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Modulation of human nuclear receptor LRH-1 activity by phospholipids and SHP

Nature Structural & Molecular Biology volume 12, pages 357–363 (2005)Cite this article

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Abstract

The human nuclear receptor liver receptor homolog 1 (hLRH-1) plays an important role in the development of breast carcinomas. This orphan receptor is efficiently downregulated by the unusual co-repressor SHP and has been thought to be ligand-independent. We present the crystal structure at a resolution of 1.9 Å of the ligand-binding domain of hLRH-1 in complex with the NR box 1 motif of human SHP, which we find contacts the AF-2 region of hLRH-1 using selective structural motifs. Electron density indicates phospholipid bound within the ligand-binding pocket, which we confirm using mass spectrometry of solvent-extracted samples. We further show that pocket mutations reduce phospholipid binding and receptor activity in vivo. Our results indicate that hLRH-1's control of gene expression is mediated by phospholipid binding, and establish hLRH-1 as a novel target for compounds designed to slow breast cancer development.

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Figure 1: Human LRH-1 LBD in complex with SHP peptide and phospholipid.
Figure 2: NR box binding to the surface of hLRH-1.
Figure 3: Phospholipid binding to the hLRH-1 LBD.
Figure 4: Phospholipid binding impacts the transcriptional activity of LRH-1 in cells.
Figure 5: Phospholipid binding impacts the interaction between hLRH-1 and co-regulators.

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  • 06 March 2005

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Notes

  1. Note: In the version of this article originally published online, Figure 4c and the legend describing it contained mistakes. The second and third lines in the graphical legends for this panel read “SRC-3” and “SRC-2”, respectively. The text read “ (c) The F342W I416W form of hLRH-1 LBD, which is reduced in phospholipid binding, shows reduced levels of coactivation by SRC-2 and SRC-3.” We apologize for any inconvenience this may have caused. This error has been corrected for the HTML and print versions of the article.

References

  1. Fayard, E., Auwerx, J. & Schoonjans, K. LRH-1: an orphan nuclear receptor involved in development, metabolism and steroidogenesis. Trends Cell Biol. 14, 250–260 (2004).

    Article  CAS  Google Scholar 

  2. Val, P., Lefrancois-Martinez, A.M., Veyssiere, G. & Martinez, A. SF-1 a key player in the development and differentiation of steroidogenic tissues. Nucl. Recept. 1, 8 (2003).

    Article  Google Scholar 

  3. Galarneau, L. et al. The α1-fetoprotein locus is activated by a nuclear receptor of the Drosophila FTZ-F1 family. Mol. Cell. Biol. 16, 3853–3865 (1996).

    Article  CAS  Google Scholar 

  4. Boerboom, D., Pilon, N., Behdjani, R., Silversides, D.W. & Sirois, J. Expression and regulation of transcripts encoding two members of the NR5A nuclear receptor subfamily of orphan nuclear receptors, steroidogenic factor-1 and NR5A2, in equine ovarian cells during the ovulatory process. Endocrinology 141, 4647–4656 (2000).

    Article  CAS  Google Scholar 

  5. Becker-Andre, M., Andre, E. & DeLamarter, J.F. Identification of nuclear receptor mRNAs by RT-PCR amplification of conserved zinc-finger motif sequences. Biochem. Biophys. Res. Commun. 194, 1371–1379 (1993).

    Article  CAS  Google Scholar 

  6. Li, M. et al. Cloning and characterization of a novel human hepatocyte transcription factor, hB1F, which binds and activates enhancer II of hepatitis B virus. J. Biol. Chem. 273, 29022–29031 (1998).

    Article  CAS  Google Scholar 

  7. Wang, Z.N., Bassett, M. & Rainey, W.E. Liver receptor homologue-1 is expressed in the adrenal and can regulate transcription of 11 β-hydroxylase. J. Mol. Endocrinol. 27, 255–258 (2001).

    Article  Google Scholar 

  8. Schoonjans, K. et al. Liver receptor homolog 1 controls the expression of the scavenger receptor class B type I. EMBO Rep. 3, 1181–1187 (2002).

    Article  CAS  Google Scholar 

  9. Hinshelwood, M.M. et al. Expression of LRH-1 and SF-1 in the mouse ovary: localization in different cell types correlates with differing function. Mol. Cell. Endocrinol. 207, 39–45 (2003).

    Article  CAS  Google Scholar 

  10. Liu, D.L. et al. Expression and functional analysis of liver receptor homologue 1 as a potential steroidogenic factor in rat ovary. Biol. Reprod. 69, 508–517 (2003).

    Article  CAS  Google Scholar 

  11. Falender, A.E., Lanz, R., Malenfant, D., Belanger, L. & Richards, J.S. Differential expression of steroidogenic factor-1 and FTF/LRH-1 in the rodent ovary. Endocrinology 144, 3598–3610 (2003).

    Article  CAS  Google Scholar 

  12. Sirianni, R. et al. Liver receptor homologue-1 is expressed in human steroidogenic tissues and activates transcription of genes encoding steroidogenic enzymes. J. Endocrinol. 174, R13–R17 (2002).

    Article  CAS  Google Scholar 

  13. Clyne, C.D., Speed, C.J., Zhou, J. & Simpson, E.R. Liver receptor homologue-1 (LRH-1) regulates expression of aromatase in preadipocytes. J. Biol. Chem. 277, 20591–20597 (2002).

    Article  CAS  Google Scholar 

  14. Parker, K.L. & Schimmer, B.P. Steroidogenic factor 1: a key determinant of endocrine development and function. Endocr. Rev. 18, 361–377 (1997).

    Article  CAS  Google Scholar 

  15. Hammer, G.D. & Ingraham, H.A. Steroidogenic factor-1: its role in endocrine organ development and differentiation. Front. Neuroendocrinol. 20, 199–223 (1999).

    Article  CAS  Google Scholar 

  16. Botrugno, O.A. et al. Synergy between LRH-1 and β-catenin induces G1 cyclin-mediated cell proliferation. Mol. Cell 15, 499–509 (2004).

    Article  CAS  Google Scholar 

  17. Kovacic, A., Speed, C.J., Simpson, E.R. & Clyne, C.D. Inhibition of aromatase transcription via promoter II by short heterodimer partner in human preadipocytes. Mol. Endocrinol. 18, 252–259 (2004).

    Article  CAS  Google Scholar 

  18. Sablin, E.P., Krylova, I.N., Fletterick, R.J. & Ingraham, H.A. Structural basis for ligand-independent activation of the orphan nuclear receptor LRH-1. Mol. Cell 11, 1575–1585 (2003).

    Article  CAS  Google Scholar 

  19. Goodwin, B. et al. A regulatory cascade of the nuclear receptors FXR, SHP-1, and LRH-1 represses bile acid biosynthesis. Mol. Cell 6, 517–526 (2000).

    Article  CAS  Google Scholar 

  20. Lu, T.T. et al. Molecular basis for feedback regulation of bile acid synthesis by nuclear receptors. Mol. Cell 6, 507–515 (2000).

    Article  CAS  Google Scholar 

  21. Goodwin, B. et al. Differential regulation of rat and human CYP7A1 by the nuclear oxysterol receptor liver X receptor-α. Mol. Endocrinol. 17, 386–394 (2003).

    Article  CAS  Google Scholar 

  22. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994).

  23. Watkins, R.E., Davis-Searles, P.R., Lambert, M.H. & Redinbo, M.R. Coactivator binding promotes the specific interaction between ligand and the pregnane X receptor. J. Mol. Biol. 331, 815–828 (2003).

    Article  CAS  Google Scholar 

  24. Darimont, B.D. et al. Structure and specificity of nuclear receptor-coactivator interactions. Genes Dev. 12, 3343–3356 (1998).

    Article  CAS  Google Scholar 

  25. He, B., Kemppainen, J.A. & Wilson, E.M. FXXLF and WXXLF sequences mediate the NH2-terminal interaction with the ligand binding domain of the androgen receptor. J. Biol. Chem. 275, 22986–22994 (2000).

    Article  CAS  Google Scholar 

  26. Greschik, H., Flaig, R., Renaud, J.P. & Moras, D. 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).

    Article  CAS  Google Scholar 

  27. Suzuki, T., Kasahara, M., Yoshioka, H., Morohashi, K. & Umesono, K. LXXLL-related motifs in Dax-1 have target specificity for the orphan nuclear receptors Ad4BP/SF-1 and LRH-1. Mol. Cell. Biol. 23, 238–249 (2003).

    Article  CAS  Google Scholar 

  28. Doig, A.J. & Baldwin, R.L. N- and C-capping preferences for all 20 amino acids in α-helical peptides. Protein Sci. 4, 1325–1336 (1995).

    Article  CAS  Google Scholar 

  29. Kallenberger, B.C., Love, J.D., Chatterjee, V.K. & Schwabe, J.W. A dynamic mechanism of nuclear receptor activation and its perturbation in a human disease. Nat. Struct. Biol. 10, 136–140 (2003).

    Article  CAS  Google Scholar 

  30. Xu, H.E. et al. Structural basis for antagonist-mediated recruitment of nuclear co-repressors by PPARα. Nature 415, 813–817 (2002).

    Article  CAS  Google Scholar 

  31. Clayton, G.M., Peak-Chew, S.Y., Evans, R.M. & Schwabe, J.W. The structure of the ultraspiracle ligand-binding domain reveals a nuclear receptor locked in an inactive conformation. Proc. Natl. Acad. Sci. USA 98, 1549–1554 (2001).

    Article  CAS  Google Scholar 

  32. Billas, I.M., Moulinier, L., Rochel, N. & Moras, D. Crystal structure of the ligand-binding domain of the ultraspiracle protein USP, the ortholog of retinoid X receptors in insects. J. Biol. Chem. 276, 7465–7474 (2001).

    Article  CAS  Google Scholar 

  33. Ahn, V.E., Faull, K.F., Whitelegge, J.P., Fluharty, A.L. & Prive, G.G. Crystal structure of saposin B reveals a dimeric shell for lipid binding. Proc. Natl. Acad. Sci. USA 100, 38–43 (2003).

    Article  CAS  Google Scholar 

  34. Roderick, S.L. et al. Structure of human phosphatidylcholine transfer protein in complex with its ligand. Nat. Struct. Biol. 9, 507–511 (2002).

    CAS  PubMed  Google Scholar 

  35. van Tilbeurgh, H. et al. Interfacial activation of the lipase-procolipase complex by mixed micells revealed by X-ray crystallography. Nature 362, 814–820 (1993).

    Article  CAS  Google Scholar 

  36. Zhou, X. & Arthur, G. Improved procedures for the determination of lipid phosphorus by malachite green. J. Lipid Res. 33, 1233–1236 (1992).

    CAS  PubMed  Google Scholar 

  37. Ikeda, Y. et al. Characterization of the mouse FTZ-F1 gene, which encodes a key regulator of steroid hydroxylase gene expression. Mol. Endocrinol. 7, 852–860 (1993).

    CAS  PubMed  Google Scholar 

  38. Albi, E. & Viola Magni, M.P. The role of intranuclear lipids. Biol. Cell. 96, 657–667 (2004).

    Article  CAS  Google Scholar 

  39. Cui, P., Qin, B., Liu, N., Pan, G. & Pei, D. Nuclear localization of the phosphatidylserine receptor protein via multiple nuclear localization signals. Exp. Cell Res. 293, 154–163 (2004).

    Article  CAS  Google Scholar 

  40. Loewen, C.J. et al. Phospholipid metabolism regulated by a transcription factor sensing phosphatidic acid. Science 304, 1644–1647 (2004).

    Article  CAS  Google Scholar 

  41. Schoonjans, K. et al. Liver receptor homolog 1 contributes to intestinal tumor formation through effects on cell cycle and inflammation. Proc. Natl. Acad. Sci. USA 2058–2062 (2005).

  42. Li, M.O., Sarkisian, M.R., Mehal, W.Z., Rakic, P. & Flavell, R.A. Phosphatidylserine receptor is required for clearance of apoptotic cells. Science 302, 1560–1563 (2003).

    Article  CAS  Google Scholar 

  43. Freeman, L.A. et al. The orphan nuclear receptor LRH-1 activates the ABCG5/ABCG8 intergenic promoter. J. Lipid Res. 45, 1197–1206 (2004).

    Article  CAS  Google Scholar 

  44. de Vree, J.M. et al. Mutations in the MDR3 gene cause progressive familial intrahepatic cholestasis. Proc. Natl. Acad. Sci. USA 95, 282–287 (1998).

    Article  CAS  Google Scholar 

  45. Jian, B. et al. Scavenger receptor class B type I as a mediator of cellular cholesterol efflux to lipoproteins and phospholipid acceptors. J. Biol. Chem. 273, 5599–5606 (1998).

    Article  CAS  Google Scholar 

  46. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  Google Scholar 

  47. Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998).

    Article  CAS  Google Scholar 

  48. Laskowski, R.A., McArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the sterechemical quality of protein structure. J. Appl. Cryst. 26, 283–291 (1993).

    Article  CAS  Google Scholar 

  49. Bligh, E.G. & Dyer, W.J. A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 37, 911–917 (1959).

    Article  CAS  Google Scholar 

  50. Lee, Y.K. & Moore, D.D. Dual mechanisms for repression of the monomeric orphan receptor liver receptor homologous protein-1 by the orphan small heterodimer partner. J. Biol. Chem. 277, 2463–2467 (2002).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank S. Lujan and G. Pielak for discussions regarding biophysical techniques; D. Fargo (UNC Center for Bioinformatics) for assistance in promoter sequence searching; and members of the Redinbo laboratory for experimental assistance and stimulating discussions. This work was supported by US National Institutes of Health grant DK62229 (M.R.R.). Nondenaturing mass spectrometry analysis was partially supported by an anonymous gift to the UNC Michael Hooker Proteomics Core Facility for research targeted to proteomics and cystic fibrosis, and was conducted by core staff members C. Scarlett and V. Mocanu. E.A.O. was supported by a Lineberger Comprehensive Cancer Center postdoctoral fellowship, and I.H.S. and J.M.H. were supported in part by the UNC Smallwood Foundation and Office of Undergraduate Research. The mass spectrometry facility in the Department of Biochemistry of the Duke University Medical Center and Z.G. were supported by Core K of LIPID MAPS consortium grant 1U54GM069338.

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Authors and Affiliations

  1. Department of Chemistry, School of Medicine, University of North Carolina at Chapel Hill, University of North Carolina at Chapel Hill, Chapel Hill, 27599, North Carolina, USA

    Eric A Ortlund, Isaac H Solomon, Janet M Hager & Matthew R Redinbo

  2. Lineberger Comprehensive Cancer Center School of Medicine, University of North Carolina at Chapel Hill, University of North Carolina at Chapel Hill, Chapel Hill, 27599, North Carolina, USA

    Eric A Ortlund & Matthew R Redinbo

  3. Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina at Chapel Hill, University of North Carolina at Chapel Hill, Chapel Hill, 27599, North Carolina, USA

    Ashutosh Tripathy & Matthew R Redinbo

  4. Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, 77030, Texas, USA

    Yoonkwang Lee, Yunhee Choi & David D Moore

  5. Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, 27710, North Carolina, USA

    Rachid Safi & Donald P McDonnell

  6. Department of Biochemistry, Duke University Medical Center, Durham, 27710, North Carolina, USA

    Ziqiang Guan & Christian R H Raetz

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Correspondence to Matthew R Redinbo.

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Ortlund, E., Lee, Y., Solomon, I. et al. Modulation of human nuclear receptor LRH-1 activity by phospholipids and SHP. Nat Struct Mol Biol 12, 357–363 (2005). https://doi.org/10.1038/nsmb910

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