Curation Information

Publication: Activation of the phz operon of Pseudomonas fluorescens 2-79 requires the LuxR homolog PhzR, N-(3-OH-Hexanoyl)-L-homoserine lactone produced by the LuxI homolog PhzI, and a cis-acting phz box.;Khan SR, Mavrodi DV, Jog GJ, Suga H, Thomashow LS, Farrand SK;Journal of bacteriology 2005 Sep; 187(18):6517-27 [16159785]
TF: PhzR [G3XD77, view regulon]
Reported TF sp.: Pseudomonas fluorescens 2-79
Reported site sp.: Pseudomonas fluorescens 2-79
Created by: Dinara Sagitova
Curation notes: P. fluorescens and P. aeruginosa genomes are not matching at the species level.

Experimental Process

Transcriptional start sites for phzA and phzR were identified by primer extension analysis. A putative PhzR binding site was identified in the phzA-phzR intergenic region by visual inspection. Beta-gal reporter fusions confirmed that an intact phz box is required for PhzR-mediated activation of the phzA and phzR genes.

Transcription Factor Binding Sites

Sites reported in the paper
Sites matched in the genome

CTACAAGATCTGGTAG

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
CTACAAGATCTGGTAG	phzA1, phzM,		Experimental technique details Beta-gal reporter assay Beta-gal reporter assay Reporter assay using the beta-galactosidase (lacZ) gene. The lacZ gene is typically fused to the promoter of interest. Differential regulation of the promoter mediated by the TF is assessed by induction of the system and evaluation of lacZ expression. Bacteria expressing lacZ appear blue when grown on a X-gal medium. The assay is often performed using a plasmid borne construction on a lacZ(def) strain. - Experimental technique details Site directed mutagenesis (ECO:0005667) Site directed mutagenesis - ECO:0005667 Target-specific mutation, as opposed to non-specific mutation. In the context of TF-binding sites, site-directed mutagenesis is typically used to establish/confirm the specific sequence and location of a site, often in tandem with EMSA. Different positions of a putative binding site are mutated to non-consensus (or random) bases and binding to the mutated site is evaluated through EMSA or other means. Often implemented only in conserved motif positions or serially through all positions of a site. - 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