Abstract
Transcriptome was analyzed in γ-irradiated green alga Pseudokirchneriella subcapitata by high coverage gene expression profiling (HiCEP). Approximately 7,800 expressed genes were detected. Expression levels of 623–707 genes were affected at 100–300 Gy. Nucleotide sequences of 41 up-regulated genes were determined. The quantitative reverse transcription polymerase chain reaction validated the up-regulation. Two genes had homology to genes related to ionizing radiation. These results indicate usefulness of HiCEP for screening of stress-responsive genes in species that are ecotoxicologically important but for which genomic sequence information is lacking.
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Aboussekhra A, Al-Sharif IS (2005) Homologous recombination is involved in transcription-coupled repair of UV damage in Saccharomyces cerevisiae. EMBO J 24:1999–2010. doi:10.1038/sj.emboj.7600665
Akhtar TA, Lampi MA, Greenberg M (2005) Identification of six differential expressed genes in response to copper exposure in the aquatic plant Lemna gibba (duckweed). Environ Toxicol Chem 24:1705–1715. doi:10.1897/04-352R.1
Araki R, Fukumura R, Sasaki N, Kasama Y, Suzuki N, Takahashi H, Tabata Y, Saito T, Abe M (2006) More than 40, 000 transcripts, including novel and noncoding transcripts, in mouse embryonic stem cells. Stem Cells 24:2522–2528. doi:10.1634/stemcells.2006-0005
Fujimori A, Okayasu R, Ishihara H, Yoshida S, Eguchi-Kasai K, Nojima K, Ebisawa S, Takahashi S (2005) Extremely low dose ionizing radiation up-regulates CXC chemokines in normal human fibroblasts. Cancer Res 65:10159–10163. doi:10.1158/0008-5472.CAN-05-2015
Fujimori A, Yaoi T, Ogi H, Wang B, Suetomi K, Sekine E, Yu D, Kato T, Takahashi S, Okayasu R, Itoh K, Fushiki S (2008) Ionizing radiation downregulates ASPM, a gene responsible for microcephaly in humans. Biochem Biophys Res Commun 369:953–957. doi:10.1016/j.bbrc.2008.02.149
Fukumura R, Takahashi H, Saito T, Tsutsumi Y, Fujimori A, Sato S, Tatsumi K, Araki R, Abe M (2003) A sensitive transcriptome analysis method that can detect unknown transcripts. Nucl Acids Res 31:e94. doi:10.1093/nar/gng094
Griffitt RJ, Chandler GT, Greig TW, Quattro JM (2006) Cathepsin B and glutathione peroxidase show differing transcriptional responses in the grass shrimp, Palaemonetes pugio following exposure to three xenobiotics. Environ Sci Technol 40:3640–3645. doi:10.1021/es052537o
Griffitt RJ, Greig TW, Chandler GT, Quattro JM (2007) Serial analysis of gene expression reveals identifiable patterns in transcriptome profiles of Palaemonetes pugio exposed to three common environmental stressors. Environ Toxicol Chem 26:2413–2419. doi:10.1897/07-158R.1
Ichimura T (1971) Sexual cell division and conjugation-papilla formation in sexual reproduction of Closterium strigosum. In: Proceedings of the seventh international seaweed symposium, University of Tokyo Press, Tokyo, pp 208–214
Klutstein M, Shaked H, Sherman A, Avivi-Ragolsky N, Shema E, Zenvirth D, Levy AA, Simchen G (2008) Functional conservation of the yeast and Arabidopsis RAD54-like genes. Genetics 178:2389–2397. doi:10.1534/genetics.108.086777
Li L, Monckton EA, Godbout R (2008) A role for DEAD box 1 at DNA double-strand breaks. Mol Cell Biol 28:6413–6425. doi:10.1128/MCB.01053-08
Merchant SS, Prochnik SE et al (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318:245–251. doi:10.1126/science.1143609
Mitani Y, Suzuki K, Kondo K, Okumura K, Tamura T (2006) Gene expression analysis using a modified HiCEP method applicable to prokaryotes: a study of the response of Rhodococcus to isoniazid and ethambutol. J Biotech 123:259–272. doi:10.1016/j.jbiotec.2005.11.004
Nakamori T, Fujimori A, Kinoshita K, Ban-nai T, Kubota Y, Yoshida S (2008) Application of HiCEP to screening of radiation stress-responsive genes in the soil microarthropod Folsomia candida (Collembola). Environ Sci Tech 42:6997–7002. doi:10.1021/es801128q
OECD (2006) OECD guidelines for the testing of chemicals: Test No. 201: Alga, growth inhibition test. Organisation for Economic Co-operation and Development, Paris
Snell TW, Brogdon SE, Morgen MB (2003) Gene expression profiling in ecotoxicology. Ecotoxicol 12:475–483. doi:10.1023/B:ECTX.0000003033.09923.a8
Suetomi K, Takahashi S, Kubota Y, Fujimori A (2008) Identification of genes responding to low-dose arsenite using HiCEP. Toxicol Mech Methods 18:605–611. doi:10.1080/15376510802335622
Acknowledgments
Gene expression profiling in this study was performed by the HiCEP unit team founded under the NIRS president’s initiative. The authors thank Syunsuke Ando, Sachi Inukai, Toshitaro Takata and Atsuko Matsumoto (NIRS) for their technical support.
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Fuma, S., Nakamori, T., Ishii, N. et al. Genome-Wide Gene Expression Profiling in γ-Irradiated Green Alga, Pseudokirchneriella subcapitata, by HiCEP. Bull Environ Contam Toxicol 83, 301–306 (2009). https://doi.org/10.1007/s00128-009-9780-y
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DOI: https://doi.org/10.1007/s00128-009-9780-y