Abstract
Ultraviolet radiation resistance-associated gene product (UVRAG) was originally identified as a protein involved in cellular responses to UV irradiation. Subsequent studies have demonstrated that UVRAG plays as an important role in autophagy, a lysosome-dependent catabolic program, as a part of a pro-autophagy PIK3C3/VPS34 lipid kinase complex. Several recent studies have shown that UVRAG is also involved in autophagy-independent cellular functions, such as DNA repair/stability and vesicular trafficking/fusion. Here, we examined the UVRAG protein interactome to obtain information about its functional network. To this end, we screened UVRAG-interacting proteins using a tandem affinity purification method coupled with MALDI-TOF/MS analysis. Our results demonstrate that UVRAG interacts with various proteins involved in a wide spectrum of cellular functions, including genome stability, protein translational elongation, protein localization (trafficking), vacuole organization, transmembrane transport as well as autophagy. Notably, the interactome list of high-confidence UVRAG-interacting proteins is enriched for proteins involved in the regulation of genome stability. Our systematic UVRAG interactome analysis should provide important clues for understanding a variety of UVRAG functions.
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Chakraborty C, Doss CG, Chen L, Zhu H (2014) Evaluating protein-protein interaction (PPI) networks for diseases pathway, target discovery, and drug-design using ‘in silico pharmacology’. Curr Protein Pept Sci 15:561–571
Feng Y, Yao Z, Klionsky DJ (2015) How to control self-digestion: transcriptional, post-transcriptional, and post-translational regulation of autophagy. Trends Cell Biol 25:354–363
He S, Ni D, Ma B, Lee JH, Zhang T, Ghozalli I, Pirooz SD, Zhao Z, Bharatham N, Li B, Oh S, Lee WH, Takahashi Y, Wang HG, Minassian A, Feng P, Deretic V, Pepperkok R, Tagaya M, Yoon HS, Liang C (2013) PtdIns(3)P-bound UVRAG coordinates Golgi-ER retrograde and Atg9 transport by differential interactions with the ER tether and the beclin 1 complex. Nat Cell Biol 15:1206–1219
Horbinski C, Stachowiak MK, Higgins D, Finnegan SG (2001) Polyethyleneimine-mediated transfection of cultured postmitotic neurons from rat sympathetic ganglia and adult human retina. BMC Neurosci 2:2
Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57
Jiang P, Nishimura T, Sakamaki Y, Itakura E, Hatta T, Natsume T, Mizushima N (2014) The HOPS complex mediates autophagosome-lysosome fusion through interaction with syntaxin 17. Mol Biol Cell 25:1327–1337
Kim J, Kim YC, Fang C, Russell RC, Kim JH, Fan W, Liu R, Zhong Q, Guan KL (2013) Differential regulation of distinct Vps34 complexes by AMPK in nutrient stress and autophagy. Cell 152:290–303
Kuzmanov U, Emili A (2013) Protein-protein interaction networks: probing disease mechanisms using model systems. Genome Med 5:37
Lage K (2014) Protein-protein interactions and genetic diseases: the interactome. Biochim Biophys Acta 1842:1971–1980
Liang C, Feng P, Ku B, Dotan I, Canaani D, Oh BH, Jung JU (2006) Autophagic and tumour suppressor activity of a novel Beclin1-binding protein UVRAG. Nat Cell Biol 8:688–699
Liang C, Lee JS, Inn KS, Gack MU, Li Q, Roberts EA, Vergne I, Deretic V, Feng P, Akazawa C, Jung JU (2008) Beclin1-binding UVRAG targets the class C Vps complex to coordinate autophagosome maturation and endocytic trafficking. Nat Cell Biol 10:776–787
Lieber MR, Ma Y, Pannicke U, Schwarz K (2003) Mechanism and regulation of human non-homologous DNA end-joining. Nat Rev Mol Cell Biol 4:712–720
Mizushima N, Komatsu M (2011) Autophagy: renovation of cells and tissues. Cell 147:728–741
Mizushima N, Yoshimori T, Ohsumi Y (2011) The role of Atg proteins in autophagosome formation. Annu Rev Cell Dev Biol 27:107–132
Park JM, Tougeron D, Huang S, Okamoto K, Sinicrope FA (2014) Beclin 1 and UVRAG confer protection from radiation-induced DNA damage and maintain centrosome stability in colorectal cancer cells. PLoS One 9:e100819
Perelman B, Dafni N, Naiman T, Eli D, Yaakov M, Feng TL, Sinha S, Weber G, Khodaei S, Sancar A, Dotan I, Canaani D (1997) Molecular cloning of a novel human gene encoding a 63-kDa protein and its sublocalization within the 11q13 locus. Genomics 41:397–405
Pirooz SD, He S, Zhang T, Zhang X, Zhao Z, Oh S, O’Connell D, Khalilzadeh P, Amini-Bavil-Olyaee S, Farzan M, Liang C (2014) UVRAG is required for virus entry through combinatorial interaction with the class C-Vps complex and SNAREs. Proc Natl Acad Sci USA 111:2716–2721
Shieh SY, Ikeda M, Taya Y, Prives C (1997) DNA damage-induced phosphorylation of p53 alleviates inhibition by MDM2. Cell 91:325–334
Shieh SY, Taya Y, Prives C (1999) DNA damage-inducible phosphorylation of p53 at N-terminal sites including a novel site, Ser20, requires tetramerization. EMBO J 18:1815–1823
Simonsen A, Tooze SA (2009) Coordination of membrane events during autophagy by multiple class III PI3-kinase complexes. J Cell Biol 186:773–782
Stelzl U, Wanker EE (2006) The value of high quality protein-protein interaction networks for systems biology. Curr Opin Chem Biol 10:551–558
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C (2015) STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 43:D447–D452
Takahashi Y, Coppola D, Matsushita N, Cualing HD, Sun M, Sato Y, Liang C, Jung JU, Cheng JQ, Mulé JJ, Pledger WJ, Wang HG (2007) Bif-1 interacts with Beclin 1 through UVRAG and regulates autophagy and tumorigenesis. Nat Cell Biol 9:1142–1151
Wodak SJ, Vlasblom J, Turinsky AL, Pu S (2013) Protein-protein interaction networks: the puzzling riches. Curr Opin Struct Biol 23:941–953
Zhao Z, Oh S, Li D, Ni D, Pirooz SD, Lee JH, Yang S, Lee JY, Ghozalli I, Costanzo V, Stark JM, Liang C (2012) A dual role for UVRAG in maintaining chromosomal stability independent of autophagy. Dev Cell 22:1001–1016
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This work was supported by the National Research Foundation of Korea (NRF) Grant funded by the Korea government (MEST, No 2012R1A5A2051387).
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Son, JH., Hwang, E.C. & Kim, J. Systematic analyses of the ultraviolet radiation resistance-associated gene product (UVRAG) protein interactome by tandem affinity purification. Arch. Pharm. Res. 39, 370–379 (2016). https://doi.org/10.1007/s12272-015-0689-1
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DOI: https://doi.org/10.1007/s12272-015-0689-1