TF | Y-naming | Publications | Comments | PMID |
AllR |
|
Ishida, Y., Kori, A. and Ishihama, A. Participation of regulator AscG of the β–glucoside utilization operon in regulation of the propionate catabolism operon. J. Bacteriol. 191(19), 6136-6144 (2009) |
|
19633077 |
AllR |
|
Hasegawa A, Ogasawara H, Kori A, Teramoto J, Ishihama A. The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines. Microbiology. 2008 Nov;154(Pt 11):3366-78. doi: 10.1099/mic.0.2008/020016-0. |
|
18957590 |
AscG |
|
Ishida, Y., Kori, A. and Ishihama, A. Participation of regulator AscG of the b–glucoside utilization operon in regulation of the propionate catabolism operon. J. Bacteriol. 191(19), 6136-6144 (2009) |
|
19633077 |
BasR |
|
Ogasawara, H., Shinohara, S. and Ishihama, A. Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli. Microbiology 158, 1482-1492 (2012) |
|
22442305 |
CitB |
|
Yamamoto, K., Matsumoto, F., Oshima, T., Fujita, N., Ogasawara, N. and Ishihama, A. Anaerobic regulation of citrate fermentation by CitAB in Escherichia coli. Biosci. Biotechnol. Biochem. 72(11), 3011-3014 (2008) |
|
18997424 |
CpxR |
|
Yamamoto, K. and Ishihama, A. Characterization of copper-inducible promoters regulated by CpxA/CpxR in Escherichia coli. Bioscience, Biotechnology and Biochemistry 70, 1688-1695 (2006) |
|
16861804 |
Cra |
|
Shimada, T., Yamamoto, K. and Ishihama, A. Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli. J. Bacteriol. 193(3), 649-659 (2011) |
|
21115656 |
Cra |
|
Shimada, T., Fujita, N., Maeda, M. and Ishihama, A. Systematic search for the Cra-binding promoters using genomic SELEX system. Genes Cells 10(9), 907-918 (2005) |
|
16115199 |
CRP |
|
Shimada, T., Fujita, N., Yamamoto, K. and Ishihama, A. Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources. PLoS ONE 6(6): e20081 (2011) |
|
21673794 |
CRP |
|
Nakano M, Ogasawara H, Shimada T, Yamamoto K, Ishihama A. Involvement of cAMP-CRP in transcription activation and repression of the pck gene encoding PEP carboxykinase, the key enzyme of gluconeogenesis. FEMS Microbiol Lett. 2014 Jun;355(2):93-9. doi: 10.1111/1574-6968.12466 |
|
24814025 |
CsgD |
|
Ogasawara, H., Yamamoto, K. and Ishihama, A. Role of the biofilm master regulator CsgD in cross-regulation between biofilm formation and flagellar synthesis. J. Bacteriol. 193(10), 2587-2597 (2011) |
|
21421764 |
CsgD |
|
Ogasawara H, Yamada K, Kori A, Yamamoto K, Ishihama A. Regulation of the Escherichia coli csgD promoter: interplay between five transcription factors. Microbiology. 2010 Aug;156(Pt 8):2470-83. doi: 10.1099/mic.0.039131-0 |
|
20466769 |
Dan |
YgiP |
Teramoto, J., Yoshimura, S.H., Takeyasu, K. and Ishihama, A. A novel nucleoid protein of Escherichia coli induced under anaerobic growth conditions. Nucleic Acids Res. 38(11), 3605-3618 (2010) |
|
20156994 |
H-NS |
|
Shimada T, Bridier A, Briandet R, Ishihama A. Novel roles of LeuO in transcription regulation of E. coli genome: antagonistic interplay with the universal silencer H-NS. Mol Microbiol. 2011 Oct;82(2):378-97. doi: 10.1111/j.1365-2958.2011.07818.x. |
|
21883529 |
LeuO |
|
Shimada, T., Bridier, A., Briandet, R. and Ishihama, A. Novel roles of LeuO in transcription regulation in E. coli: Antagonistic interplay with the universal silencer H-NS. Mol. Microbiol. 82(2), 378-397 (2011) |
|
21883529 |
LeuO |
|
Shimada, T., Yamamoto, K. and Ishihama, A. Involvement of the leucine response transcription factor LeuO in regulation of the genes for sulfa drug efflux. J. Bacteriol. 191(14), 4562-4571 (2009) |
|
19429622 |
Lrp |
|
Shimada T, Saito N, Maeda M, Tanaka K, Ishihama A. Expanded roles of leucine-responsive regulatory protein in transcription regulation of the Escherichia coli genome: Genomic SELEX screening of the regulation targets. Microbial Genomics.(2015) 1: doi:10.1099/mgen.0.000001 |
|
|
MntR |
|
Yamamoto K, Ishihama A, Busby SJ, Grainger DC. The Escherichia coli K-12 MntR miniregulon includes dps, which encodes the major stationary-phase DNA-binding protein. J. Bacteriol. 193(6), 1477-1480 (2011) |
ChIP-chip |
21239586 |
ModE |
|
Kurata T, Katayama A, Hiramatsu M, Kiguchi Y, Takeuchi M, Watanabe T, Ogasawara H, Ishihama A, Yamamoto K. Identification of the set of genes, including nonannotated morA, under the direct control of ModE in Escherichia coli. J Bacteriol. 2013 Oct;195(19):4496-505. doi: 10.1128/JB.00304-13 |
|
23913318 |
NemR |
YdhM |
Umezawa Y, Shimada T, Kori A, Yamada K, Ishihama A The uncharacterized transcription factor YdhM is the regulator of the nemA gene, encoding N-ethylmaleimide reductase. J. Bacteriol. 190(17), 5890-5897 (2008) |
|
18567656 |
NimR |
YeaM |
Ogasawara H, Ohe S, Ishihama A. Role of transcription factor NimR (YeaM) in sensitivity control of Escherichia coli to 2-nitroimidazole. FEMS Microbiol Lett. 2015 Jan;362(1):1-8. doi: 10.1093/femsle/fnu013 |
|
25790494 |
OmpR |
|
Shimada T, Takada H, Yamamoto K, Ishihama A. Expanded roles of two-component response regulator OmpR in Escherichia coli: genomic SELEX search for novel regulation targets. Genes Cells. 2015 Nov;20(11):915-31. doi: 10.1111/gtc.12282 |
|
26332955 |
PdhR |
|
Ogasawara, H., Ishida, Y., Yamada, K., Yamamoto, K. and Ishihama, A. PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli. J. Bacteriol. 189(15), 5534-5541 (2007) |
|
17513468 |
PgrR |
YcjZ |
Shimada, T., Yamazaki, K. and Ishihama, A. Novel regulator PgrR for switch control of peptidoglycan recycling in Escherichia coli. Genes Cells, 18(2),123-34 (2013) |
|
23301696 |
RcdA |
YbjK |
Shimada, T., Katayama, Y., Kawakita, S., Ogasawara, H., Nakano, M., Yamanaka, K. and Ishihama, A. A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli. Microbiologyopen 1(4), 381-394 (2012) doi: 10.1002/bo3.42 (2012) |
|
23233451 |
RpoD |
|
Shimada T., Yamazaki Y., Tanaka K., Ishihama A. The whole set of constitutive promoters recognized by RNA polymerase RpoD holoenzyme of Escherichia coli. PLoS One. 2014 Mar 6;9(3):e90447. doi: 10.1371/journal.pone.0090447. eCollection 2014. |
|
24603758 |
RpoD |
|
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. Unprecedented high-resolution view of bacterial operon architecture revealed by RNA sequencing. MBio. 2014 Jul 8;5(4):e01442-14. doi: 10.1128/mBio.01442-14. |
|
25006232 |
RstB |
|
Ogasawara, H., Hasegawa, A., Kanda, E., Miki, T., Yamamoto, K. and Ishihama, A. Genomic SELEX search for target genes under the control of PhoQP-RstBA signal relay cascade. J. Bacteriol. 189(13), 4791-4799 (2007) |
|
17468243 |
RutR |
YcdC |
Shimada, T., Hirao, K., Kori, A., Yamamoto, K. and Ishihama, A. RutR is the uracil/thymine-sensing master regulator of a set of genes for synthesis and degradation of pyrimdines. Mol. Microbiol. 66(3), 744-757 (2007) |
|
17919280 |
RutR |
YcdC |
Shimada, T., Ishihama, A., Busby, S.J.W. and Grainger, D.C. The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acids Res. 36(12), 3950-3955 (2008) |
|
18515344 |
SdiA |
|
Shimada 1, Shimada K, Matsui M, Kitai Y, Igarashi J, Suga H, Ishihama A. Roles of cell division control factor SdiA: recognition of quorum sensing signals and modulation of transcription regulation targets. Genes Cells. 2014 May;19(5):405-18. doi: 10.1111/gtc.12139 |
|
24645791 |
SutR |
YdcN |
Yamamoto K., Nakano M., Ishihama A. Regulatory role of transcription factor SutR (YdcN) in sulfur utilization in Escherichia coli. Microbiology. 2015 Jan;161(Pt 1):99-111. doi: 10.1099/mic.0.083550-0. Epub 2014 Nov 18. |
|
25406449 |
TyrR |
|
Yang, J., Ogawa, Y., Camakaris, H., Shimada, T., Ishihama, A. and Pittard, A.J. folA a new member of the TyrR regulon in Escherichia coli K-12. J. Bacteriol. 189(16), 6080-6084,(2007) |
|
17557822 |
YdeO |
|
Yamanaka Y, Oshima T, Ishihama A, Yamamoto K. Characterization of the YdeO regulon in Escherichia coli. PLoS One. 2014 Nov 6;9(11):e111962. doi: 10.1371/journal.pone.0111962 |
|
25375160 |
YedW |
|
Urano H, Umezawa Y, Yamamoto K, Ishihama A, Ogasawara H. Cooperative regulation of the common target genes between H2O2-sensing YedVW and Cu2+-sensing CusSR in Escherichia coli. Microbiology. 2015 Apr;161(Pt 4):729-38. doi: 10.1099/mic.0.000026. |
|
25568260 |