Curation Information

Publication

Transcriptional organization and regulatory elements of a Pseudomonas sp. strain ADP operon encoding a LysR-type regulator and a putative solute transport system.;Platero AI, García-Jaramillo M, Santero E, Govantes F;Journal of bacteriology 2012 Dec; 194(23):6560-73 [23042989]

TF

AtzR [Q936X4, view regulon]

Reported TF sp.

Pseudomonas sp. ADP

Reported site sp.

Pseudomonas sp. ADP

Created by

Grace Chandler

Curation notes

The proxy genome was not an adequate match for the reported genome, Pseudomonas sp. ADP. The binding site was not matched within the proxy genome, Pseudomonas putida KT2440.

Experimental Process

qRT-PCR confirmed that the atzSTUVW operon genes were co-transcribed. Beta-galactosidase assays with atzR deletion strains demonstrated the repressor activity of AtzR. Visual inspection of the atzT promoter region yielded a sequence identical to the AtzR binding site for atzDEF. Site-directed mutagenesis combined with beta-galactosidase assays identified that the integrity of this region is necessary for AtzR-dependent repression. This region was then validated with EMSA to demonstrate specific binding. DNase I footprinting localized the AtzR binding site.

Transcription Factor Binding Sites

• Sites reported in the paper
• Sites matched in the genome

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.