Malays. Appl. Biol. (2014) 43(1): 21–30
EPITOPE MAPPING OF ANTI-YB-1 ANTIBODIES USING
TRUNCATED PROTEINS
TEE CHEE WEI and SHAHARUM SHAMSUDDIN*
Advanced Molecular Biology Laboratory, School of Health Sciences,
Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
*Email:
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ABSTRACT
Increased expression and nuclear localization of Y-box-binding protein-1 (YB-1) are associated with drug resistance and tumor progression. Detection of YB-1 primarily depends on the recognition of YB-1 antibody on its epitopes. To determine the epitopes binding of anti-YB-1 A-16 and 59-Q antibodies, three YB-1 truncated proteins were generated using bacterial expression system and their aberrant migration were reported. Epitope mapping analyses revealed anti-YB-1 A-16 antibody recognized epitope at 1-127 amino acid residues of YB-1, whereas 59-Q antibody was reactive with epitope at 61-127 amino acid residues. Based on our findings, 59-Q antibody was suggested used in the future study to avoid ambiguity.
Key words: epitope mapping, YB-1, truncated protein, antibodies
REFERENCES
Armstrong, D. J.Roman, A. 1993. The anomalous electrophoretic behavior of the human papillomavirus type 16 E7 protein is due to the high content of acidic amino acid residues. Biochemical and Biophysical Research Communications. 192 (3): 1380-7.
Baerga-Ortiz, A., Hughes, C. A., Mandell, J. G.Komives, E. A. 2002. Epitope mapping of a monoclonal antibody against human thrombin by H/D-exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein. Protein Science. 11 (6): 1300-8.
Bargou, R. C., Jurchott, K., Wagener, C., Bergmann, S., Metzner, S., Bommert, K., Mapara, M. Y., Winzer, K.-J., Dietel, M., Dorken, B.Royer, H.-D. 1997. Nuclear localization and increased levels of transcription factor YB-1 in primary human breast cancers are associated with intrinsic MDR1 gene expression. Nature Medicine. 3 (4): 447-450.
Chatterjee, M., Rancso, C., Stühmer, T., Eckstein, N., Andrulis, M., Gerecke, C., Lorentz, H., Royer, H.-D.Bargou, R. C. 2008. The Y-box binding protein YB-1 is associated with progressive disease and mediates survival and drug resistance in multiple myeloma. Blood. 111 (7): 3714-3722.
Chernukhin, I. V., Shamsuddin, S., Robinson, A. F., Carne, A. F., Paul, A., El-Kady, A. I., Lobanenkov, V. V.Klenova, E. M. 2000. Physical and functional interaction between two pluripotent proteins, the Y-box DNA/RNA-binding factor, YB-1, and the multivalent zinc finger factor, CTCF. Journal of Biological Chemistry. 275 (38): 29915-21.
Chibi, M., Meyer, M., Skepu, A., G. Rees, D. J., Moolman-Smook, J. C.Pugh, D. J. R. 2008. RBBP6 Interacts with Multifunctional Protein YB-1 through Its RING Finger Domain, Leading to Ubiquitination and Proteosomal Degradation of YB-1. Journal of Molecular Biology. 384 (4): 908-916.
Cohen, S. B., Ma, W., Valova, V. A., Algie, M., Harfoot, R., Woolley, A. G., Robinson, P. J.Braithwaite, A. W. 2010. Genotoxic stress-induced nuclear localization of oncoprotein YB-1 in the absence of proteolytic processing. Oncogene. 29 (3): 403-10.
Eliseeva, I. A., Kim, E. R., Guryanov, S. G., Ovchinnikov, L. P.Lyabin, D. N. 2011. Y-box-binding protein 1 (YB-1) and its functions. Biochemistry. 76 (13): 1402-33.
Evdokimova, V. M., Wei, C. L., Sitikov, A. S., Simonenko, P. N., Lazarev, O. A., Vasilenko, K. S., Ustinov, V. A., Hershey, J. W.Ovchinnikov, L. P. 1995. The major protein of messenger ribonucleoprotein particles in somatic cells is a member of the Y-box binding transcription factor family. Journal of Biological Chemistry. 270 (7): 3186-92.
Fotovati, A., Abu-Ali, S., Wang, P.-S., Deleyrolle, L. P., Lee, C., Triscott, J., Chen, J. Y., Franciosi, S., Nakamura, Y., Sugita, Y., Uchiumi, T., Kuwano, M., Leavitt, B. R., Singh, S. K., Jury, A., Jones, C., Wakimoto, H., Reynolds, B. A., Pallen, C. J.Dunn, S. E. 2011. YB-1 Bridges Neural Stem Cells and Brain Tumor–Initiating Cells via Its Roles in Differentiation and Cell Growth. Cancer Research. 71 (16): 5569-5578.
Giménez-Bonafé, P., Fedoruk, M. N., Whitmore, T. G., Akbari, M., Ralph, J. L., Ettinger, S., Gleave, M. E.Nelson, C. C. 2004. YB-1 is upregulated during prostate cancer tumor progression and increases P-glycoprotein activity. The Prostate. 59 (3): 337-349.
Goldsmith, M. E., Madden, M. J., Morrow, C. S.Cowan, K. H. 1993. A Y-box consensus sequence is required for basal expression of the human multidrug resistance (mdr1) gene. Journal of Biological Chemistry. 268 (8): 5856-60.
Homer, C., Knight, D. A., Hananeia, L., Sheard, P., Risk, J., Lasham, A., Royds, J. A.Braithwaite, A. W. 2005. Y-box factor YB1 controls p53 apoptotic function. Oncogene. 24 (56): 8314-25.
Ito, Y., Yoshida, H., Shibahara, K., Uruno, T., Nakano, K., Takamura, Y., Miya, A., Kobayashi, K., Yokozawa, T., Matsuzuka, F., Uchimi, T., Kuwano, M., Miyoshi, E., Matsuura, N., Kuma, K.Miyauchi, A. 2003. Y-box binding protein expression in thyroid neoplasms: its linkage with anaplastic transformation. Pathology International. 53 (7): 429-33.
Khandelwal, P., Padala, M. K., Cox, J.Guntaka, R. V. 2009. The N-Terminal Domain of Y-Box Binding Protein-1 Induces Cell Cycle Arrest in G2/M Phase by Binding to Cyclin D1. International journal of cell biology. 2009.
Kloks, C. P. A. M., Spronk, C. A. E. M., Lasonder, E., Hoffmann, A., Vuister, G. W., Grzesiek, S.Hilbers, C. W. 2002. The solution structure and DNA-binding properties of the cold-shock domain of the human Y-box protein YB-1. Journal of Molecular Biology. 316 (2): 317-326.
Kojic, S., Medeot, E., Guccione, E., Krmac, H., Zara, I., Martinelli, V., Valle, G.Faulkner, G. 2004. The Ankrd2 Protein, a Link Between the Sarcomere and the Nucleus in Skeletal Muscle. Journal of Molecular Biology. 339 (2): 313-325.
Ladner, R. C. 2007. Mapping the epitopes of antibodies. Biotechnology and Genetic Engineering Reviews. 24 1-30.
Lasham, A., Print, C. G., Woolley, A. G., Dunn, S. E.Braithwaite, A. W. 2013. YB-1: oncoprotein, prognostic marker and therapeutic target? Biochemical Journal. 449 (1): 11-23.
Lu, Z. H., Books, J. T.Ley, T. J. 2005. YB-1 Is Important for Late-Stage Embryonic Development, Optimal Cellular Stress Responses, and the Prevention of Premature Senescence. Molecular and Cellular Biology. 25 (11): 4625-4637.
Manning, M.Colon, W. 2004. Structural basis of protein kinetic stability: resistance to sodium dodecyl sulfate suggests a central role for rigidity and a bias toward beta-sheet structure. Biochemistry. 43 (35): 11248-54.
Meysick, K. C., Mills, M.O'Brien, A. D. 2001. Epitope mapping of monoclonal antibodies capable of neutralizing cytotoxic necrotizing factor type 1 of uropathogenic Escherichia coli. Infection and Immunity. 69 (4): 2066-74.
Oda, Y., Ohishi, Y., Saito, T., Hinoshita, E., Uchiumi, T., Kinukawa, N., Iwamoto, Y., Kohno, K., Kuwano, M.Tsuneyoshi, M. 2003. Nuclear expression of Y-box binding protein-1 correlates with P-glycoprotein and topoisomerase II alpha expression and with poor prognosis in synovial sarcoma. Journal of Pathology. 199 251 - 258.
Oda, Y., Sakamoto, A., Shinohara, N., Ohga, T., Uchiumi, T., Kohno, K., Tsuneyoshi, M., Kuwano, M.Iwamoto, Y. 1998. Nuclear expression of YB-1 protein correlates with P-glycoprotein expression in human osteosarcoma. Clinical Cancer Research. 4 (9): 2273-2277.
Ohga, T., Uchiumi, T., Makino, Y., Koike, K., Wada, M., Kuwano, M.Kohno, K. 1998. Direct involvement of the Y-box binding protein YB-1 in genotoxic stress-induced activation of the human multidrug resistance 1 gene. Journal of Biological Chemistry. 273 (11): 5997-6000.
Perez-Leal, O., Barrero, C. A., Clarkson, A. B., Casero, R. A., Jr.Merali, S. 2012. Polyamine-regulated translation of spermidine/spermine-N1-acetyltransferase. Molecular and Cellular Biology. 32 (8): 1453-67.
Rath, A., Glibowicka, M., Nadeau, V. G., Chen, G.Deber, C. M. 2009. Detergent binding explains anomalous SDS-PAGE migration of membrane proteins. Proceedings of the National Academy of Sciences of the United States of America.
Raux, H., Iseni, F., Lafay, F.Blondel, D. 1997. Mapping of monoclonal antibody epitopes of the rabies virus P protein. Journal of General Virology. 78 ( Pt 1) 119-24.
Sano, E., Shono, S., Tashiro, K., Konishi, H., Yamauchi, E.Taniguchi, H. 2008. Novel tyrosine phosphorylated and cardiolipin-binding protein CLPABP functions as mitochondrial RNA granule. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 1783 (6): 1036-1047.
Schittek, B., Psenner, K., Sauer, B., Meier, F., Iftner, T.Garbe, C. 2007. The increased expression of Y box-binding protein 1 in melanoma stimulates proliferation and tumor invasion, antagonizes apoptosis and enhances chemoresistance. International Journal of Cancer. 120 (10): 2110-8.
Shibahara, K., Sugio, K., Osaki, T., Uchiumi, T., Maehara, Y., Kohno, K., Yasumoto, K., Sugimachi, K.Kuwano, M. 2001. Nuclear Expression of the Y-Box Binding Protein, YB-1, as a Novel Marker of Disease Progression in Non-Small Cell Lung Cancer. Clinical Cancer Research. 7 (10): 3151-3155.
Silveira, C. G., Krampe, J., Ruhland, B., Diedrich, K., Hornung, D.Agic, A. 2012. Cold-shock domain family member YB-1 expression in endometrium and endometriosis. Human Reproduction. 27 (1): 173-82.
Skabkin, M. A., Kiselyova, O. I., Chernov, K. G., Sorokin, A. V., Dubrovin, E. V., Yaminsky, I. V., Vasiliev, V. D.Ovchinnikov, L. P. 2004. Structural organization of mRNA complexes with major core mRNP protein YB-1. Nucleic Acids Research. 32 (18): 5621-35.
Sorokin, A. V., Selyutina, A. A., Skabkin, M. A., Guryanov, S. G., Nazimov, I. V., Richard, C., Th'ng, J., Yau, J., Sorensen, P. H., Ovchinnikov, L. P.Evdokimova, V. 2005. Proteasome-mediated cleavage of the Y-box-binding protein 1 is linked to DNA-damage stress response. EMBO Journal. 24 (20): 3602-12.
Swamynathan, S. K., Varma, B. R., Weber, K. T.Guntaka, R. V. 2002. Targeted disruption of one allele of the Y-box protein gene, Chk-YB-1b, in DT40 cells results in major defects in cell cycle. Biochemical and Biophysical Research Communications. 296 (2): 451-7.
Wade-Evans, A.Jenkins, J. R. 1985. Precise epitope mapping of the murine transformation-associated protein, p53. EMBO Journal. 4 (3): 699-706.
Wolffe, A. P. 1994. Structural and functional properties of the evolutionarily ancient Y-box family of nucleic acid binding proteins. Bioessays. 16 (4): 245-51.
Wolffe, A. P., Tafuri, S., Ranjan, M.Familari, M. 1992. The Y-box factors: a family of nucleic acid binding proteins conserved from Escherichia coli to man. New Biologist. 4 (4): 290-8.
Woolley, A. G., Algie, M., Samuel, W., Harfoot, R., Wiles, A., Hung, N. A., Tan, P.-H., Hains, P., Valova, V. A., Huschtscha, L., Royds, J. A., Perez, D., Yoon, H.-S., Cohen, S. B., Robinson, P. J., Bay, B.-H., Lasham, A.Braithwaite, A. W. 2011. Prognostic Association of YB-1 Expression in Breast Cancers: A Matter of Antibody. PLoS ONE. 6 (6): e20603.
Zhang, Y. F., Homer, C., Edwards, S. J., Hananeia, L., Lasham, A., Royds, J., Sheard, P.Braithwaite, A. W. 2003. Nuclear localization of Y-box factor YB1 requires wild-type p53. Oncogene. 22 (18): 2782-94.
