This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Kobayashi, T. Search for Related Content PubMed PubMed Citation Articles by Kobayashi, T.

 Previous Article  |  Next Article 

Molecular and Cellular Biology, December 2003, p. 9178-9188, Vol. 23, No. 24
0270-7306/03/$08.00+0     DOI: 10.1128/MCB.23.24.9178-9188.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.

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

National Institute for Basic Biology and The Graduate University for Advanced Studies, School of Life Science, Okazaki 444-8585, Japan

Received 23 July 2003/ Returned for modification 8 September 2003/ Accepted 17 September 2003

The replication fork barrier site (RFB) is an 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.

This article has been cited by other articles:

• Hyvarinen, A. K., Pohjoismaki, J. L. O., Reyes, A., Wanrooij, S., Yasukawa, T., Karhunen, P. J., Spelbrink, J. N., Holt, I. J., Jacobs, H. T. (2007). The mitochondrial transcription termination factor mTERF modulates replication pausing in human mitochondrial DNA. Nucleic Acids Res 35: 6458-6474 [Abstract] [Full Text]  
• Johzuka, K., Horiuchi, T. (2007). RNA polymerase I transcription obstructs condensin association with 35S rRNA coding regions and can cause contraction of long repeat in Saccharomyces cerevisiae. GENES CELLS 12: 759-771 [Abstract] [Full Text]  
• Mirkin, E. V., Mirkin, S. M. (2007). Replication Fork Stalling at Natural Impediments. Microbiol. Mol. Biol. Rev. 71: 13-35 [Abstract] [Full Text]  
• McTaggart, S. J., Dudycha, J. L., Omilian, A., Crease, T. J. (2007). Rates of Recombination in the Ribosomal DNA of Apomictically Propagated Daphnia obtusa Lines. Genetics 175: 311-320 [Abstract] [Full Text]  
• Blake, D., Luke, B., Kanellis, P., Jorgensen, P., Goh, T., Penfold, S., Breitkreutz, B.-J., Durocher, D., Peter, M., Tyers, M. (2006). The F-Box Protein Dia2 Overcomes Replication Impedance to Promote Genome Stability in Saccharomyces cerevisiae. Genetics 174: 1709-1727 [Abstract] [Full Text]  
• Calzari, L., Orlandi, I., Alberghina, L., Vai, M. (2006). The Histone Deubiquitinating Enzyme Ubp10 Is Involved in rDNA Locus Control in Saccharomyces cerevisiae by Affecting Sir2p Association. Genetics 174: 2249-2254 [Abstract] [Full Text]  
• Krings, G., Bastia, D. (2006). Molecular Architecture of a Eukaryotic DNA Replication Terminus-Terminator Protein Complex. Mol. Cell. Biol. 26: 8061-8074 [Abstract] [Full Text]  
• Grenetier, S., Bouchoux, C., Goguel, V. (2006). CTD kinase I is required for the integrity of the rDNA tandem array. Nucleic Acids Res 34: 4996-5006 [Abstract] [Full Text]  
• Huang, J., Brito, I. L., Villen, J., Gygi, S. P., Amon, A., Moazed, D. (2006). Inhibition of homologous recombination by a cohesin-associated clamp complex recruited to the rDNA recombination enhancer.. Genes Dev. 20: 2887-2901 [Abstract] [Full Text]  
• Oakes, M. L., Johzuka, K., Vu, L., Eliason, K., Nomura, M. (2006). Expression of rRNA Genes and Nucleolus Formation at Ectopic Chromosomal Sites in the Yeast Saccharomyces cerevisiae.. Mol. Cell. Biol. 26: 6223-6238 [Abstract] [Full Text]  
• Johzuka, K., Terasawa, M., Ogawa, H., Ogawa, T., Horiuchi, T. (2006). Condensin Loaded onto the Replication Fork Barrier Site in the rRNA Gene Repeats during S Phase in a FOB1-Dependent Fashion To Prevent Contraction of a Long Repetitive Array in Saccharomyces cerevisiae.. Mol. Cell. Biol. 26: 2226-2236 [Abstract] [Full Text]  
• Mohanty, B. K., Bairwa, N. K., Bastia, D. (2006). The Tof1p-Csm3p protein complex counteracts the Rrm3p helicase to control replication termination of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 103: 897-902 [Abstract] [Full Text]  
• Krings, G., Bastia, D. (2005). Sap1p Binds to Ter1 at the Ribosomal DNA of Schizosaccharomyces pombe and Causes Polar Replication Fork Arrest. J. Biol. Chem. 280: 39135-39142 [Abstract] [Full Text]  
• Di Felice, F., Cioci, F., Camilloni, G. (2005). FOB1 affects DNA topoisomerase I in vivo cleavages in the enhancer region of the Saccharomyces cerevisiae ribosomal DNA locus. Nucleic Acids Res 33: 6327-6337 [Abstract] [Full Text]  
• Mejia-Ramirez, E., Sanchez-Gorostiaga, A., Krimer, D. B., Schvartzman, J. B., Hernandez, P. (2005). The Mating Type Switch-Activating Protein Sap1 Is Required for Replication Fork Arrest at the rRNA Genes of Fission Yeast. Mol. Cell. Biol. 25: 8755-8761 [Abstract] [Full Text]  
• Ganley, A. R. D., Hayashi, K., Horiuchi, T., Kobayashi, T. (2005). Identifying gene-independent noncoding functional elements in the yeast ribosomal DNA by phylogenetic footprinting. Proc. Natl. Acad. Sci. USA 102: 11787-11792 [Abstract] [Full Text]  
• Wang, B.-D., Eyre, D., Basrai, M., Lichten, M., Strunnikov, A. (2005). Condensin Binding at Distinct and Specific Chromosomal Sites in the Saccharomyces cerevisiae Genome. Mol. Cell. Biol. 25: 7216-7225 [Abstract] [Full Text]  
• Calzada, A., Hodgson, B., Kanemaki, M., Bueno, A., Labib, K. (2005). Molecular anatomy and regulation of a stable replisome at a paused eukaryotic DNA replication fork. Genes Dev. 19: 1905-1919 [Abstract] [Full Text]  
• Michel, A. H., Kornmann, B., Dubrana, K., Shore, D. (2005). Spontaneous rDNA copy number variation modulates Sir2 levels and epigenetic gene silencing. Genes Dev. 19: 1199-1210 [Abstract] [Full Text]  
• Duggin, I. G., Matthews, J. M., Dixon, N. E., Wake, R. G., Mackay, J. P. (2005). A Complex Mechanism Determines Polarity of DNA Replication Fork Arrest by the Replication Terminator Complex of Bacillus subtilis. J. Biol. Chem. 280: 13105-13113 [Abstract] [Full Text]  
• Krings, G., Bastia, D. (2004). swi1- and swi3-dependent and independent replication fork arrest at the ribosomal DNA of Schizosaccharomyces pombe. Proc. Natl. Acad. Sci. USA 101: 14085-14090 [Abstract] [Full Text]  
• Makovets, S., Herskowitz, I., Blackburn, E. H. (2004). Anatomy and Dynamics of DNA Replication Fork Movement in Yeast Telomeric Regions. Mol. Cell. Biol. 24: 4019-4031 [Abstract] [Full Text]  
• Serizawa, N., Horiuchi, T., Kobayashi, T. (2004). Transcription-mediated hyper-recombination in HOT1. GENES CELLS 9: 305-315 [Abstract] [Full Text]