以作者查詢圖書館館藏

、以作者查詢臺灣博碩士

、以作者查詢全國書目

、勘誤回報

、線上人數：27

、訪客IP：18.191.195.110

姓名	曾祥慶(Hsiang-Ching Tseng)  查詢紙本館藏	畢業系所	生命科學系
論文名稱	(Functional analysis of biotin protein ligases from various species)
相關論文	★ Kineosphaera limosa 菌株中 phaC 基因之序列分析 ★ 剪力和組織蛋白去乙醯酶在動靜脈廔管失效扮演的角色 ★ Classification of powdery mildews on ornamental plants in northern Taiwan ★ 秀麗隱桿線蟲線粒體AlaRS通過非傳統模式識別T型無臂tRNAAla ★ Bacillus thuringiensis contains two prolyl-tRNA synthetases of different origins ★ Recognition of tRNA His isoacceptors by human HisRS isoforms ★ Functional replacement of yeast nuclear and mitochondrial RNase P by a protein-only RNase P ★ Functional characterization of a noncanonical ProRS in Toxoplasma gondii ★ tRNA aminoacylation by a naturally occurring mini-AlaRS ★ Functional Repurposing of C-Ala Domains ★ Recognition of a non-canonical tRNAAla by a non-canonical alanyl-tRNA synthetase ★ 探討Alanyl-tRNA synthetase的演化及專一性 ★ 酵母菌valyl-tRNA synthetase附加區段的 生物功能之探討 ★ 探討酵母菌glycyl-tRNA合成酵素的非傳統生物功能 ★ 探討酵母菌Valyl-tRNA synthetase的生化活性 ★ 酵母菌轉譯起始機制的研究
檔案	[Endnote RIS 格式]    [Bibtex 格式]    [相關文章]   [文章引用]   [完整記錄]   [館藏目錄]   [檢視]  [下載] 本電子論文使用權限為同意立即開放。 已達開放權限電子全文僅授權使用者為學術研究之目的，進行個人非營利性質之檢索、閱讀、列印。 請遵守中華民國著作權法之相關規定，切勿任意重製、散佈、改作、轉貼、播送，以免觸法。
摘要(中)	生物素可作為輔酶並參與生物體內一系列的羧化及去羧化反應，因此這些使用生物素當輔酶的酵素在許多重要代謝途徑中扮演不可或缺的角色，例如脂肪及含侧鏈胺基酸合成。生物素是用共價鍵結的方式與其相對應蛋白質上的離胺酸 (lysine) 做結合，過程需藉由特殊的酵素來執行，這些酵素稱為biotin protein ligase (BPL)。被修飾的離胺酸幾乎都位在羧化酶 (carboxylases) 中一段高度保守的序列AMKM。由於受質及酵素皆呈現高度保守，因此生物素化可以跨物種作用，例如酵母菌、阿拉伯芥、人類的BPL1都能有效地取代大腸桿菌的BPL (稱為birA)突變株。然而我的實驗結果卻顯示大腸桿菌的BPL不能互補酵母菌BPL1的剔除株。為了解開背後所蘊藏的分子機制，我試圖用融合蛋白、點突變、biotin濃度、和酵素濃度來研究此一現象，不幸地是所有的策略都無法讓酵素改變為正向的表現型。除此之外，本研究還想藉著融合Aquifex aeolicus BirA的催化區段與酵母菌Arc1p的tRNA結合區段，建構出能夠修飾tRNA的酵素。雖然這個融合蛋白仍具有催化的活性，不過修飾tRNA的活性不甚理想，故目前我們正改進實驗的條件。另外，我們也分析十株在演化過程相距甚遠之酵母菌BPL的序列相似性，結果發現他們的序列相似性約莫35%-60%，接著我們測試它們的跨物種互補活性，結果只有四株酵母菌株的BPL1可以將生物素加到自己的Arc1p，且這四株酵母菌的BPL1也可將生物素加至S. cerevisiae的Arc1p；另外六株則不行將生物素加到自己的Arc1p，也不可以將生物素加到S. cerevisiae的Arc1p，這些結果將有利於我們進一步分析BPL1的受質專一性。
摘要(英)	Biotin can serve as a coenzyme for a distinct set of catalytic reactions. Those biotin-dependent enzymes catalyze key steps which are involved in metabolic pathway. The covalent attachment of biotin to a conserved lysine residue in its cognate apoproteins is mediated by a specific enzyme, called biotin protein ligase (BPL). The biotinylated lysine residue is almost invariably positioned in a consensus sequence, AMKM, within the carboxylases. As a result, biotinylation can occur across widely divergent species. For example, the BPL1 homologues of yeast, Arabidopsis, and human can efficiently complement an E. coli birA mutant. Despite that, we found that some bacterial BPL1 homologues can functionally substitute for yeast BPL1, while others cannot substitute under similar conditions. To advance understanding of the functional property of this group of enzymes, we tried several different approaches, including mutagenesis, domain swapping, and gene expression. Unfortunately, none of the approaches can make the BPL rescue the negative phenotype. In addition, we tried to construct a biotin-tRNA-modifying enzyme by fusing a promiscuous Aquifex aeolicus BirA mutant and the tRNA-binding domain of yeast Arc1p. The resultant fusion protein still retained the biotin protein ligase activity, but was somehow inactive in modifying tRNA with biotin. Moreover, we have cloned BPL1 genes from ten yeast species and analyzed their sequence similarities. As it turned out, these yeast BPL1s possess 35%-60% similarities. Most interestingly, only four of the ten yeast BPL1s could biotinylate their own Arc1ps, and could biotinylate S. cerevisiae Arc1p. The remaining six yeast BPL1s failed to biotinylate their own Arc1ps, and could not biotinylate S. cerevisiae Arc1p. Such a finding may help us further delineate the substrate specificity of BPL1.
關鍵字(中)	★ 生物素 ★ 生物素化 ★ 離胺酸 ★ 蛋白質轉譯後修飾	關鍵字(英)
論文目次	摘要 Abstract Aknowledgement List of figures List of tables Appendixes Chapter Ⅰ Introduction 1 1.1. Overview of a protein post-translational modification - biotinylation 1 1.1.1. Protein biotinylation 1 1.1.2. Biotin and its physiological role 1 1.1.3. Mechanism of protein biotinylation by biotin protein ligase (BPL) 2 1.1.4. The classification of BPL 3 1.2. The structural difference and diversity of the biotinylated proteins 4 1.2.1. The structural difference of the biotinylated proteins 4 1.2.2. The diversity of the biotinylated proteins 5 1.3.. The promiscuous biotinylation activity for protein labeling 5 1.4. Specific aims 6 Chapter Ⅱ Materials and Methods 7 2.1. Strains, plasmids, and culture media 7 2.1.1. Strains 7 2.1.2. Plasmids 17 2.1.3. Culture media 8 2.2. Preparation and transformation of E. coli competent cells 9 2.2.1. Preparation of E.coli competent cells 9 2.2.2. Transformation of E. coli competent cells 10 2.3. Preparation and transformation of yeast competent cells 10 2.3.1. Preparation of yeast competent cells 10 2.3.2. Transformation of yeast competent cells 11 2.4. Construction of various BPLs and biotinylated substrates 12 2.5. Complementation assay for the cytoplasmic function of various BPLs 12 2.6 Protein preparation 12 2.7. SDS-PAGE 13 2.8. Western blot analysis 14 2.9. Purification of 6xHis-tagged proteins 16 2.10. In vitro biotinylation assay 19 2.11. Streptavidin-based gel mobility shift assay 19 Chapter Ⅲ Results 20 3.1. Properties of BPL retrieved from different species 20 3.2. Cross-species rescue activities of BPLs retrieved from distantly related organisms 20 3.3. Overexpression of EcBirA cannot rescue the yeast knockout strain 21 3.4. Effect of biotin concentration on the biotinylation activity of EcBirA 22 3.5. Switching the enzyme specificities between EcBirA and yeast BPL1 23 3.6. Not all bacterial BPLs containing a DNA binding domain failed to rescue the growth defect of the yeast knockout strain 23 3.7. Biotinylation of yeast carboxylase by EcBirA 24 3.8. Construction of a biotin tRNA ligase 25 3.9. Promiscuous biotinylation by BPL mutants 26 3.10. Expanding the substrate tolerance of BPL through exploration of BPL1 enzymes from various yeast species 26 Chapter Ⅳ Discussion 29 4.1. EcBirA cannot rescue the yeast BPL1 knockout strain 29 4.2. Construction of a biotin tRNA ligase 30 4.3. Screening for a BPL1 enzyme that can attach biotin analogues or derivaties to proteins 30 Bibliographies 32
參考文獻	Athappilly, F. K., & Hendrickson, W. A. (1995). Structure of the biotinyl domain of acetyl-coenzyme A carboxylase determined by MAD phasing. Structure, 3(12), 1407-1419 Azhar A, Booker GW, Polyak S.W. (2015) Mechanisms of Biotin Transport. Biochem Anal Biochem, 4:210 Brewster, N. K., Val, D. L., Walker, M. E., and Wallace, J. C. (1994) Arch. Biochem. Biophys, 311, 62–71 Bagautdinov, B., Kuroishi, C., Sugahara, M., & Kunishima, N. (2005). Crystal structures of biotin protein ligase from Pyrococcus horikoshii OT3 and its complexes: structural basis of biotin activation. J Mol Biol, 353(2), 322-333 Bagautdinov, B., Matsuura, Y., Bagautdinova, S., & Kunishima, N. (2008) Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate. J Biol Chem, 283(21), 14739-14750 Beckett, D. (2009). Biotin sensing at the molecular level. J Nutr, 139(1), 167-170 Bockman, M. R., Kalinda, A. S., Petrelli, R., De la Mora-Rey, T., Tiwari, D., Liu, F., . . . Aldrich, C. C. (2015). Targeting Mycobacterium tuberculosis Biotin Protein Ligase (MtBPL) with Nucleoside-Based Bisubstrate Adenylation Inhibitors. J Med Chem, 58(18), 7349-7369 Beenstock, J., Mooshayef, N., & Engelberg, D. (2016). How Do Protein Kinases Take a Selfie (Autophosphorylate)? Trends in Biochemical Sciences, 41(11), 938-953 Cronan, J. E., Jr. (1990). Biotination of proteins in vivo. A post-translational modification to label, purify, and study proteins. J Biol Chem, 265(18), 10327-10333 Chapman-Smith, A., Morris, T. W., Wallace, J. C., & Cronan, J. E., Jr. (1999). Molecular recognition in a post-translational modification of exceptional specificity. Mutants of the biotinylated domain of acetyl-CoA carboxylase defective in recognition by biotin protein ligase. J Biol Chem, 274(3), 1449-1457 Chapman-Smith, A., & Cronan, J. E., Jr. (1999a). In vivo enzymatic protein biotinylation. Biomol Eng, 16(1-4), 119-125 Chapman-Smith, A., & Cronan, J. E., Jr. (1999b). Molecular biology of biotin attachment to proteins. J Nutr, 129(2S Suppl), 477S-484S Chapman-Smith, A., Mulhern, T. D., Whelan, F., Cronan, J. E., Jr., & Wallace, J. C. (2001). The C-terminal domain of biotin protein ligase from E. coli is required for catalytic activity. Protein Sci, 10(12), 2608-2617 Campeau, E., & Gravel, R. A. (2001). Expression in Escherichia coli of N- and C-terminally deleted human holocarboxylase synthetase. Influence of the N-terminus on biotinylation and identification of a minimum functional protein. J Biol Chem, 276(15), 12310-12316 Choi-Rhee, E., Schulman, H., & Cronan, J. E. (2004). Promiscuous protein biotinylation by Escherichia coli biotin protein ligase. Protein Science : A Publication of the Protein Society, 13(11), 3043–3050 Chakravartty, V., & Cronan, J. E. (2013). The Wing of a Winged Helix-Turn-Helix Transcription Factor Organizes the Active Site of BirA, a Bifunctional Repressor/Ligase. The Journal of Biological Chemistry, 288(50), 36029–36039 Cronan, J. E. (2014). Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation. EcoSal Plus, 6(1) Cronan, J. E. (2016). Assembly of Lipoic Acid on Its Cognate Enzymes: an Extraordinary and Essential Biosynthetic Pathway. Microbiol Mol Biol Rev, 80(2), 429-450 Chapman-Smith, A., & Cronan, J. E., Jr. The enzymatic biotinylation of proteins: a post-translational modification of exceptional specificity. Trends in Biochemical Sciences, 24(9), 359-363 Duckworth, B. P., Geders, T. W., Tiwari, D., Boshoff, H. I., Sibbald, P. A., Barry, C. E., 3rd, . . . Aldrich, C. C. (2011). Bisubstrate adenylation inhibitors of biotin protein ligase from Mycobacterium tuberculosis. Chem Biol, 18(11), 1432-1441 de Oliveira, P. S. L., Ferraz, F. A. N., Pena, D. A., Pramio, D. T., Morais, F. A., & Schechtman, D. (2016). Revisiting protein kinase–substrate interactions: Toward therapeutic development. Science Signaling, 9(420), re3-re3 Eisenberg, M. A., Prakash, O., & Hsiung, S. C. (1982). Purification and properties of the biotin repressor. A bifunctional protein. J Biol Chem, 257(24), 15167-15173 Falnes, P. O., Jakobsson, M. E., Davydova, E., Ho, A., & Malecki, J. (2016). Protein lysine methylation by seven-beta-strand methyltransferases. Biochem J, 473(14), 1995-2009 Genbauffe, F. S., and Cooper, T. G. (1991) DNA Seq, 36, 19–32 Gupta, V., Gupta, R. K., Khare, G., Salunke, D. M., Surolia, A., & Tyagi, A. K. (2010). Structural ordering of disordered ligand-binding loops of biotin protein ligase into active conformations as a consequence of dehydration. PLoS One, 5(2), e9222 Hasslacher, M., Ivessa, A. S., Paltauf, F., and Kohlwein, S. D. (1993) J. Biol. Chem, 268, 10946–10952 Hoja U., Wellein C., Greiner E., Schweizer E. (1998). Pleiotropic phenotype of acetyl-CoA-carboxylase-defective yeast cells-viability of a BPL1-amber mutation depending on its readthrough by normal tRNA(Gln)(CAG). Eur J Biochem, 254(3):520-6 Hoja, U., Marthol, S., Hofmann, J., Stegner, S., Schulz, R., Meier, S., Greiner, E., and Schweizer, E. (2004) J. Biol. Chem, 279, 21779–21786 Kwon K., Streaker E.D., Ruparelia S., Beckett D. (2000). Multiple disordered loops function in corepressor-induced dimerization of the biotin repressor. J. Mol. Biol, 304:821–833 Kim, H. S., Hoja, U., Stolz, J., Sauer, G., & 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(41), 42445-42452 Kothapalli, N., Camporeale, G., Kueh, A., Chew, Y. C., Oommen, A. M., Griffin, J. B., & Zempleni, J. (2005). Biological functions of biotinylated histones. J Nutr Biochem, 16(7), 446-448 Kuroishi, T., Rios-Avila, L., Pestinger, V., Wijeratne, S. S., & Zempleni, J. (2011). Biotinylation is a natural, albeit rare, modification of human histones. Mol Genet Metab, 104(4), 537-545 Kim, D.I., Birendra, K.C., Zhu, W., Motamedchaboki, K., Doye, V., and Roux, K.J. (2014). Probing nuclear pore complex architecture with proximity-dependent biotinylation. Proceedings of the National Academy of Sciences of the United States of America, 111 E2453-2461 Leon-Del-Rio, A., Leclerc, D., Akerman, B., Wakamatsu, N., & Gravel, R. A. (1995). Isolation of a cDNA encoding human holocarboxylase synthetase by functional complementation of a biotin auxotroph of Escherichia coli. Proc Natl Acad Sci U S A, 92(10), 4626-4630 Lin, S., & Cronan, J. E. (2011). Closing in on complete pathways of biotin biosynthesis. Molecular BioSystems, 7(6), 1811-1821 Murthy P. N. A., Mistry S. P. (1974) Can. J. Biochem, 52:800–803 McAllister, H. C., & Coon, M. J. (1966). Further studies on the properties of liver propionyl coenzyme A holocarboxylase synthetase and the specificity of holocarboxylase formation. J Biol Chem, 241(12), 2855-2861 Mayende, L., Swift, R. D., Bailey, L. M., Soares da Costa, T. P., Wallace, J. C., Booker, G. W., & Polyak, S. W. (2012). A novel molecular mechanism to explain biotin-unresponsive holocarboxylase synthetase deficiency. J Mol Med (Berl), 90(1), 81-88 Ma, Q., Akhter, Y., Wilmanns, M. and Ehebauer, M. T. (2014), Active site conformational changes upon reaction intermediate biotinyl-5′-AMP binding in biotin protein ligase from Mycobacterium tuberculosis. Protein Science, 23: 932–939 Mehus, A.A., Anderson, R.H., and Roux, K.J. (2016). BioID Identification of Lamin-Associated Proteins. Methods in enzymology, 569, 3-22 Polyak, S. W., Chapman-Smith, A., Brautigan, P. J., & Wallace, J. C. (1999). Biotin protein ligase from Saccharomyces cerevisiae. The N-terminal domain is required for complete activity. J Biol Chem, 274(46), 32847-32854 Polyak, S. W., Chapman-Smith, A., Mulhern, T. D., Cronan, J. E., Jr., & Wallace, J. C. (2001). Mutational analysis of protein substrate presentation in the post-translational attachment of biotin to biotin domains. J Biol Chem, 276(5), 3037-3045 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), 973-982 Pendini, N. R., Yap, M. Y., Traore, D. A., Polyak, S. W., Cowieson, N. P., Abell, A., . . . Wilce, M. C. (2013). Structural characterization of Staphylococcus aureus biotin protein ligase and interaction partners: an antibiotic target. Protein Sci, 22(6), 762-773 Patel, D. J. (2016). A Structural Perspective on Readout of Epigenetic Histone and DNA Methylation Marks. Cold Spring Harb Perspect Biol, 8(3), a018754 Roberts, E. L., Shu, N., Howard, M. J., Broadhurst, R. W., Chapman-Smith, A., Wallace, J. C., . . . Perham, R. N. (1999). Solution structures of apo and holo biotinyl domains from acetyl coenzyme A carboxylase of Escherichia coli determined by triple-resonance nuclear magnetic resonance spectroscopy. Biochemistry, 38(16), 5045-5053 Roux, K. J., Kim, D. I., Raida, M., & Burke, B. (2012). A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells. J Cell Biol, 196(6), 801-810 Roux, K. J., Kim, D. I., & Burke, B. (2013). BioID: a screen for protein-protein interactions. Curr Protoc Protein Sci, 74, Unit 19 23 Stolz, J., Ludwig, A., & Sauer, N. (1998). Bacteriophage lambda surface display of a bacterial biotin acceptor domain reveals the minimal peptide size required for biotinylation. FEBS Lett, 440(1-2), 213-217 Slavoff, S. A., Chen, I., & Ting, A. Y. (2008). Expanding the substrate tolerance of biotin ligase through exploration of enzymes from diverse species. Journal of the American Chemical Society, 130(4), 1160–1162 Tissot, G., Douce, R., & Alban, C. (1997). Evidence for multiple forms of biotin holocarboxylase synthetase in pea (Pisum sativum) and in Arabidopsis thaliana: subcellular fractionation studies and isolation of a cDNA clone. Biochem J, 323 ( Pt 1), 179-188 Tissot, G., Pepin, R., Job, D., Douce, R., & Alban, C. (1998). Purification and properties of the chloroplastic form of biotin holocarboxylase synthetase from Arabidopsis thaliana overexpressed in Escherichia coli. Eur J Biochem, 258(2), 586-596 Tron, C. M., McNae, I. W., Nutley, M., Clarke, D. J., Cooper, A., Walkinshaw, M. D., . . . Campopiano, D. J. (2009). Structural and functional studies of the biotin protein ligase from Aquifex aeolicus reveal a critical role for a conserved residue in target specificity. J Mol Biol, 387(1), 129-146 Tong, L. (2013) Structure and function of biotin-dependnet a carboxylases. Cell. Mol. Life Sci, 70: 863 Wilson, K. P., Shewchuk, L. M., Brennan, R. G., Otsuka, A. J., & Matthews, B. W. (1992). Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains. Proc Natl Acad Sci U S A, 89(19), 9257-9261 Weaver, L. H., Kwon, K., Beckett, D., & Matthews, B. W. (2001). Corepressor-induced organization and assembly of the biotin repressor: a model for allosteric activation of a transcriptional regulator. Proc Natl Acad Sci U S A, 98(11), 6045-6050 Wood, Z. A., Weaver, L. H., Brown, P. H., Beckett, D., & Matthews, B. W. (2006). Co-repressor induced order and biotin repressor dimerization: a case for divergent followed by convergent evolution. J Mol Biol, 357(2), 509-523 Xu, Y. and Beckett, D. (1994) Kinetics of Biotinyl-5′-adenylate Synthesis Catalyzed by the Escherichia coli Repressor of Biotin Biosynthesis and the Stability of the Enzyme-Product Complex. Biochemistry, 1994, 33 (23), pp 7354–7360 Yao, X., Wei, D., Soden, C., Jr., Summers, M. F., & Beckett, D. (1997). Structure of the carboxy-terminal fragment of the apo-biotin carboxyl carrier subunit of Escherichia coli acetyl-CoA carboxylase. Biochemistry, 36(49), 15089-15100
指導教授	王健家	審核日期	2017-6-21
推文	facebook   plurk   twitter   funp   google   live   udn   HD   myshare   reddit   netvibes   friend   youpush   delicious   baidu
網路書籤	Google bookmarks   del.icio.us   hemidemi   myshare