Home LiteratureArticle Details
PMID: 11713310 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic poleta.

Nucleic acids research ·Vol. 29 ·No. 22 ·2001-11-15 ·Pages 4607-16

Boudsocq F, Iwai S, Hanaoka F, Woodgate R

Abstract

Phylogenetic analysis of Y-family DNA polymerases suggests that it can be subdivided into several discrete branches consisting of UmuC/DinB/Rev1/Rad30/Rad30A and Rad30B. The most diverse is the DinB family that is found in all three kingdoms of life. Searches of the complete genome of the crenarchaeon Sulfolobus solfataricus P2 reveal that it possesses a DinB homolog that has been termed DNA polymerase IV (Dpo4). We have overproduced and purified native Dpo4 protein and report here its enzymatic characterization. Dpo4 is thermostable, but can also synthesize DNA at 37 degrees C. Under these conditions, the enzyme exhibits misinsertion fidelities in the range of 8 x 10(-3) to 3 x 10(-4). Dpo4 is distributive but at high enzyme to template ratios can synthesize long stretches of DNA and can substitute for Taq polymerase in PCR. On damaged DNA templates, Dpo4 can facilitate translesion replication of an abasic site, a cis-syn thymine-thymine dimer, as well as acetyl aminofluorene adducted- and cisplatinated-guanine residues. Thus, although phylogenetically related to DinB polymerases, our studies suggest that the archaeal Dpo4 enzyme exhibits lesion-bypass properties that are, in fact, more akin to those of eukaryotic poleta.

MeSH Terms
Archaeal Proteins/genetics,metabolism Bacterial Proteins/genetics,metabolism DNA Polymerase beta/genetics,isolation & purification,metabolism DNA Repair DNA-Directed DNA Polymerase/genetics,metabolism Electrophoresis, Polyacrylamide Gel Enzyme Stability Escherichia coli Proteins Eukaryotic Cells/enzymology Genes, Archaeal/genetics Genome, Archaeal Nucleotides/metabolism Polymerase Chain Reaction Sulfolobus Temperature
Chemicals
Archaeal Proteins Bacterial Proteins DinB protein, E coli Escherichia coli Proteins Nucleotides DNA Polymerase beta DNA-Directed DNA Polymerase Rad30 protein
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Boudsocq F
Section on DNA Replication, Repair and Mutagenesis, National Institute of Child Health and Human Development, National Institutes of Health, MD 20892-2725, USA.
Iwai S
Hanaoka F
Woodgate R
References (51)
51 references, click to expand
  1. Misinsertion and bypass of thymine-thymine dimers by human DNA polymerase iota.
    EMBO J. 2000 Oct 2;19(19):5259-66 PMID: 11013228
  2. Human DNA polymerase kappa synthesizes DNA with extraordinarily low fidelity.
    Nucleic Acids Res. 2000 Nov 1;28(21):4147-56 PMID: 11058111
  3. Fidelity and processivity of DNA synthesis by DNA polymerase kappa, the product of the human DINB1 gene.
    J Biol Chem. 2000 Dec 15;275(50):39678-84 PMID: 11006276
  4. Purification and characterization of pol kappa, a DNA polymerase encoded by the human DINB1 gene.
    J Biol Chem. 2001 Jan 5;276(1):92-8 PMID: 11024016
  5. Phylogenetic analysis of archaeal PCNA homologues.
    Extremophiles. 2000 Dec;4(6):357-64 PMID: 11139078
  6. The expanding polymerase universe.
    Nat Rev Mol Cell Biol. 2000 Nov;1(2):101-9 PMID: 11253362
  7. The beta clamp targets DNA polymerase IV to DNA and strongly increases its processivity.
    EMBO Rep. 2000 Dec;1(6):484-8 PMID: 11263491
  8. The complete genome of the crenarchaeon Sulfolobus solfataricus P2.
    Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7835-40 PMID: 11427726
  9. The Y-family of DNA polymerases.
    Mol Cell. 2001 Jul;8(1):7-8 PMID: 11515498
  10. Detection of conserved segments in proteins: iterative scanning of sequence databases with alignment blocks.
    Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):12091-5 PMID: 7991589
  11. Gel fidelity assay measuring nucleotide misinsertion, exonucleolytic proofreading, and lesion bypass efficiencies.
    Methods Enzymol. 1995;262:232-56 PMID: 8594351
  12. Purification of a soluble UmuD'C complex from Escherichia coli. Cooperative binding of UmuD'C to single-stranded DNA.
    J Biol Chem. 1996 May 3;271(18):10767-74 PMID: 8631887
  13. Identification of a DinB/UmuC homolog in the archeon Sulfolobus solfataricus.
    Mutat Res. 1996 Oct 25;357(1-2):245-53 PMID: 8876701
  14. Intermolecular cleavage by UmuD-like mutagenesis proteins.
    Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1478-83 PMID: 9465040
  15. The mutagenesis protein MucB interacts with single strand DNA binding protein and induces a major conformational change in its complex with single-stranded DNA.
    J Biol Chem. 1998 Mar 6;273(10):5520-7 PMID: 9488676
  16. Biochemical basis of SOS-induced mutagenesis in Escherichia coli: reconstitution of in vitro lesion bypass dependent on the UmuD'2C mutagenic complex and RecA protein.
    Proc Natl Acad Sci U S A. 1998 Aug 18;95(17):9755-60 PMID: 9707548
  17. Efficient bypass of a thymine-thymine dimer by yeast DNA polymerase, Poleta.
    Science. 1999 Feb 12;283(5404):1001-4 PMID: 9974380
  18. Requirement of DNA polymerase activity of yeast Rad30 protein for its biological function.
    J Biol Chem. 1999 Jun 4;274(23):15975-7 PMID: 10347143
  19. Xeroderma pigmentosum variant (XP-V) correcting protein from HeLa cells has a thymine dimer bypass DNA polymerase activity.
    EMBO J. 1999 Jun 15;18(12):3491-501 PMID: 10369688
  20. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase eta.
    Nature. 1999 Jun 17;399(6737):700-4 PMID: 10385124
  21. hRAD30 mutations in the variant form of xeroderma pigmentosum.
    Science. 1999 Jul 9;285(5425):263-5 PMID: 10398605
  22. Archaeal DNA replication: identifying the pieces to solve a puzzle.
    Genetics. 1999 Aug;152(4):1249-67 PMID: 10430556
  23. Novel human and mouse homologs of Saccharomyces cerevisiae DNA polymerase eta.
    Genomics. 1999 Aug 15;60(1):20-30 PMID: 10458907
  24. A plethora of lesion-replicating DNA polymerases.
    Genes Dev. 1999 Sep 1;13(17):2191-5 PMID: 10485842
  25. The dinB gene encodes a novel E. coli DNA polymerase, DNA pol IV, involved in mutagenesis.
    Mol Cell. 1999 Aug;4(2):281-6 PMID: 10488344
  26. Human and mouse homologs of Escherichia coli DinB (DNA polymerase IV), members of the UmuC/DinB superfamily.
    Proc Natl Acad Sci U S A. 1999 Oct 12;96(21):11922-7 PMID: 10518552
  27. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication.
    Cell. 2001 Oct 5;107(1):91-102 PMID: 11595188
  28. DNA polymerase insertion fidelity. Gel assay for site-specific kinetics.
    J Biol Chem. 1987 Oct 25;262(30):14689-96 PMID: 3667598
  29. Use of T7 RNA polymerase to direct expression of cloned genes.
    Methods Enzymol. 1990;185:60-89 PMID: 2199796
  30. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  31. The 'A rule' of mutagen specificity: a consequence of DNA polymerase bypass of non-instructional lesions?
    Bioessays. 1991 Feb;13(2):79-84 PMID: 2029269
  32. Compilation and alignment of DNA polymerase sequences.
    Nucleic Acids Res. 1991 Aug 11;19(15):4045-57 PMID: 1870963
  33. Compilation, alignment, and phylogenetic relationships of DNA polymerases.
    Nucleic Acids Res. 1993 Feb 25;21(4):787-802 PMID: 8451181
  34. Bridging the gap: a family of novel DNA polymerases that replicate faulty DNA.
    Proc Natl Acad Sci U S A. 1999 Oct 26;96(22):12224-6 PMID: 10535901
  35. The mutagenesis protein UmuC is a DNA polymerase activated by UmuD', RecA, and SSB and is specialized for translesion replication.
    J Biol Chem. 1999 Nov 5;274(45):31763-6 PMID: 10542196
  36. Mutation enhancement by DINB1, a mammalian homologue of the Escherichia coli mutagenesis protein dinB.
    Genes Cells. 1999 Nov;4(11):607-18 PMID: 10620008
  37. Highly mutagenic replication by DNA polymerase V (UmuC) provides a mechanistic basis for SOS untargeted mutagenesis.
    Proc Natl Acad Sci U S A. 2000 Jan 18;97(2):565-70 PMID: 10639119
  38. Eukaryotic DNA polymerases, a growing family.
    Trends Biochem Sci. 2000 Mar;25(3):143-7 PMID: 10694886
  39. Fidelity of human DNA polymerase eta.
    J Biol Chem. 2000 Mar 17;275(11):7447-50 PMID: 10713043
  40. The human DINB1 gene encodes the DNA polymerase Poltheta.
    Proc Natl Acad Sci U S A. 2000 Apr 11;97(8):3838-43 PMID: 10760255
  41. Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis.
    Nature. 2000 Apr 27;404(6781):1014-8 PMID: 10801133
  42. The many faces of DNA polymerases: strategies for mutagenesis and for mutational avoidance.
    Proc Natl Acad Sci U S A. 2000 May 23;97(11):5681-3 PMID: 10811923
  43. Mechanisms of accurate translesion synthesis by human DNA polymerase eta.
    EMBO J. 2000 Jun 15;19(12):3100-9 PMID: 10856253
  44. Error-prone bypass of certain DNA lesions by the human DNA polymerase kappa.
    Genes Dev. 2000 Jul 1;14(13):1589-94 PMID: 10887153
  45. poliota, a remarkably error-prone human DNA polymerase.
    Genes Dev. 2000 Jul 1;14(13):1642-50 PMID: 10887158
  46. Eukaryotic polymerases iota and zeta act sequentially to bypass DNA lesions.
    Nature. 2000 Aug 31;406(6799):1015-9 PMID: 10984059
  47. Preferential incorporation of G opposite template T by the low-fidelity human DNA polymerase iota.
    Mol Cell Biol. 2000 Oct;20(19):7099-108 PMID: 10982826
  48. Plasmid-encoded MucB protein is a DNA polymerase (pol RI) specialized for lesion bypass in the presence of MucA', RecA, and SSB.
    Proc Natl Acad Sci U S A. 2000 Oct 10;97(21):11227-31 PMID: 11016960
  49. Genome sequence of Halobacterium species NRC-1.
    Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12176-81 PMID: 11016950
  50. Error-free and error-prone lesion bypass by human DNA polymerase kappa in vitro.
    Nucleic Acids Res. 2000 Nov 1;28(21):4138-46 PMID: 11058110
  51. All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis.
    EMBO J. 2000 Nov 15;19(22):6259-65 PMID: 11080171
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/29.22.4607
Published
2001-11-15
Pages
4607-16
Language
English
Region
England
NLM ID
0411011
PMCID
PMC92520
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/29.22.4607 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