The Replication Fork Barrier Site Forms a Unique Structure with Fob1p and Inhibits the Replication Fork

Molecular and Cellular Biology

Volumn 23, Issue 24, 2003, Pages 9178-9188

  Kobayashi, Takehiko ^a  

^a GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EXTRACHROMOSOMAL DNA; GENE PRODUCT; PROTEIN FOB1P; REPETITIVE DNA; RIBOSOME RNA; UNCLASSIFIED DRUG;

ARTICLE; ATOMIC FORCE MICROSCOPY; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; DNA FOOTPRINTING; DNA RECOMBINATION; DNA SEQUENCE; GENE STRUCTURE; IMMUNOPRECIPITATION; INHIBITION KINETICS; MOLECULAR MECHANICS; NONHUMAN; NUCLEOTIDE REPEAT; PRIORITY JOURNAL; PROTEIN BINDING; REPLICATION FORK BARRIER SITE; SACCHAROMYCES CEREVISIAE; STRUCTURE ANALYSIS; ZINC FINGER MOTIF;

BASE SEQUENCE; BINDING SITES; DNA REPLICATION; DNA, FUNGAL; DNA, RIBOSOMAL; DNA-BINDING PROTEINS; GENES, FUNGAL; PROTEIN BINDING; RECOMBINANT FUSION PROTEINS; RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; ZINC FINGERS;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0344629438     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.23.24.9178-9188.2003     Document Type: Article

References (48)

1. Bedrosian, C. L., and D. Bastia. 1991. 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. USA 88:2618-2622.
2. Brewer, B. J., and W. L. Fangman. 1987. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51:463-471.
3. Brewer, B. J., and W. L. Fangman. 1988. A replication fork barrier at the 3′ end of yeast ribosomal RNA genes. Cell 55:637-643.
4. Brewer, B. J., D. Lockshon, and W. L. Fangman. 1992. The arrest of replication forks in the rDNA of yeast occurs independently of transcription. Cell 71:267-276.
5. Carrigan, C. M., J. A. Haarsma, M. T. Smith, and R. G. Wake. 1987. Sequence features of the replication terminus of the Bacillus subtilis chromosome. Nucleic Acids Res. 15:8501-8509.
6. Defossez, P. A., R. Prusty, M. Kaeberlein, S. J. Lin, P. Ferrigno, P. A. Silver, R. L. Keil, and L. Guarente. 1999. Elimination of replication fork block protein Fob1 extends the life span of yeast mother cells. Mol. Cell 3:447-455.
7. Dlakic, M. 2002. A model of the replication fork blocking protein Fob1p based on the catalytic core domain of retroviral integrases. Protein Sci. 11:1274-1277.
8. Elion, E. A., and J. R. Warner. 1984. The major promoter element of rRNA transcription in yeast lies 2kb upstream. Cell 39:663-673.
9. French, S. L., Y. N. Osheim, F. Cioci, M. Nomura, and A. L. Beyer. 2003. 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. 23:1558-1568.
10. Fritze, C. E., K. Verschueren, R. Strich, and R. E. Esposito. 1997. Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA. EMBO J. 16:6495-6509.
11. Gadal, O., S. Labarre, C. Boschiero, and P. Thuriaux. 2002. Hmo1, an HMG-box protein, belongs to the yeast ribosomal DNA transcription system. EMBO J. 21:5498-5507.
12. Gietz, R. D., and A. Sugino. 1988. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74:527-534.
13. Hidaka, M., T. Kobayashi, Y. Ishimi, M. Seki, T. Enomoto, M. Abdel-Monem, and T. Horiuchi. 1992. Termination complex in Escherichia coli inhibits SV40 DNA replication in vitro by impeding the action of T antigen helicase. J. Biol. Chem. 267:5361-5365.
14. Hidaka, M., T. Kobayashi, S. Takenaka, H. Takeya, and T. Horiuchi. 1989. Purification of a DNA replication terminus (ter) site-binding protein in Escherichia coli and identification of the structural gene. J. Biol. Chem. 264:21031-22107.
15. Hill, T. M., M. L. Tecklenburg, A. J. Pelletier, and P. L. Kuempel. 1989. tus, the trans-acting gene required for termination of DNA replication in Escherichia coli, encodes a DNA-binding protein. Proc. Natl. Acad. Sci. USA 86:1593-1597.
16. Horiuchi, T., and Y. Fujimura. 1995. 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. 177:783-791.
17. Horiuchi, T., Y. Fujimura, H. Nishitani, T. Kobayashi, and M. Hidaka. 1994. The DNA replication fork blocked at the Ter site may be an entrance for the RecBCD enzyme into duplex DNA. J. Bacteriol. 176:4656-4663.
18. Horiuchi, T., M. Hidaka, and T. Kobayashi. 1991. Termination of chromosome duplication in bacteria, p. 25-46. In A. Ishihama and H. Yoshikawa (ed.), Control of cell growth and division. Japan Scientific Society Press, Tokyo, Japan.
19. Huang, G. S., and R. L. Keil. 1995. Requirements for activity of the yeast mitotic recombination hotspot HOTI: RNA polymerase I and multiple cisacting sequences. Genetics 141:845-855.
20. Imai, S.-I., C. M. Armstrong, M. Kaeberlein, and L. Guarente. 2000. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403:795-800.
21. Ivessa, A. S., J. Q. Zhou, and V. A. Zakian. 2000. The Saccharomyces Pif1p DNA helicase and the highly related Rrm3p have opposite effects on replication fork progression in ribosomal DNA. Cell 100:479-489.
22. Johzuka, K., and T. Horiuchi. 2002. Replication fork block protein, Fob1, acts as an rDNA region specific recombinator in S. cerevisiae. Genes Cells 7:99-113.
23. Kaeberlein, M., M. McVey, and L. Guarente. 1999. The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev. 13:2570-2580.
24. Kaiser, C., S. Michaelis, and A. Mitchell. 1994. Methods in yeast genetics, p. 207-209. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
25. Kamimura, Y., Y.-S. Tak, A. Sugino, and H. Araki. 2001. Sld3, which interacts with Cdc45 (Sld4), functions for chromosomal DNA replication in Saccharomyces cerevisiae. EMBO J. 20:2097-2107.
26. Keil, R. L., and G. S. Roeder. 1984. Cis-acting recombination-stimulating activity in a fragment of the ribosomal DNA of S. cerevisiae. Cell 39:377-386.
27. Kobayashi, T., D. J. Heck, M. Nomura, and T. Horiuchi. 1998. 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. 12:3821-3830.
28. Kobayashi, T., M. Hidaka, and T. Horiuchi. 1989. Evidence of a ter specific binding protein essential for the termination reaction of DNA replication in Escherichia coli. EMBO J. 8:2435-2441.
29. Kobayashi, T., M. Hidaka, M. Nishizawa, and T. Horiuchi. 1992. Identification of a site required for DNA replication fork blocking activity in the rRNA gene cluster in Saccharomyces cerevisiae. Mol. Gen. Genet. 233:355-362.
30. Kobayaski, T., and T. Horiuchi. 1996. A yeast gene product, Fob1 protein, required for both replication fork blocking and recombinational hotspot activities. Genes Cells 1:465-474.
31. Kobayashi, T., M. Nomura, and T. Horiuchi. 2001. Identification of DNA cis elements essential for expansion of ribosomal DNA repeats in Saccharomyces cerevisiae. Mol. Cell. Biol. 21:136-147.
32. Lee, E. H., A. Kornberg, M. Hidaka, T. Kobayashi, and T. Horluchi. 1989. Escherichia coli replication termination protein impedes the action of helicases. Proc. Natl. Acad. Sci. USA 86:9104-9108.
33. Lei, M., Y. Kawasaki, and B. K. Tye. 1996. Physical interactions among Mcm proteins and effects of Mcm dosage on DNA replication in Saccharomyces cerevisiae Mol. Cell. Biol. 16:5081-5090.
34. Lewis, P. J., M. T. Smith, and R. G. Wake. 1989. A protein involved in termination of chromosome replication in Bacillus subtilis binds specifically to the terC site. J. Bacteriol. 171:3564-3567.
35. Linskens, M. H. K., and J. A. Huberman. 1988. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:4927-4935.
36. Merker, R. J., and H. L. Klein. 2002. hpr1Δ affects ribosomal DNA recombination and cell life span in Saccharomyces cerevisiae. Mol. Cell. Biol. 22:421-429.
37. Michel, B., S. D. Ehrlich, and M. Uzest. 1997. DNA double-strand breaks caused by replication arrest. EMBO J. 16:430-438.
38. Mitchell, D. A., T. K. Marshall, and R. J. Deschenes. 1993. Vectors for the inducible overexpression of glutathione S-transferase fusion proteins in yeast. Yeast 9:715-722.
39. Nogi, Y., R. Yano, and M. Nomura. 1991. Synthesis of large rRNAs by RNA polymerase II in mutants of Saccharomyces cerevisiae defective in RNA polymerase I. Proc. Natl. Acad. Sci. USA 88:3962-3966.
40. Rothstein, R., and S. Gangloff. 1999. The shuffling of a mortal coil. Nat. Genet. 22:4-6.
41. Rothstein, R., B. Michel, and S. Gangloff. 2000. Replication fork pausing and recombination or "gimme a break." Genes Dev. 14:1-10.
42. Sinclair, D. A., and L. Guarente. 1997. Extrachromosomal rDNA circles-a cause of aging in yeast. Cell 91:1033-1042.
43. Strathern, J. N., B. K. Shafer, and C. B. McGill. 1995. DNA synthesis errors associated with double-strand-break repair. Genetics 140:965-972.
44. Takeuchi, Y., T. Horiuchi, and T. Kobayashi. 2003. Transcription-dependent recombination and the role of fork collision in yeast rDNA. Genes Dev. 17:1497-1506.
45. Tanaka, T., D. Knapp, and K. Nasmyth. 1997. Loading of a Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs. Cell 90:649-660.
46. Wai, H., K. Johzuka, L. Vu, K. Eliason, T. Kobayashi, T. Horiuchi, and M. Nomura. 2001. 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. 21:5541-5553.
47. Ward, T. R., M. L. Hoang, R. Prusty, C. K. Lau, R. L. Keil, W. L. Fangman, and B. J. Brewer. 2000. Ribosomal DNA replication fork barrier and HOT1 recombination hot spot: shared sequences but independent activities. Mol. Cell. Biol. 20:4948-4957.
48. Wu, C. 1980. The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286:854-860.