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

SNF2 family ATPases are ATP-dependent motors that often function in multisubunit complexes to regulate chromatin structure. Although the central role of SNF2 ATPases in chromatin biology is well established, mechanisms by which their catalytic activities are regulated by additional subunits of chromatin-remodeling complexes are less well understood. Here we present evidence that the human Inositol auxotrophy 80 (Ino80) SNF2 ATPase is subject to regulation at multiple levels in the INO80 chromatin-remodeling complex. The zinc finger histidine triad domain-containing protein Ies2 (Ino Eighty Subunit 2) functions as a potent activator of the intrinsic catalytic activity of the Ino80 ATPase, whereas the YL-1 family Ies6 (Ino Eighty Subunit 6) and actin-related Arp5 proteins function together to promote binding of the Ino80 ATPase to nucleosomes. These findings support the idea that both substrate recognition and the intrinsic catalytic activities of SNF2 ATPases have evolved as important sites for their regulation. Although it is well established that SNF2 family ATPases have evolved to play critical roles as ATPdependent motors that drive many types of chromatin transactions, in most cases how their intrinsic catalytic activities are regulated by their diverse array of associated proteins is poorly understood.The INO80 complex was first identified in Saccharomyces cerevisiae, where it was shown to be composed of roughly 15 subunits (1, 9). Subsequent purification of the human INO80 complex revealed that it shares with its S. cerevisiae counterpart a set of subunits including the Ino80 SNF2 ATPase, the AAA+ ATPases Tip49a and Tip49b, actin-related proteins Arp4, Arp5, and Arp8, and the Ies2 and Ies6 proteins (2, 10-12). The human INO80 complex lacks orthologs of the remaining subunits of the S. cerevisiae INO80 complex and contains instead several apparently metazoan-specific subunits including the deubiquitinating enzyme Uch37, the gene altered in glioma (GLI)-Kruppel family zinc finger transcription factor YY1, the forkhead-associated domain (FHA) containing Mcrs1, nuclear factor related to kB (Nfrkb), and the Amida, Ino80D (FLJ20309), and Ino80E (FLJ90652) proteins.The INO80 complex is capable of regulating chromatin structure in at least two ways. First, it catalyzes ATP-dependent sliding of histone octamers along DNA (1, 2). Second, it catalyzes the replacement of histone H2AZ/histone H2AB dimers in nucleosomes with histone H2A/histone H2B dimers in a reaction that in yeast has been shown to contribute to genome-wide histone H2AZ localization (13).In a recent study dissecting mechanism(s) by which the human INO80 complex catalyzes chromatin remodeling, we found that it is composed of at least three modules that assemble with three distinct domains of the Ino80 protein (14) (Fig. 1A). One module is composed of an Ino80 N-terminal domain and all of the metazoan-specific subunits except YY1. A second, the helicase-SANT-associated (HSA) module, is composed of the Ino80 HSA domain, the actin-related Arp4/Baf53a and ...

Section: Resultsmentioning

confidence: 99%

Multiple modes of regulation of the human Ino80 SNF2 ATPase by subunits of the INO80 chromatin-remodeling complex

Chen

Conaway

2013

“…Chd1, another distantly related SNF2-like family member, contains a Chd1-specific inhibitory chromodomain, which gated the interaction between ATPase motor and duplex DNA (3). In some members of the SNF2-like family of ATPase, N-terminal regions could also play positive regulatory roles, such as Ino80 (ATPase subunit in the INO80 chromatin-remodeling complex) and Sth1 (ATPase component of the RSC chromatin-remodeling complex) (6,7). The variety in the details of regulatory mechanisms by flanking regions may stem from the diverse functions and specificities of these different chromatin remodelers.…”

Section: An Emerging Theme Of Flanking Regions In Regulating Atp-depementioning

confidence: 99%

“…These SNF2-like ATPases are broadly conserved throughout evolution and share a common core ATPase domain. Whereas the core motor ATPase domain provides the driving force for DNA translocation and chromatin-remodeling activity, emerging evidence suggests important roles of the flanking regions in mediating specific interactions with nucleosomes or other protein factors, substrate specificity, and the regulation of the function of the motor (2)(3)(4)(5)(6)(7).…”

mentioning

confidence: 99%

Regulation of the Rhp26 ^ERCC6/CSB chromatin remodeler by a novel conserved leucine latch motif

Wang

Limbo

Jia

et al. 2014

CSB/ERCC6 (Cockayne syndrome B protein/excision repair crosscomplementation group 6), a member of a subfamily of SWI2/SNF2 (SWItch/sucrose nonfermentable)-related chromatin remodelers, plays crucial roles in gene expression and the maintenance of genome integrity. Here, we report the mechanism of the autoregulation of Rhp26, which is the homolog of CSB/ERCC6 in Schizosaccharomyces pombe. We identified a novel conserved protein motif, termed the "leucine latch," at the N terminus of Rhp26. The leucine latch motif mediates the autoinhibition of the ATPase and chromatin-remodeling activities of Rhp26 via its interaction with the core ATPase domain. Moreover, we found that the C terminus of the protein counteracts this autoinhibition and that both the N-and C-terminal regions of Rhp26 are needed for its proper function in DNA repair in vivo. The presence of the leucine latch motif in organisms ranging from yeast to humans suggests a conserved mechanism for the autoregulation of CSB/ERCC6 despite the otherwise highly divergent nature of the N-and C-terminal regions.chromatin remodeling | SWI2/SNF2 | SNF2-like family ATPase | enzyme autoregulation | flanking regions S WI2/SNF2 (switch/sucrose nonfermentable) and related ATPdependent chromatin-remodeling enzymes in the SNF2-like family of proteins play essential roles in many aspects of DNA metabolism, including replication, transcription, recombination, and repair (1). These SNF2-like ATPases are broadly conserved throughout evolution and share a common core ATPase domain. Whereas the core motor ATPase domain provides the driving force for DNA translocation and chromatin-remodeling activity, emerging evidence suggests important roles of the flanking regions in mediating specific interactions with nucleosomes or other protein factors, substrate specificity, and the regulation of the function of the motor (2-7).Cockayne syndrome group B protein (CSB/ERCC6) belongs to a subfamily of the SNF2-like family of ATPases (8) that plays a crucial role in transcription elongation and transcription-coupled repair (TCR), a specialized repair pathway that repairs DNA lesions in the transcribed genome (9-17). CSB is involved in the initiation steps of TCR in a manner that depends upon its chromatin remodeling and ATPase activities (18-21). Human CSB mutations are associated with Cockayne syndrome, a rare autosomal-recessive neurologic disorder characterized with progeriod features, growth failure, and photosensitivity (13,21,22).CSB/ERCC6 proteins are conserved from yeast to humans (Fig. 1A). Particularly, the core ATPase domain is highly conserved not only within the ERCC6 subfamily (Fig. 1A) but also among other SNF2-like family members. The core ATPase domain is composed of two RecA-like domains (lobe 1 and lobe 2) and shares the hallmark signature of seven SF2 helicase motifs (motif I, Ia, II, III, IV, V, and VI). In addition to two conserved lobes, the core domain contains two α-helical domain insertions (HD1 and HD2) that are present in other SNF2-like family proteins such as R...

“…Dimers or higherorder multimers of these actin/ARP proteins bind to a ∼60-residue helicase-SANT-associated (HSA) domain that is part of the ATPase subunit of remodelers and the Eaf1 subunit of NuA4 and, in remodelers, is adjacent to the N-terminal end of the ATPase domain (16). Indeed, prior biochemical experiments support roles for ARPs in regulating remodeler ATPase activity (12,13,16).…”

mentioning

confidence: 99%

“…Arp6, together with Arp5, which contains the largest Arp sequence insertion, and Arp8, which contains an additional N-terminal domain, are only observed as components of INO80. Arp8 is associated with the Ino80 HSA domain and copurifies with actin and Arp4 (16), whereas Arp5 incorporation requires the ATPase subunits Rvb1/Rvb2 (18).…”

mentioning

confidence: 99%

Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler

Schubert¹,

Wittmeyer

Kasten

et al. 2013

Self Cite

The packaging of DNA into nucleosomal structures limits access for templated processes such as transcription and DNA repair. The repositioning or ejection of nucleosomes is therefore critically important for regulated events, including gene expression. This activity is provided by chromatin remodeling complexes, or remodelers, which are typically large, multisubunit complexes that use an ATPase subunit to translocate the DNA. Many remodelers contain pairs or multimers of actin-related proteins (ARPs) that contact the helicase-SANT–associated (HSA) domain within the catalytic ATPase subunit and are thought to regulate ATPase activity. Here, we determined the structure of a four-protein subcomplex within the SWI/SNF remodeler that comprises the Snf2 HSA domain, Arp7, Arp9, and repressor of Ty1 transposition, gene 102 (Rtt102). Surprisingly, unlike characterized actin–actin associations, the two ARPs pack like spoons and straddle the HSA domain, which forms a 92-Å-long helix. The ARP–HSA interactions are reminiscent of contacts between actin and many binding partners and are quite different from those in the Arp2/3 complex. Rtt102 wraps around one side of the complex in a highly extended conformation that contacts both ARPs and therefore stabilizes the complex, yet functions to reduce by ∼2.4-fold the remodeling and ATPase activity of complexes containing the Snf2 ATPase domain. Thus, our structure provides a foundation for developing models of remodeler function, including mechanisms of coupling between ARPs and the ATPase translocation activity.