Plant Molecular Biology

, Volume 53, Issue 1–2, pp 15–25 | Cite as

Characterization of all the subunits of replication factor C from a higher plant, rice (Oryza sativa L.), and their relation to development

  • Tomoyuki Furukawa
  • Toyotaka Ishibashi
  • Seisuke Kimura
  • Hiroshi Tanaka
  • Junji Hashimoto
  • Kengo Sakaguchi


Replication factor C (RFC), which is composed of five subunits, is an important factor involved in DNA replication and repair mechanisms. Following previous studies on the RFC3 homologue from rice (Oryza sativa L. cv. Nipponbare) (OsRFC3), we succeeded in isolating and characterizing one large and three small subunits of RFC homologues from the same rice species and termed them OsRFC1, OsRFC2, OsRFC4 and OsRFC5. The plant was found to have all RFC subunits known in yeasts, human and other eukaryotes. The open reading frames of OsRFCs encoded a predicted product of 1021 amino acid residues with a molecular mass of 110.8 kDa for OsRFC1, 339 amino acid residues with a molecular mass of 37.4 kDa for OsRFC2, 335 amino acid residues with a molecular mass of 36.8 kDa for OsRFC4, and 354 amino acid residues with a molecular mass of 40.5 kDa for OsRFC5. All the OsRFC subunits have highly conserved amino acid motifs among RFC proteins, RFC box, and an unrooted phylogenetic tree shows each OsRFC subunit belongs to each RFC subunit group. These subunits showed differences in their expression patterns among tissues. The transcripts of OsRFCs were expressed strongly in the proliferating tissue, the shoot apical meristem (SAM), and very weakly in the mature leaves which have no proliferating tissues. However, in young leaves and flag leaves, tissue-specific expression of OsRFC3 and OsRFC4 was shown. On the other hand, cell cycle arrest by cell cycle inhibitors resulted in significant differences in OsRFC expression patterns. These results suggest the functional differences of each OsRFC subunit in tissues and the plant cell cycle. The roles of these molecules in plant DNA replication and DNA repair are discussed.

replication factor C (RFC) RFC expression in development RFC subunits rice (Oryza sativa L.) 


  1. Baba, A., Hasegawa, S. and Syono, K. 1986. Cultivation of rice protoplasts and their transformation mediated by Agrobacterium spheroplasts. Plant Cell Physiol. 27: 463–471.Google Scholar
  2. Batschauer, A. 1993. A plant gene for photolyase: an enzyme catalyzing the repair of UV-light-induced DNA damage. Plant J. 4: 705–709.Google Scholar
  3. Britt, A.D., Chen, J.J., Wykoff, D. and Mitchell, D. 1993. A UV-sensitive mutant of Arabidopsis defective in the repair of pyrimidine-pyrimidinone (6-4) dimers. Science 261: 1571–1574.Google Scholar
  4. Bunz, F., Kobayashi, R. and Stillman, B. 1993. cDNAs encoding the large subunit of human replication factor C. Proc. Natl. Acad. Sci. USA 90: 11014–11018.Google Scholar
  5. Chen, M., Pan, Z.Q. and Hurwitz, J. 1992. Studies of the cloned 37 kDa subunit of activator 1 (replication factor C) of HeLa cells. Proc. Natl. Acad. Sci. USA 89: 5211–5215.Google Scholar
  6. Culligan, K.M. and Hays, J.B. 1997. DNA mismatch repair in plants. Plant Physiol. 115: 833–839.Google Scholar
  7. Cullmann, G., Fien, K., Kobayashi, R. and Stillman, B. 1995. Characterization of the five replication factor C genes of Saccharomyces cerevisiae. Mol. Cell. Biol. 15: 4661–4671.Google Scholar
  8. Fien, K. and Stillman, B. 1992. Identification of replication factor C from Saccharomyces cerevisiae: a component of the leading strand DNA replication complex. Mol. Cell. Biol. 12: 155–163.Google Scholar
  9. Furukawa, T., Kimura, S., Ishibashi, T., Hashimoto, J. and Sakaguchi, K. 2001. A plant homologue of 36 kDa subunit of replication factor C: molecular cloning and characterization. Plant Sci. 161: 99–106.Google Scholar
  10. Gary, S.L. and Burgers, P.M.J. 1995. Identification of the fifth subunit of Saccharomyces cerevisiae replication factor C. Nucl. Acids Res. 23: 4986–4991.Google Scholar
  11. Gray, F.C. and MacNeill, S.A. 2000. The Schizosaccharomyces pombe rfc 3+ genes encodes a homologue of the human hRFC36 and Saccharomyces cerevisiae RFC3 subunits of replication factor C. Curr. Genet. 37: 159–167.Google Scholar
  12. Green, C.M., Erdjument-Bromage, H., Tempst, P. and Lowndes, N.F. 2000. A novel Rad24 checkpoint protein complex closely related to replication factor C. Curr Biol. 10: 39–42.Google Scholar
  13. Griffiths, D.J., Barbet, N.C., McCready, S., Lehmann, A.R. and Carr, A.M. 1995. Fission yeast rad17: a homologue of budding yeast RAD24 that shares regions of sequence similarity with DNA polymerase accessory proteins. EMBO J. 14: 5812–5822.Google Scholar
  14. Harushima, Y., Yano, M., Shomura, A., Sato, M., Shimano, T., Kuboki, Y., Yamamoto, T., Lin, S.Y., Antonio, B.A., Parco, A., Kajiya, H., Huang, N., Yamamoto, K., Nagamura, Y., Kurata, N., Khush, G.S. and Sasaki, T. 1998. A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148: 479–494.Google Scholar
  15. Ishibashi, T., Kimura, S., Furukawa, T., Hatanaka, M., Hashimoto, J. and Sakaguchi, K. 2001. Two types of replication protein A 70 kDa subunit in rice, Oryza sativa: molecular cloning, characterization, and cellular and tissue distrubution. Gene 272: 335–343.Google Scholar
  16. Kim, H.S. and Brill, S.J. 2001. Rfc4 interacts with Rpa1 and is required for both DNA replication and DNA damage chekpoints in Saccharomyces cerevisiae. Mol. Cell. Biol. 21: 3725–3737.Google Scholar
  17. Kimura, S., Ueda, T., Hatanaka, M., Takenouchi, M., Hashimoto, J. and Sakaguchi, K. 2000. Plant homologue of flap endonuclease-1: molecular cloning, characterization, and evidence of expression in meristematic tissues. Plant Mol. Biol. 42: 415–427.Google Scholar
  18. Kimura, S., Suzuki, T., Yanagawa, Y., Yamamoto, T., Nakagawa, H., Tanaka, I., Hashimoto, J. and Sakaguchi, K. 2001. Characterization of plant proliferating cell nuclear antigen (PCNA) and flap endonuclease-1 (FEN-1), and their distribution in mitotic and meiotic cell cycles. Plant J. 28: 643–653.Google Scholar
  19. Landry, L.G., Stapleton, A.E., Jim, J., Hoffman, P., Hays, J.B., Walbot, V. and Last, R.L. 1997. An Arabidopsis photolyase mutant is hypersensitive to ultraviolet-B radiation. Proc. Natl. Acad. Sci. USA 94: 328–332.Google Scholar
  20. Li, X. and Burgers, P.M.J. 1994a. Molecular cloning and expression of the Saccharomyces cerevisiae RFC3 gene, an essential componentr of replication factor C. Proc. Natl. Acad. Sci. 91: 868–872.Google Scholar
  21. Li, X. and Burgers, P.M.J. 1994b. Cloning and characterization of the essential Saccharomyces cerevisiae RFC4 gene encoding the 37 kDa subunit of replication factor C. J. Biol. Chem. 269: 21880–21884.Google Scholar
  22. Luckow, B., Bunz, F., Stillman, B., Lichter, P. and Schutz, G. 1994. Cloning, expression, and chromosomal localization of the 140-kilodalton subunit of replication factor C from mice and human. Mol. Cell. Biol. 14: 1626–1634.Google Scholar
  23. Maga, G., Stucki, M., Spadari, S. and Hubscher, U. 2000. DNA polymerase switching: replication factor C displaces DNA polymerase prior to PCNA loading. J. Mol. Biol. 295: 795–801.Google Scholar
  24. Matsumoto, Y., Kim, K., Hurwitz, J., Gary, R., Levin, D.S., Tomkinson, A.E. and Park, M.S. 1999. Reconstitution of proliferating cell nuclear antigen-dependent repair of apurinic/apyrimidinic sites with purified human proteins. J. Biol. Chem. 274: 33703–33708.Google Scholar
  25. Mayer, M.L., Gygi, S.P., Aebersold, R. and Hieter, P. 2001.Identification of RFC (Ctf18p, Ctf8p, Dcc1p): an alternative RFC complex required for sister chromatid cohesion in S. cerevisiae. Mol. Cell 7: 959–979.Google Scholar
  26. Mossi, R. and Hubscher, U. 1998. Clamping down on clamps and clamp loaders. Eur. J. Biochem. 254: 209–216.Google Scholar
  27. Mossi, R., Keller, R.C., Ferrari, E. and Hubscher, U. 2000.DNA polymerase switching: replication factor C abrogates primer synthesis by DNA polymerase α at a critical length. J. Mol. Biol. 295: 803–814.Google Scholar
  28. Nadeau, J.A., Zhang, X.S., Li, J. and O'Neill, S.D. 1996. Ovule development: identification of stage-specific and tissue-specific cDNAs. Plant Cell. 8: 213–239.Google Scholar
  29. Naiki, T., Kondo, T., Nakada, D., Matsumoto, K. and Sugimoto, K. 2001. Chl12 (Ctf18) forms a novel replication factor C-related complex and functions redundantly with Rad24 in the DNA replication checkpoint pathway. Mol. Cell. Biol. 21: 5838–5845.Google Scholar
  30. Noskov, V., Maki, S., Kawasaki, Y., Leem, S.H., Ono, B., Araki, H., Pavlov, Y. and Sugino, A. 1994. The RFC2 gene encoding a subunit of replication factor C of Saccharomyces cerevisiae. Nucl. Acids Res. 22: 1527–1535.Google Scholar
  31. Pascucci, B., Stuki, M., Jonsson, Z.O., Dogliotti, E. and Hubscher, U. 1999. Long patch base excision repair with purified human proteins. J. Biol. Chem. 274: 33696–33702.Google Scholar
  32. Reynolds, N., Fantes, P.A. and MacNeill, S.A. 1999. A key role for replication factor C in DNA replication checkpoint function in fission yeast. Nucl. Acids Res. 27: 462–469.Google Scholar
  33. Sato, Y., Hong, S.K., Tagiri, A., Kitano, H., Yamamoto, N., Nagato, Y. and Matsuoka, M. 1996. A rice homeobox gene, OSH1, is expressed before again before organ differentiation in a specific region during early embryogenesis. Proc. Natl. Acad. Sci. USA 93: 8117–8122.Google Scholar
  34. Shimada, M., Okuzaki, D., Tanaka, S., Tougan, T., Tamai, K., Shimoda, C. and Nojima, H. 1999. Replication factor C3 of Schizosaccharomyces pombe, a small subunit of replication factor c complex, plays a role in both replication and damage checkpoints. Mol. Biol. Cell. 10: 3991–4003.Google Scholar
  35. Shivji, M.K., Podust, V.N. and Hubscher, U. and Wood, R.D. 1995. Nucleotide excision repair DNA synthesis by DNA polymerase epsilon in the presence of PCNA, RFC, and RPA. Biochemistry 34: 5011–5017.Google Scholar
  36. Sugimoto, K., Ando, S., Shimomura, T. and Matsumoto, K. 1997. Rfc5, a replication factor C component, is required for regulation of Rad53 protein kinase in the yeast checkpoint pathway. Mol. Cell. Biol. 17: 5905–5914.Google Scholar
  37. Uchiyama, Y., Hatanaka, M., Kimura, S., Ishibashi, T., Ueda, T., Sakakibara, Y., Matsumoto, T., Furukawa, T., Hashimoto, J. and Sakaguchi, K. 2002. Characterization of DNA polymerase δ from a higher plant, rice (Oryza sativa L.). Gene 295: 19–26.Google Scholar

Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • Tomoyuki Furukawa
    • 1
  • Toyotaka Ishibashi
    • 2
  • Seisuke Kimura
    • 2
  • Hiroshi Tanaka
    • 3
  • Junji Hashimoto
    • 1
  • Kengo Sakaguchi
    • 2
  1. 1.National Institute of Agrobiological SciencesIbaraki-kenJapan
  2. 2.Department of Applied Biological Science, Faculty of Science and TechnologyTokyo University of ScienceNoda-shi, Chiba-kenJapan
  3. 3.National Agricultural Research CenterJyouetsu-shi, Niigata-kenJapan

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