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Egg-specific expression of protein with DNA methyltransferase activity in the biocarcinogenic liver fluke Clonorchis sinensis

  • SEON-HEE KIM (a1), HYE-JEONG CHO (a1), WOON-MOK SOHN (a2), CHUN-SEOB AHN (a3), YOON KONG (a3), HYUN-JONG YANG (a4) and YOUNG-AN BAE (a1)...

Summary

Despite recent reports regarding the biology of cytosine methylation in Schistosoma mansoni, the impact of the regulatory machinery remains unclear in diverse platyhelminthes. This ambiguity is reinforced by discoveries of DNA methyltransferase 2 (DNMT2)-only organisms and the substrate specificity of DNMT2 preferential to RNA molecules. Here, we characterized a novel DNA methyltransferase, named CsDNMT2, in a liver fluke Clonorchis sinensis. The protein exhibited structural properties conserved in other members of the DNMT2 family. The native and recombinant CsDNMT2 exhibited considerable enzymatic activity on DNA. The spatiotemporal expression of CsDNMT2 mirrored that of 5-methylcytosine (5 mC), both of which were elevated in the C. sinensis eggs. However, CsDNMT2 and 5 mC were marginally detected in other histological regions of C. sinensis adults including ovaries and seminal receptacle. The methylation site seemed not related to genomic loci occupied by progenies of an active long-terminal-repeat retrotransposon. Taken together, our data strongly suggest that C. sinensis has preserved the functional DNA methylation machinery and that DNMT2 acts as a genuine alternative to DNMT1/DNMT3 to methylate DNA in the DNMT2-only organism. The epigenetic regulation would target functional genes primarily involved in the formation and/or maturation of eggs, rather than retrotransposons.

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Corresponding author

* Corresponding author: Department of Microbiology, Graduate School of Medicine, Gachon University, 191 Hambakmoe-ro, Yeonsu-gu, Incheon 406-799, Republic of Korea. E-mail: yabae03@gmail.com

References

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Bae, Y. A., Ahn, D. W., Lee, E. G., Kim, S. H., Cai, G. B., Kang, I., Sohn, W. M. and Kong, Y. (2013 a). Differential activation of diverse glutathione transferases of Clonorchis sinensis in response to the host bile and oxidative stressors. PLoS Neglected Tropical Diseases 7, e2211.
Bae, Y. A., Cai, G. B., Kim, S. H., Sohn, W. M. and Kong, Y. (2013 b). Expression pattern and substrate specificity of Clonorchis sinensis tyrosinases. International Journal for Parasitology 43, 891900.
Bae, Y. A. and Kong, Y. (2003). Evolutionary course of CsRn1 long-terminal-repeat retrotransposon and its heterogeneous integrations into the genome of the liver fluke, Clonorchis sinensis . Korean Journal of Parasitology 41, 209219.
Bae, Y. A., Moon, S. Y., Kong, Y., Cho, S. Y. and Rhyu, M. G. (2001). CsRn1, a novel retrotransposon in a parasitic trematode, Clonorchis sinensis, discloses a new phylogenetic clade of Ty3/gypsy-like LTR retrotransposons. Molecular Biology and Evolution 18, 14741483.
Bouvard, V., Baan, R., Straif, K., Grosse, Y., Secretan, B., El Ghissassi, F., Benbrahim-Tallaa, L., Guha, N., Freeman, C., Galichet, L. and Cogliano, V., WHO International Agency for Research on Cancer Monograph Working Group (2009). A review of human carcinogens - Part B: biological agents. Lancet Oncology 10, 321322.
Cai, G. B., Bae, Y. A., Kim, S. H., Sohn, W. M., Lee, Y. S., Jiang, M. S., Kim, T. S. and Kong, Y. (2008). Vitellocyte-specific expression of phospholipid hydroperoxide glutathione peroxidases in Clonorchis sinensis . International Journal for Parasitology 38, 16131623.
DeLano, W. L. (2002). The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA.
Dong, A., Yoder, J. A., Zhang, X., Zhou, L., Bestor, T. H. and Cheng, X. (2001). Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA. Nucleic Acids Research 29, 439448.
Fisher, O., Siman-Tov, R. and Ankri, S. (2004). Characterization of cytosine methylated regions and 5-cytosine DNA methyltransferase (Ehmeth) in the protozoan parasite Entamoeba histolytica . Nucleic Acids Research 32, 287297.
Geyer, K. K., Chalmers, I. W., Mackintosh, N., Hirst, J. E., Geoghegan, R., Badets, M., Brophy, P. M., Brehm, K. and Hoffmann, K. F. (2013). Cytosine methylation is a conserved epigenetic feature found throughout the phylum Platyhelminthes. BMC Genomics 14, 462.
Geyer, K. K., Rodríguez López, C. M., Chalmers, I. W., Munshi, S. E., Truscott, M., Heald, J., Wilkinson, M. J. and Hoffmann, K. F. (2011). Cytosine methylation regulates oviposition in the pathogenic blood fluke Schistosoma mansoni . Nature Communications 2, 424.
Goll, M. G., Kirpekar, F., Maggert, K. A., Yoder, J. A., Hsieh, C. L., Zhang, X., Golic, K. G., Jacobsen, S. E. and Bestor, T. H. (2006). Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 311, 395398.
Hong, S. T. (2003). Clonorchis sinensis . In International Handbook of Foodborne Pathogens (Eds. Miliotis, M. D. and Bier, J. W.), pp. 581592, Marcel Dekker Inc., New York.
Huang, Y., Chen, W., Wang, X., Liu, H., Chen, Y., Guo, L., Luo, F., Sun, J., Mao, Q., Liang, P., Xie, Z., Zhou, C., Tian, Y., Lv, X., Huang, L., Zhou, J., Hu, Y., Li, R., Zhang, F., Lei, H., Li, W., Hu, X., Liang, C., Xu, J., Li, X. and Yu, X. (2013). The carcinogenic liver fluke, Clonorchis sinensis: new assembly, reannotation and analysis of the genome and characterization of tissue transcriptomes. PLoS ONE 8, e54732.
Jeltsch, A. (2010). Phylogeny of methylomes. Science 328, 837838.
Jeltsch, A., Nellen, W. and Lyko, F. (2006). Two substrate are better than one: dual specificities for DNMT2 methyltansferases. Trends in Biochemical Sciences 31, 306308.
Jurkowski, T. P. and Jeltsch, A. (2011). On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2. PLoS ONE 6, e28104.
Jurkowski, T. P., Meusburger, M., Phalke, S., Helm, M., Nellen, W., Reuter, G. and Jeltsch, A. (2008). Human DNMT2 methylates tRNAAsp molecules using a DNA methyltransferase-like catalytic mechanism. RNA 14, 16631670.
Kano, H., Godoy, I., Courtney, C., Vetter, M. R., Gerton, G. L., Ostertag, E. M. and Kazazian, H. H. Jr. (2009). L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes & Development 23, 13031312.
Keizer, J. and Utzinger, J. (2009). Food-borne trematodiases. Clinical Microbiology Reviews 22, 466483.
Kinney, S. R. M. and Pradhan, S. (2011). Regulation of expression and activity of DNA (cytosine-5) methyltransferases in mammalian cells. Progress in Molecular Biology and Translational Science 101, 311333.
Law, J. A. and Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews Genetics 11, 204220.
Li, S., Du, J., Yang, H., Yin, J., Ding, J. and Zhong, J. (2013). Functional and structural characterization of DNMT2 from Spodoptera frugiperda . Journal of Molecular Cell Biology 5, 6466.
Müller, S., Windhof, I. M., Maximov, V., Jurkowski, T., Jeltsch, A., Förstner, K. U., Sharma, C. M., Gräf, R. and Nellen, W. (2013). Target recognition, RNA methylation activity and transcriptional regulation of the Dictyostelium discoideum Dnmt2-homoloue (DnmA). Nucleic Acids Research 41, 86158627.
Raddatz, G., Guzzardo, P. M., Olova, N., Fantappié, M. R., Rampp, M., Schaefer, M., Reik, W., Hannon, G. J. and Lyko, F. (2013). Dnmt2-dependent methylomes lack defined DNA methylation patterns. Proceedings of the National Academy of Science of the United States of America 110, 86278631.
Rountree, M. R., Bachman, K. E. and Baylin, S. B. (2000). DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. Nature Genetics 25, 269277.
Schaefer, M. and Lyko, F. (2010). Solving the Dnmt2 enigma. Chromosoma 119, 3540.
Schultz, E. C., Roth, H. M., Ankri, S. and Finer, R. (2012). Structure analysis of Entamoeba histolytica DNMT2 (EhMeth). PLoS ONE 7, e38728.
Shin, H. R., Oh, J. K., Masuyer, E., Curado, M. P., Bouvard, V., Fang, Y. Y., Wiangnon, S., Sripa, B. and Hong, S. T. (2010). Epidemiology of cholangiocarcinoma: an update focusing on risk factors. Cancer Science 101, 579585.
Song, J., Rechkoblit, O., Bestor, T. H. and Patel, D. J. (2011). Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science 331, 10361040.
Takeshita, K., Suetake, I., Yamashita, E., Suga, M., Narita, H., Nakagawa, A. and Tajima, S. (2011). Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1). Proceedings of the National Academy of Science of the United States of America 108, 90559059.
The Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium (2009). The Schistosoma japonicum genome reveals features of host-parasite interplay. Nature 460, 345352.
Thomson, C. A., Olson, M., Jackson, L. M. and Schrader, J. W. (2012). A simplified method for the efficient refolding and purification of recombinant human GM-CSF. PLoS ONE 7, e49891.
Tsai, I. J., Zarowiecki, M., Holroyd, N., Garciarrubio, A., Sanchez-Flores, A., Brooks, K. L., Tracey, A., Bobes, R. J., Fragoso, G., Sciutto, E., Aslett, M., Beasley, H., Bennett, H. M., Cai, J., Camicia, F., Clark, R., Cucher, M., De Silva, N., Day, T. A., Deplazes, P., Estrada, K., Fernández, C., Holland, P. W. H., Hou, J., Hu, S., Huckvale, T., Hung, S. S., Kamenetzky, L., Keane, J. A., Kiss, F., The Taenia solium Genome Consortium et al. (2013). The genomes of four tapeworm species reveal adaptations to parasitism. Nature 496, 5763.
Wang, X., Chen, W., Huang, Y., Sun, J., Men, J., Liu, H., Luo, F., Guo, L., Lv, X., Deng, C., Zhou, C., Fan, Y., Li, X., Huang, L., Hu, Y., Liang, C., Hu, X., Xu, J. and Yu, X. (2011). The draft genome of the carcinogenic human liver fluke Clonorchis sinensis . Genome Biology 12, R107.
Wojciechowski, M., Czapinska, H. and Bochtler, M. (2013). CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI. Proceedings of the National Academy of Science of the United States of America 110, 105110.
Yoder, J. A., Walsh, C. P. and Bestor, T. H. (1997). Cytosine methylation and the ecology of intragenomic parasites. Trends in Genetics 13, 335–40.
Zemach, A. and Zilberman, D. (2010). Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology 20, R780R785.
Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9, 40.

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