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PMID: 14645529 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The replication fork barrier site forms a unique structure with Fob1p and inhibits the replication fork.

Molecular and cellular biology ·Vol. 23 ·No. 24 ·2003-12-00 ·Pages 9178-88

Kobayashi T

Abstract

The replication fork barrier site (RFB) is an approximately 100-bp DNA sequence located near the 3' end of the rRNA genes in the yeast Saccharomyces cerevisiae. The gene FOB1 is required for this RFB activity. FOB1 is also necessary for recombination in the ribosomal DNA (rDNA), including increase and decrease of rDNA repeat copy number, production of extrachromosomal rDNA circles, and possibly homogenization of the repeats. Despite the central role that Foblp plays in both replication fork blocking and rDNA recombination, the molecular mechanism by which Fob1p mediates these activities has not been determined. Here, I show by using chromatin immunoprecipitation, gel shift, footprinting, and atomic force microscopy assays that Fob1p directly binds to the RFB. Fob1p binds to two separated sequences in the RFB. A predicted zinc finger motif in Fob1p was shown to be essential for the RFB binding, replication fork blocking, and rDNA recombination activities. The RFB seems to wrap around Fob1p, and this wrapping structure may be important for function in the rDNA repeats.

MeSH Terms
Base Sequence Binding Sites DNA Replication DNA, Fungal/biosynthesis,genetics DNA, Ribosomal/genetics DNA-Binding Proteins/chemistry,genetics,metabolism Genes, Fungal Protein Binding Recombinant Fusion Proteins/chemistry,genetics,metabolism Recombination, Genetic Saccharomyces cerevisiae/genetics,metabolism Saccharomyces cerevisiae Proteins/chemistry,genetics,metabolism Zinc Fingers/genetics
Chemicals
DNA, Fungal DNA, Ribosomal DNA-Binding Proteins FOB1 protein, S cerevisiae Recombinant Fusion Proteins Saccharomyces cerevisiae Proteins
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Kobayashi Takehiko
National Institute for Basic Biology, 38 Nishigonaka, Myodaijicho, Okazaki 444-8585, Japan. koba@nibb.ac.jp
References (46)
46 references, click to expand
  1. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase.
    Nature. 2000 Feb 17;403(6771):795-800 PMID: 10693811
  2. Ribosomal DNA replication fork barrier and HOT1 recombination hot spot: shared sequences but independent activities.
    Mol Cell Biol. 2000 Jul;20(13):4948-57 PMID: 10848619
  3. Identification of DNA cis elements essential for expansion of ribosomal DNA repeats in Saccharomyces cerevisiae.
    Mol Cell Biol. 2001 Jan;21(1):136-47 PMID: 11113188
  4. Sld3, which interacts with Cdc45 (Sld4), functions for chromosomal DNA replication in Saccharomyces cerevisiae.
    EMBO J. 2001 Apr 17;20(8):2097-107 PMID: 11296242
  5. Yeast RNA polymerase I enhancer is dispensable for transcription of the chromosomal rRNA gene and cell growth, and its apparent transcription enhancement from ectopic promoters requires Fob1 protein.
    Mol Cell Biol. 2001 Aug;21(16):5541-53 PMID: 11463836
  6. hpr1Delta affects ribosomal DNA recombination and cell life span in Saccharomyces cerevisiae.
    Mol Cell Biol. 2002 Jan;22(2):421-9 PMID: 11756539
  7. Replication fork block protein, Fob1, acts as an rDNA region specific recombinator in S. cerevisiae.
    Genes Cells. 2002 Feb;7(2):99-113 PMID: 11895475
  8. A model of the replication fork blocking protein Fob1p based on the catalytic core domain of retroviral integrases.
    Protein Sci. 2002 May;11(5):1274-7 PMID: 11967383
  9. Hmo1, an HMG-box protein, belongs to the yeast ribosomal DNA transcription system.
    EMBO J. 2002 Oct 15;21(20):5498-507 PMID: 12374750
  10. In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes.
    Mol Cell Biol. 2003 Mar;23(5):1558-68 PMID: 12588976
  11. Transcription-dependent recombination and the role of fork collision in yeast rDNA.
    Genes Dev. 2003 Jun 15;17(12):1497-506 PMID: 12783853
  12. The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I.
    Nature. 1980 Aug 28;286(5776):854-60 PMID: 6774262
  13. Cis-acting, recombination-stimulating activity in a fragment of the ribosomal DNA of S. cerevisiae.
    Cell. 1984 Dec;39(2 Pt 1):377-86 PMID: 6094015
  14. The major promoter element of rRNA transcription in yeast lies 2 kb upstream.
    Cell. 1984 Dec;39(3 Pt 2):663-73 PMID: 6096018
  15. Replication fork pausing and recombination or "gimme a break".
    Genes Dev. 2000 Jan 1;14(1):1-10 PMID: 10640269
  16. The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA.
    Cell. 2000 Feb 18;100(4):479-89 PMID: 10693764
  17. The localization of replication origins on ARS plasmids in S. cerevisiae.
    Cell. 1987 Nov 6;51(3):463-71 PMID: 2822257
  18. Sequence features of the replication terminus of the Bacillus subtilis chromosome.
    Nucleic Acids Res. 1987 Oct 26;15(20):8501-9 PMID: 3118336
  19. A replication fork barrier at the 3' end of yeast ribosomal RNA genes.
    Cell. 1988 Nov 18;55(4):637-43 PMID: 3052854
  20. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae.
    Mol Cell Biol. 1988 Nov;8(11):4927-35 PMID: 3062373
  21. tus, the trans-acting gene required for termination of DNA replication in Escherichia coli, encodes a DNA-binding protein.
    Proc Natl Acad Sci U S A. 1989 Mar;86(5):1593-7 PMID: 2646639
  22. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites.
    Gene. 1988 Dec 30;74(2):527-34 PMID: 3073106
  23. A protein involved in termination of chromosome replication in Bacillus subtilis binds specifically to the terC site.
    J Bacteriol. 1989 Jun;171(6):3564-7 PMID: 2498294
  24. Evidence of a ter specific binding protein essential for the termination reaction of DNA replication in Escherichia coli.
    EMBO J. 1989 Aug;8(8):2435-41 PMID: 2551684
  25. Purification of a DNA replication terminus (ter) site-binding protein in Escherichia coli and identification of the structural gene.
    J Biol Chem. 1989 Dec 15;264(35):21031-7 PMID: 2687269
  26. Escherichia coli replication termination protein impedes the action of helicases.
    Proc Natl Acad Sci U S A. 1989 Dec;86(23):9104-8 PMID: 2556700
  27. Escherichia coli replication terminator protein impedes simian virus 40 (SV40) DNA replication fork movement and SV40 large tumor antigen helicase activity in vitro at a prokaryotic terminus sequence.
    Proc Natl Acad Sci U S A. 1991 Apr 1;88(7):2618-22 PMID: 1849268
  28. Synthesis of large rRNAs by RNA polymerase II in mutants of Saccharomyces cerevisiae defective in RNA polymerase I.
    Proc Natl Acad Sci U S A. 1991 May 1;88(9):3962-6 PMID: 2023944
  29. Termination complex in Escherichia coli inhibits SV40 DNA replication in vitro by impeding the action of T antigen helicase.
    J Biol Chem. 1992 Mar 15;267(8):5361-5 PMID: 1312088
  30. Identification of a site required for DNA replication fork blocking activity in the rRNA gene cluster in Saccharomyces cerevisiae.
    Mol Gen Genet. 1992 Jun;233(3):355-62 PMID: 1620093
  31. The arrest of replication forks in the rDNA of yeast occurs independently of transcription.
    Cell. 1992 Oct 16;71(2):267-76 PMID: 1423594
  32. Vectors for the inducible overexpression of glutathione S-transferase fusion proteins in yeast.
    Yeast. 1993 Jul;9(7):715-22 PMID: 8368005
  33. The DNA replication fork blocked at the Ter site may be an entrance for the RecBCD enzyme into duplex DNA.
    J Bacteriol. 1994 Aug;176(15):4656-63 PMID: 8045897
  34. Recombinational rescue of the stalled DNA replication fork: a model based on analysis of an Escherichia coli strain with a chromosome region difficult to replicate.
    J Bacteriol. 1995 Feb;177(3):783-91 PMID: 7836313
  35. DNA synthesis errors associated with double-strand-break repair.
    Genetics. 1995 Jul;140(3):965-72 PMID: 7672595
  36. Requirements for activity of the yeast mitotic recombination hotspot HOT1: RNA polymerase I and multiple cis-acting sequences.
    Genetics. 1995 Nov;141(3):845-55 PMID: 8582631
  37. Physical interactions among Mcm proteins and effects of Mcm dosage on DNA replication in Saccharomyces cerevisiae.
    Mol Cell Biol. 1996 Sep;16(9):5081-90 PMID: 8756666
  38. DNA double-strand breaks caused by replication arrest.
    EMBO J. 1997 Jan 15;16(2):430-8 PMID: 9029161
  39. A yeast gene product, Fob1 protein, required for both replication fork blocking and recombinational hotspot activities.
    Genes Cells. 1996 May;1(5):465-74 PMID: 9078378
  40. Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs.
    Cell. 1997 Aug 22;90(4):649-60 PMID: 9288745
  41. Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA.
    EMBO J. 1997 Nov 3;16(21):6495-509 PMID: 9351831
  42. Extrachromosomal rDNA circles--a cause of aging in yeast.
    Cell. 1997 Dec 26;91(7):1033-42 PMID: 9428525
  43. Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I.
    Genes Dev. 1998 Dec 15;12(24):3821-30 PMID: 9869636
  44. Elimination of replication block protein Fob1 extends the life span of yeast mother cells.
    Mol Cell. 1999 Apr;3(4):447-55 PMID: 10230397
  45. The shuffling of a mortal coil.
    Nat Genet. 1999 May;22(1):4-6 PMID: 10319847
  46. The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms.
    Genes Dev. 1999 Oct 1;13(19):2570-80 PMID: 10521401
Article Info
Journal
Molecular and cellular biology
Abbr.
Mol Cell Biol
ISSN
0270-7306
DOI
10.1128/MCB.23.24.9178-9188.2003
Email
koba@nibb.ac.jp
Published
2003-12-00
Pages
9178-88
Language
English
Region
United States
NLM ID
8109087
PMCID
PMC309713
Subset
IM
External Links
PubMed source DOI: 10.1128/MCB.23.24.9178-9188.2003 PMC Full Text View journal details
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