Eukaryotic DNA Replication Fork

Overview

Journal Annu Rev Biochem

Publisher Annual Reviews

Specialty Biochemistry

Date 2017 Mar 17

PMID 28301743

Citations 265

Authors

Peter M J Burgers

Thomas A Kunkel

Affiliations

Soon will be listed here.

Abstract

This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

Citing Articles

The p12 Subunit Choreographs the Regulation and Functions of Two Forms of DNA Polymerase δ in Mammalian Cells.

Xu D, Ayyamperumal S, Zhang S, Chen J, Lee E, Lee M Genes (Basel). 2025; 16(2).

PMID: 40004517 PMC: 11855201. DOI: 10.3390/genes16020188.

Genome-wide KAS-Seq mapping of leukocytes in ischemia-reperfusion model reveals IL7R as a potential therapeutic target for ischemia-reperfusion injury.

Zhang L, Duolikun M, Chen H, Wang Z, Li X, Xiao H Sci Rep. 2025; 15(1):6165.

PMID: 39979392 PMC: 11842730. DOI: 10.1038/s41598-025-90457-7.

Quantitative Chromatin Protein Dynamics During Replication Origin Firing in Human Cells.

Gadi S, Hendriks I, Nielsen C, Popova P, Hickson I, Nielsen M Mol Cell Proteomics. 2025; 24(3):100915.

PMID: 39880081 PMC: 11889381. DOI: 10.1016/j.mcpro.2025.100915.

A tale of two strands: Decoding chromatin replication through strand-specific sequencing.

Li Z, Zhang Z Mol Cell. 2025; 85(2):238-261.

PMID: 39824166 PMC: 11750172. DOI: 10.1016/j.molcel.2024.10.035.

The tomato gene Ty-6, encoding DNA polymerase delta subunit 1, confers broad resistance to Geminiviruses.

Shen X, Gill U, Arens M, Yan Z, Bai Y, Hutton S Theor Appl Genet. 2025; 138(1):22.

PMID: 39775891 PMC: 11711579. DOI: 10.1007/s00122-024-04803-w.

References

Calzada A, Hodgson B, Kanemaki M, Bueno A, Labib K . Molecular anatomy and regulation of a stable replisome at a paused eukaryotic DNA replication fork. Genes Dev. 2005; 19(16):1905-19. PMC: 1186190. DOI: 10.1101/gad.337205. View

Sparks J, Chon H, Cerritelli S, Kunkel T, Johansson E, Crouch R . RNase H2-initiated ribonucleotide excision repair. Mol Cell. 2012; 47(6):980-6. PMC: 3470915. DOI: 10.1016/j.molcel.2012.06.035. View

Nick McElhinny S, Kissling G, Kunkel T . Differential correction of lagging-strand replication errors made by DNA polymerases {alpha} and {delta}. Proc Natl Acad Sci U S A. 2010; 107(49):21070-5. PMC: 3000245. DOI: 10.1073/pnas.1013048107. View

Pavlov Y, Shcherbakova P, Kunkel T . In vivo consequences of putative active site mutations in yeast DNA polymerases alpha, epsilon, delta, and zeta. Genetics. 2001; 159(1):47-64. PMC: 1461793. DOI: 10.1093/genetics/159.1.47. View

Ishmael F, Trakselis M, Benkovic S . Protein-protein interactions in the bacteriophage T4 replisome. The leading strand holoenzyme is physically linked to the lagging strand holoenzyme and the primosome. J Biol Chem. 2002; 278(5):3145-52. DOI: 10.1074/jbc.M209858200. View

Kanke M, Kodama Y, Takahashi T, Nakagawa T, Masukata H . Mcm10 plays an essential role in origin DNA unwinding after loading of the CMG components. EMBO J. 2012; 31(9):2182-94. PMC: 3343466. DOI: 10.1038/emboj.2012.68. View

Indiani C, McInerney P, Georgescu R, Goodman M, ODonnell M . A sliding-clamp toolbelt binds high- and low-fidelity DNA polymerases simultaneously. Mol Cell. 2005; 19(6):805-15. DOI: 10.1016/j.molcel.2005.08.011. View

Bullock P, Seo Y, Hurwitz J . Initiation of simian virus 40 DNA synthesis in vitro. Mol Cell Biol. 1991; 11(5):2350-61. PMC: 359986. DOI: 10.1128/mcb.11.5.2350-2361.1991. View

McHenry C . DNA replicases from a bacterial perspective. Annu Rev Biochem. 2011; 80:403-36. DOI: 10.1146/annurev-biochem-061208-091655. View

10.

Kang Y, Lee C, Seo Y . Dna2 on the road to Okazaki fragment processing and genome stability in eukaryotes. Crit Rev Biochem Mol Biol. 2010; 45(2):71-96. DOI: 10.3109/10409230903578593. View

11.

Makarova K, Krupovic M, Koonin E . Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery. Front Microbiol. 2014; 5:354. PMC: 4104785. DOI: 10.3389/fmicb.2014.00354. View

12.

Ganai R, Osterman P, Johansson E . Yeast DNA polymerase ϵ catalytic core and holoenzyme have comparable catalytic rates. J Biol Chem. 2014; 290(6):3825-35. PMC: 4319046. DOI: 10.1074/jbc.M114.615278. View

13.

Stodola J, Burgers P . Resolving individual steps of Okazaki-fragment maturation at a millisecond timescale. Nat Struct Mol Biol. 2016; 23(5):402-8. PMC: 4857878. DOI: 10.1038/nsmb.3207. View

14.

Kelman Z, Lee J, Hurwitz J . The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum DeltaH contains DNA helicase activity. Proc Natl Acad Sci U S A. 1999; 96(26):14783-8. PMC: 24725. DOI: 10.1073/pnas.96.26.14783. View

15.

Villa F, Simon A, Ortiz Bazan M, Kilkenny M, Wirthensohn D, Wightman M . Ctf4 Is a Hub in the Eukaryotic Replisome that Links Multiple CIP-Box Proteins to the CMG Helicase. Mol Cell. 2016; 63(3):385-96. PMC: 4980431. DOI: 10.1016/j.molcel.2016.06.009. View

16.

Rydberg B, Game J . Excision of misincorporated ribonucleotides in DNA by RNase H (type 2) and FEN-1 in cell-free extracts. Proc Natl Acad Sci U S A. 2002; 99(26):16654-9. PMC: 139199. DOI: 10.1073/pnas.262591699. View

17.

Moyer S, Lewis P, Botchan M . Isolation of the Cdc45/Mcm2-7/GINS (CMG) complex, a candidate for the eukaryotic DNA replication fork helicase. Proc Natl Acad Sci U S A. 2006; 103(27):10236-10241. PMC: 1482467. DOI: 10.1073/pnas.0602400103. View

18.

Li N, Zhai Y, Zhang Y, Li W, Yang M, Lei J . Structure of the eukaryotic MCM complex at 3.8 Å. Nature. 2015; 524(7564):186-91. DOI: 10.1038/nature14685. View

19.

Balakrishnan L, Bambara R . Eukaryotic lagging strand DNA replication employs a multi-pathway mechanism that protects genome integrity. J Biol Chem. 2010; 286(9):6865-70. PMC: 3044941. DOI: 10.1074/jbc.R110.209502. View

20.

Baranovskiy A, Babayeva N, Zhang Y, Gu J, Suwa Y, Pavlov Y . Mechanism of Concerted RNA-DNA Primer Synthesis by the Human Primosome. J Biol Chem. 2016; 291(19):10006-20. PMC: 4858955. DOI: 10.1074/jbc.M116.717405. View