The Nod-Like Receptor (NLR) family: A tale of similarities and differences

PLoS ONE

Volumn 3, Issue 4, 2008, Pages

  Proell, Martina ^a   Riedl, Stefan J ^b   Fritz, Jörg H ^c   Rojas, Ana M ^d   Schwarzenbacher, Robert ^a  

^a UNIVERSITY OF SALZBURG   (Austria)

^b BURNHAM INSTITUTE   (United States)

^c UNIVERSITY OF TORONTO   (Canada)

^d Centro Nacional de Investigaciones Oncológicas   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

APOPTOSOME; APOPTOTIC PROTEASE ACTIVATING FACTOR 1; CELL PROTEIN; CELL RECEPTOR; LIGAND; NOD LIKE RECEPTOR; PROCASPASE 9; PROTEIN NLR; CELL SURFACE RECEPTOR; NUCLEOTIDE BINDING OLIGOMERIZATION DOMAIN PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; CELL FUNCTION; CONTROLLED STUDY; LIGAND BINDING; MOLECULAR EVOLUTION; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; OLIGOMERIZATION; PHYLOGENETIC TREE; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STRUCTURAL HOMOLOGY;

AMINO ACID SEQUENCE; BINDING SITES; EVOLUTION, MOLECULAR; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NOD SIGNALING ADAPTOR PROTEINS; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, CELL SURFACE; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 44349171085     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0002119     Document Type: Article

References (52)

1. Meylan E, Tschopp J, Karin M (2006) Intracelular pattern recognition receptors in the host response. Nature 442: 39-44.
2. Fritz JH, Ferrero RL, Philpott DJ, Girardin SE (2006) Nod-like proteins in immunity, inflammation and disease. Nat Immunol 7: 1250-1257.
3. Werts C, Girardin SE, Philpott DJ (2006) TIR, CARD and PYRIN: three domains for an antimicrobial triad. Cell Death Differ 13: 798-815.
4. Inohara N, Nunez G (2003) NODs: intracellular proteins involved in inflammation and apoptosis. Nat Rev Immunol 3: 371-382.
5. Mariathasan S, Newton K, Monack DM, Vucic D, French DM, et al. (2004) Differential activation of the inflammasome by caspase-1 adaptors ASC and lpaf. Nature 430: 213-218.
6. Inohara, Chamaillard, McDonald C, Nunez G (2005) NOD-LRR proteins: role in host-microbial interactions and inflammatory disease. Annu Rev Biochem 74: 355-383.
7. Faustin B, Reed JC (2008) Sunburned skin activates inflammasomes. Trends Cell Biol 18: 4-8.
8. Tattoli I, Travassos LH, Carneiro Lk, Magalhaes JG, Girardin SE (2007) The Nodosome: Nod1 and Nod2 control bacterial infections and inflammation. Semin Immunopathol 29: 289-301.
9. Lu C, Wang A, Wang L, Dorsch M, Ocain TD, et al. (2005) Nucleotide binding to CARD12 and its role in CARD12-mediated caspase-1 activation. Biochem Biophys Res Commun 331: 1114-1119.
10. Duncan JA, Bergstralh DT, Wang Y, Willingham SB, Ye Z, et al. (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: 8041-8046.
11. Colonna M (2007) All roads lead to CARD9. Nat Immunol 8: 554-555.
12. Martinon F (2007) Orchestration of pathogen recognition by inflammasome diversity: Variations on a common theme. Eur J Immunol 37: 3003-3006.
13. Martinon F, Gaide O, Petrilli V, Mayor A, Tschopp J (2007) NALP inflammasomes: a central role in innate immunity. Semin Immunopathol 29: 213-229.
14. Albrecht M, Takken FL (2006) Update on the domain architectures of NLRs and R proteins. Biochem Biophys Res Common 339: 459-462.
15. Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A (2005) FFAS03: a server for profile - profile sequence alignments. Nucleic Acids Res 33: W284-288.
16. Rost B, Yachdav G, Liu J (2004) The PredictProtein server. Nucleic Acids Res 32: W321-326.
17. Schultz J, Milpetz F, Bork P, Ponting CP (1998) SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A 95; 5857-5864.
18. Ammelburg M, Frickey T, Lupas AN (2006) Classification of AAA+ proteins. J Struct Biol 156: 2-11.
19. Leipe DD, Konnin EV, Aravind L (2004) STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer. J Mol Biol 343: 1-28.
20. Hu Y, Ding L, Spencer DM, Nunez G (1998) WD-40 repeat region regulates Apaf-1 self-association and procaspase-9 activation. J Biol Chem 273: 33489-33494.
21. Muhlethaler-Mottet A, Otten LA, Steimle V, Mach B (1997) Expression of MHC class II molecules in different cellular and functional compartments is controlled by differential usage of multiple promoters of the transactivator CIITA. Embo J 16: 2851-2860.
22. Iyer LM, Leipe DD, Koonin EV, Aravind L (2004) Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol 146: 11-31.
23. Edgar RC (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
24. Hanson PI, Whitcheart SW (2005) AAA+ proteins: have engine, will work. Nat Rev Mol Cell Biol 6: 519-529.
25. Ye Z, Lich JD, Moore CB, Duncan JA, Williams KL, et al. (2007) ATP binding by Monarch-1/NLRIP12 is critical for its inhibitory function. Mol Cell Biol.
26. Yan N, Chai J, Lee ES, Gu L, Liu Q, et al. (2005) Structure of the CED-4-CED-9 complex provides insights into programmed cell death in Caenorhabditis elegans. Nature 437: 831-837.
27. Rodriguez A, Oliver H, Zou H, Chen P, Wang X, et al. (1999) Dark is a Drosophila homologue of Apaf-1/CED-4 and functions in an evolutionarily conserved death pathway. Nat Cell Biol 1: 272-279.
28. Ogura T, Whiteheart SW, Wilkinson AJ (2004) Conserved arginine residues implicated in ATP hydrolysis, nucleotide-sensing, and inter-subunit interactions in AAA and AAA+ ATPases. J Struct Biol 146: 106-112.
29. Riedl SJ, Li W, Chao Y, Schwarzenbacher R, Shi Y (2005) Structure of the apoptotic protease-activating factor 1 bound to ADP. Nature 434: 926-933.
30. Yamada K, Kunishima N, Mayanagi K, Ohnishi T, Nishino T, et al. (2001) Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8. Proc Natl Acad Sci U S A 98: 1442-1447.
31. Lee SY, De La Torre A, Yan D, Kustu S, Nixon BT, et al. (2003) Regulation of the transcriptional activator NtrCl: structural studies of the regulatory and AAA+ ATPase domains. Genes Dev 17: 2552-2563.
32. Diemand AV, Lupas AN (2006) Modeling AAA+ ring complexes from monomeric structures. J Struct Biol 156: 230-243.
33. Yu X, Wang L, Acehan D, Wang X, Akey CW (2006) Three-dimensional structure of a double apoptosome formed by the Drosophila Apaf-1 related killer. J Mol Biol 355: 577-589.
34. Qui H, Srinivasula SM, Wu G, Fernandes-Alnemri T, Alnemri ES, et al. (1999) Structural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1. Nature 399: 549-557.
35. Manon F, Favier A, Nunez G, Simorre JP, Cusack S (2007) Solution structure of NOD1 CARD and mutational analysis of its interaction with the CARD of downstream kinase RICK. J Mol Biol 365: 160-174.
36. Natarajan A, Ghose R, Hill JM (2006) Structure and dynamics of ASC2, a pyrin domain-only protein that regulates inflammatory signaling. J Biel Chem 281: 31863-31875.
37. Liepinsh E, Barbals R, Dahl E, Sharipo A, Staub E, et al. (2003) The death-domain fold of the ASC PYRIN domain, presenting a basis for PYRIN/ PYRIN recognition. J Mol Biel 332: 1155-1163.
38. Enkhbayar P, Kamiya M, Osaki M, Matsumoto T, Matsushima N (2004) Structural principles of leucine-rich repeat (LRR) proteins. Proteins 54: 394-403.
39. Jin MS, Kim SE, Heo JY, Lee ME, Kim HM, et al. (2007) Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide. Cell 130: 1071-1082.
40. Kim HE, Du F, Fang M, Wang X (2005) Formation of apoptosome is initiated by cytochrome c-induced dATP hydrolysis and subsequent nucleotide exchange on Apaf-1. Proc. Natl Acad Sci U S A 102: 17545-17550.
41. Tanabe T, Chamaillard M, Ogura Y, Zhu L, Qui S, et al. (2004) Regulatory regions and critical residues of NOD2 involved in muramyl dipeptide recognition. Embo J 23: 1587-1597.
42. Kobe B, Deisenhofer J (1995) A structural basis of the interactions between leucine-rich repeats and protein ligands. Nature 374: 183-186.
43. Papageorgiou AC, Shapiro R, Acharya KR (1997) Molecular recognition of human angiogenin by placental ribionuclease inhibitor-an X-ray crystallographic study at 2.0 A resolution. Embo J 16: 5162-5177.
44. Price SR, Evans PR, Nagai K (1998) Crystal structure of the spliccosomal U2B"-U2A' protein complex bound to a fragment of U2 small nuclear RNA. Nature 394: 645-650.
45. Miceli-Richard C, Lesage S, Rybojad M, Pricur AM, Manouvrier-Hanu S, et al. (2001) CARD15 mutations in Blau syndrome. Nat Genet 29: 19-20.
46. Hugot JP, Chamaillard M, Zouali H, Lesage S, Cezard JP, et al. (2001) Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature 411: 599-603.
47. Hysi P, Kabesch M, Moffatt MF, Schedel M, Care D, et al. (2005) NOD1 variation, immunoglobulin E and asthma. Hum Mol Genet 14: 935-941.
48. 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: 301-305.
49. Feldmann J, Prieur AM, Quartier P, Berquin P, Certain S, et al. (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: 198-203.
50. Wallace IM, O'Sullivan O, Higgins DG, Notredame C (2006) M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res 34: 1692-1699.
51. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
52. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.