簡易檢索 / 詳目顯示

研究生: 曹詠翔
Cao, Yong-Shiang
論文名稱: 研究胃幽門螺旋桿菌的全面性調控蛋白CsrA功能與其X-ray晶體繞射數據分析
Functional study and X-ray diffraction analysis of the global regulator protein CsrA from Helicobacter pylori
指導教授: 王淑鶯
Wang, Shu-Ying
學位類別: 碩士
Master
系所名稱: 醫學院 - 微生物及免疫學研究所
Department of Microbiology & Immunology
論文出版年: 2014
畢業學年度: 102
語文別: 中文
論文頁數: 53
中文關鍵詞: 胃幽門螺旋桿菌碳源調控蛋白RNA結合游動力
外文關鍵詞: Helicobacter pylori, carbon storage regulator, RNA binding, motility
相關次數: 點閱:92下載:5
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
  • 全世界約有一半的人口感染了胃幽門桿菌,並且這株細菌與胃潰瘍和胃癌等疾病相關。雖然目前已經發現有許多因子對於細菌的感染所造成疾病很重要的,但是如何藉由調控基因表現改變這些因子功能的分子作用機制目前還不是很清楚。碳源調控蛋白, CsrA,是一種全面性調控蛋白,與生物膜的生成、細菌的游動能力、細菌鞭毛的合成等許多功能相關。為了了解CsrA在結構與功能是如何調控這些基因表現,以X-ray結晶學的方式研究CsrA蛋白質結構。從Escherichia coli大量表達CsrA重組蛋白,並且以親合性鎳離子螯合樹脂色層分析法與粒徑篩析層析法得到純度高的蛋白質,成功得到CsrA蛋白質結晶以及為了解出相位的硒甲硫氨酸化CsrA蛋白質結晶,並且收集了這些晶體的X光繞射數據。因為無法找出正確的晶格群 (space group),所以沒有辦法正確的解出蛋白質結構。對於CsrA的功能研究,我們發現CsrA會與flaA的RNA結合,當精胺酸(arginine) 44這個位置的胺基酸突變成丙氨酸(alanine)後,CsrA幾乎失去了與RNA結合的能力,與野生株的胃幽門桿菌相比,其游動能力也明顯的下降。

    To understand the structure-functional relationship of CsrA and the molecular mechanism by which CsrA exerts its function to regulate the gene expression, we aim to determine the crystal structure of CsrA by X-ray crystallography, SAXS, EMSA, and motility assay. We have purified CsrA and selenomethionyl CsrA protein, and get the crystals for X-ray diffraction data. But the structure of CsrA cannot be solved due to wrong space group. In the functional study of CsrA, CsrA can directly bind to flaA leader RNA, flaA1and flaA2. Residue Arg44 was involved in RNA recognition. The motility of csrA R44A mutant was significantly decreased by comparing with wild type H. pylori. In this study, CsrA can bind RNA by Arg44, and mutation of this site decrease bacteria motility.

    中文摘要 I 英文延伸摘要 II 致謝 XIII 目錄 XIV 符號及縮寫 XIX 第一章 緒論 1 1.1 胃幽門桿菌簡介 1 1.2 胃幽門桿菌致病因子 1 1.3 胃幽門桿菌游動能力 2 1.4 碳源調控蛋白 (carbon storage regulator, CsrA) 3 1.5 碳源調控蛋白與訊息RNA (mRNA) 3 1.6 碳源調控蛋白的調節 4 1.7 研究目的 4 第二章 材料與方法 5 2.1菌種及質體來源 5 2.2 實驗藥品及溶液配方 5 2.3 實驗菌種培養及保存 5 2.3.1大腸桿菌 (Escherichia coli) 5 2.3.2 胃幽門桿菌 (Helicobacter pylori) 5 2.4 CsrA突變蛋白建構 6 2.4.1萃取質體DNA 6 2.4.2 聚合酶鏈鎖反應(Polymerase chain reaction, PCR) 6 2.4.3 限制酶酵素切割 6 2.4.4 製備勝任細胞 (competent cell) 7 2.4.5大腸桿菌轉型作用 (transformation) 7 2.5 CsrA重組蛋白之表現及純化 7 2.5.1 CsrA重組蛋白之誘導 (induction) 7 2.5.2 Selenomethionyl (Se-Met) CsrA重組蛋白之誘導 (induction) 8 2.5.3 親合性鎳離子螯合樹脂色層分析法(Affinity Ni2+-chelating chromatography)純化重組蛋白CsrA與selenomethionyl CsrA 8 2.5.4 聚丙烯醯胺膠體電泳 (Sodium dodecyl sulfate polyacrylamide gel electrophoresis, SDS-PAGE) 9 2.5.5 蛋白質濃度測量 9 2.5.6 粒徑篩析層析法 (Size-exclusion chromatography) 10 2.6 CsrA與Se-Met CsrA蛋白質結晶 10 2.6.1 CsrA蛋白質結晶濃度決定 10 2.6.2 CsrA蛋白質結晶 10 2.6.3 CsrA蛋白質結晶改進 10 2.7 CsrA與Se-Met蛋白質結晶X-ray繞射數據收集 11 2.8 CsrA X光小角度散射 (Small Angle X-ray Scattering, SAXS) 11 2.8.1 CsrA的樣本準備 11 2.8.2 SAXS的數據收集 11 2.8.3 SAXS的數據分析及處理 12 2.9 H. pylori csrA R44A突變株與 CsrA R44A蛋白質體構築 12 2.9.1聚合酶鏈鎖反應 (Polymerase chain reaction, PCR) 12 2.9.2 限制酶酵素切割 12 2.9.3 以對偶基因交換作用 (allelic exchange)產生H. pylori csrA R44A突變株 13 2.9.4 胃幽門桿菌染色體DNA萃取 13 2.9.5聚合酶鏈鎖反應確認H. pylori csrA R44A突變株 13 2.10 胃幽門桿菌的游動力測試 14 2.11 CsrA與RNA結合 14 2.11.1電泳速度變動分析法 (Electrophoretic mobility shift assay, EMSA) 14 2.11.2 銀染 (silver stain) 14 第三章 結果 15 3.1 CsrA重組蛋白質表現與純化 15 3.2 Se-Met CsrA 重組蛋白質表現與純化 15 3.3 CsrA與Se-Met CsrA蛋白質結晶 16 3.4 CsrA與Se-Met CsrA蛋白質結晶數據分析 16 3.5 CsrA與Se-Met CsrA蛋白質結晶改良 17 3.6以SAXS的數據判斷CsrA為二聚體 (dimer) 17 3.7 CsrA的功能性分析 18 3.7.1 CsrA會與flaA RNA結合 18 3.7.2 CsrA R44A突變蛋白構築與純化 18 3.7.3 Arg44是CsrA與RNA結合的重要位置 18 3.7.4 H. pylori csrA R44A細菌突變株構築 19 3.7.5 H. pylori csrA R44A游動能力下降 19 第四章 討論 21 第五章 結論 25 圖 26 表 41 參考文獻 45 附錄 48 附錄1.1 藥品與廠商 48 附錄1.2 溶液配置 51 附錄1.3 flaB與rpoN上可能的CsrA結合位與RNA預測結構 53

    Altier, C., Suyemoto, M., Lawhon, S.D., 2000. Regulation of Salmonella enterica serovar typhimurium invasion genes by csrA. Infection And Immunity 68, 6790-6797.
    Barnard, F.M., Loughlin, M.F., Fainberg, H.P., Messenger, M.P., Ussery, D.W., Williams, P., Jenks, P.J., 2004. Global regulation of virulence and the stress response by CsrA in the highly adapted human gastric pathogen Helicobacter pylori. Mol Microbiol 51, 15-32.
    Censini, S., Lange, C., Xiang, Z., Crabtree, J.E., Ghiara, P., Borodovsky, M., Rappuoli, R., Covacci, A., 1996. cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors. Proceedings of the National Academy of Sciences of the United States of America 93, 14648-14653.
    Chatterjee, A., Cui, Y., Liu, Y., Dumenyo, C.K., Chatterjee, A.K., 1995. Inactivation of rsmA leads to overproduction of extracellular pectinases, cellulases, and proteases in Erwinia carotovora subsp. carotovora in the absence of the starvation/cell density-sensing signal, N-(3-oxohexanoyl)-L-homoserine lactone. Applied And Environmental Microbiology 61, 1959-1967.
    Dubey, A.K., Baker, C.S., Romeo, T., Babitzke, P., 2005. RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction. Rna 11, 1579-1587.
    Figueroa-Bossi, N., Schwartz, A., Guillemardet, B., D'Heygere, F., Bossi, L., Boudvillain, M., 2014. RNA remodeling by bacterial global regulator CsrA promotes Rho-dependent transcription termination. Genes & Development 28, 1239-1251.
    Guerrero, S.A., Hecht, H.J., Hofmann, B., Biebl, H., Singh, M., 2001. Production of selenomethionine-labelled proteins using simplified culture conditions and generally applicable host/vector systems. Applied Microbiology And Biotechnology 56, 718-723.
    Heeb, S., Kuehne, S.A., Bycroft, M., Crivii, S., Allen, M.D., Haas, D., Camara, M., Williams, P., 2006. Functional analysis of the post-transcriptional regulator RsmA reveals a novel RNA-binding site. Journal of Molecular Biology 355, 1026-1036.
    Jackson, D.W., Suzuki, K., Oakford, L., Simecka, J.W., Hart, M.E., Romeo, T., 2002. Biofilm formation and dispersal under the influence of the global regulator CsrA of Escherichia coli. Journal Of Bacteriology 184, 290-301.
    Jorgensen, M.G., Thomason, M.K., Havelund, J., Valentin-Hansen, P., Storz, G., 2013. Dual function of the McaS small RNA in controlling biofilm formation. Genes & Development 27, 1132-1145.
    Josenhans, C., Labigne, A., Suerbaum, S., 1995. Comparative ultrastructural and functional studies of Helicobacter pylori and Helicobacter mustelae flagellin mutants: both flagellin subunits, FlaA and FlaB, are necessary for full motility in Helicobacter species. Journal of Bacteriology 177, 3010-3020.
    Kao, C.Y., Sheu, B.S., Sheu, S.M., Yang, H.B., Chang, W.L., Cheng, H.C., Wu, J.J., 2012. Higher motility enhances bacterial density and inflammatory response in dyspeptic patients infected with Helicobacter pylori. Helicobacter 17, 411-416.
    Konarev, P.V., Volkov, V.V., Sokolova, A.V., Koch, M.H.J., Svergun, D.I., 2003. PRIMUS: a Windows PC-based system for small-angle scattering data analysis. Journal of Applied Crystallography 36, 1277-1282.
    Lenz, D.H., Miller, M.B., Zhu, J., Kulkarni, R.V., Bassler, B.L., 2005. CsrA and three redundant small RNAs regulate quorum sensing in Vibrio cholerae. Mol Microbiol 58, 1186-1202.
    Lertsethtakarn, P., Ottemann, K.M., Hendrixson, D.R., 2011. Motility and chemotaxis in Campylobacter and Helicobacter. Annual Review of Microbiology 65, 389-410.
    Mercante, J., Edwards, A.N., Dubey, A.K., Babitzke, P., Romeo, T., 2009. Molecular geometry of CsrA (RsmA) binding to RNA and its implications for regulated expression. Journal of Molecular Biology 392, 511-528.
    Niehus, E., Gressmann, H., Ye, F., Schlapbach, R., Dehio, M., Dehio, C., Stack, A., Meyer, T.F., Suerbaum, S., Josenhans, C., 2004. Genome-wide analysis of transcriptional hierarchy and feedback regulation in the flagellar system of Helicobacter pylori. Molecular Microbiology 52, 947-961.
    Petoukhov, M.V., Konarev, P.V., Kikhney, A.G., Svergun, D.I., 2007. ATSAS 2.1 - towards automated and web-supported small-angle scattering data analysis. Journal of Applied Crystallography 40, s223-s228.
    Phadnis, S.H., Parlow, M.H., Levy, M., Ilver, D., Caulkins, C.M., Connors, J.B., Dunn, B.E., 1996. Surface localization of Helicobacter pylori urease and a heat shock protein homolog requires bacterial autolysis. Infection And Immunity 64, 905-912.
    Polk, D.B., Peek, R.M., Jr., 2010. Helicobacter pylori: gastric cancer and beyond. Nature reviews. Cancer 10, 403-414.
    Romeo, T., Gong, M., Liu, M.Y., Brun-Zinkernagel, A.M., 1993. Identification and molecular characterization of csrA, a pleiotropic gene from Escherichia coli that affects glycogen biosynthesis, gluconeogenesis, cell size, and surface properties. Journal of Bacteriology 175, 4744-4755.
    Schubert, M., Lapouge, K., Duss, O., Oberstrass, F.C., Jelesarov, I., Haas, D., Allain, F.H., 2007. Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA. Nature Structural & Molecular Biology 14, 807-813.
    Sreenath, H.K., Bingman, C.A., Buchan, B.W., Seder, K.D., Burns, B.T., Geetha, H.V., Jeon, W.B., Vojtik, F.C., Aceti, D.J., Frederick, R.O., Phillips, G.N., Jr., Fox, B.G., 2005. Protocols for production of selenomethionine-labeled proteins in 2-L polyethylene terephthalate bottles using auto-induction medium. Protein Expression And Purification 40, 256-267.
    Sterzenbach, T., Nguyen, K.T., Nuccio, S.P., Winter, M.G., Vakulskas, C.A., Clegg, S., Romeo, T., Baumler, A.J., 2013. A novel CsrA titration mechanism regulates fimbrial gene expression in Salmonella typhimurium. The EMBO journal 32, 2872-2883.
    Sundrud, M.S., Torres, V.J., Unutmaz, D., Cover, T.L., 2004. Inhibition of primary human T cell proliferation by Helicobacter pylori vacuolating toxin (VacA) is independent of VacA effects on IL-2 secretion. Proceedings of the National Academy of Sciences of the United States of America 101, 7727-7732.
    Timmermans, J., Van Melderen, L., 2010. Post-transcriptional global regulation by CsrA in bacteria. Cellular And Molecular Life Sciences : CMLS 67, 2897-2908.
    Weilbacher, T., Suzuki, K., Dubey, A.K., Wang, X., Gudapaty, S., Morozov, I., Baker, C.S., Georgellis, D., Babitzke, P., Romeo, T., 2003. A novel sRNA component of the carbon storage regulatory system of Escherichia coli. Molecular Microbiology 48, 657-670.
    Yakhnin, A.V., Baker, C.S., Vakulskas, C.A., Yakhnin, H., Berezin, I., Romeo, T., Babitzke, P., 2013. CsrA activates flhDC expression by protecting flhDC mRNA from RNase E-mediated cleavage. Molecular Microbiology 87, 851-866.

    下載圖示 校內:2019-08-06公開
    校外:2019-08-06公開
    QR CODE