Ki-1/57 And Cgi-55 Ectopic Expression Impact Cellular Pathways Involved In Proliferation And Stress Response Regulation

Ki-1/57 (HABP4) and CGI-55 (SERBP1) are regulatory proteins and paralogs with 40.7% amino acid sequence identity and 67.4% similarity. Functionally, they have been implicated in the regulation of gene expression on both the transcriptional and mRNA metabolism levels. A link with tumorigenesis is suggested, since both paralogs show altered expression levels in tumor cells and the Ki-1/57 gene is found in a region of chromosome 9q that represents a haplotype for familiar colon cancer. However, the target genes regulated by Ki-1/57 and CGI-55 are unknown. Here, we analyzed the alterations of the global transcriptome profile after Ki-1/57 or CGI-55 overexpression in HEK293T cells by DNA microchip technology. We were able to identify 363 or 190 down-regulated and 50 or 27 up-regulated genes for Ki-1/57 and CGI-55, respectively, of which 20 were shared between both proteins. Expression levels of selected genes were confirmed by qRT-PCR both after protein overexpression and siRNA knockdown. The majority of the genes with altered expression were associated to proliferation, apoptosis and cell cycle control processes, prompting us to further explore these contexts experimentally. We observed that overexpression of Ki-1/57 or CGI-55 results in reduced cell proliferation, mainly due to a G1 phase arrest, whereas siRNA knockdown of CGI-55 caused an increase in proliferation. In the case of Ki-1/57 overexpression, we found protection from apoptosis after treatment with the ER-stress inducer thapsigargin. Together, our data give important new insights that may help to explain these proteins putative involvement in tumorigenic events.18431229442956Kobarg, J., Schnittger, S., Fonatsch, C., Lemke, H., Bowen, M.A., Buck, F., Hansen, H.P., Characterization, mapping and partial cDNA sequence of the 57-kD intracellular Ki-1 antigen (1997) Exp. Clin. Immunogenet., 14, pp. 273-280Serce, N.B., Boesl, A., Klaman, I., von Serényi, S., Noetzel, E., Press, M.F., Dimmler, A., Dahl, E., Overexpression of SERBP1 (plasminogen activator inhibitor 1 RNA binding protein) in human breast cancer is correlated with favourable prognosis (2012) BMC Cancer, 12, p. 597Heaton, J.H., Dlakic, W.M., Dlakic, M., Gelehrter, T.D., Identification and cDNA cloning of a novel RNA-binding protein that interacts with the cyclic nucleotide-responsive sequence in the type-1 plasminogen activator inhibitor mRNA (2001) J. Biol. Chem., 276, pp. 3341-3347Lemos, T.A., Passos, D.O., Nery, F.C., Kobarg, J., Characterization of a new family of proteins that interact with the C-terminal region of the chromatin-remodeling factor CHD-3 (2003) FEBS Lett., 533, pp. 14-20Kobarg, C.B., Kobarg, J., Crosara-Alberto, D.P., Theizen, T.H., Franchini, K.G., MEF2C DNA-binding activity is inhibited through its interaction with the regulatory protein Ki-1/57 (2005) FEBS Lett., 579, pp. 2615-2622Nery, F.C., Rui, E., Kuniyoshi, T.M., Kobarg, J., Evidence for the interaction of the regulatory protein Ki-1/57 with p53 and its interacting proteins (2006) Biochem. Biophys. Res. Commun., 341, pp. 847-855Bressan, G.C., Quaresma, A.J.C., Moraes, E.C., Manfiolli, A.O., Passos, D.O., Gomes, M.D., Kobarg, J., Functional association of human Ki-1/57 with pre-mRNA splicing events (2009) FEBS J., 276, pp. 3770-3783Gonçalves, K.D.A., Bressan, G.C., Saito, A., Morello, L.G., Zanchin, N.I.T., Kobarg, J., Evidence for the association of the human regulatory protein Ki-1/57 with the translational machinery (2011) FEBS Lett., 585, pp. 2556-2560Nery, F.C., Passos, D.O., Garcia, V.S., Kobarg, J., Ki-1/57 interacts with RACK1 and is a substrate for the phosphorylation by phorbol 12-myristate 13-acetate-activated protein kinase C (2004) J. Biol. Chem., 279, pp. 11444-11455Passos, D.O., Bressan, G.C., Nery, F.C., Kobarg, J., Ki-1/57 interacts with PRMT1 and is a substrate for arginine methylation (2006) FEBS J., 273, pp. 3946-3961Lemos, T.A., Kobarg, J., CGI-55 interacts with nuclear proteins and co-localizes to p80-coilin positive-coiled bodies in the nucleus (2006) Cell Biochem. Biophys., 44, pp. 463-474Bressan, G.C., Kobarg, J., From protein interaction profile to functional assignment: the human protein Ki-1/57 is associated with pre-mRNA splicing events (2010) RNA Biol., 7, pp. 268-271Gray-McGuire, C., Guda, K., Adrianto, I., Lin, C.P., Natale, L., Potter, J.D., Newcomb, P., Buchanan, D., Confirmation of linkage to and localization of familial colon cancer risk haplotype on chromosome 9q22 (2010) Cancer Res., 70, pp. 5409-5418Koensgen, D., Mustea, A., Klaman, I., Sun, P., Zafrakas, M., Lichtenegger, W., Denkert, C., Sehouli, J., Expression analysis and RNA localization of PAI-RBP1 (SERBP1) in epithelial ovarian cancer: association with tumor progression (2007) Gynecol. Oncol., 107, pp. 266-273Sun, W., Guo, C., Meng, X., Yu, Y., Jin, Y., Tong, D., Geng, J., Bai, J., Differential expression of PAI-RBP1, C1orf142, and COTL1 in non-small cell lung cancer cell lines with different tumor metastatic potential (2012) J. Investig. Med., 60, pp. 689-694Morrissey, C., True, L.D., Roudier, M.P., Coleman, I.M., Hawley, S., Nelson, P.S., Coleman, R., Vessella, R.L., Differential expression of angiogenesis associated genes in prostate cancer bone, liver and lymph node metastases (2008) Clin. Exp. Metastasis, 25, pp. 377-388Nilsson, J., Sengupta, J., Frank, J., Nissen, P., Regulation of eukaryotic translation by the RACK1 protein: a platform for signalling molecules on the ribosome (2004) EMBO Rep., 5, pp. 1137-1141Xia, Z., Zheng, X., Zheng, H., Liu, X., Yang, Z., Wang, X., Cold-inducible RNA-binding protein (CIRP) regulates target mRNA stabilization in the mouse testis (2012) FEBS Lett., 586, pp. 3299-3308Khandjian, E.W., Huot, M.-E., Tremblay, S., Davidovic, L., Mazroui, R., Bardoni, B., Biochemical evidence for the association of fragile X mental retardation protein with brain polyribosomal ribonucleoparticles (2004) Proc. Natl. Acad. Sci. U. S. A., 101, pp. 13357-13362Braunschweig, U., Gueroussov, S., Plocik, A.M., Graveley, B.R., Blencowe, B.J., Dynamic integration of splicing within gene regulatory pathways (2013) Cell, 152, pp. 1252-1269Bressan, G.C., Silva, C., Borges, C., Passos, D.O., Ramos, C.H.I., Torriani, I.L., Ma, G., Human Regulatory Protein Ki-1/57 Has Characteristics of an Intrinstrinsically Unstructured Protein (2008) J. Proteome Res., 7, pp. 4465-4474Dyson, H.J., Wright, P.E., Intrinsically unstructured proteins and their functions (2005) Nat. Rev. Mol. Cell Biol., 6, pp. 197-208Gsponer, J., Futschik, M., Teichmann, S., Babu, M., Tight regulation of unstructured proteins: from transcript synthesis to protein degradation (2008) Science, 322, pp. 1365-1368Rohde, D., Hansen, H., Hafner, M., Lange, H., Mielke, V., Hansmann, M.L., Lemke, H., Cellular localizations and processing of the two molecular forms of the Hodgkin-associated Ki-1 (CD30) antigen. The protein kinase Ki-1/57 occurs in the nucleus (1992) Am. J. Pathol., 140, pp. 473-482Goodier, J.L., Zhang, L., Vetter, M.R., Kazazian, H.H., LINE-1 ORF1 protein localizes in stress granules with other RNA-binding proteins, including components of RNA interference RNA-induced silencing complex (2007) Mol. Cell. Biol., 27, pp. 6469-6483Lee, Y.-J., Wei, H.-M., Chen, L.-Y., Li, C., Localization of SERBP1 in stress granules and nucleoli (2014) FEBS J., 281, pp. 352-364Decker, C.J., Parker, R., P-bodies and stress granules: possible roles in the control of translation and mRNA degradation (2012) Cold Spring Harb. Perspect. Biol., 4, p. a012286Anderson, P., Kedersha, N., RNA granules: post-transcriptional and epigenetic modulators of gene expression (2009) Nat. Rev. Mol. Cell Biol., 10, pp. 430-436Bressan, G.C., Moraes, E.C., Manfiolli, A.O., Kuniyoshi, T.M., Passos, D.O., Gomes, M.D., Kobarg, J., Arginine methylation analysis of the splicing-associated SR protein SFRS9/SRP30C (2009) Cell. Mol. Biol. Lett., 14, pp. 657-669Carazzolle, M.F., de Carvalho, L.M., Slepicka, H.H., Vidal, R.O., Pereira, G.A.G., Kobarg, J., Meirelles, G.V., IIS-Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools (2014) PLoS One, 9, p. e100385Chen, E.Y., Tan, C.M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G.V., Clark, N.R., Ma'ayan, A., Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool (2013) BMC Bioinforma., 14, p. 128Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Ideker, T., Cytoscape: a software environment for integrated models of biomolecular interaction (2003) Networks, pp. 2498-2504Huelsenbeck, J.P., Ronquist, F., Nielsen, R., Bollback, J.P., Bayesian inference of phylogeny and its impact on evolutionary biology (2001) Science, 294, pp. 2310-2314Katoh, K., Misawa, K., Kuma, K., Miyata, T., MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform (2002) Nucleic Acids Res., 30, pp. 3059-3066Castresana, J., Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis (2000) Mol. Biol. Evol., 17, pp. 540-552Jones, D.T., Taylor, W.R., Thornton, J.M., The rapid generation of mutation data matrices from protein sequences (1992) Comput. Appl. Biosci., 8, pp. 275-282Darriba, D., Taboada, G.L., Doallo, R., Posada, D., ProtTest 3: fast selection of best-fit models of protein evolution (2011) Bioinformatics, 27, pp. 1164-1165Huang, L., Grammatikakis, N., Yoneda, M., Banerjee, S.D., Toole, B.P., Molecular characterization of a novel intracellular hyaluronan-binding protein (2000) J. Biol. Chem., 275, pp. 29829-29839Ivanov, K.I., Tselykh, T.V., Heino, T.I., Mäkinen, K., The RISC component VIG is a target for dsRNA-independent protein kinase activity in Drosophila S2 cells (2005) J. RNAi Gene Silenc., 1, pp. 12-20Wingender, E., Schoeps, T., Dönitz, J., TFClass: an expandable hierarchical classification of human transcription factors (2013) Nucleic Acids Res., 41, pp. D165-D170Ohtomo, N., Tomiya, T., Tanoue, Y., Inoue, Y., Nishikawa, T., Ikeda, H., Seyama, Y., Fujiwara, K., Expression of α-taxilin in hepatocellular carcinoma correlates with growth activity and malignant potential of the tumor (2010) Int. J. Oncol., 37, pp. 1417-1423Mashidori, T., Shirataki, H., Kamai, T., Nakamura, F., Yoshida, K.-I., Increased alpha-taxilin protein expression is associated with the metastatic and invasive potential of renal cell cancer (2011) Biomed. Res., 32, pp. 103-110Pan, Z., Erkan, M., Streit, S., Friess, H., Kleeff, J., Silencing of GRP94 expression promotes apoptosis in pancreatic (2009) Cancer Cells, pp. 823-828Yang, X., Khosravi-Far, R., Chang, H.Y., Baltimore, D., Daxx, a novel fas-binding protein that activates JNK and apoptosis (1997) Cell, 89, pp. 1067-1076Lin, L., Ozaki, T., Takada, Y., Kageyama, H., Nakamura, Y., Hata, A., Zhang, J.-H., Koseki, H., Topors, a p53 and topoisomerase I-binding RING finger protein, is a coactivator of p53 in growth suppression induced by DNA damage (2005) Oncogene, 24, pp. 3385-3396Zhao, F., Vilardi, A., Neely, R.J., Choi, J.K., Promotion of cell cycle progression by basic helix-loop-helix E2A (2001) Mol. Cell. Biol., 21, pp. 6346-6357Davidson, G., Shen, J., Huang, Y.-L., Su, Y., Karaulanov, E., Bartscherer, K., Hassler, C., Niehrs, C., Cell cycle control of wnt receptor activation (2009) Dev. Cell, 17, pp. 788-799Hashimoto, O., Yamato, K., Koseki, T., Ohguchi, M., Ishisaki, A., Shoji, H., Nakamura, T., Nishihara, T., The role of activin type I receptors in activin A-induced growth arrest and apoptosis in mouse B-cell hybridoma cells (1998) Cell. Signal., 10, pp. 743-749Wang, X., McGowan, C.H., Zhao, M., He, L., Downey, J.S., Fearns, C., Wang, Y., Han, J., Involvement of the MKK6-p38gamma cascade in gamma-radiation-induced cell cycle arrest (2000) Mol. Cell. Biol., 20, pp. 4543-4552Liang, Y., Yu, W., Li, Y., Yu, L., Zhang, Q., Wang, F., Yang, Z., Zhu, X., Nudel modulates kinetochore association and function of cytoplasmic dynein in M phase (2007) Mol. Biol. Cell, 18, pp. 2656-2666Sütterlin, C., Polishchuk, R., Pecot, M., Malhotra, V., The golgi-associated protein GRASP65 regulates spindle dynamics and is essential for cell division (2005) Mol. Biol. Cell, 16, pp. 3211-3222Hake, S.B., Garcia, B.A., Duncan, E.M., Kauer, M., Dellaire, G., Shabanowitz, J., Bazett-Jones, D.P., Hunt, D.F., Expression patterns and post-translational modifications associated with mammalian histone H3 variants (2006) J. Biol. Chem., 281, pp. 559-568Park, C.-H., Kim, K.-T., Apoptotic phosphorylation of histone H3 on Ser-10 by protein kinase Cδ (2012) PLoS One, 7, p. e44307Lee, Y.Y., Yu, Y.B., Gunawardena, H.P., Xie, L., Chen, X., BCLAF1 is a radiation-induced H2AX-interacting partner involved in γH2AX-mediated regulation of apoptosis and DNA repair (2012) Cell Death Dis., 3, p. e359Cho, S., Park, J.S., Kang, Y.-K., Dual functions of histone-lysine N-methyltransferase Setdb1 protein at promyelocytic leukemia-nuclear body (PML-NB): maintaining PML-NB structure and regulating the expression of its associated genes (2011) J. Biol. Chem., 286, pp. 41115-41124So, C.H., Michal, A., Komolov, K.E., Luo, J., Benovic, J.L., G protein-coupled receptor kinase 2 (GRK2) is localized to centrosomes and mediates epidermal growth factor-promoted centrosomal separation (2013) Mol. Biol. Cell, 24, pp. 2795-2806Chen, X., Zhu, H., Yuan, M., Fu, J., Zhou, Y., Ma, L., G-protein-coupled receptor kinase 5 phosphorylates p53 and inhibits DNA damage-induced apoptosis (2010) J. Biol. Chem., 285, pp. 12823-12830Bando, Y., Katayama, T., Aleshin, A.N., Manabe, T., Tohyama, M., GRP94 reduces cell death in SH-SY5Y cells perturbated calcium homeostasis (2004) Apoptosis, 9, pp. 501-508Agarwal, N., Tochigi, Y., Adhikari, A.S., Cui, S., Cui, Y., Iwakuma, T., MTBP plays a crucial role in mitotic progression and chromosome segregation (2011) Cell Death Differ., 18, pp. 1208-1219Odvody, J., Vincent, T., Arrate, M.P., Grieb, B., Wang, S., Garriga, J., Lozano, G., Eischen, C.M., A deficiency in Mdm2 binding protein inhibits Myc-induced B-cell proliferation and lymphomagenesis (2010) Oncogene, 29, pp. 3287-3296Brady, M., Vlatkovic, N., Boyd, M.T., Regulation of p53 and MDM2 activity by MTBP (2005) Mol. Cell. Biol., 25, pp. 545-553Lee, Y.-J., Hsieh, W.-Y., Chen, L.-Y., Li, C., Protein arginine methylation of SERBP1 by protein arginine methyltransferase 1 affects cytoplasmic/nuclear distribution (2012) J. Cell. Biochem., 113, pp. 2721-2728Mao, Y.S., Zhang, B., Spector, D.L., Biogenesis and function of nuclear bodies (2011) Trends Genet., 27, pp. 295-306Salomoni, P., The PML-interacting protein DAXX: histone loading gets into the picture (2013) Front. Oncol., 3, p. 152Peluso, J.J., Yuan, A., Liu, X., Lodde, V., Plasminogen activator inhibitor 1 RNA-binding protein interacts with progesterone receptor membrane component 1 to regulate progesterone's ability to maintain the viability of spontaneously immortalized granulosa cells and rat granulosa cells (2013) Biol. Reprod., 88, p. 20Lallemand-Breitenbach, V., de Thé, H., PML nuclear bodies (2010) Cold Spring Harb. Perspect. Biol., 2, p. a000661Golebiowski, F., Matic, I., Tatham, M.H., Cole, C., Yin, Y., Nakamura, A., Cox, J., Hay, R.T., System-wide changes to SUMO modifications in response to heat shock (2009) Sci. Signal., 2, p. ra24Wang, J., Shiels, C., Sasieni, P., Wu, P.J., Islam, S.A., Freemont, P.S., Sheer, D., Promyelocytic leukemia nuclear bodies associate with transcriptionally active genomic regions (2004) J. Cell Biol., 164, pp. 515-526Dellaire, G., Bazett-Jones, D.P., PML nuclear bodies: dynamic sensors of DNA damage and cellular stress (2004) Bioessays, 26, pp. 963-977Sudharsan, R., Azuma, Y., The SUMO ligase PIAS1 regulates UV-induced apoptosis by recruiting Daxx to SUMOylated foci (2012) J. Cell Sci., 125, pp. 5819-582