Additions and Corrections to The ordered assembly of the ϕX174-type primosome. I. Isolation and identification of intermediate protein-DNA complexes.

Ng, Jenny Y.; Marians, Kenneth J.

doi:10.1016/s0021-9258(19)79280-1

Journal of Biological Chemistry

1996

DOI: 10.1016/s0021-9258(19)79280-1

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Additions and Corrections to The ordered assembly of the ϕX174-type primosome. I. Isolation and identification of intermediate protein-DNA complexes.

Jenny Y. Ng¹,

Kenneth J. Marians²

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Cited by 6 publications

(15 citation statements)

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“…supporting these three pathways (Heller & Marians, 2005). PriA, PriB, PriC, and DnaT were originally identified along with DnaG (primase), DnaC (helicase loader), and DnaB (replicative helicase) as being required for the primosome assembly pathway for synthesis of the RNA primer for ΦX174 DNA replication (Liu et al, 1996;Ng & Marians, 1996a, 1996bSchekman et al, 1975).…”

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Escherichia coli K‐12 has two distinguishable PriA‐PriB replication restart pathways

Sandler¹,

Leroux

Windgassen

et al. 2021

Molecular Microbiology

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DNA replication complexes (replisomes) frequently encounter obstacles that prematurely disengage the complexes from DNA templates during chromosomal replication. Such events require reloading of the replisome to prevent incomplete replication and cell death. Estimates suggest that up to 86% of Escherichia coli cells go through this process under nonstress growth condition (Maisnier-Patin et al., 2001;Mangiameli et al., 2017). Thus, it is critical to rescue incomplete replication through a process called "replication restart" to allow genome duplication (reviewed in Michel & Sandler, 2017;Windgassen et al., 2017). The central step in this process is the reloading of the replicative helicase (DnaB in gram-negative bacteria) so that primase (DnaG), clamp loader, and core DNA polymerase can associate with the repaired replication fork to continue DNA replication. This type of reloading is distinct from initiation of chromosomal DNA replication at oriC with DnaA (Kaguni, 2011) in that replication restart occurs at specific DNA structures rather than at a specific DNA sequence (for a comparison of the two processes see Heller & Marians, 2006).The proteins required for reloading the DnaB replicative helicase during replication restart in E. coli include PriA, PriB, PriC, and DnaT (reviewed in Michel & Sandler, 2017;Windgassen et al., 2017).These proteins mediate three pathways in the cell that have been defined genetically as the PriA-PriB, PriA-PriC, and PriC pathways (Sandler, 2000). There is also substantial biochemical evidence

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mentioning

confidence: 99%

Escherichia coli K‐12 has two distinguishable PriA‐PriB replication restart pathways

Sandler¹,

Leroux

Windgassen

et al. 2021

Molecular Microbiology

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“…In the PriA‐dependent pathway, which is considered a primary replication restart pathway, PriA binds to DNA by recognizing the 3′ end nucleotides of the synthesized leading strand and the D‐loop structure formed at the DNA repair site [7], and then PriA unwinds the dsDNA on the side of the lagging strand in a 3′→5′ direction to a single strand due to its own helicase activity [8–10]. Next, PriB stabilizes the PriA–ssDNA complex through binding to ssDNA [11]. DnaT then binds to the PriB–ssDNA complex, dissociates the ssDNA from the complex, binds to the dissociated ssDNA, and finally recruits the DnaB–DnaC complex [12–16].…”

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confidence: 99%

“…PriB, a basic protein with a molecular weight of approximately 11.4 kDa, consists of 104 amino acid residues. In the PriA‐dependent replication restart pathway, PriB is known to stabilize the PriA–ssDNA complex [11] and enhance the helicase activity of PriA [21]. The tertiary structure of PriB has been determined by X‐ray crystallography [22–24], and the ssDNA‐binding function was revealed by a structural similarity with single‐strand DNA‐binding protein (SSB), which is a representative of the OB‐fold family.…”

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A structural model of the PriB–DnaT complex in Escherichia coli replication restart

et al. 2020

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In Escherichia coli, DNA replication is restarted following DNA repair by the PriA‐dependent pathway, in which the binding and dissociation of proteins such as PriA, PriB, and DnaT on ssDNA lead to the formation of a protein–DNA complex for recruiting the DnaB–DnaC replication protein complex. However, the structure of the PriB–DnaT complex, which is an essential step in the PriA‐dependent pathway, remains elusive. In this study, the importance of His26 in PriB for replication restart was reconfirmed using plasmid complementation. Furthermore, we used NMR to examine the DnaT interaction sites on PriB. We also evaluated the PriB–DnaT peptide complex model, which was prepared by in silico docking, using molecular dynamic simulation. From these data, we propose a structural model that provides insight into the PriB–DnaT interaction.

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“…In vivo, PriA helicase is thought to initiate reactivation of repaired DNA replication forks by binding to specific DNA structures, such as forked DNA with three-way branches and D-loop DNA. , After binding to an appropriate DNA structure, PriA can catalyze unwinding of short stretches of duplex DNA using its 3′–5′ helicase activity and facilitate assembly of the remaining primosome proteins such as PriB and DnaT. − PriB is a primosome protein that binds to PriA and stabilizes PriA on the DNA . PriB also simulates PriA’s helicase activity and is thought to participate in recruiting DnaT to the primosome complex. − The combined activities of PriA, PriB, and DnaT facilitate recruitment of the DnaB–DnaC complex to the repaired DNA replication fork and the subsequent reloading of DnaB onto the DNA by an as yet unknown mechanism …”

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Identification of a Small Molecule PriA Helicase Inhibitor

et al. 2012

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PriA helicase catalyzes the initial steps of replisome reloading onto repaired DNA replication forks in bacterial DNA replication restart pathways. We have used a high-throughput screen to identify a small molecule inhibitor of PriA-catalyzed duplex DNA unwinding. The compound, CGS 15943, targets Neisseria gonorrhoeae PriA helicase with an IC(50) of 114 ± 24 μM. The PriA helicase of Escherichia coli is also inhibited, although to a lesser extent than N. gonorrhoeae PriA. CGS 15943 decreases rates of PriA-catalyzed ATP hydrolysis and reduces the affinity with which PriA binds DNA. Steady-state kinetic data indicate that CGS 15943 inhibits PriA through a mixed mode of inhibition with respect to ATP and with respect to DNA, indicating that it binds to a site on PriA that participates in both substrate binding and catalysis. Inhibitor binding constants derived from steady-state kinetic experiments reveal that CGS 15943 has the highest binding affinity for the PriA·PriB·ATP complex, intermediate binding affinity for the PriA·PriB·DNA complex, and the lowest binding affinity for the PriA·PriB·DNA·ATP complex, suggesting that PriA assumes different conformations in each of these complexes. We propose that CGS 15943 binds to PriA at a site distinct from the DNA and primary ATP binding sites, perhaps at PriA's weak nucleotide binding site, and induces a conformational change in PriA that renders it less catalytically proficient or prevents conformational changes in PriA that are necessary for ATP hydrolysis and duplex DNA unwinding.

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Additions and Corrections to The ordered assembly of the ϕX174-type primosome. I. Isolation and identification of intermediate protein-DNA complexes.

Cited by 6 publications

References 0 publications

Escherichia coli K‐12 has two distinguishable PriA‐PriB replication restart pathways

Escherichia coli K‐12 has two distinguishable PriA‐PriB replication restart pathways

A structural model of the PriB–DnaT complex in Escherichia coli replication restart

Identification of a Small Molecule PriA Helicase Inhibitor

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