Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Progress
  • Published:

Linear ubiquitin chains: NF-κB signalling, cell death and beyond

Abstract

Ubiquitylation is a versatile post-translational modification. Met1-linked linear ubiquitin chains are involved in nuclear factor-κB signalling and cell death, and dysfunctions in linear ubiquitylation underlie chronic inflammation. Recent identification of deubiquitylating enzymes and binding domains that are specific for linear ubiquitin chains suggests new physiological roles for linear ubiquitin chains. Moreover, the ligase required for linear ubiquitylation has a crucial role in the pathogenesis of some malignancies. Structural and functional analyses of the conjugation and deconjugation of linear ubiquitin chains have enabled the development of new probes to study the roles of linear chain ubiquitylation.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Proposed mechanism underlying linear ubiquitylation of NEMO by LUBAC.
Figure 2: Regulation of linear ubiquitin-mediated functions by interactions between DUBs and LUBAC.
Figure 3: Possible mechanism of LUBAC-mediated linear ubiquitylation of NEMO in IKK activation.

Similar content being viewed by others

References

  1. Deshaies, R. J. & Joazeiro, C. A. RING domain E3 ubiquitin ligases. Annu. Rev. Biochem. 78, 399–434 (2009).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  3. Berndsen, C. E. & Wolberger, C. New insights into ubiquitin E3 ligase mechanism. Nature Struct. Mol. Biol. 21, 301–307 (2014).

    Article  CAS  Google Scholar 

  4. Komander, D., Clague, M. J. & Urbe, S. Breaking the chains: structure and function of the deubiquitinases. Nature Rev. Mol. Cell. Biol. 10, 550–563 (2009).

    Article  CAS  Google Scholar 

  5. Iwai, K. & Tokunaga, F. Linear polyubiquitination: a new regulator of NF-κB activation. EMBO Rep. 10, 706–713 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Kirisako, T. et al. A ubiquitin ligase complex assembles linear polyubiquitin chains. EMBO J. 25, 4877–4887 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Komander, D. & Rape, M. The ubiquitin code. Annu. Rev. Biochem. 81, 203–229 (2012).

    Article  CAS  PubMed  Google Scholar 

  8. Tokunaga, F. et al. Involvement of linear polyubiquitylation of NEMO in NF-κB activation. Nature Cell Biol. 11, 123–132 (2009).

    Article  CAS  Google Scholar 

  9. Gerlach, B. et al. Linear ubiquitination prevents inflammation and regulates immune signalling. Nature 471, 591–596 (2011).

    Article  CAS  PubMed  Google Scholar 

  10. Ikeda, F. et al. SHARPIN forms a linear ubiquitin ligase complex regulating NF-κB activity and apoptosis. Nature 471, 637–641 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Lo, Y. C. et al. Structural basis for recognition of diubiquitins by NEMO. Mol. Cell 33, 602–615 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Rahighi, S. et al. Specific recognition of linear ubiquitin chains by NEMO is important for NF-κB activation. Cell 136, 1098–1109 (2009).

    Article  CAS  PubMed  Google Scholar 

  13. Keusekotten, K. et al. OTULIN antagonizes LUBAC signaling by specifically hydrolyzing Met1-linked polyubiquitin. Cell 153, 1312–1326 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Rieser, E., Cordier, S. M. & Walczak, H. Linear ubiquitination: a newly discovered regulator of cell signalling. Trends Biochem. Sci. 38, 94–102 (2013).

    Article  CAS  PubMed  Google Scholar 

  15. Sato, Y. et al. Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex. Proc. Natl Acad. Sci. USA 108, 20520–20525 (2011).

    Article  CAS  PubMed  Google Scholar 

  16. Wild, P. et al. Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth. Science 333, 228–233 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Dubois, S. M. et al. A catalytic-independent role for the LUBAC in NF-κB activation upon antigen receptor engagement and in lymphoma cells. Blood 123, 2199–2203 (2014).

    Article  CAS  PubMed  Google Scholar 

  18. Yang, Y. et al. Essential role of the linear ubiquitin chain assembly complex in lymphoma revealed by rare germline polymorphisms. Cancer Discov. 4, 480–493 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Muller-Rischart, A. K. et al. The E3 ligase parkin maintains mitochondrial integrity by increasing linear ubiquitination of NEMO. Mol. Cell 49, 908–921 (2013).

    Article  PubMed  Google Scholar 

  20. Berger, S. B. et al. Cutting edge: RIP1 kinase activity is dispensable for normal development but is a key regulator of inflammation in SHARPIN-deficient mice. J. Immunol. http://dx.doi.org/10.4049/jimmunol.1400499 (2014).

  21. Iwai, K. Diverse ubiquitin signaling in NF-κB activation. Trends Cell Biol. 22, 355–364 (2012).

    Article  CAS  PubMed  Google Scholar 

  22. Stieglitz, B., Morris-Davies, A. C., Koliopoulos, M. G., Christodoulou, E. & Rittinger, K. LUBAC synthesizes linear ubiquitin chains via a thioester intermediate. EMBO Rep. 13, 840–846 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Smit, J. J. et al. The E3 ligase HOIP specifies linear ubiquitin chain assembly through its RING-IBR-RING domain and the unique LDD extension. EMBO J. 31, 3833–3844 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Yagi, H. et al. A non-canonical UBA-UBL interaction forms the linear-ubiquitin-chain assembly complex. EMBO Rep. 13, 462–468 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Tokunaga, F. et al. SHARPIN is a component of the NF-κB-activating linear ubiquitin chain assembly complex. Nature 471, 633–636 (2011).

    Article  CAS  PubMed  Google Scholar 

  26. Wenzel, D. M., Lissounov, A., Brzovic, P. S. & Klevit, R. E. UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids. Nature 474, 105–108 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Stieglitz, B. et al. Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP. Nature 503, 422–426 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Fujita, H. et al. Mechanism underlying IκB kinase activation mediated by the linear ubiquitin chain assembly complex. Mol. Cell Biol. 34, 1322–1335 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  29. Smit, J. J. et al. Target specificity of the E3 ligase LUBAC for ubiquitin and NEMO relies on different minimal requirements. J. Biol. Chem. 288, 31728–31737 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Rantala, J. K. et al. SHARPIN is an endogenous inhibitor of β1-integrin activation. Nature Cell Biol. 13, 1315–1324 (2011).

    Article  CAS  PubMed  Google Scholar 

  31. Rivkin, E. et al. The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis. Nature 498, 318–324 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Komander, D. et al. Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains. EMBO Rep. 10, 466–473 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Sun, S. C. CYLD: a tumor suppressor deubiquitinase regulating NF-κB activation and diverse biological processes. Cell Death Differ. 17, 25–34 (2010).

    Article  CAS  Google Scholar 

  34. Harhaj, E. W. & Dixit, V. M. Regulation of NF-κB by deubiquitinases. Immunol. Rev. 246, 107–124 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  35. Hymowitz, S. G. & Wertz, I. E. A20: from ubiquitin editing to tumour suppression. Nature Rev. Cancer 10, 332–341 (2010).

    Article  CAS  Google Scholar 

  36. Verhelst, K. et al. A20 inhibits LUBAC-mediated NF-κB activation by binding linear polyubiquitin chains via its zinc finger 7. EMBO J. 31, 3845–3855 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Tokunaga, F. et al. Specific recognition of linear polyubiquitin by A20 zinc finger 7 is involved in NF-κB regulation. EMBO J. 31, 3856–3870 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Skaug, B. et al. Direct, noncatalytic mechanism of IKK inhibition by A20. Mol. Cell 44, 559–571 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Elliott, P. R. et al. Molecular basis and regulation of OTULIN–LUBAC interaction. Mol. Cell 54, 335–348 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Schaeffer, V. et al. Binding of OTULIN to the PUB Domain of HOIP Controls NF-κB Signaling. Mol. Cell 54, 349–361 (2014).

    Article  CAS  PubMed  Google Scholar 

  41. Takiuchi, T. et al. Suppression of LUBAC-mediated linear ubiquitination by a specific interaction between LUBAC and the deubiquitinases CYLD and OTULIN. Genes Cells 19, 254–272 (2014).

    Article  CAS  PubMed  Google Scholar 

  42. Sowa, M. E., Bennett, E. J., Gygi, S. P. & Harper, J. W. Defining the human deubiquitinating enzyme interaction landscape. Cell 138, 389–403 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Yeung, H. O. et al. Insights into adaptor binding to the AAA protein p97. Biochem. Soc. Trans. 36, 62–67 (2008).

    Article  CAS  PubMed  Google Scholar 

  44. Emmerich, C. H. et al. Activation of the canonical IKK complex by K63/M1-linked hybrid ubiquitin chains. Proc. Natl Acad. Sci. USA 110, 15247–15252 (2013).

    Article  CAS  PubMed  Google Scholar 

  45. Fiil, B. K. et al. OTULIN restricts Met1-linked ubiquitination to control innate immune signaling. Mol. Cell 50, 818–830 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Hayden, M. S. & Ghosh, S. Shared principles in NF-κB signaling. Cell 132, 344–362 (2008).

    Article  CAS  PubMed  Google Scholar 

  47. Chen, Z. J. Ubiquitination in signaling to and activation of IKK. Immunol. Rev. 246, 95–106 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  48. Sasaki, Y. et al. Defective immune responses in mice lacking LUBAC-mediated linear ubiquitination in B cells. EMBO J. 32, 2463–2476 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Xu, M., Skaug, B., Zeng, W. & Chen, Z. J. A ubiquitin replacement strategy in human cells reveals distinct mechanisms of IKK activation by TNFα and IL-1β. Mol. Cell 36, 302–314 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Xu, G. et al. Crystal structure of inhibitor of κB kinase β. Nature 472, 325–330 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Polley, S. et al. A structural basis for IκB kinase 2 activation via oligomerization-dependent trans auto-phosphorylation. PLoS Biol. 11, e1001581 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Clark, K., Nanda, S. & Cohen, P. Molecular control of the NEMO family of ubiquitin-binding proteins. Nature Rev. Mol. Cell Biol. 14, 673–685 (2013).

    Article  CAS  Google Scholar 

  53. Haas, T. L. et al. Recruitment of the linear ubiquitin chain assembly complex stabilizes the TNF-R1 signaling complex and is required for TNF-mediated gene induction. Mol. Cell 36, 831–844 (2009).

    Article  CAS  PubMed  Google Scholar 

  54. Inn, K. S. et al. Linear ubiquitin assembly complex negatively regulates RIG-I- and TRIM25-mediated type I interferon induction. Mol. Cell 41, 354–365 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Niu, J., Shi, Y., Iwai, K. & Wu, Z. H. LUBAC regulates NF-κB activation upon genotoxic stress by promoting linear ubiquitination of NEMO. EMBO J. 30, 3741–3753 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Belgnaoui, S. M. et al. Linear ubiquitination of NEMO negatively regulates the interferon antiviral response through disruption of the MAVS–TRAF3 complex. Cell Host Microbe 12, 211–222 (2012).

    Article  CAS  PubMed  Google Scholar 

  57. Damgaard, R. B. et al. The ubiquitin ligase XIAP recruits LUBAC for NOD2 signaling in inflammation and innate immunity. Mol. Cell 46, 746–758 (2012).

    Article  CAS  PubMed  Google Scholar 

  58. Gantke, T. Sriskantharajah, S., Sadowski, M. & Ley, S. C. IκB kinase regulation of the TPL-2/ERK MAPK pathway. Immunol. Rev. 246, 168–182 (2012).

    Article  PubMed  Google Scholar 

  59. Roget, K. et al. IKK2 regulates TPL-2 activation of ERK-1/2 MAP kinases by direct phosphorylation of TPL-2 serine 400. Mol. Cell Biol. 32, 4684–4690 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Kaiser, W. J. et al. RIP3 mediates the embryonic lethality of caspase-8-deficient mice. Nature 471, 368–372 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Green, D. R., Oberst, A., Dillon, C. P., Weinlich, R. & Salvesen, G. S. RIPK-dependent necrosis and its regulation by caspases: a mystery in five acts. Mol. Cell 44, 9–16 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Kaczmarek, A., Vandenabeele, P. & Krysko, D. V. Necroptosis: the release of damage-associated molecular patterns and its physiological relevance. Immunity 38, 209–223 (2013).

    Article  CAS  PubMed  Google Scholar 

  63. Christofferson, D. E., Li, Y. & Yuan, J. Control of life-or-death decisions by RIP1 kinase. Annu. Rev. Physiol. 76, 129–150 (2014).

    Article  CAS  PubMed  Google Scholar 

  64. Tamiya, H. et al. IFN-γ or IFN-α ameliorates chronic proliferative dermatitis by inducing expression of linear ubiquitin chain assembly complex. J. Immunol. 192, 3793–3804 (2014).

    Article  CAS  PubMed  Google Scholar 

  65. Boisson, B. et al. Immunodeficiency, autoinflammation and amylopectinosis in humans with inherited HOIL-1 and LUBAC deficiency. Nature Immunol. 13, 1178–1186 (2012).

    Article  CAS  Google Scholar 

  66. Nilsson, J. et al. Polyglucosan body myopathy caused by defective ubiquitin ligase RBCK1. Ann. Neurol. 74, 914–919 (2013).

    Article  CAS  PubMed  Google Scholar 

  67. Kato, M. et al. Frequent inactivation of A20 in B-cell lymphomas. Nature 459, 712–716 (2009).

    Article  CAS  PubMed  Google Scholar 

  68. Mackay, C. et al. E3 ubiquitin ligase HOIP attenuates apoptotic cell death induced by cisplatin. Cancer Res. 74, 2246–2257 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Tomonaga, M. et al. Activation of nuclear factor-κ B by linear ubiquitin chain assembly complex contributes to lung metastasis of osteosarcoma cells. Int. J. Oncol. 40, 409–417 (2012).

    CAS  PubMed  Google Scholar 

  70. van Wijk, S. J. et al. Fluorescence-based sensors to monitor localization and functions of linear and K63-linked ubiquitin chains in cells. Mol. Cell 47, 797–809 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Wickliffe, K. E., Williamson, A., Meyer, H. J., Kelly, A. & Rape, M. K11-linked ubiquitin chains as novel regulators of cell division. Trends Cell Biol. 21, 656–663 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The authors are grateful to members of the Iwai laboratory for valuable discussions and insightful comments. The authors apologize to colleagues whose work could not be cited owing to space limitations. Work in the Iwai laboratory is partly supported by the Targeted Proteins Research Program (TPRP), the Project for Development of Innovative Research on Cancer Therapeutics, and by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan (Grant Numbers 22249008, 24112002 and 25253019).

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Kazuhiro Iwai, Hiroaki Fujita or Yoshiteru Sasaki.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Iwai, K., Fujita, H. & Sasaki, Y. Linear ubiquitin chains: NF-κB signalling, cell death and beyond. Nat Rev Mol Cell Biol 15, 503–508 (2014). https://doi.org/10.1038/nrm3836

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrm3836

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing