Structure of Actin-related protein 8 and its contribution to nucleosome binding.

Christian B Gerhold,Christian B Gerhold,Christian B Gerhold,Sebastian Fenn,Sebastian Fenn,Sebastian Fenn,Brigitte Kessler,Karolin Luger,Karolin Luger,Karolin Luger,Karl-Peter Hopfner,Karl-Peter Hopfner,Karl-Peter Hopfner,Duane D Winkler,Duane D Winkler,Duane D Winkler,Kristina Lakomek,Gregor Witte,Gregor Witte,Gregor Witte,Kristina Lakomek,Kristina Lakomek,Florian U Seifert,Florian U Seifert,Florian U Seifert

doi:10.1093/nar/gks842

Abstract

Nuclear actin-related proteins (Arps) are subunits of several chromatin remodelers, but their molecular functions within these complexes are unclear. We report the crystal structure of the INO80 complex subunit Arp8 in its ATP-bound form. Human Arp8 has several insertions in the conserved actin fold that explain its inability to polymerize. Most remarkably, one insertion wraps over the active site cleft and appears to rigidify the domain architecture, while active site features shared with actin suggest an allosterically controlled ATPase activity. Quantitative binding studies with nucleosomes and histone complexes reveal that Arp8 and the Arp8–Arp4–actin-HSA sub-complex of INO80 strongly prefer nucleosomes and H3–H4 tetramers over H2A–H2B dimers, suggesting that Arp8 functions as a nucleosome recognition module. In contrast, Arp4 prefers free (H3–H4)2 over nucleosomes and may serve remodelers through binding to (dis)assembly intermediates in the remodeling reaction.

Highlights

Chromatin remodeling and modifying complexes regulate or facilitate chromosomal processes such as transcription, replication and DNA repair by changing the position, spacing, histone composition or histone modification pattern of nucleosomes
We found that human Arp8 (hArp8), like Arp4, stably binds ATP
In contrast to Arp4, we found that Arp8 has a low basal ATPase activity, suggesting that ATP-hydrolysis could contribute to Arp8 function

Summary

Introduction

Chromatin remodeling and modifying complexes regulate or facilitate chromosomal processes such as transcription, replication and DNA repair by changing the position, spacing, histone composition or histone modification pattern of nucleosomes. Deleting Arp8 in Saccharomyces cerevisiae results in an INO80 complex that lacks Arp4 and actin, in addition to the losses of DNA binding and ATPase activities [12]. To dissect the role of Arp8 and Arp4 in targeting the INO80 complex to chromatin, we quantitatively analysed the binding of Arp8, Arp4 and the intact Arp8–Arp4–actin-HSA sub-complex I to the histone complexes H2A–H2B, (H3–H4)2, DNA and to nucleosomes.

Results

Conclusion