Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

A nuclear FK506-binding protein is a histone chaperone regulating rDNA silencing

Nature Structural & Molecular Biology volume 11, pages 275–283 (2004)Cite this article

Abstract

We report a novel chromatin-modulating factor, nuclear FK506-binding protein (FKBP). It is a member of the peptidyl prolyl cis-trans isomerase (PPIase) family, whose members were originally identified as enzymes that assist in the proper folding of polypeptides. The endogenous FKBP gene is required for the in vivo silencing of gene expression at the rDNA locus and FKBP has histone chaperone activity in vitro. Both of these properties depend on the N-terminal non-PPIase domain of the protein. The C-terminal PPIase domain is not essential for the histone chaperone activity in vitro, but it regulates rDNA silencing in vivo. Chromatin immunoprecipitation showed that nuclear FKBP associates with chromatin at rDNA loci in vivo. These in vivo and in vitro findings in nuclear FKBPs reveal a hitherto unsuspected link between PPIases and the alteration of chromatin structure.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Histone chaperone activity of a nuclear FKBP PPIase.
Figure 2: Difference between the histone chaperone reactions promoted by nuclear FKBP and the classical histone chaperone NAP-I.
Figure 3: The histone chaperone domain is distinct from the PPIase domain.
Figure 4: Conservation of the histone chaperone activities of nuclear FKBPs.
Figure 5: The association of nuclear FKBP with chromatin at rDNA loci in vivo.
Figure 6: Endogenous nuclear FKBP is essential for silencing at the rDNA locus.
Figure 7: Regulation of rDNA silencing by the C-terminal PPIase pocket in vivo.

Similar content being viewed by others

References

  1. Workman, J.L. & Kingston, R.E. Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu. Rev. Biochem. 67, 545–579 (1998).

    Article  CAS  Google Scholar 

  2. Wolffe, A. Chromatin 3rd edn (Academic, San Diego, 1998).

    Google Scholar 

  3. Fan, Z., Beresford, P.J., Oh, D.Y., Zhang, D. & Lieberman, J. Tumor suppressor NM23-H1 is a granzyme A-activated DNase during CTL-mediated apoptosis, and the nucleosome assembly protein SET is its inhibitor. Cell 112, 659–672 (2003).

    Article  CAS  Google Scholar 

  4. Ito, T., Bulger, M., Pazin, M.J., Kobayashi, R. & Kadonaga, J.T. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90, 145–155 (1997).

    Article  CAS  Google Scholar 

  5. Seo, S. et al. Regulation of histone acetylation and transcription by INHAT, a human cellular complex containing the Set oncoprotein. Cell 104, 119–130 (2001).

    Article  CAS  Google Scholar 

  6. Galat, A. & Riviere, S. Peptidyl-prolyl cis/trans Isomerases (Oxford Univ. Press, Oxford, 1998).

    Google Scholar 

  7. Hunter, T. Prolyl isomerase and nuclear function. Cell 92, 141–143 (1998).

    Article  CAS  Google Scholar 

  8. Himukai, R., Kuzuhara, T. & Horikoshi, M. Relationship between the subcellular localization and structures of catalytic domains of FKBP-type PPIases. J. Biochem. 126, 879–888 (1999).

    Article  CAS  Google Scholar 

  9. Leverson, J.D. & Ness, S.A. Point mutations in v-Myb disrupt a cyclophilin-catalyzed negative regulatory mechanism. Mol. Cell 1, 203–211 (1998).

    Article  CAS  Google Scholar 

  10. Mamane, Y., Sharma, S., Petropoulos, L., Lin, R. & Hiscott, J. Posttranslational regulation of IRF-4 activity by the immunophilin FKBP52. Immunity 12, 129–140 (2000).

    Article  CAS  Google Scholar 

  11. Pratt, W.B. Control of steroid receptor function and cytoplasmic-nuclear transport by heat shock proteins. Bioessays 14, 841–848 (1992).

    Article  CAS  Google Scholar 

  12. Tai, P.K., Albers, M.W., Chang, H., Faber, L.E. & Schreiber, S.L. Association of a 59-kiloDalton immunophilin with the glucocorticoid receptor complex. Science 256, 1315–1318 (1992).

    Article  CAS  Google Scholar 

  13. Sinars, C.R. et al. Structure of the large FK506-binding protein FKBP51, an Hsp90-binding protein and a component of steroid receptor complexes. Proc. Natl. Acad. Sci. USA 100, 868–873 (2003).

    Article  CAS  Google Scholar 

  14. Rycyzyn, M.A. & Clevenger, C.V. The intranuclear prolactin/cyclophilin B complex as a transcriptional inducer. Proc. Natl. Acad. Sci. USA 99, 6790–6795 (2002).

    Article  CAS  Google Scholar 

  15. Lu, P.-J., Wulf, G., Zhou, X.Z., Davies, P. & Lu, K.P. The prolyl isomerase Pin1 restores the function of Alzheimer-associated phosphorylated tau protein. Nature 399, 784–788 (1999).

    Article  CAS  Google Scholar 

  16. Lavoie, S.B., Albert, A.L., Handa, H., Vincent, M. & Bensaude, O. The peptidyl-prolyl isomerase Pin1 interacts with hSpt5 phosphorylated by Cdk9. J. Mol. Biol. 312, 675–685 (2001).

    Article  CAS  Google Scholar 

  17. Zacchi, P. et al. The prolyl isomerase Pin1 reveals a mechanism to control p53 functions after genotoxic insults. Nature 419, 853–857 (2002).

    Article  CAS  Google Scholar 

  18. Zheng, H. et al. The prolyl isomerase Pin1 is a regulator of p53 in genotoxic response. Nature 419, 849–853 (2002).

    Article  CAS  Google Scholar 

  19. Ryan, K.M. & Vousden, K.H. Cancer: pinning a change on p53. Nature 419, 795–797 (2002).

    Article  CAS  Google Scholar 

  20. Shan, X., Xue, Z. & Melese, T. Yeast NPI46 encodes a novel prolyl cis/trans isomerase that is located in the nucleolus. J. Cell Biol. 126, 853–862 (1994).

    Article  CAS  Google Scholar 

  21. Arévalo-Rodríguez, M., Cardenas, M.E., Wu, X., Hanes, S.D. & Heitman, J. Cyclophilin A and Ess1 interact with and regulate silencing by the Sin3-Rpd3 histone deacetylase. EMBO J. 19, 3739–3749 (2000).

    Article  Google Scholar 

  22. Wu, X. et al. The Ess1 prolyl isomerase is linked to chromatin remodeling complexes and the general transcription machinery. EMBO J. 19, 3727–3738 (2000).

    Article  CAS  Google Scholar 

  23. Yang, W.-M., Yao, Y.-L. & Seto, E. The FK506-binding protein 25 functionally associates with histone deacetylases and with transcription factor YY1. EMBO J. 20, 4814–4825 (2001).

    Article  CAS  Google Scholar 

  24. Laskey, R.A., Honda, B.M., Mills, A.D. & Finch, J.T. Nucleosome are assembled by an acidic protein which binds histones and transfers them to DNA. Nature 275, 416–420 (1978).

    Article  CAS  Google Scholar 

  25. Ishimi, Y., Yasuda, H., Hirosumi, J., Hanaoka, F. & Yamada, M. A protein which facilitates assembly of nucleosome-like structure in vitro in mammalian cells. J. Biochem. 94, 735–744 (1983).

    Article  CAS  Google Scholar 

  26. Harding, M.W., Galat, A., Uehling, D.E. & Schreiber, S.L. A receptor for the immunosuppressant FK506 is a cis/trans peptidyl-prolyl isomerase. Nature 341, 758–760 (1989).

    Article  CAS  Google Scholar 

  27. Siekierka, J.J., Hung, S.H.Y., Poe, M., Lin, C.S. & Sigal, N.H. A cytosolic binding protein for the immunosuppressant FK506 has peptidyl-prolyl isomerase activity but is distinct from cyclophilin. Nature 341, 755–757 (1989).

    Article  CAS  Google Scholar 

  28. Kleinschmidt, J.A. & Franke, W.W. Soluble acidic complexes containing histones H3 and H4 in nuclei of Xenopus laevis oocytes. Cell 29, 799–809 (1982).

    Article  CAS  Google Scholar 

  29. Matsumoto, K., Nagata, K., Ui, M. & Hanaoka, F. Template activating factor I, a novel host factor required to stimulate the adenovirus core DNA replication. J. Biol. Chem. 268, 10582–10587 (1993).

    CAS  PubMed  Google Scholar 

  30. Kaufman, P.D., Kobayashi, R. & Stillman, B. Ultraviolet radiation sensitivity and reduction of telomeric silencing in Saccharomyces cerevisiae cells lacking chromatin assembly factor-I. Genes Dev. 11, 345–357 (1997).

    Article  CAS  Google Scholar 

  31. Tyler, J.K. et al. The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature 402, 555–560 (1999).

    Article  CAS  Google Scholar 

  32. Munakata, T., Adachi, N., Yokoyama, N., Kuzuhara, T. & Horikoshi M. A human homologue of yeast anti-silencing factor has histone chaperone activity. Genes Cells 5, 221–233 (2000).

    Article  CAS  Google Scholar 

  33. Chimura, T., Kuzuhara, T. & Horikoshi, M. Identification and characterization of CIA/ASF1 as an interactor of bromodomains associated with TFIID. Proc. Natl. Acad. Sci. USA 99, 9334–9339 (2002).

    Article  CAS  Google Scholar 

  34. Umehara, T., Chimura, T., Ichikawa, N. & Horikoshi, M. Polyanionic stretch-deleted histone chaperone cia1/Asf1p is functional both in vivo and in vitro. Genes Cells 7, 59–73 (2002).

    Article  CAS  Google Scholar 

  35. Benton, B.M., Zang, J.H. & Thorner, J. A novel FK506- and rapamycin-binding protein (FPR3 gene product) in the yeast Saccharomyces cerevisiae is a proline rotamase localized to the nucleolus. J. Cell Biol. 127, 623–639 (1994).

    Article  CAS  Google Scholar 

  36. Hecht, A., Strahl-Bolsinger, S. & Grunstein, M. Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature 383, 92–96 (1996).

    Article  CAS  Google Scholar 

  37. Smith, J.S., Caputo, E. & Boeke, J.D. A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol. Cell. Biol. 19, 3184–3197 (1999).

    Article  CAS  Google Scholar 

  38. Dolinski, K., Muir, S., Cardenas, M. & Heitman, J. All cyclophilins and FK506 binding proteins are, individually and collectively, dispensable for viability in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 94, 13093–13098 (1997).

    Article  CAS  Google Scholar 

  39. Dolinski, K. et al. Functions of FKBP12 and mitochondrial cyclophilin active site residues in vitro and in vivo in Saccharomyces cerevisiae. Mol. Biol. Cell 8, 2267–2280 (1997).

    Article  CAS  Google Scholar 

  40. Singer, M.S. et al. Identification of high-copy disruptors of telomeric silencing in Saccharomyces cerevisiae. Genetics 150, 613–632 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Dittmer, D. et al. Gain of function mutations in p53. Nat. Genet. 4, 42–46 (1993).

    Article  CAS  Google Scholar 

  42. Fritze, C.E., Verschueren, K., Strich, R. & Easton Esposito, R. Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA. EMBO J. 16, 6495–6509 (1997).

    Article  CAS  Google Scholar 

  43. Ratajczak, T. & Carrello, A. Cyclophilin 40 (CyP-40), mapping of its hsp90 binding domain and evidence that FKBP52 competes with CyP-40 for hsp90 binding. J. Biol. Chem. 271, 2961–2965 (1996).

    Article  CAS  Google Scholar 

  44. Lu, P.J., Zhou, X.Z., Shen, M. & Lu, K.P. Function of WW domains as phosphoserine- or phosphothreonine-binding modules. Science 283, 1325–1328 (1999).

    Article  CAS  Google Scholar 

  45. Verdecia, M.A., Bowman, M.E., Lu, K.P., Hunter, T. & Noel, J.P. Structural basis for phosphoserine-proline recognition by group IV WW domains. Nat. Struct. Biol. 7, 639–643 (2000).

    Article  CAS  Google Scholar 

  46. Zarrinpar, A. & Lim, W.A. Converging on proline: the mechanism of WW domain peptide recognition. Nat. Struct. Biol. 7, 611–613 (2000).

    Article  CAS  Google Scholar 

  47. Morris, D.P., Phatnani, H.P. & Greenleaf, A.L. Phospho-carboxyl-terminal domain binding and the role of a prolyl isomerase in pre-mRNA 3′-end formation. J. Biol. Chem. 274, 31583–31587 (1999).

    Article  CAS  Google Scholar 

  48. Silverstein, A.M. et al. Different regions of the immunophilin FKBP52 determine its association with the glucocorticoid receptor, hsp90, and cytoplasmic dynein. J. Biol. Chem. 274, 36980–36986 (1999).

    Article  CAS  Google Scholar 

  49. Albert, A, Lavoie, S. & Vincent, M. A hyperphosphorylated form of RNA polymerase II is the major interphase antigen of the phosphoprotein antibody MPM-2 and interacts with the peptidyl-prolyl isomerase Pin1. J. Cell Sci. 112, 2493–2500 (1999).

    CAS  PubMed  Google Scholar 

  50. Wu, X., Chang, A., Sudol, M. & Hanes, S.D. Genetic interactions between the ESS1 prolyl-isomerase and the RSP5 ubiquitin ligase reveal opposing effects on RNA polymerase II function. Curr. Genet. 40, 234–242 (2001).

    Article  CAS  Google Scholar 

  51. Hoffmann, A. & Roeder, R.G. Purification of his-tagged proteins in non-denaturing conditions suggests a convenient method for protein interaction studies. Nucleic Acids Res. 19, 6337–6338 (1991).

    Article  CAS  Google Scholar 

  52. Simon, R.H. & Felsenfeld, G. A new procedure for purifying histone pairs H2A + H2B and H3 + H4 from chromatin using hydroxyapatite. Nucleic Acids Res. 6, 689–696 (1979).

    Article  CAS  Google Scholar 

  53. Rothstein, R.J. One-step gene disruption in yeast. Methods Enzymol. 101, 202–211 (1983).

    Article  CAS  Google Scholar 

  54. Van Duyne, G.D., Standaert, R.F., Karplus, P.A., Schreiber, S.L. & Clardy, J. Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex. Science 252, 839–842 (1991).

    Article  CAS  Google Scholar 

  55. Michnick, S.W., Rosen, M.K., Wandless, T.J., Karplus, M. & Schreiber, S.L. Solution structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin. Science 252, 836–839 (1991).

    Article  CAS  Google Scholar 

  56. Moore, J.M., Peattie, D.A., Fitzgibbon, M.J. & Thomson, J.A. Solution structure of the major binding protein for the immunosuppressant FK506. Nature 351, 248–250 (1991).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank J. Smith and J.D. Boeke for the gift of the yeast strain JS237 and Y. Ohya for the Candida glabrata genes. We also thank R. Himukai and N. Shinjyo for the construction of SpFkbp39p plasmids and purification of Fpr4 proteins, and N. Adachi, T. Chimura, K. Hasegawa, A. Kimura, S. Muto, M. Ohara, T. Suzuki, T. Umehara and P.A. Weil for critically reading the manuscript. This work was supported in part by a grant-in-aid for scientific research from the Ministry of Education, Culture, Sports, Science and Technology of Japan, New Energy and Industrial Technology Development Organization (NEDO) of the Ministry of Economy, Trade and Industry of Japan, and the Exploratory Research for Advanced Technology (ERATO) of the Japan Science Technology Corporation (JST).

Author information

Authors and Affiliations

  1. Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan

    Takashi Kuzuhara & Masami Horikoshi

  2. Horikoshi Gene Selector Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), 5-9-6 Tokodai, Tsukuba, 300-2535, Ibaraki, Japan

    Masami Horikoshi

Authors
  1. Takashi Kuzuhara
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Masami Horikoshi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Masami Horikoshi.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kuzuhara, T., Horikoshi, M. A nuclear FK506-binding protein is a histone chaperone regulating rDNA silencing. Nat Struct Mol Biol 11, 275–283 (2004). https://doi.org/10.1038/nsmb733

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb733

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing