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
YodB [O34844, 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

Northern blot analysis using a YodB deletion mutant demonstrated negative control of catDE operon expression by YodB. Northern blot experiments were further sued to determine the Cys7 residue is critical in YodB 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 the YodB binding sites for catD, yocJ, yodC and spx further characterized the YodB consensus sequence. Repression of yocJ, yodC and spx were previously reported in other papers.

Transcription Factor Binding Sites


TACTTGACGTAAACA
TACTATTTGTAAGTA
TACATTTAGTAAGCT
TACTTTTTTATAGTA
TACTTGACGTAAACA
TACTATTTGTAAGTA
TACATTTAGTAAGCT
TACTTTTTTATAGTA

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
TACTTGACGTAAACA catE, catD,
... ... catE catD yfiF
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
TACTATTTGTAAGTA yocJ
... ... yocJ
Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - repressor not specified
TACATTTAGTAAGCT yodC,
... ... yodC yodB
Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - repressor not specified
TACTTTTTTATAGTA spxA
... ... spxA
Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - repressor not specified