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Efficient Enhancement of Signalling Capacity: The Ubiquitin System

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Abstract

Ubiquitin (Ub) has emerged as a potent cellular signal that regulates a wide variety of processes in normal as well as malignant cells. Its potency is based on an elaborate system of “writing” and “reading” a diverse Ub code on substrate proteins. In this chapter we give an overview on the principles of Ub-based signalling and explain how efficiency and specificity is ensured in the cell. Moreover, we discuss how the capacity of Ub signalling is further enhanced by crosstalk with other post-translational modifications such as phosphorylation and acetylation.

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References

  1. Al-Hakim AK, Zagorska A, Chapman L, Deak M, Peggie M, Alessi DR (2008) Control of AMPK-related kinases by USP9X and atypical Lys(29)/Lys(33)-linked polyubiquitin chains. Biochem J 411(2):249–260

    Article  PubMed  CAS  Google Scholar 

  2. Amerik AY, Hochstrasser M (2004) Mechanism and function of deubiquitinating enzymes. Biochim Biophys Acta 1695(1–3):189–207

    Article  PubMed  CAS  Google Scholar 

  3. Bienko M, Green CM, Crosetto N, Rudolf F, Zapart G, Coull B, Kannouche P, Wider G, Peter M, Lehmann AR, Hofmann K, Dikic I (2005) Ubiquitin-binding domains in Y-family polymerases regulate translesion synthesis. Science 310(5755):1821–1824

    Article  PubMed  CAS  Google Scholar 

  4. Brzovic PS, Keeffe JR, Nishikawa H, Miyamoto K, Fox D III, Ohta T, Fukuda M, Klevit R (2003) Binding and recognition in the assembly of an active BRCA1/BARD1 ubiquitin-ligase complex. Proc Natl Acad Sci U S A 100(10):5646–5651

    Article  PubMed  CAS  Google Scholar 

  5. Cadwell K, Coscoy L (2005) Ubiquitination on nonlysine residues by a viral E3 ubiquitin ligase. Science 309(5731):127–130

    Article  PubMed  CAS  Google Scholar 

  6. Chen ZJ (2012) Ubiquitination in signaling to and activation of IKK. Immunol Rev 246(1):95–106

    Article  PubMed  CAS  Google Scholar 

  7. Christensen DE, Brzovic PS, Klevit RE (2007) E2-BRCA1 RING interactions dictate synthesis of mono- or specific polyubiquitin chain linkages. Nat Struct Mol Biol 14(10):941–948

    Article  PubMed  CAS  Google Scholar 

  8. Ciechanover A, Ben-Saadon R (2004) N-terminal ubiquitination: more protein substrates join in. Trends Cell Biol 14(3):103–106

    Article  PubMed  CAS  Google Scholar 

  9. Deshaies RJ, Joazeiro CA (2009) RING domain E3 ubiquitin ligases. Annu Rev Biochem 78:399–434

    Article  PubMed  CAS  Google Scholar 

  10. Dikic I, Wakatsuki S, Walters KJ (2009) Ubiquitin-binding domains—from structures to functions. Nat Rev Mol Cell Biol 10(10):659–671

    Article  PubMed  CAS  Google Scholar 

  11. Dou H, Buetow L, Hock A, Sibbet GJ, Vousden KH, Huang DT (2012) Structural basis for autoinhibition and phosphorylation-dependent activation of c-Cbl. Nat Struct Mol Biol 19(2):184–192

    Article  PubMed  CAS  Google Scholar 

  12. Gallagher E, Gao M, Liu YC, Karin M (2006) Activation of the E3 ubiquitin ligase Itch through a phosphorylation-induced conformational change. Proc Natl Acad Sci USA 103(6):1717–1722

    Article  PubMed  CAS  Google Scholar 

  13. Geisler S, Holmstrom KM, Skujat D, Fiesel FC, Rothfuss OC, Kahle PJ, Springer W (2010) PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1. Nat Cell Biol 12(2):119–131

    Article  PubMed  CAS  Google Scholar 

  14. Grabbe C, Husnjak K, Dikic I (2011) The spatial and temporal organization of ubiquitin networks. Nat Rev Mol Cell Biol 12(5):295–307

    Article  PubMed  CAS  Google Scholar 

  15. Grovdal LM, Stang E, Sorkin A, Madshus IH (2004) Direct interaction of Cbl with pTyr 1045 of the EGF receptor (EGFR) is required to sort the EGFR to lysosomes for degradation. Exp Cell Res 300(2):388–395

    Article  PubMed  CAS  Google Scholar 

  16. Guarani V, Deflorian G, Franco CA, Kruger M, Phng LK, Bentley K, Toussaint L, Dequiedt F, Mostoslavsky R, Schmidt MH, Zimmermann B, Brandes RP, Mione M, Westphal CH, Braun T, Zeiher AM, Gerhardt H, Dimmeler S, Potente M (2011) Acetylation-dependent regulation of endothelial Notch signalling by the SIRT1 deacetylase. Nature 473(7346):234–238

    Article  PubMed  CAS  Google Scholar 

  17. Haglund K, Di Fiore PP, Dikic I (2003) Distinct monoubiquitin signals in receptor endocytosis. Trends Biochem Sci 28(11):598–603

    Article  PubMed  CAS  Google Scholar 

  18. Hershko A, Ciechanover A (1998) The ubiquitin system. Annu Rev Biochem 67:425–479

    Article  PubMed  CAS  Google Scholar 

  19. Hoeller D, Dikic I (2009) Targeting the ubiquitin system in cancer therapy. Nature 458(7237):438–444

    Article  PubMed  CAS  Google Scholar 

  20. Hoeller D, Volarevic S, Dikic I (2005) Compartmentalization of growth factor receptor signalling. Curr Opin Cell Biol 17(2):107–111

    Article  PubMed  CAS  Google Scholar 

  21. Hunter T (2007) The age of crosstalk: phosphorylation, ubiquitination, and beyond. Mol Cell 28(5):730–738

    Article  PubMed  CAS  Google Scholar 

  22. Hurley JH, Stenmark H (2011) Molecular mechanisms of ubiquitin-dependent membrane traffic. Annu Rev Biophys 40:119–142

    Article  PubMed  CAS  Google Scholar 

  23. Ikeda F, Crosetto N, Dikic I (2010) What determines the specificity and outcomes of ubiquitin signaling? Cell 143(5):677–681

    Article  PubMed  CAS  Google Scholar 

  24. Ikeda F, Dikic I (2008) Atypical ubiquitin chains: new molecular signals. ‘Protein Modifications: Beyond the Usual Suspects’ review series. EMBO Rep 9(6):536–542

    Article  PubMed  CAS  Google Scholar 

  25. Jin L, Williamson A, Banerjee S, Philipp I, Rape M (2008) Mechanism of ubiquitin-chain formation by the human anaphase-promoting complex. Cell 133(4):653–665

    Article  PubMed  CAS  Google Scholar 

  26. Kamura T, Hara T, Matsumoto M, Ishida N, Okumura F, Hatakeyama S, Yoshida M, Nakayama K, Nakayama KI (2004) Cytoplasmic ubiquitin ligase KPC regulates proteolysis of p27(Kip1) at G1 phase. Nat Cell Biol 6(12):1229–1235

    Article  PubMed  CAS  Google Scholar 

  27. Kawakami T, Chiba T, Suzuki T, Iwai K, Yamanaka K, Minato N, Suzuki H, Shimbara N, Hidaka Y, Osaka F, Omata M, Tanaka K (2001) NEDD8 recruits E2-ubiquitin to SCF E3 ligase. EMBO J 20(15):4003–4012

    Article  PubMed  CAS  Google Scholar 

  28. Kim HC, Huibregtse JM (2009) Polyubiquitination by HECT E3s and the determinants of chain type specificity. Mol Cell Biol 29(12):3307–3318

    Article  PubMed  CAS  Google Scholar 

  29. Komander D, Clague MJ, Urbe S (2009) Breaking the chains: structure and function of the deubiquitinases. Nat Rev Mol Cell Biol 10(8):550–563

    Article  PubMed  CAS  Google Scholar 

  30. Matsuda N, Sato S, Shiba K, Okatsu K, Saisho K, Gautier CA, Sou YS, Saiki S, Kawajiri S, Sato F, Kimura M, Komatsu M, Hattori N, Tanaka K (2010) PINK1 stabilized by mitochondrial depolarization recruits Parkin to damaged mitochondria and activates latent Parkin for mitophagy. J Cell Biol 189(2):211–221

    Article  PubMed  CAS  Google Scholar 

  31. Matsumoto G, Wada K, Okuno M, Kurosawa M, Nukina N (2011) Serine 403 phosphorylation of p62/SQSTM1 regulates selective autophagic clearance of ubiquitinated proteins. Mol Cell 44(2):279–289

    Article  PubMed  CAS  Google Scholar 

  32. Miaczynska M, Bar-Sagi D (2010) Signaling endosomes: seeing is believing. Curr Opin Cell Biol 22(4):535–540

    Article  PubMed  CAS  Google Scholar 

  33. Nakayama KI, Nakayama K (2006) Ubiquitin ligases: cell-cycle control and cancer. Nat Rev Cancer 6(5):369–381

    Article  PubMed  CAS  Google Scholar 

  34. Pickart CM (2004) Back to the future with ubiquitin. Cell 116(2):181–190

    Article  PubMed  CAS  Google Scholar 

  35. Rahighi S, Ikeda F, Kawasaki M, Akutsu M, Suzuki N, Kato R, Kensche T, Uejima T, Bloor S, Komander D, Randow F, Wakatsuki S, Dikic I (2009) Specific recognition of linear ubiquitin chains by NEMO is important for NF-kappaB activation. Cell 136(6):1098–1109

    Article  PubMed  CAS  Google Scholar 

  36. Rajesh S, Bago R, Odintsova E, Muratov G, Baldwin G, Sridhar P, Overduin M, Berditchevski F (2011) Binding to syntenin-1 protein defines a new mode of ubiquitin-based interactions regulated by phosphorylation. J Biol Chem 286(45):39606–39614

    Article  PubMed  CAS  Google Scholar 

  37. Ravid T, Hochstrasser M (2007) Autoregulation of an E2 enzyme by ubiquitin-chain assembly on its catalytic residue. Nat Cell Biol 9(4):422–427

    Article  PubMed  CAS  Google Scholar 

  38. Rohaim A, Kawasaki M, Kato R, Dikic I, Wakatsuki S (2012) Structure of a compact conformation of linear diubiquitin. Acta Crystallogr D Biol Crystallogr 68(Pt 2):102–108

    Article  PubMed  Google Scholar 

  39. Rotin D, Kumar S (2009) Physiological functions of the HECT family of ubiquitin ligases. Nat Rev Mol Cell Biol 10(6):398–409

    Article  PubMed  CAS  Google Scholar 

  40. Ryabov Y, Fushman D (2006) Interdomain mobility in di-ubiquitin revealed by NMR. Proteins 63(4):787–796

    Article  PubMed  CAS  Google Scholar 

  41. Sriram SM, Kim BY, Kwon YT (2011) The N-end rule pathway: emerging functions and molecular principles of substrate recognition. Nat Rev Mol Cell Biol 12(11):735–747

    Article  PubMed  CAS  Google Scholar 

  42. Varshavsky A (2005) Regulated protein degradation. Trends Biochem Sci 30(6):283–286

    Article  PubMed  CAS  Google Scholar 

  43. Walczak H, Iwai K, Dikic I (2012) Generation and physiological roles of linear ubiquitin chains. BMC Biol 10:23

    Article  PubMed  CAS  Google Scholar 

  44. Wang X, Herr RA, Chua WJ, Lybarger L, Wiertz EJ, Hansen TH (2007) Ubiquitination of serine, threonine, or lysine residues on the cytoplasmic tail can induce ERAD of MHC-I by viral E3 ligase mK3. J Cell Biol 177(4):613–624

    Article  PubMed  CAS  Google Scholar 

  45. Wortzel I, Seger R (2011) The ERK cascade: distinct functions within various subcellular organelles. Genes Cancer 2(3):195–209

    Article  PubMed  CAS  Google Scholar 

  46. Wu T, Merbl Y, Huo Y, Gallop JL, Tzur A, Kirschner MW (2010) UBE2S drives elongation of K11-linked ubiquitin chains by the anaphase-promoting complex. Proc Natl Acad Sci USA 107(4):1355–1360

    Article  PubMed  CAS  Google Scholar 

  47. Wu-Baer F, Lagrazon K, Yuan W, Baer R (2003) The BRCA1/BARD1 heterodimer assembles polyubiquitin chains through an unconventional linkage involving lysine residue K6 of ubiquitin. J Biol Chem 278(37):34743–34746

    Article  PubMed  CAS  Google Scholar 

  48. Xu L, Lubkov V, Taylor LJ, Bar-Sagi D (2010) Feedback regulation of Ras signaling by Rabex-5-mediated ubiquitination. Curr Biol 20(15):1372–1377

    Article  PubMed  CAS  Google Scholar 

  49. Xu P, Duong DM, Seyfried NT, Cheng D, Xie Y, Robert J, Rush J, Hochstrasser M, Finley D, Peng J (2009) Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell 137(1):133–145

    Article  PubMed  CAS  Google Scholar 

  50. Yang C, Zhou W, Jeon MS, Demydenko D, Harada Y, Zhou H, Liu YC (2006) Negative regulation of the E3 ubiquitin ligase itch via Fyn-mediated tyrosine phosphorylation. Mol Cell 21(1):135–141

    Article  PubMed  Google Scholar 

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Acknowledgement

We would like to thank Tobias Kensche for his help with references and comments on the manuscript.

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Correspondence to Daniela Hoeller or Ivan Dikic .

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Hoeller, D., Dikic, I. (2013). Efficient Enhancement of Signalling Capacity: The Ubiquitin System. In: Yarden, Y., Tarcic, G. (eds) Vesicle Trafficking in Cancer. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-6528-7_9

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