Exploring the diversity of SPRY/B30.2-mediated interactions

Trends in Biochemical Sciences

Volumn 38, Issue 1, 2013, Pages 38-46

  Perfetto, Livia ^a   Gherardini, Pier Federico ^a   Davey, Norman E ^c   Diella, Francesca ^c,d   Helmer Citterich, Manuela ^a   Cesareni, Gianni ^a,b  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b IRCCS FONDAZIONE SANTA LUCIA   (Italy)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^d Molecular Health GmbH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

INTERLEUKIN 1BETA; INTERLEUKIN 1BETA CONVERTING ENZYME;

BETA SHEET; BINDING AFFINITY; CARCINOGENESIS; CYTOKINE RELEASE; FAMILIAL MEDITERRANEAN FEVER; GENE; HUMAN; MUTATION; NONHUMAN; OPITZ SYNDROME; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; TRIM GENE; TRIM18 GENE; TRIM27 GENE; TRIM5ALPHA GENE; UBIQUITINATION;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; ANIMALS; CARRIER PROTEINS; HUMANS; MACROMOLECULAR SUBSTANCES; MEMBRANE PROTEINS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY;

EUKARYOTA;

EID: 84871474752     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibs.2012.10.001     Document Type: Review

References (80)

1. Bhattacharyya R.P., et al. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu. Rev. Biochem. 2006, 75:655-680.
2. Modular Protein Domains 2004, InterScience. G. Cesareni (Ed.).
3. Copley R.R., et al. Eukaryotic domain evolution inferred from genome comparisons. Curr. Opin. Genet. Dev. 2003, 13:623-628.
4. Tonikian R., et al. Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol. 2009, 7:e1000218.
5. Carducci M., et al. The protein interaction network mediated by human SH3 domains. Biotechnol. Adv. 2012, 30:4-15.
6. Vogel C., Chothia C. Protein family expansions and biological complexity. PLoS Comput. Biol. 2006, 2:e48.
7. Sigrist C.J., et al. PROSITE, a protein domain database for functional characterization and annotation. Nucleic. Acids Res. 2010, 38:D161-D166.
8. Rhodes D.A., et al. Relationship between SPRY and B30.2 protein domains. Evolution of a component of immune defence?. Immunology 2005, 116:411-417.
9. Vernet C., et al. Evolutionary study of multigenic families mapping close to the human MHC class I region. J. Mol. Evol. 1993, 37:600-612.
10. Meyer M., et al. Cluster of TRIM genes in the human MHC class I region sharing the B30.2 domain. Tissue Antigens 2003, 61:63-71.
11. Henry J., et al. Cloning, structural analysis, and mapping of the B30 and B7 multigenic families to the major histocompatibility complex (MHC) and other chromosomal regions. Immunogenetics 1997, 46:383-395.
12. Henry J., et al. B30.2-like domain proteins: update and new insights into a rapidly expanding family of proteins. Mol. Biol. Evol. 1998, 15:1696-1705.
13. Ponting C., et al. SPRY domains in ryanodine receptors (Ca(2+)-release channels). Trends Biochem. Sci. 1997, 22:193-194.
14. Woo J.S., et al. Structural and functional insights into the B30.2/SPRY domain. EMBO J. 2006, 25:1353-1363.
15. Tae H., et al. Ubiquitous SPRY domains and their role in the skeletal type ryanodine receptor. Eur. Biophys. J. 2009, 39:51-59.
16. Seto M.H., et al. Protein fold analysis of the B30.2-like domain. Proteins 1999, 35:235-249.
17. Sardiello M., et al. Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties. BMC Evol. Biol. 2008, 8:225.
18. Ozato K., et al. TRIM family proteins and their emerging roles in innate immunity. Nat. Rev. Immunol. 2008, 8:849-860.
19. Kawai T., Akira S. Regulation of innate immune signalling pathways by the tripartite motif (TRIM) family proteins. EMBO Mol. Med. 2011, 3:513-527.
20. Carthagena L., et al. Human TRIM gene expression in response to interferons. PLoS ONE 2009, 4:e4894.
21. Stremlau M., et al. The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in Old World monkeys. Nature 2004, 427:848-853.
22. Ganser-Pornillos B.K., et al. Hexagonal assembly of a restricting TRIM5alpha protein. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:534-539.
23. Nakayama E.E., Shioda T. Role of human TRIM5alpha in intrinsic immunity. Front Microbiol. 2012, 3:97.
24. Diaz-Griffero F. Caging the beast: TRIM5alpha binding to the HIV-1 core. Viruses 2011, 3:423-428.
25. Li Y., et al. Removal of arginine 332 allows human TRIM5alpha to bind human immunodeficiency virus capsids and to restrict infection. J. Virol. 2006, 80:6738-6744.
26. Abeler-Dorner L., et al. Butyrophilins: an emerging family of immune regulators. Trends Immunol. 2012, 33:34-41.
27. Jeong J., et al. The PRY/SPRY/B30.2 domain of butyrophilin 1A1 (BTN1A1) binds to xanthine oxidoreductase: implications for the function of BTN1A1 in the mammary gland and other tissues. J. Biol. Chem. 2009, 284:22444-22456.
28. Zhang J.G., et al. The conserved SOCS box motif in suppressors of cytokine signaling binds to elongins B and C and may couple bound proteins to proteasomal degradation. Proc. Natl. Acad. Sci. U.S.A. 1999, 96:2071-2076.
29. Kile B.T., et al. The SOCS box: a tale of destruction and degradation. Trends Biochem. Sci. 2002, 27:235-241.
30. Li W., et al. Genome-wide and functional annotation of human E3 ubiquitin ligases identifies MULAN, a mitochondrial E3 that regulates the organelle's dynamics and signaling. PLoS ONE 2008, 3:e1487.
31. Huang da W., et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4:44-57.
32. Weinert C., et al. The crystal structure of human pyrin b30.2 domain: implications for mutations associated with familial Mediterranean fever. J. Mol. Biol. 2009, 394:226-236.
33. Chae J.J., et al. The familial Mediterranean fever protein, pyrin, is cleaved by caspase-1 and activates NF-kappaB through its N-terminal fragment. Blood 2008, 112:1794-1803.
34. Chae J.J., et al. The B30.2 domain of pyrin, the familial Mediterranean fever protein, interacts directly with caspase-1 to modulate IL-1beta production. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:9982-9987.
35. Ferrentino R., et al. MID1 mutation screening in a large cohort of Opitz G/BBB syndrome patients: twenty-nine novel mutations identified. Hum. Mutat. 2007, 28:206-207.
36. Aranda-Orgilles B., et al. The Opitz syndrome gene product MID1 assembles a microtubule-associated ribonucleoprotein complex. Hum. Genet. 2008, 123:163-176.
37. Trockenbacher A., et al. MID1, mutated in Opitz syndrome, encodes an ubiquitin ligase that targets phosphatase 2A for degradation. Nat. Genet. 2001, 29:287-294.
38. Hu C.H., et al. A MID1 gene mutation in a patient with Opitz G/BBB syndrome that altered the 3D structure of SPRY domain. Am. J. Med. Genet. A 2012, 158A:726-731.
39. Schweiger S., et al. The Opitz syndrome gene product, MID1, associates with microtubules. Proc. Natl. Acad. Sci. U.S.A. 1999, 96:2794-2799.
40. Hsieh E.W., et al. Clinical and molecular studies of patients with characteristics of Opitz G/BBB syndrome shows a novel MID1 mutation. Am. J. Med. Genet. A 2008, 146A:2337-2345.
41. Krutzfeldt M., et al. Selective ablation of retinoblastoma protein function by the RET finger protein. Mol. Cell 2005, 18:213-224.
42. Zoumpoulidou G., et al. Role of the tripartite motif protein 27 in cancer development. J. Natl. Cancer Inst. 2012, 104:941-952.
43. Forbes S.A., et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011, 39:D945-D950.
44. Andreeva A., et al. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 2008, 36:D419-D425.
45. Kuang Z., et al. SPRY domain-containing SOCS box protein 2: crystal structure and residues critical for protein binding. J. Mol. Biol. 2009, 386:662-674.
46. Masters S.L., et al. The SPRY domain of SSB-2 adopts a novel fold that presents conserved Par-4-binding residues. Nat. Struct. Mol. Biol. 2006, 13:77-84.
47. James L.C., et al. Structural basis for PRYSPRY-mediated tripartite motif (TRIM) protein function. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:6200-6205.
48. Woo J.S., et al. Structural basis for protein recognition by B30.2/SPRY domains. Mol. Cell 2006, 24:967-976.
49. Filippakopoulos P., et al. Structural basis for Par-4 recognition by the SPRY domain- and SOCS box-containing proteins SPSB1, SPSB2, and SPSB4. J. Mol. Biol. 2010, 401:389-402.
50. He F., et al. Structural and functional characterization of the NHR1 domain of the Drosophila neuralized E3 ligase in the notch signaling pathway. J. Mol. Biol. 2009, 393:478-495.
51. Fontana J.R., Posakony J.W. Both inhibition and activation of Notch signaling rely on a conserved Neuralized-binding motif in Bearded proteins and the Notch ligand Delta. Dev. Biol. 2009, 333:373-385.
52. Grutter C., et al. Structure of the PRYSPRY-domain: implications for autoinflammatory diseases. FEBS Lett. 2006, 580:99-106.
53. Li X., et al. Determinants of the higher order association of the restriction factor TRIM5alpha and other tripartite motif (TRIM) proteins. J. Biol. Chem. 2011, 286:27959-27970.
54. Zhai L., et al. Structure-function analysis of GNIP, the glycogenin-interacting protein. Arch. Biochem. Biophys. 2004, 421:236-242.
55. Stirnimann C.U., et al. WD40 proteins propel cellular networks. Trends Biochem. Sci. 2010, 35:565-574.
56. Punta M., et al. The Pfam protein families database. Nucleic Acids Res. 2012, 40:D290-D301.
57. Larkin M.A., et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
58. Crooks G.E., et al. WebLogo: a sequence logo generator. Genome Res. 2004, 14:1188-1190.
59. Liu E., et al. Control of mTORC1 signaling by the Opitz syndrome protein MID1. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:8680-8685.
60. Stacey K.B., et al. Tyrosine phosphorylation of the E3 ubiquitin ligase TRIM21 positively regulates interaction with IRF3 and hence TRIM21 activity. PLoS ONE 2012, 7:e34041.
61. Tanaka M., Kamitani T. Cytoplasmic relocation of Daxx induced by Ro52 and FLASH. Histochem. Cell Biol. 2010, 134:297-306.
62. Sivaramakrishnan G., et al. B30.2/SPRY domain in tripartite motif-containing 22 is essential for the formation of distinct nuclear bodies. FEBS Lett. 2009, 583:2093-2099.
63. Yu S., et al. Identification of tripartite motif-containing 22 (TRIM22) as a novel NF-kappaB activator. Biochem. Biophys. Res. Commun. 2011, 410:247-251.
64. Morris-Desbois C., et al. Interaction between the Ret finger protein and the Int-6 gene product and co-localisation into nuclear bodies. J. Cell Sci. 1999, 112:3331-3342.
65. Ogg S.L., et al. Expression of butyrophilin (Btn1a1) in lactating mammary gland is essential for the regulated secretion of milk-lipid droplets. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:10084-10089.
66. Chaudhury A., et al. Heterogeneous nuclear ribonucleoproteins (hnRNPs) in cellular processes: focus on hnRNP E1's multifunctional regulatory roles. RNA 2010, 16:1449-1462.
67. Kim M.K., Nikodem V.M. hnRNP U inhibits carboxy-terminal domain phosphorylation by TFIIH and represses RNA polymerase II elongation. Mol. Cell Biol. 1999, 19:6833-6844.
68. Piessevaux J., et al. The many faces of the SOCS box. Cytokine Growth Factor Rev. 2008, 19:371-381.
69. Wang D., et al. The SPRY domain-containing SOCS box protein 1 (SSB-1) interacts with MET and enhances the hepatocyte growth factor-induced Erk-Elk-1-serum response element pathway. J. Biol. Chem. 2005, 280:16393-16401.
70. Lewis R.S., et al. TLR regulation of SPSB1 controls inducible nitric oxide synthase induction. J. Immunol. 2011, 187:3798-3805.
71. Kuang Z., et al. The SPRY domain-containing SOCS box protein SPSB2 targets iNOS for proteasomal degradation. J. Cell Biol. 2010, 190:129-141.
72. Styhler S., et al. VASA localization requires the SPRY-domain and SOCS-box containing protein, GUSTAVUS. Dev. Cell 2002, 3:865-876.
73. Wang D., et al. Activation of Ras/Erk pathway by a novel MET-interacting protein RanBPM. J. Biol. Chem. 2002, 277:36216-36222.
74. Suresh B., et al. Stability and function of mammalian lethal giant larvae-1 oncoprotein are regulated by the scaffolding protein RanBPM. J. Biol. Chem. 2010, 285:35340-35349.
75. Kramer S., et al. Protein stability and function of p73 are modulated by a physical interaction with RanBPM in mammalian cultured cells. Oncogene 2005, 24:938-944.
76. Wu H.H., et al. Ryanodine receptors, a family of intracellular calcium ion channels, are expressed throughout early vertebrate development. BMC Res. Notes 2011, 4:541.
77. Tae H., et al. The elusive role of the SPRY2 domain in RyR1. Channels (Austin) 2011, 5:148-160.
78. Peschiaroli A., et al. The F-box protein FBXO45 promotes the proteasome-dependent degradation of p73. Oncogene 2009, 28:3157-3166.
79. Saiga T., et al. Fbxo45 forms a novel ubiquitin ligase complex and is required for neuronal development. Mol Cell Biol 2009, 29:3529-3543.
80. Cao F., et al. An Ash2L/RbBP5 heterodimer stimulates the MLL1 methyltransferase activity through coordinated substrate interactions with the MLL1 SET domain. PLoS ONE 2010, 5:e14102.