Curation Information

Catabolism of phenylalanine by Pseudomonas putida: the NtrC-family PhhR regulator binds to two sites upstream from the phhA gene and stimulates transcription with sigma70.;Herrera MC, Ramos JL;Journal of molecular biology 2007 Mar 9; 366(5):1374-86 [17217960]
PhhR [Q88EH4, view regulon]
Reported TF sp.
Pseudomonas putida KT2440
Reported site sp.
Pseudomonas putida KT2440
Created by
Kathryn Cronise
Curation notes

Experimental Process

A beta-gal assay was used to show that PhhR activates phhA expression. A PSSM search was used with IHF (another NtrC TF) motifs to identify a proximal and distal site. A beta-gal assay was used with site directed mutagenesis to show that the proximal site is necessary for phhA activation. EMSA followed by DNAse footprinting was used to show binding.

Transcription Factor Binding Sites


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
... ... phhA phhR phhB
Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator dimer