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shows TF lists uploaded
TF namedate
ArcA2013-12-10
ArgP2012-08-17
ArgPArg2013-12-11
ArgPLys2013-12-11
ArgR2013-12-10
AscG2013-12-10
AsnC2013-12-10
BasR2015-06-30
BasRAcP2013-12-11
BetI2013-12-11
BetICholine2013-12-11
CbpB2012-08-17
CitB2015-06-30
Cra2013-02-04
CraFruBP2013-12-10
CreBP2013-12-10
CRP2013-02-04
CRPnoncAMP2013-12-10
CynR2013-12-10
CynRcyanate2013-12-10
CytR2015-06-30
Dan2015-06-30
DcuRP2013-12-10
DeoR2013-12-10
DeoT2013-12-10
DhaR2016-05-09
DicA2013-12-10
Dps2012-08-17
DsdC2013-12-10
DsdCSer2013-12-10
EbgR2013-12-10
EvgA2013-12-10
EvgAP2013-12-10
ExuR2013-12-10
Fis2012-08-17
FlhA2013-12-10
FlhAformate2013-12-10
FrlR2016-05-09
Fur2013-12-10
GalR2013-12-11
GusR2013-12-10
HcaR2013-12-11
Hfq2013-12-10
HipB2013-12-11
HNS2015-07-01
HNSHha2013-12-10
HU2013-12-10
IclR2013-12-10
IHF2012-08-17
IlvY2013-12-11
IlvYhydroxybutyrate2013-12-11
KdpE2013-12-11
KdpEP2013-12-10
LctR2013-12-11
LctRlactate2013-12-11
LeuO2015-07-01
LrhA2013-12-11
Lrp2013-12-10
Lrpleucine2013-12-10
MalI2013-12-11
MalImaltose2013-12-11
MarR2013-12-11
MarRsalicylate2013-12-11
Mlc2013-12-11
MlrA2013-12-11
MntR2015-07-01
MntRMn2013-12-10
ModE2013-12-10
ModEMo2013-12-10
MrlA2013-12-10
NadR2013-12-11
NadRNMN2013-12-11
NanR2013-12-11
NanRnana2013-12-11
NhaR2013-12-10
NhaRNa2013-12-11
NorR2013-12-11
NtrC2013-12-10
OmpR2013-12-11
OxyR2013-12-10
PepA2013-12-11
PgrR2013-12-10
PhnF2013-12-11
PhoB2013-12-11
PspF2013-12-10
PutA2013-12-11
PutAProline2013-12-11
QseA2013-12-10
QseAPHBA2013-12-10
QseB2013-12-11
QseBP2013-12-11
RbsR2013-12-11
RbsRribose2013-12-11
RcdA2013-12-10
RcsB2013-12-10
RpiR2013-12-11
RpoD2012-08-17
RpoE2017-04-25
RpoF2017-04-25
RpoH2017-04-25
RpoS2017-04-25
RpoZ_ChIP2018-01-23
RutR2015-07-01
SdiA2013-12-10
SdiAA2013-12-10
SdiAF2013-12-10
SdiAK2013-12-10
SdiAOC2013-12-10
SfsA2013-12-11
SfsAmaltose2013-12-11
SlmA2013-12-11
SoxRDTT2013-12-11
SoxRFe2013-12-11
SoxSDTT2013-12-11
SoxSFe2013-12-11
SrlR2013-12-10
TorR2013-12-11
TorRP2013-12-11
TreR2013-12-11
TreRtrehalose2013-12-11
UlaR2013-12-11
UlaRP2013-12-11
UvrY2013-12-11
UvrYP2013-12-11
uxuR2013-12-11
UxuRglucronate2013-12-11
YagI2016-05-09
YahA2013-12-11
YahAcdiGMP2013-12-10
YahB2016-05-09
YbaO2013-12-11
YbiH2013-12-10
YcaN2016-05-09
YcfQ2013-12-10
YciT2013-12-11
YdcN2013-12-11
YdfH2013-12-10
YeaM2013-12-11
YedW2013-12-11
YegW2016-05-09
YfaX2016-05-09
YfeR2016-05-09
YfgA2013-12-10
YfhH2016-05-09
YgfB2013-12-10
YgfI2016-05-09
YheR2013-12-10
YiaJ2016-05-09
YiaU2016-05-09
YidZ2016-05-09
YifA2013-12-10
YihW2018-05-16
YijO2013-12-10
YjgJ2013-12-11
YjiE2013-12-11
YkgA2013-12-10
YkgD2013-12-10
YneJ2016-05-09
YnfL2016-05-09
YpdB2013-12-10
YpdBP2013-12-10
ZraR2013-12-11
Zur2013-12-10
ZurZn2013-12-10

List of Publications from TF-SELEX Research Group


TF name (space separated):

   TF   Y-namingPublicationsCommentsPMID
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