Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/21856
標題: 可辨識 SmaI 延伸序列的 XveII 突變酵素之生化與蛋白結構分析
Biochemical and protein structural analyses of XveII mutant enzymes that recognize extended SmaI cognate sequence
作者: 于玉珍
Yu, Yu-Jen
關鍵字: XveII;限制酶突變;restriction endonuclease;mutant;flanking sequence;protein structure;相鄰序列;蛋白結構
出版社: 分子生物學研究所
引用: 于玉珍 (1997) Xanthomonas campestris pv. vesicatoria XveI 及 XveII 限制修飾系統基因之選殖與特性研究。國立中興大學分子生物學研究所碩士論文。 賴靜瑩 (2000) Xanthomonas campestris pv. phaseoli xphI 限制修飾系統基因及其上下游片段之選殖及特性研究。國立中興大學分子生物學研究所博士論文。 Acharya, A.S., and Roy, K.B. (2001) Reduced activity of BamHI variants C54I, C64W, and C54D/C64R is consistent with the substrate-assisted catalysis model. Biochem Biophys Res Commun 287: 153-159. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. Arber, W., and Dussoix, D. (1962) Host specificity of DNA produced by Escherichia coli. I. Host controlled modification of bacteriophage lambda. J Mol Biol 5: 18-36. Choi, S.H., and Leach, J.E. (1994) Identification of the XorII methyltransferase gene and a vsr homolog from Xanthomonas oryzae pv. oryzae. Mol Gen Genet 244: 383-390. 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. Danna, K., and Nathans, D. (1971) Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae. Proc Natl Acad Sci USA 68: 2913-2917. Endow, S.A., and Roberts, R.J. (1977) Two restriction-like enzymes from Xanthomonas malvacearum. J Mol Biol 112: 521-529. Froman, B.E., Tait, R.C., Kado, C.I., and Rodriguez, R.L. (1984) Purification of restriction endonuclease XcyI from Xanthomonas cyanopsidis. Gene 28: 331-335. Gingeras, T.R., Myers, P.A., Olson, J.A., Hanberg, F.A., and Roberts, R.J. (1978) A new specific endonuclease present in Xanthomonas holcicola, Xanthomonas papavericola and Brevibacterium luteum. J Mol Biol 118: 113-122. Gomez, P., Ribas-Aparicio, R.M., Pelaez, A.I., Gomez, A., and Rodicio, M.R. (1997) Isolation and nucleotide sequence of the gene encoding the XamI DNA methyltransferase of Xanthomonas campestris pv. amaranthicola. Biochim Biophys Acta 1351: 261-266. Heidmann, S., Seifert, W., Kessler, C., and Domdey, H. (1989) Cloning, characterization and heterologous expression of the SmaI restriction-modification system. Nucleic Acids Res 17: 9783-9796. Kelly, T.J., Jr., and Smith, H.O. (1970) A restriction enzyme from Hemophilus influenzae. II. J Mol Biol 51: 393-409. Kim, J.G., Choi, S., Oh, J., Moon, J.S., and Hwang, I. (2006) Comparative analysis of three indigenous plasmids from Xanthomonas axonopodis pv. glycines. Plasmid 56: 79-87. Klimašauskas, S., Steponavičienė, D., Manelienė, Z., Petrušytė, M., Butkus, V., and Janulaitis, A. (1990) M.SmaI is an N 4-methylcytosine specific DNA-methylase. Nucleic Acids Res 18: 6607-6609. Kunkel, L.M., Silberklang, M., and McCarthy, B.J. (1979) A third restriction endonuclease from Xanthomonas malvacearum. J Mol Biol 132: 133-139. Lee, B.M., Park, Y.J., Park, D.S., Kang, H.W., Kim, J.G., Song, E.S., Park, I.C., Yoon, U.H., Hahn, J.H., Koo, B.S., Lee, G.B., Kim, H., Park, H.S., Yoon, K.O., Kim, J.H., Jung, C.H., Koh, N.H., Seo, J.S., and Go, S.J. (2005) The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice. Nucleic Acids Res 33: 577-586. Lin, B.C., Chien, M.C., and Lou, S.Y. (1980) A sequence-specific endonuclease (Xmn I) from Xanthomonas manihotis. Nucleic Acids Res 8: 6189-6198. Linn, S., and Arber, W. (1968) Host specificity of DNA produced by Escherichia coli, X. in vitro restriction of phage fd replicative form. Proc Natl Acad Sci USA 59: 1300-1306. Luria, S.E., and Human, M.L. (1952) A nonhereditary, host-induced variation of bacterial viruses. J Bacteriol 64: 557-569. Meselson, M., and Yuan, R. (1968) DNA restriction enzyme from E. coli. Nature 217: 1110-1114. Nwankwo, D.O., Lynch, J.J., Moran, L.S., Fomenkov, A., and Slatko, B.E. (1996) The XmnI restriction-modification system: cloning, expression, sequence organization and similarity between the R and M genes. Gene 173: 121-127. Ochiai, H., Inoue, Y., Takeya, M., Sasaki, A., and Kaku, H. (2005) Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity. Jpn Agric Res Q 39: 275-287. Roberts, R.J., Belfort, M., Bestor, T., Bhagwat, A.S., Bickle, T.A., Bitinaite, J., Blumenthal, R.M., Degtyarev, S.K., Dryden, D.T.F., Dybvig, K., Firman, K., Gromova, E.S., Gumport, R.I., Halford, S.E., Hattman, S., Heitman, J., Hornby, D.P., Janulaitis, A., Jeltsch, A., Josephsen, J., Kiss, A., Klaenhammer, T.R., Kobayashi, I., Kong, H., Krüger, D.H., Lacks, S., Marinus, M.G., Miyahara, M., Morgan, R.D., Murray, N.E., Nagaraja, V., Piekarowicz, A., Pingoud, A., Raleigh, E., Rao, D.N., Reich, N., Repin, V.E., Selker, E.U., Shaw, P.-C., Stein, D.C., Stoddard, B.L., Szybalski, W., Trautner, T.A., Van Etten, J.L., Vitor, J.M.B., Wilson, G.G., and Xu, S.-y. (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 31: 1805-1812. Roberts, R.J. (2005) How restriction enzymes became the workhorses of molecular biology. Proc Natl Acad Sci USA 102: 5905-5908. Roberts, R.J., Vincze, T., Pósfai, J., and Macelis, D. (2007) REBASE--enzymes and genes for DNA restriction and modification. Nucleic Acids Res 35: D269-270. Shaw, P.C., and Mok, Y.K. (1993) XcmI as a universal restriction enzyme for single-stranded DNA. Gene 133: 85-89. Smith, H.O., and Wilcox, K.W. (1970) A restriction enzyme from Hemophilus influenzae. I. Purification and general properties. J Mol Biol 51: 379-391. Smith, H.O., and Nathans, D. (1973) Letter: A suggested nomenclature for bacterial host modification and restriction systems and their enzymes. J Mol Biol 81: 419-423. Song, T., Sik Kang, B., and Min Kim, Y. (1998) XspI, a new type II restriction endonuclease from a Xanthomonas species. Mol Cells 8: 370-373. Thieme, F., Koebnik, R., Bekel, T., Berger, C., Boch, J., Büttner, D., Caldana, C., Gaigalat, L., Goesmann, A., Kay, S., Kirchner, O., Lanz, C., Linke, B., McHardy, A.C., Meyer, F., Mittenhuber, G., Nies, D.H., Niesbach-Klösgen, U., Patschkowski, T., Rückert, C., Rupp, O., Schneiker, S., Schuster, S.C., Vorhölter, F.-J., Weber, E., Pühler, A., Bonas, U., Bartels, D., and Kaiser, O. (2005) Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol 187: 7254-7266. Wang, R.Y., Shedlarski, J.G., Farber, M.B., Kuebbing, D., and Ehrlich, M. (1980) Two sequence-specific endonucleases from Xanthomonas oryzae. Characterization and unusual properties. Biochim Biophys Acta 606: 371-385. Weng, S.F., Fan, Y.F., Tseng, Y.H., and Lin, J.W. (1997) Sequence analysis of the small cryptic Xanthomonas campestris pv. vesicatoria plasmid pXV64 encoding a Rep protein similar to gene II protein of phage 12-2. Biochem Biophys Res Commun 231: 121-125. Wilson, G.G., and Murray, N.E. (1991) Restriction and Modification Systems. Annu Rev Genet 25: 585-627. Wu, L.T., and Tseng, Y.H. (2000) Characterization of the IncW cryptic plasmid pXV2 from Xanthomonas campestris pv. vesicatoria. Plasmid 44: 163-172. Yu, Y.J., and Yang, M.T. (2007) A novel restriction-modification system from Xanthomonas campestris pv. vesicatoria encodes a m4C-methyltransferase and a nonfunctional restriction endonuclease. FEMS Microbiol Lett 272: 83-90. Zain, B.S., and Roberts, R.J. (1977) A new specific endonuclease from Xanthomonas badrii. J Mol Biol 115: 249-255. 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。 許佳智 (2000) 十字花科黑腐病菌 groESL 基因之選殖及特性之研究。國立中興大學分子生物學研究所碩士論文。 黃建富 (1995) 十字花科黑病菌 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。 戴盤銘 (1997) 十字花科蔬菜黑腐菌 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。 Alvarez, M.A., Chater, K.F., and Rodicio, M.R. (1993) Complex transcription of an operon encoding the SalI restriction-modification system of Streptomyces albus G. Mol Microbiol 8: 243-252. Alvarez, M.A., Gomez, A., Gomez, P., Brooks, J.E., and Rodicio, M.R. (1996) Comparative analysis of expression of the SalI restriction-modification system in Escherichia coli and Streptomyces. Mol Gen Genet 253: 74-80. Alves, J., Pingoud, A., Haupt, W., Langowski, J., Peters, F., Maass, G., and Wolff, C. (1984) The influence of sequences adjacent to the recognition site on the cleavage of oligodeoxynucleotides by the EcoRI endonuclease. Eur J Biochem 140: 83-92. Barany, F., Slatko, B., Danzitz, M., Cowburn, D., Schildkraut, I., and Wilson, G.G. (1992) The corrected nucleotide sequences of the TaqI restriction and modification enzymes reveal a thirteen-codon overlap. Gene 112: 91-95. Barcus, V.A., Titheradge, A.J., and Murray, N.E. (1995) The diversity of alleles at the hsd locus in natural populations of Escherichia coli. Genetics 140: 1187-1197. Bickle, T.A., and Krüger, D.H. (1993) Biology of DNA restriction. Microbiol Rev 57: 434-450. Bilcock, D.T., and Halford, S.E. (1999) DNA restriction dependent on two recognition sites: activities of the SfiI restriction-modification system in Escherichia coli. Mol Microbiol 31: 1243-1254. Birnboim, H.C., and Doly, J. (1979) A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7: 1513-1523. Bist, P., Sistla, S., Krishnamurthy, V., Acharya, A., Chandrakala, B., and Rao, D.N. (2001) S-adenosyl-L-methionine is required for DNA cleavage by type III restriction enzymes. J Mol Biol 310: 93-109. Bradford, M.M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72: 248-254. Bujnicki, J.M. (2001) Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons. Acta Biochim Pol 48: 935-967. Bujnicki, J.M., Rotkiewicz, P., Kolinski, A., and Rychlewski, L. (2001) Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics. Protein Eng 14: 717-721. Butler, D., and Fitzgerald, G.F. (2001) Transcriptional analysis and regulation of expression of the ScrFI restriction-modification system of Lactococcus lactis subsp. cremoris UC503. J Bacteriol 183: 4668-4673. Cao, W. (1999) Binding kinetics and footprinting of TaqI endonuclease: effects of metal cofactors on sequence-specific interactions. Biochemistry 38: 8080-8087. Cesnaviciene, E., Mitkaite, G., Stankevicius, K., Janulaitis, A., and Lubys, A. (2003) Esp1396I restriction-modification system: structural organization and mode of regulation. Nucleic Acids Res 31: 743-749. Cha, J., Bishai, W., and Chandrasegaran, S. (1993) New vectors for direct cloning of PCR products. Gene 136: 369-370. Chang, A.C., and Cohen, S.N. (1978) Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol 134: 1141-1156. Chang, W.H., Lee, M.C., Yang, M.T., and Tseng, Y.H. (2005) Expression of heat-shock genes groESL in Xanthomonas campestris is upregulated by CLP in an indirect manner. FEMS Microbiol Lett 243: 365-372. Chen, W.P., and Kuo, T.T. (1993) A simple and rapid method for the preparation of gram-negative bacterial genomic DNA. Nucleic Acids Res 21: 2260. Chin, V., Valinluck, V., Magaki, S., and Ryu, J. (2004) KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system. Nucleic Acids Res 32: e138. Chinen, A., Naito, Y., Handa, N., and Kobayashi, I. (2000) Evolution of sequence recognition by restriction-modification enzymes: selective pressure for specificity decrease. Mol Biol Evol 17: 1610-1619. Connolly, B.A., Liu, H.H., Parry, D., Engler, L.E., Kurpiewski, M.R., and Jen-Jacobson, L. (2001) Assay of restriction endonucleases using oligonucleotides. Methods Mol Biol 148: 465-490. Cooper, L.P., and Dryden, D.T. (1994) The domains of a type I DNA methyltransferase. Interactions and role in recognition of DNA methylation. J Mol Biol 236: 1011-1021. Daniels, L.E., Wood, K.M., Scott, D.J., and Halford, S.E. (2003) Subunit assembly for DNA cleavage by restriction endonuclease SgrAI. J Mol Biol 327: 579-591. Dar, M.E., and Bhagwat, A.S. (1993) Mechanism of expression of DNA repair gene vsr, an Escherichia coli gene that overlaps the DNA cytosine methylase gene, dcm. Mol Microbiol 9: 823-833. Das, R., Laederach, A., Pearlman, S.M., Herschlag, D., and Altman, R.B. (2005) SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA 11: 344-354. Dower, W.J., Miller, J.F., and Ragsdale, C.W. (1988) High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res 16: 6127-6145. Dryden, D.T., Murray, N.E., and Rao, D.N. (2001) Nucleoside triphosphate-dependent restriction enzymes. Nucleic Acids Res 29: 3728-3741. Fomenkov, A., Xiao, J.P., Dila, D., Raleigh, E., and Xu, S.Y. (1994) The ‘endo-blue method’ for direct cloning of restriction endonuclease genes in E. coli. Nucleic Acids Res 22: 2399-2403. Galburt, E.A., and Stoddard, B.L. (2002) Catalytic mechanisms of restriction and homing endonucleases. Biochemistry 41: 13851-13860. Gonzalez-Nicieza, R., Turner, D.P., and Connolly, B.A. (2001) DNA binding and cleavage selectivity of the Escherichia coli DNA G:T-mismatch endonuclease (vsr protein). J Mol Biol 310: 501-508. Handa, N., Ichige, A., Kusano, K., and Kobayashi, I. (2000) Cellular responses to postsegregational killing by restriction-modification genes. J Bacteriol 182: 2218-2229. Harlow, E., and Lane, D. (1988) Antibodies: A Laboratory Manual. NY: Cold Spring Harbor Laboratory Press, Cold Spring Harbor. Heidmann, S., Seifert, W., Kessler, C., and Domdey, H. (1989) Cloning, characterization and heterologous expression of the SmaI restriction-modification system. Nucleic Acids Res 17: 9783-9796. Heitman, J., Ivanenko, T., and Kiss, A. (1999) DNA nicks inflicted by restriction endonucleases are repaired by a RecA- and RecB-dependent pathway in Escherichia coli. Mol Microbiol 33: 1141-1151. Henikoff, S. (1987) Unidirectional digestion with exonuclease III in DNA sequence analysis. Methods Enzymol 155: 156-165. Heukeshoven, J., and Dernick, R. (1985) Simplified method for silver staining of proteins in polyacrylamide gels and the mechanism of silver staining. Electrophoresis 6: 103-112. Huai, Q., Colandene, J.D., Chen, Y., Luo, F., Zhao, Y., Topal, M.D., and Ke, H. (2000) Crystal structure of NaeI--an evolutionary bridge between DNA endonuclease and topoisomerase. EMBO J. 19: 3110-3118. Huai, Q., Colandene, J.D., Topal, M.D., and Ke, H. (2001) Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement. Nat Struct Biol 8: 665-669. Hung, C.-H., Wu, H.-C., and Tseng, Y.-H. (2002) Mutation in the Xanthomonas campestris xanA gene required for synthesis of xanthan and lipopolysaccharide drastically reduces the efficiency of bacteriophage ΦL7 adsorption. Biochem Biophy Res Comm 291: 338-343. Janscak, P., Dryden, D.T., and Firman, K. (1998) Analysis of the subunit assembly of the typeIC restriction-modification enzyme EcoR124I. Nucleic Acids Res 26: 4439-4445. Janscak, P., Sandmeier, U., Szczelkun, M.D., and Bickle, T.A. (2001) Subunit assembly and mode of DNA cleavage of the type III restriction endonucleases EcoP1I and EcoP15I. J Mol Biol 306: 417-431. Jeltsch, A., and Pingoud, A.M. (2001) Methods for determining activity and specificity of DNA binding and DNA cleavage by class II restriction endonucleases. Methods Mol Biol 160: 287-308. Jensen, R.B., and Gerdes, K. (1995) Programmed cell death in bacteria: proteic plasmid stabilization systems. Mol Microbiol 17: 205-210. Jindrova, E., Schmid-Nuoffer, S., Hamburger, F., Janscak, P., and Bickle, T.A. (2005) On the DNA cleavage mechanism of Type I restriction enzymes. Nucleic Acids Res 33: 1760-1766. Karyagina, A., Shilov, I., Tashlitskii, V., Khodoun, M., Vasil''ev, S., Lau, P.C., and Nikolskaya, I. (1997) Specific binding of SsoII DNA methyltransferase to its promoter region provides the regulation of SsoII restriction-modification gene expression. Nucleic Acids Res 25: 2114-2120. Kita, K., Kotani, H., Sugisaki, H., and Takanami, M. (1989) The FokI restriction-modification system. I. Organization and nucleotide sequences of the restriction and modification genes. J Biol Chem 264: 5751-5756. Kita, K., Tsuda, J., and Nakai, S.Y. (2002) C.EcoO109I, a regulatory protein for production of EcoO109I restriction endonuclease, specifically binds to and bends DNA upstream of its translational start site. Nucleic Acids Res 30: 3558-3565. Kleanthous, C., James, R., Hemmings, A.M., and Moore, G.R. (1999) Protein antibiotics and their inhibitors. Biochem Soc Trans 27: 63-67. Knowle, D., Lintner, R.E., Touma, Y.M., and Blumenthal, R.M. (2005) Nature of the promoter activated by C.PvuII, an unusual regulatory protein conserved among restriction-modification systems. J Bacteriol 187: 488-497. Kobayashi, I. (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 29: 3742-3756. Kong, H., Roemer, S.E., Waite-Rees, P.A., Benner, J.S., Wilson, G.G., and Nwankwo, D.O. (1994) Characterization of BcgI, a new kind of restriction-modification system. J Biol Chem 269: 683-690. Kong, H. (1998) Analyzing the functional organization of a novel restriction modification system, the BcgI system. J Mol Biol 279: 823-832. Kong, H., Lin, L.F., Porter, N., Stickel, S., Byrd, D., Posfai, J., and Roberts, R.J. (2000) Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome. Nucleic Acids Res. 28: 3216-3223. Kraft, R., Tardiff, J., Krauter, K.S., and Leinwand, L.A. (1988) Using mini-prep plasmid DNA for sequencing double stranded templates with Sequenase. Biotechniques 6: 544-546, 549. Krishnan, B.R., Blakesley, R.W., and Berg, D.E. (1991) Linear amplification DNA sequencing directly from single phage plaques and bacterial colonies. Nucleic Acids Res. 19: 1153. Kulakauskas, S., Lubys, A., and Ehrlich, S.D. (1995) DNA restriction-modification systems mediate plasmid maintenance. J Bacteriol 177: 3451-3454. Kunkel, T.A. (1985) Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci USA 82: 488-492. Kusano, K., Naito, T., Handa, N., and Kobayashi, I. (1995) Restriction-modification systems as genomic parasites in competition for specific sequences. Proc Natl Acad Sci USA 92: 11095-11099. Ladurner, A.G., and Fersht, A.R. (1997) Glutamine, alanine or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates. J Mol Biol 273: 330-337. Laemmli, U.K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685. Lee, E.C., Gumport, R.I., and Gardner, J.F. (1990) Genetic analysis of bacteriophage lambda integrase interactions with arm-type attachment site sequences. J. Bacteriol. 172: 1529-1538. Lennox, E.S. (1955) Transduction of linked genetic characters of the host by bacteriophage P1. Virology 1: 190-206. Loenen, W.A., Daniel, A.S., Braymer, H.D., and Murray, N.E. (1987) Organization and sequence of the hsd genes of Escherichia coli K-12. J Mol Biol 198: 159-170. Lubys, A., Menkevicius, S., Timinskas, A., Butkus, V., and Janulaitis, A. (1994) Cloning and analysis of translational control for genes encoding the Cfr9I restriction-modification system. Gene 141: 85-89. Lubys, A., Lubiene, J., Kulakauskas, S., Stankevicius, K., Timinskas, A., and Janulaitis, A. (1996) Cloning and analysis of the genes encoding the type IIS restriction-modification system HphI from Haemophilus parahaemolyticus. Nucleic Acids Res 24: 2760-2766. Malone, T., Blumenthal, R.M., and Cheng, X. (1995) Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J Mol Biol 253: 618-632. Marks, P., McGeehan, J., Wilson, G., Errington, N., and Kneale, G. (2003) Purification and characterisation of a novel DNA methyltransferase, M.AhdI. Nucleic Acids Res 31: 2803-2810. Marshall, J.J., Gowers, D.M., and Halford, S.E. (2007) Restriction endonucleases that bridge and excise two recognition sites from DNA. J Mol Biol 367: 419-431. McGeehan, J.E., Streeter, S.D., Papapanagiotou, I., Fox, G.C., and Kneale, G.G. (2005) High-resolution crystal structure of the restriction-modification controller protein C.AhdI from Aeromonas hydrophila. J Mol Biol 346: 689-701. McGeehan, J.E., Papapanagiotou, I., Streeter, S.D., and Kneale, G.G. (2006) Cooperative binding of the C.AhdI controller protein to the C/R promoter and its role in endonuclease gene expression. J Mol Biol 358: 523-531. Miller, J.H. (1992) A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria. NY: Cold Spring Harbor Laboratory Press, Cold Spring Harbor. Morgan, R.D., Calvet, C., Demeter, M., Agra, R., and Kong, H. (2000) Characterization of the specific DNA nicking activity of restriction endonuclease N.BstNBI. Biol Chem 381: 1123-1125. Morrison, D.A. (1977) Transformation in Escherichia coli: cryogenic preservation of competent cells. J Bacteriol 132: 349-351. Mücke, M., Lurz, R., Mackeldanz, P., Behlke, J., Krüger, D.H., and Reuter, M. (2000) Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage. J Biol Chem 275: 30631-30637. Murray, N.E., Gough, J.A., Suri, B., and Bickle, T.A. (1982) Structural homologies among Type I restriction-modification systems. EMBO J 1: 535-539. Murray, N.E. (2000) Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle). Microbiol. Mol. Biol. Rev. 64: 412-434. Naito, T., Kusano, K., and Kobayashi, I. (1995) Selfish behavior of restriction-modification systems. Science 267: 897-899. Naito, Y., Naito, T., and Kobayashi, I. (1998) Selfish restriction modification genes: resistance of a resident R/M plasmid to displacement by an incompatible plasmid mediated by host killing. Biol Chem 379: 429-436. Nakayama, Y., and Kobayashi, I. (1998) Restriction-modification gene complexes as selfish gene entities: Roles of a regulatory system in their establishment, maintenance, and apoptotic mutual exclusion. Proc Natl Acad Sci USA 95: 6442-6447. Nastri, H.G., Evans, P.D., Walker, I.H., and Riggs, P.D. (1997) Catalytic and DNA binding properties of PvuII restriction endonuclease mutants. J Biol Chem 272: 25761-25767. Noyer-Weidner, M., and Trautner, T.A. (1993) Methylation of DNA in prokaryotes. EXS 64: 39-108. Palmer, B.R., and Marinus, M.G. (1994) The dam and dcm strains of Escherichia coli--a review. Gene 143: 1-12. Papapanagiotou, I., Streeter, S.D., Cary, P.D., and Kneale, G.G. (2007) DNA structural deformations in the interaction of the controller protein C.AhdI with its operator sequence. Nucleic Acids Res 35: 2643-2650. Pélaez, A.I., Ribas-Aparicio, R.M., Gómez, A., and Rodicio, M.R. (1998) Establishment of a hybrid SalI-HgiDII type II restriction-modification system. Biol Chem 379: 583-584. Perona, J.J. (2002) Type II restriction endonucleases. Methods 28: 353-364. Petrusyte, M., Bitinaite, J., Menkevicius, S., Klimasauskas, S., Butkus, V., and Janulaitis, A. (1988) Restriction endonucleases of a new type. Gene 74: 89-91. Pingoud, A., and Jeltsch, A. (2001) Structure and function of type II restriction endonucleases. Nucleic Acids Res 29: 3705-3727. Pingoud, A. (2004) Restriction Endonucleases. Berlin, Heidelberg: Springer-Verlag. Pingoud, V., Geyer, H., Geyer, R., Kubareva, E., Bujnicki, J.M., and Pingoud, A. (2005) Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII. Mol Biosyst 1: 135-141. Price, C., and Bickle, T.A. (1986) A possible role for DNA restriction in bacterial evolution. Microbiol Sci 3: 296-299. Raleigh, E.A., Murray, N.E., Revel, H., Blumenthal, R.M., Westaway, D., Reith, A.D., Rigby, P.W., Elhai, J., and Hanahan, D. (1988) McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning. Nucleic Acids Res 16: 1563-1575. Raleigh, E.A. (1992) Organization and function of the mcrBC genes of Escherichia coli K-12. Mol Microbiol 6: 1079-1086. Reuter, M., Kupper, D., Meisel, A., Schroeder, C., and Krüger, D.H. (1998) Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites. J Biol Chem 273: 8294-8300. Roberts, R.J., Belfort, M., Bestor, T., Bhagwat, A.S., Bickle, T.A., Bitinaite, J., Blumenthal, R.M., Degtyarev, S.K., Dryden, D.T.F., Dybvig, K., Firman, K., Gromova, E.S., Gumport, R.I., Halford, S.E., Hattman, S., Heitman, J., Hornby, D.P., Janulaitis, A., Jeltsch, A., Josephsen, J., Kiss, A., Klaenhammer, T.R., Kobayashi, I., Kong, H., Krüger, D.H., Lacks, S., Marinus, M.G., Miyahara, M., Morgan, R.D., Murray, N.E., Nagaraja, V., Piekarowicz, A., Pingoud, A., Raleigh, E., Rao, D.N., Reich, N., Repin, V.E., Selker, E.U., Shaw, P.-C., Stein, D.C., Stoddard, B.L., Szybalski, W., Trautner, T.A., Van Etten, J.L., Vitor, J.M.B., Wilson, G.G., and Xu, S.-y. (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 31: 1805-1812. Roberts, R.J., Vincze, T., Pósfai, J., and Macelis, D. (2007) REBASE--enzymes and genes for DNA restriction and modification. Nucleic Acids Res 35: D269-270. Robinson, C.R., and Sligar, S.G. (1995) Heterogeneity in molecular recognition by restriction endonucleases: osmotic and hydrostatic pressure effects on BamHI, Pvu II, and EcoRV specificity. Proc Natl Acad Sci U S A 92: 3444-3448. Robinson, C.R., and Sauer, R.T. (1998) Optimizing the stability of single-chain proteins by linker length and composition mutagenesis. Proc Natl Acad Sci U S A 95: 5929-5934. Saha, S., Ahmad, I., Reddy, Y.V., Krishnamurthy, V., and Rao, D.N. (1998) Functional analysis of conserved motifs in type III restriction-modification enzymes. Biol Chem 379: 511-517. Sambrook, J., and Russell, D.W. (2001) Molecular Cloning: A Laboratory Manual. NY: Cold Spring Harbor Laboratory Press, Cold Spring Harbor. Samuelson, J.C., Zhu, Z., and Xu, S.Y. (2004) The isolation of strand-specific nicking endonucleases from a randomized SapI expression library. Nucleic Acids Res 32: 3661-3671. Sanger, F., Nicklen, S., and Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74: 5463-5467. Sawaya, M.R., Zhu, Z., Mersha, F., Chan, S.H., Dabur, R., Xu, S.Y., and Balendiran, G.K. (2005) Crystal structure of the restriction-modification system control element C.Bcll and mapping of its binding site. Structure 13: 1837-1847. Schweizer, H.D. (1993) Small broad-host-range gentamycin resistance gene cassettes for site-specific insertion and deletion mutagenesis. Biotechniques 15: 831-834. Semenova, E., Minakhin, L., Bogdanova, E., Nagornykh, M., Vasilov, A., Heyduk, T., Solonin, A., Zakharova, M., and Severinov, K. (2005) Transcription regulation of the EcoRV restriction-modification system. Nucleic Acids Res 33: 6942-6951. Senejani, A.G., and Gogarten, J.P. (2007) Structural stability and endonuclease activity of a PI-SceI GFP-fusion protein. Int J Biol Sci 3: 205-211. Shilov, I., Tashlitsky, V., Khodoun, M., Vasil''ev, S., Alekseev, Y., Kuzubov, A., Kubareva, E., and Karyagina, A. (1998) DNA-methyltransferase SsoII interaction with own promoter region binding site. Nucleic Acids Res 26: 2659-2664. Simoncsits, A., Tjörnhammar, M.L., Raskó, T., Kiss, A., and Pongor, S. (2001) Covalent joining of the subunits of a homodimeric type II restriction endonuclease: single-chain PvuII endonuclease. J Mol Biol 309: 89-97. Sistla, S., and Rao, D.N. (2004) S-Adenosyl-L-methionine-dependent restriction enzymes. Crit Rev Biochem Mol Biol 39: 1-19. Sohail, A., Lieb, M., Dar, M., and Bhagwat, A.S. (1990) A gene required for very short patch repair in Escherichia coli is adjacent to the DNA cytosine methylase gene. J Bacteriol 172: 4214-4221. Som, S., and Friedman, S. (1993) Autogenous regulation of the EcoRII methylase gene at the transcriptional level: effect of 5-azacytidine. EMBO J 12: 4297-4303. Som, S., and Friedman, S. (1994) Regulation of EcoRII methyltransferase: effect of mutations on gene expression and in vitro binding to the promoter region. Nucleic Acids Res 22: 5347-5353. Spanakis, E., and Horne, M.T. (1987) Co-adaptation of Escherichia coli and coliphage lambda vir in continuous culture. J. Gen. Microbiol. 133: 353-360. Stoddard, B.L. (2005) Homing endonuclease structure and function. Q Rev Biophys 38: 49-95. Studier, F.W., and Bandyopadhyay, P.K. (1988) Model for how type I restriction enzymes select cleavage sites in DNA. Proc Natl Acad Sci USA 85: 4677-4681. Su, M.J., Lai, M.C., Weng, S.F., and Tseng, Y.H. (1990) Characterization of phage ΦL7 and transfection of Xanthomonas campestris pv. campestris by the phage DNA. Bot Bull Acad Sin 31: 197-203. Sugisaki, H., Kita, K., and Takanami, M. (1989) The FokI restriction-modification system. II. Presence of two domains in FokI methylase responsible for modification of different DNA strands. J Biol Chem 264: 5757-5761. Sukchawalit, R., Vattanaviboon, P., Sallabhan, R., and Mongkolsuk, S. (1999) Construction and characterization of regulated L-arabinose-inducible broad host range expression vectors in Xanthomonas. FEMS Microbiol Lett 181: 217-223. Suri, B., and Bickle, T.A. (1985) EcoA: the first member of a new family of type I restriction modification systems. Gene organization and enzymatic activities. J Mol Biol 186: 77-85. Takahashi, N., Naito, Y., Handa, N., and Kobayashi, I. (2002) A DNA methyltransferase can protect the genome from postdisturbance attack by a restriction-modification gene complex. J Bacteriol 184: 6100-6108. Takeshita, S., Sato, M., Toba, M., Masahashi, W., and Hashimoto-Gotoh, T. (1987) High-copy-number and low-copy-number plasmid vectors for lacZ alpha- complementation and chloramphenicol- or kanamycin-resistance selection. Gene 61: 63-74. Tao, T., Bourne, J.C., and Blumenthal, R.M. (1991) A family of regulatory genes associated with type II restriction-modification systems. J Bacteriol 173: 1367-1375. Taylor, J.D., and Halford, S.E. (1992) The activity of the EcoRV restriction endonuclease is influenced by flanking DNA sequences both inside and outside the DNA-protein complex. Biochemistry 31: 90-97. Terry, B.J., Jack, W.E., Rubin, R.A., and Modrich, P. (1983) Thermodynamic parameters governing interaction of EcoRI endonuclease with specific and nonspecific DNA sequences. J Biol Chem 258: 9820-9825. Thieme, F., Koebnik, R., Bekel, T., Berger, C., Boch, J., Büttner, D., Caldana, C., Gaigalat, L., Goesmann, A., Kay, S., Kirchner, O., Lanz, C., Linke, B., McHardy, A.C., Meyer, F., Mittenhuber, G., Nies, D.H., Niesbach-Klösgen, U., Patschkowski, T., Rückert, C., Rupp, O., Schneiker, S., Schuster, S.C., Vorhölter, F.-J., Weber, E., Pühler, A., Bonas, U., Bartels, D., and Kaiser, O. (2005) Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol 187: 7254-7266. Titheradge, A.J.B., King, J., Ryu, J., and Murray, N.E. (2001) Families of restriction enzymes: an analysis prompted by molecular and genetic data for
摘要: 
The XveII restriction-modification (R-M) system, xveIIM and xveIIR, is a SmaI-like R-M system and cloned from Xanthomonas campestris pv. vesicatoria strain 7-1 (Xcv7-1). The xveIIM encoding the XveII methyltransferase (M.XveII) methylates the second cytosine of the 5'-CCCGGG-3' recognition sequence and belongs to the m4C-methyltransferase family. However, an internal TAA stop codon was found to locate at nucleotide 484 - 486 (the 162nd amino acid residue) of the predicted xveIIR ORF resulting in an 18.3 kDa nonfunctional protein product. Site-directed mutagenesis was applied to replace the internal TAA stop codon of the xveIIR gene with twenty different amino acid codons and designated as xveIIR-mut. Each of the recombinant XveII-mut was overexpressed and purified from E. coli ER2566 and most of the 31 kDa XveII mutant enzymes restore restriction activities. The specificities of XveII mutant enzymes, being identical to SmaI, cleave between C and G of the 5'-CCCGGG recognition sequence and yield a blunt-ended product. The cleavage activity of the tryptophan substituted enzyme (XveII-W) is the highest among the mutants, however, still lower than that of SmaI. The mutant XveII-S was found to have the highest binding affinity to the cognate DNA (KD = 97.4 nM). According to the results of glutaraldehyde cross-linking experiments and size exclusion chromatography, XveII-mut was determined to exist as a dimer. XveII-mutD was constructed by ligating two xveIIR-mut genes with 4 continuous glycine codons and expressed as a single polypeptide dimer of XveII-mut with 63 kDa molecular weight. The specificities of XveII-mutD were the same as those of the XveII-muts while the DNA cleavage, binding activities, and stability of XveII-mutD were higher than those of the corresponding XveII-mut. The mutant enzymes exhibited different activities, indicating that different amino acid substitutions at the 162nd position might play an important role in XveII. Results showed that the cleavage rate and the DNA binding activites of XveII-mut were influenced by different flanking sequences of the recognition site. Plasmid and linealized DNA with different flanking sequence of the recognition site were used for digestion and revealed that XveII-WD prefer A or T immediately adjacent to the SmaI sites. Base composition next to the CC flanking sequence of the SmaI site had influence on the cleavage rate. Moreover, the one with GC flanking sequence had the lowest cleavage rate. To explore the roles of the 162nd amino acid in XveII-mut the crystal structure of the DNA-free XveII-I was determined and analyzed at 2.7Å resolution. Results showed that structure of XveII-I spatial superimposed with the Endo domain of NaeI and suggested that E80-YD105-K116 is the active site motif and Asp241, Glu245 and Lys247 are involved in DNA binding. Alanine-substitution at these predicted amino acid residues were constructed and found that these XveII-I mutants lost cleavage activity on double-stranded DNA. In addition, mutant XveIIK247A was almost completely lost DNA binding activity. Amino acid alignment revealed that E72-HD98-K109 are the catalytic residues of SmaI and both of XveII and SmaI are not typical PD-(D/E)XK superfamily nucleases. Based on the crystal structure of XveII-I, we proposed that the three hydrophobic residues, Ile21 and Val24 and Phe69, are responsible for its dimerization by hydrophobic contacts between helix bundles in its N-terminal region. The 162nd amino acid residue of XveII is located between α4 and α5 of the α/β core structure near the metal ion binding region. The differences in cleavage activities of the XveII-mut may due to comformational change when variants of the XveII-mut binding with substrate DNA.

XveII 限制修飾系統是由 Xanthomonas campestris pv. vesicatoria 7-1 (Xcv7-1) 菌株中所選殖出來,包含 xveIIM 及 xveIIR 基因,為一種 SmaI-like 限制修飾系統。xveIIM 基因可轉譯出 XveII 甲基轉移酶 (M.XveII),會將 5′-CCCGGG-3′ 中第二個 C 進行甲基化,是屬於 m4C-甲基轉移酶。而 xveIIR 基因預測為一含 813 鹼基對之 ORF,但在第 484 至 486 個鹼基對 (即第 162 個胺基酸位置) 具有一內在 TAA 終止密碼,其表現出來的 XveII 分子量僅 18.3 kDa 為一無功能蛋白。為探討第 162 胺基酸位置在 XveII 所扮演的角色,本研究針對 xveIIR 基因,以定點突變的方法將此基因內在 TAA 終止密碼以二十種不同胺基酸密碼子取代,並命名為 xveIIR-mut 基因。突變基因於 E. coli ER2566 菌株表現與純化後,可得到約 31 kDa 的 XveII-mut,並發現大部份取代株可以恢復限制酶活性,切割在5′-CCCGGG-3′辨識序列的 C 與 G 之間形成平端的產物 (CCC↓GGG),且切割活性以 tryptophan 取代株 (XveII-W) 最高,但卻遠低於 SmaI 的切割活性;而與 DNA 的親和力則是以 XveII-S 為最佳 (KD = 97.4 nM)。藉由交聯反應與分子篩管柱分析,XveII-mut 是以雙隅體的構形呈現。因此亦利用四個連續 glycine 的密碼子 (GGC) 將二個相同之 xveIIR-mut 基因串聯,可以表現出由 555 個胺基酸所構成之單一胜肽雙隅體 (XveII-mutD)。所表現之 XveII-mutD 並未改變其專一性,且其切割活性與 DNA 結合能力及穩定性等皆優於 XveII-mut。在第 162 位置由不同胺基酸取代株,會造成活性之差異,顯示此位置之胺基酸在 XveII 中可能扮演重要角色。根據 DNA 切割的結果分析,XveII-mut 對於帶有不同鄰邊序列的辨識切位,具有不同的切割效率與結合能力。利用帶有不同鄰邊序列的質體或線形 DNA 的切割實驗,顯示 XveII-WD 較偏好 A 或 T 之相鄰序列;至於 CC 的組合要視更外側的核苷酸序列才可決定其切割速率;對於 GC 鄰邊序列切割速率則最慢。進一步藉由 XveII-I 結構分析,了解 XveII 中第 162 胺基酸位置可能扮演之角色,同時推測 SmaI 中重要胺基酸位置。由 XveII-I 結晶繞射得到 2.7Å 的解析度,經比對與 NaeI 限制酶的 Endo domain 具有空間上的重疊性,推測活性中心區域為 E80-YD105-K116,而參與 DNA 結合的胺基酸為 Asp241、Glu245 與 Lys247,將這些位置以 alanine 取代後皆喪失切割能力,其中 XveII-IK247A 則幾乎喪失了 DNA 結合能力。藉由胺基酸序列的比對,推測 SmaI 的活性中心胺基酸為 E72-HD98-K109,與 XveII-I 的活性中心皆為非典型的 PD-(D/E)XK superfamily。XveII-I 形成雙隅體介面是位在 N-端區域 helix bundles 間形成疏水性作用力,即由胺基酸 Ile21、Val24和 Phe69 所形成。至於第 162 胺基酸位置是座落於 α/β 結構中心的 α4 與 α5 之間,接近金屬離子結合區域,因此推測 XveII 第 162 位置由不同胺基酸的取代,會改變與 DNA 之間構形改變,進而導致活性的差異性。
URI: http://hdl.handle.net/11455/21856
其他識別: U0005-2408200712272800
Appears in Collections:分子生物學研究所

Show full item record
 

Google ScholarTM

Check


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.