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The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases

Abstract

We identify the helicase-SANT–associated (HSA) domain as the primary binding platform for nuclear actin-related proteins (ARPs) and actin. Individual HSA domains from chromatin remodelers (RSC, yeast SWI-SNF, human SWI-SNF, SWR1 and INO80) or modifiers (NuA4) reconstitute their respective ARP–ARP or ARP–actin modules. In RSC, the HSA domain resides on the catalytic ATPase subunit Sth1. The Sth1 HSA is essential in vivo, and its omission causes the specific loss of ARPs and a moderate reduction in ATPase activity. Genetic selections for arp suppressors yielded specific gain-of-function mutations in two new domains in Sth1, the post-HSA domain and protrusion 1, which are essential for RSC function in vivo but not ARP association. Taken together, we define the role of the HSA domain and provide evidence for a regulatory relationship involving the ARP–HSA module and two new functional domains conserved in remodeler ATPases that contain ARPs.

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Figure 1: HSA, post-HSA (PTH) and protrusion 1 domains in ARP-containing remodeling complexes are conserved; arpΔ suppressors cluster in Sth1.
Figure 2: Particular sth1 mutations suppress arpΔ mutations.
Figure 3: The HSA domain of Sth1 is sufficient to bind Arp7 and Arp9.
Figure 4: Individual HSA domains are sufficient to bind actin and particular ARPs.
Figure 5: The HSA domains of Sth1 and NuA4 are required for Arp and actin binding, and, in RSC, full ATPase activity.
Figure 6: The HSA, post-HSA and protrusion 1 domains are essential for viability.
Figure 7: Summary of HSA domain complexes and a model for HSA–ARP regulation of ATPase activity via the adjacent post-HSA domain and protrusion 1.

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References

  1. Havas, K., Whitehouse, I. & Owen-Hughes, T. ATP-dependent chromatin remodeling activities. Cell. Mol. Life Sci. 58, 673–682 (2001).

    Article  CAS  Google Scholar 

  2. Narlikar, G.J., Fan, H.Y. & Kingston, R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell 108, 475–487 (2002).

    Article  CAS  Google Scholar 

  3. Vignali, M., Hassan, A.H., Neely, K.E. & Workman, J.L. ATP-dependent chromatin-remodeling complexes. Mol. Cell. Biol. 20, 1899–1910 (2000).

    Article  CAS  Google Scholar 

  4. Saha, A., Wittmeyer, J. & Cairns, B.R. Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev. 16, 2120–2134 (2002).

    Article  CAS  Google Scholar 

  5. Brown, C.E., Lechner, T., Howe, L. & Workman, J.L. The many HATs of transcription coactivators. Trends Biochem. Sci. 25, 15–19 (2000).

    Article  CAS  Google Scholar 

  6. Sterner, D.E. & Berger, S.L. Acetylation of histones and transcription-related factors. Microbiol. Mol. Biol. Rev. 64, 435–459 (2000).

    Article  CAS  Google Scholar 

  7. Olave, I.A., Reck-Peterson, S.L. & Crabtree, G.R. Nuclear actin and actin-related proteins in chromatin remodeling. Annu. Rev. Biochem. 71, 755–781 (2002).

    Article  CAS  Google Scholar 

  8. Blessing, C.A., Ugrinova, G.T. & Goodson, H.V. Actin and ARPs: action in the nucleus. Trends Cell Biol. 14, 435–442 (2004).

    Article  CAS  Google Scholar 

  9. Chen, M. & Shen, X. Nuclear actin and actin-related proteins in chromatin dynamics. Curr. Opin. Cell Biol. 19, 326–330 (2007).

    Article  CAS  Google Scholar 

  10. Poch, O. & Winsor, B. Who's who among the Saccharomyces cerevisiae actin-related proteins? A classification and nomenclature proposal for a large family. Yeast 13, 1053–1058 (1997).

    Article  CAS  Google Scholar 

  11. Peterson, C.L., Zhao, Y. & Chait, B.T. Subunits of the yeast SWI/SNF complex are members of the actin-related protein (ARP) family. J. Biol. Chem. 273, 23641–23644 (1998).

    Article  CAS  Google Scholar 

  12. Cairns, B.R., Erdjument-Bromage, H., Tempst, P., Winston, F. & Kornberg, R.D. Two actin-related proteins are shared functional components of the chromatin-remodeling complexes RSC and SWI/SNF. Mol. Cell 2, 639–651 (1998).

    Article  CAS  Google Scholar 

  13. Krogan, N.J. et al. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol. Cell 12, 1565–1576 (2003).

    Article  CAS  Google Scholar 

  14. Shen, X., Mizuguchi, G., Hamiche, A. & Wu, C. A chromatin remodelling complex involved in transcription and DNA processing. Nature 406, 541–544 (2000).

    Article  CAS  Google Scholar 

  15. Galarneau, L. et al. Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Mol. Cell 5, 927–937 (2000).

    Article  CAS  Google Scholar 

  16. 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 

  17. Ikura, T. et al. Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Cell 102, 463–473 (2000).

    Article  CAS  Google Scholar 

  18. Grant, P.A. et al. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 11, 1640–1650 (1997).

    Article  CAS  Google Scholar 

  19. Osada, S. et al. The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1. Genes Dev. 15, 3155–3168 (2001).

    Article  CAS  Google Scholar 

  20. Zhao, K. et al. Rapid and phosphoinositol-dependent binding of the SWI/SNF-like BAF complex to chromatin after T lymphocyte receptor signaling. Cell 95, 625–636 (1998).

    Article  CAS  Google Scholar 

  21. Mizuguchi, G. et al. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303, 343–348 (2004).

    Article  CAS  Google Scholar 

  22. Szerlong, H., Saha, A. & Cairns, B.R. The nuclear actin-related proteins Arp7 and Arp9: a dimeric module that cooperates with architectural proteins for chromatin remodeling. EMBO J. 22, 3175–3187 (2003).

    Article  CAS  Google Scholar 

  23. Yang, X., Zaurin, R., Beato, M. & Peterson, C.L. Swi3p controls SWI/SNF assembly and ATP-dependent H2A–H2B displacement. Nat. Struct. Mol. Biol. 14, 540–547 (2007).

    Article  CAS  Google Scholar 

  24. Shen, X., Ranallo, R., Choi, E. & Wu, C. Involvement of actin-related proteins in ATP-dependent chromatin remodeling. Mol. Cell 12, 147–155 (2003).

    Article  CAS  Google Scholar 

  25. Wu, W.H. et al. Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange. Nat. Struct. Mol. Biol. 12, 1064–1071 (2005).

    Article  CAS  Google Scholar 

  26. Letunic, I. et al. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30, 242–244 (2002).

    Article  CAS  Google Scholar 

  27. Jorgensen, P. et al. High-resolution genetic mapping with ordered arrays of Saccharomyces cerevisiae deletion mutants. Genetics 162, 1091–1099 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Subramanya, H.S., Bird, L.E., Brannigan, J.A. & Wigley, D.B. Crystal structure of a DExx box DNA helicase. Nature 384, 379–383 (1996).

    Article  CAS  Google Scholar 

  29. Flaus, A., Martin, D.M., Barton, G.J. & Owen-Hughes, T. Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res. 34, 2887–2905 (2006).

    Article  CAS  Google Scholar 

  30. Thoma, N.H. et al. Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nat. Struct. Mol. Biol. 12, 350–356 (2005).

    Article  Google Scholar 

  31. Winzeler, E.A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901–906 (1999).

    Article  CAS  Google Scholar 

  32. Fiori, A. et al. Disruption of six novel genes from chromosome VII of Saccharomyces cerevisiae reveals one essential gene and one gene which affects the growth rate. Yeast 16, 377–386 (2000).

    Article  CAS  Google Scholar 

  33. Hitchcock-DeGregori, S.E. Now, swing your partner! 3D-domain switching of WASP activates Arp2/3 complex. Nat. Struct. Biol. 10, 583–584 (2003).

    Article  CAS  Google Scholar 

  34. Jonsson, Z.O., Jha, S., Wohlschlegel, J.A. & Dutta, A. Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin remodeling complex. Mol. Cell 16, 465–477 (2004).

    Article  CAS  Google Scholar 

  35. Tong, A.H. et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294, 2364–2368 (2001).

    Article  CAS  Google Scholar 

  36. Park, J., Wood, M.A. & Cole, M.D. BAF53 forms distinct nuclear complexes and functions as a critical c-Myc-interacting nuclear cofactor for oncogenic transformation. Mol. Cell. Biol. 22, 1307–1316 (2002).

    Article  CAS  Google Scholar 

  37. Cairns, B.R. et al. Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. Mol. Cell 4, 715–723 (1999).

    Article  CAS  Google Scholar 

  38. Puig, O. et al. The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24, 218–229 (2001).

    Article  CAS  Google Scholar 

  39. Bateman, A. et al. The Pfam protein families database. Nucleic Acids Res. 32, D138–D141 (2004).

    Article  CAS  Google Scholar 

  40. Clamp, M., Cuff, J., Searle, S.M. & Barton, G.J. The Jalview Java alignment editor. Bioinformatics 20, 426–427 (2004).

    Article  CAS  Google Scholar 

  41. Katoh, K., Kuma, K., Toh, H. & Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33, 511–518 (2005).

    Article  CAS  Google Scholar 

  42. Jones, D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195–202 (1999).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank J. Wittmeyer and A. Saha (Cairns laboratory) for plasmids, strains and expertise on protein purification. We thank J. Shaw, D. Close, M. Kasten, T. Parnell and J. Lenkart (all University of Utah) for reagents and advice. We thank W. Wang (US National Institutes of Health (NIH)) and M. Cole (Dartmouth University) for antibodies and plasmids, P. Hollenhorst and C. Foulds (University of Utah) for cell culture reagents and advice. This work was supported by the NIH (GM60415 to B.R.C., and support of H.S.), CA24014 for core facilities, and the Howard Hughes Medical Institute (support of B.R.C. and K.H.).

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H.S., K.H. and B.R.C. designed and interpreted experiments; H.S. and K.H. executed experiments and generated figures; R.V., H.S. and B.R.C. isolated and characterized sth1 alleles.; P.T. and H.E.-B. performed MS analysis; B.R.C., H.S. and K.H. wrote the manuscript.

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Correspondence to Bradley R Cairns.

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Szerlong, H., Hinata, K., Viswanathan, R. et al. The HSA domain binds nuclear actin-related proteins to regulate chromatin-remodeling ATPases. Nat Struct Mol Biol 15, 469–476 (2008). https://doi.org/10.1038/nsmb.1403

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