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The nonconserved hinge region and distinct amino-terminal domains of the ROR alpha orphan nuclear receptor isoforms are required for proper DNA bending and ROR alpha-DNA interactions.

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  • 1. Department of Biochemistry, McGill University, Royal Victoria Hospital, Montréal, Québec, Canada.
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    • McBroom LD 1
    (1 author)

Molecular and Cellular Biology, 01 Feb 1995, 15(2):796-808
https://doi.org/10.1128/mcb.15.2.796 PMID: 7823947 PMCID: PMC231954

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Abstract 

ROR alpha 1 and ROR alpha 2 are two isoforms of a novel member of the steroid-thyroid-retinoid receptor superfamily and are considered orphan receptors since their cognate ligand has yet to be identified. These putative receptors have previously been shown to bind as monomers to a DNA recognition sequence composed of two distinct moieties, a 3' nuclear receptor core half-site AGGTCA preceded by a 5' AT-rich sequence. Recognition of this bipartite hormone response element (RORE) requires both the zinc-binding motifs and a group of amino acid residues located at the carboxy-terminal end of the DNA-binding domain (DBD) which is referred to here as the carboxy-terminal extension. In this report, we show that binding of ROR alpha 1 and ROR alpha 2 to the RORE induces a large DNA bend of approximately 130 degrees which may be important for receptor function. The overall direction of the DNA bend is towards the major groove at the center of the 3' AGGTCA half-site. The presence of the nonconserved hinge region which is located between the DBD and the putative ligand-binding domain (LBD) or ROR alpha is required for maximal DNA bending. Deletion of a large portion of the amino-terminal domain (NTD) of the ROR alpha protein does not alter the DNA bend angle but shifts the DNA bend center 5' relative to the bend induced by intact ROR alpha. Methylation interference studies using the NTD-deleted ROR alpha 1 mutant indicate that some DNA contacts in the 5' AT-rich half of the RORE are also shifted 5', while those in the 3' AGGTCA half-site are unaffected. These results are consistent with a model in which the ROR alpha NTD and the nonconserved hinge region orient the zinc-binding motifs and the carboxy-terminal extension of the ROR alpha DBD relative to each other to achieve proper interactions with the two halves of its recognition site. Transactivation studies suggest that both protein-induced DNA bending and protein-protein interactions are important for receptor function.

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Mol Cell Biol. 1995 Feb; 15(2): 796–808.
PMCID: PMC231954
PMID: 7823947

The nonconserved hinge region and distinct amino-terminal domains of the ROR alpha orphan nuclear receptor isoforms are required for proper DNA bending and ROR alpha-DNA interactions.

L D McBroom, G Flock, and V Giguère
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Abstract

ROR alpha 1 and ROR alpha 2 are two isoforms of a novel member of the steroid-thyroid-retinoid receptor superfamily and are considered orphan receptors since their cognate ligand has yet to be identified. These putative receptors have previously been shown to bind as monomers to a DNA recognition sequence composed of two distinct moieties, a 3' nuclear receptor core half-site AGGTCA preceded by a 5' AT-rich sequence. Recognition of this bipartite hormone response element (RORE) requires both the zinc-binding motifs and a group of amino acid residues located at the carboxy-terminal end of the DNA-binding domain (DBD) which is referred to here as the carboxy-terminal extension. In this report, we show that binding of ROR alpha 1 and ROR alpha 2 to the RORE induces a large DNA bend of approximately 130 degrees which may be important for receptor function. The overall direction of the DNA bend is towards the major groove at the center of the 3' AGGTCA half-site. The presence of the nonconserved hinge region which is located between the DBD and the putative ligand-binding domain (LBD) or ROR alpha is required for maximal DNA bending. Deletion of a large portion of the amino-terminal domain (NTD) of the ROR alpha protein does not alter the DNA bend angle but shifts the DNA bend center 5' relative to the bend induced by intact ROR alpha. Methylation interference studies using the NTD-deleted ROR alpha 1 mutant indicate that some DNA contacts in the 5' AT-rich half of the RORE are also shifted 5', while those in the 3' AGGTCA half-site are unaffected. These results are consistent with a model in which the ROR alpha NTD and the nonconserved hinge region orient the zinc-binding motifs and the carboxy-terminal extension of the ROR alpha DBD relative to each other to achieve proper interactions with the two halves of its recognition site. Transactivation studies suggest that both protein-induced DNA bending and protein-protein interactions are important for receptor function.

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Selected References

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  • Baur CP, Knippers R. Protein-induced bending of the simian virus 40 origin of replication. J Mol Biol. 1988 Oct 20;203(4):1009–1019. [Abstract] [Google Scholar]
  • Bracco L, Kotlarz D, Kolb A, Diekmann S, Buc H. Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. EMBO J. 1989 Dec 20;8(13):4289–4296. [Europe PMC free article] [Abstract] [Google Scholar]
  • Bradshaw MS, Tsai SY, Leng XH, Dobson AD, Conneely OM, O'Malley BW, Tsai MJ. Studies on the mechanism of functional cooperativity between progesterone and estrogen receptors. J Biol Chem. 1991 Sep 5;266(25):16684–16690. [Abstract] [Google Scholar]
  • Bugge TH, Pohl J, Lonnoy O, Stunnenberg HG. RXR alpha, a promiscuous partner of retinoic acid and thyroid hormone receptors. EMBO J. 1992 Apr;11(4):1409–1418. [Europe PMC free article] [Abstract] [Google Scholar]
  • Drouin J, Sun YL, Tremblay S, Lavender P, Schmidt TJ, de Léan A, Nemer M. Homodimer formation is rate-limiting for high affinity DNA binding by glucocorticoid receptor. Mol Endocrinol. 1992 Aug;6(8):1299–1309. [Abstract] [Google Scholar]
  • Espinás ML, Roux J, Ghysdael J, Pictet R, Grange T. Participation of Ets transcription factors in the glucocorticoid response of the rat tyrosine aminotransferase gene. Mol Cell Biol. 1994 Jun;14(6):4116–4125. [Europe PMC free article] [Abstract] [Google Scholar]
  • Evans RM. The steroid and thyroid hormone receptor superfamily. Science. 1988 May 13;240(4854):889–895. [Europe PMC free article] [Abstract] [Google Scholar]
  • Freedman LP. Anatomy of the steroid receptor zinc finger region. Endocr Rev. 1992 May;13(2):129–145. [Abstract] [Google Scholar]
  • Giese K, Cox J, Grosschedl R. The HMG domain of lymphoid enhancer factor 1 bends DNA and facilitates assembly of functional nucleoprotein structures. Cell. 1992 Apr 3;69(1):185–195. [Abstract] [Google Scholar]
  • Giese K, Grosschedl R. LEF-1 contains an activation domain that stimulates transcription only in a specific context of factor-binding sites. EMBO J. 1993 Dec;12(12):4667–4676. [Europe PMC free article] [Abstract] [Google Scholar]
  • Giguère V, Hollenberg SM, Rosenfeld MG, Evans RM. Functional domains of the human glucocorticoid receptor. Cell. 1986 Aug 29;46(5):645–652. [Abstract] [Google Scholar]
  • Giguere V, Ong ES, Segui P, Evans RM. Identification of a receptor for the morphogen retinoic acid. Nature. 1987 Dec 17;330(6149):624–629. [Abstract] [Google Scholar]
  • Giguère V, Tini M, Flock G, Ong E, Evans RM, Otulakowski G. Isoform-specific amino-terminal domains dictate DNA-binding properties of ROR alpha, a novel family of orphan hormone nuclear receptors. Genes Dev. 1994 Mar 1;8(5):538–553. [Abstract] [Google Scholar]
  • Gilson E, Roberge M, Giraldo R, Rhodes D, Gasser SM. Distortion of the DNA double helix by RAP1 at silencers and multiple telomeric binding sites. J Mol Biol. 1993 May 20;231(2):293–310. [Abstract] [Google Scholar]
  • Gober JW, Shapiro L. Integration host factor is required for the activation of developmentally regulated genes in Caulobacter. Genes Dev. 1990 Sep;4(9):1494–1504. [Abstract] [Google Scholar]
  • Goodman SD, Nash HA. Functional replacement of a protein-induced bend in a DNA recombination site. Nature. 1989 Sep 21;341(6239):251–254. [Abstract] [Google Scholar]
  • Harding HP, Lazar MA. The orphan receptor Rev-ErbA alpha activates transcription via a novel response element. Mol Cell Biol. 1993 May;13(5):3113–3121. [Europe PMC free article] [Abstract] [Google Scholar]
  • Hoover TR, Santero E, Porter S, Kustu S. The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons. Cell. 1990 Oct 5;63(1):11–22. [Abstract] [Google Scholar]
  • Kerppola TK, Curran T. DNA bending by Fos and Jun: the flexible hinge model. Science. 1991 Nov 22;254(5035):1210–1214. [Abstract] [Google Scholar]
  • Kerppola TK, Curran T. Fos-Jun heterodimers and Jun homodimers bend DNA in opposite orientations: implications for transcription factor cooperativity. Cell. 1991 Jul 26;66(2):317–326. [Abstract] [Google Scholar]
  • King IN, de Soyza T, Catanzaro DF, Lavin TN. Thyroid hormone receptor-induced bending of specific DNA sequences is modified by an accessory factor. J Biol Chem. 1993 Jan 5;268(1):495–501. [Abstract] [Google Scholar]
  • Kliewer SA, Umesono K, Mangelsdorf DJ, Evans RM. Retinoid X receptor interacts with nuclear receptors in retinoic acid, thyroid hormone and vitamin D3 signalling. Nature. 1992 Jan 30;355(6359):446–449. [Europe PMC free article] [Abstract] [Google Scholar]
  • Klock G, Strähle U, Schütz G. Oestrogen and glucocorticoid responsive elements are closely related but distinct. Nature. 1987 Oct 22;329(6141):734–736. [Abstract] [Google Scholar]
  • Knegtel RM, Katahira M, Schilthuis JG, Bonvin AM, Boelens R, Eib D, van der Saag PT, Kaptein R. The solution structure of the human retinoic acid receptor-beta DNA-binding domain. J Biomol NMR. 1993 Jan;3(1):1–17. [Abstract] [Google Scholar]
  • Krust A, Green S, Argos P, Kumar V, Walter P, Bornert JM, Chambon P. The chicken oestrogen receptor sequence: homology with v-erbA and the human oestrogen and glucocorticoid receptors. EMBO J. 1986 May;5(5):891–897. [Europe PMC free article] [Abstract] [Google Scholar]
  • Kumar V, Chambon P. The estrogen receptor binds tightly to its responsive element as a ligand-induced homodimer. Cell. 1988 Oct 7;55(1):145–156. [Abstract] [Google Scholar]
  • Laudet V, Hänni C, Coll J, Catzeflis F, Stéhelin D. Evolution of the nuclear receptor gene superfamily. EMBO J. 1992 Mar;11(3):1003–1013. [Europe PMC free article] [Abstract] [Google Scholar]
  • Lavorgna G, Ueda H, Clos J, Wu C. FTZ-F1, a steroid hormone receptor-like protein implicated in the activation of fushi tarazu. Science. 1991 May 10;252(5007):848–851. [Abstract] [Google Scholar]
  • Lazar MA, Hodin RA, Darling DS, Chin WW. A novel member of the thyroid/steroid hormone receptor family is encoded by the opposite strand of the rat c-erbA alpha transcriptional unit. Mol Cell Biol. 1989 Mar;9(3):1128–1136. [Europe PMC free article] [Abstract] [Google Scholar]
  • Lee MS, Kliewer SA, Provencal J, Wright PE, Evans RM. Structure of the retinoid X receptor alpha DNA binding domain: a helix required for homodimeric DNA binding. Science. 1993 May 21;260(5111):1117–1121. [Abstract] [Google Scholar]
  • Leid M, Kastner P, Lyons R, Nakshatri H, Saunders M, Zacharewski T, Chen JY, Staub A, Garnier JM, Mader S, et al. Purification, cloning, and RXR identity of the HeLa cell factor with which RAR or TR heterodimerizes to bind target sequences efficiently. Cell. 1992 Jan 24;68(2):377–395. [Abstract] [Google Scholar]
  • Leidig F, Shepard AR, Zhang WG, Stelter A, Cattini PA, Baxter JD, Eberhardt NL. Thyroid hormone responsiveness in human growth hormone-related genes. Possible correlation with receptor-induced DNA conformational changes. J Biol Chem. 1992 Jan 15;267(2):913–921. [Abstract] [Google Scholar]
  • Lu XP, Eberhardt NL, Pfahl M. DNA bending by retinoid X receptor-containing retinoid and thyroid hormone receptor complexes. Mol Cell Biol. 1993 Oct;13(10):6509–6519. [Europe PMC free article] [Abstract] [Google Scholar]
  • Luisi BF, Xu WX, Otwinowski Z, Freedman LP, Yamamoto KR, Sigler PB. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature. 1991 Aug 8;352(6335):497–505. [Abstract] [Google Scholar]
  • Mangelsdorf DJ, Ong ES, Dyck JA, Evans RM. Nuclear receptor that identifies a novel retinoic acid response pathway. Nature. 1990 May 17;345(6272):224–229. [Abstract] [Google Scholar]
  • Marks MS, Hallenbeck PL, Nagata T, Segars JH, Appella E, Nikodem VM, Ozato K. H-2RIIBP (RXR beta) heterodimerization provides a mechanism for combinatorial diversity in the regulation of retinoic acid and thyroid hormone responsive genes. EMBO J. 1992 Apr;11(4):1419–1435. [Europe PMC free article] [Abstract] [Google Scholar]
  • Martinez E, Givel F, Wahli W. The estrogen-responsive element as an inducible enhancer: DNA sequence requirements and conversion to a glucocorticoid-responsive element. EMBO J. 1987 Dec 1;6(12):3719–3727. [Europe PMC free article] [Abstract] [Google Scholar]
  • McBroom LD, Sadowski PD. DNA bending by Saccharomyces cerevisiae ABF1 and its proteolytic fragments. J Biol Chem. 1994 Jun 10;269(23):16461–16468. [Abstract] [Google Scholar]
  • När AM, Boutin JM, Lipkin SM, Yu VC, Holloway JM, Glass CK, Rosenfeld MG. The orientation and spacing of core DNA-binding motifs dictate selective transcriptional responses to three nuclear receptors. Cell. 1991 Jun 28;65(7):1267–1279. [Abstract] [Google Scholar]
  • Nardulli AM, Shapiro DJ. Binding of the estrogen receptor DNA-binding domain to the estrogen response element induces DNA bending. Mol Cell Biol. 1992 May;12(5):2037–2042. [Europe PMC free article] [Abstract] [Google Scholar]
  • Natesan S, Gilman MZ. DNA bending and orientation-dependent function of YY1 in the c-fos promoter. Genes Dev. 1993 Dec;7(12B):2497–2509. [Abstract] [Google Scholar]
  • Oñate SA, Prendergast P, Wagner JP, Nissen M, Reeves R, Pettijohn DE, Edwards DP. The DNA-bending protein HMG-1 enhances progesterone receptor binding to its target DNA sequences. Mol Cell Biol. 1994 May;14(5):3376–3391. [Europe PMC free article] [Abstract] [Google Scholar]
  • Pérez-Martín J, Espinosa M. Protein-induced bending as a transcriptional switch. Science. 1993 May 7;260(5109):805–807. [Abstract] [Google Scholar]
  • Retnakaran R, Flock G, Giguère V. Identification of RVR, a novel orphan nuclear receptor that acts as a negative transcriptional regulator. Mol Endocrinol. 1994 Sep;8(9):1234–1244. [Abstract] [Google Scholar]
  • Rhodes SJ, Chen R, DiMattia GE, Scully KM, Kalla KA, Lin SC, Yu VC, Rosenfeld MG. A tissue-specific enhancer confers Pit-1-dependent morphogen inducibility and autoregulation on the pit-1 gene. Genes Dev. 1993 Jun;7(6):913–932. [Abstract] [Google Scholar]
  • Rojo F, Zaballos A, Salas M. Bend induced by the phage phi 29 transcriptional activator in the viral late promoter is required for activation. J Mol Biol. 1990 Feb 20;211(4):713–725. [Abstract] [Google Scholar]
  • Russo FD, Silhavy TJ. Alpha: the Cinderella subunit of RNA polymerase. J Biol Chem. 1992 Jul 25;267(21):14515–14518. [Abstract] [Google Scholar]
  • Sabbah M, Le Ricousse S, Redeuilh G, Baulieu EE. Estrogen receptor-induced bending of the Xenopus vitellogenin A2 gene hormone response element. Biochem Biophys Res Commun. 1992 Jun 30;185(3):944–952. [Abstract] [Google Scholar]
  • Salvo JJ, Grindley ND. The gamma delta resolvase bends the res site into a recombinogenic complex. EMBO J. 1988 Nov;7(11):3609–3616. [Europe PMC free article] [Abstract] [Google Scholar]
  • Schwabe JW, Chapman L, Finch JT, Rhodes D. The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements. Cell. 1993 Nov 5;75(3):567–578. [Abstract] [Google Scholar]
  • Schwartz CJ, Sadowski PD. FLP recombinase of the 2 microns circle plasmid of Saccharomyces cerevisiae bends its DNA target. Isolation of FLP mutants defective in DNA bending. J Mol Biol. 1989 Feb 20;205(4):647–658. [Abstract] [Google Scholar]
  • Siebenlist U, Gilbert W. Contacts between Escherichia coli RNA polymerase and an early promoter of phage T7. Proc Natl Acad Sci U S A. 1980 Jan;77(1):122–126. [Europe PMC free article] [Abstract] [Google Scholar]
  • Stenzel TT, MacAllister T, Bastia D. Cooperativity at a distance promoted by the combined action of two replication initiator proteins and a DNA bending protein at the replication origin of pSC101. Genes Dev. 1991 Aug;5(8):1453–1463. [Abstract] [Google Scholar]
  • Thompson JF, Landy A. Empirical estimation of protein-induced DNA bending angles: applications to lambda site-specific recombination complexes. Nucleic Acids Res. 1988 Oct 25;16(20):9687–9705. [Europe PMC free article] [Abstract] [Google Scholar]
  • Tini M, Otulakowski G, Breitman ML, Tsui LC, Giguère V. An everted repeat mediates retinoic acid induction of the gamma F-crystallin gene: evidence of a direct role for retinoids in lens development. Genes Dev. 1993 Feb;7(2):295–307. [Abstract] [Google Scholar]
  • Truss M, Beato M. Steroid hormone receptors: interaction with deoxyribonucleic acid and transcription factors. Endocr Rev. 1993 Aug;14(4):459–479. [Abstract] [Google Scholar]
  • Truss M, Chalepakis G, Slater EP, Mader S, Beato M. Functional interaction of hybrid response elements with wild-type and mutant steroid hormone receptors. Mol Cell Biol. 1991 Jun;11(6):3247–3258. [Europe PMC free article] [Abstract] [Google Scholar]
  • Tsukiyama T, Ueda H, Hirose S, Niwa O. Embryonal long terminal repeat-binding protein is a murine homolog of FTZ-F1, a member of the steroid receptor superfamily. Mol Cell Biol. 1992 Mar;12(3):1286–1291. [Europe PMC free article] [Abstract] [Google Scholar]
  • Ueda H, Sun GC, Murata T, Hirose S. A novel DNA-binding motif abuts the zinc finger domain of insect nuclear hormone receptor FTZ-F1 and mouse embryonal long terminal repeat-binding protein. Mol Cell Biol. 1992 Dec;12(12):5667–5672. [Europe PMC free article] [Abstract] [Google Scholar]
  • Umesono K, Murakami KK, Thompson CC, Evans RM. Direct repeats as selective response elements for the thyroid hormone, retinoic acid, and vitamin D3 receptors. Cell. 1991 Jun 28;65(7):1255–1266. [Europe PMC free article] [Abstract] [Google Scholar]
  • Williams JS, Eckdahl TT, Anderson JN. Bent DNA functions as a replication enhancer in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Jul;8(7):2763–2769. [Europe PMC free article] [Abstract] [Google Scholar]
  • Wilson TE, Fahrner TJ, Johnston M, Milbrandt J. Identification of the DNA binding site for NGFI-B by genetic selection in yeast. Science. 1991 May 31;252(5010):1296–1300. [Abstract] [Google Scholar]
  • Wilson TE, Fahrner TJ, Milbrandt J. The orphan receptors NGFI-B and steroidogenic factor 1 establish monomer binding as a third paradigm of nuclear receptor-DNA interaction. Mol Cell Biol. 1993 Sep;13(9):5794–5804. [Europe PMC free article] [Abstract] [Google Scholar]
  • Wilson TE, Paulsen RE, Padgett KA, Milbrandt J. Participation of non-zinc finger residues in DNA binding by two nuclear orphan receptors. Science. 1992 Apr 3;256(5053):107–110. [Abstract] [Google Scholar]
  • Wu HM, Crothers DM. The locus of sequence-directed and protein-induced DNA bending. Nature. 1984 Apr 5;308(5959):509–513. [Abstract] [Google Scholar]
  • Yu VC, Delsert C, Andersen B, Holloway JM, Devary OV, När AM, Kim SY, Boutin JM, Glass CK, Rosenfeld MG. RXR beta: a coregulator that enhances binding of retinoic acid, thyroid hormone, and vitamin D receptors to their cognate response elements. Cell. 1991 Dec 20;67(6):1251–1266. [Abstract] [Google Scholar]
  • Zhang XK, Hoffmann B, Tran PB, Graupner G, Pfahl M. Retinoid X receptor is an auxiliary protein for thyroid hormone and retinoic acid receptors. Nature. 1992 Jan 30;355(6359):441–446. [Abstract] [Google Scholar]
  • Zinkel SS, Crothers DM. DNA bend direction by phase sensitive detection. Nature. 1987 Jul 9;328(6126):178–181. [Abstract] [Google Scholar]
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