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:

Histone chaperone specificity in Rtt109 activation

Abstract

Rtt109 is a histone acetyltransferase that requires a histone chaperone for the acetylation of histone 3 at lysine 56 (H3K56). Rtt109 forms a complex with the chaperone Vps75 in vivo and is implicated in DNA replication and repair. Here we show that both Rtt109 and Vps75 bind histones with high affinity, but only the complex is efficient for catalysis. The C-terminal acidic domain of Vps75 contributes to activation of Rtt109 and is necessary for in vivo functionality of Vps75, but it is not required for interaction with either Rtt109 or histones. We demonstrate that Vps75 is a structural homolog of yeast Nap1 by solving its crystal structure. Nap1 and Vps75 interact with histones and Rtt109 with comparable affinities. However, only Vps75 stimulates Rtt109 enzymatic activity. Our data highlight the functional specificity of Vps75 in Rtt109 activation.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

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

Figure 1: Vps75 is a distinct member of the Nap1 family.
Figure 2: Vps75 binds histones with high affinity.
Figure 3: The C-terminal acidic domain of Vps75 contributes to in vivo and in vitro functions.
Figure 4: Nap1 does not stimulate Rtt109 HAT activity.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

References

  1. De Koning, L., Corpet, A., Haber, J.E. & Almouzni, G. Histone chaperones: an escort network regulating histone traffic. Nat. Struct. Mol. Biol. 14, 997–1007 (2007).

    Article  CAS  PubMed  Google Scholar 

  2. Eitoku, M., Sato, L., Senda, T. & Horikoshi, M. Histone chaperones: 30 years from isolation to elucidation of the mechanisms of nucleosome assembly and disassembly. Cell. Mol. Life Sci. 65, 414–444 (2008).

    Article  CAS  PubMed  Google Scholar 

  3. Shikama, N. et al. Functional interaction between nucleosome assembly proteins and p300/CREB-binding protein family coactivators. Mol. Cell. Biol. 20, 8933–8943 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Krogan, N.J. et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637–643 (2006).

    Article  CAS  PubMed  Google Scholar 

  5. Collins, S.R. et al. Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae. Mol. Cell. Proteomics 6, 439–450 (2007).

    Article  CAS  PubMed  Google Scholar 

  6. Tsubota, T. et al. Histone H3–K56 acetylation is catalyzed by histone chaperone-dependent complexes. Mol. Cell 25, 703–712 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Driscoll, R., Hudson, A. & Jackson, S.P. Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56. Science 315, 649–652 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Schneider, J., Bajwa, P., Johnson, F.C., Bhaumik, S.R. & Shilatifard, A. Rtt109 is required for proper H3K56 acetylation: a chromatin mark associated with the elongating RNA polymerase II. J. Biol. Chem. 281, 37270–37274 (2006).

    Article  CAS  PubMed  Google Scholar 

  9. Han, J. et al. Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. Science 315, 653–655 (2007).

    Article  CAS  PubMed  Google Scholar 

  10. Jessulat, M. et al. Interacting proteins Rtt109 and Vps75 affect the efficiency of non-homologous end-joining in Saccharomyces cerevisiae. Arch. Biochem. Biophys. 469, 157–164 (2008).

    Article  CAS  PubMed  Google Scholar 

  11. Fillingham, J. et al. Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109. Mol. Cell Biol. 28, 4342–4353 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Han, J., Zhou, H., Li, Z., Xu, R.M. & Zhang, Z. The Rtt109-Vps75 histone acetyltransferase complex acetylates non-nucleosomal histone H3. J. Biol. Chem. 282, 14158–14164 (2007).

    Article  CAS  PubMed  Google Scholar 

  13. Kelly, T.J., Qin, S., Gottschling, D.E. & Parthun, M.R. Type B histone acetyltransferase Hat1p participates in telomeric silencing. Mol. Cell. Biol. 20, 7051–7058 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Selth, L. & Svejstrup, J.Q. Vps75, a new yeast member of the NAP histone chaperone family. J. Biol. Chem. 282, 12358–12362 (2007).

    Article  CAS  PubMed  Google Scholar 

  15. Zlatanova, J., Seebart, C. & Tomschik, M. Nap1: taking a closer look at a juggler protein of extraordinary skills. FASEB J. 21, 1294–1310 (2007).

    Article  CAS  PubMed  Google Scholar 

  16. Park, Y.J. & Luger, K. Structure and function of nucleosome assembly proteins. Biochem. Cell Biol. 84, 549–558 (2006).

    Article  CAS  PubMed  Google Scholar 

  17. Adkins, M.W., Carson, J.J., English, C.M., Ramey, C.J. & Tyler, J.K. The histone chaperone anti-silencing function 1 stimulates the acetylation of newly synthesized histone H3 in S-phase. J. Biol. Chem. 282, 1334–1340 (2007).

    Article  CAS  PubMed  Google Scholar 

  18. Park, Y.J. & Luger, K. The structure of nucleosome assembly protein 1. Proc. Natl. Acad. Sci. USA 103, 1248–1253 (2006).

    Article  CAS  PubMed  Google Scholar 

  19. Park, Y.J., McBryant, S.J. & Luger, K. A β-hairpin comprising the nuclear localization sequence sustains the self-associated states of nucleosome assembly protein 1. J. Mol. Biol. 375, 1076–1085 (2008).

    Article  CAS  PubMed  Google Scholar 

  20. Park, Y.J., Chodaparambil, J.V., Bao, Y., McBryant, S.J. & Luger, K. Nucleosome assembly protein 1 exchanges histone H2A–H2B dimers and assists nucleosome sliding. J. Biol. Chem. 280, 1817–1825 (2005).

    Article  CAS  PubMed  Google Scholar 

  21. Giaever, G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387–391 (2002).

    Article  CAS  PubMed  Google Scholar 

  22. Hampsey, M. A review of phenotypes in Saccharomyces cerevisiae. Yeast 13, 1099–1133 (1997).

    Article  CAS  PubMed  Google Scholar 

  23. Seo, S.B. 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  PubMed  Google Scholar 

  24. Muto, S. et al. Relationship between the structure of SET/TAF-Iβ/INHAT and its histone chaperone activity. Proc. Natl. Acad. Sci. USA 104, 4285–4290 (2007).

    Article  CAS  PubMed  Google Scholar 

  25. Lee, M.W. et al. Global protein expression profiling of budding yeast in response to DNA damage. Yeast 24, 145–154 (2007).

    Article  CAS  PubMed  Google Scholar 

  26. English, C.M., Maluf, N.K., Tripet, B., Churchill, M.E. & Tyler, J.K. ASF1 binds to a heterodimer of histones H3 and H4: a two-step mechanism for the assembly of the H3–H4 heterotetramer on DNA. Biochemistry 44, 13673–13682 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Pflugrath, J.W. The finer things in X-ray diffraction data collection. Acta Crystallogr. D Biol. Crystallogr. 55, 1718–1725 (1999).

    Article  CAS  PubMed  Google Scholar 

  28. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjelgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).

    Article  PubMed  Google Scholar 

  29. Brunger, A.T., Adams, P.D. & Rice, L.M. New applications of simulated annealing in X-ray crystallography and solution NMR. Structure 5, 325–336 (1997).

    Article  CAS  PubMed  Google Scholar 

  30. Kleywegt, G.J. Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr. D Biol. Crystallogr. 52, 842–857 (1996).

    Article  CAS  PubMed  Google Scholar 

  31. Shechter, D., Dormann, H.L., Allis, C.D. & Hake, S.B. Extraction, purification and analysis of histones. Nat. Protoc. 2, 1445–1457 (2007).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank S. McBryant for help with analytical ultracentrifugation, N.J. Krogan, D.A. Goldstrohm and C.A. Radebaugh for discussion, and K. Brown for critical reading of the manuscript. We also thank J. Nix at MBC 4.2.2., Advanced Light Source, for data collection. This work was funded by the US National Institutes of Health (NIH) grant GM067777 to K.L. and by NIH grant GM056884 to L.A.S. Y.-J.P., A.J.A. and K.L. are supported by the Howard Hughes Medical Institute.

Author information

Authors and Affiliations

Authors

Contributions

Y.-.J.P. performed crystallography, gel shifts, enzymatic assays and initial yeast genetics studies; K.B.S. performed in vivo experiments; A.J.A. performed quantitative protein-protein interaction assays, MS and enzymatic assays; L.A.S. performed planning and advice for in vivo experiments; K.L. and Y.-J.P. planned and supervised the structural and biochemical experimental sections.

Corresponding author

Correspondence to Karolin Luger.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5 and Supplementary Methods (PDF 500 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Park, YJ., Sudhoff, K., Andrews, A. et al. Histone chaperone specificity in Rtt109 activation. Nat Struct Mol Biol 15, 957–964 (2008). https://doi.org/10.1038/nsmb.1480

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.1480

This article is cited by

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