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

Published online by Cambridge University Press:  03 June 2015

SEON-HEE KIM
Affiliation:
Department of Microbiology, Graduate School of Medicine, Gachon University, 191 Hambakmoe-ro, Yeonsu-gu, Incheon 406-799, Republic of Korea
HYE-JEONG CHO
Affiliation:
Department of Microbiology, Graduate School of Medicine, Gachon University, 191 Hambakmoe-ro, Yeonsu-gu, Incheon 406-799, Republic of Korea
WOON-MOK SOHN
Affiliation:
Department of Parasitology and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Republic of Korea
CHUN-SEOB AHN
Affiliation:
Department of Molecular Parasitology, Sungkyunkwan University School of Medicine and Center for Molecular Medicine, Samsung Biomedical Research Institute, Suwon, Republic of Korea
YOON KONG
Affiliation:
Department of Molecular Parasitology, Sungkyunkwan University School of Medicine and Center for Molecular Medicine, Samsung Biomedical Research Institute, Suwon, Republic of Korea
HYUN-JONG YANG
Affiliation:
Department of Parasitology, Ewha Womans University School of Medicine, Seoul, Republic of Korea
YOUNG-AN BAE*
Affiliation:
Department of Microbiology, Graduate School of Medicine, Gachon University, 191 Hambakmoe-ro, Yeonsu-gu, Incheon 406-799, Republic of Korea
*
*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

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.

Type
Research Article
Copyright
Copyright © Cambridge University Press 2015 

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References

REFERENCES

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.Google Scholar
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.Google Scholar
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.CrossRefGoogle ScholarPubMed
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.Google Scholar
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.Google Scholar
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.Google Scholar
DeLano, W. L. (2002). The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA.Google Scholar
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.Google Scholar
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.CrossRefGoogle ScholarPubMed
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.Google Scholar
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.CrossRefGoogle ScholarPubMed
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.Google Scholar
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.Google Scholar
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.Google ScholarPubMed
Jeltsch, A. (2010). Phylogeny of methylomes. Science 328, 837838.Google Scholar
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.Google Scholar
Jurkowski, T. P. and Jeltsch, A. (2011). On the evolutionary origin of eukaryotic DNA methyltransferases and Dnmt2. PLoS ONE 6, e28104.Google Scholar
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.Google Scholar
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.CrossRefGoogle ScholarPubMed
Keizer, J. and Utzinger, J. (2009). Food-borne trematodiases. Clinical Microbiology Reviews 22, 466483.Google Scholar
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.Google Scholar
Law, J. A. and Jacobsen, S. E. (2010). Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nature Reviews Genetics 11, 204220.Google Scholar
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.Google Scholar
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.Google Scholar
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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
Schaefer, M. and Lyko, F. (2010). Solving the Dnmt2 enigma. Chromosoma 119, 3540.Google Scholar
Schultz, E. C., Roth, H. M., Ankri, S. and Finer, R. (2012). Structure analysis of Entamoeba histolytica DNMT2 (EhMeth). PLoS ONE 7, e38728.Google Scholar
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.Google Scholar
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.Google Scholar
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.Google Scholar
The Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium (2009). The Schistosoma japonicum genome reveals features of host-parasite interplay. Nature 460, 345352.Google Scholar
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.Google Scholar
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.Google Scholar
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.Google Scholar
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.Google Scholar
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.Google Scholar
Zemach, A. and Zilberman, D. (2010). Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology 20, R780R785.Google Scholar
Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9, 40.Google Scholar
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