Polymerase Dynamics at the Eukaryotic DNA Replication Fork

Peter M.J Burgers

doi:10.1074/jbc.r800062200

Abstract

This review discusses recent insights in the roles of DNA polymerases (Pol) delta and epsilon in eukaryotic DNA replication. A growing body of evidence specifies Pol epsilon as the leading strand DNA polymerase and Pol delta as the lagging strand polymerase during undisturbed DNA replication. New evidence supporting this model comes from the use of polymerase mutants that show an asymmetric mutator phenotype for certain mispairs, allowing an unambiguous strand assignment for these enzymes. On the lagging strand, Pol delta corrects errors made by Pol alpha during Okazaki fragment initiation. During Okazaki fragment maturation, the extent of strand displacement synthesis by Pol delta determines whether maturation proceeds by the short or long flap processing pathway. In the more common short flap pathway, Pol delta coordinates with the flap endonuclease FEN1 to degrade initiator RNA, whereas in the long flap pathway, RNA removal is initiated by the Dna2 nuclease/helicase.

Highlights

How are three DNA polymerases distributed over two strands at one single replication fork? For several decades, researchers have been faced with the enigmatic problem of assigning functions to the three major replicative DNA polymerases in the nucleus: Pol2 ␣, Pol ␦, and Pol ⑀
For the lagging strand machinery, strand placement of Pol ␦ has been inferred from genetic interactions between polymerase mutants and other lagging strand replication genes
A second approach has relied on the analysis of mutation spectra produced by the use of mutator DNA polymerases

Summary

Polymerase Dynamics at the Eukaryotic DNA Replication Fork*

Cated, whereas on the lagging strand, an iterative switch between Pol ␣ and Pol ␦ ensures initiation and elongation of Okazaki fragments, respectively (reviewed in Ref. 2). In this compact and efficient replication system, there was no necessity for a third DNA polymerase. Researchers have been faced with the enigmatic problem of assigning functions to the three major replicative DNA polymerases in the nucleus: Pol2 ␣, Pol ␦, and Pol ⑀. For all other elongation factors including DNA polymerase(s), the virus depends on the host cell This system quickly led to the discovery of the single-stranded binding protein RPA and implicated Pol ␦ and the replication clamp PCNA in SV40 DNA replication. E-mail: burgers@ biochem.wustl.edu. 2 The abbreviations used are: Pol, DNA polymerase; RPA, replication protein A; PCNA, proliferating cell nuclear antigen; nt, nucleotide(s)

Division of Labor at the Fork

Replication fork DNA polymerases

DNA binding