Structural mechanisms of PriA-mediated DNA replication restart

Bhattacharyya, Basudeb; George, Nicholas P.; Thurmes, Tiffany; Zhou, Ruobo; Jani, Niketa; Wessel, Sarah R.; Sandler, Steven J.; Ha, Taekjip; Keck, James L.

doi:10.1073/pnas.1318001111

Cited by 99 publications

(212 citation statements)

References 47 publications

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“…This feature appears to arise from the juxtaposition of motif II and the ARL within RecQ enzymes. A similar motif II-ARL arrangement is present in the SF2 PriA DNA helicase (39), indicating that the DNA-dependent changes observed in RecQ could apply to other DNA helicase families as well.…”

Section: Discussionmentioning

confidence: 74%

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Manthei

Hill

Burke

et al. 2015

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

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RecQ helicases unwind remarkably diverse DNA structures as key components of many cellular processes. How RecQ enzymes accommodate different substrates in a unified mechanism that couples ATP hydrolysis to DNA unwinding is unknown. Here, the X-ray crystal structure of the Cronobacter sakazakii RecQ catalytic core domain bound to duplex DNA with a 3′ single-stranded extension identifies two DNA-dependent conformational rearrangements: a winged-helix domain pivots ∼90°to close onto duplex DNA, and a conserved aromatic-rich loop is remodeled to bind ssDNA. These changes coincide with a restructuring of the RecQ ATPase active site that positions catalytic residues for ATP hydrolysis. Complex formation also induces a tight bend in the DNA and melts a portion of the duplex. This bending, coupled with translocation, could provide RecQ with a mechanism for unwinding duplex and other DNA structures.helicase | RecQ | mechanism | aromatic-rich loop | DNA bending H elicases are motor proteins that convert the chemical energy of nucleoside triphosphate (NTP) hydrolysis into the mechanical energy needed to separate nucleic acid strands (1). The largest and most diverse helicase superfamilies, SF1 and SF2, use conserved sequence motifs (I, Ia, II-VI) within their helicase domains to couple NTP hydrolysis to conformational changes that mediate DNA translocation and unwinding (1, 2). Although the DNA-unwinding mechanisms of SF1 helicases have been examined extensively, far less is known about SF2 enzymes, in part because of the smaller number of available helicase/substrate complex structures.RecQ DNA helicases are SF2 enzymes with broad roles in promoting genomic stability in eubacterial and eukaryotic species (3). Their importance is underscored by the multiple genomic instability diseases caused by mutations in human recQ genes (4-8). At a structural level, most RecQ helicases share a similar domain architecture that includes a helicase domain, a RecQ C-terminal (RQC) element comprised of Zn 2+ -binding and winged-helix (WH) domains, and a helicase and RNaseD C-terminal (HDRC) domain (Fig. 1A) (9, 10). The helicase and RQC domains combine to form a catalytic core that is sufficient for DNA-unwinding activity in many RecQ proteins. Crystal structures of several RecQ catalytic cores have been determined, including Escherichia coli RecQ (EcRecQ), human RecQ1, and human Bloom syndrome protein (BLM) [refs. 10-12 and unpublished structures (4CDG, 2WWY, and 4CGZ) available through the Protein Data Bank (PDB)]. A comparison of these structures reveals strong similarities among domains within the catalytic core but also differences in the relative positioning of these domains among RecQ proteins. The EcRecQ and antibody-bound BLM structures form an open arrangement in which the WH domain is centered relative to the helicase and Zn 2+ -binding domains, but in RecQ1 and DNA-bound BLM a closed arrangement is observed with the WH domain positioned laterally to the helicase domain (Fig. 1B and Fig. S1) (10-12). The functional relevance of...

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Section: Discussionmentioning

confidence: 74%

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Manthei

Hill

Burke

et al. 2015

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

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“…Although our analysis does not allow evaluation of these transitions directly, we observe that the stimulation of HsPol ␥ activity corresponds with a transition from the collapsed to a less dense species. Interestingly, recent studies on replication restart in bacteria have shown that the 65-nt binding mode can be reverted actively to the 35-nt binding mode by interaction with the protein machinery required for reinitiating prematurely terminated replication (42). Despite its similar DNA binding affinity and mode of DNA binding, HsmtSSB stimulates Pol ␥ activity and facilitates template DNA opening at concentrations exceeding that required for template saturation, whereas for DmSSB and EcSSB, template saturation corresponds roughly to the maximal stimulation phase and the transition from partially to fully open template molecules.…”

Section: Discussionmentioning

confidence: 99%

Mitochondrial Single-stranded DNA-binding Proteins Stimulate the Activity of DNA Polymerase γ by Organization of the Template DNA

Ciesielski

Bermek

Rosado-Ruiz

et al. 2015

Journal of Biological Chemistry

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Background: mtSSB stimulates the activity of Pol ␥. Results: Stimulation of Pol ␥ activity by SSB correlates with the organization of ssDNA templates in a species-independent manner. Conclusion: Organization of the template DNA by mtSSB is the major factor contributing to the stimulation of Pol ␥ activity. Significance: This study provides insight into the functional relationship of Pol ␥ and mtSSB and a general mechanism for it.

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“…SSB 35 is associated with DNA replication, and SSB 65 is associated with DNA repair. Single-molecule experiments have shown that both PriA and PriC promote shifting of the SSB binding mode from SSB 65 to SSB 35 (44,53). It was proposed that PriA and PriC might thus release a small region of ssDNA where DnaC can load DnaB.…”

Section: Biochemistry Of Pria and Its Partnersmentioning

confidence: 99%

“…A full-length structure of PriA from K. pneumoniae with 88% identity with E. coli PriA and the ability to complement PriA mutants of E. coli revealed a structure with six tightly clustered domains (53). The first domain has been crystallized before from the E. coli protein and shown to be able to bind the 3=-OH group of ssDNA (41).…”

Section: Biochemistry Of Pria and Its Partnersmentioning

confidence: 99%

Replication Restart in Bacteria

Michel

Sandler²

2017

J Bacteriol

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In bacteria, replication forks assembled at a replication origin travel to the terminus, often a few megabases away. They may encounter obstacles that trigger replisome disassembly, rendering replication restart from abandoned forks crucial for cell viability. During the past 25 years, the genes that encode replication restart proteins have been identified and genetically characterized. In parallel, the enzymes were purified and analyzed in vitro, where they can catalyze replication initiation in a sequence-independent manner from fork-like DNA structures. This work also revealed a close link between replication and homologous recombination, as replication restart from recombination intermediates is an essential step of DNA double-strand break repair in bacteria and, conversely, arrested replication forks can be acted upon by recombination proteins and converted into various recombination substrates. In this review, we summarize this intense period of research that led to the characterization of the ubiquitous replication restart protein PriA and its partners, to the definition of several replication restart pathways in vivo, and to the description of tight links between replication and homologous recombination, responsible for the importance of replication restart in the maintenance of genome stability.KEYWORDS DNA replication, homologous recombination R eplication of a circular bacterial chromosome normally initiates at a unique origin. For bidirectional DNA replication, two replication forks are established that replicate the DNA in opposite directions until they meet in the terminus region. Replication fork progression involves the coordinated action of two complexes, the primosome to open the DNA duplex and synthesize primers and the replisome to catalyze the concerted DNA synthesis of both DNA strands. The two DNA strands at the replication fork are antiparallel, and DNA synthesis occurs only in the 5=-to-3= direction. Therefore, to synthesize both strands in a concerted and semiconservative fashion, one strand is synthesized mainly continuously (the leading strand) and the other is synthesized discontinuously (the lagging strand). The fragments generated on the discontinuous strand are 1 to 2 kb in length and are called Okazaki fragments (OF). In Escherichia coli, the primosome is composed of the DnaB helicase that opens the parental strands and the DnaG primase that interacts transiently with DnaB and synthesizes the RNA primers at the onset of each OF synthesis. DnaB is a hexameric helicase that encircles singlestranded DNA (ssDNA) and translocates on the lagging-strand template in a 5=-to-3= direction. The DNA polymerase III holoenzyme (Pol III HE) synthesizes both nascent DNA strands, and its action is stimulated by interactions with DnaB and with the ssDNA binding protein (SSB) that covers the lagging-strand template (1).The first committed step in the assembly of a replication fork is DnaB loading. In bacteria, two pathways for DnaB loading have been described, a sequence-specific, DnaA-dep...

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Structural mechanisms of PriA-mediated DNA replication restart

Cited by 99 publications

References 47 publications

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases

Mitochondrial Single-stranded DNA-binding Proteins Stimulate the Activity of DNA Polymerase γ by Organization of the Template DNA

Replication Restart in Bacteria

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