Structure and functional interactions of INO80 actin/Arp module.

Xuan Zhang,Xuejuan Wang,Gang Cai,Zhihui Zhang,Haian Fu

doi:10.1093/jmcb/mjy062

Abstract

The presence and functions of nuclear actin have been controversial due to the lack of molecular mechanisms. Nuclear actin and actin-related proteins (Arps) are subunits of several chromatin remodelers, including the evolutionarily conserved INO80 chromatin-remodeling complex. Here, we present an improved cryo-EM structure of the yeast INO80 complex and the first 3D reconstruction of the INO80 actin/Arp module. The modular and subunit architecture is defined using a combination of subunit deletion analysis and published crosslinking-mass spectrometry. The functional interactions of the INO80 actin/Arp module with a nucleosome is 3D EM reconstructed in two different binding states. Nucleosomes initially bind to the Arp8 subunit and the substantial conformational changes maximize nucleosome contacts of the actin/Arp module, which could promote the bound nucleosome to be engaged onto the INO80 ATPase domain. Our findings suggest that the conserved nuclear actin/Arp module acts a conformational switch of the INO80 for nucleosome binding.

Highlights

The basic unit of chromatin organization is the nucleosome, which comprises 147 bp of DNA wrapped around a core of histone proteins (Kornberg, 1974; Luger et al, 1997)
The actin/actin-related proteins (Arps) module has been implicated in nucleosomebinding of INO80 complex (Shen et al, 2003; Tosi et al, 2013; Watanabe et al, 2015), we found that the actin/Arp module stably binds to chromatin independently of the ATPase subunit with a 1:1 stoichiometry
These observations consistently suggest that the actin/Arp initiates the nucleosome binding for the INO80 complex

Summary

Introduction

The basic unit of chromatin organization is the nucleosome, which comprises 147 bp of DNA wrapped around a core of histone proteins (Kornberg, 1974; Luger et al, 1997). ATP-dependent chromatin-remodeling complexes are characterized by the presence of an ATPase subunit belonging to the superfamily II helicase-related proteins (Singleton and Wigley, 2002; Flaus et al, 2006).

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