Curation Information

Publication
The paralogous MarR/DUF24-family repressors YodB and CatR control expression of the catechol dioxygenase CatE in Bacillus subtilis.;Chi BK, Kobayashi K, Albrecht D, Hecker M, Antelmann H;Journal of bacteriology 2010 Sep; 192(18):4571-81 [20639328]
TF
CatR [O32238, view regulon]
Reported TF sp.
Bacillus subtilis subsp. subtilis str. 168
Reported site sp.
Bacillus subtilis subsp. subtilis str. 168
Created by
Grace Chandler
Curation notes
-

Experimental Process

Transcription Factor arrays utilizing a catE-lacZ fusion identified CatR(YvaP) as a repressor of the catDE operon. Microarray analysis validated catDE repression by CatR. Northern blot analysis using a CatR deletion mutant demonstrated negative control of catDE operon expression by CatR. Northern blot experiments were further sued to determine the Cys7 residue is critical in CatR binding. DNase I footprinting localized overlapping CatR/YodB binding sites in the catDE promoter region. Site-directed mutagenesis in conjunction with EMSA confirmed the specificity of the binding regions by showing that as IR sequences were deleted, binding was reduced. MALDI-TOF, Western blot and Northern blot experiments were performed, proving that CatR and YodB do not form a complex. Multiple sequence alignment using CatR binding sites from other Bacillus species further characterized the CatR consensus sequence.

Transcription Factor Binding Sites


TTACTTGACGTAA
TTACATTAAGTAA
TTACTTGACGTAA
TTACATTAAGTAA

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
TTACTTGACGTAA catE, catD,
... ... catE catD yfiF
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) - Experimental technique details MALDI-TOF Mass Spectrometry (ECO:0005527) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Western blot (quantitative) expression analysis (ECO:0000279) - repressor not specified
TTACATTAAGTAA catD, catE,
... ... catD catE yfiF
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) - Experimental technique details MALDI-TOF Mass Spectrometry (ECO:0005527) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Western blot (quantitative) expression analysis (ECO:0000279) - repressor not specified