Curation Information

Publication: Cloning and functional characterization of the Pseudomonas aeruginosa rhlC gene that encodes rhamnosyltransferase 2, an enzyme responsible for di-rhamnolipid biosynthesis.;Rahim R, Ochsner UA, Olvera C, Graninger M, Messner P, Lam JS, Soberón-Chávez G;Molecular microbiology 2001 May; 40(3):708-18 [11359576]
TF: LasR [P54292, view regulon]
Reported TF sp.: Pseudomonas aeruginosa PAO1
Reported site sp.: Pseudomonas aeruginosa PAO1
Created by: Matthew Coveyou
Curation notes: -

Experimental Process

The absence of an immediate upstream promoter region for the P. aeruginosa PAO1 gene rhlC was supported by the total lack of beta-gal reporter activity and complete mRNA binding of an upstream probe in RNase protection assays. However, protection assays were also performed on the putative gene PA1131 (immediately upstream of rhlC), and a single start site was identified, suggesting rhlC and PA1131 are organized in an operon. RNase protection of start site regions for both rhlC and PA1131 were performed with rhlR, lasR, and rhlR/lasR mutant PAO1 strains, which demonstrated identical expression patterns of strong, limited, and total loss (respectively) for each. This indicated strong up-regulation by rhlR and independent, meager up-regulation by lasR, and further supported rhlC/PA1131 activity as an operon. Expression patterns were identical to a comparative assay of the PAO1 rhlAB operon, known to be recognized by rhlR and lasR. Sequence alignment of the PA1131 and rhlA promoter regions confirmed a conserved lux box and rpoN consensus region.

Transcription Factor Binding Sites

Sites reported in the paper
Sites matched in the genome

CCTGTGAATTCCGGTAGTT

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
CCTGTGAATTCCGGTAGTT	PA1131, rhlC,		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 RNAse protection (ECO:0000288) RNAse protection - ECO:0000288 This is a technique used to detect typically mRNA with greater precision than Northern blot or RT-PCR. Therefore, it is commonly used to assess gene expression (specifically transcription). RNAse protection uses labelled RNA probes to bind desired targets. RNAses are then added to the mix and degrade all RNA that is not bound to probes. The remaining RNA is typically run on a gel to detect the size (and label) of the probe and determine which RNA it is. -	activator	not specified