Curation Information

Publication
The Fur regulon in anaerobically grown Salmonella enterica sv. Typhimurium: identification of new Fur targets.;Troxell B, Fink RC, Porwollik S, McClelland M, Hassan HM;BMC microbiology 2011 Oct 21; 11():236 [22017966]
TF
Fur [Q7CQY3, view regulon]
Reported TF sp.
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Reported site sp.
Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Created by
Dinara Sagitova
Curation notes
-

Experimental Process

DNA microarray analysis and the β-galactosidase assay were used to identify differentially expressed genes. Putative Fur-binding sites of each gene were identified and the sequence logo was constructed.

Transcription Factor Binding Sites


GAAATAGATATAATTTAT
AAATTGAGAATAGTTATT
ATAATGCCCATCGTTTCC
AAACTGATAAACATTGCC
CTGATGCTCATCATTATT
ATAAACATTATAATTATA
CAAATAACAACAATTTAA
AAAGTAAAAATCATTGGC
GAAATAGATATAATTTAT
AAATTGAGAATAGTTATT
ATAATGCCCATCGTTTCC
AAACTGATAAACATTGCC
CTGATGCTCATCATTATT
ATAAACATTATAATTATA
CAAATAACAACAATTTAA
AAAGTAAAAATCATTGGC

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
GAAATAGATATAATTTAT ynaF,
... ... ynaF STM14_1996 nifJ STM14_1998
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - activator dimer
AAATTGAGAATAGTTATT STM14_2693,
... ... STM14_2693 STM14_2692 sanA yeiA
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - activator dimer
ATAATGCCCATCGTTTCC eutC,
... ... eutC eutB eutL eutK eutR eutA eutH
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - activator dimer
AAACTGATAAACATTGCC eutB,
... ... eutB eutC eutL eutK eutR eutA eutH
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - activator dimer
CTGATGCTCATCATTATT STM14_4330,
... ... STM14_4330 STM14_4329 STM14_4331
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - activator dimer
ATAAACATTATAATTATA STM14_4449,
... ... STM14_4449 STM14_4448 yibL STM14_4450
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - activator dimer
CAAATAACAACAATTTAA dcuA,
... ... dcuA aspA STM14_5203
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - activator dimer
AAAGTAAAAATCATTGGC aspA,
... ... aspA STM14_5203 fxsA
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details PSSM site search (ECO:0005659) - activator dimer