A Dynamic Polymerase Exchange with Escherichia coli DNA Polymerase IV Replacing DNA Polymerase III on the Sliding Clamp*

Furukohri, Asako; Goodman, Myron F.; Maki, Hisaji

doi:10.1074/jbc.m709689200

Cited by 87 publications

(139 citation statements)

References 32 publications

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“…Moreover, it has been shown that replication forks slow down in response to DNA damage, when RecA and TLS Pols are produced (3). In vivo overexpression of Pol IV greatly slows DNA replication (2,15). Additional genetic studies also indicate that Pols II and IV gain access to the replication fork in a RecA-mediated fashion (52).…”

Section: Discussionmentioning

confidence: 99%

“…Both in vivo and in vitro studies indicate that TLS Pols can switch with the Pol III replicase during replication and that the switching process mainly occurs by simple mass action (2,15,17). Although mass action may be an important determinant, most likely the process is more complex (14,38).…”

Section: Discussionmentioning

confidence: 99%

“…Upon DNA damage, the induced levels of TLS Pols take over the cellular replicase (2,14,15). Our previous studies have shown that Pols II and IV replace Pol III within the replisome without causing fork collapse, as they preserve the DNAbound helicase and sliding clamp to form TLS Pol replisomes (2).…”

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confidence: 99%

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RecA acts as a switch to regulate polymerase occupancy in a moving replication fork

Indiani

Patel

Goodman

et al. 2013

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

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This report discovers a role of Escherichia coli RecA, the cellular recombinase, in directing the action of several DNA polymerases at the replication fork. Bulk chromosome replication is performed by DNA polymerase (Pol) III. However, E. coli contains translesion synthesis (TLS) Pols II, IV, and V that also function with the helicase, primase, and sliding clamp in the replisome. Surprisingly, we find that RecA specifically activates replisomes that contain TLS Pols. In sharp contrast, RecA severely inhibits the Pol III replisome. Given the opposite effects of RecA on Pol III and TLS replisomes, we propose that RecA acts as a switch to regulate the occupancy of polymerases within a moving replisome. Previous studies have shown that all three Pols function at replication forks with DnaB helicase, primase, the β sliding clamp, and the clamp loader (2). Bulk chromosome replication is performed by Pol III, and the mechanism that regulates the access of TLS Pols to the replisome is largely unexplored.Heavy DNA damage in E. coli induces the SOS response, which slows down chromosomal replication (3) and expresses over 40 proteins that aid cell survival and enable genome replication to continue (4, 5). Induction of the SOS response requires formation of ssDNA by replication forks to which the cellular recombinase, RecA, binds. The binding of RecA to ssDNA facilitates RecAmediated self-cleavage of the LexA repressor, thereby activating the SOS response genes (6). Among these are TLS Pol II (polB) and TLS Pol IV (dinB), which are rapidly (<5 min) up-regulated during the SOS response (7-10). TLS Pol V (UmuD′ 2 C) is induced late (≥45 min) and requires RecA bound to ssDNA (RecA*) for synthetic activity (8,11,12). Pol IV and Pol V belong to the Yfamily Pols (1), whereas Pol II, even though involved in TLS and mutagenesis, is a B-family polymerase (13).During normal chromosome duplication, the intracellular levels of Pols II and IV are not sufficient to take over Pol III-based replisomes (2). Upon DNA damage, the induced levels of TLS Pols take over the cellular replicase (2, 14, 15). Our previous studies have shown that Pols II and IV replace Pol III within the replisome without causing fork collapse, as they preserve the DNAbound helicase and sliding clamp to form TLS Pol replisomes (2). Pol II and Pol IV replisomes progress at significantly slower rates than the intrinsic rate of DnaB helicase, and thus regulate the speed of helicase unwinding. Slower fork progression may give the cell additional time to repair DNA lesions using normal repair processes (e.g., nucleotide excision repair), thereby preventing direct encounters of the replication fork with DNA lesions.It has been suggested that polymerase selection at the replication fork is mainly guided by mass action dictated by the concentration of each polymerase and its affinity for the clamp (1,14,16,17). However, the findings of this report demonstrate that RecA adds an additional level of control, acting as a switch that regulates DNA polymerase access to the replicat...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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RecA acts as a switch to regulate polymerase occupancy in a moving replication fork

Indiani

Patel

Goodman

et al. 2013

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

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“…In bacteria, the homodimeric clamp utilizes twin peptide-binding pockets on the monomer subunits to facilitate dynamic switching between the replicative polymerase and various repair polymerases (26,27). During active DNA synthesis by the replicative polymerase, our model suggests that a repair polymerase bound to the second peptide-binding site on the clamp would be physically blocked from accessing the primer-template junction by the exonuclease domain (Fig.…”

Section: Structural Clues To the Evolution Of The 3 -5 Exonuclease Inmentioning

confidence: 99%

Structure of PolC reveals unique DNA binding and fidelity determinants

Evans

Davies²,

Bullard

et al. 2008

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

124

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PolC is the polymerase responsible for genome duplication in many Gram-positive bacteria and represents an attractive target for antibacterial development. We have determined the 2.4-Å resolution crystal structure of Geobacillus kaustophilus PolC in a ternary complex with DNA and dGTP. The structure reveals nascent base pair interactions that lead to highly accurate nucleotide incorporation. A unique ␤-strand motif in the PolC thumb domain contacts the minor groove, allowing replication errors to be sensed up to 8 nt upstream of the active site. PolC exhibits the potential for large-scale conformational flexibility, which could encompass the catalytic residues. The structure suggests a mechanism by which the active site can communicate with the rest of the replisome to trigger proofreading after nucleotide misincorporation, leading to an integrated model for controlling the dynamic switch between replicative and repair polymerases. This ternary complex of a cellular replicative polymerase affords insights into polymerase fidelity, evolution, and structural diversity.DNA polymerase III ͉ DNA replication ͉ Gram-positive polymerase ͉ polymerase and histidinol phosphatase (PHP) ͉ ternary complex D NA polymerases are the enzymes responsible for DNA synthesis. Cellular organisms typically use multiple DNA polymerase types. The ''replicative'' polymerase performs the bulk of genome duplication, whereas various specialty polymerases repair damaged DNA and resolve Okazaki fragments. Across every kingdom of life, replicative polymerases exhibit certain hallmarks such as high fidelity, speed, and processivity (1). Polymerase holoenzyme accessory proteins play an integral role in achieving the extraordinary efficiency and accuracy of the replicative polymerase complex. These include a ''sliding clamp'' that encircles the DNA and increases processivity (2).Bacterial replicative polymerases comprise the C family of DNA polymerases (3) and differ significantly from the replicative polymerases of eukaryotes, bacteriophage, and archaea, which belong to the B family. The major C family replicative polymerases are DnaE (PolIII), found primarily in Gram-negative bacteria, and PolC (PolIIIC), found primarily in Gram-positive bacteria (4). Apoenzyme crystal structures of DnaE have revealed surprising structural differences in the catalytic center of the enzyme compared with B family polymerases, suggesting a separate evolutionary origin for the C family (5, 6).As the core component of the replicative polymerase complex in Gram-positive pathogens such as Staphylococcus aureus, PolC has received considerable attention as a potential target for antibacterial drug discovery (7,8). No currently marketed antibiotics target the central replication apparatus, making PolC a novel target for antibacterial development. Gram-negative and Gram-positive bacteria are separated by Ͼ1 billion years of evolution, and PolC and DnaE share Ͻ20% sequence identity; PolC is further differentiated from DnaE by domain rearrangements and by the presence of an ...

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“…Such a mechanism is certainly possible under irradiation of ionizing radiation of DNA molecule. The action of the free radicals, mainly singlet oxygen leads to spontaneous mutagenesis [137,138]. In these cases, as is known, a large number of damages of DNA bases and of sugar-phosphate backbone are formed [137,138].…”

Section: /14mentioning

confidence: 99%

A Polymerase Tautomeric Model for Radiation Induced Bystander Effects: A Model for Untargeted Base Substitution Mutagenesis during Error Prone and SOS Replication of Double Stranded DNA Containing Thymine and Adenine in Rare Tautomeric Forms

Grebneva¹

2017

IJMBOA

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Currently, untargeted mutations are studied in the context of bystander effects. Up to now the nature and mechanisms of formation of untargeted mutations is poorly understood. Untargeted base substitution mutations are base substitution mutations then one or some nucleotides are inserted in DNA molecule on, so called, undamaged sites of DNA. Here the polymerase-tautomeric models of ultraviolet mutagenesis and bystander effects are developed. The mechanisms of untargeted base substitution mutations formation caused by cis-syn cyclobutane thymine dimers and bases pairs of adenine-thymine or thymine-adenine in rare tautomeric forms that are in small neighbor from any cyclobutane dimers are proposed. Five rare tautomeric forms may form for thymine and adenine. These rare tautomeric forms will be stable if corresponding nucleotides are part of cyclobutane pyrimidine dimers or are in small neighbor of the cyclobutane dimers and during DNA synthesis. Structural analysis of bases incorporation shown that adenine in rare tautomeric form A 1

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A Dynamic Polymerase Exchange with Escherichia coli DNA Polymerase IV Replacing DNA Polymerase III on the Sliding Clamp*

Cited by 87 publications

References 32 publications

RecA acts as a switch to regulate polymerase occupancy in a moving replication fork

RecA acts as a switch to regulate polymerase occupancy in a moving replication fork

Structure of PolC reveals unique DNA binding and fidelity determinants

A Polymerase Tautomeric Model for Radiation Induced Bystander Effects: A Model for Untargeted Base Substitution Mutagenesis during Error Prone and SOS Replication of Double Stranded DNA Containing Thymine and Adenine in Rare Tautomeric Forms

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