Curation Information

Publication
PhhR binds to target sequences at different distances with respect to RNA polymerase in order to activate transcription.;Herrera MC, Krell T, Zhang X, Ramos JL;Journal of molecular biology 2009 Dec 4; 394(3):576-86 [19781550]
TF
PhhR [Q88EH4, view regulon]
Reported TF sp.
Pseudomonas putida KT2440
Reported site sp.
Pseudomonas putida KT2440
Created by
Kathryn Cronise
Curation notes
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Experimental Process

A PSSM search was used with known phhA sites and the consensus sequence to identify potential binding sites. A beta-gal assay was performed to show that PhhR up-regulates the genes. EMSA and DNase footprinting was used to prove binding and ITC (isothermal titration calorimetry) was performed to show that binding is favorable.

Transcription Factor Binding Sites


GTTTTGTAAAAATTATCAATCGATGA
TTGCGGTGAAGATGTCTGCACACGCT
GTTTTGTAAAAATTATCAATCGATGA
TTGCGGTGAAGATGTCTGCACACGCT

Quantitative data format: Kd from quantitative EMSA.

GTTTTGTAAAAATTATCAATCGATGA 1.71
TTGCGGTGAAGATGTCTGCACACGCT 2.2

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
GTTTTGTAAAAATTATCAATCGATGA PP_3122,
... ... PP_3122 PP_3121 PP_3120 PP_3123
Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Isothermal titration calorimetry (ECO:0005647) - Experimental technique details PSSM site search (ECO:0005659) - activator dimer
TTGCGGTGAAGATGTCTGCACACGCT PP_3122,
... ... PP_3122 PP_3121 PP_3120 PP_3123
Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Isothermal titration calorimetry (ECO:0005647) - Experimental technique details PSSM site search (ECO:0005659) - activator dimer