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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 吳蕙芬(Whei-Fen Wu) | |
| dc.contributor.author | Chih-Hsuan Tsai | en |
| dc.contributor.author | 蔡智瑄 | zh_TW |
| dc.date.accessioned | 2021-06-16T10:16:27Z | - |
| dc.date.available | 2018-08-23 | |
| dc.date.copyright | 2013-08-23 | |
| dc.date.issued | 2013 | |
| dc.date.submitted | 2013-08-18 | |
| dc.identifier.citation | 胡惠婷. (2012).大腸桿菌莢膜生合成調節蛋白RcsA為ClpYQ蛋白酶的基質之研究. 國立臺灣大學農業化學研究所.
Azim, M. K., Goehring, W., Song, H. K., Ramachandran, R., Bochtler, M. &Goettig, P. (2005). Characterization of the HslU chaperone affinity for HslV protease. Protein Sci 14(5): 1357-1362. Babu, M., Beloglazova, N., Flick, R., Graham, C., Skarina, T., Nocek, B., Gagarinova, A., Pogoutse, O., Brown, G., Binkowski, A., Phanse, S., Joachimiak, A., Koonin, E. V., Savchenko, A., Emili, A., Greenblatt, J., Edwards, A. M. &Yakunin, A. F. (2011). A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol 79(2): 484-502. Baker, T. A. &Sauer, R. T. (2006). ATP-dependent proteases of bacteria: recognition logic and operating principles. Trends Biochem Sci 31(12): 647-653. Bhaya, D., Davison, M. &Barrangou, R. (2011). CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet 45: 273-297. Bi, E. &Lutkenhaus, J. (1990). Analysis of ftsZ mutations that confer resistance to the cell division inhibitor SulA (SfiA). J Bacteriol 172(10): 5602-5609. Bochtler, M., Ditzel, L., Groll, M. &Huber, R. (1997). Crystal structure of heat shock locus V (HslV) from Escherichia coli. Proc Natl Acad Sci U S A 94(12): 6070-6074. Bochtler, M., Hartmann, C., Song, H. K., Bourenkov, G. P., Bartunik, H. D. &Huber, R. (2000). The structures of HsIU and the ATP-dependent protease HsIU-HsIV. Nature 403(6771): 800-805. Bukau, B., Weissman, J. &Horwich, A. (2006). Molecular chaperones and protein quality control. Cell 125(3): 443-451. Chandu, D. &Nandi, D. (2004). Comparative genomics and functional roles of the ATP-dependent proteases Lon and Clp during cytosolic protein degradation. Res Microbiol 155(9): 710-719. Chen, C. S., Sullivan, S., Anderson, T., Tan, A. C., Alex, P. J., Brant, S. R., Cuffari, C., Bayless, T. M., Talor, M. V., Burek, C. L., Wang, H., Li, R., Datta, L. W., Wu, Y., Winslow, R. L., Zhu, H. &Li, X. (2009). Identification of novel serological biomarkers for inflammatory bowel disease using Escherichia coli proteome chip. Mol Cell Proteomics 8(8): 1765-1776. Chuang, S. E., Burland, V., Plunkett, G., 3rd, Daniels, D. L. &Blattner, F. R. (1993). Sequence analysis of four new heat-shock genes constituting the hslTS/ibpAB and hslVU operons in Escherichia coli. Gene 134(1): 1-6. Cooley, A. E., Riley, S. P., Kral, K., Miller, M. C., DeMoll, E., Fried, M. G. &Stevenson, B. (2009). DNA-binding by Haemophilus influenzae and Escherichia coli YbaB, members of a widely-distributed bacterial protein family. BMC Microbiol 9: 137. Feng, Y., Jiao, W., Fu, X. &Chang, Z. (2006). Stepwise disassembly and apparent nonstepwise reassembly for the oligomeric RbsD protein. Protein Sci 15(6): 1441-1448. Flynn, J. M., Neher, S. B., Kim, Y. I., Sauer, R. T. &Baker, T. A. (2003). Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Mol Cell 11(3): 671-683. Gottesman, S. (2003). Proteolysis in bacterial regulatory circuits. Annu Rev Cell Dev Biol 19: 565-587. Gottesman, S., Roche, E., Zhou, Y. &Sauer, R. T. (1998). The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev 12(9): 1338-1347. Gottesman, S., Trisler, P. &Torres-Cabassa, A. (1985). Regulation of capsular polysaccharide synthesis in Escherichia coli K-12: characterization of three regulatory genes. J Bacteriol 162(3): 1111-1119. Guo, F., Maurizi, M. R., Esser, L. &Xia, D. (2002). Crystal structure of ClpA, an Hsp100 chaperone and regulator of ClpAP protease. J Biol Chem 277(48): 46743-46752. Gur, E., Biran, D. &Ron, E. Z. (2011). Regulated proteolysis in Gram-negative bacteria--how and when? Nat Rev Microbiol 9(12): 839-848. Hsieh, F. C., Chen, C. T., Weng, Y. T., Peng, S. S., Chen, Y. C., Huang, L. Y., Hu, H. T., Wu, Y. L., Lin, N. C. &Wu, W. F. (2011). Stepwise activity of ClpY (HslU) mutants in the processive degradation of Escherichia coli ClpYQ (HslUV) protease substrates. J Bacteriol 193(19): 5465-5476. Ikeda, Y., Yagi, M., Morita, T. &Aiba, H. (2011). Hfq binding at RhlB-recognition region of RNase E is crucial for the rapid degradation of target mRNAs mediated by sRNAs in Escherichia coli. Mol Microbiol 79(2): 419-432. Jutras, B. L., Bowman, A., Brissette, C. A., Adams, C. A., Verma, A., Chenail, A. M. &Stevenson, B. (2012). EbfC (YbaB) is a new type of bacterial nucleoid-associated protein and a global regulator of gene expression in the Lyme disease spirochete. J Bacteriol 194(13): 3395-3406. Kanemori, M., Nishihara, K., Yanagi, H. &Yura, T. (1997). Synergistic roles of HslVU and other ATP-dependent proteases in controlling in vivo turnover of sigma32 and abnormal proteins in Escherichia coli. J Bacteriol 179(23): 7219-7225. Kanemori, M., Yanagi, H. &Yura, T. (1999). Marked instability of the sigma (32) heat shock transcription factor at high temperature. Implications for heat shock regulation. J Biol Chem 274(31): 22002-22007. Kang, S. G., Ortega, J., Singh, S. K., Wang, N., Huang, N. N., Steven, A. C. &Maurizi, M. R. (2002). Functional proteolytic complexes of the human mitochondrial ATP-dependent protease, hClpXP. J Biol Chem 277(23): 21095-21102. Katayama-Fujimura, Y., Gottesman, S. &Maurizi, M. R. (1987). A multiple-component, ATP-dependent protease from Escherichia coli. J Biol Chem 262(10): 4477-4485. Khattar, M. M. (1997). Overexpression of the hslVU operon suppresses SOS-mediated inhibition of cell division in Escherichia coli. FEBS Lett 414(2): 402-404. Kitagawa, M., Ara, T., Arifuzzaman, M., Ioka-Nakamichi, T., Inamoto, E., Toyonaga, H. &Mori, H. (2005). Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res 12(5): 291-299. Kuo, M. S., Chen, K. P. &Wu, W. F. (2004). Regulation of RcsA by the ClpYQ (HslUV) protease in Escherichia coli. Microbiology 150(Pt 2): 437-446. Lau-Wong, I. C., Locke, T., Ellison, M. J., Raivio, T. L. &Frost, L. S. (2008). Activation of the Cpx regulon destabilizes the F plasmid transfer activator, TraJ, via the HslVU protease in Escherichia coli. Mol Microbiol 67(3): 516-527. Lee, Y. Y., Chang, C. F., Kuo, C. L., Chen, M. C., Yu, C. H., Lin, P. I. &Wu, W. F. (2003). Subunit oligomerization and substrate recognition of the Escherichia coli ClpYQ (HslUV) protease implicated by in vivo protein-protein interactions in the yeast two-hybrid system. J Bacteriol 185(8): 2393-2401. Li, R., Gu, J., Chen, Y. Y., Xiao, C. L., Wang, L. W., Zhang, Z. P., Bi, L. J., Wei, H. P., Wang, X. D., Deng, J. Y. &Zhang, X. E. (2010). CobB regulates Escherichia coli chemotaxis by deacetylating the response regulator CheY. Mol Microbiol 76(5): 1162-1174. Liang, W. &Deutscher, M. P. (2010). A novel mechanism for ribonuclease regulation: transfer-messenger RNA (tmRNA) and its associated protein SmpB regulate the stability of RNase R. J Biol Chem 285(38): 29054-29058. Liang, W. &Deutscher, M. P. (2012). Transfer-messenger RNA-SmpB protein regulates ribonuclease R turnover by promoting binding of HslUV and Lon proteases. J Biol Chem 287(40): 33472-33479. Lim, K., Tempczyk, A., Parsons, J. F., Bonander, N., Toedt, J., Kelman, Z., Howard, A., Eisenstein, E. &Herzberg, O. (2003). Crystal structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function coexpressed with the recombinational DNA repair protein RecR. Proteins 50(2): 375-379. Lima, B. P., Antelmann, H., Gronau, K., Chi, B. K., Becher, D., Brinsmade, S. R. &Wolfe, A. J. (2011). Involvement of protein acetylation in glucose-induced transcription of a stress-responsive promoter. Mol Microbiol 81(5): 1190-1204. Missiakas, D., Schwager, F., Betton, J. M., Georgopoulos, C. &Raina, S. (1996). Identification and characterization of HsIV HsIU (ClpQ ClpY) proteins involved in overall proteolysis of misfolded proteins in Escherichia coli. EMBO J 15(24): 6899-6909. Mizusawa, S. &Gottesman, S. (1983). Protein degradation in Escherichia coli: the lon gene controls the stability of sulA protein. Proc Natl Acad Sci U S A 80(2): 358-362. Park, E., Rho, Y. M., Koh, O. J., Ahn, S. W., Seong, I. S., Song, J. J., Bang, O., Seol, J. H., Wang, J., Eom, S. H. &Chung, C. H. (2005). Role of the GYVG pore motif of HslU ATPase in protein unfolding and translocation for degradation by HslV peptidase. J Biol Chem 280(24): 22892-22898. Riley, S. P., Bykowski, T., Cooley, A. E., Burns, L. H., Babb, K., Brissette, C. A., Bowman, A., Rotondi, M., Miller, M. C., DeMoll, E., Lim, K., Fried, M. G. &Stevenson, B. (2009). Borrelia burgdorferi EbfC defines a newly-identified, widespread family of bacterial DNA-binding proteins. Nucleic Acids Res 37(6): 1973-1983. Rohrwild, M., Coux, O., Huang, H. C., Moerschell, R. P., Yoo, S. J., Seol, J. H., Chung, C. H. &Goldberg, A. L. (1996). HslV-HslU: A novel ATP-dependent protease complex in Escherichia coli related to the eukaryotic proteasome. Proc Natl Acad Sci U S A 93(12): 5808-5813. Rohrwild, M., Pfeifer, G., Santarius, U., Muller, S. A., Huang, H. C., Engel, A., Baumeister, W. &Goldberg, A. L. (1997). The ATP-dependent HslVU protease from Escherichia coli is a four-ring structure resembling the proteasome. Nat Struct Biol 4(2): 133-139. Ryu, K. S., Kim, C., Kim, I., Yoo, S., Choi, B. S. &Park, C. (2004). NMR application probes a novel and ubiquitous family of enzymes that alter monosaccharide configuration. J Biol Chem 279(24): 25544-25548. Sauer, R. T., Bolon, D. N., Burton, B. M., Burton, R. E., Flynn, J. M., Grant, R. A., Hersch, G. L., Joshi, S. A., Kenniston, J. A., Levchenko, I., Neher, S. B., Oakes, E. S., Siddiqui, S. M., Wah, D. A. &Baker, T. A. (2004). Sculpting the proteome with AAA(+) proteases and disassembly machines. Cell 119(1): 9-18. Schirmer, E. C., Glover, J. R., Singer, M. A. &Lindquist, S. (1996). HSP100/Clp proteins: a common mechanism explains diverse functions. Trends Biochem Sci 21(8): 289-296. Song, H. K., Hartmann, C., Ramachandran, R., Bochtler, M., Behrendt, R., Moroder, L. &Huber, R. (2000). Mutational studies on HslU and its docking mode with HslV. Proc Natl Acad Sci U S A 97(26): 14103-14108. Starai, V. J., Celic, I., Cole, R. N., Boeke, J. D. &Escalante-Semerena, J. C. (2002). Sir2-dependent activation of acetyl-CoA synthetase by deacetylation of active lysine. Science 298(5602): 2390-2392. Sundar, S., Baker, T. A. &Sauer, R. T. (2012). The I domain of the AAA+ HslUV protease coordinates substrate binding, ATP hydrolysis, and protein degradation. Protein Sci 21(2): 188-198. Sundar, S., McGinness, K. E., Baker, T. A. &Sauer, R. T. (2010). Multiple sequence signals direct recognition and degradation of protein substrates by the AAA+ protease HslUV. J Mol Biol 403(3): 420-429. Thao, S., Chen, C. S., Zhu, H. &Escalante-Semerena, J. C. (2010). Nepsilon-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity. PLoS One 5(12): e15123. Thiel, A., Valens, M., Vallet-Gely, I., Espeli, O. &Boccard, F. (2012). Long-range chromosome organization in E. coli: a site-specific system isolates the Ter macrodomain. PLoS Genet 8(4): e1002672. Tomoyasu, T., Gamer, J., Bukau, B., Kanemori, M., Mori, H., Rutman, A. J., Oppenheim, A. B., Yura, T., Yamanaka, K., Niki, H. &et al. (1995). Escherichia coli FtsH is a membrane-bound, ATP-dependent protease which degrades the heat-shock transcription factor sigma 32. EMBO J 14(11): 2551-2560. Voges, D., Zwickl, P. &Baumeister, W. (1999). The 26S proteasome: a molecular machine designed for controlled proteolysis. Annu Rev Biochem 68: 1015-1068. Wang, H., Wang, F., Hua, X., Ma, T., Chen, J., Xu, X., Wang, L., Tian, B. &Hua, Y. (2012). Genetic and biochemical characteristics of the histone-like protein DR0199 in Deinococcus radiodurans. Microbiology 158(Pt 4): 936-943. Westphal, K., Langklotz, S., Thomanek, N. &Narberhaus, F. (2012). A trapping approach reveals novel substrates and physiological functions of the essential protease FtsH in Escherichia coli. J Biol Chem 287(51): 42962-42971. Wickner, S., Maurizi, M. R. &Gottesman, S. (1999). Posttranslational quality control: folding, refolding, and degrading proteins. Science 286(5446): 1888-1893. Wu, W. F., Zhou, Y. &Gottesman, S. (1999). Redundant in vivo proteolytic activities of Escherichia coli Lon and the ClpYQ (HslUV) protease. J Bacteriol 181(12): 3681-3687. Yosef, I., Goren, M. G. &Qimron, U. (2012). Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res 40(12): 5569-5576. Zhao, K., Chai, X. &Marmorstein, R. (2004). Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Escherichia coli. J Mol Biol 337(3): 731-741. Zwickl, P., Baumeister, W. &Steven, A. (2000). Dis-assembly lines: the proteasome and related ATPase-assisted proteases. Curr Opin Struct Biol 10(2): 242-250. | |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/60366 | - |
| dc.description.abstract | 蛋白質的降解為調控生物體中蛋白體組成的重要機制，而ATP依賴型蛋白酶即是負責蛋白質降解的重要一員。在大腸桿菌中，ClpYQ蛋白酶為三個主要的ATP依賴型蛋白酶之一，其由具有ATPase活性的ClpY和具有分解酶活性的ClpQ所組成。除了分解菌體內摺疊錯誤的蛋白質之外，ClpYQ還會在必要情況下分解具有活性的調控蛋白以改變細胞的生理狀態，使其得以適應外在環境條件。已知的ClpYQ的基質包含SulA、RcsA、RpoH、TraJ及RNase R。
由於ClpY在ClpYQ的作用過程中負責辨認、解開，和轉送基質進入負責分解的ClpQ活性位，因此能與ClpY產生交互作用的蛋白即有可能為ClpYQ的基質。由大腸桿菌K12蛋白質晶片分析結果發現大腸桿菌體內六個功能各異的蛋白質YbaB、YfbV、RbsD、CobB、RhlB和YgbT，與ATPase ClpY之間有較強的交互作用。本研究試圖確認此六個蛋白質是否為ClpYQ的基質，首先以酵母菌雙雜交系統和胞內共沉澱試驗測定ClpY和此六個蛋白之間的交互作用，並針對其中作用力最強之YbaB蛋白進行Kd值測定。基質確認部分則分別以胞外和胞內降解試驗分析ClpYQ是否會分解這六個蛋白質。 酵母菌雙雜交系統及胞內共沉澱試驗結果共確定YbaB、RhlB和YfbV與ClpY具有交互作用。以胞外和胞內的降解試驗所進行之基質確認結果發現MBP-YbaB、MBP-YgbT和MBP-RbsD可在胞外降解試驗中被ClpYQ分解，而MBP-CobB和MBP-RhlB則可在胞內降解試驗中觀察到分解情形。此外，MBP-YfbV在胞內共沉澱試驗中被確認為ClpXP之基質，然而其被ClpXP分解之過程會受ClpYQ影響。 | zh_TW |
| dc.description.abstract | Proteolysis is a vital mechanism to regulate the cellular proteome in all kingdoms of life, and ATP-dependent proteases take a crucial role within that process. In Escherichia coli, ClpYQ is one of the three primary ATP-dependent proteases. ClpYQ contains ClpY (HslU), an ATPase with unfolding activity, and ClpQ (HslV), the peptidase responsible for proteolysis. Besides removals of abnormal peptides in cell, ClpYQ degrades regulatory proteins if necessary and thus let cells adjust to various environmental conditions. In E. coli, SulA, RcsA, RpoH and TraJ as well as RNase R, have been identified as natural protein substrates of ClpYQ.
As the ATPase ClpY is responsible for protein recognition, unfolding, and translocation into the catalytic core of ClpQ, the interactions with ClpY suggested previously unknown substrates of ClpYQ. According to the analysis of protein interaction using E. coli K12 proteome chips, there are six proteins, YbaB, YfbV, RbsD, CobB, RhlB, and YgbT, interacting strongly with ClpY. With an attempt to find novel substrates of ClpYQ, various methods were used to verify the six putative substrates in this study. The yeast two-hybrid assay and in vivo pull-down assay were performed to confirm the interactions with ClpY, and the YbaB protein, which has the strongest interaction, was chosen to determine the Kd value. In vitro degradation and in vivo degradation were carried out for the direct observations of degradation. The results of yeast two-hybrid assay and pull-down assay showed that YbaB, RhlB, and YfbV do have interactions with ClpY under different conditions. In the test of degradation, MBP-RbsD and MBP-YbaB and MBP-YgbT could be degraded by ClpYQ in vitro while MBP-CobB and MBP-RhlB have shown decay in vivo. In addition, the results of in vivo degradation indicated that MBP-YfbV is the substrates of ClpXP, but the proteolysis process is likely to be affected by ClpYQ. | en |
| dc.description.provenance | Made available in DSpace on 2021-06-16T10:16:27Z (GMT). No. of bitstreams: 1 ntu-102-R00623006-1.pdf: 1675160 bytes, checksum: f6e11d5a6c9a55e6eb15da214a6cf95c (MD5) Previous issue date: 2013 | en |
| dc.description.tableofcontents | 目錄
致謝 I 摘要 II Abstract III 目錄 V 表目錄 VIII 圖目錄 IX 壹、前言 1 一、 蛋白質降解 (protein degradation) 1 二、 ATP依賴蛋白酶 2 三、 ClpYQ蛋白酶 3 四、 已知ClpYQ蛋白酶之基質 5 五、 與ClpY具交互作用之蛋白 8 六、 研究動機與目的 14 貳、材料與方法 15 一、 實驗材料 15 (一) 菌株與質體 15 (二) 藥品與試劑 17 (三) 器材設備 18 (四) 分析軟體 19 二、 實驗方法 19 (一) 一般實驗方法 19 (二) 基因表現質體的建構 24 (三) 酵母菌雙雜交實驗 25 (四) in vitro實驗系統 27 (五) in vivo實驗系統 36 叁、結果 44 一、 六個蛋白質與ClpY之間的交互作用 44 (一) 酵母菌雙雜交系統分析結果 44 (二) 胞內共沉澱實驗 45 (三) YbaB之Kd值測定 45 二、 胞外降解試驗結果 46 三、 胞內降解試驗結果 47 (一) 六蛋白質之胞內降解情形 47 (二) MBP-YfbV之胞內降解受溫度變化之影響 49 (三) 分解MBP-YfbV之可能蛋白酶 49 肆、討論 50 伍、結論 55 陸、參考文獻 56 表目錄 表一、本論文所使用的菌株 63 表二、本論文所使用的質體 64 表三、本論文所使用的引子對 65 圖目錄 圖一、由大腸桿菌蛋白質晶片篩選之與ClpY具交互作用之六蛋白質 68 圖二、酵母菌雙雜交系統之X-gal測試結果 69 圖三、胞內共沉澱試驗結果 70 圖四、以QCM測分析ClpY和MBP-YbaB之交互作用 71 圖五、胞外降解試驗結果 72 圖六、MBP-CobB及MBP-RbsD之胞內降解結果 73 圖七、MBP-RhlB及MBP-YbaB之胞內降解結果 74 圖八、MBP-YfbV、及MBP-YgbT之胞內降解結果 75 圖九、改變胞內降解試驗溫度對MBP-YfbV降解之影響 76 圖十、分解MBP-YfbV之可能蛋白酶 77 附圖一、大腸桿菌ClpYQ結構圖 78 | |
| dc.language.iso | zh-TW | |
| dc.subject | 基質確認 | zh_TW |
| dc.subject | ATP依賴蛋白酶 | zh_TW |
| dc.subject | ClpYQ蛋白酶 | zh_TW |
| dc.subject | 交互作用 | zh_TW |
| dc.subject | interaction | en |
| dc.subject | substrate identification | en |
| dc.subject | ClpYQ | en |
| dc.subject | ATP-dependent protease | en |
| dc.title | 大腸桿菌ClpYQ蛋白酶可能基質之研究 | zh_TW |
| dc.title | Identification of putative substrates of ClpYQ protease in Escherichia coli | en |
| dc.type | Thesis | |
| dc.date.schoolyear | 101-2 | |
| dc.description.degree | 碩士 | |
| dc.contributor.oralexamcommittee | 陳健生(Chien-Sheng Chen),林乃君(Nai-Chun Lin),黃楓婷(Feng-Ting Huang),羅凱尹(Kai-Yin Lo) | |
| dc.subject.keyword | ATP依賴蛋白酶,ClpYQ蛋白酶,交互作用,基質確認, | zh_TW |
| dc.subject.keyword | ATP-dependent protease,ClpYQ,interaction,substrate identification, | en |
| dc.relation.page | 78 | |
| dc.rights.note | 有償授權 | |
| dc.date.accepted | 2013-08-18 | |
| dc.contributor.author-college | 生物資源暨農學院 | zh_TW |
| dc.contributor.author-dept | 農業化學研究所 | zh_TW |
| 顯示於系所單位： | 農業化學系 | |
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