DNA polymerase delta in DNA replication and genome maintenance

Abstract

The eukaryotic genome is in a constant state of modification and repair. Faithful transmission of the genomic information from parent to daughter cells depends upon an extensive system of surveillance, signaling, and DNA repair, as well as accurate synthesis of DNA during replication. Often, replicative synthesis occurs over regions of DNA that have not yet been repaired, presenting further challenges to genomic stability. DNA polymerase δ (pol δ) occupies a central role in all of these processes: catalyzing the accurate replication of a majority of the genome, participating in several DNA repair synthetic pathways, and contributing structurally to the accurate bypass of problematic lesions during translesion synthesis. The concerted actions of pol δ on the lagging strand, pol ϵ on the leading strand, associated replicative factors, and the mismatch repair (MMR) proteins results in a mutation rate of less than one misincorporation per genome per replication cycle. This low mutation rate provides a high level of protection against genetic defects during development and may prevent the initiation of malignancies in somatic cells. This review explores the role of pol δ in replication fidelity and genome maintenance.

Fig. 1

Structure of the Pol δ holoenzyme, catalytic subunit, and DNA binding pocket. A. A conceptual depiction of the four-subunit human Pol δ holoenzyme, based on demonstrated interactions of subunits and a small-angle X-ray scattering study (see text). B. Cartoon representation of the crystal structure of the p125 catalytic subunit in complex with DNA and the incoming dCTP (black) bound at the active site. Ca²⁺ ions are shown as purple spheres, representing the location of the Mg²⁺ atoms at the polymerase and exonuclease active sites. C. Pol δ active site and DNA binding channel, highlighting important side chains for polymerase fidelity, as well as purported “sensing” side chains along the minor groove. Palm residues are green, fingers residues are red, N-terminal domain residues are silver, β-hairpin site is purple, DNA template strand is yellow, and DNA primer strand is blue. The incoming dCTP and its template G are shown in black, and active site metals are shown as light blue spheres. Hydrogen bonds (yellow) are shown for the nascent base pair and for the active site metals. (Structure images generated in The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC. from PDB accession code 3IAY).

Fig. 2

Model of the Eukaryotic Replication Fork. The current model, showing Okazaki fragments at three stages of formation. Next to the MCM helicase, the primase Pol α synthesizes an RNA primer (pink box with lines) and a small amount of DNA, beginning lagging strand synthesis. Replication protein A (RPA) coats the single stranded DNA between the Pol α-catalyzed primers. The next primer has been extended by the lagging strand replisome, represented by Pol δ and PCNA. The third Okazaki fragment has been completely extended, and Okazaki fragment maturation, directed by Pol δ, Fen1, and Lig1, is underway. The leading strand is shown as being copied by Pol ε and PCNA, although Pol δ may be responsible for some leading strand synthesis as well. Several important cofactors are not shown for simplicity. Figure inspired by and adapted from [Burgers 2009].