Curation Information

Publication: Pseudomonas aeruginosa PA14 cupD transcription is activated by the RcsB response regulator, but repressed by its putative cognate sensor RcsC.;Nicastro GG, Boechat AL, Abe CM, Kaihami GH, Baldini RL;FEMS microbiology letters 2009 Nov; 301(1):115-23 [19832907]
TF: RcsB [A0A0H2ZHG6, view regulon]
Reported TF sp.: Pseudomonas aeruginosa PA14
Reported site sp.: Pseudomonas aeruginosa PA14
Created by: Grace Chandler
Curation notes: -

Experimental Process

Visual inspection of the cupD upstream region identified a putative RcsB binding site. RACE PCR determined the transcriptional start site location of cupD. qRT-PCR demonstrated RcsB-mediated activation of cupD transcription. These results were confirmed with cupD'-lacZ reporter assays. Multiple sequence alignment of RcsB-binding regions and putative binding sites further characterized the RcsB binding motif.

Transcription Factor Binding Sites

Sites reported in the paper
Sites matched in the genome

TAAGAAACGTCCTAAA

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
TAAGAAACGTCCTAAA	cupD1, cupD2, cupD3, cupD4, cupD5		Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) Multiple sequence alignment (MSA) - ECO:0005556 MSA can be used to align promoter regions and highlight regions of conservation that may be indicative of transcription factor binding sites. - Experimental technique details qRT-PCR [RNA] (ECO:0001808) qRT-PCR [RNA] - ECO:0001808 Quantitative Reverse-Transcription PCR is a modification of PCR in which RNA is first reverse transcribed into cDNA and this is amplified measuring the product (qPCR) in real time. It therefore allows one to analyze transcription by directly measuring the product (RNA) of a gene's transcription. If the gene is transcribed more, the starting product for PCR is larger and the corresponding volume of amplification is also larger. - Experimental technique details RACE PCR (ECO:0005661) RACE PCR - ECO:0005661 Rapid Amplification of cDNA Ends is a technique to obtain the full length sequence of an RNA transcript. Most succinctly, the technique exploits the fact that PCR will stop at the ends of a mRNA. Basically, a primer mapping a "center" region of the mRNA is used to perform RT-PCR and terminal deoxynucleotidyl transferase (TdT) is used to add identical nucleotides to the 3' end of the cDNA. Standard PCR using another primer and the TdT-oligomer is performed in the other sense. The technique is frequently used to verify transcription start sites, which are relevant to the function (e.g. repression) of transcription factor binding sites. - Experimental technique details Visual sequence inspection (nan) Visual sequence inspection - nan Visual inspection of promoter region to identify putative binding sites based on previous knowledge -	activator	not specified