Home LiteratureArticle Details
PMID: 18835809 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Review

Polymerase dynamics at the eukaryotic DNA replication fork.

The Journal of biological chemistry ·Vol. 284 ·No. 7 ·2009-02-13 ·Pages 4041-5

Burgers PM

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.

MeSH Terms
Animals DNA/genetics,metabolism DNA Helicases/genetics,metabolism DNA Polymerase II/genetics,metabolism DNA Polymerase III/genetics,metabolism DNA Replication/physiology Eukaryotic Cells/cytology,enzymology Flap Endonucleases/genetics,metabolism Humans Mutation
Chemicals
Okazaki fragments DNA DNA Polymerase II DNA Polymerase III Flap Endonucleases FEN1 protein, human DNA Helicases DNA2 protein, human
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Burgers Peter M J
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA. burgers@biochem.wustl.edu
References (38)
38 references, click to expand
  1. The nuclease activity of the yeast DNA2 protein, which is related to the RecB-like nucleases, is essential in vivo.
    J Biol Chem. 2000 Jun 2;275(22):16518-29 PMID: 10748138
  2. Evidence suggesting that Pif1 helicase functions in DNA replication with the Dna2 helicase/nuclease and DNA polymerase delta.
    Mol Cell Biol. 2006 Apr;26(7):2490-500 PMID: 16537895
  3. Characterization of the enzymatic properties of the yeast dna2 Helicase/endonuclease suggests a new model for Okazaki fragment processing.
    J Biol Chem. 2000 Dec 1;275(48):38022-31 PMID: 10984490
  4. The 3'-->5' exonuclease of DNA polymerase delta can substitute for the 5' flap endonuclease Rad27/Fen1 in processing Okazaki fragments and preventing genome instability.
    Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5122-7 PMID: 11309502
  5. Schizosaccharomyces pombe cells lacking the amino-terminal catalytic domains of DNA polymerase epsilon are viable but require the DNA damage checkpoint control.
    Mol Cell Biol. 2001 Jul;21(14):4495-504 PMID: 11416129
  6. RPA governs endonuclease switching during processing of Okazaki fragments in eukaryotes.
    Nature. 2001 Jul 26;412(6845):456-61 PMID: 11473323
  7. Okazaki fragment processing: modulation of the strand displacement activity of DNA polymerase delta by the concerted action of replication protein A, proliferating cell nuclear antigen, and flap endonuclease-1.
    Proc Natl Acad Sci U S A. 2001 Dec 4;98(25):14298-303 PMID: 11724925
  8. Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects.
    Science. 2002 Jul 26;297(5581):599-602 PMID: 12142537
  9. The DNA polymerase domain of pol(epsilon) is required for rapid, efficient, and highly accurate chromosomal DNA replication, telomere length maintenance, and normal cell senescence in Saccharomyces cerevisiae.
    J Biol Chem. 2002 Aug 2;277(31):28099-108 PMID: 12015307
  10. Okazaki fragment maturation in yeast. II. Cooperation between the polymerase and 3'-5'-exonuclease activities of Pol delta in the creation of a ligatable nick.
    J Biol Chem. 2003 Jan 17;278(3):1626-33 PMID: 12424237
  11. Characterization of nuclease-dependent functions of Exo1p in Saccharomyces cerevisiae.
    DNA Repair (Amst). 2002 Nov 3;1(11):895-912 PMID: 12531018
  12. A heterotrimeric PCNA in the hyperthermophilic archaeon Sulfolobus solfataricus.
    Mol Cell. 2003 Jan;11(1):275-82 PMID: 12535540
  13. The protein components and mechanism of eukaryotic Okazaki fragment maturation.
    Crit Rev Biochem Mol Biol. 2003;38(5):433-52 PMID: 14693726
  14. On the roles of Saccharomyces cerevisiae Dna2p and Flap endonuclease 1 in Okazaki fragment processing.
    J Biol Chem. 2004 Apr 9;279(15):15014-24 PMID: 14747468
  15. Simian virus 40 DNA replication in vitro.
    Proc Natl Acad Sci U S A. 1984 Nov;81(22):6973-7 PMID: 6095264
  16. A third essential DNA polymerase in S. cerevisiae.
    Cell. 1990 Sep 21;62(6):1143-51 PMID: 2169349
  17. Calf 5' to 3' exo/endonuclease must slide from a 5' end of the substrate to perform structure-specific cleavage.
    J Biol Chem. 1995 Dec 22;270(51):30377-83 PMID: 8530463
  18. DNA polymerase epsilon may be dispensable for SV40- but not cellular-DNA replication.
    EMBO J. 1996 May 1;15(9):2298-305 PMID: 8641295
  19. 3'-->5' exonucleases of DNA polymerases epsilon and delta correct base analog induced DNA replication errors on opposite DNA strands in Saccharomyces cerevisiae.
    Genetics. 1996 Mar;142(3):717-26 PMID: 8849882
  20. A novel mutation avoidance mechanism dependent on S. cerevisiae RAD27 is distinct from DNA mismatch repair.
    Cell. 1997 Jan 24;88(2):253-63 PMID: 9008166
  21. A yeast replicative helicase, Dna2 helicase, interacts with yeast FEN-1 nuclease in carrying out its essential function.
    Mol Cell Biol. 1997 Apr;17(4):2136-42 PMID: 9121462
  22. Repeat expansion--all in a flap?
    Nat Genet. 1997 Jun;16(2):116-8 PMID: 9171819
  23. Identification and characterization of Saccharomyces cerevisiae EXO1, a gene encoding an exonuclease that interacts with MSH2.
    Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7487-92 PMID: 9207118
  24. Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase.
    Cell. 1997 Oct 3;91(1):59-69 PMID: 9335335
  25. Structure and processivity of two forms of Saccharomyces cerevisiae DNA polymerase delta.
    J Biol Chem. 1998 Jul 31;273(31):19756-62 PMID: 9677406
  26. The DNA replication fork in eukaryotic cells.
    Annu Rev Biochem. 1998;67:721-51 PMID: 9759502
  27. DNA polymerase epsilon catalytic domains are dispensable for DNA replication, DNA repair, and cell viability.
    Mol Cell. 1999 May;3(5):679-85 PMID: 10360184
  28. Analysis of the essential functions of the C-terminal protein/protein interaction domain of Saccharomyces cerevisiae pol epsilon and its unexpected ability to support growth in the absence of the DNA polymerase domain.
    J Biol Chem. 1999 Aug 6;274(32):22283-8 PMID: 10428796
  29. Idling by DNA polymerase delta maintains a ligatable nick during lagging-strand DNA replication.
    Genes Dev. 2004 Nov 15;18(22):2764-73 PMID: 15520275
  30. DNA polymerases that propagate the eukaryotic DNA replication fork.
    Crit Rev Biochem Mol Biol. 2005 Mar-Apr;40(2):115-28 PMID: 15814431
  31. Cellular DNA replicases: components and dynamics at the replication fork.
    Annu Rev Biochem. 2005;74:283-315 PMID: 15952889
  32. Evidence that errors made by DNA polymerase alpha are corrected by DNA polymerase delta.
    Curr Biol. 2006 Jan 24;16(2):202-7 PMID: 16431373
  33. Roles of Pif1-like helicases in the maintenance of genomic stability.
    Nucleic Acids Res. 2006;34(15):4147-53 PMID: 16935874
  34. Yeast DNA polymerase epsilon participates in leading-strand DNA replication.
    Science. 2007 Jul 6;317(5834):127-30 PMID: 17615360
  35. Division of labor at the eukaryotic replication fork.
    Mol Cell. 2008 Apr 25;30(2):137-44 PMID: 18439893
  36. Pif1 helicase directs eukaryotic Okazaki fragments toward the two-nuclease cleavage pathway for primer removal.
    J Biol Chem. 2008 Oct 10;283(41):27483-93 PMID: 18689797
  37. Flexibility of eukaryotic Okazaki fragment maturation through regulated strand displacement synthesis.
    J Biol Chem. 2008 Dec 5;283(49):34129-40 PMID: 18927077
  38. The endonuclease activity of the yeast Dna2 enzyme is essential in vivo.
    Nucleic Acids Res. 2000 Aug 1;28(15):2873-81 PMID: 10908349
Article Info
Journal
The Journal of biological chemistry
Abbr.
J Biol Chem
ISSN
0021-9258
Published
2009-02-13
Epub
2008-00-03
Pages
4041-5
Language
English
Region
United States
NLM ID
2985121R
PMCID
PMC2640984
Subset
IM
Grants
NIGMS NIH HHS · R01 GM032431 · United States
NIGMS NIH HHS · GM32431 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com