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Regulatory roles of pyruvate-sensing two-component system PyrSR (YpdAB) in Escherichia coli K-12.

Miyake Y, Inaba T, Watanabe H, Teramoto J, Yamamoto K, Ishihama A.

FEMS Microbiol Lett. 2019 Jan 1;366(2). doi: 10.1093/femsle/fnz009.


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.

Microbiology. 2019 Jan;165(1):78-89. doi: 10.1099/mic.0.000740. Epub 2018 Oct 29.


Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of Escherichia coli to Stationary Phase.

Yoshida H, Shimada T, Ishihama A.

mSystems. 2018 Sep 11;3(5). pii: e00057-18. doi: 10.1128/mSystems.00057-18. eCollection 2018 Sep-Oct.


Genomic SELEX Screening of Regulatory Targets of Escherichia coli Transcription Factors.

Shimada T, Ogasawara H, Ishihama A.

Methods Mol Biol. 2018;1837:49-69. doi: 10.1007/978-1-4939-8675-0_4.


Dimerization site 2 of the bacterial DNA-binding protein H-NS is required for gene silencing and stiffened nucleoprotein filament formation.

Yamanaka Y, Winardhi RS, Yamauchi E, Nishiyama SI, Sowa Y, Yan J, Kawagishi I, Ishihama A, Yamamoto K.

J Biol Chem. 2018 Jun 15;293(24):9496-9505. doi: 10.1074/jbc.RA117.001425. Epub 2018 Apr 25.


Single-target regulators form a minor group of transcription factors in Escherichia coli K-12.

Shimada T, Ogasawara H, Ishihama A.

Nucleic Acids Res. 2018 May 4;46(8):3921-3936. doi: 10.1093/nar/gky138.


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.

mSystems. 2018 Feb 13;3(1). pii: e00172-17. doi: 10.1128/mSystems.00172-17. eCollection 2018 Jan-Feb.


Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia coli K-12.

Shimada T, Momiyama E, Yamanaka Y, Watanabe H, Yamamoto K, Ishihama A.

FEMS Microbiol Lett. 2017 Dec 1;364(22). doi: 10.1093/femsle/fnx220.


Building a complete image of genome regulation in the model organism Escherichia coli.

Ishihama A.

J Gen Appl Microbiol. 2018 Jan 15;63(6):311-324. doi: 10.2323/jgam.2017.01.002. Epub 2017 Sep 12. Review.


The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase.

Shimada T, Tanaka K, Ishihama A.

PLoS One. 2017 Jun 30;12(6):e0179181. doi: 10.1371/journal.pone.0179181. eCollection 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.

FEBS Lett. 2017 Jul;591(13):2019-2031. doi: 10.1002/1873-3468.12713. Epub 2017 Jun 26.


Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli.

Takada H, Shimada T, Dey D, Quyyum MZ, Nakano M, Ishiguro A, Yoshida H, Yamamoto K, Sen R, Ishihama A.

PLoS One. 2016 Dec 22;11(12):e0163057. doi: 10.1371/journal.pone.0163057. eCollection 2016.


Cross-regulation between two common ancestral response regulators, HprR and CusR, in Escherichia coli.

Urano H, Yoshida M, Ogawa A, Yamamoto K, Ishihama A, Ogasawara H.

Microbiology. 2017 Feb;163(2):243-252. doi: 10.1099/mic.0.000410. Epub 2017 Mar 9.


Transcription factor DecR (YbaO) controls detoxification of L-cysteine in Escherichia coli.

Shimada T, Tanaka K, Ishihama A.

Microbiology. 2016 Sep;162(9):1698-1707. doi: 10.1099/mic.0.000337. Epub 2016 Jul 19.


Effect of Spermidine Analogues on Cell Growth of Escherichia coli Polyamine Requiring Mutant MA261.

Yoshida T, Sakamoto A, Terui Y, Takao K, Sugita Y, Yamamoto K, Ishihama A, Igarashi K, Kashiwagi K.

PLoS One. 2016 Jul 19;11(7):e0159494. doi: 10.1371/journal.pone.0159494. eCollection 2016.


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.

Microbiology. 2016 Jul;162(7):1253-1264. doi: 10.1099/mic.0.000292. Epub 2016 Apr 25.


TDP-43 binds and transports G-quadruplex-containing mRNAs into neurites for local translation.

Ishiguro A, Kimura N, Watanabe Y, Watanabe S, Ishihama A.

Genes Cells. 2016 May;21(5):466-81. doi: 10.1111/gtc.12352. Epub 2016 Feb 24.


Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors.

Ishihama A, Shimada T, Yamazaki Y.

Nucleic Acids Res. 2016 Mar 18;44(5):2058-74. doi: 10.1093/nar/gkw051. Epub 2016 Feb 3.


Strength and Regulation of Seven rRNA Promoters in Escherichia coli.

Maeda M, Shimada T, Ishihama A.

PLoS One. 2015 Dec 30;10(12):e0144697. doi: 10.1371/journal.pone.0144697. eCollection 2015.



Ishihama A.

Seikagaku. 2015 Oct;87(5):499. Japanese. No abstract available.


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.

Genes Cells. 2015 Nov;20(11):915-31. doi: 10.1111/gtc.12282. Epub 2015 Sep 2.


Growth phase dependent changes in the structure and protein composition of nucleoid in Escherichia coli.

Talukder A, Ishihama A.

Sci China Life Sci. 2015 Sep;58(9):902-11. doi: 10.1007/s11427-015-4898-0. Epub 2015 Jul 24.


Expanded roles of leucine-responsive regulatory protein in transcription regulation of the Escherichia coli genome: Genomic SELEX screening of the regulation targets.

Shimada T, Saito N, Maeda M, Tanaka K, Ishihama A.

Microb Genom. 2015 Jul 15;1(1):e000001. doi: 10.1099/mgen.0.000001. eCollection 2015 Jul.


Cross talk in promoter recognition between six NarL-family response regulators of Escherichia coli two-component system.

Yoshida M, Ishihama A, Yamamoto K.

Genes Cells. 2015 Jul;20(7):601-12. doi: 10.1111/gtc.12251. Epub 2015 May 26.


Three members of polyamine modulon under oxidative stress conditions: two transcription factors (SoxR and EmrR) and a glutathione synthetic enzyme (GshA).

Sakamoto A, Terui Y, Yoshida T, Yamamoto T, Suzuki H, Yamamoto K, Ishihama A, Igarashi K, Kashiwagi K.

PLoS One. 2015 Apr 21;10(4):e0124883. doi: 10.1371/journal.pone.0124883. eCollection 2015.


Role of transcription factor NimR (YeaM) in sensitivity control of Escherichia coli to 2-nitroimidazole.

Ogasawara H, Ohe S, Ishihama A.

FEMS Microbiol Lett. 2015 Jan;362(1):1-8. doi: 10.1093/femsle/fnu013. Epub 2014 Dec 4.


Cooperative regulation of the common target genes between H₂O₂-sensing YedVW and Cu²⁺-sensing CusSR in Escherichia coli.

Urano H, Umezawa Y, Yamamoto K, Ishihama A, Ogasawara H.

Microbiology. 2015 Apr;161(Pt 4):729-38. doi: 10.1099/mic.0.000026. Epub 2015 Jan 7.


Regulatory role of transcription factor SutR (YdcN) in sulfur utilization in Escherichia coli.

Yamamoto K, Nakano M, Ishihama A.

Microbiology. 2015 Jan;161(Pt 1):99-111. doi: 10.1099/mic.0.083550-0. Epub 2014 Nov 18.


Characterization of the YdeO regulon in Escherichia coli.

Yamanaka Y, Oshima T, Ishihama A, Yamamoto K.

PLoS One. 2014 Nov 6;9(11):e111962. doi: 10.1371/journal.pone.0111962. eCollection 2014.


Induction of the Escherichia coli yijE gene expression by cystine.

Yamamoto K, Nonaka G, Ozawa T, Takumi K, Ishihama A.

Biosci Biotechnol Biochem. 2015;79(2):218-22. doi: 10.1080/09168451.2014.972328. Epub 2014 Oct 27.


Expression levels of transcription factors in Escherichia coli: growth phase- and growth condition-dependent variation of 90 regulators from six families.

Yamamoto K, Watanabe H, Ishihama A.

Microbiology. 2014 Sep;160(Pt 9):1903-13. doi: 10.1099/mic.0.079889-0. Epub 2014 Jul 18.


Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing.

Conway T, Creecy JP, Maddox SM, Grissom JE, Conkle TL, Shadid TM, Teramoto J, San Miguel P, Shimada T, Ishihama A, Mori H, Wanner BL.

MBio. 2014 Jul 8;5(4):e01442-14. doi: 10.1128/mBio.01442-14.


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, Fujita N.

J Bacteriol. 2014 Aug;196(15):2718-27. doi: 10.1128/JB.01579-14. Epub 2014 May 16.


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.

FEMS Microbiol Lett. 2014 Jun;355(2):93-9. doi: 10.1111/1574-6968.12466. Epub 2014 May 27.


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.

Genes Cells. 2014 May;19(5):405-18. doi: 10.1111/gtc.12139. Epub 2014 Mar 19.


The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli.

Shimada T, Yamazaki Y, Tanaka K, Ishihama A.

PLoS One. 2014 Mar 6;9(3):e90447. doi: 10.1371/journal.pone.0090447. eCollection 2014. Erratum in: PLoS One. 2014;9(6):e100908.


Role for σ38 in prolonged survival of Escherichia coli in Drosophila melanogaster.

Shiratsuchi A, Shimamoto N, Nitta M, Tuan TQ, Firdausi A, Gawasawa M, Yamamoto K, Ishihama A, Nakanishi Y.

J Immunol. 2014 Jan 15;192(2):666-75. doi: 10.4049/jimmunol.1300968. Epub 2013 Dec 13.


Repression of flagellar genes in exponential phase by CsgD and CpxR, two crucial modulators of Escherichia coli biofilm formation.

Dudin O, Geiselmann J, Ogasawara H, Ishihama A, Lacour S.

J Bacteriol. 2014 Feb;196(3):707-15. doi: 10.1128/JB.00938-13. Epub 2013 Nov 22.


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.

Microbiology. 2013 Dec;159(Pt 12):2501-12. doi: 10.1099/mic.0.067538-0. Epub 2013 Sep 11.


Structural change of DNA induced by nucleoid proteins: growth phase-specific Fis and stationary phase-specific Dps.

Sato YT, Watanabe S, Kenmotsu T, Ichikawa M, Yoshikawa Y, Teramoto J, Imanaka T, Ishihama A, Yoshikawa K.

Biophys J. 2013 Aug 20;105(4):1037-44. doi: 10.1016/j.bpj.2013.07.025.


Identification of the set of genes, including nonannotated morA, under the direct control of ModE in Escherichia coli.

Kurata T, Katayama A, Hiramatsu M, Kiguchi Y, Takeuchi M, Watanabe T, Ogasawara H, Ishihama A, Yamamoto K.

J Bacteriol. 2013 Oct;195(19):4496-505. doi: 10.1128/JB.00304-13. Epub 2013 Aug 2.


Involvement of EnvZ-OmpR two-component system in virulence control of Escherichia coli in Drosophila melanogaster.

Pukklay P, Nakanishi Y, Nitta M, Yamamoto K, Ishihama A, Shiratsuchi A.

Biochem Biophys Res Commun. 2013 Aug 23;438(2):306-11. doi: 10.1016/j.bbrc.2013.07.062. Epub 2013 Jul 22.


Involvement of the ribose operon repressor RbsR in regulation of purine nucleotide synthesis in Escherichia coli.

Shimada T, Kori A, Ishihama A.

FEMS Microbiol Lett. 2013 Jul;344(2):159-65. doi: 10.1111/1574-6968.12172. Epub 2013 Jun 3.


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.

J Bacteriol. 2013 May;195(10):2212-9. doi: 10.1128/JB.02279-12. Epub 2013 Mar 8.


Novel regulator PgrR for switch control of peptidoglycan recycling in Escherichia coli.

Shimada T, Yamazaki K, Ishihama A.

Genes Cells. 2013 Feb;18(2):123-34. doi: 10.1111/gtc.12026. Epub 2013 Jan 10.


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.

Microbiologyopen. 2012 Dec;1(4):381-94. doi: 10.1002/mbo3.42. Epub 2012 Oct 8.


The nucleoid-associated protein Dan organizes chromosomal DNA through rigid nucleoprotein filament formation in E. coli during anoxia.

Lim CJ, Lee SY, Teramoto J, Ishihama A, Yan J.

Nucleic Acids Res. 2013 Jan;41(2):746-53. doi: 10.1093/nar/gks1126. Epub 2012 Nov 23.


Prokaryotic genome regulation: a revolutionary paradigm.

Ishihama A.

Proc Jpn Acad Ser B Phys Biol Sci. 2012;88(9):485-508. Review.


Enhanced biofilm formation and/or cell viability by polyamines through stimulation of response regulators UvrY and CpxR in the two-component signal transducing systems, and ribosome recycling factor.

Sakamoto A, Terui Y, Yamamoto T, Kasahara T, Nakamura M, Tomitori H, Yamamoto K, Ishihama A, Michael AJ, Igarashi K, Kashiwagi K.

Int J Biochem Cell Biol. 2012 Nov;44(11):1877-86. doi: 10.1016/j.biocel.2012.07.010. Epub 2012 Jul 17.


Induction of YdeO, a regulator for acid resistance genes, by ultraviolet irradiation in Escherichia coli.

Yamanaka Y, Ishihama A, Yamamoto K.

Biosci Biotechnol Biochem. 2012;76(6):1236-8. Epub 2012 Jun 7.

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