Escherichia coli PriA Protein, Two Modes of DNA Binding and Activation of ATP Hydrolysis

Tanaka, Taku; Mizukoshi, Toshimi; Sasaki, Kaori; Kohda, Daisuke; Masai, Hisao

doi:10.1074/jbc.m701848200

Cited by 44 publications

(64 citation statements)

References 36 publications

(66 reference statements)

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“…S2). Despite these differences, an EcPriA fragment comprising just the WH domain is able to bind partial duplex DNA in vitro, and a longer fragment that includes both the 3′BD and WH domains binds DNA replication fork structures with higher affinity than either domain alone, indicating that the two domains functionally cooperate (9). The most conserved surface of the WH domain presents a highly basic patch from the helix-turn-helix motif on the concave face of PriA that we speculate is important in replication fork DNA binding (below).…”

Section: Resultsmentioning

confidence: 99%

Structural mechanisms of PriA-mediated DNA replication restart

Bhattacharyya

George

Thurmes

et al. 2013

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

205

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Collisions between cellular DNA replication machinery (replisomes) and damaged DNA or immovable protein complexes can dissociate replisomes before the completion of replication. This potentially lethal problem is resolved by cellular "replication restart" reactions that recognize the structures of prematurely abandoned replication forks and mediate replisomal reloading. In bacteria, this essential activity is orchestrated by the PriA DNA helicase, which identifies replication forks via structure-specific DNA binding and interactions with fork-associated ssDNA-binding proteins (SSBs). However, the mechanisms by which PriA binds replication fork DNA and coordinates subsequent replication restart reactions have remained unclear due to the dearth of high-resolution structural information available for the protein. Here, we describe the crystal structures of full-length PriA and PriA bound to SSB. The structures reveal a modular arrangement for PriA in which several DNA-binding domains surround its helicase core in a manner that appears to be poised for binding to branched replication fork DNA structures while simultaneously allowing complex formation with SSB. PriA interaction with SSB is shown to modulate SSB/DNA complexes in a manner that exposes a potential replication initiation site. From these observations, a model emerges to explain how PriA links recognition of diverse replication forks to replication restart.X-ray crystal structure | single-molecule FRET

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Section: Resultsmentioning

confidence: 99%

Structural mechanisms of PriA-mediated DNA replication restart

Bhattacharyya

George

Thurmes

et al. 2013

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

205

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“…2, A and B) or 0.04 units of P1 nuclease (Fig. 2C) (38). Unexpectedly, specific protection was not detected on both template strands in DNase I footprinting on D-loop or bubble-related structures ( Fig.…”

Section: Binding Of Mrc1 Protein To D-loop or Bubble-like Structures-mentioning

confidence: 99%

“…Nuclease Footprinting-Reactions were performed as described previously (38). 0.002 units of DNase I (TAKARA) or 0.04 units of P1 nuclease (Roche Applied Science) was added in each reaction.…”

Section: Methodsmentioning

confidence: 99%

Fission Yeast Swi1-Swi3 Complex Facilitates DNA Binding of Mrc1

Tanaka

Yokoyama

Matsumoto

et al. 2010

Journal of Biological Chemistry

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Replication fork protection complex Swi1-Swi3 and replication checkpoint mediator Mrc1 are required for maintenance of replication fork integrity during the course of DNA replication in the fission yeast Schizosaccharomyces pombe. These proteins play crucial roles in stabilizing stalled forks and activating replication checkpoint signaling pathways. Although they are conserved replication fork components, precise biochemical roles of these proteins are not known. Here we purified Mrc1 and Swi1-Swi3 proteins and show that these proteins bind to DNA independently but synergistically in vitro. Mrc1 binds preferentially to arrested fork or D-loop-like structures, although the affinity is relatively low, whereas the Swi1-Swi3 complex binds to double-stranded DNA with higher affinity. In the presence of a low concentration of Swi1-Swi3, Mrc1 generates a novel ternary complex and binds to various types of DNA with higher affinity. Moreover, purified Mrc1 and Swi1-Swi3 physically interact with each other, and this interaction is lost by mutations in the known DNA binding domain of Mrc1 (K235E,K236E). The interaction is also lost in a mutant form of Swi1 (E662K) that is specifically defective in polar fork arrest at a site called RTS1 and causes sensitivity to genotoxic agents, although the DNA binding affinity of Swi1-Swi3 is not affected by this mutation. As expected, the synergistic effect of the Swi1-Swi3 on DNA binding of Mrc1 is also lost by these mutations affecting the interaction between Mrc1 and Swi1-Swi3. Our results reveal an aspect of molecular interactions that may play an important role in replication pausing and fork stabilization.

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“…A stem-loop formed on a single strand can indeed be viewed as a branched structure between a double strand and two singlestrand components (a Y fork). PriA was recently shown to bind Y forks (146). This is an illustration of hairpins that have evolved to be recognized by a host protein to direct primosome assembly (Fig.…”

Section: Dna Hairpin Biological Functions Hairpins and Replication Ormentioning

confidence: 99%

Folded DNA in Action: Hairpin Formation and Biological Functions in Prokaryotes

Bikard

Loot

Baharoglu

et al. 2010

Microbiol Mol Biol Rev

165

151

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SUMMARY Structured forms of DNA with intrastrand pairing are generated in several cellular processes and are involved in biological functions. These structures may arise on single-stranded DNA (ssDNA) produced during replication, bacterial conjugation, natural transformation, or viral infections. Furthermore, negatively supercoiled DNA can extrude inverted repeats as hairpins in structures called cruciforms. Whether they are on ssDNA or as cruciforms, hairpins can modify the access of proteins to DNA, and in some cases, they can be directly recognized by proteins. Folded DNAs have been found to play an important role in replication, transcription regulation, and recognition of the origins of transfer in conjugative elements. More recently, they were shown to be used as recombination sites. Many of these functions are found on mobile genetic elements likely to be single stranded, including viruses, plasmids, transposons, and integrons, thus giving some clues as to the manner in which they might have evolved. We review here, with special focus on prokaryotes, the functions in which DNA secondary structures play a role and the cellular processes giving rise to them. Finally, we attempt to shed light on the selective pressures leading to the acquisition of functions for DNA secondary structures.

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Escherichia coli PriA Protein, Two Modes of DNA Binding and Activation of ATP Hydrolysis

Cited by 44 publications

References 36 publications

Structural mechanisms of PriA-mediated DNA replication restart

Structural mechanisms of PriA-mediated DNA replication restart

Fission Yeast Swi1-Swi3 Complex Facilitates DNA Binding of Mrc1

Folded DNA in Action: Hairpin Formation and Biological Functions in Prokaryotes

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