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. LacZ reporter fusions were constructed to verify Fur-mediated expression regulation.

Transcription Factor Binding Sites


AATGATAATCATTATCAAT
ATTGATAATGATAATCATT
AATGATTATCAATATCGTT
GGTGATAATGATTCTCATT
AATGATAATGATAATCAAT
ATTGAAAATGATTTTCAAA
TATCGGAATCATTTGCATT
AATGATAATCATTATCAAT
ATTGATAATGATAATCATT
AATGATTATCAATATCGTT
GGTGATAATGATTCTCATT
AATGATAATGATAATCAAT
ATTGAAAATGATTTTCAAA
TATCGGAATCATTTGCATT

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
AATGATAATCATTATCAAT dhbA,
... ... dhbA dhbC dhbE dhbB dhbF ybdZ yukJ ald yukF besA
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
ATTGATAATGATAATCATT yxeB,
... ... yxeB yxeC yxeD yxeA yxdM yxdL yxdK yxdJ iolJ iolI iolH iolG iolF iolE iolD iolC iolB mmsA
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AATGATTATCAATATCGTT ydbN,
... ... ydbN ydbM ydbL ydbK ydbJ ydbO ydbP
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
GGTGATAATGATTCTCATT yhfO,
... ... yhfO yhfP yhfQ phoE yhfS yhfT bioY hemAT yhfW yhxC yhzC
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
AATGATAATGATAATCAAT yclN,
... ... yclN yclM yclO yclP yclQ ycnB ycnC
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
ATTGAAAATGATTTTCAAA yusV,
... ... yusV yusU yusT yusS yusR yusQ yusP yusO yusW yusY yusY yusZ mrgA htrB
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer
TATCGGAATCATTTGCATT yusV,
... ... yusV yusU yusT yusS yusR yusQ yusP yusO yusW yusY yusY yusZ mrgA htrB
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - repressor dimer