Curation Information

Publication
Global analysis of the Bacillus subtilis Fur regulon and the iron starvation stimulon.;Baichoo N, Wang T, Ye R, Helmann JD;Molecular microbiology 2002 Sep; 45(6):1613-29 [12354229]
TF
Fur [P54574, view regulon]
Reported TF sp.
Bacillus subtilis subsp. subtilis str. 168
Reported site sp.
Bacillus subtilis subsp. subtilis str. 168
Created by
Dinara Sagitova
Curation notes
-

Experimental Process

DNA microarrays were used to identify genes whose expression is regulated by Fur. EMSAs were done to confirm binding of Fur to its target promoters. DNase I footprinting analysis was performed to localize the binding sites on promoters of the identified genes.

Transcription Factor Binding Sites


AATGAAAATCATTATCATT
ATTGAAAATCATTATCAAC
ATTGATAATAGTTATCAAT
AATGATAATGAATTTCAAT
ATTGAAAATGATTATCAAT
AAAGAGAATCATTATCATC
ATTGAGAAATATTATCAGT
AATGATAATCATTTTCAAT
TGTGATAATGATTCTCATT
GATTAGGCTAAGTATCATA
AATGATAATCATTTTCAAT
AATGAAAATCATTATCATT
ATTGAAAATCATTATCAAC
ATTGATAATAGTTATCAAT
AATGATAATGAATTTCAAT
ATTGAAAATGATTATCAAT
AAAGAGAATCATTATCATC
ATTGAGAAATATTATCAGT
AATGATAATCATTTTCAAT
TGTGATAATGATTCTCATT
GATTAGGCTAAGTATCATA
AATGATAATCATTTTCAAT

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
AATGAAAATCATTATCATT ykuN,
... ... ykuN dapL dapH ykuP ykuO ykuJ ykuK ykzF ykuL ccpC ykuS ykuT
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
ATTGAAAATCATTATCAAC ykuN,
... ... ykuN ccpC ykuL ykzF ykuK ykuJ ykuO ykuP dapH dapL ykuS ykuT
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
ATTGATAATAGTTATCAAT feuA, feuB, feuC, ybbA,
... ... feuA feuB feuC ybbA ybaS ybaR ybbB
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AATGATAATGAATTTCAAT yfiY,
... ... yfiY mprF yfiZ yfhA yfhB yfhC yfhD yfhE yfhF recX yfhH yfhI sspK yfhJ yfhK yfhL yfhM
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
ATTGAAAATGATTATCAAT ybbB,
... ... ybbB feuA feuB feuC ybbA ybaS ybaR ybbC ybbD ybbE ybbF ybbH murQ ybbJ ybbK
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AAAGAGAATCATTATCATC fhuD,
... ... fhuD fhuB fhuG fhuC
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
ATTGAGAAATATTATCAGT ywjA,
... ... ywjA ywjB ywjC uvsE clsB ywiE
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AATGATAATCATTTTCAAT ywbI,
... ... ywbI efeU efeM efeN thiE thiM ywbH lrgB ywbF ywbE ywbD ywbC ywbB ywbA
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
TGTGATAATGATTCTCATT yfmC,
... ... yfmC yfmD yfmE yfmF yfmB yfmA yflT
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
GATTAGGCTAAGTATCATA yfkM,
... ... yfkM yfkN yfkO treR treA treP yfkL yfkK
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AATGATAATCATTTTCAAT yfhC,
... ... yfhC yfhB yfhA yfiZ yfiY mprF yfhD yfhE yfhF recX yfhH yfhI sspK yfhJ yfhK yfhL yfhM
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer