Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/22044
標題: Xanthomonas campestris pv. campestris RNA 聚合酶相關次單元蛋白之探討
Characterization the Functional RNA Polymerase Subunits of Xanthomonas campestris pv. campestris
作者: 鄭景元
Cheng, Ching-Yuan
關鍵字: 十字花科黑腐病菌
Xanthomonas campestris
RNA 聚合酶共同表現
σ 因子
RNA polymerase
coexpression
σ factor
出版社: 分子生物學研究所
引用: CH1 方文岑 (2003) 十字花科黑腐病菌 rseA 與 mucD 基因之功能表現對 rpoE 調控之研究。國立中興大學分子生物學研究所碩士論文。 王昭仁 (1996) 十字花科黑腐病菌 RNA 聚合酶 Beta 次單位基因之選殖與分析。國立中興大學分子生物學研究所碩士論文。 王彩諭 (1999) 十字花科黑腐病菌聚合酶之重組及特性研究。國立中興大學分子生物學研究所碩士論文。 許朝欽 (2001) 十字花科黑腐病菌 sigma E 因子 (rpoE) 下游基因的特性分析。國立中興大學分子生物學研究所碩士論文。 陳世真 (1997) 十字花科蔬菜黑腐病菌 RNA 聚合酶 β'' 次單位基因之選殖及分析。國立中興大學分子生物學研究所碩士論文。 蔚承太 (1994) 十字花科黑腐病菌 RNA 聚合酶之純化與分析。國立中興大學分子生物學研究所碩士論文。 謝小燕 (2000) 十字花科黑腐病菌 rpoE 基因之選殖及其啟動子之探討。國立中興大學分子生物學研究所碩士論文。 Archambault, J., and Friesen, J.D. (1993) Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol Rev 57: 703–724. Becker, A., Katzen, F., Puhler, A., and Ielpi, L. (1998) Xanthan gum biosynthesis and application: a biochemical/genetic perspective. Appl Microbiol Biotechnol 50: 145–152. Blatter, E.E., Ross, W., Tang, H., Gourse, R.L., and Ebright, R.H. (1994) Domain organization of RNA polymerase α subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell 78: 889–896. Burgess, R.R., Travers, A.A., Dunn, J.J., and Bautz, E.K. (1969) Factor stimulating transcription by RNA polymerase. Nature 221: 43–46. Burgess, R.R., and Travers, A.A. (1970) Escherichia coli RNA polymerase: purification, subunit structure, and factor requirements. Fed Proc 29: 1164-1169. Busby, S., and Ebright, R.H. (1994) Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79: 743–746. Camarero, J.A., Shekhtman, A., Campbell, E.A., Chlenov, M., Gruber, T.M., Bryant, D.A., Darst, S.A., Cowburn, D., and Muir, T.W. (2002) Autoregulation of a bacterial sigma factor explored by using segmental isotopic labeling and NMR. Proc Natl Acad Sci U S A 99: 8536–8541. da Silva, A.C., Ferro, J.A., Reinach, F.C., Farah, C.S., Furlan, L.R., Quaggio, R.B., Monteiro-Vitorello, C.B., Van Sluys, M.A., Almeida, N.F., Alves, L.M., do Amaral, A.M., Bertolini, M.C., Camargo, L.E., Camarotte, G., Cannavan, F., Cardozo, J., Chambergo, F., Ciapina, L.P., Cicarelli, R.M., Coutinho, L.L., Cursino-Santos, J.R., El-Dorry, H., Faria, J.B., Ferreira, A.J., Ferreira, R.C., Ferro, M.I., Formighieri, E.F., Franco, M.C., Greggio, C.C., Gruber, A., Katsuyama, A.M., Kishi, L.T., Leite, R.P., Lemos, E.G., Lemos, M.V., Locali, E.C., Machado, M.A., Madeira, A.M., Martinez-Rossi, N.M., Martins, E.C., Meidanis, J., Menck, C.F., Miyaki, C.Y., Moon, D.H., Moreira, L.M., Novo, M.T., Okura, V.K., Oliveira, M.C., Oliveira, V.R., Pereira, H.A., Rossi, A., Sena, J.A., Silva, C., de Souza, R.F., Spinola, L.A., Takita, M.A., Tamura, R.E., Teixeira, E.C., Tezza, R.I., Trindade dos Santos, M., Truffi, D., Tsai, S.M., White, F.F., Setubal, J.C., and Kitajima, J.P. (2002) Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417: 459–463. Delcuve, G., Downing, W., Lewis, H., and Dennis, P.P. (1980) Nucleotide sequence of the proximal portion of the RNA polymerase β subunit gene of Escherichia coli. Gene 11: 367–373. Dove, S.L., and Hochschild, A. (1998) Conversion of the ω subunit of Escherichia coli RNA polymerase into a transcriptional activator or an activation target. Genes Dev 12: 745–754. Dow, J.M., and Daniels, M.J. (1994) Pathogenicity determinants and global regulation of pathogenicity of Xanthomonas campestris pv. campestris. Curr Top Microbiol Immunol 192: 29–41. Ebright, R.H. (2000) RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J Mol Biol 304: 687–698. Estrem, S.T., Gaal, T., Ross, W., and Gourse, R.L. (1998) Identification of an UP element consensus sequence for bacterial promoters. Proc Natl Acad Sci U S A 95: 9761–9766. Finn, R.D., Orlova, E.V., Gowen, B., Buck, M., and van Heel, M. (2000) Escherichia coli RNA polymerase core and holoenzyme structures. EMBO J 19: 6833–6844. Gentry, D., Xiao, H., Burgess, R., and Cashel, M. (1991) The ω subunit of Escherichia coli K-12 RNA polymerase is not required for stringent RNA control in vivo. J Bacteriol 173: 3901–3903. Gentry, D.R., and Burgess, R.R. (1989) rpoZ, encoding the ω subunit of Escherichia coli RNA polymerase, is in the same operon as spoT. J Bacteriol 171: 1271–1277. Glass, R.E., Jones, S.T., and Ishihama, A. (1986) Genetic studies on the β subunit of Escherichia coli RNA polymerase. VII. RNA polymerase is a target for ppGpp. Mol Gen Genet 203: 265–268. Heil, A., and Zillig, W. (1970) Reconstitution of bacterial DNA-dependent RNA-polymerase from isolated subunits as a tool for the elucidation of the role of the subunits in transcription. FEBS Lett 11: 165–168. Hochschild, A., and Dove, S.L. (1998) Protein-protein contacts that activate and repress prokaryotic transcription. Cell 92: 597–600. Huang, L.H., Tseng, Y.H., and Yang, M.T. (1998) Isolation and characterization of the Xanthomonas campestris rpoH gene coding for a 32-kDa heat shock sigma factor. Biochem Biophys Res Commun 244: 854–860. Hurwitz, J., Bresler, A., and Diringer, R. (1960) The enzymic incorporation of ribonucleotides into polyribonucleotides and the effect of DNA. Biochem Biophys Res Commun 3: 15–18. Ishihama, A. (1981) Subunit of assembly of Escherichia coli RNA polymerase. Adv Biophys 14: 1–35. Jaskunas, S.R., Burgess, R.R., and Nomura, M. (1975) Identification of a gene for the α-subunit of RNA polymerase at the str-spc region of the Escherichia coli chromosome. Proc Natl Acad Sci U S A 72: 5036–5040. Jeon, Y.H., Yamazaki, T., Otomo, T., Ishihama, A., and Kyogoku, Y. (1997) Flexible linker in the RNA polymerase α subunit facilitates the independent motion of the C-terminal activator contact domain. J Mol Biol 267: 953–962. Jin, D.J., and Gross, C.A. (1988) Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistance. J Mol Biol 202: 45–58. Kashlev, M., Martin, E., Polyakov, A., Severinov, K., Nikiforov, V., and Goldfarb, A. (1993) Histidine-tagged RNA polymerase: dissection of the transcription cycle using immobilized enzyme. Gene 130: 9–14. Krummel, B., and Chamberlin, M.J. (1989) RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes. Biochemistry 28: 7829–7842. Krummel, B., and Chamberlin, M.J. (1992) Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Individual complexes halted along different transcription units have distinct and unexpected biochemical properties. J Mol Biol 225: 221–237. Lai, J.Y., Huang, C.F., Tseng, Y.H., and Yang, M.T. (2000) Sequence and molecular analysis of the rpoA cluster genes from Xanthomonas campestris pv. campestris. Biochim Biophys Acta 1492: 553–559. Levin, J.R., Krummel, B., and Chamberlin, M.J. (1987) Isolation and properties of transcribing ternary complexes of Escherichia coli RNA polymerase positioned at a single template base. J Mol Biol 196: 85–100. Markov, D., Naryshkina, T., Mustaev, A., and Severinov, K. (1999) A zinc-binding site in the largest subunit of DNA-dependent RNA polymerase is involved in enzyme assembly. Genes Dev 13: 2439–2448. McMeechan, A., Roberts, M., Cogan, T.A., Jorgensen, F., Stevenson, A., Lewis, C., Rowley, G., and Humphrey, T.J. (2007) Role of the alternative sigma factors σE and σS in survival of Salmonella enterica serovar Typhimurium during starvation, refrigeration and osmotic shock. Microbiology 153: 263–269. Minakhin, L., Nechaev, S., Campbell, E.A., and Severinov, K. (2001) Recombinant Thermus aquaticus RNA polymerase, a new tool for structure-based analysis of transcription. J Bacteriol 183: 71–76. Mukherjee, K., and Chatterji, D. (1997) Studies on the omega subunit of Escherichia coli RNA polymerase--its role in the recovery of denatured enzyme activity. Eur J Biochem 247: 884–889. Mukherjee, K., Nagai, H., Shimamoto, N., and Chatterji, D. (1999) GroEL is involved in activation of Escherichia coli RNA polymerase devoid of the ω subunit in vivo. Eur J Biochem 266: 228–235. Negishi, T., Fujita, N., and Ishihama, A. (1995) Structural map of the α subunit of Escherichia coli RNA polymerase: structural domains identified by proteolytic cleavage. J Mol Biol 248: 723–728. Nene, V., and Glass, R.E. (1982) Genetic studies on the β subunit of Escherichia coli RNA polymerase. II. Evidence that large N-terminal amber fragments of the β subunit interfere with RNA polymerase function. Mol Gen Genet 188: 405–409. Ross, W., Gosink, K.K., Salomon, J., Igarashi, K., Zou, C., Ishihama, A., Severinov, K., and Gourse, R.L. (1993) A third recognition element in bacterial promoters: DNA binding by the α subunit of RNA polymerase. Science 262: 1407–1413. Saecker, R.M., Tsodikov, O.V., McQuade, K.L., Schlax, P.E., Jr., Capp, M.W., and Record, M.T., Jr. (2002) Kinetic studies and structural models of the association of E. coli σ70 RNA polymerase with the lPR promoter: large scale conformational changes in forming the kinetically significant intermediates. J Mol Biol 319: 649–671. Schurr, M.J., Yu, H., Martinez-Salazar, J.M., Boucher, J.C., and Deretic, V. (1996) Control of AlgU, a member of the σE-like family of stress sigma factors, by the negative regulators MucA and MucB and Pseudomonas aeruginosa conversion to mucoidy in cystic fibrosis. J Bacteriol 178: 4997–5004. Severinov, K. (2000) RNA polymerase structure-function: insights into points of transcriptional regulation. Curr Opin Microbiol 3: 118–125. Starr, M.P., Jenkins, C.L., Bussey, L.B., and Andrewes, A.G. (1977) Chemotaxonomic significance of the xanthomonadins, novel brominated aryl-polyene pigments produced by bacteria of the genus Xanthomonas. Arch Microbiol 113: 1–9. Swings, J.G., and Civerolo, E.L. (1993) Xanthomonas. London, England: Chapman & Hall. Testerman, T.L., Vazquez-Torres, A., Xu, Y., Jones-Carson, J., Libby, S.J., and Fang, F.C. (2002) The alternative sigma factor σE controls antioxidant defences required for Salmonella virulence and stationary-phase survival. Mol Microbiol 43: 771–782. Travers, A.A. (1969) Bacteriophage sigma factor for RNA polymerase. Nature 223: 1107–1110. Tseng, Y.S., Yu, C.T., Tseng, Y.H., and Yang, M.T. (1997) Cloning, sequencing, and expression of the rpoD gene encoding the primary sigma factor of Xanthomonas campestris. Biochem Biophys Res Commun 232: 712–718. Vauterin, L., Rademaker, J., and Swings, J. (2000) Synopsis on the Taxonomy of the Genus Xanthomonas. Phytopathol 90: 677–682. Vo, N.V., Hsu, L.M., Kane, C.M., and Chamberlin, M.J. (2003) In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 3. Influences of individual DNA elements within the promoter recognition region on abortive initiation and promoter escape. Biochemistry 42: 3798–3811. Vogel, U., and Jensen, K.F. (1994) The RNA chain elongation rate in Escherichia coli depends on the growth rate. J Bacteriol 176: 2807–2813. Weiss, S.B., and Gladstone, L. (1959) A mammalian system for the incorporation of cytidine triphosphate into ribonucleic acid. J Am Chem Soci 81: 4118–4119. Wu, C.W., Wu, F.Y., and Speckhard, D.C. (1977) Subunit location of the intrinsic divalent metal ions in RNA polymerase from Escherichia coli. Biochemistry 16: 5449–5454. Zhang, G., Campbell, E.A., Minakhin, L., Richter, C., Severinov, K., and Darst, S.A. (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98: 811–824. CH2 于玉珍 (2007) 可辨識 SmaI 延伸序列的 XveII 突變酵素之生化與蛋白結構分析。國立中興大學分子生物學研究所博士論文。 王彩諭 (1999) 十字花科黑腐病菌聚合酶之重組及特性研究。國立中興大學分子生物學研究所碩士論文。 馬宜恭 (1999) 十字花科黑腐病菌 RNA 聚合酶對 σ70 及 σ32 類型啟動子辨識之探討。國立中興大學分子生物學研究所碩士論文。 曾雅詩 (1994) 十字花科蔬菜黑腐病菌主要 sigma 因子基因之選殖。國立中興大學分子生物學研究所碩士論文。 黃建富 (1996) 十字花科黑腐病菌 RNA 聚合酶 Alpha 次單位基因及其操縱組之選殖與分析。國立中興大學分子生物學研究所碩士論文。 楊政華 (1999) 十字花科黑腐病菌 dnaK 操縱組啟動子之選殖與分析。國立中興大學分子生物學研究所碩士論文。 蔚承太 (1994) 十字花科黑腐病菌 RNA 聚合酶之純化與分析。國立中興大學分子生物學研究所碩士論文。 戴盤銘 (1997) 十字花科黑腐病菌 dnaK 及其上下游基因之選殖與定序。國立中興大學分子生物學研究所碩士論文。 謝小燕 (2000) 十字花科黑腐病菌 rpoE 基因之選殖及其啟動子之探討。國立中興大學分子生物學研究所碩士論文。 Artsimovitch, I., Svetlov, V., Murakami, K.S. & Landick, R. (2003) Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions. J Biol Chem 278: 12344–12355. Babcock, M.J., Buttner, M.J., Keler, C.H., Clarke, B.R., Morris, R.A., Lewis, C.G. & Brawner, M.E. (1997) Characterization of the rpoC gene of Streptomyces coelicolor A3(2) and its use to develop a simple and rapid method for the purification of RNA polymerase. Gene 196: 31–42. Bader, G.D. & Hogue, C.W. (2002) Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol 20: 991–997. Blatter, E.E., Ross, W., Tang, H., Gourse, R.L. & Ebright, R.H. (1994) Domain organization of RNA polymerase α subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell 78: 889–896. Borsig, L., Berger, E.G. & Malissard, M. (1997) Expression and purification of His-tagged β-1,4-galactosyltransferase in yeast and in COS cells. Biochem Biophys Res Commun 240: 586–589. Burgess, R.R. & Jendrisak, J.J. (1975) A procedure for the rapid, large-scall purification of Escherichia coli DNA-dependent RNA polymerase involving Polymin P precipitation and DNA-cellulose chromatography. Biochemistry 14: 4634-4638. Burgess, R.R., Travers, A.A., Dunn, J.J. & Bautz, E.K. (1969) Factor stimulating transcription by RNA polymerase. Nature 221: 43–46. Carroll, P., Brown, A.C., Hartridge, A.R. & Parish, T. (2007) Expression of Mycobacterium tuberculosis Rv1991c using an arabinose-inducible promoter demonstrates its role as a toxin. FEMS Microbiol Lett 274: 73–82. Chaga, G., Bochkariov, D.E., Jokhadze, G.G., Hopp, J. & Nelson, P. (1999a) Natural poly-histidine affinity tag for purification of recombinant proteins on cobalt(II)-carboxymethylaspartate crosslinked agarose. J Chromatogr A 864: 247–256. Chaga, G., Hopp, J. & Nelson, P. (1999b) Immobilized metal ion affinity chromatography on Co2+-carboxymethylaspartate-agarose Superflow, as demonstrated by one-step purification of lactate dehydrogenase from chicken breast muscle. Biotechnol Appl Biochem 29 19–24. Chamberlin, M.J., Nierman, W.C., Wiggs, J. & Neff, N. (1979) A quantitative assay for bacterial RNA polymerases. J Biol Chem 254: 10061–10069. Chan, C.L. & Landick, R. (1989) The Salmonella typhimurium his operon leader region contains an RNA hairpin-dependent transcription pause site. Mechanistic implications of the effect on pausing of altered RNA hairpins. J Biol Chem 264: 20796–20804. Chen, C.K., Tu, J. & Kuo, T.T. (1989) A new protein subunit k for RNA polymerase from Xanthomonas campestris pv. oryzae. J Biol Chem 264: 4362–4366. Cheng, C.Y., Shieh, S.Y., Hsu, C.C. & Yang, M.T. (2008) Characterization and transcriptional analysis of an ECF sigma factor from Xanthomonas campestris pv. campestris FEMS Microbiol Lett 289: 250–257. Chesnokov, I., Gossen, M., Remus, D. & Botchan, M. (1999) Assembly of functionally active Drosophila origin recognition complex from recombinant proteins. Genes Dev 13: 1289–1296. Colland, F., Barth, M., Hengge-Aronis, R. & Kolb, A. (2000) σ factor selectivity of Escherichia coli RNA polymerase: role for CRP, IHF and Lrp transcription factors. EMBO J 19: 3028–3037. da Silva, A.C., Ferro, J.A., Reinach, F.C., Farah, C.S., Furlan, L.R., Quaggio, R.B., Monteiro-Vitorello, C.B., Van Sluys, M.A., Almeida, N.F., Alves, L.M., do Amaral, A.M., Bertolini, M.C., Camargo, L.E., Camarotte, G., Cannavan, F., Cardozo, J., Chambergo, F., Ciapina, L.P., Cicarelli, R.M., Coutinho, L.L., Cursino-Santos, J.R., El-Dorry, H., Faria, J.B., Ferreira, A.J., Ferreira, R.C., Ferro, M.I., Formighieri, E.F., Franco, M.C., Greggio, C.C., Gruber, A., Katsuyama, A.M., Kishi, L.T., Leite, R.P., Lemos, E.G., Lemos, M.V., Locali, E.C., Machado, M.A., Madeira, A.M., Martinez-Rossi, N.M., Martins, E.C., Meidanis, J., Menck, C.F., Miyaki, C.Y., Moon, D.H., Moreira, L.M., Novo, M.T., Okura, V.K., Oliveira, M.C., Oliveira, V.R., Pereira, H.A., Rossi, A., Sena, J.A., Silva, C., de Souza, R.F., Spinola, L.A., Takita, M.A., Tamura, R.E., Teixeira, E.C., Tezza, R.I., Trindade dos Santos, M., Truffi, D., Tsai, S.M., White, F.F., Setubal, J.C. & Kitajima, J.P. (2002) Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417: 459–463. de Lorenzo, V., Herrero, M., Jakubzik, U. & Timmis, K.N. (1990) Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria. J Bacteriol 172: 6568–6572. Fribourg, S., Romier, C., Werten, S., Gangloff, Y.G., Poterszman, A. & Moras, D. (2001) Dissecting the interaction network of multiprotein complexes by pairwise coexpression of subunits in E. coli. J Mol Biol 306: 363–373. Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M.A., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G. & Superti-Furga, G. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141–147. Gourse, R.L., Ross, W. & Gaal, T. (2000) UPs and downs in bacterial transcription initiation: the role of the α subunit of RNA polymerase in promoter recognition. Mol Microbiol 37: 687–695. Guzman, L.M., Belin, D., Carson, M.J. & Beckwith, J. (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol 177: 4121–4130. Hefti, M.H., Van Vugt-Van der Toorn, C.J., Dixon, R. & Vervoort, J. (2001) A novel purification method for histidine-tagged proteins containing a thrombin cleavage site. Anal Biochem 295: 180–185. Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolting, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A.R., Sassi, H., Nielsen, P.A., Rasmussen, K.J., Andersen, J.R., Johansen, L.E., Hansen, L.H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sorensen, B.D., Matthiesen, J., Hendrickson, R.C., Gleeson, F., Pawson, T., Moran, M.F., Durocher, D., Mann, M., Hogue, C.W., Figeys, D. & Tyers, M. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180–183. Hochuli, E., Bannwarth, W., Döebeli, H., Gentz, R. & Stueber, D. (1988) Genetic approach to facilitate purification of recombinant proteins with a novel metal chelate adsorbent. Bio/Technology 6: 1321–1325. Huang, L.H., Tseng, Y.H. & Yang, M.T. (1998) Isolation and characterization of the Xanthomonas campestris rpoH gene coding for a 32-kDa heat shock sigma factor. Biochem Biophys Res Commun 244: 854–860. Ishihama, A. (1981) Subunit of assembly of Escherichia coli RNA polymerase. Adv Biophys 14: 1–35. Ishihama, A. & Ito, K. (1972) Subunits of RNA polymerase in function and structure. II. Reconstitution of Escherichia coli RNA polymerase from isolated subunits. J Mol Biol 72: 111–123. Janaszak, A., Nadratowska-Wesołowska, B., Konopa, G. & Taylor, A. (2009) The P1 promoter of the Escherichia coli rpoH gene is utilized by σ70 -RNAP or σS -RNAP depending on growth phase. FEMS Microbiol Lett 291: 65-72. Janknecht, R., de Martynoff, G., Lou, J., Hipskind, R.A., Nordheim, A. & Stunnenberg, H.G. (1991) Rapid and efficient purification of native histidine-tagged protein expressed by recombinant vaccinia virus. Proc Natl Acad Sci U S A 88: 8972–8976. Johnston, K., Clements, A., Venkataramani, R.N., Trievel, R.C. & Marmorstein, R. (2000) Coexpression of proteins in bacteria using T7-based expression plasmids: expression of heteromeric cell-cycle and transcriptional regulatory complexes. Protein Expr Purif 20: 435–443. Kümmel, D., Müller, J.J., Roske, Y., Henke, N. & Heinemann, U. (2006) Structure of the Bet3-Tpc6B core of TRAPP: two Tpc6 paralogs form trimeric complexes with Bet3 and Mum2. J Mol Biol 361: 22–32. Kümmel, D., Müller, J.J., Roske, Y., Misselwitz, R., Büssow, K. & Heinemann, U. (2005) The structure of the TRAPP subunit TPC6 suggests a model for a TRAPP subcomplex. EMBO Rep 6: 787–793. Kashlev, M., Martin, E., Polyakov, A., Severinov, K., Nikiforov, V. & Goldfarb, A. (1993) Histidine-tagged RNA polymerase: dissection of the transcription cycle using immobilized enzyme. Gene 130: 9–14. Kim, K.J., Kim, H.E., Lee, K.H., Han, W., Yi, M.J., Jeong, J. & Oh, B.H. (2004) Two-promoter vector is highly efficient for overproduction of protein complexes. Protein Sci 13: 1698–1703. Klančnik, A., Botteldoorn, N., Herman, L. & Možina, S.S. (2006) Survival and stress induced expression of groEL and rpoD of Campylobacter jejuni from different growth phases. Int J Food Microbiol 112: 200-207. Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685. Lai, J.Y., Huang, C.F., Tseng, Y.H. & Yang, M.T. (2000) Sequence and molecular analysis of the rpoA cluster genes from Xanthomonas campestris pv. campestris. Biochim Biophys Acta 1492: 553–559. Landick, R., Colwell, A. & Stewart, J. (1990) Insertional mutagenesis of a plasmid-borne Escherichia coli rpoB gene reveals alterations that inhibitβ-subunit assembly into RNA polymerase. J Bacteriol 172: 2844–2854. Luger, K., Rechsteiner, T.J., Flaus, A.J., Waye, M.M. & Richmond, T.J. (1997) Characterization of nucleosome core particles containing histone proteins made in bacteria. J Mol Biol 272: 301–311. Maeda, H., Fujita, N. & Ishihama, A. (2000) Competition among seven Escherichia coli σ subunits: relative binding affinities to the core RNA polymerase. Nucleic Acids Res 28: 3497–3503. Minakhin, L., Bhagat, S., Brunning, A., Campbell, E.A., Darst, S.A., Ebright, R.H. & Severinov, K. (2001a) Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly. Proc Natl Acad Sci U S A 98: 892–897. Minakhin, L., Nechaev, S., Campbell, E.A. & Severinov, K. (2001b) Recombinant Thermus aquaticus RNA polymerase, a new tool for structure-based analysis of transcription. J Bacteriol 183: 71–76. Olekhnovich, I.N. & Kadner, R.J. (2004) Contribution of the RpoA C-terminal domain to stimulation of the Salmonella enterica hilA promoter by HilC and HilD. J Bacteriol 186: 3249–3253. Palmer, B.R. & Marinus, M.G. (1994) The dam and dcm strains of Escherichia coli--a review. Gene 143: 1-12. Porath, J., Carlsson, J., Olsson, I. & Belfrage, G. (1975) Metal chelate affinity chromatography, a new approach to protein fractionation. Nature 258: 598–599. Rank, K.B., Mildner, A.M., Leone, J.W., Koeplinger, K.A., Chou, K.C., Tomasselli, A.G., Heinrikson, R.L. & Sharma, S.K. (2001) [W206R]-procaspase 3: an inactivatable substrate for caspase 8. Protein Expr Purif 22: 258–266. Romier, C., Ben Jelloul, M., Albeck, S., Buchwald, G., Busso, D., Celie, P.H., Christodoulou, E., De Marco, V., van Gerwen, S., Knipscheer, P., Lebbink, J.H., Notenboom, V., Poterszman, A., Rochel, N., Cohen, S.X., Unger, T., Sussman, J.L., Moras, D., Sixma, T.K. & Perrakis, A. (2006) Co-expression of protein complexes in prokaryotic and eukaryotic hosts: experimental procedures, database tracking and case studies. Acta Crystallogr. D Biol Crystallogr 62: 1232–1242. Sambrook, J. & Russell, D.W., (2001) Molecular Cloning, A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Schagger, H., and von Jagow, G. (1987) Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem 166: 368-379. Scheich, C., Kummel, D., Soumailakakis, D., Heinemann, U. & Bussow, K. (2007) Vectors for co-expression of an unrestricted number of proteins. Nucleic Acids Res 35: e43. Schmidt, M., Tuominen, N., Johansson, T., Weiss, S.A., Keinanen, K. & Oker-Blom, C. (1998) Baculovirus-mediated large-scale expression and purification of a polyhistidine-tagged rubella virus capsid protein. Protein Expr Purif 12: 323–330. Schweizer, H.D. (1993) Small broad-host-range gentamycin resistance gene cassettes for site-specific insertion and deletion mutagenesis. Biotechniques 15: 831-834. Setlow, J.K., (2001) Genetic Engineering: Principles and Methods. Kluwer Academic Publishers, New York. Studier, F.W. & Moffatt, B.A. (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol 189: 113–130. Sukchawalit, R., Vattanaviboon, P., Sallabhan, R. & Mongkolsuk, S. (1999) Construction and characterization of regulated L-arabinose-inducible broad host range expression vectors in Xanthomonas. FEMS Microbiol Lett 181: 217–223. Tan, S., Hunziker, Y., Sargent, D.F. & Richmond, T.J. (1996) Crystal structure of a yeast TFIIA/TBP/DNA complex. Nature 381: 127–151. Tan, S., Kern, R.C. & Selleck, W. (2005) The pST44 polycistronic expression system for producing protein complexes in Escherichia coli. Protein Expr Purif 40: 385–395. Tang, H., Severinov, K., Goldfarb, A. & Ebright, R.H. (1995) Rapid RNA polymerase genetics: one-day, no-column preparation of reconstituted recombinant Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A 92: 4902–4906. Taylor, L.A. & Rose, R.E. (1988) A correction in the nucleotide sequence of the Tn903 kanamycin resistance determinant in pUC4K. Nucleic Acids Res 16: 358. Terpe, K. (2003) Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol 60: 523–533. Vrentas, C.E., Gaal, T., Ross, W., Ebright, R.H. & Gourse, R.L. (2005) Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA. Genes Dev 19: 2378–2387. Wang, T.W. & Tseng, Y.H. (1992) Electrotransformation of Xanthomonas campestris by RF DNA of filamentous phage ØLf. Lett Appl Microbiol 14: 65–68. White, T.J. & Gonzalez, C.F. (1995) Electroporation of Xanthomonas. Methods Mol Biol 47: 135–141. Wu, J. & Filutowicz, M. (1999) Hexahistidine (His6)-tag dependent protein dimerization: a cautionary tale. Acta Biochim Pol 46: 591–599. Yang, B.Y. & Tseng, Y.H. (1988) Production of exopolysaccharide and exocellular enzymes in virulent and avirulent strains of Xanthomonas campestris pv. campestris. Bot Bull Acad Sin 29: 93–99. Yang, X. & Lewis, P.J. (2008) Overproduction and purification of recombinant Bacillus subtilis RNA polymerase. Protein Expr Purif 59: 86–93. Zalenskaya, K., Lee, J., Gujuluva, C.N., Shin, Y.K., Slutsky, M. & Goldfarb, A. (1990) Recombinant RNA polymerase: inducible overexpression, purification and assembly of Escherichia coli rpo gene products. Gene 89: 7–12. CH3 于玉珍 (2007) 可辨識 SmaI 延伸序列的 XveII 突變酵素之生化與蛋白結構分析。國立中興大學分子生物學研究所博士論文。 江玉玲 (1999) 十字花科黑腐病菌 secE 及 secY 基因選殖及特性的研究。國立中興大學分子生物學研究所碩士論文。 馬宜恭 (1999) 十字花科黑腐病菌 RNA 聚合酶對 σ70 及 σ32 類型啟動子辨識之探討。國立中興大學分子生物學研究所碩士論文。 陳稜穎 (2008) Xanthomonas campestris pv. campestris RecX 與 RecA 交互作用及 recA 基因調控者之探討。國立中興大學分子生物學研究所碩士論文。 楊明浩 (1998) 線狀噬菌體 ØLf 啟動子之選殖與分析。國立中興大學植物學研究所碩士論文。 謝小燕 (2000) 十字花科黑腐病菌 rpoE 基因之選殖及其啟動子之探討。國立中興大學分子生物學研究所碩士論文。 An, G., Justesen, J., Watson, R.J. & Friesen, J.D. (1979) Cloning the spoT gene of Escherichia coli: identification of the spoT gene product. J Bacteriol 137: 1100–1110. Anantharaman, V., Koonin, E.V. & Aravind, L. (2002) SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases. J Mol Microbiol Biotechnol 4: 71–75. Artsimovitch, I., Svetlov, V., Murakami, K.S. & Landick, R. (2003) Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions. J Biol Chem 278: 12344–12355. Barker, M.M., Gaal, T., Josaitis, C.A. & Gourse, R.L. (2001) Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J Mol Biol 305: 673–688. Burgess, R.R., Travers, A.A., Dunn, J.J. & Bautz, E.K. (1969) Factor stimulating transcription by RNA polymerase. Nature 221: 43–46. Cashel, M., Gentry, D.R., Hernandez, V.J. & Vinella, D., (1996) The stringent response. In: Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. Neidhardt, F. C., Curtiss III, R., Ingraham, J. L., C., L. E. C., Low, K. B., Magasanik, B., Reznikoff, W. S., Riley, M., Schaechter, M. & Umbarger, H. E. (eds). ASM Press, Washington, DC, pp. 1458–1496. Chatterji, D., Ogawa, Y., Shimada, T. & Ishihama, A. (2007) The role of the ω subunit of RNA polymerase in expression of the relA gene in Escherichia coli. FEMS Microbiol Lett 267: 51–55. Chen, W.P. & Kuo, T.T. (1993) A simple and rapid method for the preparation of gram-negative bacterial genomic DNA. Nucleic Acids Res 21: 2260. Chung, W.J., Shu, H.Y., Lu, C.Y., Wu, C.Y., Tseng, Y.H., Tsai, S.F. & Lin, C.H. (2007) Qualitative and comparative proteomic analysis of Xanthomonas campestris pv. campestris 17. Proteomics 7: 2047–2058. Costanzo, A. & Ades, S.E. (2006) Growth phase-dependent regulation of the extracytoplasmic stress factor, σE, by guanosine 3'',5''-bispyrophosphate (ppGpp). J Bacteriol 188: 4627–4634. Dillingham, M.S. & Kowalczykowski, S.C. (2001) A step backward in advancing DNA replication: rescue of stalled replication forks by RecG. Mol Cell 8: 734–736. Dubois, M., Gilles, K.A., Hamilton, J.K., Rebers, P.A. & Smith, F. (1956) Colorimetric method for determination of sugars and related substances. Anal Chem 28: 350–356. Gentry, D., Bengra, C., Ikehara, K. & Cashel, M. (1993a) Guanylate kinase of Escherichia coli K-12. J Biol Chem 268: 14316–14321. Gentry, D.R. & Burgess, R.R. (1989) rpoZ, encoding the ω subunit of Escherichia coli RNA polymerase, is in the same operon as spoT. J Bacteriol 171: 1271–1277. Gentry, D.R. & Burgess, R.R. (1993) Cross-linking of Escherichia coli RNA polymerase subunits: identification ofβ'' as the binding site of ω. Biochemistry 32: 11224–11227. Gentry, D.R., Hernandez, V.J., Nguyen, L.H., Jensen, D.B. & Cashel, M. (1993b) Synthesis of the stationary-phase sigma factor σS is positively regulated by ppGpp. J Bacteriol 175: 7982–7989. Gentry, D., Xiao, H., Burgess, R. & Cashel, M. (1991) The ω subunit of Escherichia coli K-12 RNA polymerase is not required for stringent RNA control in vivo. J Bacteriol 173: 3901–3903. Ghosh, P., Ishihama, A. & Chatterji, D. (2001) Escherichia coli RNA polymerase subunit omega and its N-terminal domain bind full-length β'' to facilitate incorporation into theα2βsubassembly. Eur J Biochem 268: 4621–4627. Gralla, J.D. (2005) Escherichia coli ribosomal RNA transcription: regulatory roles for ppGpp, NTPs, architectural proteins and a polymerase-binding protein. Mol Microbiol 55: 973–977. Harlow, E. & Lane, D., (1988) Antibodies: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Helmann, J.D. (2003) Purification of Bacillus subtilis RNA polymerase and associated factors. Methods Enzymol 370: 10–24. Helmann, J.D. & Moran, J.C.P., (2002) Bacillus subtilis and its closest relatives: From genes to cells. In: RNA polymerase and sigma factors. Sonenshine, A. L., Hoch, J. A. & Losick, R. (eds). ASM Press, Washington, DC, USA, pp. 289–312. Hung, C.H., Wu, H.C. & Tseng, Y.H. (2002) Mutation in the Xanthomonas campestris xanA gene required for synthesis of xanthan and lipopolysaccharide drastically reduces the efficiency of bacteriophage adsorption. Biochem Biophys Res Commun 291: 338–343. Igarashi, K., Fujita, N. & Ishihama, A. (1989) Promoter selectivity of Escherichia coli RNA polymerase: omega factor is responsible for the ppGpp sensitivity. Nucleic Acids Res 17: 8755–8765. Kojima, I., Kasuga, K., Kobayashi, M., Fukasawa, A., Mizuno, S., Arisawa, A. & Akagawa, H. (2002) The rpoZ gene, encoding the RNA polymerase omega subunit, is required for antibiotic production and morphological differentiation in Streptomyces kasugaensis. J Bacteriol 184: 6417–6423. Kvint, K., Farewell, A. & Nystrom, T. (2000) RpoS-dependent promoters require guanosine tetraphosphate for induction even in the presence of high levels of σS. J Biol Chem 275: 14795–14798. Lee, T.C., Lin, N.T. & Tseng, Y.H. (1996) Isolation and characterization of the recA gene of Xanthomonas campestris pv. campestris. Biochem Bioph
摘要: 原核生物中 RNA polymerase (RNAP) 為負責基因轉錄表現的蛋白複合體,分別由 α、β、β′ 以及 ω 所組成。藉由與 σ 因子重組後辨識位於基因上游的啟動子序列,而得以起始基因的轉錄並達到調控表現的目的。雖然在 E. coli 的研究中對 RNAP 的功能已有諸多的探討,而透過 Thermus aquaticus RNAP 的結構解析對於各次單元間的交互作用也有了進一步的瞭解;但對於 AT-rich 的革蘭氏陽性菌,如 Bacillus subtilis,或是高 G+C 值的 α-proteobacteria 菌屬 Rhodobacter capsulatus,相關研究顯現出這些 RNAP 有著不同於 E. coli RNAP 的轉錄調控機制。而對於 G+C 值高達 65% 的 Xanthomonas campestris pv. campestris (Xcc),其 RNAP 的轉錄調控機制應當仍有許多值得探討的地方。本論文針對 Xcc RNAP 的研究分為三部分,第一部分為探討不同 Xcc RNAP 純化方式的比較。透過基因重組技術改造 Xcc 野生株 Xc11 從而衍生出 Xc1009 以及 TY109,為分別在 rpoA 以及 rpoC 基因 3′ 端序列上具有 6 × His 的轉譯密碼。在蛋白層析過程中發現,相較於 β′His-tag RNAP,αHis-tag RNAP 對於 Ni-NTA 有較強的結合能力,可獲得較佳的純化結果。體外實驗結果則顯示 αHis-tag 不會影響 core RNAP 與 σ 因子之間的重組。將各次單元基因以 rpoC-rpoB-rpoAHis-tag 的順序選殖到單一質體上,經誘導後可成功於 E. coli 宿主細胞中大量表現重組成為完整的 core RNAP 分子,此方法可簡化純化步驟並縮短過程中所耗費的時間。第二部分乃針對可轉譯出 ω 次單元的 rpoZ 基因進行探討。該基因的表現隨著菌體生長時期而逐漸增加,當 rpoZ 發生突變會造成其下游 spoT 基因的表現受到影響,並且降低了菌體對於環境中營養源的感受性而使生長速度受到影響,推測 rpoZ 參與了菌體中 stringent response 的調節機制。另一方面,ω 次單元與其他 RNAP 次單元共同表現後,所獲得的 core RNAP (α2ββ′ω) 其轉錄活性高於不具 ω 的 core RNAP (α2ββ′) 約 13 倍,顯示 ω 次單元為維持 RNAP 活性的重要因子。第三部分則探討 ECF σ 因子,RpoE (σE),的表現及調控。RT-PCR 的結果顯示 rpoE 與下游基因 rseA 屬於同一操縱子 (operon),而 DNase I footprint 的分析結果顯示 rpoE 與 rseA 基因上游皆具有受 σE 所辨識的啟動子序列。於高溫環境 (42℃) 或 5% 乙醇誘導下,σE 的表現量可上升 20% ~ 40%,有助於菌體在逆境中的存活。進一步分析 Xcc 在遭受熱誘導時,σE 對另一熱誘導 σ 因子,σ32,在表現上的影響,結果發現 σ32 的表現量會因 rpoE 的突變而略為下降,推測 σE 在 σ32 因應熱誘導時具有調控的功能。
Prokaryotic RNA polymerase (RNAP) is a protein complex responsible for gene expression, consisting of α dimer, β, β', and ω subunits. Initiation of gene transcription is allowed to proceed when a dissociable σ subunit associates with the core RNAP to form the holoenzyme, directing the holoenzyme to bind to the promoter upstream of the target gene. Functions of RNAP in E. coli have been well characterized, and the crystal structure analysis of Thermus aquaticus (Taq) RNAP has provided detail information about interactions among RNAP subunits. However, results of studies in AT-rich gram-positive bacteria, such as Bacillus subtilis, or Rhodobacter capsulatus with high G+C content showed that transcriptional regulation mechanisms of RNAPs of these bacteria are different from that of E. coli RNAP. Xanthomonas campestris pv. campestris (Xcc) has a G+C content of 65%, and the transcriptional mechanisms of this bacterium are not well-defined. The aim of this dissertation was to characterize the functions of RNAP subunits in Xcc, and results of this study were divided into three sections. In the first section, purification and characterization of Xcc RNAP with a His-tag fusion at either the C-terminus of α or β' subunit were compared. Result showed that αHis-tag RNAP renders its binding to Ni-NTA stronger than β'His-tag RNAP. Further analyses demonstrated that αHis-tag core RNAP keeps the same ability to interact with σ factors. In addition, coexpression of Xcc RNAP subunits was carried out in E. coli with a plasmid bearing rpoC-rpoB-rpoAHis-tag genes, and in vivo reconstitution of Xcc RNAP subunits to form a core RNAP was successfully achieved. By using this approach, the purification of Xcc RNAP was simplified and the time-cost was reduced. The second section demonstrates the physiological roles of ω in Xcc. Expression of rpoZ was found to be closely related to the cell growth phase. Mutation in rpoZ had influence on expression of the downstream spoT gene. Additionally, the rpoZ mutant exhibited slower growth rate than that of the wild type, suggesting that rpoZ might be involved in regulating the stringent response of Xcc. Moreover, transcriptional activity of the recombinant Xcc core RNAP with ω coexpressed in E. coli had a 13-fold increase than that of the one lacking ω, indicating ω is an important element in maintenance the enzymatic activity of Xcc RNAP. The third section was focused on the expression and regulation of the ECF σ factor, RpoE (σE). RT-PCR analyses demonstrated that rpoE and rseA are in the same operon. The results of DNase I footprint analyses showed the binding by EσE on the σE-dependent upstream promoters of rpoE and rseA. The expression level of σE increases 20 ~ 40% in response to 42℃ or 5% EtOH stresses. Expression of heat-inducible σ32 decreased in rpoE mutant under heat shock, suggesting the role of σE in σ32 expression in response to heat shock.
URI: http://hdl.handle.net/11455/22044
其他識別: U0005-1908200912023300
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