年別の研究成果
年別の研究成果
- 49 件
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2021
Acetate overflow metabolism regulates a major metabolic shift after glucose depletion in Escherichia coli
Shimada, T., Nakazawa, K., Tachikawa, T., Saito, N., Niwa, T., Taguchi, H. & Tanaka, K., 8月 2021, In: FEBS Letters. 595, 15, p. 2047-2056 10 p.研究成果: Article › 査読
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Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis
Sharma, M., Abayakoon, P., Epa, R., Jin, Y., Lingford, J. P., Shimada, T., Nakano, M., Mui, J. W. Y., Ishihama, A., Goddard-Borger, E. D., Davies, G. J. & Williams, S. J., 24 3月 2021, In: ACS Central Science. 7, 3, p. 476-487 12 p.研究成果: Article › 査読
Open Access3 被引用数 (Scopus) -
Single-Target Regulators Constitute the Minority Group of Transcription Factors in Escherichia coli K-12
Shimada, T., Ogasawara, H., Kobayashi, I., Kobayashi, N. & Ishihama, A., 18 6月 2021, In: Frontiers in Microbiology. 12, 697803.研究成果: Article › 査読
Open Access -
Whole set of constitutive promoters for RpoN sigma factor and the regulatory role of its enhancer protein NtrC in Escherichia coli K-12
Shimada, T., Furuhata, S. & Ishihama, A., 2021, In: Microbial genomics. 7, 11, 000653.研究成果: Article › 査読
Open Access1 被引用数 (Scopus) -
2020
Expanded roles of pyruvate-sensing pdhr in transcription regulation of the escherichia coli K-12 genome: Fatty acid catabolism and cell motility
Anzai, T., Imamura, S., Ishihama, A. & Shimada, T., 2020, In: Microbial genomics. 6, 10, p. 1-14 14 p., 000442.研究成果: Article › 査読
Open Access5 被引用数 (Scopus) -
Novel regulators of the CSGD gene encoding the master regulator of biofilm formation in Escherichia coli K-12
Ogasawara, H., Ishizuka, T., Hotta, S., Aoki, M., Shimada, T. & Ishihama, A., 2020, In: Microbiology (United Kingdom). 166, 9, p. 880-890 11 p., 000947.研究成果: Article › 査読
8 被引用数 (Scopus) -
Proteomic analysis of haem-binding protein from Arabidopsis thaliana and Cyanidioschyzon merolae
Shimizu, T., Yasuda, R., Mukai, Y., Tanoue, R., Shimada, T., Imamura, S., Tanaka, K., Watanabe, S. & Masuda, T., 22 6月 2020, In: Philosophical Transactions of the Royal Society B: Biological Sciences. 375, 1801, 20190488.研究成果: Article › 査読
Open Access6 被引用数 (Scopus) -
Regulatory role of pyruvate-sensing BtsSR in biofilm formation by Escherichia coli K-12
Ogasawara, H., Ishizuka, T., Yamaji, K., Kato, Y., Shimada, T. & Ishihama, A., 3 1月 2020, In: FEMS microbiology letters. 366, 24, fnz251.研究成果: Article › 査読
6 被引用数 (Scopus) -
2019
C-terminal regulatory domain of the ε subunit of FoF1 ATP synthase enhances the ATP-dependent H+ pumping that is involved in the maintenance of cellular membrane potential in Bacillus subtilis
Akanuma, G., Tagana, T., Sawada, M., Suzuki, S., Shimada, T., Tanaka, K., Kawamura, F. & Kato-Yamada, Y., 8月 2019, In: MicrobiologyOpen. 8, 8, e00815.研究成果: Article › 査読
Open Access4 被引用数 (Scopus) -
Large expert-curated database for benchmarking document similarity detection in biomedical literature search
RELISH Consortium, 2019, In: Database : the journal of biological databases and curation. 2019, p. 1-67 67 p.研究成果: Article › 査読
Open Access5 被引用数 (Scopus) -
Regulatory role of CsqR (YihW) in transcription of the genes for catabolism of the anionic sugar sulfoquinovose (SQ) in escherichia coli K-12
Shimada, T., Yamamoto, K., Nakano, M., Watanabe, H., Schleheck, D. & Ishihama, A., 1月 2019, In: Microbiology (United Kingdom). 165, 1, p. 78-89 12 p., 000740.研究成果: Article › 査読
10 被引用数 (Scopus) -
Regulatory Role of PlaR (YiaJ) for Plant Utilization in Escherichia coli K-12
Shimada, T., Yokoyama, Y., Anzai, T., Yamamoto, K. & Ishihama, A., 1 12月 2019, In: Scientific reports. 9, 1, 20415.研究成果: Article › 査読
Open Access9 被引用数 (Scopus) -
The retrograde signaling protein GUN1 regulates tetrapyrrole biosynthesis
Shimizu, T., Kacprzak, S. M., Mochizuki, N., Nagatani, A., Watanabe, S., Shimada, T., Tanaka, K., Hayashi, Y., Arai, M., Leister, D., Okamoto, H., Terry, M. J. & Masuda, T., 3 12月 2019, In: Proceedings of the National Academy of Sciences of the United States of America. 116, 49, p. 24900-24906 7 p.研究成果: Article › 査読
Open Access19 被引用数 (Scopus) -
2018
Altered distribution of RNA polymerase lacking the omega subunit within the prophages along the Escherichia coli K-12 genome
Yamamoto, K., Yamanaka, Y., Shimada, T., Sarkar, P., Yoshida, M., Bhardwaj, N., Watanabe, H., Taira, Y., Chatterji, D. & Ishihama, A., 2018, In: mSystems. 3, 1, e00172-17.研究成果: Article › 査読
Open Access12 被引用数 (Scopus) -
Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of Escherichia coli to Stationary Phase
Yoshida, H., Shimada, T. & Ishihama, A., 1 9月 2018, In: mSystems. 3, 5, e0005718.研究成果: Article › 査読
Open Access18 被引用数 (Scopus) -
Single-target regulators form a minor group of transcription factors in Escherichia coli K-12
Shimada, T., Ogasawara, H. & Ishihama, A., 4 5月 2018, In: Nucleic Acids Research. 46, 8, p. 3921-3936 16 p.研究成果: Article › 査読
Open Access14 被引用数 (Scopus) -
2017
A structural sketch of RcdA, a transcription factor controlling the master regulator of biofilm formation
Sugino, H., Usui, T., Shimada, T., Nakano, M., Ogasawara, H., Ishihama, A. & Hirata, A., 1 7月 2017, In: FEBS Letters. 591, 13, p. 2019-2031 13 p.研究成果: Article › 査読
5 被引用数 (Scopus) -
Conserved two-component Hik34-Rre1 module directly activates heat-stress inducible transcription of major chaperone and other genes in Synechococcus elongatus PCC 7942
Kobayashi, I., Watanabe, S., Kanesaki, Y., Shimada, T., Yoshikawa, H. & Tanaka, K., 1 4月 2017, In: Molecular Microbiology. 104, 2, p. 260-277 18 p.研究成果: Article › 査読
Open Access10 被引用数 (Scopus) -
Identification of YbhA as the pyridoxal 5'-phosphate (PLP) phosphatase in escherichia coli: Importance of PLP homeostasis on the bacterial growth
Sugimoto, R., Saito, N., Shimada, T. & Tanaka, K., 2017, In: Journal of General and Applied Microbiology. 63, 6, p. 362-368 7 p.研究成果: Article › 査読
Open Access15 被引用数 (Scopus) -
The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase
Shimada, T., Tanaka, K. & Ishihama, A., 6月 2017, In: PLoS ONE. 12, 6, e0179181.研究成果: Article › 査読
Open Access26 被引用数 (Scopus) -
2016
Differential regulation of rRNA and tRNA transcription from the rRNA-tRNA composite operon in Escherichia coli
Takada, H., Shimada, T., Dey, D., Quyyum, M. Z., Nakano, M., Ishiguro, A., Yoshida, H., Yamamoto, K., Sen, R. & Ishihama, A., 12月 2016, In: PLoS ONE. 11, 12, e0163057.研究成果: Article › 査読
Open Access3 被引用数 (Scopus) -
Growth inhibition by external potassium of Escherichia coli lacking PtsN (EIIANtr) is caused by potassium limitation mediated by YcgO
Sharma, R., Shimada, T., Mishra, V. K., Upreti, S. & Sardesai, A. A., 2016, In: Journal of Bacteriology. 198, 13, p. 1868-1882 15 p.研究成果: Article › 査読
Open Access9 被引用数 (Scopus) -
Transcription factor CecR (YbiH) regulates a set of genes affecting the sensitivity of Escherichia coli against cefoperazone and chloramphenicol
Yamanaka, Y., Shimada, T., Yamamoto, K. & Ishihama, A., 7月 2016, In: Microbiology (United Kingdom). 162, 7, p. 1253-1264 12 p.研究成果: Article › 査読
Open Access24 被引用数 (Scopus) -
Transcription factor DecR (YbaO) controls detoxification of L-cysteine in Escherichia coli
Shimada, T., Tanaka, K. & Ishihama, A., 9月 2016, In: Microbiology (United Kingdom). 162, 9, p. 1698-1707 10 p.研究成果: Article › 査読
Open Access28 被引用数 (Scopus) -
Transcription profile of Escherichia coli: Genomic SELEX search for regulatory targets of transcription factors
Ishihama, A., Shimada, T. & Yamazaki, Y., 3 2月 2016, In: Nucleic Acids Research. 44, 5, p. 2058-2074 17 p.研究成果: Article › 査読
Open Access66 被引用数 (Scopus) -
Use of a bacterial luciferase monitoring system to estimate real-time dynamics of intracellular metabolism in Escherichia coli
Shimada, T. & Tanaka, K., 2016, In: Applied and Environmental Microbiology. 82, 19, p. 5960-5968 9 p.研究成果: Article › 査読
Open Access5 被引用数 (Scopus) -
2015
Expanded roles of two-component response regulator OmpR in Escherichia coli: Genomic SELEX search for novel regulation targets
Shimada, T., Takada, H., Yamamoto, K. & Ishihama, A., 11月 2015, In: Genes to Cells. 20, 11, p. 915-931 17 p.研究成果: Article › 査読
Open Access22 被引用数 (Scopus) -
Strength and Regulation of Seven rRNA Promoters in Escherichia coli
Maeda, M., Shimada, T. & Ishihama, A., 1 12月 2015, In: PLoS ONE. 10, 12, e0144697.研究成果: Article › 査読
Open Access26 被引用数 (Scopus) -
2014
Intracellular concentrations of 65 species of transcription factors with known regulatory functions in Escherichia coli
Ishihama, A., Kori, A., Koshio, E., Yamada, K., Maeda, H., Shimada, T., Makinoshima, H., Iwata, A. & Fujitac, N., 2014, In: Journal of Bacteriology. 196, 15, p. 2718-2727 10 p.研究成果: Article › 査読
66 被引用数 (Scopus) -
Involvement of cAMP-CRP in transcription activation and repression of the pck gene encoding PEP carboxykinase, the key enzyme of gluconeogenesis
Nakano, M., Ogasawara, H., Shimada, T., Yamamoto, K. & Ishihama, A., 6月 2014, In: FEMS microbiology letters. 355, 2, p. 93-99 7 p.研究成果: Article › 査読
Open Access11 被引用数 (Scopus) -
Roles of cell division control factor SdiA: Recognition of quorum sensing signals and modulation of transcription regulation targets
Shimada, T., Shimada, K., Matsui, M., Kitai, Y., Igarashi, J., Suga, H. & Ishihama, A., 5月 2014, In: Genes to Cells. 19, 5, p. 405-418 14 p.研究成果: Article › 査読
Open Access21 被引用数 (Scopus) -
The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli
Shimada, T., Yamazaki, Y., Tanaka, K. & Ishihama, A., 6 3月 2014, In: PLoS ONE. 9, 3, e90447.研究成果: Article › 査読
Open Access63 被引用数 (Scopus) -
Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing
Conway, T., Creecy, J. P., Maddox, S. M., Grissom, J. E., Conkle, T. L., Shadid, T. M., Teramoto, J., Miguel, P. S., Shimada, T., Ishihama, A., Mori, H. & Wanner, B. L., 8 7月 2014, In: mBio. 5, 4, e01442-14.研究成果: Article › 査読
Open Access115 被引用数 (Scopus) -
2013
Involvement of cyclic AMP receptor protein in regulation of the rmf gene encoding the ribosome modulation factor in escherichia coli
Shimada, T., Yoshida, H. & Ishihama, A., 5月 2013, In: Journal of Bacteriology. 195, 10, p. 2212-2219 8 p.研究成果: Article › 査読
34 被引用数 (Scopus) -
Involvement of the ribose operon repressor RbsR in regulation of purine nucleotide synthesis in Escherichia coli
Shimada, T., Kori, A. & Ishihama, A., 7月 2013, In: FEMS microbiology letters. 344, 2, p. 159-165 7 p.研究成果: Article › 査読
Open Access21 被引用数 (Scopus) -
Novel regulator PgrR for switch control of peptidoglycan recycling in Escherichia coli
Shimada, T., Yamazaki, K. & Ishihama, A., 2月 2013, In: Genes to Cells. 18, 2, p. 123-134 12 p.研究成果: Article › 査読
13 被引用数 (Scopus) -
Screening of promoter-specific transcription factors: Multiple regulators for the sdiA gene involved in cell division control and quorum sensing
Shimada, K., Ogasawara, H., Yamada, K., Shimura, M., Kori, A., Shimada, T., Yamanaka, Y., Yamamoto, K. & Ishihama, A., 12月 2013, In: Microbiology (United Kingdom). 159, PART 12, p. 2501-2512 12 p.研究成果: Article › 査読
Open Access21 被引用数 (Scopus) -
2012
A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli
Shimada, T., Katayama, Y., Kawakita, S., Ogasawara, H., Nakano, M., Yamamoto, K. & Ishihama, A., 12月 2012, In: MicrobiologyOpen. 1, 4, p. 381-394 14 p.研究成果: Article › 査読
Open Access21 被引用数 (Scopus) -
2011
Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli
Shimada, T., Yamamoto, K. & Ishihama, A., 2月 2011, In: Journal of Bacteriology. 193, 3, p. 649-659 11 p.研究成果: Article › 査読
80 被引用数 (Scopus) -
Novel roles of camp receptor protein (CRP) in regulation of transport and metabolism of carbon sources
Shimada, T., Fujita, N., Yamamoto, K. & Ishihama, A., 2011, In: PLoS ONE. 6, 6, e20081.研究成果: Article › 査読
Open Access171 被引用数 (Scopus) -
Novel roles of LeuO in transcription regulation of E. coli genome: Antagonistic interplay with the universal silencer H-NS
Shimada, T., Bridier, A., Briandet, R. & Ishihama, A., 10月 2011, In: Molecular Microbiology. 82, 2, p. 378-397 20 p.研究成果: Article › 査読
Open Access74 被引用数 (Scopus) -
2009
Involvement of the leucine response transcription factor LeuO in regulation of the genes for sulfa drug efflux
Shimada, T., Yamamoto, K. & Ishihama, A., 7月 2009, In: Journal of Bacteriology. 191, 14, p. 4562-4571 10 p.研究成果: Article › 査読
48 被引用数 (Scopus) -
2008
The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions
Shimada, T., Ishihama, A., Busby, S. J. W. & Grainger, D. C., 7月 2008, In: Nucleic Acids Research. 36, 12, p. 3950-3955 6 p.研究成果: Article › 査読
Open Access107 被引用数 (Scopus) -
The uncharacterized transcription factor YdhM is the regulator of the nemA gene, encoding N-ethylmaleimide reductase
Umezawa, Y., Shimada, T., Kori, A., Yamada, K. & Ishihama, A., 9月 2008, In: Journal of Bacteriology. 190, 17, p. 5890-5897 8 p.研究成果: Article › 査読
47 被引用数 (Scopus) -
2007
folA, a new member of the TyrR regulon in Escherichia coli K-12
Yang, J., Ogawa, Y., Camakaris, H., Shimada, T., Ishihama, A. & Pittard, A. J., 8月 2007, In: Journal of Bacteriology. 189, 16, p. 6080-6084 5 p.研究成果: Article › 査読
24 被引用数 (Scopus) -
RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines
Shimada, T., Hirao, K., Kori, A., Yamamoto, K. & Ishihama, A., 1 11月 2007, In: Molecular Microbiology. 66, 3, p. 744-757 14 p.研究成果: Article › 査読
74 被引用数 (Scopus) -
The role of the omega subunit of RNA polymerase in expression of the relA gene in Escherichia coli
Chatterji, D., Ogawa, Y., Shimada, T. & Ishihama, A., 1 2月 2007, In: FEMS Microbiology Letters. 267, 1, p. 51-55 5 p.研究成果: Article › 査読
Open Access20 被引用数 (Scopus) -
2005
Systematic search for the Cra-binding promoters using genomic SELEX system
Shimada, T., Fujita, N., Maeda, M. & Ishihama, A., 1 9月 2005, In: Genes to Cells. 10, 9, p. 907-918 12 p.研究成果: Article › 査読
137 被引用数 (Scopus) -
2004
Classification and strength measurement of stationary-phase promoters by use of a newly developed promoter cloning vector
Shimada, T., Makinoshima, H., Ogawa, Y., Miki, T., Maeda, M. & Ishihama, A., 11月 2004, In: Journal of Bacteriology. 186, 21, p. 7112-7122 11 p.研究成果: Article › 査読
61 被引用数 (Scopus)