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

Gerhold, Christian-Benedikt; Winkler, Duane D.; Lakomek, K.; Seifert, Florian Ulrich; Fenn, Sebastian; Keßler, Brigitte; Witte, Gregor; Luger, Karolin; Hopfner, Karl‐Peter

doi:10.1093/nar/gks842

Cited by 52 publications

(68 citation statements)

References 56 publications

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“…S1). Similar levels of structural overlap (2.2-3.9 Å) are seen for Arp7 and Arp9 with Arp2, Arp3, Arp4, and Arp8 (19,24,25). Arp7 and Arp9 therefore adopt the canonical actin fold comprising four globular subdomains surrounding a central cleft that, in actin and Arp4, contain the ATPase active site (30).…”

Section: Resultsmentioning

confidence: 65%

“…It is presently unknown whether Arp8 uses its hydrophobic cleft to interact with the HSA specifically or with other subunits in the complex. Large insertions in Arp8 may also be responsible for alternative quaternary interactions (25).…”

Section: Resultsmentioning

confidence: 99%

“…Similar to actin, both Arp2 and Arp3 bind nucleotides, although structural data suggest that nucleotide binding alone is not sufficient to generate the conformational changes required for full activation of the complex (20,23). In addition to Arp2/3, the monomeric structures of Arp4 and Arp8 bound to ATP were recently determined and reveal how the actin structural fold accommodates large sequence insertions that likely preclude any potential actin-like "pointed end" interactions (24,25). In contrast, the ATPase "active site" residues within Arp7 and Arp9 are not conserved with actin, and their mutation does not result in observable phenotypes, suggesting they do not bind or hydrolyze ATP (11).…”

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confidence: 99%

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

Schubert¹,

Wittmeyer

Kasten

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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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.

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Section: Resultsmentioning

confidence: 65%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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

Schubert¹,

Wittmeyer

Kasten

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…Actin-related proteins, including the HSA module subunits Arp4 and Arp8, have been reported to be capable of binding directly to histones (9,(29)(30)(31). In addition, Ies6 includes a conserved domain shared with the SRCAP complex subunit YL1 and its yeast counterpart Swc2; the Swc2 YL1 domain has been shown to bind the histone variant H2AZ (17).…”

Section: Insertion Region Of the Ino80 Snf2-like Atpase Domain Directsmentioning

confidence: 99%

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

Chen

Conaway

2013

Proc. Natl. Acad. Sci. U.S.A.

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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 ...

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“…This Arp4/ Arp8/actin module is important for nucleosome recognition, which stimulates ATP hydrolysis and nucleosome sliding in vitro (21,(23)(24)(25)(26)(27). In addition, the Arp5 and INO80 subunit 6 (Ies6) subunits comprise a separate module that is particularly interesting because of its structural placement at the "enzymatic center" of the complex, between the ATPase domain of Ino80 and the large Rvb1-Rvb2 helicase module (21).…”

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confidence: 99%

The INO80 Complex Requires the Arp5-Ies6 Subcomplex for Chromatin Remodeling and Metabolic Regulation

Yao

King

Beckwith

et al. 2016

Molecular and Cellular Biology

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d ATP-dependent chromatin remodeling complexes are essential for transcription regulation, and yet it is unclear how these multisubunit complexes coordinate their activities to facilitate diverse transcriptional responses. In this study, we found that the conserved Arp5 and Ies6 subunits of the Saccharomyces cerevisiae INO80 chromatin-remodeler form an abundant and distinct subcomplex in vivo and stimulate INO80-mediated activity in vitro. Moreover, our genomic studies reveal that the relative occupancy of Arp5-Ies6 correlates with nucleosome positioning at transcriptional start sites and expression levels of >1,000 INO80-regulated genes. Notably, these genes are significantly enriched in energy metabolism pathways. Specifically, arp5⌬, ies6⌬, and ino80⌬ mutants demonstrate decreased expression of genes involved in glycolysis and increased expression of genes in the oxidative phosphorylation pathway. Deregulation of these metabolic pathways results in constitutively elevated mitochondrial potential and oxygen consumption. Our results illustrate the dynamic nature of the INO80 complex assembly and demonstrate for the first time that a chromatin remodeler regulates glycolytic and respiratory capacity, thereby maintaining metabolic stability. E ukaryotic genomic DNA is assembled with histones to form chromatin, a complex structure that undergoes constant dynamic reorganization in coordination with DNA-templated processes. Chromatin remodeling, an ATP-dependent mechanism by which nucleosomes are repositioned and reconstructed, is a fundamental component of chromatin manipulation and influences numerous DNA-templated pathways. Because chromatin remodelers are involved in essential cellular processes, defects in remodeling activity directly result in fitness deficiencies in lower eukaryotes, as well as developmental defects and disease in higher eukaryotes (1, 2).In particular, disruption of INO80, an evolutionarily conserved chromatin remodeling complex, results in pluripotency defects and carcinogenesis (3-6). The INO80 complex has demonstrated roles in transcription (7-9), replication (10-12), DNA damage responses (13-16), telomere regulation (17), and mitotic stability (18,19). These studies exemplify the functional diversity of the INO80 complex in different pathways (20). Moreover, they highlight the need for regulatory mechanisms that direct its activity among, and within, these processes.Ample opportunities for regulation of chromatin remodeling exist at the level of individual remodeler complex subunits. For example, different subunits of the INO80 complex are involved in DNA repair and cell cycle checkpoint responses (13, 16). Structural studies demonstrate that these subunits are components of different modules that interact with distinct domains of the S. cerevisiae Ino80 ATPase subunit (21) and thus may impart regulatory functions on ATP-dependent activities of the INO80 complex.For example, a module consisting of actin and actin-related proteins (Arps) Arp8 and Arp4 interacts with the helicase-associated...

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

Cited by 52 publications

References 56 publications

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

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

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

The INO80 Complex Requires the Arp5-Ies6 Subcomplex for Chromatin Remodeling and Metabolic Regulation

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