A protein interaction atlas for the nuclear receptors: Properties and quality of a hub-based dimerisation network

BMC Systems Biology

Volumn 1, Issue , 2007, Pages

  Amoutzias, Gregory D ^a,b,c,d   Pichler, Elgar E ^c   Mian, Nina ^c   De Graaf, David ^c,e   Imsiridou, Anastasia ^f   Robinson Rechavi, Marc ^b   Bornberg Bauer, Erich ^a,g   Robertson, David L ^a   Oliver, Stephen G ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITY OF LAUSANNE   (Switzerland)

^c ASTRAZENECA   (United Kingdom)

^d GHENT UNIVERSITY   (Belgium)

^e PFIZER INC   (United States)

^f ALEXANDER TECHNOLOGICAL EDUCATIONAL INSTITUTE OF THESSALONIKI   (Greece)

^g UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

CELL RECEPTOR; DNA; TRANSCRIPTION FACTOR;

ANIMAL; ARTICLE; CLASSIFICATION; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; MOLECULAR EVOLUTION; MOUSE; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DATABASE;

ANIMALS; DATABASES, PROTEIN; DNA; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MICE; PHYLOGENY; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; RECEPTORS, CYTOPLASMIC AND NUCLEAR; TRANSCRIPTION FACTORS;

EID: 34548570117     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-1-34     Document Type: Article

References (67)

1. Robinson-Rechavi M Escriva Garcia H Laudet V The nuclear receptor superfamily J Cell Sci 2003, 116(Pt 4):585-586. 10.1242/jcs.00247 12538758
2. Bookout AL Jeong Y Downes M Yu RT Evans RM Mangelsdorf DJ Anatomical profiling of nuclear receptor expression reveals a hierarchical transcriptional network Cell 2006, 126(4):789-799. 10.1016/ j.cell.2006.06.049 16923397
3. Gronemeyer H Gustafsson JA Laudet V Principles for modulation of the nuclear receptor superfamily Nat Rev Drug Discov 2004, 3(11):950-964. 10.1038/nrd1551 15520817
4. Shulman AI Mangelsdorf DJ Retinoid x receptor heterodimers in the metabolic syndrome N Engl J Med 2005, 353(6):604-615. 10.1056/ NEJMra043590 16093469
5. Aranda A Pascual A Nuclear hormone receptors and gene expression Physiol Rev 2001, 81(3):1269-1304. 11427696
6. Khorasanizadeh S Rastinejad F Nuclear-receptor interactions on DNA-response elements Trends Biochem Sci 2001, 26(6):384-390. 10.1016/ S0968-0004(01)01800-X 11406412
7. Desvergne B RXR: From Partnership to Leadership in Metabolic Regulations Vitam Horm 2007, 75:1-32. 17368310
8. Mangelsdorf DJ Evans RM The RXR heterodimers and orphan receptors Cell 1995, 83(6):841-850. 10.1016/0092-8674(95)90200-7 8521508
9. Perlmann T Umesono K Rangarajan PN Forman BM Evans RM Two distinct dimerization interfaces differentially modulate target gene specificity of nuclear hormone receptors Mol Endocrinol 1996, 10(8):958-966. 10.1210/ me.10.8.958 8843412
10. Sugiyama T Wang JC Scott DK Granner DK Transcription activation by the orphan nuclear receptor, chicken ovalbumin upstream promoter-transcription factor I (COUP-TFI). Definition of the domain involved in the glucocorticoid response of the phosphoenolpyruvate carboxykinase gene J Biol Chem 2000, 275(5):3446-3454. 10.1074/ jbc.275.5.3446 10652338
11. Miyata KS McCaw SE Patel HV Rachubinski RA Capone JP The orphan nuclear hormone receptor LXR alpha interacts with the peroxisome proliferator-activated receptor and inhibits peroxisome proliferator signaling J Biol Chem 1996, 271(16):9189-9192. 10.1074/jbc.271.16.9189 8621574
12. Shyr CR Hu YC Kim E Chang C Modulation of estrogen receptor-mediated transactivation by orphan receptor TR4 in MCF-7 cells J Biol Chem 2002, 277(17):14622-14628. 10.1074/jbc.M110051200 11844790
13. Giot L Bader JS Brouwer C Chaudhuri A Kuang B Li Y Hao YL Ooi CE Godwin B Vitols E Vijayadamodar G Pochart P Machineni H Welsh M Kong Y Zerhusen B Malcolm R Varrone Z Collis A Minto M Burgess S McDaniel L Stimpson E Spriggs F Williams J Neurath K Ioime N Agee M Voss E Furtak K Renzulli R Aanensen N Carrolla S Bickelhaupt E Lazovatsky Y DaSilva A Zhong J Stanyon CA Finley RL Jr. White KP Braverman M Jarvie T Gold S Leach M Knight J Shimkets RA McKenna MP Chant J Rothberg JM A protein interaction map of Drosophila melanogaster Science 2003, 302(5651):1727-1736. 10.1126/science.1090289 14605208
14. Ito T Chiba T Ozawa R Yoshida M Hattori M Sakaki Y A comprehensive two-hybrid analysis to explore the yeast protein interactome Proc Natl Acad Sci U S A 2001, 98(8):4569-4574. 31875 11283351 10.1073/ pnas.061034498
15. Uetz P Giot L Cagney G Mansfield TA Judson RS Knight JR Lockshon D Narayan V Srinivasan M Pochart P Qureshi-Emili A Li Y Godwin B Conover D Kalbfleisch T Vijayadamodar G Yang M Johnston M Fields S Rothberg JM A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae Nature 2000, 403(6770):623-627. 10.1038/35001009 10688190
16. Lockhart DJ Dong H Byrne MC Follettie MT Gallo MV Chee MS Mittmann M Wang C Kobayashi M Horton H Brown EL Expression monitoring by hybridization to high-density oligonucleotide arrays Nat Biotechnol 1996, 14(13):1675-1680. 10.1038/nbt1296-1675 9634850
17. Newman JR Keating AE Comprehensive identification of human bZIP interactions with coiled-coil arrays Science 2003, 300(5628):2097-2101. 10.1126/science.1084648 12805554
18. Peri S Navarro JD Kristiansen TZ Amanchy R Surendranath V Muthusamy B Gandhi TK Chandrika KN Deshpande N Suresh S Rashmi BP Shanker K Padma N Niranjan V Harsha HC Talreja N Vrushabendra BM Ramya MA Yatish AJ Joy M Shivashankar HN Kavitha MP Menezes M Choudhury DR Ghosh N Saravana R Chandran S Mohan S Jonnalagadda CK Prasad CK Kumar-Sinha C Deshpande KS Pandey A Human protein reference database as a discovery resource for proteomics Nucleic Acids Res 2004 32(Database issue):D497-501. 308804 14681466 10.1093/nar/gkh070
19. Barabasi AL Oltvai ZN Network biology: Understanding the cell's functional organization Nat Rev Genet 2004, 5(2):101-113. 10.1038/ nrg1272 14735121
20. Jeong H Mason SP Barabasi AL Oltvai ZN Lethality and centrality in protein networks Nature 2001, 411(6833):41-42. 10.1038/35075138 11333967
21. Albert R Jeong H Barabasi AL Error and attack tolerance of complex networks Nature 2000, 406(6794):378-382. 10.1038/35019019 10935628
22. Wagner A Fell DA The small world inside large metabolic networks Proc Biol Sci 2001, 268(1478):1803-1810. 10.1098/rspb.2001.1711 11522199 1088812
23. Watts DJ Strogatz SH Collective dynamics of 'small-world' networks Nature 1998, 393(6684):440-442. 10.1038/30918 9623998
24. Papp B Oliver S Genome-wide analysis of the context-dependence of regulatory networks Genome Biol 2005, 6(2):206. 551525 15693953 10.1186/ gb-2005-6-2-206
25. Albert S Gaudan S Knigge H Raetsch A Delgado A Huhse B Kirsch H Albers M Rebholz-Schuhmann D Koegl M Computer-assisted generation of a protein-interaction database for nuclear receptors Mol Endocrinol 2003, 17(8):1555-1567. 10.1210/me.2002-0424 12738764
26. Albers M Kranz H Kober I Kaiser C Klink M Suckow J Kern R Koegl M Automated yeast two-hybrid screening for nuclear receptor-interacting proteins Mol Cell Proteomics 2005, 4(2):205-213. 10.1074/ mcp.M400169-MCP200 15604093
27. Rual JF Venkatesan K Hao T Hirozane-Kishikawa T Dricot A Li N Berriz GF Gibbons FD Dreze M Ayivi-Guedehoussou N Klitgord N Simon C Boxem M Milstein S Rosenberg J Goldberg DS Zhang LV Wong SL Franklin G Li S Albala JS Lim J Fraughton C Llamosas E Cevik S Bex C Lamesch P Sikorski RS Vandenhaute J Zoghbi HY Smolyar A Bosak S Sequerra R Doucette-Stamm L Cusick ME Hill DE Roth FP Vidal M Towards a proteome-scale map of the human protein-protein interaction network Nature 2005, 437(7062):1173-1178. 10.1038/nature04209 16189514
28. Stelzl U Worm U Lalowski M Haenig C Brembeck FH Goehler H Stroedicke M Zenkner M Schoenherr A Koeppen S Timm J Mintzlaff S Abraham C Bock N Kietzmann S Goedde A Toksoz E Droege A Krobitsch S Korn B Birchmeier W Lehrach H Wanker EE A human protein-protein interaction network: A resource for annotating the proteome Cell 2005, 122(6):957-968. 10.1016/ j.cell.2005.08.029 16169070
29. Amoutzias GD Robertson DL Oliver SG Bornberg-Bauer E Convergent evolution of gene networks by single-gene duplications in higher eukaryotes EMBO Rep 2004, 5(3):274-279. 1299007 14968135 10.1038/ sj.embor.7400096
30. Zetterstrom RH Solomin L Mitsiadis T Olson L Perlmann T Retinoid X receptor heterodimerization and developmental expression distinguish the orphan nuclear receptors NGFI-B, Nurr1, and Nor1 Mol Endocrinol 1996, 10(12):1656-1666. 10.1210/me.10.12.1656 8961274
31. Mathivanan S Periaswamy B Gandhi TK Kandasamy K Suresh S Mohmood R Ramachandra Y Pandey A An evaluation of human protein-protein interaction data in the public domain BMC Bioinformatics 2006, 7(Suppl 5):S19. 1764475 17254303 10.1186/1471-2105-7-S5-S19
32. Giguere V Orphan nuclear receptors: From gene to function Endocr Rev 1999, 20(5):689-725. 10.1210/er.20.5.689 10529899
33. Amoutzias GD Robertson DL Bornberg-Bauer E The evolution of protein interaction networks in regulatory proteins Comparative & Functional Genomics 2004, 5:79-84. 10.1002/cfg.365
34. Benoit G Cooney A Giguere V Ingraham H Lazar M Muscat G Perlmann T Renaud JP Schwabe J Sladek F Tsai MJ Laudet V International Union of Pharmacology. LXVI. Orphan nuclear receptors Pharmacological reviews 2006, 58(4):798-836. 10.1124/pr.58.4.10 17132856
35. Dahlman-Wright K Cavailles V Fuqua SA Jordan VC Katzenellenbogen JA Korach KS Maggi A Muramatsu M Parker MG Gustafsson JA International Union of Pharmacology. LXIV. Estrogen receptors Pharmacological reviews 2006, 58(4):773-781. 10.1124/pr.58.4.8 17132854
36. Flamant F Baxter JD Forrest D Refetoff S Samuels H Scanlan TS Vennstrom B Samarut J International Union of Pharmacology. LIX. The pharmacology and classification of the nuclear receptor superfamily: Thyroid hormone receptors Pharmacological reviews 2006, 58(4):705-711. 10.1124/pr.58.4.3 17132849
37. Germain P Chambon P Eichele G Evans RM Lazar MA Leid M De Lera AR Lotan R Mangelsdorf DJ Gronemeyer H International Union of Pharmacology. LXIII. Retinoid X receptors Pharmacological reviews 2006, 58(4):760-772. 10.1124/pr.58.4.7 17132853
38. Germain P Chambon P Eichele G Evans RM Lazar MA Leid M De Lera AR Lotan R Mangelsdorf DJ Gronemeyer H International Union of Pharmacology. LX. Retinoic acid receptors Pharmacological reviews 2006, 58(4):712-725. 10.1124/pr.58.4.4 17132850
39. Lu NZ Wardell SE Burnstein KL Defranco D Fuller PJ Giguere V Hochberg RB McKay L Renoir JM Weigel NL Wilson EM McDonnell DP Cidlowski JA International Union of Pharmacology. LXV. The pharmacology and classification of the nuclear receptor superfamily: Glucocorticoid, mineralocorticoid, progesterone, and androgen receptors Pharmacological reviews 2006, 58(4):782-797. 10.1124/pr.58.4.9 17132855
40. Michalik L Auwerx J Berger JP Chatterjee VK Glass CK Gonzalez FJ Grimaldi PA Kadowaki T Lazar MA O'Rahilly S Palmer CN Plutzky J Reddy JK Spiegelman BM Staels B Wahli W International Union of Pharmacology. LXI. Peroxisome proliferator-activated receptors Pharmacological reviews 2006, 58(4):726-741. 10.1124/pr.58.4.5 17132851
41. Moore DD Kato S Xie W Mangelsdorf DJ Schmidt DR Xiao R Kliewer SA International Union of Pharmacology. LXII. The NR1H and NR1I receptors: constitutive androstane receptor, pregnene X receptor, farnesoid X receptor alpha, farnesoid X receptor beta, liver X receptor alpha, liver X receptor beta, and vitamin D receptor Pharmacological reviews 2006, 58(4):742-759. 10.1124/pr.58.4.6 17132852
42. Seol W Choi HS Moore DD An orphan nuclear hormone receptor that lacks a DNA binding domain and heterodimerizes with other receptors Science 1996, 272(5266):1336-1339. 10.1126/science.272.5266.1336 8650544
43. Seol W Chung M Moore DD Novel receptor interaction and repression domains in the orphan receptor SHP Mol Cell Biol 1997, 17(12):7126-7131. 232569 9372944
44. Lee YK Parker KL Choi HS Moore DD Activation of the promoter of the orphan receptor SHP by orphan receptors that bind DNA as monomers J Biol Chem 1999, 274(30):20869-20873. 10.1074/jbc.274.30.20869 10409629
45. Smolen P Baxter DA Byrne JH Mathematical modeling of gene networks Neuron 2000, 26(3):567-580. 10.1016/S0896-6273(00)81194-0 10896154
46. Shen-Orr SS Milo R Mangan S Alon U Network motifs in the transcriptional regulation network of Escherichia coli Nat Genet 2002, 31(1):64-68. 10.1038/ng881 11967538
47. Spiegelman BM Heinrich R Biological control through regulated transcriptional coactivators Cell 2004, 119(2):157-167. 10.1016/ j.cell.2004.09.037 15479634
48. Levine M Tjian R Transcription regulation and animal diversity Nature 2003, 424(6945):147-151. 10.1038/nature01763 12853946
49. Ranea JA Grant A Thornton JM Orengo CA Microeconomic principles explain an optimal genome size in bacteria Trends Genet 2005, 21(1):21-25. 10.1016/j.tig.2004.11.014 15680509
50. van Nimwegen E Scaling laws in the functional content of genomes Trends Genet 2003, 19(9):479-484. 10.1016/S0168-9525(03)00203-8 12957540
51. Davidson EH The regulatory genome Academic Press; 2006.
52. Klemm JD Schreiber SL Crabtree GR Dimerization as a regulatory mechanism in signal transduction Annu Rev Immunol 1998, 16:569-592. 10.1146/ annurev.immunol.16.1.569 9597142
53. Luscombe NM Babu MM Yu H Snyder M Teichmann SA Gerstein M Genomic analysis of regulatory network dynamics reveals large topological changes Nature 2004, 431(7006):308-312. 10.1038/nature02782 15372033
54. Teichmann SA Babu MM Gene regulatory network growth by duplication Nat Genet 2004, 36(5):492-496. 10.1038/ng1340 15107850
55. Dosztanyi Z Chen J Dunker AK Simon I Tompa P Disorder and sequence repeats in hub proteins and their implications for network evolution Journal of proteome research 2006, 5(11):2985-2995. 10.1021/pr060171o 17081050
56. Dehal P Boore JL Two rounds of whole genome duplication in the ancestral vertebrate PLoS Biol 2005, 3(10):e314. 1197285 16128622 10.1371/ journal.pbio.0030314
57. Amoutzias GD Bornberg-Bauer E Oliver SG Robertson DL Reduction/ oxidation-phosphorylation control of DNA binding in the bZIP dimerization network BMC Genomics 2006, 7:107. 1479340 16674813 10.1186/ 1471-2164-7-107
58. Amoutzias GD Veron AS Weiner J 3rd Robinson-Rechavi M Bornberg-Bauer E Oliver SG Robertson DL One billion years of bZIP transcription factor evolution: Conservation and change in dimerization and DNA-binding site specificity Mol Biol Evol 2007, 24(3):827-835. 10.1093/molbev/msl211 17194801
59. Pereira-Leal JB Teichmann SA Novel specificities emerge by stepwise duplication of functional modules Genome Res 2005, 15(4):552-559. 1074369 15805495 10.1101/gr.3102105
60. Ben-Shushan E Sharir H Pikarsky E Bergman Y A dynamic balance between ARP-1/COUP-TFII, EAR-3/COUP-TFI, and retinoic acid receptor: retinoid X receptor heterodimers regulates Oct-3/4 expression in embryonal carcinoma cells Mol Cell Biol 1995, 15(2):1034-1048. 232002 7823919
61. Johansson L Thomsen JS Damdimopoulos AE Spyrou G Gustafsson JA Treuter E The orphan nuclear receptor SHP inhibits agonist-dependent transcriptional activity of estrogen receptors ERalpha and ERbeta J Biol Chem 1999, 274(1):345-353. 10.1074/jbc.274.1.345 9867849
62. QUOSA http://www.quosa.com
63. MULTIVALENT http://multivalent.sourceforge.net/
64. HTMLESS http://www.oz.net/~sorth/
65. R gplots package http://cran.r-project.org/src/contrib/ gplots_2.3.2.tar.gz
66. Kostrouch Z Kostrouchova M Love W Jannini E Piatigorsky J Rall JE Retinoic acid X receptor in the diploblast, Tripedalia cystophora Proc Natl Acad Sci U S A 1998, 95(23):13442-13447. 24838 9811819 10.1073/ pnas.95.23.13442
67. Laudet V Gronemeyer H The Nuclear Receptor FactsBook Academic Press; 2001.