Curation Information

Publication
Integration of metabolism and virulence by Clostridium difficile CodY.;Dineen SS, McBride SM, Sonenshein AL;Journal of bacteriology 2010 Oct; 192(20):5350-62 [20709897]
TF
CodY [Q18BE1, view regulon]
Reported TF sp.
Clostridium difficile 630
Reported site sp.
Clostridium difficile 630
Created by
Dinara Sagitova
Curation notes
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Experimental Process

CodY-regulated genes were identified by DNA microarray analysis. qRT-PCR analyses were performed to confirm the gene expression results obtained from the microarray analysis. EMSAs were done to validate that CodY directly interacts with the promoters of the identified genes. DNase I footprinting was used to identify specific binding sites for CodY.

Transcription Factor Binding Sites


AATTCTCTGAAACAC
AAGTTTTTGATATTT
AATTAACAGAATCTT
AATCTTTATACAATT
AATTCTCTGAAACAC
AAGTTTTTGATATTT
AATTAACAGAATCTT
AATCTTTATACAATT

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
AATTCTCTGAAACAC hisZ,
... ... hisZ CD630_15461 CD630_15460 hisG hisC hisB hisH hisA hisF hisI
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 qRT-PCR [RNA] (ECO:0001808) - repressor not specified
AAGTTTTTGATATTT CD630_23440,
... ... CD630_23440 cat1 sucD CD630_23450
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 qRT-PCR [RNA] (ECO:0001808) - repressor not specified
AATTAACAGAATCTT glgC,
... ... glgC CD630_08810 CD630_08800 glgD glgA glgP CD630_08860
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 qRT-PCR [RNA] (ECO:0001808) - repressor not specified
AATCTTTATACAATT glgC,
... ... glgC CD630_08810 CD630_08800 glgD glgA glgP CD630_08860
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 qRT-PCR [RNA] (ECO:0001808) - repressor not specified