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Molecular functions of the histone acetyltransferase chaperone complex Rtt109–Vps75

Nature Structural & Molecular Biology volume 15, pages 948–956 (2008)Cite this article

Abstract

Histone acetylation and nucleosome remodeling regulate DNA damage repair, replication and transcription. Rtt109, a recently discovered histone acetyltransferase (HAT) from Saccharomyces cerevisiae, functions with the histone chaperone Asf1 to acetylate lysine K56 on histone H3 (H3K56), a modification associated with newly synthesized histones. In vitro analysis of Rtt109 revealed that Vps75, a Nap1 family histone chaperone, could also stimulate Rtt109-dependent acetylation of H3K56. However, the molecular function of the Rtt109–Vps75 complex remains elusive. Here we have probed the molecular functions of Vps75 and the Rtt109–Vps75 complex through biochemical, structural and genetic means. We find that Vps75 stimulates the kcat of histone acetylation by ∼100-fold relative to Rtt109 alone and enhances acetylation of K9 in the H3 histone tail. Consistent with the in vitro evidence, cells lacking Vps75 showed a substantial reduction (60%) in H3K9 acetylation during S phase. X-ray structural, biochemical and genetic analyses of Vps75 indicate a unique, structurally dynamic Nap1-like fold that suggests a potential mechanism of Vps75-dependent activation of Rtt109. Together, these data provide evidence for a multifunctional HAT–chaperone complex that acetylates histone H3 and deposits H3-H4 onto DNA, linking histone modification and nucleosome assembly.

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Figure 1: Rtt109–Vps75 acetylates residues within the H3 tail.
Figure 2: Rtt109 stimulates histone-deposition activity of Vps75.
Figure 3: Structure of Vps75.
Figure 4: Dimerization between domain I of Vps75 monomers.
Figure 5: Comparison of surface electrostatics of the Nap1 family of histone chaperones.
Figure 6: Characterization of Vps75 acidic cavity mutants.

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Acknowledgements

We wish to thank S. Anderson at the Life Sciences Collaborative Access Team (LS-CAT) for assistance in data collection on the native Vps75. We also thank K. Satyshur for assistance in crystal screening, and we thank M. Foley and K. Crowley for assistance with the AUC experiment. Finally, we thank members of the Denu and Keck laboratories for helpful comments and critique of the work, especially K. Arnold, B. Smith, L. Li and M. Killoran. This work was supported in part by a predoctoral fellowship from the American Heart Association to C.E.B., US National Institutes of Health (NIH) grant GM059785 to J.M.D., a Shaw award from the Greater Milwaukee Foundation to J.L.K. and NIH grant GM055712 to P.D.K.

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Authors and Affiliations

  1. Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, 1300 University Avenue, Madison, 53706, Wisconsin, USA

    Christopher E Berndsen, Scott E Lindner, Susan Lee, James L Keck & John M Denu

  2. Programs in Gene Function and Expression and Molecular Medicine, University of Massachusetts Medical School, 364 Plantation Street #506, Worcester, 01605, Massachusetts, USA

    Toshiaki Tsubota & Paul D Kaufman

  3. Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, 94720, California, USA

    James M Holton

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Contributions

J.M.D., J.L.K., P.D.K., T.T. and C.E.B. developed experiments; C.E.B. performed biochemical analyses of Rtt109–Vps75; S.L. performed MS experiments; T.T. performed yeast cell-cycle analyses; C.E.B., S.E.L., J.M.H. and J.L.K. performed crystallographic experiments; C.E.B., T.T., S.L., J.L.K., P.D.K. and J.M.D. made figures and wrote the manuscript; all authors read and approved the final submission of manuscript.

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Correspondence to Paul D Kaufman, James L Keck or John M Denu.

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Berndsen, C., Tsubota, T., Lindner, S. et al. Molecular functions of the histone acetyltransferase chaperone complex Rtt109–Vps75. Nat Struct Mol Biol 15, 948–956 (2008). https://doi.org/10.1038/nsmb.1459

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