Bio Nano Tools, Nano Kelvin, T. Fukuda, F. Arai, L. Dong, T. Fukuda, ...
motor Toshio Fukuda (Nagoya Univ.) To construct the Bio-Nano tools, such as Nano pipette, injector, Nano Kelvin scanner, Mass flow sensor and so on To investigate the cell dynamics due to changes of...
Negre, D, Bonod-Bidaud, C, Oudot, C, Prost, JF, Kolb, A, Ishihama, A, ...
Tang, Y, Murakami, K, Ishihama, A, DeHaseth, P L
The rightward regulatory region of bacteriophage lambda contains two promoters, pRM and pR, which direct the synthesis of nonoverlapping divergent transcripts from start sites 82 bp apart. Each of...
Tanaka, K, Takayanagi, Y, Fujita, N, Ishihama, A, Takahashi, H
The rpoS gene of Escherichia coli encodes a putative RNA polymerase sigma factor that is considered to be the central regulator of gene expression in stationary phase. The gene product (sigma 38) was...
Yamanaka, K, Ogasawara, N, Yoshikawa, H, Ishihama, A, Nagata, K
A system for the expression of a foreign gene derived from negative polarity RNA was developed using influenza virus, a negative-stranded RNA virus. From cDNA for the influenza virus RNA genome...
Igarashi, K, Hanamura, A, Makino, K, Aiba, H, Aiba, H, Mizuno, T, ...
The role of the alpha subunit of Escherichia coli RNA polymerase in transcription activation by positive factors was investigated using two reconstituted mutant RNA polymerases (containing...
Wada, A, Yamazaki, Y, Fujita, N, Ishihama, A
The decrease in overall translation activity occurring concomitantly with the transition from the exponential growth phase to the stationary phase of Escherichia coli cells was found to be...
Belyaeva, T A, Bown, J A, Fujita, N, Ishihama, A, Busby, S J
Hydroxyl radical footprinting has been used to study different open complexes between Escherichia coli RNA polymerase and the galactose operon regulatory region, which contains two overlapping...
Nègre, D, Bonod-Bidaud, C, Oudot, C, Prost, J F, Kolb, A, Ishihama, A, ...
The specific interaction of the upstream element-containing promoter of the Escherichia coli acetate operon with either the RNA polymerase holoenzyme or its alpha subunit has been analyzed by the...
Kang, J G, Hahn, M Y, Ishihama, A, Roe, J H
We examined the promoter selectivity of RNA polymerase (RNAP) from Streptomyces coelicolor at two growth phases by in vitro transcription. Distinct sets of promoters were preferentially recognized by...
Burns, H D, Ishihama, A, Minchin, S D
We have studied the role of the C-terminal domain of the alpha subunit (alphaCTD) of Escherichia coli RNA polymerase during transcription initiation at promoters lacking an UP-element. The...
The TyrR protein of Escherichia coli is a class I transcription activator.
Lawley, B, Fujita, N, Ishihama, A, Pittard, A J
The purified TyrR protein and phenylalanine were sufficient to activate in vitro transcription from the tyrP promoter by wild-type RNA polymerase. Such TyrR-mediated activation did not occur when the...
Liu, X, Fujita, N, Ishihama, A, Matsumura, P
A number of transcription activators have been found to activate transcription via protein-protein contact between RNA polymerase alpha subunits and transcription factors; they are classified as...
A partially functional 245-amino-acid internal deletion derivative of Escherichia coli sigma 70.
Kumar, A, Williamson, H S, Fujita, N, Ishihama, A, Hayward, R S
Two hundred forty-five consecutive amino acids of the sigma 70 subunit of Escherichia coli RNA polymerase are not conserved in the homologous protein of Bacillus subtilis. We show that their deletion...
Mapping of the OxyR protein contact site in the C-terminal region of RNA polymerase alpha subunit.
Tao, K, Zou, C, Fujita, N, Ishihama, A
The Escherichia coli OxyR protein requires the C-terminal contact site I region of the RNA polymerase alpha subunit for cooperative interaction with and transcription activation at OxyR-dependent...
The intracellular levels of two principal sigma subunits, sigma 70 (sigma D, the rpoD gene product) and sigma 38 (sigma s, the rpoS gene product), in Escherichia coli MC4100 were determined by a...
Jair, K W, Martin, R G, Rosner, J L, Fujita, N, Ishihama, A, Wolf, R E
Expression of the marA or soxS genes is induced by exposure of Escherichia coli to salicylate or superoxides, respectively. This, in turn, enhances the expression of a common set of promoters (the...
Jair, K W, Yu, X, Skarstad, K, Thöny, B, Fujita, N, Ishihama, A, ...
The Rob protein, isolated on the basis of its ability to bind to the right arm of the Escherichia coli origin of chromosomal replication, is about 50% identical in amino acid sequence to SoxS and...
Rajkumari, K, Kusano, S, Ishihama, A, Mizuno, T, Gowrishankar, J
We have used supercoiled DNA templates in this study to demonstrate that transcription in vitro from the P1 and P2 promoters of the osmoresponsive proU operon of Escherichia coli is preferentially...
Jishage, M, Iwata, A, Ueda, S, Ishihama, A
By a quantitative Western immunoblot analysis, the intracellular levels of two principal sigma subunits, sigma 70 (sigma D, the rpoD gene product) and sigma 38 (sigma S, the rpoS gene product), and...
Tang, Y, Murakami, K, Ishihama, A, DeHaseth, P L
The rightward regulatory region of bacteriophage lambda contains two promoters, pRM and pR, which direct the synthesis of nonoverlapping divergent transcripts from start sites 82 bp apart. Each of...
The composition of RNA polymerase sigma subunits was analyzed for stock strains of Escherichia coli K-12 W3110 in Japan. Heterogeneity was discovered with respect to two sigma subunits, sigma28...
Boucher, P E, Murakami, K, Ishihama, A, Stibitz, S
The expression of virulence factor genes in Bordetella pertussis is mediated by the BvgA-BvgS two-component signal transduction system. The response regulator, BvgA, acts directly as a...
Chugani, S A, Parsek, M R, Hershberger, C D, Murakami, K, Ishihama, A, Chakrabarty, A M
The soil bacterium Pseudomonas putida is capable of degrading many aromatic compounds, including benzoate, through catechol as an intermediate. The catabolism of catechol is mediated by the catBCA...
The intracellular concentration of trehalose increases in the stationary-phase cells of Escherichia coli. The effects of trehalose on transcription in vitro by E. coli RNA polymerase were compared...
Kundu, T K, Kusano, S, Ishihama, A
The rpoF gene of Escherichia coli codes for the RNA polymerase sigmaF (or sigma28) subunit, which is involved in transcription of the flagellar and chemotaxis genes. Both sigmaF and sigma70 (the...
Yang, J, Murakami, K, Camakaris, H, Fujita, N, Ishihama, A, Pittard, A J
To examine the role of the amino acid residues (between positions 258 and 275 and positions 297 and 298) of the alpha-subunit of RNA polymerase in TyrR-mediated activation of the mtr promoter, we...
Rajkumari, K, Ishihama, A, Gowrishankar, J
The osmotically regulated proU locus in Escherichia coli has two promoters, P1 and P2, that are recognized, respectively, by the sigmaS- and sigma70-bearing RNA polymerase holoenzymes. However, the...
Nakagawa, Y, Kimura, N, Toyoda, T, Mizumoto, K, Ishihama, A, Oda, K, ...
An established cell line, clone 64, in which the expression of the RNA polymerase PB1 and PA subunit genes and the nucleoprotein (NP) gene but not the PB2 subunit gene of influenza virus can be...
The Ada protein is a class I transcription factor of Escherichia coli.
Sakumi, K, Igarashi, K, Sekiguchi, M, Ishihama, A
The methylated Ada protein of Escherichia coli, a regulatory protein for the adaptive response, binds to a target DNA from positions -62 to -31 upstream of the ada gene and facilitates the binding of...
Lee, H S, Ishihama, A, Kustu, S
Several activators of sigma 70 holoenzyme whose binding sites lie upstream of the -35 region of promoters require the C-terminal region of the alpha subunit of RNA polymerase to activate...
Regulation of the Escherichia coli hfq gene encoding the host factor for phage Q beta.
Kajitani, M, Kato, A, Wada, A, Inokuchi, Y, Ishihama, A
The host factor (HF-I) for phage Q beta RNA replication is a small protein of 102 amino acid residues encoded by the hfq gene at 94.8 min on the Escherichia coli chromosome. The synthesis rate of...
Activation defects caused by mutations in Escherichia coli rpoA are promoter specific.
Gussin, G N, Olson, C, Igarashi, K, Ishihama, A
Escherichia coli RNA polymerases containing mutated alpha subunits were tested for their ability to respond to three different positive regulators (activators) in vitro. The two alpha (rpoA) mutants,...
Yasuda, J, Bucher, D J, Ishihama, A
Analysis of fast-growing reassortants (AWM viruses) of influenza A virus produced by mixed infection with a fast-growing WSN strain and a slowly growing Aichi strain indicated that the M gene plays a...
Molecular dissection of influenza virus nucleoprotein: deletion mapping of the RNA binding domain.
Kobayashi, M, Toyoda, T, Adyshev, D M, Azuma, Y, Ishihama, A
Influenza virus nucleoprotein (NP) is associated with the genome RNA, forming ribonucleoprotein cores. To identify the amino acid sequence involved in RNA binding, we performed Northwestern blot...
Promoter analysis of influenza virus RNA polymerase.
Parvin, J D, Palese, P, Honda, A, Ishihama, A, Krystal, M
Influenza virus polymerase, which was prepared depleted of viral RNA, was used to copy small RNA templates prepared from plasmid-encoded sequences. Template constructions containing only the 3' end...
Solubilization and promoter analysis of RNA polymerase from rice stripe virus.
Barbier, P, Takahashi, M, Nakamura, I, Toriyama, S, Ishihama, A
The RNA-dependent RNA polymerase associated with rice stripe virus was dissociated from viral RNA (vRNA) by CsCl centrifugation. The solubilized RNA-free RNA polymerase transcribed a model RNA...
Kolb, A, Kotlarz, D, Kusano, S, Ishihama, A
A series of gal promoter mutants has been used to compare the in vitro selectivities of the two forms of Escherichia coli RNA polymerase, E sigma 38 and E sigma 70. In the absence of the CRP-cAMP...
Tanaka, K, Kusano, S, Fujita, N, Ishihama, A, Takahashi, H
Sequence determinants responsible for promoter recognition by RNA polymerase holoenzyme containing sigma 38, the rpoS gene product, were analyzed. In a previous study [Tanaka et al. (1993) Proc....
Fujita, N, Mori, H, Yura, T, Ishihama, A
The complete sequence analysis of the E. coli genome was initiated as a collaborative study in Japan. Following the initial analysis of the 0-2.4 min region (Yura, T. et al. (1992) Nucleic Acids Res....
Attey, A, Belyaeva, T, Savery, N, Hoggett, J, Fujita, N, Ishihama, A, ...
DNAase I footprinting has been used to study open complexes between Escherichia coli RNA polymerase and the galactose operon P1 promoter, both in the absence and the presence of CRP (the cyclic AMP...
Kolb, A, Igarashi, K, Ishihama, A, Lavigne, M, Buckle, M, Buc, H
A deletion of the C-terminal part of the alpha-subunit of RNA polymerase is known to affect differently promoters activated by CRP depending on the location of the CRP binding site at the promoter....
Kawagishi, M, Yamagishi, M, Ishihama, A
The gene, rpb2, encoding the second largest subunit, subunit 2, of RNA polymerase II has been cloned from Schizosaccharomyces pombe using the corresponding gene, RPB2, of Saccharomyces cerevisiae as...
Azuma, Y, Yamagishi, M, Ishihama, A
To improve our understanding of the structure and function of eukaryotic RNA polymerase II, we purified the enzyme from the fission yeast Schizosaccharomyces pombe. The highly purified RNA polymerase...
Ozaki, M, Fujita, N, Wada, A, Ishihama, A
Upon growth transition of Escherichia coli cells from exponential to stationary phase, RNA polymerase is converted into at least three different forms (S1, S2 and S3), which could be separately...
Promoter selectivity of Escherichia coli RNA polymerase: alteration by fMet-tRNAfMet.
Nomura, T, Fujita, N, Ishihama, A
An in vitro mixed transcription system was employed to examine the possible alteration of the promoter selectivity of Escherichia coli RNA polymerase by specific tRNAs. Transcription in vitro was...
"Opening potential"s of DNA segments of about ten base pairs in length were calculated for eleven promoters of Escherichia coli using the thermodynamic parameter values [Gotoh and Tagashira (1981)...
Nomura, T, Fujita, N, Ishihama, A
Promoter properties were analyzed for the convergently-overlapped E. coli genes coding for the DNA polymerase III epsilon subunit (dnaQ) and the ribonuclease H (rnh). The rates of open complex...
In vitro transcription was performed in a single reaction mixture, which contained three species of truncated E. coli DNA template, each carrying one specific promoter, lacP (UV5), trpP or rplJp, and...
Cloning and promoter analysis of the Escherichia coli adenylate cyclase gene.
Aiba, H, Kawamukai, M, Ishihama, A
The gene for adenylate cyclase of E. coli has been cloned in the plasmid pBR322. The Cya- strain transformed with the isolated plasmids produces significant amounts of adenylate cyclase and cAMP....
Kawakami, K, Mizumoto, K, Ishihama, A
Catalytic properties of the capped RNA-specific endonuclease associated with the influenza virus RNA polymerase were analyzed with use of synthetic hetero- and homopolymers containing 32P-labeled CAP...
Using the in vitro mixed transcription system (Kajitani, M. and Ishihama, A. (1983) Nucleic Acids Res. 11, 671-686), we determined the two parameters of the promoter strength, i.e., the rate of open...
Igarashi, K, Fujita, N, Ishihama, A
The rpoA gene of Escherichia coli encodes the alpha subunit of the DNA-dependent RNA polymerase. Two mutant alleles, rpoA101 and rpoA112, both of which produce RNA polymerase with altered...
Kobayashi, M, Nagata, K, Ishihama, A
A set of 18 variant lac UV5 promoters was constructed, each carrying a single base substitution within the -35 region (nucleotide positions from -36 to -31 relative to the transcription start site)....
Azuma, Y, Yamagishi, M, Ueshima, R, Ishihama, A
The gene, rpb1, encoding the largest subunit of RNA polymerase II has been cloned from Schizosaccharomyces pombe using the corresponding gene, RPB1, of Saccharomyces cerevisiae as a...
Identification and sequence determination of the host factor gene for bacteriophage Q beta.
The host factor (HF-I) required for phage Q beta RNA-directed synthesis of complementary minus-strand RNA was purified to homogeneity from phage-infected Escherichia coli cells. The hfq gene encoding...
Igarashi, K, Fujita, N, Ishihama, A
Transcription in vitro of stringently controlled Escherichia coli genes by purified RNA polymerase holoenzyme is inhibited by guanosine tetraphosphate (ppGpp). In order to examine possible role of...
Promoter analysis of the phosphoenolpyruvate carboxylase gene of Escherichia coli.
Izui, K, Miwa, T, Kajitani, M, Fujita, N, Sabe, H, Ishihama, A, ...
In order to find the promoter region of phosphoenolpyruvate carboxylase [EC 4.1.1.31] gene (ppc), in vitro transcription was performed using truncated DNA fragments as templates. Transcription...
Tatei, K, Takemura, K, Mayeda, A, Fujiwara, Y, Tanaka, H, Ishihama, A, ...
We have investigated factors that recognize the splice junctions for mRNA by means of a rapid and sensitive filter binding assay using chemically synthesized single-stranded (ss) DNA (16-21...
Choy, H E, Park, S W, Aki, T, Parrack, P, Fujita, N, Ishihama, A, ...
Gal or Lac repressor binding to an upstream DNA segment, in the absence of DNA looping, represses the P1 promoter located on the same face and activates the P2 promoter situated on the opposite face...
Yamagishi, M, Matsushima, H, Wada, A, Sakagami, M, Fujita, N, Ishihama, A
Ribosome modulation factor (RMF) is a protein specifically associated with 100S ribosome dimers which start to accumulate in Escherichia coli cells upon growth transition from exponential to...
Murakami, K, Fujita, N, Ishihama, A
The carboxy-terminal one-third of Escherichia coli RNA polymerase alpha subunit plays a key role in transcription regulation by a group of protein transcription factors and DNA enhancer (UP)...
A novel function of RNase P from Escherichia coli: processing of a suppressor tRNA precursor.
The leuX gene of Escherichia coli codes for a suppressor tRNA and forms a single gene operon containing its own promoter and Q-independent terminator. An analysis of the in vitro processing of leuX...
Bertoni, G, Fujita, N, Ishihama, A, De Lorenzo, V
The sequence elements determining the binding of the sigma54-containing RNA polymerase (sigma54-RNAP) to the Pu promoter of Pseudomonas putida have been examined. Contrary to previous results in...
Colland, F, Fujita, N, Kotlarz, D, Bown, J A, Meares, C F, Ishihama, A, ...
The sigma(S) subunit of RNA polymerase is the master regulator of the general stress response in Escherichia coli and is required for promoter recognition of many stationary phase genes. We have...
Single-molecule imaging of RNA polymerase-DNA interactions in real time.
Harada, Y, Funatsu, T, Murakami, K, Nonoyama, Y, Ishihama, A, Yanagida, T
Using total internal reflection fluorescence microscopy, we have directly observed individual interactions of single RNA polymerase molecules with a single molecule of lambda-phage DNA suspended in...
Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region.
Yura, T, Mori, H, Nagai, H, Nagata, T, Ishihama, A, Fujita, N, ...
A contiguous 111,402-nucleotide sequence corresponding to the 0 to 2.4 min region of the E. coli chromosome was determined as a first step to complete structural analysis of the genome. The resulting...
Tanaka, K, Takayanagi, Y, Fujita, N, Ishihama, A, Takahashi, H
The rpoS gene of Escherichia coli encodes a putative RNA polymerase sigma factor that is considered to be the central regulator of gene expression in stationary phase. The gene product (sigma 38) was...
Yamanaka, K, Ogasawara, N, Yoshikawa, H, Ishihama, A, Nagata, K
A system for the expression of a foreign gene derived from negative polarity RNA was developed using influenza virus, a negative-stranded RNA virus. From cDNA for the influenza virus RNA genome...
Igarashi, K, Hanamura, A, Makino, K, Aiba, H, Aiba, H, Mizuno, T, ...
The role of the alpha subunit of Escherichia coli RNA polymerase in transcription activation by positive factors was investigated using two reconstituted mutant RNA polymerases (containing...
Wada, A, Yamazaki, Y, Fujita, N, Ishihama, A
The decrease in overall translation activity occurring concomitantly with the transition from the exponential growth phase to the stationary phase of Escherichia coli cells was found to be...
Belyaeva, T A, Bown, J A, Fujita, N, Ishihama, A, Busby, S J
Hydroxyl radical footprinting has been used to study different open complexes between Escherichia coli RNA polymerase and the galactose operon regulatory region, which contains two overlapping...
Nègre, D, Bonod-Bidaud, C, Oudot, C, Prost, J F, Kolb, A, Ishihama, A, ...
The specific interaction of the upstream element-containing promoter of the Escherichia coli acetate operon with either the RNA polymerase holoenzyme or its alpha subunit has been analyzed by the...
Kang, J G, Hahn, M Y, Ishihama, A, Roe, J H
We examined the promoter selectivity of RNA polymerase (RNAP) from Streptomyces coelicolor at two growth phases by in vitro transcription. Distinct sets of promoters were preferentially recognized by...
Burns, H D, Ishihama, A, Minchin, S D
We have studied the role of the C-terminal domain of the alpha subunit (alphaCTD) of Escherichia coli RNA polymerase during transcription initiation at promoters lacking an UP-element. The...
The TyrR protein of Escherichia coli is a class I transcription activator.
Lawley, B, Fujita, N, Ishihama, A, Pittard, A J
The purified TyrR protein and phenylalanine were sufficient to activate in vitro transcription from the tyrP promoter by wild-type RNA polymerase. Such TyrR-mediated activation did not occur when the...
Liu, X, Fujita, N, Ishihama, A, Matsumura, P
A number of transcription activators have been found to activate transcription via protein-protein contact between RNA polymerase alpha subunits and transcription factors; they are classified as...
A partially functional 245-amino-acid internal deletion derivative of Escherichia coli sigma 70.
Kumar, A, Williamson, H S, Fujita, N, Ishihama, A, Hayward, R S
Two hundred forty-five consecutive amino acids of the sigma 70 subunit of Escherichia coli RNA polymerase are not conserved in the homologous protein of Bacillus subtilis. We show that their deletion...
Mapping of the OxyR protein contact site in the C-terminal region of RNA polymerase alpha subunit.
Tao, K, Zou, C, Fujita, N, Ishihama, A
The Escherichia coli OxyR protein requires the C-terminal contact site I region of the RNA polymerase alpha subunit for cooperative interaction with and transcription activation at OxyR-dependent...
The intracellular levels of two principal sigma subunits, sigma 70 (sigma D, the rpoD gene product) and sigma 38 (sigma s, the rpoS gene product), in Escherichia coli MC4100 were determined by a...
Jair, K W, Martin, R G, Rosner, J L, Fujita, N, Ishihama, A, Wolf, R E
Expression of the marA or soxS genes is induced by exposure of Escherichia coli to salicylate or superoxides, respectively. This, in turn, enhances the expression of a common set of promoters (the...
Jair, K W, Yu, X, Skarstad, K, Thöny, B, Fujita, N, Ishihama, A, ...
The Rob protein, isolated on the basis of its ability to bind to the right arm of the Escherichia coli origin of chromosomal replication, is about 50% identical in amino acid sequence to SoxS and...
Rajkumari, K, Kusano, S, Ishihama, A, Mizuno, T, Gowrishankar, J
We have used supercoiled DNA templates in this study to demonstrate that transcription in vitro from the P1 and P2 promoters of the osmoresponsive proU operon of Escherichia coli is preferentially...
Jishage, M, Iwata, A, Ueda, S, Ishihama, A
By a quantitative Western immunoblot analysis, the intracellular levels of two principal sigma subunits, sigma 70 (sigma D, the rpoD gene product) and sigma 38 (sigma S, the rpoS gene product), and...
Tang, Y, Murakami, K, Ishihama, A, DeHaseth, P L
The rightward regulatory region of bacteriophage lambda contains two promoters, pRM and pR, which direct the synthesis of nonoverlapping divergent transcripts from start sites 82 bp apart. Each of...
The composition of RNA polymerase sigma subunits was analyzed for stock strains of Escherichia coli K-12 W3110 in Japan. Heterogeneity was discovered with respect to two sigma subunits, sigma28...
Boucher, P E, Murakami, K, Ishihama, A, Stibitz, S
The expression of virulence factor genes in Bordetella pertussis is mediated by the BvgA-BvgS two-component signal transduction system. The response regulator, BvgA, acts directly as a...
Chugani, S A, Parsek, M R, Hershberger, C D, Murakami, K, Ishihama, A, Chakrabarty, A M
The soil bacterium Pseudomonas putida is capable of degrading many aromatic compounds, including benzoate, through catechol as an intermediate. The catabolism of catechol is mediated by the catBCA...
The intracellular concentration of trehalose increases in the stationary-phase cells of Escherichia coli. The effects of trehalose on transcription in vitro by E. coli RNA polymerase were compared...
Kundu, T K, Kusano, S, Ishihama, A
The rpoF gene of Escherichia coli codes for the RNA polymerase sigmaF (or sigma28) subunit, which is involved in transcription of the flagellar and chemotaxis genes. Both sigmaF and sigma70 (the...
Yang, J, Murakami, K, Camakaris, H, Fujita, N, Ishihama, A, Pittard, A J
To examine the role of the amino acid residues (between positions 258 and 275 and positions 297 and 298) of the alpha-subunit of RNA polymerase in TyrR-mediated activation of the mtr promoter, we...
Rajkumari, K, Ishihama, A, Gowrishankar, J
The osmotically regulated proU locus in Escherichia coli has two promoters, P1 and P2, that are recognized, respectively, by the sigmaS- and sigma70-bearing RNA polymerase holoenzymes. However, the...
Nakagawa, Y, Kimura, N, Toyoda, T, Mizumoto, K, Ishihama, A, Oda, K, ...
An established cell line, clone 64, in which the expression of the RNA polymerase PB1 and PA subunit genes and the nucleoprotein (NP) gene but not the PB2 subunit gene of influenza virus can be...
The Ada protein is a class I transcription factor of Escherichia coli.
Sakumi, K, Igarashi, K, Sekiguchi, M, Ishihama, A
The methylated Ada protein of Escherichia coli, a regulatory protein for the adaptive response, binds to a target DNA from positions -62 to -31 upstream of the ada gene and facilitates the binding of...
Lee, H S, Ishihama, A, Kustu, S
Several activators of sigma 70 holoenzyme whose binding sites lie upstream of the -35 region of promoters require the C-terminal region of the alpha subunit of RNA polymerase to activate...
Regulation of the Escherichia coli hfq gene encoding the host factor for phage Q beta.
Kajitani, M, Kato, A, Wada, A, Inokuchi, Y, Ishihama, A
The host factor (HF-I) for phage Q beta RNA replication is a small protein of 102 amino acid residues encoded by the hfq gene at 94.8 min on the Escherichia coli chromosome. The synthesis rate of...
Activation defects caused by mutations in Escherichia coli rpoA are promoter specific.
Gussin, G N, Olson, C, Igarashi, K, Ishihama, A
Escherichia coli RNA polymerases containing mutated alpha subunits were tested for their ability to respond to three different positive regulators (activators) in vitro. The two alpha (rpoA) mutants,...
Yasuda, J, Bucher, D J, Ishihama, A
Analysis of fast-growing reassortants (AWM viruses) of influenza A virus produced by mixed infection with a fast-growing WSN strain and a slowly growing Aichi strain indicated that the M gene plays a...
Molecular dissection of influenza virus nucleoprotein: deletion mapping of the RNA binding domain.
Kobayashi, M, Toyoda, T, Adyshev, D M, Azuma, Y, Ishihama, A
Influenza virus nucleoprotein (NP) is associated with the genome RNA, forming ribonucleoprotein cores. To identify the amino acid sequence involved in RNA binding, we performed Northwestern blot...
Promoter analysis of influenza virus RNA polymerase.
Parvin, J D, Palese, P, Honda, A, Ishihama, A, Krystal, M
Influenza virus polymerase, which was prepared depleted of viral RNA, was used to copy small RNA templates prepared from plasmid-encoded sequences. Template constructions containing only the 3' end...
Solubilization and promoter analysis of RNA polymerase from rice stripe virus.
Barbier, P, Takahashi, M, Nakamura, I, Toriyama, S, Ishihama, A
The RNA-dependent RNA polymerase associated with rice stripe virus was dissociated from viral RNA (vRNA) by CsCl centrifugation. The solubilized RNA-free RNA polymerase transcribed a model RNA...
Kolb, A, Kotlarz, D, Kusano, S, Ishihama, A
A series of gal promoter mutants has been used to compare the in vitro selectivities of the two forms of Escherichia coli RNA polymerase, E sigma 38 and E sigma 70. In the absence of the CRP-cAMP...
Tanaka, K, Kusano, S, Fujita, N, Ishihama, A, Takahashi, H
Sequence determinants responsible for promoter recognition by RNA polymerase holoenzyme containing sigma 38, the rpoS gene product, were analyzed. In a previous study [Tanaka et al. (1993) Proc....
Fujita, N, Mori, H, Yura, T, Ishihama, A
The complete sequence analysis of the E. coli genome was initiated as a collaborative study in Japan. Following the initial analysis of the 0-2.4 min region (Yura, T. et al. (1992) Nucleic Acids Res....
Attey, A, Belyaeva, T, Savery, N, Hoggett, J, Fujita, N, Ishihama, A, ...
DNAase I footprinting has been used to study open complexes between Escherichia coli RNA polymerase and the galactose operon P1 promoter, both in the absence and the presence of CRP (the cyclic AMP...
Kolb, A, Igarashi, K, Ishihama, A, Lavigne, M, Buckle, M, Buc, H
A deletion of the C-terminal part of the alpha-subunit of RNA polymerase is known to affect differently promoters activated by CRP depending on the location of the CRP binding site at the promoter....
Kawagishi, M, Yamagishi, M, Ishihama, A
The gene, rpb2, encoding the second largest subunit, subunit 2, of RNA polymerase II has been cloned from Schizosaccharomyces pombe using the corresponding gene, RPB2, of Saccharomyces cerevisiae as...
Azuma, Y, Yamagishi, M, Ishihama, A
To improve our understanding of the structure and function of eukaryotic RNA polymerase II, we purified the enzyme from the fission yeast Schizosaccharomyces pombe. The highly purified RNA polymerase...
Ozaki, M, Fujita, N, Wada, A, Ishihama, A
Upon growth transition of Escherichia coli cells from exponential to stationary phase, RNA polymerase is converted into at least three different forms (S1, S2 and S3), which could be separately...
Promoter selectivity of Escherichia coli RNA polymerase: alteration by fMet-tRNAfMet.
Nomura, T, Fujita, N, Ishihama, A
An in vitro mixed transcription system was employed to examine the possible alteration of the promoter selectivity of Escherichia coli RNA polymerase by specific tRNAs. Transcription in vitro was...
Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region.
Yura, T, Mori, H, Nagai, H, Nagata, T, Ishihama, A, Fujita, N, ...
A contiguous 111,402-nucleotide sequence corresponding to the 0 to 2.4 min region of the E. coli chromosome was determined as a first step to complete structural analysis of the genome. The resulting...
"Opening potential"s of DNA segments of about ten base pairs in length were calculated for eleven promoters of Escherichia coli using the thermodynamic parameter values [Gotoh and Tagashira (1981)...
Nomura, T, Fujita, N, Ishihama, A
Promoter properties were analyzed for the convergently-overlapped E. coli genes coding for the DNA polymerase III epsilon subunit (dnaQ) and the ribonuclease H (rnh). The rates of open complex...
In vitro transcription was performed in a single reaction mixture, which contained three species of truncated E. coli DNA template, each carrying one specific promoter, lacP (UV5), trpP or rplJp, and...
Cloning and promoter analysis of the Escherichia coli adenylate cyclase gene.
Aiba, H, Kawamukai, M, Ishihama, A
The gene for adenylate cyclase of E. coli has been cloned in the plasmid pBR322. The Cya- strain transformed with the isolated plasmids produces significant amounts of adenylate cyclase and cAMP....
Kawakami, K, Mizumoto, K, Ishihama, A
Catalytic properties of the capped RNA-specific endonuclease associated with the influenza virus RNA polymerase were analyzed with use of synthetic hetero- and homopolymers containing 32P-labeled CAP...
Using the in vitro mixed transcription system (Kajitani, M. and Ishihama, A. (1983) Nucleic Acids Res. 11, 671-686), we determined the two parameters of the promoter strength, i.e., the rate of open...
Igarashi, K, Fujita, N, Ishihama, A
The rpoA gene of Escherichia coli encodes the alpha subunit of the DNA-dependent RNA polymerase. Two mutant alleles, rpoA101 and rpoA112, both of which produce RNA polymerase with altered...
Kobayashi, M, Nagata, K, Ishihama, A
A set of 18 variant lac UV5 promoters was constructed, each carrying a single base substitution within the -35 region (nucleotide positions from -36 to -31 relative to the transcription start site)....
Azuma, Y, Yamagishi, M, Ueshima, R, Ishihama, A
The gene, rpb1, encoding the largest subunit of RNA polymerase II has been cloned from Schizosaccharomyces pombe using the corresponding gene, RPB1, of Saccharomyces cerevisiae as a...
Identification and sequence determination of the host factor gene for bacteriophage Q beta.
The host factor (HF-I) required for phage Q beta RNA-directed synthesis of complementary minus-strand RNA was purified to homogeneity from phage-infected Escherichia coli cells. The hfq gene encoding...
Igarashi, K, Fujita, N, Ishihama, A
Transcription in vitro of stringently controlled Escherichia coli genes by purified RNA polymerase holoenzyme is inhibited by guanosine tetraphosphate (ppGpp). In order to examine possible role of...
Promoter analysis of the phosphoenolpyruvate carboxylase gene of Escherichia coli.
Izui, K, Miwa, T, Kajitani, M, Fujita, N, Sabe, H, Ishihama, A, ...
In order to find the promoter region of phosphoenolpyruvate carboxylase [EC 4.1.1.31] gene (ppc), in vitro transcription was performed using truncated DNA fragments as templates. Transcription...
Tatei, K, Takemura, K, Mayeda, A, Fujiwara, Y, Tanaka, H, Ishihama, A, ...
We have investigated factors that recognize the splice junctions for mRNA by means of a rapid and sensitive filter binding assay using chemically synthesized single-stranded (ss) DNA (16-21...
Choy, H E, Park, S W, Aki, T, Parrack, P, Fujita, N, Ishihama, A, ...
Gal or Lac repressor binding to an upstream DNA segment, in the absence of DNA looping, represses the P1 promoter located on the same face and activates the P2 promoter situated on the opposite face...
Yamagishi, M, Matsushima, H, Wada, A, Sakagami, M, Fujita, N, Ishihama, A
Ribosome modulation factor (RMF) is a protein specifically associated with 100S ribosome dimers which start to accumulate in Escherichia coli cells upon growth transition from exponential to...
Murakami, K, Fujita, N, Ishihama, A
The carboxy-terminal one-third of Escherichia coli RNA polymerase alpha subunit plays a key role in transcription regulation by a group of protein transcription factors and DNA enhancer (UP)...
A novel function of RNase P from Escherichia coli: processing of a suppressor tRNA precursor.
The leuX gene of Escherichia coli codes for a suppressor tRNA and forms a single gene operon containing its own promoter and Q-independent terminator. An analysis of the in vitro processing of leuX...
Bertoni, G, Fujita, N, Ishihama, A, De Lorenzo, V
The sequence elements determining the binding of the sigma54-containing RNA polymerase (sigma54-RNAP) to the Pu promoter of Pseudomonas putida have been examined. Contrary to previous results in...
Colland, F, Fujita, N, Kotlarz, D, Bown, J A, Meares, C F, Ishihama, A, ...
The sigma(S) subunit of RNA polymerase is the master regulator of the general stress response in Escherichia coli and is required for promoter recognition of many stationary phase genes. We have...
Single-molecule imaging of RNA polymerase-DNA interactions in real time.
Harada, Y, Funatsu, T, Murakami, K, Nonoyama, Y, Ishihama, A, Yanagida, T
Using total internal reflection fluorescence microscopy, we have directly observed individual interactions of single RNA polymerase molecules with a single molecule of lambda-phage DNA suspended in...