Design principles of nuclear receptor signaling: How complex networking improves signal transduction

Molecular Systems Biology

Volumn 6, Issue , 2010, Pages

  Kolodkin, Alexey N ^a   Bruggeman, Frank J ^a,b,c   Plant, Nick ^d   Moné, Martijn J ^a   Bakker, Barbara M ^a,e   Campbell, Moray J ^f   Van Leeuwen, Johannes P T M ^g   Carlberg, Carsten ^h   Snoep, Jacky L ^a,i,j   Westerhoff, Hans V ^a,j  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

^b Netherlands Institute of Systems Biology   (Netherlands)

^c CWI   (Netherlands)

^d UNIVERSITY OF SURREY   (United Kingdom)

^e UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

^f ROSWELL PARK CANCER INSTITUTE   (United States)

^g ERASMUS MEDICAL CENTER   (Netherlands)

^h UNIVERSITY OF LUXEMBOURG   (Luxembourg)

ⁱ STELLENBOSCH UNIVERSITY   (South Africa)

^j UNIVERSITY OF MANCHESTER   (United Kingdom)

more..

Author keywords

biochemical network; kinetic model; nuclear receptor; signaling; systems biology

Indexed keywords

CELL NUCLEUS RECEPTOR; DNA; KARYOPHERIN; LIGAND; RECEPTOR PROTEIN; RNA; CELL RECEPTOR; GUANOSINE TRIPHOSPHATE;

ARTICLE; CANONICAL ANALYSIS; CELL NUCLEUS MEMBRANE; CYTOPLASM; CYTOSOL; GENETIC TRANSCRIPTION; KINETICS; NUCLEAR PORE; PRIORITY JOURNAL; PROTEIN LOCALIZATION; SENSITIVITY ANALYSIS; SIGNAL TRANSDUCTION; CELL MEMBRANE; CELL NUCLEUS; GENE EXPRESSION; HUMAN; METABOLISM; SYSTEMS BIOLOGY;

CELL MEMBRANE; CELL NUCLEUS; CYTOPLASM; GENE EXPRESSION; GUANOSINE TRIPHOSPHATE; HUMANS; KARYOPHERINS; LIGANDS; NUCLEAR PORE; RECEPTORS, CYTOPLASMIC AND NUCLEAR; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 78650646102     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2010.102     Document Type: Article

References (62)

1. Aouabdi S, Gibson G, Plant N (2006) Transcriptional regulation of the PXR gene: identification and characterization of a functional peroxisome proliferator-activated receptor alpha binding site within the proximal promoter of PXR. Drug Metab Disp 34: 138-144
2. Brink M, Humbel BM, De Kloet ER, Van Driel R (1992) The unliganded glucocorticoid receptor is localized in the nucleus, not in the cytoplasm. Endocrinol 130: 3575-3581
3. Bunce CM, Campbell MJ (eds.) (2010) Nuclear receptors, Proteins and Cell Regulation 8, 455-457. DOI 10.1007/978-90-481-3303-1, Springer Science Business Media BV
4. Burns JA, Cornish-Bowden A, Groen AK, Heinrich R, Kacser H, Porteous JW, Rapoport SM, Rapoport TA, Stucki JW, Tager JM, Wanders RJA, Westerhoff HV (1985) Control analysis of metabolic systems. Trends Biochem Sci 10: 16
5. Cao HJ, Lin HY, Luidens MK, Davis FB, Davis PJ (2009) Cytoplasm-tonucleus shuttling of thyroid hormone receptor-1 (Tr1) is directed from a plasma membrane integrin receptor by thyroid hormone. Endocr Res 34: 31-42
6. Carlberg C, Dunlop TW (2006) An integrated biological approach to nuclear receptor signaling in physiological control and disease. Crit Rev Eukar Gene Expr 16: 1-22
7. Catimel B, Teh T, Fontes MRM, Jennings IG, Jans DA, Howlett GJ, Nice EC, Kobe B (2001) Biophysical characterization of interactions involving importin-alpha during nuclear import. J Biol Chem 276: 34189-34198
8. Charmandari E, Kino T, Ichijo T, Jubiz W, Mejia L, Zachman K, Chrousos GP (2007) A novel point mutation in helix 11 of the ligand-binding domain of the human glucocorticoid receptor gene causing generalized glucocorticoid resistance. J Clin Endocrinol Metab 92: 3986-3990
9. Charmandari E, Raji A, Kino T, Ichijo T, Tiulpakov A, Zachman K, Chrousos GP (2005) A novel point mutation in the ligand-binding domain (LBD) of the human glucocorticoid receptor (hGR) causing generalized glucocorticoid resistance: the importance of the C terminus of hGR LBD in conferring transactivational activity. J Clin Endocrinol Metab 90: 3696-3705
10. Cutress ML, Whitaker HC, Mills IG, Stewart M, Neal DE (2008) Structural basis for the nuclear import of the human androgen receptor. J Cell Sci 121: 957-968
11. Dange T, Grunwald D, Grunwald A, Peters R, Kubitscheck U (2008) Autonomy and robustness of translocation through the nuclear pore complex: a single-molecule study. J Cell Biol 183: 77-86
12. Dayel MJ, Hom EFY, Verkman AS (1999) Diffusion of green fluorescent protein in the aqueous-phase lumen of endoplasmic reticulum. Biophys J 76: 2843-2851
13. De Kloet ER, Meijer OC, Vreugdenhil E, Joels M (2000) The Yin and Yang of nuclear receptors: symposium on nuclear receptors in brain, Oegstgeest, The Netherlands, 13-14 April 2000. Trends Endocrinol Metab 11: 245-248
14. Drouin J, Sun YL, Tremblay S, Lavender P, Schmidt TJ, Delean A, Nemer M (1992) Homodimer formation is rate-limiting for highaffinity DNA-binding by glucocorticoid receptor. Mol Endocrinol 6: 1299-1309
15. Dupont S, Mamidi A, Cordenonsi M, Montagner M, Zacchigna L, Adorno M, Martello G, Stinchfield MJ, Soligo S, Morsut L, Inui M, Moro S, Modena N, Argenton F, Newfeld SJ, Piccolo S (2009) FAM/ USP9x, a deubiquitinating enzyme essential for TGFbeta signaling, controls Smad4 monoubiquitination. Cell 136: 123-135
16. Ebert R, Schutze N, Adamski J, Jakob F (2006) Vitamin D signaling is modulated on multiple levels in health and disease. Mol Cell Endocrinol 248: 149-159
17. El-Sankary W, Bombail V, Gibson GG, Plant N (2002) Glucocorticoidmediated induction of CYP3A4 is decreased by disruption of a protein: DNA interaction distinct from the pregnane X receptor response element. Drug Metab Disp 30: 1029-1034
18. El-Sankary W, Gibson GG, Ayrton A, Plant N (2001) Use of a reporter gene assay to predict and rank the potency and efficacy of CYP3A4 inducers. Drug Metab Disposit 29: 1499-1504
19. Fanestil DD, Edelman IS (1966) Characteristics of renal nuclear receptors for aldosterone. Proc Natl Acad Sci USA 56: 872-879
20. Gardner RS (1975) Nuclear thyroid-hormone receptors-evidence for association with nucleolar chromatin. Biochem Biophys Res Commun 67: 625-633
21. Garlatti M, Daheshia M, Slater E, Bouguet J, Hanoune J, Beato M, Barouki R (1994) A functional glucocorticoid-responsive unit composed of 2 overlapping inactive receptor-binding sites- evidence for formation of a receptor tetramer. Mol Cell Biol 14: 8007-8017
22. Heitzer MD, Wolf IM, Sanchez ER, Witchel SF, DeFranco DB (2007) Glucocorticoid receptor physiology. Rev Endocr Metab Dis 8: 321-330
23. Kahn D, Westerhoff HV (1991) Control-theory of regulatory cascades. J Theo Biol 153: 255-285
24. Kholodenko BN, Brown GC, Hoek JB (2000a) Diffusion control of protein phosphorylation in signal transduction pathways. Biochem J 350: 901-907
25. Kholodenko BN, Hoek JB, Westerhoff HV (2000b) Why cytoplasmic signalling proteins should be recruited to cell membranes. Trends Cell Biol 10: 173-178
26. Kitano H, Funahashi A, Matsuoka Y, Oda K (2005) Using process diagrams for the graphical representation of biological networks. Nat Biotech 23: 961-966
27. Kopito RB, Elbaum M (2007) Reversibility in nucleocytoplasmic transport. Proc Nat Acad Sci USA 104: 12743-12748
28. Kumar S, Chaturvedi NK, Nishi M, Kawata M, Tyagi RK (2004) Shuttling components of nuclear import machinery involved in nuclear translocation of steroid receptors exit nucleus via exportin- 1/CRM-1 independent pathway. Biochim Biophys Acta-Mol Cell Res 1691: 73-77
29. Kumar S, Saradhi M, Chaturvedi NK, Tyagi RK (2006) Intracellular localization and nucleocytoplasmic trafficking of steroid receptors: an overview. Mol Cell Endocrinol 246: 147-156
30. Levin ER (2009a) Membrane oestrogen receptor alpha signalling to cell functions. J Physiol 587: 5019-5023
31. Levin ER (2009b) Plasma membrane estrogen receptors. Trends Endocrinol Metab 20: 477-482
32. Lin CY, Vega VB, Thomsen JS, Zhang T, Kong SL, Xie M, Chiu KP, Lipovich L, Barnett DH, Stossi F, Yeo A, George J, Kuznetsov VA, Lee YK, Charn TH, Palanisamy N, Miller LD, Cheung E, Katzenellenbogen BS, Ruan Y, et al. (2007) Whole-genome cartography of estrogen receptor alpha binding sites. PloS Gen 3: 867-885
33. Liu JM, DeFranco DB (2000) Protracted nuclear export of glucocorticoid receptor limits its turnover and does not require the exportin 1/CRM1-directed nuclear export pathway. Molecul Endocrinol 14: 40-51
34. Macara IG (2001) Transport into and out of the nucleus. Microbiol Mol Biol Rev 65: 570-594
35. Marissal-Arvy N, Mormede P, Sarrieau A (1999) Strain differences in corticosteroid receptor efficiencies and regulation in Brown Norway and Fischer 344 rats. J Neuroendocrinol 11: 267-273
36. Menezes RJ, Cheney RT, Husain A, Tretiakova M, Loewen G, Johnson CS, Jayaprakash V, Moysich KB, Salgia R, Reid ME (2008) Vitamin D receptor expression in normal, premalignant, and malignant human lung tissue. Cancer Epidemiol Biom Preven 17: 1104-1110
37. Nicolas FJ, De Bosscher K, Schmierer B, Hill CS (2004) Analysis of Smad nucleocytoplasmic shuttling in living cells. J Cell Sci 117: 4113-4125
38. Nordeen SK, Kuhnel B, Lawlerheavner J, Barber DA, Edwards DP (1989) A quantitative comparison of dual control of a hormone response element by progestins and glucocorticoids in the same cell-line. Mol Endocrinol 3: 1270-1278
39. Olivier BG, Snoep JL (2004) Web-based kinetic modelling using JWS Online. Bioinformatics 20: 2143-2144
40. Ong DB, Colley SM, Norman MR, Kitazawa S, Tobias JH (2004) Transcriptional regulation of a BMP-6 promoter by estrogen receptor alpha. J Bone Miner Res 19: 447-454
41. Oren I, Fleishman SJ, Kessel A, Ben-Tal N (2004) Free diffusion of steroid hormones across biomembranes: a simplex search with implicit solvent model calculations. Biophys J 87: 768-779
42. Pemberton LF, Paschal BM (2005) Mechanisms of receptor-mediated nuclear import and nuclear export. Traffic 6: 187-198
43. Phillips AL, Hood SR, Gibson GG, Plant NJ (2003) CYP3A and nuclear receptor messenger RNA expression in liver and HuH7 cells. Drug Metabol Rev 35: 83
44. Poon IKH, Jans DA (2005) Regulation of nuclear transport: central role in development and transformation? Traffic 6: 173-186
45. Pratt WB, Sanchez ER, Bresnick EH, Meshinchi S, Scherrer LC, Dalman FC, Welsh MJ (1989) Interaction of the glucocorticoid receptor with the Mr 90,000 heat shock protein: an evolving model of ligandmediated receptor transformation and translocation. Cancer Res 49: 2222s-2229s
46. Prüfer K, Boudreaux J (2007) Nuclear localization of liver X receptor alpha and beta is differentially regulated. J Cell Biochem 100: 69-85
47. Racz A, Barsony J (1999) Hormone-dependent translocation of vitamin D receptors is linked to transactivation. J Biol Chem 274: 19352-19360
48. Reddy TE, Pauli F, Sprouse RO, Neff NF, Newberry KM, Garabedian MJ, Myers RM (2009) Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res 19: 2163-2171
49. Ricketson D, Hostick U, Fang L, Yamamoto KR, Darimont BD (2007) A conformational switch in the ligand-binding domain regulates the dependence of the glucocorticold receptor on Hsp90. J Molecul Biol 368: 729-741
50. Riddick G, Macara IG (2005) A systems analysis of importin-alpha-beta mediated nuclear protein import. J Cell Biol 168: 1027-1038
51. Riddick G, Macara IG (2007) The adapter importin-alpha provides flexible control of nuclear import at the expense of efficiency. Mol Sys Biol 3: 118
52. Sharova EI (2002) Protein transport in plant cells. Russ J Plant Physiol 49: 255-268
53. Snoep JL, Olivier BG (2002) Java Web Simulation (JWS); a web based database of kinetic models. Mol Biol Rep 29: 259-263
54. Spona J, Leibl H, Bieglmayer C (1980) Nuclear translocation of estrogen-receptor complex and stimulation of Rna-synthesis by estrogens of different biological potencies in the female rat pituitary. Biochim Biophys Acta 607: 189-200
55. Stavreva DA, Wiench M, John S, Conway-Campbell BL, McKenna MA, Pooley JR, Johnson TA, Voss TC, Lightman SL, Hager GL (2009) Ultradian hormone stimulation induces glucocorticoid receptor-mediated pulses of gene transcription. Nat Cell Biol 11: 1093-1111
56. Tanaka M, Nishi M, Morimoto M, Sugimoto T, Kawata M (2005) Imaging analysis of mineralocorticoid receptor and importins in single living cells by using GFP color variants. Cell Tiss Res 320: 447-453
57. Tran EJ, Wente SR (2006) Dynamic nuclear pore complexes: life on the edge. Cell 125: 1041-1053
58. Van Steensel B, Brink M, Van der Meulen K, Van Binnendijk EP, Wansink DG, De Jong L, De Kloet ER, Van Driel R (1995) Localization of the glucocorticoid receptor in discrete clusters in the cell nucleus. J Cell Sci 108 (Pt 9): 3003-3011
59. Von Knethen A, Tzieply N, Jennewein C, Brune B (2010) Caseinkinase- II-dependent phosphorylation of PPAR gamma provokes CRM1-mediated shuttling of PPAR gamma from the nucleus to the cytosol. J Cell Sci 123: 192-201
60. Voss TC, Schiltz RL, Sung MH, Johnson TA, John S, Hager GL (2009) Combinatorial probabilistic chromatin interactions produce transcriptional heterogeneity. J Cell Sci 122: 345-356
61. Weisiger RA (2002) Cytosolic fatty acid binding proteins catalyze two distinct steps in intracellular transport of their ligands. Mol Cell Biochem 239: 35-43
62. Westerhoff HV (1985) Thermodynamics and control of proton motive free-energy transduction. Biomedica Biochimica Acta 44: 929-941