The ATPase domain of ISWI is an autonomous nucleosome remodeling machine

Abstract

ISWI slides nucleosomes along DNA, enabling the structural changes of chromatin required for the regulated use of eukaryotic genomes. Prominent mechanistic models imply cooperation of the ISWI ATPase domain with a C-terminal DNA-binding function residing in the HAND-SANT-SLIDE (HSS) domain. Contrary to these models, we show by quantitative biochemical means that all fundamental aspects of nucleosome remodeling are contained within the compact ATPase module of Drosophila ISWI. This domain can independently associate with DNA and nucleosomes, which in turn activate ATP turnover by inducing a conformational change in the enzyme, and it can autonomously reposition nucleosomes. The role of the HSS domain is to increase the affinity and specificity for nucleosomes. Nucleosome-remodeling enzymes may thus have evolved directly from ancestral helicase-type motors, and peripheral domains have furnished regulatory capabilities that bias the remodeling reaction toward different structural outcomes.

Molecular Mechanism of Mot1, a TATA-binding Protein (TBP)-DNA Dissociating Enzyme

“…Our observation of the open form of Mot1 in 6Fe DNA complexes is consistent with the open form of the ATPase in the SsoRad54-DNA co-complex (28). In contrast, in solution, interconversion between conformational forms of Swi/Snf ATPases has been observed (31,58), and the closed form predominated when bound to DNA in solution (31), consistent with results using the Moyle6Fe template. We favor a model in which the Mot1 open and closed forms both exist in solution in the absence of ATP.…”

Regulation of ISWI chromatin remodelling activity

“…In this work the authors found that ISWI lacking its HSS domain can still remodel nucleosomes, with an intrinsic ability to bind nucleosomes and to interact with histone H4 N terminus, revealing a positive role for the HSS domain in increasing the affinity and specificity of ISWI ATPase for nucleosome ( Fig. 2) (Mueller-Planitz et al 2013). Similarly, another study showed a regulatory function for the SLIDE domain of Saccharomyces cerevisiae Isw2 subunit to help maintaining the directionality of DNA movement into nucleosomes (Hota et al 2013).…”

“…Over the past few years, in vivo and in vitro studies have led to a broadly accepted model in which the HSS domain plays an integral part during the remodelling reaction (Boyer et al 2004;Grune et al 2003a;Boyer et al 2002). Unexpectedly, a recent study conducted on Drosophila ISWI (d ISWI) showed that most of the fundamental regulatory aspects of nucleosome remodelling are contained around the compact ATPase module (Mueller-Planitz et al 2013). In this work the authors found that ISWI lacking its HSS domain can still remodel nucleosomes, with an intrinsic ability to bind nucleosomes and to interact with histone H4 N terminus, revealing a positive role for the HSS domain in increasing the affinity and specificity of ISWI ATPase for nucleosome ( Fig.…”

“…In particular, ATPase kinetic studies indicate that ISWI is present in two distinct conformations in absence of DNA. Indeed, the addition of DNA causes a dramatic ISWI protease hypersensitivity at level of residues adjacent to NegC and AutoN (Mueller-Planitz et al 2013). On the basis of the characterization of AutoN and NegC inhibitory function, the conformational change triggered by nucleosomal epitopes binding probably involves the removal of both of these ATPase brakes (Manning and Peterson 2013).…”

“…Recent works have shed light into the function of ISWI intrinsic domains. Interestingly, studies conducted in vitro, demonstrated that the conserved ATPase domain has autonomous nucleosome remodelling activity, while domains adjacent to the ATPase module have regulatory function (Mueller-Planitz et al 2013;Hota et al 2013;Clapier and Cairns 2012).…”