishima A, Terashima T, Kikkawa S, Tohyama M, Sakanaka M, Tanaka J, Maeda N, Vitek MP, Mitsuda N. Apolipoprotein E and Reelin ligands modulate tau phosphorylation through an apolipoprotein E receptor/disabled-1/glycogen synthase kinase-3ß cascade.FASEB J 2003; 17:295–297.

    PubMed  CAS  Google Scholar 

  31. 31.

    McKee AC, Kosik KS, Kennedy MB, Kowall NW. Hippocampal neurons predisposed to neurofibrillary tangle formation are enriched in type II calcium/calmodulin-dependent protein kinase.J Neuropath Exp Neur 1990; 49:49–63.

    PubMed  Article  CAS  Google Scholar 

  32. 32.

    Perry G, Friedman R, Shaw G, Chau V. Ubiquitin is detected in neurofibrillary tangles and senile plaque neurites of Alzheimer disease brains.Proc Natl Acad Sci 1987;84:3033–3036.

    PubMed  Article  CAS  Google Scholar 

  33. 33.

    Kuusisto E, Salminen A, Alafuzoff I. Early accumulation of p62 in neurofibrillary tangles in Alzheimer’s disease: possible role in tangle formation.Neuropath Appl Neuro 2002; 28:228–237.

    Article  CAS  Google Scholar 

  34. 34.

    Choe SK, Vlachakis N, Sagerstrom CG. Meis family proteins are required for hindbrain development in the zebrafish.Development 2002; 129:585–595.

    PubMed  CAS  Google Scholar 

  35. 35.

    Hedgecock EM, Culotti JG, Thomson JN, Perkins LA. Axonal guidance mutants ofCaenorhabditis elegans identified by filling sensory neurons with fluorescein dyes.Dev Bio 1985; 111:158–170.

    Article  CAS  Google Scholar 

  36. 36.

    Okazaki N, Yan J, Yuasa S, Ueno T, Kominami E, Masuho Y, Koga H, Muramatsu M. Interaction of the Unc-51-like kinase and microtubule-associated protein light chain 3 related proteins in the brain: possible role of vesicular transport in axonal elongation.Mol Brain Res 2000; 85:1–12.

    PubMed  Article  CAS  Google Scholar 

  37. 37.

    Fung JJ, Starzl TE. FK506 in solid organ transplantation.Ther Drug Monit 1995; 17:592–595.

    PubMed  Article  CAS  Google Scholar 

  38. 38.

    Schreiber SL, Crabtree GR. The mechanism of action of cyclosporin A and FK506.Immunol Today 1992; 13:136–142.

    PubMed  Article  CAS  Google Scholar 

  39. 39.

    Christner C, Herdegen T, Fischer G. FKBP ligands as novel therapeutics for neurological disorders.Mini-Reviews in Medicinal Chemistry 2001; 1:377–397.

    PubMed  Article  CAS  Google Scholar 

  40. 40.

    Avramut M, Zeevi A, Achim CL. The immunosuppressant drug FK506 is a potent trophic agent for human fetal neurons.Dev Brain Res 2001; 132:151–157.

    Article  CAS  Google Scholar 

  41. 41.

    Boutell JM, Thomas P, Neal JW, Weston VJ, Duce J, Harper PS, Jones AL. Aberrant interactions of transcriptional repressor proteins with the Huntington’s disease gene product, huntingtin.Hum Mol Genet 1999; 8:1647–1655.

    PubMed  Article  CAS  Google Scholar 

  42. 42.

    Chau V, Tobias JW, Bachmair A, Marriott D, Ecker DJ, Gonda DK, Varshavsky A. A multiubiquitin chain is confined to specific lysine in a targeted short-lived protein.Science 1989; 243:1576–1583.

    PubMed  Article  CAS  Google Scholar 

  43. 43.

    Gregori L, Poosch MS, Cousins G, Chau V. A uniform isopeptide-linked multiubiquitin chain is sufficient to target substrate for degradation in ubiquitin-mediated proteolysis.J Biol Chem 1990; 265:8354–8357.

    PubMed  CAS  Google Scholar 

  44. 44.

    Finley D, Sadis S, Monia BP, Boucher P, Ecker DJ, Crooke ST, Chau V. Inhibition of proteolysis and cell cycle progression in a multiubiquitination-deficient yeast mutant.Mol Cell Biol 1994; 14:5501–5509.

    PubMed  CAS  Google Scholar 

  45. 45.

    Jiang J, Ballinger CA, Wu Y, Dai Q, Cyr DM, Hohfeld J, Patterson C. CHIP is a U-box-dependent E3 ubiquitin ligase: identification of Hsc70 as a target for ubiquitylation.J Biol Chem 2001; 276:42938–42944.

    PubMed  Article  CAS  Google Scholar 

  46. 46.

    Wooten MW, Seibenhener ML, Mamidipudi V, Diaz-Meco MT, Barker PA, Moscat J. The atypical protein kinase C-interacting protein p62 is a scaffold for NF-kappaB activation by nerve growth factor.J Biol Chem 2001;276:7709–7712.

    PubMed  Article  CAS  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding author

Correspondence to Marie W. Wooten.

Additional information

Published: December 12, 2003.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Pridgeon, J.W., Geetha, T. & Wooten, M.W. A method to identify p62’s UBA domain interacting proteins. Biol. Proced. Online 5, 228–237 (2003). https://doi.org/10.1251/bpo66

Download citation

Indexing terms

  • Ubiquitin
  • Alzheimer Disease