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Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases

Nature Structural & Molecular Biology volume 20, pages 502–507 (2013)Cite this article

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Abstract

ADP-ribosylation is an important post-translational protein modification (PTM) that regulates diverse biological processes. ADP-ribosyltransferase diphtheria toxin-like 10 (ARTD10, also known as PARP10) mono-ADP-ribosylates acidic side chains and is one of eighteen ADP-ribosyltransferases that catalyze mono- or poly-ADP-ribosylation of target proteins. Currently, no enzyme is known that reverses ARTD10-catalyzed mono-ADP-ribosylation. Here we report that ARTD10-modified targets are substrates for the macrodomain proteins MacroD1, MacroD2 and C6orf130 from Homo sapiens as well as for the macrodomain protein Af1521 from archaebacteria. Structural modeling and mutagenesis of MacroD1 and MacroD2 revealed a common core structure with Asp102 and His106 of MacroD2 implicated in the hydrolytic reaction. Notably, MacroD2 reversed the ARTD10-catalyzed, mono-ADP-ribose–mediated inhibition of glycogen synthase kinase 3β (GSK3β) in vitro and in cells, thus underlining the physiological and regulatory importance of mono-ADP-ribosylhydrolase activity. Our results establish macrodomain-containing proteins as mono-ADP-ribosylhydrolases and define a class of enzymes that renders mono-ADP-ribosylation a reversible modification.

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Figure 1: MacroD1, MacroD2, C6orf130 and Af1521 hydrolyze mono-ADP-ribose modifications.
Figure 2: MacroD2 is a mono-ADP-ribosylhydrolase specific for aspartates and glutamates.
Figure 3: Structural and mutational analysis of the mono-ADP-ribosylhydrolase activity of MacroD2.
Figure 4: MacroD2 functionally and specifically regulates mono-ADP-ribosylation of GSK3β in vitro and in cells.

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References

  1. Erener, S. et al. ARTD1 deletion causes increased hepatic lipid accumulation in mice fed a high-fat diet and impairs adipocyte function and differentiation. FASEB J. 26, 2631–2638 (2012).

    Article  CAS  PubMed  Google Scholar 

  2. Altmeyer, M. & Hottiger, M.O. Poly(ADP-ribose) polymerase 1 at the crossroad of metabolic stress and inflammation in aging. Aging 1, 458–469 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  3. Hassa, P.O., Haenni, S., Elser, M. & Hottiger, M.O. Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going? Microbiol. Mol. Biol. Rev. 70, 789–829 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Telli, M.L. PARP inhibitors in cancer: moving beyond BRCA. Lancet Oncol. 12, 827–828 (2011).

    Article  PubMed  Google Scholar 

  5. Curtin, N.J. PARP inhibitors for cancer therapy. Expert Rev. Mol. Med. 7, 1–20 (2005).

    Article  PubMed  Google Scholar 

  6. Schreiber, V., Dantzer, F., Ame, J.-C. & De Murcia, G. Poly(ADP-ribose): novel functions for an old molecule. Nat. Rev. Mol. Cell Biol. 7, 517–528 (2006).

    Article  CAS  PubMed  Google Scholar 

  7. Kleine, H. et al. Substrate-assisted catalysis by PARP10 limits its activity to mono-ADP-ribosylation. Mol. Cell 32, 57–69 (2008).

    Article  CAS  PubMed  Google Scholar 

  8. Feijs, K.L.H. et al. ARTD10 substrate identification on protein microarrays: regulation of GSK3β by mono-ADP-ribosylation. Cell Commun. Signal published online, doi:10.1186/1478-811X-11-5 (19 January 2013).

  9. Hottiger, M.O., Hassa, P.O., Lüscher, B., Schüler, H. & Koch-Nolte, F. Toward a unified nomenclature for mammalian ADP-ribosyltransferases. Trends Biochem. Sci. 35, 208–219 (2010).

    Article  CAS  PubMed  Google Scholar 

  10. Hanai, S. et al. Loss of poly(ADP-ribose) glycohydrolase causes progressive neurodegeneration in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 101, 82–86 (2004).

    Article  CAS  PubMed  Google Scholar 

  11. Koh, D.W. et al. Failure to degrade poly(ADP-ribose) causes increased sensitivity to cytotoxicity and early embryonic lethality. Proc. Natl. Acad. Sci. USA 101, 17699–17704 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Williams, J.C., Chambers, J.P. & Liehr, J.G. Glutamyl ribose 5-phosphate storage disease. A hereditary defect in the degradation of poly(ADP-ribosylated) proteins. J. Biol. Chem. 259, 1037–1042 (1984).

    CAS  PubMed  Google Scholar 

  13. Slade, D. et al. The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase. Nature 477, 616–620 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Dunstan, M.S. et al. Structure and mechanism of a canonical poly(ADP-ribose) glycohydrolase. Nat. Commun. 3, 878 (2012).

    Article  PubMed  Google Scholar 

  15. Han, W., Li, X. & Fu, X. The macro domain protein family: structure, functions, and their potential therapeutic implications. Mutat. Res. 727, 86–103 (2011).

    Article  CAS  PubMed  Google Scholar 

  16. Kim, I.K. et al. Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element. Nat. Struct. Mol. Biol. 19, 653–656 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Karras, G.I. et al. The macro domain is an ADP-ribose binding module. EMBO J. 24, 1911–1920 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Neuvonen, M. & Ahola, T. Differential activities of cellular and viral macro domain proteins in binding of ADP-ribose metabolites. J. Mol. Biol. 385, 212–225 (2009).

    Article  CAS  PubMed  Google Scholar 

  19. Angelov, D. et al. The histone variant macroH2A interferes with transcription factor binding and SWI/SNF nucleosome remodeling. Mol. Cell 11, 1033–1041 (2003).

    Article  CAS  PubMed  Google Scholar 

  20. Buschbeck, M. et al. The histone variant macroH2A is an epigenetic regulator of key developmental genes. Nat. Struct. Mol. Biol. 16, 1074–1079 (2009).

    Article  CAS  PubMed  Google Scholar 

  21. Changolkar, L.N. et al. Developmental changes in histone macroH2A1-mediated gene regulation. Mol. Cell Biol. 27, 2758–2764 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Goenka, S., Cho, S.H. & Boothby, M. Collaborator of Stat6 (CoaSt6)-associated poly(ADP-ribose) polymerase activity modulates Stat6-dependent gene transcription. J. Biol. Chem. 282, 18732–18739 (2007).

    Article  CAS  PubMed  Google Scholar 

  23. Ahel, D. et al. Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1. Science 325, 1240–1243 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Gottschalk, A.J. et al. Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler. Proc. Natl. Acad. Sci. USA 106, 13770–13774 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Aguiar, R.C., Takeyama, K., He, C., Kreinbrink, K. & Shipp, M.A. B-aggressive lymphoma family proteins have unique domains that modulate transcription and exhibit poly(ADP-ribose) polymerase activity. J. Biol. Chem. 280, 33756–33765 (2005).

    Article  CAS  PubMed  Google Scholar 

  26. Aguiar, R.C. et al. BAL is a novel risk-related gene in diffuse large B-cell lymphomas that enhances cellular migration. Blood 96, 4328–4334 (2000).

    CAS  PubMed  Google Scholar 

  27. Cho, S.H. et al. Glycolytic rate and lymphomagenesis depend on PARP14, an ADP ribosyltransferase of the B aggressive lymphoma (BAL) family. Proc. Natl. Acad. Sci. USA 108, 15972–15977 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Chen, D. et al. Identification of macrodomain proteins as novel O-acetyl-ADP-ribose deacetylases. J. Biol. Chem. 286, 13261–13271 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Peterson, F.C. et al. Orphan macrodomain protein (human C6orf130) is an O-acyl-ADP-ribose deacylase: solution structure and catalytic properties. J. Biol. Chem. 286, 35955–35965 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Hofmann, A. et al. Structure and mechanism of activity of the cyclic phosphodiesterase of Appr>p, a product of the tRNA splicing reaction. EMBO J. 19, 6207–6217 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Sawaya, R., Schwer, B. & Shuman, S. Structure-function analysis of the yeast NAD+-dependent tRNA 2′-phosphotransferase Tpt1. RNA 11, 107–113 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Stone, P.R. & Hilz, H. Quantitation of hydroxylamine sensitive mono(adenosine diphosphate ribose) residues in different hepatic tissues. FEBS Lett. 57, 209–212 (1975).

    Article  CAS  PubMed  Google Scholar 

  33. Barth, H., Aktories, K., Popoff, M.R. & Stiles, B.G. Binary bacterial toxins: biochemistry, biology, and applications of common Clostridium and Bacillus proteins. Microbiol. Mol. Biol. Rev. 68, 373–402 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Lang, A.E. et al. Photorhabdus luminescens toxins ADP-ribosylate actin and RhoA to force actin clustering. Science 327, 1139–1142 (2010).

    Article  CAS  PubMed  Google Scholar 

  35. Timinszky, G. et al. A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation. Nat. Struct. Mol. Biol. 16, 923–929 (2009).

    Article  CAS  PubMed  Google Scholar 

  36. Jope, R.S. & Johnson, G.V. The glamour and gloom of glycogen synthase kinase-3. Trends Biochem. Sci. 29, 95–102 (2004).

    Article  CAS  PubMed  Google Scholar 

  37. Jackson, M.D. & Denu, J.M. Structural identification of 2′- and 3′-O-acetyl-ADP-ribose as novel metabolites derived from the Sir2 family of β-NAD+-dependent histone/protein deacetylases. J. Biol. Chem. 277, 18535–18544 (2002).

    Article  CAS  PubMed  Google Scholar 

  38. Sauve, A.A. et al. Chemistry of gene silencing: the mechanism of NAD+-dependent deacetylation reactions. Biochemistry 40, 15456–15463 (2001).

    Article  CAS  PubMed  Google Scholar 

  39. Jackson, M.D., Schmidt, M.T., Oppenheimer, N.J. & Denu, J.M. Mechanism of nicotinamide inhibition and transglycosidation by Sir2 histone/protein deacetylases. J. Biol. Chem. 278, 50985–50998 (2003).

    Article  CAS  PubMed  Google Scholar 

  40. Kleine, H. et al. Dynamic subcellular localization of the mono-ADP-ribosyltransferase ARTD10 and interaction with the ubiquitin receptor p62. Cell Commun. Signal. 10, 28 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Forst, A.H. et al. Recognition of mono-ADP-ribosylated ARTD10 substrates by ART8 macrodomains. Structure (in the press).

  42. Gülke, I. et al. Characterization of the enzymatic component of the ADP-ribosyltransferase toxin CDTa from Clostridium difficile. Infect. Immun. 69, 6004–6011 (2001).

    Article  PubMed  PubMed Central  Google Scholar 

  43. Eswar, N. et al. Comparative protein structure modeling using Modeller. in Curr. Protoc. Bioinformatics 15, 5.6 (2006).

    Article  Google Scholar 

  44. Martí-Renom, M.A. et al. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291–325 (2000).

    Article  PubMed  Google Scholar 

  45. Sali, A. & Blundell, T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779–815 (1993).

    Article  CAS  PubMed  Google Scholar 

  46. Fiser, A., Do, R.K. & Sali, A. Modeling of loops in protein structures. Protein Sci. 9, 1753–1773 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Shen, M.Y. & Sali, A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 15, 2507–2524 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Seeber, M., Cecchini, M., Rao, F., Settanni, G. & Caflisch, A. Wordom: a program for efficient analysis of molecular dynamics simulations. Bioinformatics 23, 2625–2627 (2007).

    Article  CAS  PubMed  Google Scholar 

  49. Seeber, M. et al. Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. J. Comput. Chem. 32, 1183–1194 (2011).

    Article  CAS  PubMed  Google Scholar 

  50. Trott, O. & Olson, A.J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 31, 455–461 (2010).

    CAS  PubMed Central  PubMed  Google Scholar 

  51. Vanommeslaeghe, K. et al. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem. 31, 671–690 (2010).

    CAS  PubMed Central  PubMed  Google Scholar 

  52. Brooks, B.R. et al. CHARMM: the biomolecular simulation program. J. Comput. Chem. 30, 1545–1614 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We are grateful to I. Ahel (Paterson Institute for Cancer Research, Manchester, UK) and M. Neuvonen (Institute of Biotechnology, University of Helsinki, Helsinki, Finland) for MacroD1 and MacroD2 constructs and J. Moss (National Institutes of Health, Bethesda, Maryland, USA) for the ARH1 construct. F. Althaus (University of Zurich, Zurich, Switzerland) and K. Aktories (University of Freiburg, Freiburg, Germany) are acknowledged for generously providing a baculovirus expressing PARG and the CDTa and TccC3 enzymes together with purified actin, respectively. F. Freimoser (University of Zurich, Zurich, Switzerland) provided editorial assistance and critical input during the writing and M. Fey technical assistance. This work was supported by the Deutsche Forschungsgemeinschaft DFG (LU 466/15-1) to B.L. and in part by the University of Zurich (Forschungskredit 54041205 to E.F.), the Swiss National Science Foundation (SNF-31003A_125190 (to P.O.H.) and 31-122421 (to M.O.H.)) and the Kanton of Zurich (to M.O.H.).

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  1. Florian Rosenthal and Karla L H Feijs: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland

    Florian Rosenthal, Mario Bonalli, Ralph Imhof, Hans C Winkler, Paul O Hassa & Michael O Hottiger

  2. Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland

    Florian Rosenthal

  3. Institute of Biochemistry and Molecular Biology, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany

    Karla L H Feijs, Alexandra H Forst & Bernhard Lüscher

  4. Department of Biochemistry, University of Zurich, Zurich, Switzerland

    Emilie Frugier & Amedeo Caflisch

  5. Functional Genomics Center Zurich, University of Zurich, Zurich, Switzerland

    David Fischer

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Contributions

F.R. and P.O.H. performed experiments with MacroD1, MacroD2 and other macrodomains, and MS analysis was done together with D.F.; K.L.H.F. analyzed the influence of MacroD2 on GSK3β; E.F. performed the computer modeling; E.F. and A.C. analyzed the modeling and simulation results; M.B. identified MacroD2 as an ADP-ribosylhydrolase; A.H.F. cloned and purified mMacro1 and mMacro2; R.I. performed the HPLC analysis; H.C.W. compared the macro sequences; A.C., P.O.H., B.L. and M.O.H. supervised the work. B.L. and M.O.H. wrote the manuscript.

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Correspondence to Bernhard Lüscher or Michael O Hottiger.

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Rosenthal, F., Feijs, K., Frugier, E. et al. Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases. Nat Struct Mol Biol 20, 502–507 (2013). https://doi.org/10.1038/nsmb.2521

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