Direct observation of DNA rotation during branch migration of Holliday junction DNA by
            <i>Escherichia coli</i>
            RuvA–RuvB protein complex

Han, Yong-Woon; Tani, Tomomi; Hayashi, Masahito; Hishida, Takashi; Iwasaki, Hiroshi; Shinagawa, Hideo; Harada, Yoshie

doi:10.1073/pnas.0600753103

Cited by 29 publications

(30 citation statements)

References 25 publications

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“…Some hexameric dsDNA translocation motors such as RuvA/RuvB involved in DNA homologous recombination (Han et al,2006; Rafferty et al,1996) are sophisticated, and some other dsDNA riding motors such as those involved in DNA repair only display two protein subunits. The mechanisms of these motors are so complicated that they go beyond the scope of this review and will not be addressed here.…”

Section: Rotational Dsdna Translocases With Only One Ssdna Strand mentioning

confidence: 99%

Common mechanisms of DNA translocation motors in bacteria and viruses using one-way revolution mechanism without rotation

Guo

Zhao

Haak

et al. 2014

Biotechnology Advances

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Biomotors were once classified into two categories: linear motor and rotation motor. For decades, the viral DNA-packaging motor has been popularly believed to be a five-fold rotation motor. Recently, a third type of biomotor with revolution mechanism without rotation has been discovered. By analogy, rotation resembles the Earth rotating on its axis in a complete cycle every 24 hours, while revolution resembles the Earth revolving around the Sun one circle per 365 days (see animations http://nanobio.uky.edu/movie.html). The action of revolution that enables a motor free of coiling and torque has solved many puzzles and debates that have occurred throughout the history of viral DNA packaging motor studies. It also settles the discrepancies concerning the structure, stoichiometry, and functioning of DNA translocation motors. This review uses bacteriophages Phi29, HK97, SPP1, P22, T4, T7 as well as bacterial DNA translocase FtsK and SpoIIIE as examples to elucidate the puzzles. These motors use a ATPase, some of which have been confirmed to be a hexamer, to revolve around the dsDNA sequentially. ATP binding induces conformational change and possibly an entropy alteration in ATPase to a high affinity toward dsDNA; but ATP hydrolysis triggers another entropic and conformational change in ATPase to a low affinity for DNA, by which dsDNA is pushed toward an adjacent ATPase subunit. The rotation and revolution mechanisms can be distinguished by the size of channel: the channels of rotation motors are equal to or smaller than 2 nm, whereas channels of revolution motors are larger than 3 nm. Rotation motors use parallel threads to operate with a right-handed channel, while revolution motors use a left-handed channel to drive the right-handed DNA in an anti-parallel arrangement. Coordination of several vector factors in the same direction makes viral DNA-packaging motors unusually powerful and effective. Revolution mechanism avoids DNA coiling in translocating the lengthy genomic dsDNA helix could be advantage for cell replication such as bacterial binary fission and cell mitosis without the need for topoisomerase or helicase to consume additional energy.

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Section: Rotational Dsdna Translocases With Only One Ssdna Strand mentioning

confidence: 99%

Common mechanisms of DNA translocation motors in bacteria and viruses using one-way revolution mechanism without rotation

Guo

Zhao

Haak

et al. 2014

Biotechnology Advances

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“…Notably, Kinosita and coworkers[12] used this configuration to directly confirm that the DNA template rotates relative to RNA polymerase during transcription. Important new contributions of FOMT include dispensing with marker beads[12-14], incorporating simultaneous extension measurements, and introducing an alignment procedure that reduces the residual horizontal component of the field[13,14] to a negligible contribution. In a demonstration of a promising application area, FOMT was used to follow DNA stretching and untwisting during assembly of a RecA filament on dsDNA.…”

Section: Dissecting the Structural Dynamics Of Nucleoprotein Complexesmentioning

confidence: 99%

Recent developments in single-molecule DNA mechanics

Bryant

Oberstrass

Basu

2012

Current Opinion in Structural Biology

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Over the past two decades, measurements on individual stretched and twisted DNA molecules have helped define the basic elastic properties of the double helix and enabled real-time functional assays of DNA-associated molecular machines. Recently, new magnetic tweezers approaches for simultaneously measuring freely fluctuating twist and extension have begun to shed light on the structural dynamics of large nucleoprotein complexes. Related technical advances have facilitated direct measurements of DNA torque, contributing to a better understanding of abrupt structural transitions in mechanically stressed DNA. The new measurements have also been exploited in studies that hint at a developing synergistic relationship between single-molecule manipulation and structural DNA nanotechnology.

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“…A single step of branch migration requires the breakage of two base pairs at the point of strand exchange located on diametrically opposite arms, rotation around, and formation of the terminal base pairs on the remaining two arms. Rotation of DNA strands during branch migration promoted by RuvAB was observed in real time using single-molecule techniques [146]. In the absence of bivalent ions, when the Holliday junction exists in the open conformation, preferable for branch migration (Fig.…”

Section: Branch Migration Activity Of Rad54 Proteinmentioning

confidence: 99%

Rad54, the motor of homologous recombination

Mazin¹,

Mazina²,

Bugreev³

et al. 2010

DNA Repair

159

153

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Homologous recombination (HR) performs crucial functions including DNA repair, segregation of homologous chromosomes, propagation of genetic diversity, and maintenance of telomeres. HR is responsible for the repair of DNA double-strand breaks and DNA interstrand cross-links. The process of HR is initiated at the site of DNA breaks and gaps and involves a search for homologous sequences promoted by Rad51 and auxiliary proteins followed by the subsequent invasion of broken DNA ends into the homologous duplex DNA that then serves as a template for repair. The invasion produces a cross-stranded structure, known as the Holliday junction. Here, we describe the properties of Rad54, an important and versatile HR protein that is evolutionarily conserved in eukaryotes. Rad54 is a motor protein that translocates along dsDNA and performs several important functions in HR. The current review focuses on the recently identified Rad54 activities which contribute to the late phase of HR, especially the branch migration of Holliday junctions.

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Direct observation of DNA rotation during branch migration of Holliday junction DNA by Escherichia coli RuvA–RuvB protein complex

Cited by 29 publications

References 25 publications

Common mechanisms of DNA translocation motors in bacteria and viruses using one-way revolution mechanism without rotation

Common mechanisms of DNA translocation motors in bacteria and viruses using one-way revolution mechanism without rotation

Recent developments in single-molecule DNA mechanics

Rad54, the motor of homologous recombination

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