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Chapter 10 : DNA Elongation

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Abstract:

This chapter describes the structure and mechanisms of action of bacterial DNA replication proteins, and how their activities are coordinated for efficient duplication of chromosomal DNA. The proteins holoenzyme/replicase function together as catalytic or structural components of the chromosomal DNA replication machinery known as a replisome. At the heart of the replisome is the replicase, or DNA polymerase holoenzyme-itself a complex protein machine comprising DNA polymerase and the accessory clamp and clamp loader proteins. Prokaryotic single-stranded DNA-binding protein (SSB) and eukaryotic replication protein A (RPA) are known to bind several proteins involved in DNA metabolism. The interactions between SSB and primase and between SSB and χ protein of γ/τ complex are critical for assembly of DNA polymerase onto primed DNA. Each replisomal protein provides a specific function or interaction at a specific point in the DNA replication pathway, enabling highly efficient DNA synthesis. Cell survival depends on the ability of the replisomal protein machinery to overcome such blocks in the path of DNA elongation. Bypass polymerase activity appears to be distributive, suggesting that once the polymerase traverses the lesion it "falls off," allowing reassembly of the replicative DNA polymerase and continued DNA elongation. The processes described clearly indicate that the pathways of DNA replication, recombination, and repair are intimately intertwined.

Citation: Hingorani M, O'Donnell M. 2005. DNA Elongation, p 193-216. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch10

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DNA Replication Proteins
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Figures

Image of Figure 1
Figure 1

Replisome. At the DNA replication fork the helicase unwinds dsDNA, making ssDNA templates that are stabilized by SSB. Primase synthesizes RNA primers around which a clamp loader assembles circular clamps for use by the DNA polymerase. The holoenzyme, comprising two core DNA polymerases (αεθ), a connector protein (τ) and clamp loader (γ/τ complex), and two clamps (β), replicates leading and lagging DNA strands simultaneously. A connection between the holoenzyme (via t) and DnaB helicase stimulates DNA unwinding up to the speed of the DNA polymerase. Additional connections between the helicase and primase, the clamp loader, and SSB help coordinate the activities of the various protein components and help stabilize the replisome at the fork junction.

Citation: Hingorani M, O'Donnell M. 2005. DNA Elongation, p 193-216. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch10
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Image of Figure 2
Figure 2

DNA polymerase structure and catalytic site geometry. (A and B) The polymerase structure comprises the "fingers," "palm," and "thumb" domains arranged to form a DNA binding cleft with the active site at the base (in the palm domain). (B and C) The template strand is bent to expose a nucleotide for base pairing with the incoming dNTP (shown for T7 DNA polymerase), while the primer 3′-OH end and the new base pair are held snugly within the active site to facilitate correct base pairing and nucleotidyl transfer. (D) At the active site, two metal ions (A and B) are coordinated by conserved acidic residues and water molecules, and in turn coordinate the phosphate group oxygens of the incoming dNTP. The primer 3′-OH initiates nucleophilic attack on the a phosphate of dNTP, resulting in phosphodiester bond formation and pyrophosphate release.

Citation: Hingorani M, O'Donnell M. 2005. DNA Elongation, p 193-216. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch10
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Image of Figure 3
Figure 3

DNA polymerase mechanism of action. The DNA synthesis pathway (shown here for T7 DNA polymerase) initiates with rapid and high-affinity binding of primer-template DNA and dNTP to the polymerase. Next, the polymerase undergoes a slow, rate-limiting conformation in preparation for nucleotidyl transfer. The fast chemistry step is followed by another conformational change that allows product release and translocation of the new 3′-OH terminus into the active site. (A) An image of the Klentaq1●DNA “open” complex with primed DNA in the binding cleft. The arrow predicts translocation of the primer-template following nucleotidyl transfer. (B) A Klentaq1*●DNA●dNTP “closed” ternary complex, with DNA and dNTP trapped securely within the active site due to the inward movement of the fingers domain.

Citation: Hingorani M, O'Donnell M. 2005. DNA Elongation, p 193-216. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch10
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Image of Figure 4
Figure 4

Circular clamps. (A) Circular sliding clamps from (β dimer), bacteriophages T4 (gp45 trimer) and RB69, and and humans (PCNA trimer). The central cavity averages 35 Å in diameter, sufficient to encircle dsDNA without any steric hindrance. (B) A model structure of the bacteriophage RB69 DNA polymerase tethered by its circular clamp (onto DNA) via a short C-terminal polymerase peptide connector.

Citation: Hingorani M, O'Donnell M. 2005. DNA Elongation, p 193-216. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch10
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Image of Figure 5
Figure 5

Clamp loader. (A) A model pathway of clamp assembly by the clamp loader begins with ATP binding to the γ/τ subunits, which triggers a change in the complex conformation from "closed" (in which the β-binding element on d is buried) to "open," allowing interaction between γ/τ complex and b. The clamp loader • clamp complex binds primed DNA with high affinity, which triggers rapid ATP hydrolysis and clamp assembly around DNA. The ADP-bound γ/τ complex releases both β and DNA linked topologically to each other. ADP dissociation recycles the clamp loader for the next round of clamp assembly on DNA. (B) A crystal structure of the γδδ′ clamp loader (χ and ψ are not essential for clamp assembly) reveals three γ subunits, one δ, and one δ' subunit arranged in a pentamer. The C-terminal domains of all five proteins are arranged in a closed ring, but a large separation between the N-terminal domains of δ and d0 in an open conformation exposes the β-binding element on δ.

Citation: Hingorani M, O'Donnell M. 2005. DNA Elongation, p 193-216. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch10
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Image of Figure 6
Figure 6

Additional DNA replication proteins. (A) Crystal structure of the phage T7 gp4 helicase domain, looking down the 61-symmetry axis, and a model of the gp4 helicase/primase at the DNA replication fork junction (based on electron microscopy data). (B) Crystal structure of the primase catalytic domain indicating the active site. (C) Crystal structure of the SSB tetramer showing the oligonucleotide-binding domain (five-stranded antiparallel β barrel) per monomer. (D) Crystal structure of the T. filiformis NAD-dependent DNA ligase with DNA modeled within the central channel. (E) Crystal structure of type IA topoisomerase III. (F) The DNA binding/cleavage fragment of type II topoisomerase II (analogous to DNA gyrase).

Citation: Hingorani M, O'Donnell M. 2005. DNA Elongation, p 193-216. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch10
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Image of Figure 7
Figure 7

Protein switching during lagging DNA synthesis. (A) After synthesizing a primer, the primase maintains its grip on the site aided by interaction with SSB. (B) The χ subunit disrupts the primase-SSB contact, which triggers primase recycling to an upstream site and allows the clamp loader to assemble a circular clamp around the primed DNA. Meanwhile, the lagging strand polymerase finishes an Okazaki fragment and releases its clamp and DNA. The clamp on DNA is likely bound next by Pol I and DNA ligase for processing of Okazaki fragments into a continuous lagging strand. (C) The lagging strand polymerase replaces the clamp loader at the upstream primed DNA (with β on it) and initiates a new fragment. Meanwhile, the leftover β clamp on DNA is free to be recycled by the δ clamp unloader.

Citation: Hingorani M, O'Donnell M. 2005. DNA Elongation, p 193-216. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch10
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Tables

Generic image for table
Table 1

DNA replication proteins in E. coli

Citation: Hingorani M, O'Donnell M. 2005. DNA Elongation, p 193-216. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch10

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