No need for a power stroke in ISWI‐mediated nucleosome sliding

Ludwigsen, Johanna; Klinker, Henrike; Mueller-Planitz, Felix

doi:10.1038/embor.2013.160

Cited by 19 publications

(15 citation statements)

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“…These include potential Mot1-mediated changes in TBP conformation and a proposed "spring-loaded" mechanism that exploits the severely bent DNA in the TBP-DNA complex (4, 20 -22). Moreover, recent work on related enzymes has shown that rigid coupling of the motor domain to the target complex is not required for catalytic activity (23,24). These observations challenge prior models for Mot1 action in which it functions by pulling or pushing TBP along DNA (4).…”

contrasting

confidence: 50%

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

Viswanathan

True

Auble

2016

Journal of Biological Chemistry

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The essential Saccharomyces cerevisiae ATPase Mot1 globally regulates transcription by impacting the genomic distribution and activity of the TATA-binding protein (TBP). In vitro, Mot1 forms a ternary complex with TBP and DNA and can use ATP hydrolysis to dissociate the TBP-DNA complex. Prior work suggested an interaction between the ATPase domain and a functionally important segment of DNA flanking the TATA sequence. However, how ATP hydrolysis facilitates removal of TBP from DNA is not well understood, and several models have been proposed. To gain insight into the Mot1 mechanism, we dissected the role of the flanking DNA segment by biochemical analysis of complexes formed using DNAs with short singlestranded gaps. In parallel, we used a DNA tethered cleavage approach to map regions of Mot1 in proximity to the DNA under different conditions. Our results define non-equivalent roles for bases within a broad segment of flanking DNA required for Mot1 action. Moreover, we present biochemical evidence for two distinct conformations of the Mot1 ATPase, the detection of which can be modulated by ATP analogs as well as DNA sequence flanking the TATA sequence. We also show using purified complexes that Mot1 dissociation of a stable, high affinity TBP-DNA interaction is surprisingly inefficient, suggesting how other transcription factors that bind to TBP may compete with Mot1. Taken together, these results suggest that TBP-DNA affinity as well as other aspects of promoter sequence influence Mot1 function in vivo.Snf2/Swi2 enzymes play critical roles in regulation of essentially all DNA metabolic processes by utilizing the energy of ATP hydrolysis to alter protein-DNA interactions (1-4). Mot1, 2 a Snf2/Swi2 protein, dissociates the TATA-binding protein (TBP) from promoters and thereby regulates TBP distribution in the cell (5-9). By exploiting the Mot1 experimental system, biochemical analyses of the TBP-DNA dissociation reaction have provided general insight into mechanisms by which Snf2/Swi2 ATPases catalyze rearrangements of stable protein-DNA complexes (4). The N terminus of Mot1 interacts with TBP through its flexible HEAT repeats and in this way recruits Mot1 to TBP-DNA (7, 10 -14). The C-terminal region of Mot1, which comprises the ATPase domain, interacts with DNA upstream of the TATA box (13,14). Given the sequence and structural similarity among Snf2/Swi2 ATPase domains (15, 16), a central goal in the field has been to decipher the mechanisms by which these enzymes couple ATP hydrolysis to dissociation or rearrangement of protein-DNA complexes.The Snf2/Swi2 ATPases comprise a group within the SF2 helicase superfamily (17). Thus, their mechanisms are proposed to be similar to those of helicases except that they do not catalyze DNA strand separation (15,18). Nonetheless, the Snf2/ Swi2 family has well over a thousand members, and the great majority of them have not been characterized biochemically (19). Biochemical studies of helicases have revealed diverse mechanistic properties (3), suggesting that Snf2/Swi2 enz...

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confidence: 50%

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

Viswanathan

True

Auble

2016

Journal of Biological Chemistry

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“…However, it remains unclear whether or how DNA binding by the HSS domain is coupled to the action of the ATPase domain (Clapier and Cairns, 2012; Hota et al, 2013; Ludwigsen et al, 2013; Mueller-Planitz et al, 2013). Our observations above suggested that the state of the ATPase active site may influence the HSS domain in cis to affect the remodeling reaction (Figure 1F, [wt]-[WB] vs. [ΔHSS/WB]-[wt]).…”

Section: Resultsmentioning

confidence: 99%

“…However, it is unclear how the HSS contributes to nucleosome movement, as well as whether and how it communicates with the ATPase domain (Clapier and Cairns, 2012; Ludwigsen et al, 2013; Mueller-Planitz et al, 2013; Nodelman and Bowman, 2013). Our work indicates that the nucleotide state of the active site controls binding of the HSS domain to different regions of the nucleosome (Figures 2, 3).…”

Section: Discussionmentioning

confidence: 99%

“…Recent studies demonstrated that ISWI and related Chd1 remodelers do not require rigid mechanical coupling between the flanking DNA binding domain and the ATPase domain in order to efficiently move nucleosomes (Ludwigsen et al, 2013; Nodelman and Bowman, 2013). Instead, the authors suggest that binding of the HSS to flanking DNA enhances enzymatic activity by productively anchoring the ATPase domain.…”

Section: Introductionmentioning

confidence: 99%

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A Nucleotide-Driven Switch Regulates Flanking DNA Length Sensing by a Dimeric Chromatin Remodeler

Leonard

Narlikar

2015

Molecular Cell

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SUMMARY The ATP-dependent chromatin assembly factor (ACF) is a dimeric motor that spaces nucleosomes to promote formation of silent chromatin. Two copies of its ATPase subunit SNF2h bind opposite sides of a nucleosome, but how these protomers avoid competition is unknown. SNF2h senses the length of DNA flanking a nucleosome via its HAND-SANT-SLIDE (HSS) domain, yet it is unclear how this interaction enhances remodeling. Using covalently connected SNF2h dimers we show that dimerization accelerates remodeling and that the HSS contributes to communication between protomers. We further identify a nucleotide-dependent conformational change in SNF2h. In one conformation the HSS binds flanking DNA, and in another conformation the HSS engages the nucleosome core. Based on these results, we propose a model in which DNA length sensing and translocation are performed by two distinct conformational states of SNF2h. Such separation of function suggests that these activities could be independently regulated to affect remodeling outcomes.

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“…We showed recently that a rigid connection between HSS and ATPase domains was not necessary for remodeling as would be expected for a power stroke-like energy coupling (43). Nonetheless, it was possible that the connecting length influenced the resulting spacing.…”

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confidence: 97%

Nucleosome Spacing Generated by ISWI and CHD1 Remodelers Is Constant Regardless of Nucleosome Density

Lieleg¹,

Ketterer

Nuebler

et al. 2015

Molecular and Cellular Biology

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Arrays of regularly spaced nucleosomes are a hallmark of chromatin, but it remains unclear how they are generated. Recent genome-wide studies, in vitro and in vivo, showed constant nucleosome spacing even if the histone concentration was experimentally reduced. This counters the long-held assumption that nucleosome density determines spacing and calls for factors keeping spacing constant regardless of nucleosome density. We call this a clamping activity. Here, we show in a purified system that ISWI-and CHD1-type nucleosome remodelers have a clamping activity such that they not only generate regularly spaced nucleosome arrays but also generate constant spacing regardless of nucleosome density. This points to a functionally attractive nucleosome interaction that could be mediated either directly by nucleosome-nucleosome contacts or indirectly through the remodelers. Mutant Drosophila melanogaster ISWI without the HAND-SANT-SLIDE (HSS) domain had no detectable spacing activity even though it is known to remodel and slide nucleosomes. This suggests that the role of ISWI remodelers in generating constant spacing is not just to mediate nucleosome sliding; they actively contribute to the attractive interaction. Additional factors are necessary to set physiological spacing in absolute terms.

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No need for a power stroke in ISWI‐mediated nucleosome sliding

Cited by 19 publications

References 31 publications

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

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

A Nucleotide-Driven Switch Regulates Flanking DNA Length Sensing by a Dimeric Chromatin Remodeler

Nucleosome Spacing Generated by ISWI and CHD1 Remodelers Is Constant Regardless of Nucleosome Density

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