Curation Information

Publication
Identification and molecular characterization of the Mg2+ stimulon of Escherichia coli.;Minagawa S, Ogasawara H, Kato A, Yamamoto K, Eguchi Y, Oshima T, Mori H, Ishihama A, Utsumi R;Journal of bacteriology 2003 Jul; 185(13):3696-702 [12813061]
TF
PhoP [P23836, view regulon]
Reported TF sp.
Escherichia coli str. K-12 substr. W3110
Reported site sp.
Escherichia coli str. K-12 substr. W3110
Created by
Erill Lab
Curation notes
-
External databases
Custom URL (http://www.nara.kindai.ac.jp/nogei/seiken/array.html) .

Experimental Process

Analysis of microarray data for repressed genes. Putative PhoP sites indentified by consensus search on promoter regions of repressed genes. Regulation by Mg+ further validated by S1 nuclease assays. Specific PhoP binding validated by EMSA. Binding site further identified by DNAse footprinting.

Transcription Factor Binding Sites


TGTTTAGGTTTTGTTTA
TGTTTAGGGTTTGTTTA
TGTTTAGAAACGATTGA
TGTTTATAATTGGTTGA
TAGTTAGGCGCTGTTTA
GGTTTATCGTTGGTTTA
GGTTTATTTAATGTTTA
TGTTTAGGTTTTGTTTA
TGTTTAGGGTTTGTTTA
TGTTTAGAAACGATTGA
TGTTTATAATTGGTTGA
TAGTTAGGCGCTGTTTA
GGTTTATCGTTGGTTTA
GGTTTATTTAATGTTTA

Quantitative data format: Quantitative EMSA. Range: 0.88-9.66

TGTTTAGGTTTTGTTTA 1.0
TGTTTAGGGTTTGTTTA 0.94
TGTTTAGAAACGATTGA 2.37
TGTTTATAATTGGTTGA 2.3
TAGTTAGGCGCTGTTTA 2.25
GGTTTATCGTTGGTTTA 0.88
GGTTTATTTAATGTTTA 1.54

Gene Regulation

Regulated genes for each binding site are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation. For each indvidual site, experimental techniques used to determine the site are also given.

Site sequence Regulated genes Gene diagram Experimental techniques TF function TF type
TGTTTAGGTTTTGTTTA yrbL,
... ... yrbL yhcC arcB ryhA elbB mtgA yrbG kdsD kdsC yrbK yhbN yhbG rpoN yhbH ptsN yhbJ npr
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details S1 nuclease protection (ECO:0005666) - activator dimer
TGTTTAGGGTTTGTTTA borD,
... ... borD ybcV essD ybcS rzpD rzoD
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details S1 nuclease protection (ECO:0005666) - activator dimer
TGTTTAGAAACGATTGA rstB, rstA,
... ... rstB rstA ydgI folM ydgC fumA fumC tus
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details S1 nuclease protection (ECO:0005666) - activator dimer
TGTTTATAATTGGTTGA slyB,
... ... slyB slyA ydgR gst pdxY tyrS pdxH ydhA ydhH
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details S1 nuclease protection (ECO:0005666) - activator dimer
TAGTTAGGCGCTGTTTA yebO,
... ... yebO kdgR yobH yobG
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details S1 nuclease protection (ECO:0005666) - activator dimer
GGTTTATCGTTGGTTTA mgtA,
... ... mgtA treC treB treR
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details S1 nuclease protection (ECO:0005666) - activator dimer
GGTTTATTTAATGTTTA phoQ, phoP,
... ... phoQ phoP ymfC ymfB trmU hflD purB pepT ycfD
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details S1 nuclease protection (ECO:0005666) - activator dimer