Faculty Database - SHIMADA TOMOHIRO

Works

Books and Papers

Research Topics, Consignment Studies & KAKENHI Researches

Web Sites

Current Specialized Field

KAKENHI Researcher Number

（Last updated : 2023-05-18 10:44:17）

SHIMADA TOMOHIRO
Department Undergraduate School , School of Agriculture

Position Associate Professor

■ Works

■ Books and Papers

1.	2023/04	Article	Overview of the Molecular Mechanism of Bacterial Environmental Adaptation by Comprehensive Analysis. International journal of molecular sciences 24(8) (Collaboration)
2.	2023/03	Article	Metal-Responsive Transcription Factors Co-Regulate Anti-Sigma Factor (Rsd) and Ribosome Dimerization Factor Expression. International journal of molecular sciences 24(5) (Collaboration)
3.	2023/02	Article	Genomic SELEX Reveals Pervasive Role of the Flagella Master Regulator FlhDC in Carbon Metabolism. International journal of molecular sciences 24(4) (Collaboration)
4.	2022/05	Article	Transcription Factor SrsR (YgfI) Is a Novel Regulator for the Stress-Response Genes in Stationary Phase in Escherichia coli K-12 International Journal of Molecular Sciences 23(11),pp.6055-6055 (Collaboration)
5.	2022/04	Article	Regulatory role of CsuR (YiaU) in determination of cell surface properties of Escherichia coli K-12. Microbiology (Reading, England) 168(4) (Collaboration)
6.	2021/11	Article	Whole set of constitutive promoters for RpoN sigma factor and the regulatory role of its enhancer protein NtrC in Escherichia coli K-12. Microbial genomics 7(11) (Collaboration)
7.	2021/08	Article	Acetate overflow metabolism regulates a major metabolic shift after glucose depletion in Escherichia coli. FEBS letters 595(15),pp.2047-2056 (Collaboration)
8.	2021/07	Article	Hierarchy of transcription factor network in Escherichia coli K-12: H-NS-mediated silencing and Anti-silencing by global regulators. FEMS microbiology reviews (Collaboration)
9.	2021/03	Article	Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis. ACS central science 7(3),pp.476-487 (Collaboration)
10.	2021	Article	Single-Target Regulators Constitute the Minority Group of Transcription Factors in Escherichia coli K-12. Frontiers in microbiology 12,pp.697803-697803 (Collaboration)
11.	2020/10	Article	Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility. Microbial genomics 6(10) (Collaboration)
12.	2018/05	Article	Single-target regulators form a minor group of transcription factors in Escherichia coli K-12. Nucleic acids research 46(8),pp.3921-3936 (Collaboration)
13.	2018/01	Article	Identification of YbhA as the pyridoxal 5'-phosphate (PLP) phosphatase in Escherichia coli: Importance of PLP homeostasis on the bacterial growth. The Journal of general and applied microbiology 63(6),pp.362-368 (Collaboration)
14.	2018	Article	Altered distribution of RNA polymerase lacking the omega subunit within the prophages along the Escherichia coli K-12 genome. mSystems (Collaboration)
15.	2018	Article	Single-target regulators form a minor group of transcription factors in Escherichia coli. Nucleic Acids Research (Collaboration)
16.	2017/12	Article	Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia coli K-12. FEMS microbiology letters 364(22) (Collaboration)
17.	2017/07	Article	A structural sketch of RcdA, a transcription factor controlling the master regulator of biofilm formation. FEBS letters 591(13),pp.2019-2031 (Collaboration)
18.	2017/04	Article	Conserved two-component Hik34-Rre1 module directly activates heat-stress inducible transcription of major chaperone and other genes in Synechococcus elongatus PCC 7942. Molecular microbiology 104(2),pp.260-277 (Collaboration)
19.	2017	Article	A structural sketch of RcdA, a transcription factor controlling the master regulator of biofilm formation. FEBS Letters (Collaboration)
20.	2017	Article	Conserved two-component Hik34-Rre1 module directly activates heat-stress inducible transcription of major chaperone and other genes in Synechococcus elongatus PCC 7942. Mol Microbiol. (Collaboration)
21.	2017	Article	Identification of YbhA as the pyridoxal 5'-phosphate (PLP) phosphatase in Escherichia coli: Importance of PLP homeostasis on the bacterial growth. J. Gen. Appl. Microbiol. (Collaboration)
22.	2017	Article	Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia coli K-12. FEMS Microbiology Letters (Collaboration)
23.	2017	Article	The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase. PLoS ONE 12,pp.e0179181 (Collaboration)
24.	2017	Article	The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase. PloS one 12(6),pp.e0179181 (Collaboration)
25.	2016/10	Article	Use of a Bacterial Luciferase Monitoring System To Estimate Real-Time Dynamics of Intracellular Metabolism in Escherichia coli. Applied and environmental microbiology 82(19),pp.5960-8 (Collaboration)
26.	2016/09	Article	Transcription factor DecR (YbaO) controls detoxification of L-cysteine in Escherichia coli. Microbiology (Reading, England) 162(9),pp.1698-1707 (Collaboration)
27.	2016/07	Article	Growth Inhibition by External Potassium of Escherichia coli Lacking PtsN (EIIANtr) Is Caused by Potassium Limitation Mediated by YcgO. Journal of bacteriology 198(13),pp.1868-1882 (Collaboration)
28.	2016/07	Article	Transcription factor CecR (YbiH) regulates a set of genes affecting the sensitivity of Escherichia coli against cefoperazone and chloramphenicol. Microbiology (Reading, England) 162(7),pp.1253-1264 (Collaboration)
29.	2016/03	Article	Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors. Nucleic acids research 44(5),pp.2058-74 (Collaboration)
30.	2016	Article	Differential regulation of rRNA and tRNA transcription from the rRNA-tRNA composite operon in Escherichia coli. PLoS One (Collaboration)
31.	2016	Article	Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli. PloS one 11(12),pp.e0163057 (Collaboration)
32.	2016	Article	Growth inhibition by external potassium of Escherichia coli lacking PtsN (EIIANtr) is caused by potassium limitation mediated by YcgO. J Bacteriol. (Collaboration)
33.	2016	Article	Transcription factor CecR (YbiH) regulates a set of genes affecting the sensitivity of Escherichia coli against cefoperazone and chloramphenicol. Microbiology (Collaboration)
34.	2016	Article	Transcription factor DecR (YbaO) controls detoxification of L-cysteine in Escherichia coli. Microbiology (Collaboration)
35.	2016	Article	Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors. Nucleic Acids Res. (Collaboration)
36.	2016	Article	Use of a bacterial luciferase monitoring system to estimate real-time dynamics of intracellular metabolism in Escherichia coli. Appl Environ Microbiol. (Collaboration)
37.	2015/11	Article	Expanded roles of two-component response regulator OmpR in Escherichia coli: genomic SELEX search for novel regulation targets. Genes to cells : devoted to molecular & cellular mechanisms 20(11),pp.915-31 (Collaboration)
38.	2015/07	Article	Expanded roles of leucine-responsive regulatory protein in transcription regulation of the Escherichia coli genome: Genomic SELEX screening of the regulation targets. Microbial genomics 1(1),pp.e000001 (Collaboration)
39.	2015	Article	Expanded roles of leucine-responsive regulatory protein in transcription regulation of the Escherichia coli genome: Genomic SELEX screening of the regulation targets. Microbial Genomics. (Collaboration)
40.	2015	Article	Expanded roles of two-component response regulator OmpR in Escherichia coli: Genomic SELEX search for novel regulation targets. Genes Cells. (Collaboration)
41.	2015	Article	Strength and regulation of seven rRNA promoters in Escherichia coli. PLoS ONE. (Collaboration)
42.	2014/08	Article	Intracellular concentrations of 65 species of transcription factors with known regulatory functions in Escherichia coli. Journal of bacteriology 196(15),pp.2718-27 (Collaboration)
43.	2014/07	Article	Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing. mBio 5(4),pp.e01442-14 (Collaboration)
44.	2014/06	Article	Involvement of cAMP-CRP in transcription activation and repression of the pck gene encoding PEP carboxykinase, the key enzyme of gluconeogenesis. FEMS microbiology letters 355(2),pp.93-9 (Collaboration)
45.	2014/05	Article	Roles of cell division control factor SdiA: recognition of quorum sensing signals and modulation of transcription regulation targets. Genes to cells : devoted to molecular & cellular mechanisms 19(5),pp.405-18 (Collaboration)
46.	2014	Article	Intracellular Concentrations of Transcription Factors in Escherichia coli: 65 species with known regulatory functions. Journal of Bacteriology (Collaboration)
47.	2014	Article	Involvement of cAMP-CRP in transcription activation and repression of the pck gene encoding PEP carboxykinase, the key enzyme of gluconeogenesis. FEMS Microbiology Letters. (Collaboration)
48.	2014	Article	Roles of Cell Division Control Factor SdiA: Recognition of Quorum Sensing Signals and Modulation of Transcription Regulation Targets. Genes Cells. (Collaboration)
49.	2014	Article	The Whole Set of Constitutive Promoters Recognized by RNA polymerase RpoD Holoenzyme of Escherichia coli. PLoS ONE (Collaboration)
50.	2014	Article	Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing. MBio. (Collaboration)
51.	2013/12	Article	Screening of promoter-specific transcription factors: multiple regulators for the sdiA gene involved in cell division control and quorum sensing. Microbiology (Reading, England) 159(Pt 12),pp.2501-2512 (Collaboration)
52.	2013/07	Article	Involvement of the ribose operon repressor RbsR in regulation of purine nucleotide synthesis in Escherichia coli. FEMS microbiology letters 344(2),pp.159-65 (Collaboration)
53.	2013/05	Article	Involvement of cyclic AMP receptor protein in regulation of the rmf gene encoding the ribosome modulation factor in Escherichia coli. Journal of bacteriology 195(10),pp.2212-9 (Collaboration)
54.	2013/02	Article	Novel regulator PgrR for switch control of peptidoglycan recycling in Escherichia coli. Genes to cells : devoted to molecular & cellular mechanisms 18(2),pp.123-34 (Collaboration)
55.	2013	Article	A novel regulator PgrR for switch control of peptideglycan recycling in Escherichia coli. Genes Cells. (Collaboration)
56.	2013	Article	Involvement of Cyclic AMP Receptor Protein in Regulation of the rmf Gene Encoding the Ribosome Modulation Factor in Escherichia coli. Journal of Bacteriology. (Collaboration)
57.	2013	Article	Involvement of the Ribose operon Repressor RbsR in Regulation of Purine Nucleotide Synthesis in Escherichia coli. FEMS Microbiology Letters (Collaboration)
58.	2013	Article	Screening of Promoter-Specific Transcription Factors: Multiple Regulators for the sdiA Gene Involved in Cell Division Control and Quorum Sensing. Microbiology. (Collaboration)
59.	2012/12	Article	A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli. MicrobiologyOpen 1(4),pp.381-94 (Collaboration)
60.	2012	Article	A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli. MicrobiologyOpen. 1, 381-394. (2012) (Collaboration)
61.	2011/10	Article	Novel roles of LeuO in transcription regulation of E. coli genome: antagonistic interplay with the universal silencer H-NS. Molecular microbiology 82(2),pp.378-97 (Collaboration)
62.	2011/02	Article	Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli. Journal of bacteriology 193(3),pp.649-59 (Collaboration)
63.	2011	Article	Novel Members of the cAMP Receptor Protein (CRP) Regulon for Transport and Metabolism of Carbon Sources. PLoS ONE. (Collaboration)
64.	2011	Article	Novel Members of the Cra Regulon Involved in Carbon Metabolism in Escherichia coli. Journal of Bacteriology (Collaboration)
65.	2011	Article	Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources. PloS one 6(6),pp.e20081 (Collaboration)
66.	2011	Article	Novel roles of LeuO in transcription regulation of E.coli genome: antagonistic interplay with the universal silencer H-NS. Mol Microbiol. (Collaboration)
67.	2009	Article	Involvement of the leucine response transcription factor LeuO in regulation of the genes for sulfa drug efflux. Journal of Bacteriology. (Collaboration)
68.	2008/09	Article	The uncharacterized transcription factor YdhM is the regulator of the nemA gene, encoding N-ethylmaleimide reductase. Journal of bacteriology 190(17),pp.5890-7 (Collaboration)
69.	2008	Article	The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acid Research (Collaboration)
70.	2007/11	Article	RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines. Molecular microbiology 66(3),pp.744-57 (Collaboration)
71.	2007/08	Article	folA, a new member of the TyrR regulon in Escherichia coli K-12. Journal of bacteriology 189(16),pp.6080-4 (Collaboration)
72.	2007/02	Article	The role of the omega subunit of RNA polymerase in expression of the relA gene in Escherichia coli. FEMS microbiology letters 267(1),pp.51-5 (Collaboration)
73.	2007	Article	folA, a new member of the TyrR regulon in Escherichia coli K-12. Journal of Bacteriology (Collaboration)
74.	2007	Article	RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimidines. Molecular Microbiology (Collaboration)
75.	2007	Article	The role of the omega subunit of RNA polymerase in expression of the relA gene in Escherichia coli. FEMS Microbiology Letters (Collaboration)
76.	2005	Article	Systematic search for the Cra-binding promoters using genomic SELEX system. Genes to Cells (Collaboration)
77.	2004	Article	Classification and strength measurement of stationary phase promoters by use of a newly developed promoter cloning vector. Journal of Bacteriology (Collaboration)
Display 5 items
Display all(77)

■ Research Topics, Consignment Studies & KAKENHI Researches

1.	2022/04～2025/03	Identification of the regulatory network of all functionally unknown transcription factors in Escherichia coli. (Key Word : )
2.	2019/04～2022/03	Identification of the whole set of the constitutive promoters in Escherichia coli (Key Word : )
3.	2016/04～2019/03	Identification of the whole set of constitutive promoters in Escherichia coli (Key Word : )
4.	2012/04～2015/03	Role of acetylation of transcription factor CRP in network of metabolic regulation (Key Word : )
5.	2009～2010	Analysis of Transcriptional Regulation of Genome by Pathogenicity Transcription Factor LeuO. (Key Word : )

■ Web Sites

http://genomeregulation.planet.bindcloud.jp

■ Current Specialized Field

Genome biology

■ KAKENHI Researcher Number

10535230