跳到主要內容

簡易檢索 / 詳目顯示

研究生: 尼古拉
Restu Nugraha
論文名稱: Effect of Biotinylation on the Structure and Function of a Yeast tRNA-Binding Protein
Effect of Biotinylation on the Structure and Function of a Yeast tRNA-Binding Protein
指導教授: 王健家
Chien-Chia Wang
Widodo
Widodo
口試委員:
學位類別: 碩士
Master
系所名稱: 生醫理工學院 - 生命科學系
Department of Life Science
論文出版年: 2018
畢業學年度: 106
語文別: 英文
論文頁數: 47
中文關鍵詞: 生物素化突變
外文關鍵詞: Biotinylation, Arc1p
相關次數: 點閱:23下載:0
分享至:
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報
  • 中文摘要

    Arc1p是一個酵母菌tRNA結合蛋白質,它能與細胞質中的 glutamyl-tRNA synthetase(GluRSc)和 methionyl-tRNA Synthetase(MetRS)形成三元複合物。形成複合物可以顯著提高這兩種酵素對其相對應tRNA的胺醯化效率。最近的研究發現,Arc1p 的 N 端區域Lys86可以被轉譯後修飾,加上一個生物素(biotin)為了進一步研究生物素化(biotinylation)對Arc1p的結構及功能影響,我們進一步純化及比較野生型及突變型Arc1p的結構差異,結果發現發現:K86R和K86A突變完全阻斷了Arc1p生物素化,但是不會影響該蛋白質的細胞內功能,突變Arc1p仍能解救ARC1剔除株的cold sensitive外表型。然而,生物素化將會將影響Arc1p的熱穩定性,且 K86R在蛋白酶處理下看起來更耐受,而K86A更敏感。

    關鍵詞:Arc1p,生物素化,K86R,K86A,突變


    Abstract

    Arc1p is a yeast-specific tRNA-binding protein that has ability to form a ternary complex with glutamyl-tRNA synthetase (GluRSc) and methionyl-tRNA synthetase (MetRS) in the cytoplasm. This complex can significantly enhance the aminoacylation efficiency of these two aaRSs to their respective cognate tRNAs. Recently, it was found that Arc1p can be biotinylated via post-translational modification at Lys86 (K86) in the N-domain. We herein studied the effect of K86 mutation on Arc1p’s structure and function. We found that mutation in K86R and K86A dramatically decreased the biotinylation level of Arc1p and altered its secondary structure. However, the mutant Arc1p could effectively rescue the cold-sensitive phenotype of an ARC1- strain, suggesting that biotinylation is dispensable for the rescue activity of Arc1p. Interestingly, K86R was more resistant to protease treatment than the wild-type, while K86A was more sensitive.

    Keywords: Arc1p, biotinylation, K86A, K86R, mutation.

    Table of Content Abstract i Acknowledgments ii Table of content iii List of Figure iv Abbreviation v Chapter I – Introduction 1 Background 1 Objectives 2 Outlines 2 Chapter II – Literature Review 3 2. 1 Arc1p and Its Properties 3 2. 2 Role and Function of Arc1p 4 2. 3 Aminoacyl-tRNA Synthetase (aaRS) 4 2. 4 Multi-aminoacyl-tRNA Synthetase 6 2. 5 Biotinylation 7 Chapter III – Materials and Methods 9 3. 1 Strain, Culture Medium, and Transformation 9 3. 2 Plasmid Construction 11 3. 3 Arc1p Purification 11 3. 4 Western Blotting Method 13 3. 5 Streptavidin-based Gel Mobility Shift Assay 14 3. 6 Circular Dichroism (CD) Spectroscopy 15 3. 7 Limited Proteolysis 15 Chapter IV – Result 16 4.1 Biotinylation of Yeast Arc1p and Variants 16 4.2 Biotinylation of Arc1p’s is not Required for the Rescue Activity 16 4.3 Effect of Biotinylation on the Secondary Structure in Vitro of Arc1p 17 4.4 Purification and Characterization of Arc1p Variant 17 Chapter V – Discussion and Conclusion 19 5.1 Discussion 19 5.2 Conclusion 20 Reference 21 Appendix 25

    References
    1. Alegria-Schaffer, Alice. (2014) Chapter Ten - Protein Biotinylation. Methods in Enzymology. 536, 109-114
    2. Awasthi, Niranjan, Margaret A. S., Varun V., Clint C., Roderich E S. (2009) Endothelial monocyte activating polypeptide II interferes with VEGF-induced proangiogenic signaling. Laboratory Investigation. 89, 38–46 doi:10.1038/labinvest.2008.106
    3. Beckett, D. (2007) Biotin sensing: universal influence of biotin status on transcription. Annu. Rev. Genet. 41, 443–464
    4. Betts, Matthew J. and Robert B. R. (2003) Amino Acid Properties and Consequences of Substitutions. Bioinformatics for Geneticists. Edited by Michael R. Barnes and Ian C. Gray Copyright. John Wiley & Sons, Ltd
    5. Chang, Chia-Pei., Yi-Kuan T., Chou-Yuan Ko., and Chien-Chia W. (2011) Alanyl-tRNA synthetase genes of Vanderwaltozyma polyspora arose from duplication of a dual-functional predecessor of mitochondrial origin. Nucleic Acids Research. 40, No. 1
    6. Copley R.R., Barton G, J. (1994) A structural analysis of phosphate and sulphate binding sites in proteins. Estimation of propensities for binding and conservation of phosphate binding sites. J Mol Biol 242, 321–329
    7. Cronan, J. E., Jr. (1990) J. Biol. Chem. 265, 10327–10333
    8. Deinert, K., Fasiolo, F., Hurt, E.C. and Simos, G. (2001) Arc1p organizes the yeast aminoacyl-tRNA synthetase complex and stabilizes its interaction with the cognate tRNAs. J. Biol. Chem. 276, 6000–6008
    9. Dmitry. (1999) An introduction to circular dichroism spectroscopy. https://www.chem.uci.edu/
    10. Edvardson S, Shaag A, Kolesnikova O et al. (2007) Deleterious mutation in the mitochondrial arginyl-transfer RNA synthetase gene is associated with pontocerebellar hypoplasia. Am J Hum Genet 81, 857–862
    11. Filonenko V.V., Deutscher M, P. (1994) Evidence for similar structural organization of the multienzyme aminoacyl-tRNA synthetase complex in vivo and in vitro. J. Biol. Chem. 269, 17375–17378
    12. Finkenwirth, Friedrich., Franziska K., and Thomas E. (2014) A versatile Escherichia coli strain for identification of biotin transporters and for biotin quantification. Bioengineered. 5(2), 129–132
    13. Frechin, M., Daniel K., Robert P. M., Hubert D. B., Bruno S. (2010) Arc1p: Anchoring, routing, coordinating. FEBS Letters 584, 427–433
    14. Golinelli-Cohen, M.P. and Mirande, M. (2007) Arc1p is required for cytoplasmic confinement of synthetases and tRNA. Mol. Cell. Biochem. 300, 47–59
    15. Graindorge, J.S., Senger, B., Tritch, D., Simos, G. and Fasiolo, F. (2005) Role of Arc1p in the modulation of yeast glutamyl-tRNA synthetase activity. Biochemistry 44, 1344–1352
    16. Green, N.M. (1990) Avidin and streptavidin. Method Enzymol 184, 51–67
    17. Ibba, M. and Soll, D. (2000) Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69, 617–650
    18. Kaminska, M., Havrylenko, S., Decottignies, P., Gillet, S., Le Marechal, P., Negrutskii, B. and Mirande, M. (2009) Dissection of the structural organization of the aminoacyl-tRNA synthetase complex. J. Biol. Chem. 284, 6053–6060
    19. Kern, D., Dietrich, A., Fasiolo, F., Renaud, M., Giege, R. and Ebel, J.P. (1977) The yeast aminoacyl-tRNA synthetases. Methodology for their complete or partial purification and comparison of their relative activities under various extraction conditions. Biochimie 59, 453–462
    20. Kern, D. and Lapointe, J. (1979) The twenty aminoacyl-tRNA synthetases from Escherichia coli. General separation procedure, and comparison of the influence of pH and divalent cations on their catalytic activities. Biochimie 61, 1257–1272
    21. Kim, H. S., Hoja, U., Stolz, J., Sauer, G., and Schweizer, E. (2004) Identification of the tRNA-binding protein Arc1p as a novel target of in vivo biotinylation in Saccharomyces cerevisiae. J. Biol. Chem. 279, 42445– 42452
    22. Kim, Sunghoon Ed. (2014) Aminoacyl-tRNA Synthetases in Biology and Medicine. Springer Dordrecht Heidelberg New York London
    23. Labauge P, Dorboz I, Eymard-Pierre E, Dereeper O, Boespflug-Tanguy O. (2011) Clinically asymptomatic adult patient with extensive LBSL MRI pattern and DARS2 mutations. J Neurol 258: 335-337
    24. Lane, M. D., Young, D. L., and Lynen, F. (1964) J. Biol. Chem. 239, 2858–2864
    25. Laporte D., Jonathan L. H., Gaétan B., Ludovic E., Bruno S., Hubert D. B. (2014) Exploring the evolutionary diversity and assembly modes of multi-aminoacyl-tRNA synthetase complexes: Lessons from unicellular organisms. FEBS Letters 588, 4268–4278
    26. Mirande M., et al. (1985) A complex from cultured Chinese hamster ovary cells containing nine aminoacyltRNA synthetases. Thermolabile leucyl-tRNA synthetase from the tsH1 mutant cell line is an integral component of this complex. Eur. J. Biochem. 147, 281–289
    27. Nakama, T., Nureki, O., Yokoyama, S., (2001) Structural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase. J. Biol. Chem. 276, 47387–47393
    28. Nathanson L., Deutscher M, P. (2000) Active aminoacyl-tRNA synthetases are present in nuclei as a high molecular weight multienzyme complex. J. Biol. Chem. 275, 31559–31562
    29. Negrutskii B, S., Deutscher M, P. (1991) Channeling of aminoacyl-tRNA for protein synthesis in vivo. Proc. Natl. Acad. Sci. U.S.A. 88, 4991–4995
    30. Pendini N.R., Bailey L.M., Booker G.W., Wilce M.C., Wallace J.C., Polyak S.W. (2008) Microbial biotin protein ligases aid in understanding holocarboxylase synthetase deficiency. Biochim Biophys Acta. 1784(7-8):973-82
    31. Ray P, S., et al. (2007) Macromolecular complexes as depots for releasable regulatory proteins. Trends Biochem. Sci. 32, 158–164
    32. Sandeepa M., Eswarappa. and Paul L. Fox. (2013) Citric acid cycle and the origin of MARS. Trends Biochem Sci. 38(5), 222–228. doi:10.1016/j.tibs.2013.01.005
    33. Schechter, I., Berger A. (1967) On the size of the active site in proteases. I. Papain. Biochem Biophys Res Commun. 27, 157–62
    34. Simader, H., Hothorn, M., Kohler, C., Basquin, J., Simos, G. and Suck, D. (2006) Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes. Nucleic Acids Res. 34, 3968–3979
    35. Simos, George., Alexandra S., Franco F., Klaus H., Andrei S., Mattias M., Eduard C.H. (1996) The yeast protein Arcip binds to tRNA and functions as a cofactor for the methionyl- and glutamyl-tRNA synthetases. The EMBO Journal. 15 no.19, 5437-5448
    36. Simos, G., Sauer, A., Fasiolo, F. and Hurt, E.C. (1998) A conserved domain within Arc1p delivers tRNA to aminoacyl-tRNA synthetases. Mol. Cell. 1, 235–242
    37. Srimonti, S., and Hopper, A. K. (1998) Mol. Biol. Cell 9, 3041–3055.
    38. Yadavalli SS, Ibba M. (2012) Quality control in aminoacyl-tRNA synthesis its role in translational fidelity. Adv Protein Chem Struct Biol 86, 1–43
    39. Yao, C.C., Chia-Pei C., Shruti C., Shao-Win W., Yi-Kuan T. and Chien-Chia W. (2016) Modulating the Structure and Function of an Aminoacyl-tRNA Synthetase Cofactor by Biotinylation. The Journal of Biological Chemistry. 291, No. 33, 17102–17111
    40. Yao, Peng and Paul L. Fox. (2013) Aminoacyl-tRNA synthetases in medicine and disease. EMBO Mol Med. 5, 332–343
    41. Zempleni J., Teixeira D.C., Kuroishi T., Cordonier E, L., Baier S. (2011) Biotin requirements for DNA damage prevention. Mutat Res. 733, 58–60.

    QR CODE
    :::