Growth Retardation and Death of Rice Plants Irradiated with Carbon Ion Beams Is Preceded by Very Early Dose- and Time-dependent Gene Expression Changes

  • Rakwal, Randeep (Human Stress Signal Research Center (HSS), National Institute of Advanced Industrial Science and Technology (AIST)) ;
  • Kimura, Shinzo (Hazard Assessment and Epidemiology Research Group, Japan National Institute of Occupational Safety and Health (Japan NIOSH)) ;
  • Shibato, Junko (Human Stress Signal Research Center (HSS), National Institute of Advanced Industrial Science and Technology (AIST)) ;
  • Nojima, Kumie (Research Center for Charged Particle Therapy, National Institute of Radiological Sciences (NIRS)) ;
  • Kim, Yeon-Ki (Division of Bioscience and Bioinformatics, Myongji University, GreenGene BioTech Inc.) ;
  • Nahm, Baek Hie (Division of Bioscience and Bioinformatics, Myongji University, GreenGene BioTech Inc.) ;
  • Jwa, Nam-Soo (Department of Molecular Biology, College of Natural Science, Sejong University) ;
  • Endo, Satoru (Research Institute for Radiation Biology and Medicine, Hiroshima University) ;
  • Tanaka, Kenichi (Research Institute for Radiation Biology and Medicine, Hiroshima University) ;
  • Iwahashi, Hitoshi (Human Stress Signal Research Center (HSS), National Institute of Advanced Industrial Science and Technology (AIST))
  • 투고 : 2007.07.13
  • 심사 : 2007.12.12
  • 발행 : 2008.04.30

초록

The carbon-ion beam (CIB) generated by the heavy-ion medical accelerator in Chiba (HIMAC) was targeted to 7-day-old rice. Physiological parameters such as growth, and gene expression profiles were examined immediately after CIB irradiation. Dose-dependent growth suppression was seen three days post-irradiation (PI), and all the irradiated plants died by 15 days PI. Microarray (Agilent rice 22K) analysis of the plants immediately after irradiation (iai) revealed effects on gene expression at 270 Gy; 353 genes were up-regulated and 87 down-regulated. Exactly the same set of genes was affected at 90 Gy. Among the highly induced genes were genes involved in information storage and processing, cellular processes and signaling, and metabolism. RT-PCR analysis confirmed the microarray data.

키워드

과제정보

연구 과제 주관 기관 : Atomic Energy Commission

참고문헌

  1. Agrawal, G.K., and Rakwal, R. (2006). Rice proteomics: A cornerstone for cereal food crop proteomes. Mass Spec. Rev. 2, 51-53
  2. Altman, N. (2005). Replication, variation and normalisation in microarray experiments. Appl. Bioinformatics 4, 33-44 https://doi.org/10.2165/00822942-200504010-00004
  3. DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997). Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686 https://doi.org/10.1126/science.278.5338.680
  4. Fukumura, A., Hiraoka, T., Omata, K., Takeshita, M., Kawachi, K., Kanai, T., Matsufuji, M., Tomura, H., Futami, Y., Kaizuka, Y., et al. (1998). Carbon beam dosimetry intercomparison at HIMAC. Phys. Med. Biol. 43, 3459-3463 https://doi.org/10.1088/0031-9155/43/12/005
  5. Hase, Y., Shimono, K., Inoue, M., Tanaka, A., and Watanabe, H. (1999). Biological effects of ion beams in Nicotiana tabacum L. Radiat. Environ. Biophys. 38, 111-1115 https://doi.org/10.1007/s004110050146
  6. 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 distribution. Gene 272, 335-343 https://doi.org/10.1016/S0378-1119(01)00555-8
  7. Jwa, N.S., Agrawal, G.K., Tamogami, S., Yonekura, M., Han, O., Iwahashi, H., and Rakwal, R. (2006). Defense/stress-related marker genes, proteins and secondary metabolites in defining rice self-defense mechanisms. Plant Physiol. Biochem. 44, 261-273 https://doi.org/10.1016/j.plaphy.2006.06.010
  8. Kim, S.T., Kim, S.G., Hwang, D.H., Kang, S.Y., Kim, H.J., Lee, B.H., Lee, J.J., and Kang, K.Y. (2004). Proteomic analysis of pathogen-responsive proteins from rice leaves induced by rice blast fungus, Magnaporthe grisea. Proteomics 11, 3569-3578
  9. 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 https://doi.org/10.1023/A:1006349511964
  10. Kimura, S., Tahira, Y., Ishibashi, T., Mori, Y., Mori, T., Hashimoto, J., and Sakaguchi, K. (2004). DNA repair in higher plants; photoreactivation is the major DNA repair pathway in nonproliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cells. Nucleic. Acids Res. 32, 2760-2767 https://doi.org/10.1093/nar/gkh591
  11. Kimura, S., Ishidou, E., Kurita, S., Suzuki, Y., Shibato, J., Rakwal, R., and Iwahashi, H. (2006a). DNA microarray analyses reveal a post-irradiation differential time-dependent gene expression profile in yeast cells exposed to X-rays and $\gamma$-rays. Biochem. Biophys. Res. Commun. 346, 51-60 https://doi.org/10.1016/j.bbrc.2006.05.126
  12. Kimura, S., Sahoo, S.K., Shiraishi, K., Watanabe, Y., Ban-nai, T., Los, I.P., Koruzn, V.N., Tsygankov, N.Y., Zamostyan, P.V., and Shevchuk, V.E. (2006b). Radiation monitoring using imaging plate technology: a case study of plant leaves affected due to Chernobyl nuclear power plant accident and JCO critically accident. Nucl. Tech. Rad. Protec. 21, 41-47 https://doi.org/10.2298/NTRP0601041K
  13. Kimura, S., Shibato, J., Agrawal, G.K., Kim, Y.K., Nahm, B.H., Jwa, N.S., Iwahashi, H., and Rakwal, R. (2007). Microarray analysis of rice leaf response to radioactivity from contaminated Chernobyl soil. Rice Gent. Newsletter 24
  14. Maekawa, M., Hase, Y., Shikazono, N., and Tanaka, A. (2003). Induction of somatic instability in stable yellow leaf mutant of rice by ion beam irradiation. Nucl. Instrum. Methods Phys. Res. B. 206, 579-585 https://doi.org/10.1016/S0168-583X(03)00839-5
  15. Martin-Magniette, M.L., Aubert, J., Cabannes, E., and Daudin, J.J. (2005). Evaluation of the gene-specific dye bias in cDNA microarray experiments. Bioinformatics 21, 1995-2000 https://doi.org/10.1093/bioinformatics/bti302
  16. Rosenzweig, B.A., Pine, P.S., Domon, O.E., Morris, M., Chen, J.J., and Sistare, F.D. (2004). Dye bias correction in dual-labeled cDNA microarray gene expression measurements. Environ. Health Perspect. 112, 480-487 https://doi.org/10.1289/ehp.6694
  17. Shikazono, N., Yokota, Y., Kitamura, S., Suzuki, C., Watanabe, H., Tano, S., and Tanaka, A. (2003). Mutation rate and novel tt mutants of Arabidopsis thaliana induced by carbon ions. Genetics 163, 1449-1455
  18. Shikazono, N., Suzuki, C., Kitamura, S., Watanabe, H., Tano, S., and Tanaka, A. (2005). Analysis of mutations induced by carbon ions in Arabidopsis thaliana. J. Exp. Bot. 56, 587-596 https://doi.org/10.1093/jxb/eri047
  19. Shimizu, T., Satoh, K., Kikuchi, S., and Omura, T. (2006). The repression of cell wall- and plastid-related genes and the induction of defense-related genes in rice plants infected with Rice dwarf virus. Mol. Plant-Microbe Inter. 20, 247-254 https://doi.org/10.1094/MPMI-20-3-0247
  20. Stone, R. (2006). Return to the inferno: Chornobyl after 20 years. Science 312, 180-182 https://doi.org/10.1126/science.312.5771.180
  21. Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N., et al. (2003). The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41 https://doi.org/10.1186/1471-2105-4-41
  22. Tsujii, H., Mizoe, J.E., Kamada, T., Baba, M., Kato, S., Kato, H., Tsuji, H., Yamada, S., Yasuda, S., Ohno, T., et al. (2004). Overview of clinical experiences on carbon ion radiotherapy at NIRS. Radiother. Oncol. 73, Suppl 2: S41-49
  23. Yan, S., Tang, Z., Su, W., and Sun, W. (2005). Proteome analysis of salt-responsive proteins in rice roots. Proteomics 5, 235-244 https://doi.org/10.1002/pmic.200400853
  24. Yokota, Y., Hase, Y., Shikazono, N., Tanaka, A., and Inoue, M. (2003). LET dependence of lethality of carbon ion irradiation to single tobacco cells. Int. J. Radiat. Biol. 79, 681-685 https://doi.org/10.1080/09553000310001622832
  25. Yokota, Y., Yamada, S., Hase, Y., Shikazono, N., Narumi, I., Tanaka, A., and Inoue, M. (2007). Initial yields of DNA double strand breaks and DNA Fragmentation patterns depend on linear energy transfer in tobacco BY-2 protoplasts irradiated with helium, carbon and neon ions. Radiat. Res. 167, 94-101 https://doi.org/10.1667/RR0701.1