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Volumn 8, Issue 10, 2010, Pages

Protein evolution by molecular tinkering: Diversification of the nuclear receptor superfamily from a ligand-dependent ancestor

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS RECEPTOR; FATTY ACID;

EID: 78149390724     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.1000497     Document Type: Article
Times cited : (193)

References (52)
  • 1
    • 39149110563 scopus 로고    scopus 로고
    • The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans
    • King N, Westbrook MJ, Young SL, Kuo A, Abedin M, et al. (2008) The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451: 783-788.
    • (2008) Nature , vol.451 , pp. 783-788
    • King, N.1    Westbrook, M.J.2    Young, S.L.3    Kuo, A.4    Abedin, M.5
  • 3
    • 34447300950 scopus 로고    scopus 로고
    • Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization
    • Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, et al. (2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317: 86-94.
    • (2007) Science , vol.317 , pp. 86-94
    • Putnam, N.H.1    Srivastava, M.2    Hellsten, U.3    Dirks, B.4    Chapman, J.5
  • 4
    • 60149092301 scopus 로고    scopus 로고
    • Deep homology and the origins of evolutionary novelty
    • Shubin N, Tabin C, Carroll S (2009) Deep homology and the origins of evolutionary novelty. Nature 457: 818-823.
    • (2009) Nature , vol.457 , pp. 818-823
    • Shubin, N.1    Tabin, C.2    Carroll, S.3
  • 5
    • 8844262660 scopus 로고    scopus 로고
    • Principles for modulation of the nuclear receptor superfamily
    • Gronemeyer H, Gustafsson JA, Laudet V (2004) Principles for modulation of the nuclear receptor superfamily. Nat Rev Drug Discov 3: 950-964.
    • (2004) Nat Rev Drug Discov , vol.3 , pp. 950-964
    • Gronemeyer, H.1    Gustafsson, J.A.2    Laudet, V.3
  • 6
    • 0037931737 scopus 로고    scopus 로고
    • Identification of a novel human constitutive androstane receptor (CAR) agonist and its use in the identification of CAR target genes
    • Maglich JM, Parks DJ, Moore LB, Collins JL, Goodwin B, et al. (2003) Identification of a novel human constitutive androstane receptor (CAR) agonist and its use in the identification of CAR target genes. J Biol Chem 278: 17277-17283.
    • (2003) J Biol Chem , vol.278 , pp. 17277-17283
    • Maglich, J.M.1    Parks, D.J.2    Moore, L.B.3    Collins, J.L.4    Goodwin, B.5
  • 7
    • 70349330695 scopus 로고    scopus 로고
    • Efficient discovery of selective small molecule agonists of estrogen-related receptor gamma using combinatorial approach
    • Kim Y, Koh M, Kim DK, Choi HS, Park SB (2009) Efficient discovery of selective small molecule agonists of estrogen-related receptor gamma using combinatorial approach. J Comb Chem 11: 928-937.
    • (2009) J Comb Chem , vol.11 , pp. 928-937
    • Kim, Y.1    Koh, M.2    Kim, D.K.3    Choi, H.S.4    Park, S.B.5
  • 8
    • 4043176291 scopus 로고    scopus 로고
    • Structural basis for the deactivation of the estrogen-related receptor gamma by diethylstilbestrol or 4-hydroxytamoxifen and determinants of selectivity
    • Greschik H, Flaig R, Renaud JP, Moras D (2004) Structural basis for the deactivation of the estrogen-related receptor gamma by diethylstilbestrol or 4-hydroxytamoxifen and determinants of selectivity. J Biol Chem 279: 33639-33646.
    • (2004) J Biol Chem , vol.279 , pp. 33639-33646
    • Greschik, H.1    Flaig, R.2    Renaud, J.P.3    Moras, D.4
  • 9
    • 3042753852 scopus 로고    scopus 로고
    • Digging deep into the pockets of orphan nuclear receptors: Insights from structural studies
    • Benoit G, Malewicz M, Perlmann T (2004) Digging deep into the pockets of orphan nuclear receptors: insights from structural studies. Trends Cell Biol 14: 369-376.
    • (2004) Trends Cell Biol , vol.14 , pp. 369-376
    • Benoit, G.1    Malewicz, M.2    Perlmann, T.3
  • 10
    • 34848818037 scopus 로고    scopus 로고
    • Orphan nuclear receptor TLX recruits histone deacetylases to repress transcription and regulate neural stem cell proliferation
    • Sun G, Yu RT, Evans RM, Shi Y (2007) Orphan nuclear receptor TLX recruits histone deacetylases to repress transcription and regulate neural stem cell proliferation. Proc Natl Acad Sci U S A 104: 15282-15287.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 15282-15287
    • Sun, G.1    Yu, R.T.2    Evans, R.M.3    Shi, Y.4
  • 11
    • 52949135190 scopus 로고    scopus 로고
    • Evolution of a new function by degenerative mutation in cephalochordate steroid receptors
    • doi:10.1371/journal.pgen.1000191
    • Bridgham JT, Brown JE, Rodriguez-Mari A, Catchen JM, Thornton JW (2008) Evolution of a new function by degenerative mutation in cephalochordate steroid receptors. PLoS Genet 4: e1000191. doi:10.1371/journal.pgen.1000191.
    • (2008) PLoS Genet , vol.4
    • Bridgham, J.T.1    Brown, J.E.2    Rodriguez-Mari, A.3    Catchen, J.M.4    Thornton, J.W.5
  • 12
    • 61349184546 scopus 로고    scopus 로고
    • The structural basis of gas-responsive transcription by the human nuclear hormone receptor REV-ERBbeta
    • doi:10.1371/journal.pbio.1000043
    • Pardee KI, Xu X, Reinking J, Schuetz A, Dong A, et al. (2009) The structural basis of gas-responsive transcription by the human nuclear hormone receptor REV-ERBbeta. PLoS Biol 7: e43. doi:10.1371/journal.pbio.1000043.
    • (2009) PLoS Biol , vol.7
    • Pardee, K.I.1    Xu, X.2    Reinking, J.3    Schuetz, A.4    Dong, A.5
  • 13
    • 0033858499 scopus 로고    scopus 로고
    • Ligand binding and nuclear receptor evolution
    • Escriva H, Delaunay F, Laudet V (2000) Ligand binding and nuclear receptor evolution. Bioessays 22: 717-727.
    • (2000) Bioessays , vol.22 , pp. 717-727
    • Escriva, H.1    Delaunay, F.2    Laudet, V.3
  • 17
    • 0017771466 scopus 로고
    • Evolution and tinkering
    • Jacob F (1977) Evolution and tinkering. Science 196: 1161-1166.
    • (1977) Science , vol.196 , pp. 1161-1166
    • Jacob, F.1
  • 18
    • 4944258189 scopus 로고    scopus 로고
    • Evolutionary genomics of nuclear receptors: From twenty-five ancestral genes to derived endocrine systems
    • Bertrand S, Brunet FG, Escriva H, Parmentier G, Laudet V, et al. (2004) Evolutionary genomics of nuclear receptors: from twenty-five ancestral genes to derived endocrine systems. Mol Biol Evol 21: 1923-1937.
    • (2004) Mol Biol Evol , vol.21 , pp. 1923-1937
    • Bertrand, S.1    Brunet, F.G.2    Escriva, H.3    Parmentier, G.4    Laudet, V.5
  • 19
    • 77955490196 scopus 로고    scopus 로고
    • The Amphimedon queenslandica genome and the evolution of animal complexity
    • Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier MEA, et al. (2010) The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466: 720.
    • (2010) Nature , vol.466 , pp. 720
    • Srivastava, M.1    Simakov, O.2    Chapman, J.3    Fahey, B.4    Gauthier, M.E.A.5
  • 20
    • 70349577811 scopus 로고    scopus 로고
    • Nuclear receptor complement of the cnidarian Nematostella vectensis: Phylogenetic relationships and developmental expression patterns
    • Reitzel AM, Tarrant AM (2009) Nuclear receptor complement of the cnidarian Nematostella vectensis: phylogenetic relationships and developmental expression patterns. BMC Evol Biol 9: 230.
    • (2009) BMC Evol Biol , vol.9 , pp. 230
    • Reitzel, A.M.1    Tarrant, A.M.2
  • 21
    • 0032023889 scopus 로고    scopus 로고
    • Taxonomic sampling, phylogenetic accuracy, and investigator bias
    • Hillis DM (1998) Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst Biol 47: 3-8.
    • (1998) Syst Biol , vol.47 , pp. 3-8
    • Hillis, D.M.1
  • 22
    • 0034350428 scopus 로고    scopus 로고
    • A new method to localize and test the significance of incongruence: Detecting domain shuffling in the nuclear receptor superfamily
    • Thornton JW, DeSalle R (2000) A new method to localize and test the significance of incongruence: detecting domain shuffling in the nuclear receptor superfamily. Syst Biol 49: 183-201.
    • (2000) Syst Biol , vol.49 , pp. 183-201
    • Thornton, J.W.1    Desalle, R.2
  • 23
    • 0036710140 scopus 로고    scopus 로고
    • Hepatocyte nuclear factor 4 is a transcription factor that constitutively binds fatty acids
    • Wisely GB, Miller AB, Davis RG, Thornquest ADJ, Johnson R, et al. (2002) Hepatocyte nuclear factor 4 is a transcription factor that constitutively binds fatty acids. Structure 10: 1225-1234.
    • (2002) Structure , vol.10 , pp. 1225-1234
    • Wisely, G.B.1    Miller, A.B.2    Davis, R.G.3    Thornquest, A.D.J.4    Johnson, R.5
  • 24
  • 25
    • 66049149024 scopus 로고    scopus 로고
    • Identification of an endogenous ligand bound to a native orphan nuclear receptor
    • doi:10.1371/journal.pone.0005609
    • Yuan X, Ta TC, Lin M, Evans JR, Dong Y, et al. (2009) Identification of an endogenous ligand bound to a native orphan nuclear receptor. PLoS One 4: e5609. doi:10.1371/journal.pone.0005609.
    • (2009) PLoS One , vol.4
    • Yuan, X.1    Ta, T.C.2    Lin, M.3    Evans, J.R.4    Dong, Y.5
  • 26
    • 0033711971 scopus 로고    scopus 로고
    • Structural studies on nuclear receptors
    • Renaud JP, Moras D (2000) Structural studies on nuclear receptors. Cell Mol Life Sci 57: 1748-1769.
    • (2000) Cell Mol Life Sci , vol.57 , pp. 1748-1769
    • Renaud, J.P.1    Moras, D.2
  • 27
    • 0032511086 scopus 로고    scopus 로고
    • Hormone-dependent coactivator binding to a hydrophobic cleft on nuclear receptors
    • Feng W, Ribeiro RC, Wagner RL, Nguyen H, Apriletti JW, et al. (1998) Hormone-dependent coactivator binding to a hydrophobic cleft on nuclear receptors. Science 280: 1747-1749.
    • (1998) Science , vol.280 , pp. 1747-1749
    • Feng, W.1    Ribeiro, R.C.2    Wagner, R.L.3    Nguyen, H.4    Apriletti, J.W.5
  • 28
    • 0038526314 scopus 로고    scopus 로고
    • Structure and function of Nurr1 identifies a class of ligand-independent nuclear receptors
    • Wang Z, Benoit G, Liu J, Prasad S, Aarnisalo P, et al. (2003) Structure and function of Nurr1 identifies a class of ligand-independent nuclear receptors. Nature 423: 555-560.
    • (2003) Nature , vol.423 , pp. 555-560
    • Wang, Z.1    Benoit, G.2    Liu, J.3    Prasad, S.4    Aarnisalo, P.5
  • 29
    • 0038508965 scopus 로고    scopus 로고
    • The Drosophila orphan nuclear receptor DHR38 mediates an atypical ecdysteroid signaling pathway
    • Baker KD, Shewchuk LM, Kozlova T, Makishima M, Hassell A, et al. (2003) The Drosophila orphan nuclear receptor DHR38 mediates an atypical ecdysteroid signaling pathway. Cell 113: 731-742.
    • (2003) Cell , vol.113 , pp. 731-742
    • Baker, K.D.1    Shewchuk, L.M.2    Kozlova, T.3    Makishima, M.4    Hassell, A.5
  • 30
    • 10944250224 scopus 로고    scopus 로고
    • The nuclear xenobiotic receptor CAR: Structural determinants of constitutive activation and hetero-dimerization
    • Suino K, Peng L, Reynolds R, Li Y, Cha JY, et al. (2004) The nuclear xenobiotic receptor CAR: structural determinants of constitutive activation and hetero-dimerization. Mol Cell 16: 893-905.
    • (2004) Mol Cell , vol.16 , pp. 893-905
    • Suino, K.1    Peng, L.2    Reynolds, R.3    Li, Y.4    Cha, J.Y.5
  • 31
    • 19944372389 scopus 로고    scopus 로고
    • A structural basis for constitutive activity in the human CAR/RXRalpha heterodimer
    • Xu RX, Lambert MH, Wisely BB, Warren EN, Weinert EE, et al. (2004) A structural basis for constitutive activity in the human CAR/RXRalpha heterodimer. Mol Cell 16: 919-928.
    • (2004) Mol Cell , vol.16 , pp. 919-928
    • Xu, R.X.1    Lambert, M.H.2    Wisely, B.B.3    Warren, E.N.4    Weinert, E.E.5
  • 32
    • 10944229118 scopus 로고    scopus 로고
    • Structure of the murine constitutive androstane receptor complexed to androstenol: A molecular basis for inverse agonism
    • Shan L, Vincent J, Brunzelle JS, Dussault I, Lin M, et al. (2004) Structure of the murine constitutive androstane receptor complexed to androstenol: a molecular basis for inverse agonism. Mol Cell 16: 907-917.
    • (2004) Mol Cell , vol.16 , pp. 907-917
    • Shan, L.1    Vincent, J.2    Brunzelle, J.S.3    Dussault, I.4    Lin, M.5
  • 33
    • 13544263313 scopus 로고    scopus 로고
    • Structural analyses reveal phosphatidyl inositols as ligands for the NR5 orphan receptors SF-1 and LRH-1
    • Krylova IN, Sablin EP, Moore J, Xu RX, Waitt GM, et al. (2005) Structural analyses reveal phosphatidyl inositols as ligands for the NR5 orphan receptors SF-1 and LRH-1. Cell 120: 343-355.
    • (2005) Cell , vol.120 , pp. 343-355
    • Krylova, I.N.1    Sablin, E.P.2    Moore, J.3    Xu, R.X.4    Waitt, G.M.5
  • 34
    • 34548040966 scopus 로고    scopus 로고
    • Crystal structure of an ancient protein: Evolution by conformational epistasis
    • Ortlund EA, Bridgham JT, Redinbo MR, Thornton JW (2007) Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317: 1544-1548.
    • (2007) Science , vol.317 , pp. 1544-1548
    • Ortlund, E.A.1    Bridgham, J.T.2    Redinbo, M.R.3    Thornton, J.W.4
  • 35
    • 0035893393 scopus 로고    scopus 로고
    • Glucocorticoids manifest androgenic activity in a cell line derived from a metastatic prostate cancer
    • Chang CY, Walther PJ, McDonnell DP (2001) Glucocorticoids manifest androgenic activity in a cell line derived from a metastatic prostate cancer. Cancer Res 61: 8712-8717.
    • (2001) Cancer Res , vol.61 , pp. 8712-8717
    • Chang, C.Y.1    Walther, P.J.2    McDonnell, D.P.3
  • 36
    • 0034617130 scopus 로고    scopus 로고
    • Activating mineralocorticoid receptor mutation in hypertension exacerbated by pregnancy
    • Geller DS, Farhi A, Pinkerton N, Fradley M, Moritz M, et al. (2000) Activating mineralocorticoid receptor mutation in hypertension exacerbated by pregnancy. Science 289: 119-123.
    • (2000) Science , vol.289 , pp. 119-123
    • Geller, D.S.1    Farhi, A.2    Pinkerton, N.3    Fradley, M.4    Moritz, M.5
  • 37
    • 0035958922 scopus 로고    scopus 로고
    • Molecular basis for the constitutive activity of estrogen-related receptor alpha-1
    • Chen S, Zhou D, Yang C, Sherman M (2001) Molecular basis for the constitutive activity of estrogen-related receptor alpha-1. J Biol Chem 276: 28465-28470.
    • (2001) J Biol Chem , vol.276 , pp. 28465-28470
    • Chen, S.1    Zhou, D.2    Yang, C.3    Sherman, M.4
  • 39
    • 0141742293 scopus 로고    scopus 로고
    • PANTHER: A library of protein families and subfamilies indexed by function
    • Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, et al. (2003) PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 13: 2129-2141.
    • (2003) Genome Res , vol.13 , pp. 2129-2141
    • Thomas, P.D.1    Campbell, M.J.2    Kejariwal, A.3    Mi, H.4    Karlak, B.5
  • 40
    • 0032568655 scopus 로고    scopus 로고
    • SMART, a simple modular architecture research tool: Identification of signaling domains
    • 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.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 5857-5864
    • Schultz, J.1    Milpetz, F.2    Bork, P.3    Ponting, C.P.4
  • 41
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 42
    • 33747877691 scopus 로고    scopus 로고
    • The iRMSD: A local measure of sequence alignment accuracy using structural information
    • Armougom F, Moretti S, Keduas V, Notredame C (2006) The iRMSD: a local measure of sequence alignment accuracy using structural information. Bioinfor-matics 22: e35-e39.
    • (2006) Bioinfor-matics , vol.22
    • Armougom, F.1    Moretti, S.2    Keduas, V.3    Notredame, C.4
  • 43
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
    • (2003) Syst Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 44
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 45
    • 33745256005 scopus 로고    scopus 로고
    • Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
    • Anisimova M, Gascuel O (2006) Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol 55: 539-552.
    • (2006) Syst Biol , vol.55 , pp. 539-552
    • Anisimova, M.1    Gascuel, O.2
  • 46
    • 33846141299 scopus 로고    scopus 로고
    • Searching for convergence in phylogenetic Markov chain Monte Carlo
    • Beiko RG, Keith JM, Harlow TJ, Ragan MA (2006) Searching for convergence in phylogenetic Markov chain Monte Carlo. Syst Biol 55: 553-565.
    • (2006) Syst Biol , vol.55 , pp. 553-565
    • Beiko, R.G.1    Keith, J.M.2    Harlow, T.J.3    Ragan, M.A.4
  • 47
    • 39149141072 scopus 로고    scopus 로고
    • AWTY (are we there yet?): A system for graphical exploration of MCMC convergence in Bayesian phylogenetics
    • Nylander JA, Wilgenbusch JC, Warren DL, Swofford DL (2008) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24: 581-583.
    • (2008) Bioinformatics , vol.24 , pp. 581-583
    • Nylander, J.A.1    Wilgenbusch, J.C.2    Warren, D.L.3    Swofford, D.L.4
  • 48
    • 0141677722 scopus 로고    scopus 로고
    • Retinoid X receptor and retinoic acid response in the marine sponge Suberites domuncula
    • Wiens M, Batel R, Korzhev M, Muller WE (2003) Retinoid X receptor and retinoic acid response in the marine sponge Suberites domuncula. J Exp Biol 206: 3261-3271.
    • (2003) J Exp Biol , vol.206 , pp. 3261-3271
    • Wiens, M.1    Batel, R.2    Korzhev, M.3    Muller, W.E.4
  • 49
    • 33646485296 scopus 로고    scopus 로고
    • Developmental expression of transcription factor genes in a demosponge: Insights into the origin of metazoan multicellularity
    • Larroux C, Fahey B, Liubicich D, Hinman VF, Gauthier M, et al. (2006) Developmental expression of transcription factor genes in a demosponge: insights into the origin of metazoan multicellularity. Evol Dev 8: 150-173.
    • (2006) Evol Dev , vol.8 , pp. 150-173
    • Larroux, C.1    Fahey, B.2    Liubicich, D.3    Hinman, V.F.4    Gauthier, M.5
  • 50
    • 0034791426 scopus 로고    scopus 로고
    • A simple algorithm to infer gene duplication and speciation events on a gene tree
    • Zmasek CM, Eddy SR (2001) A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17: 821-828.
    • (2001) Bioinformatics , vol.17 , pp. 821-828
    • Zmasek, C.M.1    Eddy, S.R.2
  • 51
    • 0027995683 scopus 로고
    • Detection, delineation, measurement and display of cavities in macromolecular structures
    • Kleywegt GJ, Jones TA (1994) Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr D Biol Crystallogr 50: 178-185.
    • (1994) Acta Crystallogr D Biol Crystallogr , vol.50 , pp. 178-185
    • Kleywegt, G.J.1    Jones, T.A.2


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