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Assessing ATP Binding and Hydrolysis by NLR Proteins

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The Inflammasome

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1040))

Abstract

Nucleotide-binding and leucine rich repeat domain-containing proteins (NLRs) are central to the formation of many inflammasome complexes. Several inflammasome forming NLR proteins are known to be ATPases, but the nucleotide binding specificity of many remains to be characterized. The oligomerization of NLR proteins and assembly of inflammasomes require the ATP (or other nucleotide) binding activity of the NLR proteins. Quantitative and qualitative studies of the nucleotide binding properties of these proteins are useful tools in studying the regulation of inflammasome activity, and are outlined in this Chapter.

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References

  1. Martinon F, Burns K, Tschopp J (2002) The inflammasome: a molecular platform triggering activation of inflammatory caspases and processing of proIL-beta. Mol Cell 10(2):417–426

    Article  PubMed  CAS  Google Scholar 

  2. Agostini L, Martinon F, Burns K, McDermott MF, Hawkins PN, Tschopp J (2004) NALP3 forms an IL-1beta-processing inflammasome with increased activity in Muckle-Wells autoinflammatory disorder. Immunity 20(3):319–325

    Article  PubMed  CAS  Google Scholar 

  3. Hornung V, Ablasser A, Charrel-Dennis M, Bauernfeind F, Horvath G, Caffrey DR, Latz E, Fitzgerald KA (2009) AIM2 recognizes cytosolic dsDNA and forms a caspase-1-­activating inflammasome with ASC. Nature 458(7237):514–518. doi:10.1038/nature07725

    Article  PubMed  CAS  Google Scholar 

  4. Duncan JA, Bergstralh DT, Wang Y, Willingham SB, Ye Z, Zimmermann AG, Ting JP (2007) Cryopyrin/NALP3 binds ATP/dATP, is an ATPase, and requires ATP binding to mediate inflammatory signaling. Proc Natl Acad Sci U S A 104(19):8041–8046

    Article  PubMed  CAS  Google Scholar 

  5. Faustin B, Lartigue L, Bruey JM, Luciano F, Sergienko E, Bailly-Maitre B, Volkmann N, Hanein D, Rouiller I, Reed JC (2007) Reconstituted NALP1 inflammasome reveals two-step mechanism of caspase-1 activation. Mol Cell 25(5):713–724

    Article  PubMed  CAS  Google Scholar 

  6. Ting JP, Lovering RC, Alnemri ES, Bertin J, Boss JM, Davis BK, Flavell RA, Girardin SE, Godzik A, Harton JA, Hoffman HM, Hugot JP, Inohara N, Mackenzie A, Maltais LJ, Nunez G, Ogura Y, Otten LA, Philpott D, Reed JC, Reith W, Schreiber S, Steimle V, Ward PA (2008) The NLR gene family: a standard nomenclature. Immunity 28(3):285–287

    Article  PubMed  CAS  Google Scholar 

  7. Genini D, Budihardjo I, Plunkett W, Wang X, Carrera CJ, Cottam HB, Carson DA, Leoni LM (2000) Nucleotide requirements for the in vitro activation of the apoptosis protein-­activating factor-1-mediated caspase pathway. J Biol Chem 275(1):29–34

    Article  PubMed  CAS  Google Scholar 

  8. Jiang X, Wang X (2000) Cytochrome c promotes caspase-9 activation by inducing nucleotide binding to Apaf-1. J Biol Chem 275(40):31199–31203. doi:10.1074/jbc.C000405200

    Article  PubMed  CAS  Google Scholar 

  9. Tameling WI, Elzinga SD, Darmin PS, Vossen JH, Takken FL, Haring MA, Cornelissen BJ (2002) The tomato R gene products I-2 and MI-1 are functional ATP binding proteins with ATPase activity. Plant Cell 14(11):2929–2939

    Article  PubMed  CAS  Google Scholar 

  10. Tameling WI, Vossen JH, Albrecht M, Lengauer T, Berden JA, Haring MA, Cornelissen BJ, Takken FL (2006) Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation. Plant Physiol 140(4):1233–1245

    Article  PubMed  CAS  Google Scholar 

  11. Ting JP, Kastner DL, Hoffman HM (2006) CATERPILLERs, pyrin and hereditary immunological disorders. Nat Rev Immunol 6(3):183–195

    Article  PubMed  CAS  Google Scholar 

  12. Hugot JP, Chamaillard M, Zouali H, Lesage S, Cezard JP, Belaiche J, Almer S, Tysk C, O’Morain CA, Gassull M, Binder V, Finkel Y, Cortot A, Modigliani R, Laurent-Puig P, Gower-Rousseau C, Macry J, Colombel JF, Sahbatou M, Thomas G (2001) Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn’s disease. Nature 411(6837):599–603

    Article  PubMed  CAS  Google Scholar 

  13. Miceli-Richard C, Lesage S, Rybojad M, Prieur AM, Manouvrier-Hanu S, Hafner R, Chamaillard M, Zouali H, Thomas G, Hugot JP (2001) CARD15 mutations in Blau syndrome. Nat Genet 29(1):19–20

    Article  PubMed  CAS  Google Scholar 

  14. Ogura Y, Bonen DK, Inohara N, Nicolae DL, Chen FF, Ramos R, Britton H, Moran T, Karaliuskas R, Duerr RH, Achkar JP, Brant SR, Bayless TM, Kirschner BS, Hanauer SB, Nunez G, Cho JH (2001) A frameshift mutation in NOD2 associated with susceptibility to Crohn’s disease. Nature 411(6837):603–606

    Article  PubMed  CAS  Google Scholar 

  15. Hampe J, Cuthbert A, Croucher PJ, Mirza MM, Mascheretti S, Fisher S, Frenzel H, King K, Hasselmeyer A, MacPherson AJ, Bridger S, van Deventer S, Forbes A, Nikolaus S, Lennard-Jones JE, Foelsch UR, Krawczak M, Lewis C, Schreiber S, Mathew CG (2001) Association between insertion mutation in NOD2 gene and Crohn’s disease in German and British populations. Lancet 357(9272):1925–1928

    Article  PubMed  CAS  Google Scholar 

  16. Hoffman HM, Mueller JL, Broide DH, Wanderer AA, Kolodner RD (2001) Mutation of a new gene encoding a putative pyrin-like protein causes familial cold autoinflammatory syndrome and Muckle-Wells syndrome. Nat Genet 29(3):301–305

    Article  PubMed  CAS  Google Scholar 

  17. Wang X, Kuivaniemi H, Bonavita G, Mutkus L, Mau U, Blau E, Inohara N, Nunez G, Tromp G, Williams CJ (2002) CARD15 mutations in familial granulomatosis syndromes: a study of the original Blau syndrome kindred and other families with large-vessel arteritis and cranial neuropathy. Arthritis Rheum 46(11):3041–3045

    Article  PubMed  CAS  Google Scholar 

  18. Aganna E, Martinon F, Hawkins PN, Ross JB, Swan DC, Booth DR, Lachmann HJ, Bybee A, Gaudet R, Woo P, Feighery C, Cotter FE, Thome M, Hitman GA, Tschopp J, McDermott MF (2002) Association of mutations in the NALP3/CIAS1/PYPAF1 gene with a broad phenotype including recurrent fever, cold sensitivity, sensorineural deafness, and AA amyloidosis. Arthritis Rheum 46(9):2445–2452

    Article  PubMed  CAS  Google Scholar 

  19. Aksentijevich I, Nowak M, Mallah M, Chae JJ, Watford WT, Hofmann SR, Stein L, Russo R, Goldsmith D, Dent P, Rosenberg HF, Austin F, Remmers EF, Balow JE Jr, Rosenzweig S, Komarow H, Shoham NG, Wood G, Jones J, Mangra N, Carrero H, Adams BS, Moore TL, Schikler K, Hoffman H, Lovell DJ, Lipnick R, Barron K, O’Shea JJ, Kastner DL, Goldbach-­Mansky R (2002) De novo CIAS1 mutations, cytokine activation, and evidence for genetic heterogeneity in patients with neonatal-onset multisystem inflammatory disease (NOMID): a new member of the expanding family of pyrin-associated autoinflammatory diseases. Arthritis Rheum 46(12):3340–3348

    Article  PubMed  CAS  Google Scholar 

  20. Dode C, Le Du N, Cuisset L, Letourneur F, Berthelot JM, Vaudour G, Meyrier A, Watts RA, Scott DG, Nicholls A, Granel B, Frances C, Garcier F, Edery P, Boulinguez S, Domergues JP, Delpech M, Grateau G (2002) New mutations of CIAS1 that are responsible for Muckle-Wells syndrome and familial cold urticaria: a novel mutation underlies both ­syndromes. Am J Hum Genet 70(6):1498–1506

    Article  PubMed  CAS  Google Scholar 

  21. Feldmann J, Prieur AM, Quartier P, Berquin P, Certain S, Cortis E, Teillac-Hamel D, Fischer A, de Saint Basile G (2002) Chronic infantile neurological cutaneous and articular syndrome is caused by mutations in CIAS1, a gene highly expressed in polymorphonuclear cells and chondrocytes. Am J Hum Genet 71(1):198–203

    Article  PubMed  CAS  Google Scholar 

  22. Dowds TA, Masumoto J, Chen FF, Ogura Y, Inohara N, Nunez G (2003) Regulation of cryopyrin/Pypaf1 signaling by pyrin, the familial Mediterranean fever gene product. Biochem Biophys Res Commun 302(3):575–580

    Article  PubMed  CAS  Google Scholar 

  23. Goldbach-Mansky R, Dailey NJ, Canna SW, Gelabert A, Jones J, Rubin BI, Kim HJ, Brewer C, Zalewski C, Wiggs E, Hill S, Turner ML, Karp BI, Aksentijevich I, Pucino F, Penzak SR, Haverkamp MH, Stein L, Adams BS, Moore TL, Fuhlbrigge RC, Shaham B, Jarvis JN, O’Neil K, Vehe RK, Beitz LO, Gardner G, Hannan WP, Warren RW, Horn W, Cole JL, Paul SM, Hawkins PN, Pham TH, Snyder C, Wesley RA, Hoffmann SC, Holland SM, Butman JA, Kastner DL (2006) Neonatal-­onset multisystem inflammatory disease responsive to interleukin-1beta inhibition. N Engl J Med 355(6):581–592

    Article  PubMed  CAS  Google Scholar 

  24. Harton JA, Cressman DE, Chin KC, Der CJ, Ting JP (1999) GTP binding by class II transactivator: role in nuclear import. Science 285(5432):1402–1405

    Article  PubMed  CAS  Google Scholar 

  25. Lu C, Wang A, Wang L, Dorsch M, Ocain TD, Xu Y (2005) Nucleotide binding to CARD12 and its role in CARD12-mediated caspase-1 activation. Biochem Biophys Res Commun 331(4):1114–1119. doi:10.1016/j.bbrc.2005.04.027

    Article  PubMed  CAS  Google Scholar 

  26. Ye Z, Lich JD, Moore CB, Duncan JA, Williams KL, Ting JP (2008) ATP binding by monarch-1/NLRP12 is critical for its inhibitory function. Mol Cell Biol 28(5):1841–1850

    Article  PubMed  CAS  Google Scholar 

  27. Askari N, Correa RG, Zhai D, Reed JC (2012) Expression, purification, and characterization of recombinant NOD1 (NLRC1): a NLR family member. J Biotechnol 157(1):75–81. doi:10.1016/j.jbiotec.2011.10.007

    Article  PubMed  CAS  Google Scholar 

  28. Mo J, Boyle JP, Howard CB, Monie TP, Davis BK, Duncan JA (2012) Pathogen sensing by nucleotide-binding oligomerization domain-­containing protein 2 (NOD2) is mediated by direct binding to muramyl dipeptide and ATP. J Biol Chem 287(27):23057–23067. doi:10.1074/jbc.M112.344283

    Article  PubMed  CAS  Google Scholar 

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Acknowledgment

This work was supported by the National Institutes of Health through grant AI088255 and the Burroughs Wellcome Fund Career Award for Medical Scientists.

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Authors and Affiliations

  1. Division of Infectious Diseases, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA

    Jinyao Mo & Joseph A. Duncan

Authors
  1. Jinyao Mo
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  2. Joseph A. Duncan
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Editor information

Editors and Affiliations

  1. , Institute of Innate Immunity, University of Bonn, Sigmund-Freud-Strasse 25, Bonn, 53105, Germany

    Christine M. De Nardo

  2. , Institute of Innate Immunity, University of Bonn, Sigmund-Freud-Str. 25, Bonn, 53105, Germany

    Eicke Latz

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Mo, J., Duncan, J.A. (2013). Assessing ATP Binding and Hydrolysis by NLR Proteins. In: De Nardo, C., Latz, E. (eds) The Inflammasome. Methods in Molecular Biology, vol 1040. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-523-1_12

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  • DOI: https://doi.org/10.1007/978-1-62703-523-1_12

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-522-4

  • Online ISBN: 978-1-62703-523-1

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