Curation Information

Publication
A novel copper-responsive regulon in Mycobacterium tuberculosis.;Festa RA, Jones MB, Butler-Wu S, Sinsimer D, Gerads R, Bishai WR, Peterson SN, Darwin KH;Molecular microbiology 2011 Jan; 79(1):133-48 [21166899]
TF
RicR [O07434, view regulon]
Reported TF sp.
Mycobacterium tuberculosis H37Rv
Reported site sp.
Mycobacterium tuberculosis H37Rv
Created by
Erill Lab
Curation notes
-
External databases
NCBI GEO (GSE23947) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23947. NCBI GEO (GSE23498) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23498.

Experimental Process

A regulatory element controlling promoters repressed in proteasome degradation-defective Mtb (Rv0847 and Rv2963) was identified by visual inspection. RACE-PCR determined that these elements were close to the transcriptional start site. Additional promoters containing the TACCC-N5-G/AGGTA element were identified with consensus Search Pattern (http://genodb.pasteur.fr). These correspond to Rv0190 (ricR), mymT and ppe23 (Rv1706c). Again RACE-PCR confirmed their proximity to the TSS. qRT-PCR showed that these genes are induced by copper, and further qRT-PCR and array anaylsis revealed that these genes are induced in a ricR, but not csoR mutant. Co-purification of the biotinylated lpqS promoter with RicR, in combination with site-directed mutagenesis, revealed that RicR bound the palindromic element.

Transcription Factor Binding Sites


CTACCCCTATAGGGTAT
ATACCCCCGGGTGGTAT
ATACCCGTATAGGGTAT
ATACCCCGCTGGGGTAC
ATACCCCATAGGGGTAT
CTACCCCTATAGGGTAT
ATACCCCCGGGTGGTAT
ATACCCGTATAGGGTAT
ATACCCCGCTGGGGTAC
ATACCCCATAGGGGTAT

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
CTACCCCTATAGGGTAT lpqS,
... ... lpqS Rv0846c
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA affinity purification (ECO:0005629) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) - repressor not specified
ATACCCCCGGGTGGTAT Rv2963,
... ... Rv2963 Rv2962c purU
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Visual sequence inspection (nan) - repressor not specified
ATACCCGTATAGGGTAT mymT,
... ... mymT Rv0187 Rv0188
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor not specified
ATACCCCGCTGGGGTAC Rv0190,
... ... Rv0190 ilvD Rv0191 Rv0192 Rv0192A
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor not specified
ATACCCCATAGGGGTAT
... ... PPE23 PPE22 cycA Rv1703c
Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor not specified