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Divergent allosteric control of the IRE1α endoribonuclease using kinase inhibitors

Nature Chemical Biology volume 8, pages 982–989 (2012)Cite this article

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Abstract

Under endoplasmic reticulum stress, unfolded protein accumulation leads to activation of the endoplasmic reticulum transmembrane kinase/endoRNase (RNase) IRE1α. IRE1α oligomerizes, autophosphorylates and initiates splicing of XBP1 mRNA, thus triggering the unfolded protein response (UPR). Here we show that IRE1α's kinase-controlled RNase can be regulated in two distinct modes with kinase inhibitors: one class of ligands occupies IRE1α's kinase ATP-binding site to activate RNase-mediated XBP1 mRNA splicing even without upstream endoplasmic reticulum stress, whereas a second class can inhibit the RNase through the same ATP-binding site, even under endoplasmic reticulum stress. Thus, alternative kinase conformations stabilized by distinct classes of ATP-competitive inhibitors can cause allosteric switching of IRE1α's RNase—either on or off. As dysregulation of the UPR has been implicated in a variety of cell degenerative and neoplastic disorders, small-molecule control over IRE1α should advance efforts to understand the UPR's role in pathophysiology and to develop drugs for endoplasmic reticulum stress–related diseases.

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Figure 1: Interaction of ATP-competitive inhibitors with the bifunctional kinase/RNase, IRE1α.
Figure 2: APY29 and 3 divergently modulate the RNase activity and oligomerization state of IRE1α*.
Figure 3: Characterization of 3′s interaction with the ATP-binding site of IRE1α.
Figure 4: APY29 and 3 differentially affect the oligomerization state of IRE1α*.
Figure 5: Chemical-genetic modulation of IRE1α kinase and RNase activity in vivo.
Figure 6: Divergent modulation of endogenous IRE1α RNase activity under endoplasmic reticulum stress with type I and type II kinase inhibitors.

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References

  1. Walter, P. & Ron, D. The unfolded protein response: from stress pathway to homeostatic regulation. Science 334, 1081–1086 (2011).

    Article  CAS  Google Scholar 

  2. Merksamer, P.I. & Papa, F.R. The UPR and cell fate at a glance. J. Cell Sci. 123, 1003–1006 (2010).

    Article  CAS  Google Scholar 

  3. Scheuner, D. & Kaufman, R.J. The unfolded protein response: a pathway that links insulin demand with β-cell failure and diabetes. Endocr. Rev. 29, 317–333 (2008).

    Article  CAS  Google Scholar 

  4. Carrasco, D.R. et al. The differentiation and stress response factor XBP-1 drives multiple myeloma pathogenesis. Cancer Cell 11, 349–360 (2007).

    Article  CAS  Google Scholar 

  5. Tabas, I. & Ron, D. Integrating the mechanisms of apoptosis induced by endoplasmic reticulum stress. Nat. Cell Biol. 13, 184–190 (2011).

    Article  CAS  Google Scholar 

  6. Tirasophon, W., Welihinda, A.A. & Kaufman, R.J. A stress response pathway from the endoplasmic reticulum to the nucleus requires a novel bifunctional protein kinase/endoribonuclease (Ire1p) in mammalian cells. Genes Dev. 12, 1812–1824 (1998).

    Article  CAS  Google Scholar 

  7. Han, D. et al. IRE1α kinase activation modes control alternate endoribonuclease outputs to determine divergent cell fates. Cell 138, 562–575 (2009).

    Article  CAS  Google Scholar 

  8. Han, D. et al. A kinase inhibitor activates the IRE1α RNase to confer cytoprotection against ER stress. Biochem. Biophys. Res. Commun. 365, 777–783 (2008).

    Article  CAS  Google Scholar 

  9. Credle, J.J., Finer-Moore, J.S., Papa, F.R., Stroud, R.M. & Walter, P. On the mechanism of sensing unfolded protein in the endoplasmic reticulum. Proc. Natl. Acad. Sci. USA 102, 18773–18784 (2005).

    Article  CAS  Google Scholar 

  10. Zhou, J. et al. The crystal structure of human IRE1 luminal domain reveals a conserved dimerization interface required for activation of the unfolded protein response. Proc. Natl. Acad. Sci. USA 103, 14343–14348 (2006).

    Article  CAS  Google Scholar 

  11. Gardner, B.M. & Walter, P. Unfolded proteins are Ire1-activating ligands that directly induce the unfolded protein response. Science 333, 1891–1894 (2011).

    Article  CAS  Google Scholar 

  12. Calfon, M. et al. IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA. Nature 415, 92–96 (2002).

    Article  CAS  Google Scholar 

  13. Yoshida, H., Matsui, T., Yamamoto, A., Okada, T. & Mori, K. XBP1 mRNA is induced by ATF6 and spliced by IRE1 in response to ER stress to produce a highly active transcription factor. Cell 107, 881–891 (2001).

    Article  CAS  Google Scholar 

  14. Papa, F.R., Zhang, C., Shokat, K. & Walter, P. Bypassing a kinase activity with an ATP-competitive drug. Science 302, 1533–1537 (2003).

    Article  CAS  Google Scholar 

  15. Lin, J.H. et al. IRE1 signaling affects cell fate during the unfolded protein response. Science 318, 944–949 (2007).

    Article  CAS  Google Scholar 

  16. Korennykh, A.V. et al. The unfolded protein response signals through high-order assembly of Ire1. Nature 457, 687–693 (2009).

    Article  CAS  Google Scholar 

  17. Liu, Y. & Gray, N.S. Rational design of inhibitors that bind to inactive kinase conformations. Nat. Chem. Biol. 2, 358–364 (2006).

    Article  CAS  Google Scholar 

  18. Korennykh, A.V. et al. Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1. BMC Biol. 9, 48 (2011).

    Article  CAS  Google Scholar 

  19. Ali, M.M. et al. Structure of the Ire1 autophosphorylation complex and implications for the unfolded protein response. EMBO J. 30, 894–905 (2011).

    Article  CAS  Google Scholar 

  20. Lee, K.P. et al. Structure of the dual enzyme Ire1 reveals the basis for catalysis and regulation in nonconventional RNA splicing. Cell 132, 89–100 (2008).

    Article  CAS  Google Scholar 

  21. Wan, P.T. et al. Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF. Cell 116, 855–867 (2004).

    Article  CAS  Google Scholar 

  22. Schindler, T. et al. Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. Science 289, 1938–1942 (2000).

    Article  CAS  Google Scholar 

  23. Ranjitkar, P., Brock, A.M. & Maly, D.J. Affinity reagents that target a specific inactive form of protein kinases. Chem. Biol. 17, 195–206 (2010).

    Article  CAS  Google Scholar 

  24. Dar, A.C., Lopez, M.S. & Shokat, K.M. Small molecule recognition of c-Src via the Imatinib-binding conformation. Chem. Biol. 15, 1015–1022 (2008).

    Article  CAS  Google Scholar 

  25. Papandreou, I. et al. Identification of an Ire1α endonuclease specific inhibitor with cytotoxic activity against human multiple myeloma. Blood 117, 1311–1314 (2011).

    Article  CAS  Google Scholar 

  26. Tu, B.P. & Wang, J.C. Protein footprinting at cysteines: probing ATP-modulated contacts in cysteine-substitution mutants of yeast DNA topoisomerase II. Proc. Natl. Acad. Sci. USA 96, 4862–4867 (1999).

    Article  CAS  Google Scholar 

  27. Underbakke, E.S., Zhu, Y. & Kiessling, L.L. Isotope-coded affinity tags with tunable reactivities for protein footprinting. Angew. Chem. Int. Ed. Engl. 47, 9677–9680 (2008).

    Article  CAS  Google Scholar 

  28. Bowers, K.J. et al. in Proceedings of the ACM/IEEE Conference on Supercomputing (SC06) (Tampa, Florida, USA, 2006).

  29. Yoshida, H. et al. A time-dependent phase shift in the mammalian unfolded protein response. Dev. Cell 4, 265–271 (2003).

    Article  CAS  Google Scholar 

  30. Lu, P.D. et al. Cytoprotection by pre-emptive conditional phosphorylation of translation initiation factor 2. EMBO J. 23, 169–179 (2004).

    Article  CAS  Google Scholar 

  31. Huang, C.J. et al. High expression rates of human islet amyloid polypeptide induce endoplasmic reticulum stress–mediated β-cell apoptosis, a characteristic of humans with type 2 but not type 1 diabetes. Diabetes 56, 2016–2027 (2007).

    Article  CAS  Google Scholar 

  32. Oyadomari, S. et al. Targeted disruption of the Chop gene delays endoplasmic reticulum stress-mediated diabetes. J. Clin. Invest. 109, 525–532 (2002).

    Article  CAS  Google Scholar 

  33. Feldman, D.E., Chauhan, V. & Koong, A.C. The unfolded protein response: a novel component of the hypoxic stress response in tumors. Mol. Cancer Res. 3, 597–605 (2005).

    Article  CAS  Google Scholar 

  34. Cross, B.C. et al. The molecular basis for selective inhibition of unconventional mRNA splicing by an IRE1-binding small molecule. Proc. Natl. Acad. Sci. USA 109, E869–E878 (2012).

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by the US National Institutes of Health Director's New Innovator Award DP2 OD001925 (F.R.P.), RO1 DK080955 (F.R.P.), RO1 CA136577 (S.A.O.), R00 GM080097 (M.A.S.) and R01 GM086858 (D.J.M.), an American Cancer Society Research Scholar Award (S.A.O.) and the Burroughs Wellcome (F.R.P.), Juvenile Diabetes Research (F.R.P.) and Sloan (D.J.M.) Foundations. S.B.H. was supported by a predoctoral fellowship from the American Heart Association.

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Author notes

  1. Likun Wang, B Gayani K Perera, Feroz R Papa and Dustin J Maly: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Medicine, University of California–San Francisco, San Francisco, California, USA

    Likun Wang, Bradley J Backes & Feroz R Papa

  2. Lung Biology Center, University of California–San Francisco, San Francisco, California, USA

    Likun Wang, Bradley J Backes & Feroz R Papa

  3. Diabetes Center, University of California–San Francisco, San Francisco, California, USA

    Likun Wang & Feroz R Papa

  4. California Institute for Quantitative Biosciences, University of California–San Francisco, San Francisco, California, USA

    Likun Wang & Feroz R Papa

  5. Department of Pathology, University of California–San Francisco, San Francisco, California, USA

    Scott A Oakes

  6. Department of Chemistry, University of Washington, Seattle, Washington, USA

    B Gayani K Perera, Sanjay B Hari & Dustin J Maly

  7. Department of Pharmacological Sciences, Stony Brook University Medical School, Stony Brook, New York, USA

    Markus A Seeliger

  8. Center for Computational Science, University of Miami, Florida, USA

    Barun Bhhatarai & Stephan C Schürer

  9. Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Florida, USA.,

    Stephan C Schürer

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Contributions

F.R.P. and D.J.M. contributed equally as senior authors to the study. F.R.P. and D.J.M. conceived the idea and designed the study. With the guidance of F.R.P. and D.J.M., L.W. designed and performed the biochemical and cellular studies. B.G.K.P. designed and performed all of the chemical syntheses. S.B.H. performed footprinting experiments. B.B. and S.C.S. performed molecular modeling studies. All authors designed experiments, analyzed data and commented on the manuscript. F.R.P. and D.J.M. cowrote the paper.

Corresponding authors

Correspondence to Feroz R Papa or Dustin J Maly.

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Wang, L., Perera, B., Hari, S. et al. Divergent allosteric control of the IRE1α endoribonuclease using kinase inhibitors. Nat Chem Biol 8, 982–989 (2012). https://doi.org/10.1038/nchembio.1094

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