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01-03-2017 | Original Paper

Identification of Novel SCIRR69-Interacting Proteins During ER Stress Using SILAC-Immunoprecipitation Quantitative Proteomics Approach

Authors: Yujian Chen, Yong Liu, Shide Lin, Shuguang Yang, Haiping Que, Shaojun Liu

Published in: NeuroMolecular Medicine | Issue 1/2017

Abstract

Spinal cord injury and regeneration-related protein #69 (SCIRR69),also known as cAMP-responsive element-binding protein 3-like 2, belongs to the CREB/ATF family, some members of which play significant roles in ER stress. However, it is still not fully elucidated whether SCIRR69 involves in ER stress and its biochemical and functional roles during ER stress. In this study, we firstly treated fetal rat spinal cord neuron cells (SCN) and PC12 cells with ER stress activator thapsigargin (TG) or tunicamycin (TM) and then detected the expression pattern of SCIRR69 in response to ER stress at mRNA and protein levels using real-time PCR assay and immunoblotting. Results showed that the expression pattern of SCIRR69 was largely consistent with those of ER stress marker (ATF6, BIP and CHOP) at either mRNA level or protein level, implying that SCIRR69 may play important roles in ER stress. Subsequently, we used stable isotope labeling by amino acids in cell culture (SILAC)-immunoprecipitation quantitative proteomics to identify interaction partners of SCIRR69 during TG-induced ER stress in PC12 cells and found that transitional endoplasmic reticulum ATPase (TERA) and sideroflexin-1 (SFXN1) were potential SCIRR69-interacting proteins. The interaction between SCIRR69 and TERA or SFXN1 was validated using co-immunoprecipitation. Those results provide some clues for novel signaling nexuses that made by interactions between SCIRR69 and TERA or SFXN1. Our findings may facilitate a better understanding of the fundamental functions of SCIRR69 during ER stress.

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Acs, K., Luijsterburg, M. S., Ackermann, L., Salomons, F. A., Hoppe, T., & Dantuma, N. P. (2011). The AAA-ATPase VCP/p97 promotes 53BP1 recruitment by removing L3MBTL1 from DNA double-strand breaks. Nature Structural & Molecular Biology, 18(12), 1345–1350.CrossRef

Cox, J., & Mann, M. (2008). MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nature Biotechnology, 26(12), 1367–1372.CrossRefPubMed

Emmott, E., Munday, D., Bickerton, E., Britton, P., Rodgers, M. A., Whitehouse, A., et al. (2013). The cellular interactome of the coronavirus infectious bronchitis virus nucleocapsid protein and functional implications for virus biology. Journal of Virology, 87(17), 9486–9500.CrossRefPubMedPubMedCentral

Engin, F., & Hotamisligil, G. S. (2010). Restoring endoplasmic reticulum function by chemical chaperones: an emerging therapeutic approach for metabolic diseases. Diabetes, Obesity & Metabolism, 12(Suppl 2), 108–115.CrossRef

Fleming, M. D., Campagna, D. R., Haslett, J. N., Trenor, C. C, 3rd, & Andrews, N. C. (2001). A mutation in a mitochondrial transmembrane protein is responsible for the pleiotropic hematological and skeletal phenotype of flexed-tail (f/f) mice. Genes & Development, 15(6), 652–657.CrossRef

Fowler, S. L., Akins, M., Zhou, H., Figeys, D., & Bennett, S. A. (2013). The liver connexin32 interactome is a novel plasma membrane-mitochondrial signaling nexus. Journal of Proteome Research, 12(6), 2597–2610.CrossRefPubMedPubMedCentral

Fujita, K., Nakamura, Y., Oka, T., Ito, H., Tamura, T., Tagawa, K., et al. (2013). A functional deficiency of TERA/VCP/p97 contributes to impaired DNA repair in multiple polyglutamine diseases. Nat Commun, 4, 1816.CrossRefPubMedPubMedCentral

Kehat, I., Hasin, T., & Aronheim, A. (2006). The role of basic leucine zipper protein-mediated transcription in physiological and pathological myocardial hypertrophy. Annals of the New York Academy of Sciences, 1080, 97–109.CrossRefPubMed

Keller, A., Nesvizhskii, A. I., Kolker, E., & Aebersold, R. (2002). Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Analytical Chemistry, 74(20), 5383–5392.CrossRefPubMed

Kittler, R., Putz, G., Pelletier, L., Poser, I., Heninger, A. K., Drechsel, D., et al. (2004). An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division. Nature, 432(7020), 1036–1040.CrossRefPubMed

Li, X., Han, D., Kin Ting Kam, R., Guo, X., Chen, M., Yang, Y., et al. (2010). Developmental expression of sideroflexin family genes in Xenopus embryos. Developmental Dynamics, 239(10), 2742–2747.CrossRefPubMed

Liu, Y., Que, H., Ma, Z., Yang, S., Ni, Y., Luo, Z., et al. (2013). Transcription factor SCIRR69 involved in the activation of brain-derived neurotrophic factor gene promoter II in mechanically injured neurons. Neuromolecular Med, 15(3), 605–622.CrossRefPubMed

Ma, Z., Que, H., Ni, Y., Huang, H., Liu, Y., Liu, T., et al. (2012). Cloning and characterization of SCIRR69: a novel transcriptional factor belonging to the CREB/ATF family. Molecular Biology Reports, 39(7), 7665–7672.CrossRefPubMed

Meerang, M., Ritz, D., Paliwal, S., Garajova, Z., Bosshard, M., Mailand, N., et al. (2011). The ubiquitin-selective segregase VCP/p97 orchestrates the response to DNA double-strand breaks. Nature Cell Biology, 13(11), 1376–1382.CrossRefPubMed

Miotto, G., Tessaro, S., Rotta, G. A., & Bonatto, D. (2007). In silico analyses of Fsf1 sequences, a new group of fungal proteins orthologous to the metazoan sideroblastic anemia-related sideroflexin family. Fungal Genetics and Biology, 44(8), 740–753.CrossRefPubMed

Murakami, T., Kondo, S., Ogata, M., Kanemoto, S., Saito, A., Wanaka, A., et al. (2006). Cleavage of the membrane-bound transcription factor OASIS in response to endoplasmic reticulum stress. Journal of Neurochemistry, 96(4), 1090–1100.CrossRefPubMed

Nesvizhskii, A. I., Keller, A., Kolker, E., & Aebersold, R. (2003). A statistical model for identifying proteins by tandem mass spectrometry. Analytical Chemistry, 75(17), 4646–4658.CrossRefPubMed

Omori, Y., Imai, J., Watanabe, M., Komatsu, T., Suzuki, Y., Kataoka, K., et al. (2001). CREB-H: a novel mammalian transcription factor belonging to the CREB/ATF family and functioning via the box-B element with a liver-specific expression. Nucleic Acids Research, 29(10), 2154–2162.CrossRefPubMedPubMedCentral

Ribeiro, A., Brown, A., & Lee, K. A. (1994). An in vivo assay for members of the cAMP response element-binding protein family of transcription factors. Journal of Biological Chemistry, 269(49), 31124–31128.PubMed

Roy, B., & Lee, A. S. (1999). The mammalian endoplasmic reticulum stress response element consists of an evolutionarily conserved tripartite structure and interacts with a novel stress-inducible complex. Nucleic Acids Research, 27(6), 1437–1443.CrossRefPubMedPubMedCentral

Shen, J., & Prywes, R. (2005). ER stress signaling by regulated proteolysis of ATF6. Methods, 35(4), 382–389.CrossRefPubMed

Trinkle-Mulcahy, L. (2012). Resolving protein interactions and complexes by affinity purification followed by label-based quantitative mass spectrometry. Proteomics, 12(10), 1623–1638.CrossRefPubMed

Trinkle-Mulcahy, L., Boulon, S., Lam, Y. W., Urcia, R., Boisvert, F. M., Vandermoere, F., et al. (2008). Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. Journal of Cell Biology, 183(2), 223–239.CrossRefPubMedPubMedCentral

Walter, P., & Ron, D. (2011). The unfolded protein response: from stress pathway to homeostatic regulation. Science, 334(6059), 1081–1086.CrossRefPubMed

Wang, S., & Kaufman, R. J. (2012). The impact of the unfolded protein response on human disease. Journal of Cell Biology, 197(7), 857–867.CrossRefPubMedPubMedCentral

Williamson, M. P., & Sutcliffe, M. J. (2010). Protein-protein interactions. Biochemical Society Transactions, 38(4), 875–878.CrossRefPubMed

Woodman, P. G. (2003). p97, a protein coping with multiple identities. Journal of Cell Science, 116(Pt 21), 4283–4290.CrossRefPubMed

Ye, Y., Meyer, H. H., & Rapoport, T. A. (2001). The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol. Nature, 414(6864), 652–656.CrossRefPubMed

Ye, Y., Shibata, Y., Yun, C., Ron, D., & Rapoport, T. A. (2004). A membrane protein complex mediates retro-translocation from the ER lumen into the cytosol. Nature, 429(6994), 841–847.CrossRefPubMed

Ye, X., Xu, J., Cheng, C., Yin, G., Zeng, L., Ji, C., et al. (2003). Isolation and characterization of a novel human putative anemia-related gene homologous to mouse sideroflexin. Biochemical Genetics, 41(3–4), 119–125.CrossRefPubMed

Yoshida, H., Haze, K., Yanagi, H., Yura, T., & Mori, K. (1998). Identification of the cis-acting endoplasmic reticulum stress response element responsible for transcriptional induction of mammalian glucose-regulated proteins. Involvement of basic leucine zipper transcription factors. Journal of Biological Chemistry, 273(50), 33741–33749.CrossRefPubMed

Yoshida, H., Okada, T., Haze, K., Yanagi, H., Yura, T., Negishi, M., et al. (2000). ATF6 activated by proteolysis binds in the presence of NF-Y (CBF) directly to the cis-acting element responsible for the mammalian unfolded protein response. Molecular and Cellular Biology, 20(18), 6755–6767.CrossRefPubMedPubMedCentral

Zhong, X., Shen, Y., Ballar, P., Apostolou, A., Agami, R., & Fang, S. (2004). AAA ATPase p97/valosin-containing protein interacts with gp78, a ubiquitin ligase for endoplasmic reticulum-associated degradation. Journal of Biological Chemistry, 279(44), 45676–45684.CrossRefPubMed

Title: Identification of Novel SCIRR69-Interacting Proteins During ER Stress Using SILAC-Immunoprecipitation Quantitative Proteomics Approach
Authors: Yujian Chen
Yong Liu
Shide Lin
Shuguang Yang
Haiping Que
Shaojun Liu
Publication date: 01-03-2017
Publisher: Springer US
Published in: NeuroMolecular Medicine / Issue 1/2017
Print ISSN: 1535-1084
Electronic ISSN: 1559-1174
DOI: https://doi.org/10.1007/s12017-016-8431-9

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

Identification of Novel SCIRR69-Interacting Proteins During ER Stress Using SILAC-Immunoprecipitation Quantitative Proteomics Approach

Abstract

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

Abstract

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