Home LiteratureArticle Details
PMID: 23042675 Published · ppublish English Journal Article Research Support, N.I.H., Intramural

Pol β associated complex and base excision repair factors in mouse fibroblasts.

Nucleic acids research ·Vol. 40 ·No. 22 ·2012-12-00 ·Pages 11571-82

Prasad R, Williams JG, Hou EW, Wilson SH

Abstract

During mammalian base excision repair (BER) of lesion-containing DNA, it is proposed that toxic strand-break intermediates generated throughout the pathway are sequestered and passed from one step to the next until repair is complete. This stepwise process is termed substrate channeling. A working model evaluated here is that a complex of BER factors may facilitate the BER process. FLAG-tagged DNA polymerase (pol) β was expressed in mouse fibroblasts carrying a deletion in the endogenous pol β gene, and the cell extract was subjected to an 'affinity-capture' procedure using anti-FLAG antibody. The pol β affinity-capture fraction (ACF) was found to contain several BER factors including polymerase-1, X-ray cross-complementing factor1-DNA ligase III and enzymes involved in processing 3'-blocked ends of BER intermediates, e.g. polynucleotide kinase and tyrosyl-DNA phosphodiesterase 1. In contrast, DNA glycosylases, apurinic/aprymidinic endonuclease 1 and flap endonuclease 1 and several other factors involved in BER were not present. Some of the BER factors in the pol β ACF were in a multi-protein complex as observed by sucrose gradient centrifugation. The pol β ACF was capable of substrate channeling for steps in vitro BER and was proficient in in vitro repair of substrates mimicking a 3'-blocked topoisomerase I covalent intermediate or an oxidative stress-induced 3'-blocked intermediate.

MeSH Terms
Animals Cell Extracts DNA/metabolism DNA Contamination DNA Polymerase beta/metabolism DNA Repair DNA Repair Enzymes/isolation & purification,metabolism Fibroblasts/metabolism Mice Poly (ADP-Ribose) Polymerase-1 Poly(ADP-ribose) Polymerases/isolation & purification
Chemicals
Cell Extracts DNA Parp1 protein, mouse Poly (ADP-Ribose) Polymerase-1 Poly(ADP-ribose) Polymerases DNA Polymerase beta DNA Repair Enzymes
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Prasad Rajendra
Laboratory of Structural Biology, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA.
Williams Jason G
Hou Esther W
Wilson Samuel H
References (82)
82 references, click to expand
  1. Direct interaction between XRCC1 and UNG2 facilitates rapid repair of uracil in DNA by XRCC1 complexes.
    DNA Repair (Amst). 2010 Jul 1;9(7):785-95 PMID: 20466601
  2. DNA polymerases beta and lambda bypass thymine glycol in gapped DNA structures.
    Biochemistry. 2010 Jun 8;49(22):4695-704 PMID: 20423048
  3. Cellular localisation of the ataxia-telangiectasia (ATM) gene product and discrimination between mutated and normal forms.
    Oncogene. 1997 Apr 24;14(16):1911-21 PMID: 9150358
  4. Mutation of TDP1, encoding a topoisomerase I-dependent DNA damage repair enzyme, in spinocerebellar ataxia with axonal neuropathy.
    Nat Genet. 2002 Oct;32(2):267-72 PMID: 12244316
  5. FEN1 stimulation of DNA polymerase beta mediates an excision step in mammalian long patch base excision repair.
    J Biol Chem. 2000 Feb 11;275(6):4460-6 PMID: 10660619
  6. Second pathway for completion of human DNA base excision-repair: reconstitution with purified proteins and requirement for DNase IV (FEN1).
    EMBO J. 1997 Jun 2;16(11):3341-8 PMID: 9214649
  7. The Arg280His polymorphism in X-ray repair cross-complementing gene 1 impairs DNA repair ability.
    Mutat Res. 2005 Apr 4;582(1-2):135-45 PMID: 15781218
  8. Chromatin 3'-phosphatase/5'-OH kinase cannot transfer phosphate from 3' to 5' across a strand nick in DNA.
    Nucleic Acids Res. 1986 Oct 24;14(20):8103-10 PMID: 3022244
  9. AP endonuclease-independent DNA base excision repair in human cells.
    Mol Cell. 2004 Jul 23;15(2):209-20 PMID: 15260972
  10. Interaction of human apurinic endonuclease and DNA polymerase beta in the base excision repair pathway.
    Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7166-9 PMID: 9207062
  11. Mammalian DNA ligase II is highly homologous with vaccinia DNA ligase. Identification of the DNA ligase II active site for enzyme-adenylate formation.
    J Biol Chem. 1994 Dec 16;269(50):31923-8 PMID: 7989368
  12. Subunits of human replication protein A are crosslinked by photoreactive primers synthesized by DNA polymerases.
    Nucleic Acids Res. 1998 Jan 15;26(2):602-7 PMID: 9421522
  13. Different DNA polymerases are involved in the short- and long-patch base excision repair in mammalian cells.
    Biochemistry. 1998 Mar 17;37(11):3575-80 PMID: 9530283
  14. The tandem affinity purification (TAP) method: a general procedure of protein complex purification.
    Methods. 2001 Jul;24(3):218-29 PMID: 11403571
  15. Substrate channeling in mammalian base excision repair pathways: passing the baton.
    J Biol Chem. 2010 Dec 24;285(52):40479-88 PMID: 20952393
  16. Properties of a recombinant human uracil-DNA glycosylase from the UNG gene and evidence that UNG encodes the major uracil-DNA glycosylase.
    Biochemistry. 1995 Jan 10;34(1):128-38 PMID: 7819187
  17. Interaction of poly(ADP-ribose) polymerase 1 with apurinic/apyrimidinic sites within clustered DNA damage.
    Biochemistry (Mosc). 2011 Jan;76(1):147-56 PMID: 21568846
  18. Human DNA polymerase beta deoxyribose phosphate lyase. Substrate specificity and catalytic mechanism.
    J Biol Chem. 1998 Jun 12;273(24):15263-70 PMID: 9614142
  19. Coordination of steps in single-nucleotide base excision repair mediated by apurinic/apyrimidinic endonuclease 1 and DNA polymerase beta.
    J Biol Chem. 2007 May 4;282(18):13532-41 PMID: 17355977
  20. Quality control by DNA repair.
    Science. 1999 Dec 3;286(5446):1897-905 PMID: 10583946
  21. HMGB1 is a cofactor in mammalian base excision repair.
    Mol Cell. 2007 Sep 7;27(5):829-41 PMID: 17803946
  22. Tidying up loose ends: the role of polynucleotide kinase/phosphatase in DNA strand break repair.
    Trends Biochem Sci. 2011 May;36(5):262-71 PMID: 21353781
  23. The genesis of cerebellar interneurons and the prevention of neural DNA damage require XRCC1.
    Nat Neurosci. 2009 Aug;12(8):973-80 PMID: 19633665
  24. Accumulation of premutagenic DNA lesions in mice defective in removal of oxidative base damage.
    Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13300-5 PMID: 10557315
  25. Generation of single-nucleotide repair patches following excision of uracil residues from DNA.
    Mol Cell Biol. 1992 Apr;12(4):1605-12 PMID: 1549115
  26. Photoaffinity labeling of mouse fibroblast enzymes by a base excision repair intermediate. Evidence for the role of poly(ADP-ribose) polymerase-1 in DNA repair.
    J Biol Chem. 2001 Jul 6;276(27):25541-8 PMID: 11340072
  27. Protection against methylation-induced cytotoxicity by DNA polymerase beta-dependent long patch base excision repair.
    J Biol Chem. 2000 Jan 21;275(3):2211-8 PMID: 10636928
  28. Heat-shock proteins associated with base excision repair enzymes in HeLa cells.
    Radiat Res. 2000 Feb;153(2):186-95 PMID: 10629618
  29. Excision of deoxyribose phosphate residues by DNA polymerase beta during DNA repair.
    Science. 1995 Aug 4;269(5224):699-702 PMID: 7624801
  30. The lyase activity of the DNA repair protein beta-polymerase protects from DNA-damage-induced cytotoxicity.
    Nature. 2000 Jun 15;405(6788):807-10 PMID: 10866204
  31. Repair of oxidative damage to DNA: enzymology and biology.
    Annu Rev Biochem. 1994;63:915-48 PMID: 7979257
  32. Single-strand break repair and genetic disease.
    Nat Rev Genet. 2008 Aug;9(8):619-31 PMID: 18626472
  33. Mutations in PNKP cause microcephaly, seizures and defects in DNA repair.
    Nat Genet. 2010 Mar;42(3):245-9 PMID: 20118933
  34. Direct interaction between mammalian DNA polymerase beta and proliferating cell nuclear antigen.
    J Biol Chem. 2002 Aug 23;277(34):31115-23 PMID: 12063248
  35. Protein-protein interactions during mammalian DNA single-strand break repair.
    Biochem Soc Trans. 2003 Feb;31(Pt 1):247-51 PMID: 12546695
  36. Molecular cloning of the human gene, PNKP, encoding a polynucleotide kinase 3'-phosphatase and evidence for its role in repair of DNA strand breaks caused by oxidative damage.
    J Biol Chem. 1999 Aug 20;274(34):24176-86 PMID: 10446192
  37. A role for p53 in base excision repair.
    EMBO J. 2001 Feb 15;20(4):914-23 PMID: 11179235
  38. Mutagenesis by apurinic/apyrimidinic sites.
    Annu Rev Genet. 1986;20:201-30 PMID: 3545059
  39. Aberrant DNA repair and DNA replication due to an inherited enzymatic defect in human DNA ligase I.
    Mol Cell Biol. 1994 Jan;14(1):310-7 PMID: 8264597
  40. Implication of p53 in base excision DNA repair: in vivo evidence.
    Oncogene. 2002 Jan 24;21(5):731-7 PMID: 11850801
  41. Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells.
    Cell Res. 2008 Jan;18(1):27-47 PMID: 18166975
  42. RPA physically interacts with the human DNA glycosylase NEIL1 to regulate excision of oxidative DNA base damage in primer-template structures.
    DNA Repair (Amst). 2010 Jun 4;9(6):643-52 PMID: 20338831
  43. NEIL2-initiated, APE-independent repair of oxidized bases in DNA: Evidence for a repair complex in human cells.
    DNA Repair (Amst). 2006 Dec 9;5(12):1439-48 PMID: 16982218
  44. Base excision repair.
    Adv Protein Chem. 2004;69:1-41 PMID: 15588838
  45. Yeast gene for a Tyr-DNA phosphodiesterase that repairs topoisomerase I complexes.
    Science. 1999 Oct 15;286(5439):552-5 PMID: 10521354
  46. Apurinic/apyrimidinic (AP) site recognition by the 5'-dRP/AP lyase in poly(ADP-ribose) polymerase-1 (PARP-1).
    Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22090-5 PMID: 21127267
  47. Involvement of poly(ADP-ribose) polymerase activity in regulating Chk1-dependent apoptotic cell death.
    DNA Repair (Amst). 2005 Sep 28;4(10):1111-20 PMID: 16002346
  48. Specific interaction of DNA polymerase beta and DNA ligase I in a multiprotein base excision repair complex from bovine testis.
    J Biol Chem. 1996 Jul 5;271(27):16000-7 PMID: 8663274
  49. XRCC1 coordinates disparate responses and multiprotein repair complexes depending on the nature and context of the DNA damage.
    Environ Mol Mutagen. 2011 Oct;52(8):623-35 PMID: 21786338
  50. A unified view of base excision repair: lesion-dependent protein complexes regulated by post-translational modification.
    DNA Repair (Amst). 2007 Jun 1;6(6):695-711 PMID: 17337257
  51. The human Rad9/Rad1/Hus1 damage sensor clamp interacts with DNA polymerase beta and increases its DNA substrate utilisation efficiency: implications for DNA repair.
    Nucleic Acids Res. 2004 Jun 22;32(11):3316-24 PMID: 15314187
  52. Tumor suppressor APC blocks DNA polymerase beta-dependent strand displacement synthesis during long patch but not short patch base excision repair and increases sensitivity to methylmethane sulfonate.
    J Biol Chem. 2005 Feb 25;280(8):6942-9 PMID: 15548520
  53. Substrate binding by human apurinic/apyrimidinic endonuclease indicates a Briggs-Haldane mechanism.
    J Biol Chem. 1997 Jan 10;272(2):1302-7 PMID: 8995436
  54. Evidence for an imino intermediate in the DNA polymerase beta deoxyribose phosphate excision reaction.
    J Biol Chem. 1996 Jul 26;271(30):17811-5 PMID: 8663612
  55. A requirement for PARP-1 for the assembly or stability of XRCC1 nuclear foci at sites of oxidative DNA damage.
    Nucleic Acids Res. 2003 Oct 1;31(19):5526-33 PMID: 14500814
  56. A new XRCC1-containing complex and its role in cellular survival of methyl methanesulfonate treatment.
    Mol Cell Biol. 2004 Oct;24(19):8356-65 PMID: 15367657
  57. Characterization of the interactome of the human MutL homologues MLH1, PMS1, and PMS2.
    J Biol Chem. 2007 Feb 2;282(5):2976-86 PMID: 17148452
  58. Association of XRCC1 and tyrosyl DNA phosphodiesterase (Tdp1) for the repair of topoisomerase I-mediated DNA lesions.
    DNA Repair (Amst). 2003 Oct 7;2(10):1087-100 PMID: 13679147
  59. Processing of nucleopeptides mimicking the topoisomerase I-DNA covalent complex by tyrosyl-DNA phosphodiesterase.
    Nucleic Acids Res. 2002 Mar 1;30(5):1198-204 PMID: 11861912
  60. XRCC1-DNA polymerase beta interaction is required for efficient base excision repair.
    Nucleic Acids Res. 2004 May 11;32(8):2550-5 PMID: 15141024
  61. Purification and domain-mapping of mammalian DNA polymerase beta.
    Methods Enzymol. 1995;262:98-107 PMID: 8594388
  62. DNA topoisomerases.
    Annu Rev Biochem. 1996;65:635-92 PMID: 8811192
  63. Topoisomerase I-mediated DNA damage.
    Adv Cancer Res. 2001;80:189-216 PMID: 11034544
  64. Base excision repair intermediates are mutagenic in mammalian cells.
    Nucleic Acids Res. 2005 Aug 02;33(14):4404-11 PMID: 16077026
  65. Involvement of poly(ADP-ribose) polymerase in base excision repair.
    Biochimie. 1999 Jan-Feb;81(1-2):69-75 PMID: 10214912
  66. Single-nucleotide base excision repair DNA polymerase activity in C. elegans in the absence of DNA polymerase β.
    Nucleic Acids Res. 2012 Jan;40(2):670-81 PMID: 21917855
  67. The alternative end-joining pathway for repair of DNA double-strand breaks requires PARP1 but is not dependent upon microhomologies.
    Nucleic Acids Res. 2010 Oct;38(18):6065-77 PMID: 20483915
  68. Requirement of mammalian DNA polymerase-beta in base-excision repair.
    Nature. 1996 Jan 11;379(6561):183-6 PMID: 8538772
  69. Long patch base excision repair proceeds via coordinated stimulation of the multienzyme DNA repair complex.
    J Biol Chem. 2009 May 29;284(22):15158-72 PMID: 19329425
  70. Characterization of the XRCC1-DNA ligase III complex in vitro and its absence from mutant hamster cells.
    Nucleic Acids Res. 1995 Dec 11;23(23):4836-43 PMID: 8532526
  71. DNA polymerase beta conducts the gap-filling step in uracil-initiated base excision repair in a bovine testis nuclear extract.
    J Biol Chem. 1995 Jan 13;270(2):949-57 PMID: 7822335
  72. DNA repair enzymes.
    Annu Rev Biochem. 1982;51:61-87 PMID: 6287922
  73. Two pathways for base excision repair in mammalian cells.
    J Biol Chem. 1996 Apr 19;271(16):9573-8 PMID: 8621631
  74. Human Mre11/human Rad50/Nbs1 and DNA ligase IIIalpha/XRCC1 protein complexes act together in an alternative nonhomologous end joining pathway.
    J Biol Chem. 2011 Sep 30;286(39):33845-53 PMID: 21816818
  75. XRCC1 stimulates human polynucleotide kinase activity at damaged DNA termini and accelerates DNA single-strand break repair.
    Cell. 2001 Jan 12;104(1):107-17 PMID: 11163244
  76. An interaction between the mammalian DNA repair protein XRCC1 and DNA ligase III.
    Mol Cell Biol. 1994 Jan;14(1):68-76 PMID: 8264637
  77. DNA topoisomerase poisons as antitumor drugs.
    Annu Rev Biochem. 1989;58:351-75 PMID: 2549853
  78. The checkpoint clamp, Rad9-Rad1-Hus1 complex, preferentially stimulates the activity of apurinic/apyrimidinic endonuclease 1 and DNA polymerase beta in long patch base excision repair.
    Nucleic Acids Res. 2007;35(8):2596-608 PMID: 17426133
  79. Impairment of proliferating cell nuclear antigen-dependent apurinic/apyrimidinic site repair on linear DNA.
    J Biol Chem. 1998 Jan 9;273(2):898-902 PMID: 9422747
  80. Uracil-excision DNA repair.
    Prog Nucleic Acid Res Mol Biol. 1994;48:315-70 PMID: 7938553
  81. TDP1-dependent DNA single-strand break repair and neurodegeneration.
    Mutagenesis. 2006 Jul;21(4):219-24 PMID: 16775218
  82. Effect of 8-oxoguanine and abasic site DNA lesions on in vitro elongation by human DNA polymerase in the presence of replication protein A and proliferating-cell nuclear antigen.
    Biochem J. 2010 Aug 1;429(3):573-82 PMID: 20528769
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gks898
Published
2012-12-00
Epub
2012-00-05
Pages
11571-82
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3526277
Subset
IM
Grants
NIEHS NIH HHS · Z01ES050158 · United States
NIEHS NIH HHS · Z01ES50159 · United States
Intramural NIH HHS · United States
External Links
PubMed source DOI: 10.1093/nar/gks898 PMC Full Text View journal details
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

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2