研究生: |
潘韻如 Pan, Yun-Ru Anka |
---|---|
論文名稱: |
結構導向功能:克雷伯氏肺炎桿菌中之碲酸鹽抗藥蛋白之核磁共振研究 Structure as a Guide to Function: NMR Studies on Tellurite Resistance Proteins from Klebsiella pneumoniae |
指導教授: |
陳金榜
Chen, Chinpan 呂平江 Lyu, Ping-Chiang |
口試委員: |
余靖
Yu, Chin 黃太煌 Huang, Tai-Huang 徐尚德 Hsu, Shang-Te Danny |
學位類別: |
博士 Doctor |
系所名稱: |
生命科學暨醫學院 - 生物資訊與結構生物研究所 Institute of Bioinformatics and Structural Biology |
論文出版年: | 2012 |
畢業學年度: | 100 |
語文別: | 英文 |
論文頁數: | 91 |
中文關鍵詞: | 核磁共振 、碲酸鹽抗藥性蛋白 、鈣離子結合蛋白 、鈣離子訊息傳導 |
外文關鍵詞: | NMR, tellurite resistance, Ca2+ binding protein, KP-TerD, calcium signaling |
相關次數: | 點閱:2 下載:0 |
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Ter proteins mediate tellurite resistance and other responses to extracellular stimuli, but their functions are not understood yet. To shed light into the function of KP-TerD, a 20.5 kDa tellurite resistance protein from a plasmid of Klebsiella pneumoniae, we solved its three-dimensional structure in solution by multidimensional NMR spectroscopy. The structure consists of a beta-sandwich formed by two five-stranded beta-sheets and six short helices. Interestingly, the structure contains two clusters of negatively charged residues, which suggested that KP-TerD might bind some metal ions. Using NMR, CD and ICP-OES, we demonstrate that KP-TerD binds two calcium ions. An EDTA competition assay monitored by 1D NMR spectroscopy showed the estimated dissociation constants of KP-TerD. Since the Ca2+ concentration in the cytoplasm of bacteria is estimated to be 90-300 nM, the estimated Kd of site Ca2 of KP-TerD (200 nM) is well suited to sense changes in the cytoplasmic Ca2+ concentrations of bacteria. The calcium ligands are highly conserved in TerD proteins, suggesting that calcium binding is a conserved property of this family. Moreover, the calcium-binding motif of KP-TerD is conserved in TerE and TerZ. Using analogous methodology, we show that KP-TerE and KP-TerZ also bind two calcium ions, but their affinties are different from KP-TerD. These results show that three out of seven Ter proteins bind calcium and their affinities cover a wide range (from □M to nM) that is ideal to respond to changes in cytoplasmic calcium concentration. Overall, these data suggest that TerD, TerE and TerZ function as calcium sensors and that some form of calcium signaling is critical for the Ter response to extracellular stimuli.
中文摘要
克雷伯氏肺炎桿菌屬於腸道革蘭氏陰性桿菌G (-),會對醫院內住院,衰弱或免疫功能低下的病人造成感染。碲酸鹽化合物(TeO32-)早期被應用於治療由結核分枝桿菌引起的傳染病,並且廣泛的被應用在工業界。目前為止已有數個碲酸鹽抗藥性基因早就被分離鑑定出來,但是對於這些基因如何調控不同的細胞外刺激,例如對噬菌體(phage)、大腸桿菌素(colicin)、碲酸鹽類存在威脅時所做出反應的機制仍然是未知的。亞碲酸鉀(potassium tellurite)可以抑制大多數革蘭氏陰性菌的生長,但是克雷伯氏菌可以在含有亞碲酸鉀的環境下生長。為了闡明克雷伯氏肺炎桿菌質粒(plasmid)中的KP- TerD,20.5 kDa的碲酸鹽抗藥性蛋白的功能,我們運用核磁共振光譜的方法解出其三維立體結構。KP- TerD的蛋白質結構包含兩邊各由五個β-摺版所形成的類似三明治夾層及六個短的螺旋構型。在結構的上方顯示有兩個負電聚集的區域,這表示KP- TerD可能會與帶正電的金屬離子結合。接著我們運用了圓二色譜(circular dichroism)、核磁共振(NMR)以及感應耦合電漿-光學放射光譜(ICP-OES)實驗證實KP-TerD可與鈣離子以1:2結合比例結合,且鈣離子結合的區域的確是在KP-TerD的上方負電聚集的區域。TerD蛋白質家族有獨特的蛋白折疊法和新型的鈣離子結合模式。用EDTA競爭的方法,再藉由一維核磁共振光譜測量,可得到KP- TerD的鈣離子解離常數的估計值,已知在細菌細胞質內的鈣離子濃度估計值為90-300 nM,而KP- TerD之第二個鈣離子的解離常數估計值200 nM是非常適合用來感應在細菌細胞質內鈣離子濃度的變化。與鈣離子結合的配體在不同種類的細菌內的TerD蛋白質是非常一致的,這使人聯想到與鈣離子結合是的TerD蛋白質家族一致的特性。此外,KP- TerD鈣離子結合的區塊也一致的存在於TerE和TerZ蛋白質中。使用類似的方法,我們證明KP-TerE和KP-TerZ也結合兩個鈣離子,但他們的對鈣離子的親和力與KP- TerD不同。這些結果顯示,在七個碲酸鹽抗藥性蛋白質之中有三個會與鈣離子結合,且其與鈣離子的結合親合力涵蓋的範圍很廣(從□M到nM),對於細胞漿內的鈣離子濃度變化可做出理想的回應。總體而言,這些實驗結果推測出TerD,TerE和TerZ這三個蛋白質的功能可能是做為鈣離子傳導感應器,並且可能是碲酸鹽抗藥性以及細胞外刺激所引起的某種形式的鈣離子訊息傳導重要的關鍵。
References
1 Guentzel, M. N. Escherichia, Klebsiella, Enterobacter, Serratia, Citrobacter. [book] (1996).
2 Podschun, R. & Ullmann, U. Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev 11, 589-603 (1998).
3 Fang, C. T., Chen, Y. C., Chang, S. C., Sau, W. Y. & Luh, K. T. Klebsiella pneumoniae meningitis: timing of antimicrobial therapy and prognosis. QJM 93, 45-53 (2000).
4 Naito, T. et al. A case of endophthalmitis and abscesses in the liver and the lung caused by Klebsiella pneumoniae. Kansenshogaku Zasshi 73, 935-938 (1999).
5 Ohmori, S. et al. Septic endophthalmitis and meningitis associated with Klebsiella pneumoniae liver abscess. Hepatol Res 22, 307-312 (2002).
6 Saccente, M. Klebsiella pneumoniae liver abscess, endophthalmitis, and meningitis in a man with newly recognized diabetes mellitus. Clin Infect Dis 29, 1570-1571 (1999).
7 Cahill, M., Chang, B. & Murray, A. Bilateral endogenous bacterial endophthalmitis associated with pyogenic hepatic abscess. Br J Ophthalmol 84, 1436 (2000).
8 Aguilar, J., Cruz, A. & Ortega, C. [Multiple hepatic and pulmonary abscesses caused by Klebsiella pneumoniae]. Enferm Infecc Microbiol Clin 12, 270-271 (1994).
9 Couez, D., Libon, E., Wasteels, M., Derue, G. & Gilbeau, J. P. Klebsiella pneumoniae liver abscess with septic endophthalmitis. The role of computed tomography. J Belge Radiol 74, 41-44 (1991).
10 Barton, E. N., Daisley, H., Gilbert, D. T. & Roberts, L. Diabetes mellitus and Klebsiella pneumoniae liver abscess in adults. Trop Geogr Med 43, 100-104 (1991).
11 Casanova, C., Lorente, J. A., Carrillo, F., Perez-Rodriguez, E. & Nunez, N. Klebsiella pneumoniae liver abscess associated with septic endophthalmitis. Arch Intern Med 149, 1467 (1989).
12 Podschun, R., Sievers, D., Fischer, A. & Ullmann, U. Serotypes, hemagglutinins, siderophore synthesis, and serum resistance of Klebsiella isolates causing human urinary tract infections. J Infect Dis 168, 1415-1421 (1993).
13 Chang, S. C., Fang, C. T., Hsueh, P. R., Luh, K. T. & Hsieh, W. C. In vitro activity of quinupristin/dalfopristin against clinical isolates of common gram-positive bacteria in Taiwan. Diagn Microbiol Infect Dis 33, 299-303 (1999).
14 Taylor, D. E. Bacterial tellurite resistance. Trends Microbiol 7, 111-115 (1999).
15 Turner, R. J., Weiner, J. H. & Taylor, D. E. Tellurite-mediated thiol oxidation in Escherichia coli. Microbiology 145 ( Pt 9), 2549-2557 (1999).
16 Borghese, R., Borsetti, F., Foladori, P., Ziglio, G. & Zannoni, D. Effects of the metalloid oxyanion tellurite (TeO32-) on growth characteristics of the phototrophic bacterium Rhodobacter capsulatus. Appl Environ Microbiol 70, 6595-6602 (2004).
17 Summers, A. O. & Jacoby, G. A. Plasmid-determined resistance to tellurium compounds. J Bacteriol 129, 276-281 (1977).
18 Jobling, M. G. & Ritchie, D. A. Genetic and physical analysis of plasmid genes expressing inducible resistance of tellurite in Escherichia coli. Mol Gen Genet 208, 288-293 (1987).
19 Toptchieva, A., Sisson, G., Bryden, L. J., Taylor, D. E. & Hoffman, P. S. An inducible tellurite-resistance operon in Proteus mirabilis. Microbiology 149, 1285-1295 (2003).
20 Dyllick-Brenzinger, M., Liu, M., Winstone, T. L., Taylor, D. E. & Turner, R. J. The role of cysteine residues in tellurite resistance mediated by the TehAB determinant. Biochem Biophys Res Commun 277, 394-400 (2000).
21 Chasteen, T. G., Fuentes, D. E., Tantalean, J. C. & Vasquez, C. C. Tellurite: history, oxidative stress, and molecular mechanisms of resistance. FEMS Microbiol Rev 33, 820-832 (2009).
22 Taylor, D. E. & Grant, R. B. Inhibition of bacteriophage lambda, T1, and T7 development by R plasmids of the H incompatibility group. Antimicrob Agents Chemother 10, 762-764 (1976).
23 Vilchez, G., Alonso, G. & Rodriguez Lemoine, V. Cloning of the PacB-Ter region from plasmid Mip233 (IncHI3) and their expression in E. coli ton, tol mutants. Zentralbl Bakteriol 286, 1-8 (1997).
24 Whelan, K. F., Colleran, E. & Taylor, D. E. Phage inhibition, colicin resistance, and tellurite resistance are encoded by a single cluster of genes on the IncHI2 plasmid R478. J Bacteriol 177, 5016-5027 (1995).
25 Bax, A. et al. Measurement of homo- and heteronuclear J couplings from quantitative J correlation. Methods Enzymol 239, 79-105 (1994).
26 Kay, L. E. Pulsed field gradient multi-dimensional NMR methods for the study of protein structure and dynamics in solution. Prog Biophys Mol Biol 63, 277-299 (1995).
27 Delaglio, F. et al. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6, 277-293 (1995).
28 Kalbitzer, H. R. AURELIA, a program for computer-aided analysis of multidimensional NMR spectra. J Biomol NMR 6, 255-270 (1995).
29 Johnson, B. A. B., R. A. NMRView: a computer program for the visualization and analysis of NMR data. J Biomol NMR 4, 603-614 (1994).
30 Wishart, D. S. et al. 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J Biomol NMR 6, 135-140 (1995).
31 Cornilescu, G., Delaglio, F. & Bax, A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13, 289-302 (1999).
32 Schwieters, C. D., Kuszewski, J. J., Tjandra, N. & Clore, G. M. The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160, 65-73 (2003).
33 Koradi, R., Billeter, M. & Wuthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14, 51-55, 29-32 (1996).
34 DeLano, W. L. The PyMOL Molecular Graphics System. http://www.pymol.org. (2002).
35 Laskowski, R. A., Rullmannn, J. A., MacArthur, M. W., Kaptein, R. & Thornton, J. M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8, 477-486 (1996 ).
36 Wishart, D. S. & Sykes, B. D. The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR 4, 171-180 (1994).
37 Herbaud, M. L., Guiseppi, A., Denizot, F., Haiech, J. & Kilhoffer, M. C. Calcium signalling in Bacillus subtilis. Biochim Biophys Acta 1448, 212-226 (1998).
38 Norris, V. et al. Calcium signalling in bacteria. J Bacteriol 178, 3677-3682 (1996).
39 Whelan, K. F., Sherburne, R. K. & Taylor, D. E. Characterization of a region of the IncHI2 plasmid R478 which protects Escherichia coli from toxic effects specified by components of the tellurite, phage, and colicin resistance cluster. J Bacteriol 179, 63-71 (1997).
40 Sneddon, I. N. 166-167 (Pergamon Press, Oxford, 1976).
41 Patton, C., Thompson, S. & Epel, D. Some precautions in using chelators to buffer metals in biological solutions. Cell Calcium 35, 427-431 (2004).
42 Holm, L., Kaariainen, S., Rosenstrom, P. & Schenkel, A. Searching protein structure databases with DaliLite v.3. Bioinformatics 24, 2780-2781 (2008).
43 Novotna, J. et al. Proteomic studies of diauxic lag in the differentiating prokaryote Streptomyces coelicolor reveal a regulatory network of stress-induced proteins and central metabolic enzymes. Mol Microbiol 48, 1289-1303 (2003).
44 De Mot, R., Schoofs, G. & Nagy, I. Proteome analysis of Streptomyces coelicolor mutants affected in the proteasome system reveals changes in stress-responsive proteins. Arch Microbiol 188, 257-271 (2007).
45 Kretsinger, R. H. & Nockolds, C. E. Carp muscle calcium-binding protein. II. Structure determination and general description. J Biol Chem 248, 3313-3326 (1973).
46 Herzberg, O. & James, M. N. Common structural framework of the two Ca2+/Mg2+ binding loops of troponin C and other Ca2+ binding proteins. Biochemistry 24, 5298-5302 (1985).
47 Satyshur, K. A. et al. Refined structure of chicken skeletal muscle troponin C in the two-calcium state at 2-A resolution. J Biol Chem 263, 1628-1647 (1988).
48 Szebenyi, D. M. & Moffat, K. The refined structure of vitamin D-dependent calcium-binding protein from bovine intestine. Molecular details, ion binding, and implications for the structure of other calcium-binding proteins. J Biol Chem 261, 8761-8777 (1986).
49 Ubach, J., Zhang, X., Shao, X., Sudhof, T. C. & Rizo, J. Ca2+ binding to synaptotagmin: how many Ca2+ ions bind to the tip of a C2-domain? EMBO J 17, 3921-3930 (1998).
50 Ubach, J., Garcia, J., Nittler, M. P., Sudhof, T. C. & Rizo, J. Structure of the Janus-faced C2B domain of rabphilin. Nat Cell Biol 1, 106-112 (1999).
51 Garcia, J., Gerber, S. H., Sugita, S., Sudhof, T. C. & Rizo, J. A conformational switch in the Piccolo C2A domain regulated by alternative splicing. Nat Struct Mol Biol 11, 45-53 (2004).
52 Pan, Y. R., Lou, Y. C., Seven, A. B., Rizo, J. & Chen, C. NMR structure and calcium-binding properties of the tellurite resistance protein TerD from Klebsiella pneumoniae. J Mol Biol 405, 1188-1201 (2011).
53 Wu, K. M. et al. Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis. J Bacteriol 191, 4492-4501 (2009).
54 Johnson, B. A. Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol Biol 278, 313-352 (2004).
55 Wishart, D. S. & Sykes, B. D. Chemical shifts as a tool for structure determination. Methods Enzymol 239, 363-392 (1994).