Preferential relaxation of positively supercoiled DNA by <i>E. coli</i> topoisomerase IV in single-molecule and ensemble measurements

Crisona, Nancy J.; Strick, Térence; Bensimon, David; Croquette, Vincent; Cozzarelli, Nicholas R.

doi:10.1101/gad.838900

Cited by 185 publications

(215 citation statements)

References 49 publications

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“…However, in sharp contrast to the eukaryotic type IIA Topos, which act indistinguishably on the supercoils of both signs, recent studies show that Topo IV relaxes (ϩ) supercoils much faster than (Ϫ) supercoils (17)(18)(19). Although this distinctive substrate specificity provides an explanation of why Topo IV can promote replication elongation without counteracting the activity of DNA gyrase, it raises the question of how Topo IV preferentially recognizes (ϩ) supercoiled DNA as preferred substrate.…”

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confidence: 77%

“…Roles of CTD in Topo IV Catalysis-Unlike eukaryotic type IIA Topos, which exhibit similar activities on (ϩ) and (Ϫ) supercoiled DNA substrates, it is well documented that Topo IV can distinguish the spatial arrangement of the T-and G-segments imposed by the superhelix and preferentially resolves left-handed cross-overs of (ϩ) supercoiled DNA (17)(18)(19). Furthermore, the activity of Topo IV is sensitive to the superhelical density ( ) (as defined by Bates and Maxwell (54)).…”

Section: Resultsmentioning

confidence: 99%

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Structure of the Topoisomerase IV C-terminal Domain

Hsieh

Farh

Huang

et al. 2004

Journal of Biological Chemistry

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Bacteria possess two closely related yet functionally distinct essential type IIA topoisomerases (Topos). DNA gyrase supports replication and transcription with its unique supercoiling activity, whereas Topo IV preferentially relaxes (؉) supercoils and is a decatenating enzyme required for chromosome segregation. Here we report the crystal structure of the C-terminal domain of Topo IV ParC subunit (ParC-CTD) from Bacillus stearothermophilus and provide a structure-based explanation for how Topo IV and DNA gyrase execute distinct activities. Although the topological connectivity of ParC-CTD is similar to the recently determined CTD structure of DNA gyrase GyrA subunit (GyrA-CTD), ParC-CTD surprisingly folds as a previously unseen broken form of a six-bladed ␤-propeller. Propeller breakage is due to the absence of a DNA gyrase-specific GyrA box motif, resulting in the reduction of curvature of the proposed DNA binding region, which explains why ParC-CTD is less efficient than GyrA-CTD in mediating DNA bending, a difference that leads to divergent activities of the two homologous enzymes. Moreover, we found that the topology of the propeller blades observed in ParC-CTD and GyrA-CTD can be achieved from a concerted ␤-hairpin invasion-induced fold change event of a canonical six-bladed ␤-propeller; hence, we proposed to name this new fold as "hairpininvaded ␤-propeller" to highlight the high degree of similarity and a potential evolutionary linkage between them. The possible role of ParC-CTD as a geometry facilitator during various catalytic events and the evolutionary relationships between prokaryotic type IIA Topos have also been discussed according to these new structural insights.

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mentioning

confidence: 77%

Section: Resultsmentioning

confidence: 99%

Structure of the Topoisomerase IV C-terminal Domain

Hsieh

Farh

Huang

et al. 2004

Journal of Biological Chemistry

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“…Other studies have utilized linear nucleic acid substrates, especially for mapping sites of drug-induced DNA scission. Recent reports have begun to describe interactions between type II topoisomerases and positively supercoiled substrates [61,62,64,65,187,188]. Several unexpected findings have emerged from these experiments.…”

Section: Effects Of Dna Supercoiling On Topoisomerase Ii-mediated Dnamentioning

confidence: 99%

DNA topoisomerase II, genotoxicity, and cancer

McClendon

Osheroff

2007

Mutation Research/Fundamental and Molecular Mechanisms of Mutag

365

466

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Type II topoisomerases are ubiquitous enzymes that play essential roles in a number of fundamental DNA processes. They regulate DNA under-and overwinding, and resolve knots and tangles in the genetic material by passing an intact double helix through a transient double-stranded break that they generate in a separate segment of DNA. Because type II topoisomerases generate DNA strand breaks as a requisite intermediate in their catalytic cycle, they have the potential to fragment the genome every time they function. Thus, while these enzymes are essential to the survival of proliferating cells, they also have significant genotoxic effects. This latter aspect of type II topoisomerase has been exploited for the development of several classes of anticancer drugs that are widely employed for the clinical treatment of human malignancies. However, considerable evidence indicates that these enzymes also trigger specific leukemic chromosomal translocations. In light of the impact, both positive and negative, of type II topoisomerases on human cells, it is important to understand how these enzymes function and how their actions can destablize the genome. This article discusses both aspects of human type II topoisomerases.

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“…Both human Topo IIα and E coli Topo IV preferentially relax positive supercoils (Charvin et al 2003;Crisona et al 2000;McClendon et al 2005McClendon et al , 2008Neuman et al 2009;Seol et al 2013a;Stone et al 2003). The underlying mechanism for this chiral discrimination is embedded in differential interactions between positive and negative writhe and the C-terminal domains of the topoisomerases (Corbett et al 2005;McClendon et al 2008;Neuman et al 2009;Seol et al 2013a).…”

Section: Dna Twist (Torsion)-dependent Protein Activitymentioning

confidence: 99%

The dynamic interplay between DNA topoisomerases and DNA topology

Seol

Neuman

2016

Biophys Rev

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Topological properties of DNA influence its structure and biochemical interactions. Within the cell, DNA topology is constantly in flux. Transcription and other essential processes, including DNA replication and repair, not only alter the topology of the genome but also introduce additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that has established the fundamental mechanistic basis of topoisomerase activity, scientists have begun to explore the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases. In this review we survey established and emerging DNA topology-dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.

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Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements

Cited by 185 publications

References 49 publications

Structure of the Topoisomerase IV C-terminal Domain

Structure of the Topoisomerase IV C-terminal Domain

DNA topoisomerase II, genotoxicity, and cancer

The dynamic interplay between DNA topoisomerases and DNA topology

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