Curation Information

Publication
A non-classical LysR-type transcriptional regulator PA2206 is required for an effective oxidative stress response in Pseudomonas aeruginosa.;Reen FJ, Haynes JM, Mooij MJ, O'Gara F;PloS one 2013; 8(1):e54479 [23382903]
TF
PA2206 [Q9I1R1, view regulon]
Reported TF sp.
Pseudomonas aeruginosa PAO1
Reported site sp.
Pseudomonas aeruginosa PAO1
Created by
Dinara Sagitova
Curation notes
-
External databases
NCBI GEO (GSE23367) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23367.

Experimental Process

RT-PCR shows induction of PA2206 in response to oxidative damage, but beta-galactosidase assays reveal that gene is not autoregulated. Phenotypic analysis shows that induction leads to increased survival. DNA-arrays and RT-PCR show that PA2214-15 is substantially lower in a PA2206 mutant. This was further validated with beta-gal assays in P. aeruginosa and in E. coli harboring a PA2206 copy, suggesting direct control. Binding at pPA2214 was confirmed through EMSA, showing several conformations. Several LysR-type boxes were identified, but one was shown to be sufficient for binding. Sequence search was performed to identify additional sites in the genome and a site upstream of pvdS and PA4881 was verified through EMSA.

Transcription Factor Binding Sites


TTGCCTGGGGTTA
TTCGCAGCGGCTA
TTAAATCGACTTA
TTGCCGAAGCCTA
TTCCACAGGCATA
TTGCCTGGGGTTA
TTCGCAGCGGCTA
TTAAATCGACTTA
TTGCCGAAGCCTA
TTCCACAGGCATA

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
TTGCCTGGGGTTA PA2214, PA2215,
... ... PA2214 PA2215 PA2216 PA2217
Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTCGCAGCGGCTA pvdS,
... ... pvdS pvdG pvdL
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTAAATCGACTTA PA4881
... ... PA4881
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTGCCGAAGCCTA ilvH,
... ... ilvH ilvI ilvC PA4697
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTCCACAGGCATA trpG,
... ... trpG trpD trpC
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified