Modularity and Specialization in Superfamily 1 and 2 Helicases

Singleton, Martin R.; Wigley, Dale B.

doi:10.1128/jb.184.7.1819-1826.2002

Cited by 198 publications

(178 citation statements)

References 72 publications

Supporting

Mentioning

172

Contrasting

Unclassified

Order By: Relevance

“…Notably, remodeler ATPases lack the 'pin' motif required for DNA strand separation and are therefore DNA translocases but not helicases 5,39 . One consistent feature of SF2 translocases is their tracking along the phosphate backbone of one of the two DNA strands, with limited interaction with the bases themselves 39,40 . Consistent with the notion of tracking, the results of triplex-displacement assays suggest that SWI/SNF, ISWI and Rad54 track in a 3′-to-5′ direction along one strand of the DNA duplex and are impeded if the tracking strand bears a gap in the phosphodiester backbone 4,36,38,41 .…”

Section: Remodelers Can Translocate Dna From a Fixed Internal Sitementioning

confidence: 99%

“…Crystal structures, biochemical studies and single-molecule analyses of both SF1-and SF2-family translocases (PcrA, RecG, UvrD, NS3 and others) have provided many important insights into these issues 39,40,[57][58][59] . Currently, there is no crystal structure of the ATPase domain of a nucleosome-binding remodeler (SWI/SNF or ISWI), but recent structures of the SWI/SNF-family member Rad54 (with DNA) show remarkable structural homology to the SF2 family of RNA and DNA translocases (see Fig.…”

Section: Remodeler Atpases Resemble 'Dna Inchworms'mentioning

confidence: 99%

“…Although there is some diversity in their mechanisms, most monomeric SF1 and SF2 translocases conform to a 'DNA-inchworm' model of movement, which involves the coordinated movement of two domains: a DBD and a DNA-tracking domain 39,40 . The DNAtracking domain has two RecA-like motifs, and between them is a pocket for nucleotide binding as well as a platform for DNA interaction.…”

Section: Remodeler Atpases Resemble 'Dna Inchworms'mentioning

confidence: 99%

See 2 more Smart Citations

Chromatin remodeling: insights and intrigue from single-molecule studies

Cairns

2007

Nat Struct Mol Biol

227

208

View full text Add to dashboard Cite

Chromatin remodelers are ATP-hydrolyzing machines specialized to restructure, mobilize or eject nucleosomes, allowing regulated exposure of DNA in chromatin. Recently, remodelers have been analyzed using single-molecule techniques in real time, revealing them to be complex DNA-pumping machines. The results both support and challenge aspects of current models of remodeling, supporting the idea that the remodeler translocates or pumps DNA loops into and around the nucleosome, while also challenging earlier concepts about loop formation, the character of the loop and how it propagates. Several complex behaviors were observed, such as reverse translocation and long translocation bursts of the remodeler, without appreciable DNA twist. This review presents and discusses revised models for nucleosome sliding and ejection that integrate this new information with the earlier biochemical studies.Many processes involving chromosomes are guided by DNA-binding proteins, and the access of these proteins to DNA is regulated by chromatin. Nucleosomes, the primary repeating unit of chromatin, package DNA by wrapping 147 base pairs (bp) around an octamer of histone proteins in ∼1.7 helical turns 1-3 . This packaging provides topological order but occludes one face of the DNA, which slows or prevents the recognition of DNA sequences by DNA-binding proteins. To maintain topological order, and also to allow rapid and regulated access to the DNA, cells have evolved a set of chromatin-remodeling machines that alter nucleosome position, presence and structure.Remodelers can be separated into several families on the basis of their composition and activities: SWI/SNF, ISWI, NURD/Mi-2/CHD and the 'split ATPases' INO80 and SWR1 (which bear an insertion within their ATPase domains). Rad54 may represent an additional family, as it perturbs chromatin in vitro, but it apparently lacks specific nucleosome-interacting domains 4,5 . The participation of remodelers in various chromosomal processes has been the subject of many reviews 6-9 . The present work focuses solely on remodeler mechanisms, and primarily on the function of their conserved catalytic subunit, a superfamily 2 (SF2) ATPdependent DNA translocase. Recently, single-molecule approaches have been used to examine several remodelers, providing many new insights into their behavior. Here I discuss these recent studies, compare them with previous biochemical studies and suggest refinements to existing models to account for some of the observations. Remodelers slide, eject and restructure nucleosomesRemodelers can affect nucleosomes in at least four ways ( Fig. 1): (i) sliding, or moving the histone octamer to a new position, which exposes DNA 10-12 ; (ii) ejection, or completely displacing the octamer to expose DNA [13][14][15][16] ; (iii) removal of H2A-H2B dimers, leaving only the central H3-H4 tetramer, which exposes DNA and destabilizes the nucleosome 17,18 ; and (iv) dimer replacement-for example, exchanging the resident H2A-H2B dimers for dimers NIH Public Access

show abstract

Section: Remodelers Can Translocate Dna From a Fixed Internal Sitementioning

confidence: 99%

Section: Remodeler Atpases Resemble 'Dna Inchworms'mentioning

confidence: 99%

Section: Remodeler Atpases Resemble 'Dna Inchworms'mentioning

confidence: 99%

See 1 more Smart Citation

Chromatin remodeling: insights and intrigue from single-molecule studies

Cairns

2007

Nat Struct Mol Biol

227

208

View full text Add to dashboard Cite

show abstract

“…In the last 5 years, the helicase superfamilies I and II (SF1 and SF2, based on sequence comparison) have been discovered; this work led to a revision of the view that helicase function requires a multimeric protein. For a review of the SF1 and SF2 helicases see [3]. This paper was inspired by experiments on the SF1 and SF2 helicases.…”

Section: Introductionmentioning

confidence: 99%

A Motor that Makes Its Own Track: Helicase Unwinding of DNA

Betterton

Jülicher

2003

Phys. Rev. Lett.

View full text Add to dashboard Cite

Helicase opening of double-stranded nucleic acids may be "active" (the helicase directly destabilizes the dsNA to promote opening) or "passive" (the helicase binds ssNA available due to a thermal fluctuation which opens part of the dsNA). We describe helicase opening of dsNA, based on helicases which bind single NA strands and move towards the double-stranded region, using a discrete "hopping" model. The interaction between the helicase and the junction where the double strand opens is characterized by an interaction potential. The form of the potential determines whether the opening is active or passive. We calculate the rate of passive opening for the helicase PcrA, and show that the rate increases when the opening is active. Finally, we examine how to choose the interaction potential to optimize the rate of strand separation. One important result is our finding that active opening can increase the unwinding rate by 7 fold compared to passive opening.

show abstract

“…This group of proteins shares structural and sequence similarity with SF2 DNA helicases, but they are unable to catalyze strand separation typical for DNA helicases (5). Instead, these proteins likely translocate on dsDNA inducing topological changes.…”

mentioning

confidence: 99%

Terminal association of Rad54 protein with the Rad51–dsDNA filament

Kiianitsa

Solinger

Heyer

2006

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

View full text Add to dashboard Cite

Rad54 protein is a Snf2-related dsDNA-specific ATPase essential for homologous recombination mediated by Rad51 protein, the eukaryotic RecA ortholog. Snf2-related enzymes couple ATP hydrolysis with translocation on dsDNA to remodel or dissociate a wide variety of protein-dsDNA complexes. Rad54 and Rad51 interact through species-specific contacts and mutually stimulate their biochemical activities. Specifically, Rad51 bound to dsDNA, the product of homologous recombination after DNA-strand exchange, stimulates the Rad54 ATPase up to 6-fold, leading to the turnover of Rad51 in the product complex. Electron microscopy visualized the Rad51-Rad54 interaction on dsDNA, showing that an oligomeric form of Rad54 associates preferentially with termini of the Rad51-dsDNA filament. Our data support a mechanism of processive dsDNA-Rad51 filament dissociation by the translocating Rad54 protein.recombination ͉ ATPase ͉ Snf2-like proteins H omologous recombination (HR) is a high-fidelity, templatedependent pathway involved in the nonmutagenic tolerance of DNA damage, the repair of complex DNA damage, and the recovery of stalled and collapsed replication forks (1, 2). The Rad52 group proteins define the HR pathway. Initially, RPA, the eukaryotic ssDNA-binding protein, binds to ssDNA exposed by doublestrand break processing or discoordination of leading and lagging strands at stalled replication forks. Mediator proteins (Rad52, Brca2, and Rad51 paralogs) orchestrate the assembly of Rad51 protein on ssDNA to form the nucleoprotein filament, which performs homology search and DNA-strand invasion to prime repair synthesis by using the undamaged sister chromatid or homolog as a template. After resolution of the pairing intermediates, HR has restored the contiguity of the chromosomes with a crossover or noncrossover outcome.Eukaryotes contain a large number of Snf2-related proteins (3, 4). This group of proteins shares structural and sequence similarity with SF2 DNA helicases, but they are unable to catalyze strand separation typical for DNA helicases (5). Instead, these proteins likely translocate on dsDNA inducing topological changes. Using the energy of ATP hydrolysis, their action leads to the remodeling or dissociation of protein-dsDNA complexes (4, 6). Prominent members of this group are the chromatin-remodeling factors Snf2, Isw1, Isw2, or Chd1. Each eukaryotic genome codes for a variety of Snf2-related proteins. Saccharomyces cerevisiae alone has 17 paralogs, and a number of these proteins appear to function outside a nucleosome remodeling context; for example, the Mot1 protein was found to dissociate the TATA box-binding protein from dsDNA (7). DNA repair pathways are richly endowed with specific, largely nonredundant Snf2-related proteins that function in transcriptioncoupled repair (Cockayne's Syndrome B͞Rad26 in S. cerevisiae; ref. Rad54 is a critical member of the Rad52 group, and its absence leads to catastrophic sensitivity to double-strand breaks in yeast (2,11,12). This protein displays robust dsDNA-specific ATPase ac...

show abstract

Modularity and Specialization in Superfamily 1 and 2 Helicases

Cited by 198 publications

References 72 publications

Chromatin remodeling: insights and intrigue from single-molecule studies

Chromatin remodeling: insights and intrigue from single-molecule studies

A Motor that Makes Its Own Track: Helicase Unwinding of DNA

Terminal association of Rad54 protein with the Rad51–dsDNA filament

Contact Info

Product

Resources

About