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(In Japanese)ゲノム全遺伝子の発現ヒエラルキー決定機構の解明

Research report code R000000121
Posted date Sep 30, 2002
  • (In Japanese)石浜 明
  • (In Japanese)国立遺伝学研究所
Research organization
  • (In Japanese)国立遺伝学研究所
Report name (In Japanese)ゲノム全遺伝子の発現ヒエラルキー決定機構の解明
Technology summary (In Japanese)全遺伝子のなかから,どれをどの程度に発現し利用するかを決定する機構の解明が,ポストゲノムプロジェクトの最も重要な研究課題との立場から,本研究が開始された。転写酵素RNAポリメラーゼが,ゲノム全遺伝子から発現遺伝子を選択し,またそれぞれの発現水準を決め,遺伝子間の発現水準の順位を決定していると考えた理論を提唱し,その実証を目指した研究を実施した。研究対象として,主として原核生物の代表大腸菌と真核生物の代表として分裂酵母を解析し,またこのモデルを検証するための最も単純なウイルスを解析した。大腸菌における遺伝子発現ヒエラルキー決定機構の研究,分裂酵母の遺伝子発現ヒエラルキー決定機構の研究およびウイルスにおける遺伝子発現ヒエラルキー決定機構の研究についての研究実施概要を述べた。
Research field
  • Genetics in general
  • Gene expression
  • Cell physiology in general
  • Microorganism biochemistry
  • Virus biochemistry
Published papers related (In Japanese)(1)Hwang, J.-S., Yamda, K., Honda, A., Nakade, K. and Ishihama, A.: Expression of functional influenza viral RNA polymerase in the methylotrophic yeast Pichia pastoris. J. Virol. 74, 4074-4084 (2000)
(2)Ishiguro, A., Nogi, Y., Hisatake, K., Muramatsu, M. and Ishihama, A.: Ppb6 subunit of the fission yeast RNA polymerase II is a contact target of the transcription elongation factor TFIIS. Mol. Cell. Biol. 20, 1263-1270 (2000)
(3)Katayama, A., Fujita, N. and Ishihama, A.: Mapping of subunit-subunit contact surfaces on the β′ subunit of Escherichia coli RNA polymerase. J. Biol. Chem. 275, 3583-3592 (2000)
(4)Kimura, M. and Ishihama, A.: Involvement of multiple subunit-subunit contacts in the assembly of RNA polymerase II. Nucleic Acids Res. 28, 952-959 (2000)
(5)Maeda, H., Jishage, M., Nomura, T., Fujita, N. and Ishihama, A.: Promoter selectivity of the RNA polymerase holoenzyme containing the extracytoplasmic function (ECF) sigma subunit σE or σFecI. J. Bacteriol. 182, 1181-1184 (2000)
(6)Ozoline, O., Fujita, N. and Ishihama, A.: Transcription activation mediated by the carboxy-terminal domain of RNA polymerase alpha-subunit: Multipoint monitoring ssing fluorescent probe. J. Biol. Chem. 275, 1119-1127 (2000)
(7)Schpakovski, G.V., Gadal, O., Lararre-Mariotte, S., Lebedenko, E.N., Miklos, I., Sakurai, H., Proshkin, S.A., van Mullem, V., Ishihama, A. and Thuriaux, P.: Functional conservation of RNA polymerase II subunits between the fission and budding yeasts. J. Mol. Biol. 295, 1119-1127 (2000)
(8)Yamamoto, K., Nagura, R., Tanabe, H., Fujita, N., Ishihama, A. and Utsumi, R.: Negative regulation of the bolA1p of Escherichia coli K-12 by the transcription factor OmpR for osmolarity response genes. FEMS Microbiol. Lett. 186, 257-262 (2000)
(9)Apirakaramwong, A., Kashiwagi, K., Raj, V.S., Sakata, K., Kakinuma, A., Ishihama, A. and Igarashi, K.: Involvement of ppGpp, ribosome modulation factor, and stationary phase-specific sigma factor σS in the decrease in cell viability caused by spermidine. Biochem. Biophys. Res. Commun. 264, 643-647 (1999)
(10)Bown, J.A., Owens, J.T., Meares, C.F., Fujita, N., Ishihama, A., Busby, S.J. and Minchin, S.D.: Organisation of open complexes at Escherichia coli promoters: mapping the promoter DNA sites close to region 2.5 of the σ70 subunit of RNA polymerase. J. Biol. Chem. 274, 2263-2270 (1999)
(11)Burns, H.D., Ishihama, A. and Minchin, S.D.: Open complex formation during transcription initiation at the Escherichia coli galP1 promoter: the role of the RNA polymerase a subunit at promoters lacking an UP-element. Nucleic Acids Res. 27, 2051-2056 (1999)
(12)Colland, F., Fujita, N., Kotlarz, D., Bown, J.A., Meares, C.F., Ishihama, A. and Kolb, A.: Positioning of σS, the stationary phase σ factor, in Escherichia coli RNA polymerase-promoter open complexes. EMBO J. 18, 4049-4059 (1999)
(13)Harada, Y., Funatsu, T., Murakami, K., Nonoyama, Y., Ishihama, A. and Yanagida, T.: Single molecule imaging of RNA polymerase-DNA interactions in real time. Biophys. J. 76, 709-715 (1999)
(14)Honda, A., Mizumoto, K. and Ishihama, A.: Two separate sequences of PB2 subunit consitute the RNA cap-binding site of influenza virus RNA polymerase. Genes Cells 4, 475-485 (1999)
(15)Ishihama, A.: Stringent control. In: Encyclopedia of Molecular Biology, T.E. Creighton, Ed., John Wiley & Sons, Inc., New York, pp.2451-2455 (1999)
(16)Ishihama, A.: Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival. Genes Cells 3, 135-143 (1999)
(17)Jishage, M. and Ishihama, A.: Transcriptional organization and in vivo role of the Escherichia coli rsd gene, encoding the regulator of RNA polymerase sigma D. J. Bacteriol. 181, 3768-3776 (1999)
(18)Masuda, H., Suzuki, T., Sugiyama, Y., Murakami, K., Miyamoto, D., Jwa Hidari, K.I., Ito, T., Kida, M., Fukunaga, K., Obuchi, M., Toyoda, T., Ishihama, A., Kawaoka, Y. and Suzuki, Y.: Substitution of amino acid residue in influenza A virus hemagglutinin aggects recognition of glycosphingolipid containing N-glycolylneuraminic acid. FEBS Lett. 464, 71-74 (1999)
(19)Masunaga, K., Mizumoto, K., Kato, H., Ishihama, A. and Toyoda, T.: Molecular mapping of influenza virus RNA polymerase by site-specific antibodies. Virology 256, 130-141 (1999)
(20)Mitobe, J., Mitsuzawa, H. and Ishihama, A.: Isolation and characterization of temperature-sensitive mutations in the subunit 3 gene (rpb3) of RNA polymerase II of the fission yeast Schizosaccharomyces pombe. Mol. Gen. Genet. 262, 73-84 (1999)
(21)Nomura, T., Fujita, N. and Ishihama, A.: Mapping of subunit-subunit contact sites on the β subunit of Escherichia coli RNA polymerase. Biochemistry 38, 1346-1355 (1999)
(22)Ozoline, O.N., Fujita, N. and Ishihama, A.: Functional topology of the bacterial RNA polymerase. Multipoint monitoring by a fluorescent probe. In: Spectroscopy of Biological Molecules: New Directions (eds. J. Greve, G.J. Puppels, C. Otto), Kluwer Academic Publ., Dordrecht, Netherland. pp.87-89, 1999.
(23)Prost, J.-F., Negre, D., Oudot, C., Murakami, K., Ishihama, A., Cozzone, A.J. and Cortay, J.-C.: Cra-dependent transcriptional activation of the icd gene of Escherichia coli. J. Bacteriol. 181, 893-898 (1999)
(24)Sakurai, H., Mitsuzawa, H., Kimura, M. and Ishihama, A.: Rpb4 subunit of the fission yeast Schizosaccharomyces pombe RNA polymerase II is essential for cell viability and similar in structure to the corresponding subunits of higher eukaryotes. Mol. Cell. Biol. 19, 7511-7518 (1999)
(25)Stevens, A.M., Fujita, N., Ishihama, A. and Greenberg, E.P.: Involvement of the RNA polymerase a subunit C-terminal domain in LuxR-dependent activation of the Vibrio fischeri luminescence genes. J. Bacteriol. 181, 4704-4707 (1999)
(26)Talukder A.Z. and Ishihama, A.: Twelve species of DNA-binding protein from Escherichia coli: Sequence recognition specificity and DNA binding affinity. J. Biol. Chem. 274, 33105-33113 (1999)
(27)Talukder A.Z., Iwata, A., Ueda, A. and Ishihama, A.: Growth phase-dependent variation in the protein composition of Escherichia coli nucleoid. J. Bacteriol. 181, 6361-6370 (1999)
(28)Traviglia, S.L., Datwyler, S.A., Yan, D., Ishihama, A. and Meares, C.F.: Targeted protein footprinting: Where different transcription factors bind to RNA polymerase. Biochemistry 38, 15774-15778 (1999).
(29)Watanabe, T., Honda, A., Iwata, A., Ueda, S., Hibi, T. and Ishihama, A.: Isolation of 130K/180K heterodimer with RNA-dependent RNA polymerase activity from TMV-infected tobacco. J. Virol. 73, 2633-2640 (1999)
(30)Wlassoff, W.A., Kimura, M. and Ishihama, A.: Functional organization of two large subunits of the fission yeast Schizosaccharomyces pombe RNA polymerase II: Location of the catalytic sites. J. Biol. Chem. 274, 5104-5113 (1999)
(31)Bown, J.A., Kolb, A., Meares, C.F., Ishihama, A., Minchin, S.D. and Busby, S. J. W.: Positioning of region 4 of the Escherichia coli RNA polymerase σ70 subunit by a transcription activator. J. Bacteriol. 182, 2982-2984 (2000)
(32)Fujita, N., Endo, S. and Ishihama, A.: Structual requirements for the interdomain linker of α subunit of Escherichia coli RNA polymerase. Biochemistry 39, 6243-6249 (2000)
(33)Hatta, M., Asano, Y., Masunaga, K., Ito, T., Okazaki, T., Toyoda, T., Kawaoka, Y., Ishihama, A. and Kida, H.: Epitope mapping of the influenza A virus polymerase PA using monoclonal anbitodies. Arch Virol. 145, 957-964 (2000)
(34)Hatta, M., Asano, Y., Masunaga, K., Ito, T., Okazaki, T., Toyoda, T., Kawaoka, Y., Ishihama, A. and Kida, H.: Mapping of functional domains on the influenza A virus RNA polymerase PB2 molecule using monoclonal antibodies. Arch. Virol. 145, 1947-1961 (2000)
(35)Ishihama, A.: Functional modulation of Escherichia coli RNA polymerase. Ann. Rev. Microbiol. 54, 499-518 (2000)
(36)Ishihama, A.: Molecular anatomy of RNA polymerase using protein-conjugated metal probes with nuclease and protease activities. Chem. Commun. 2000. 1091-1094 (2000)
(37)Maeda, H., Fujita, N. and Ishihama, A.: Sigma competition: Comparison of binding affinity to the core RNA polymerase among seven E. coli sigma subunits. Nucleic Acids Res. 28, 3497-3503 (2000)
(38)Ohnuma, M., Fujita, N., Ishihama, A., Tanaka, K. and Takahashi, H.: A carboxy-terminal 16 amino acid region of _38 of Escherichia coli is important for transcription under high-salt conditions and sigma activities in vivo. J. Bacteriol. 182, 4628-4631 (2000)
(39)Otomo, T., Yamazaki, T., Murakami, K., Ishihama, A. and Kyogoku, Y.: Structural study of the N-terminal domain of the alpha subunit of Escherichia coli solubilized with non-denaturing deteregents. J. Biochem. 128, 337-344 (2000)
(39)Talukder A.A., Hiraga, S. and Ishihama, A.: Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells 5, 613-626 (2000)
(40)Wada, A., Mikkola, R., Kurland, C.G. and Ishihama, A.: Growth phase-coupled changes of the ribosome pattern in Escherichia coli. J. Bacteriol. 182, 2893-2899 (2000)
Wigneshweraraj, S.R., Fujita, N., Ishihama, A. and Buck, M.: Conservation of sigma-core RNA polymerase proximity relationships between the enhancer independent an denhancer-dependent sigma classes. EMBO J. 19, 3038-3048 (2000)
Research project
  • Core Research for Evolutional Science and Technology;Genetic Programming
Information research report
  • (In Japanese)石浜 明. 生命活動のプログラム ゲノム全遺伝子の発現ヒエラルキー決定機構の解明. 戦略的基礎研究推進事業 平成11年度 研究年報.科学技術振興事業団, 2000. p.68 - 76.