Curation Information

Publication
Pseudomonas syringae two-component response regulator RhpR regulates promoters carrying an inverted repeat element.;Deng X, Lan L, Xiao Y, Kennelly M, Zhou JM, Tang X;Molecular plant-microbe interactions : MPMI 2010 Jul; 23(7):927-39 [20521955]
TF
RhpR [Q883X4, view regulon]
Reported TF sp.
Pseudomonas syringae pv. tomato str. DC3000
Reported site sp.
Pseudomonas syringae pv. tomato str. DC3000
Created by
Dinara Sagitova
Curation notes
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Experimental Process

Northern blot hybridization in wild-type DC3000 and rhpS mutant showed that rhpR was expressed at a much higher level in the rhpS– mutant than in the WT strain. rhpR-luc reporter assay showed that activity was 10-fold higher in the rhpS– mutant than in the WT, indicating an autoactivation of rhpR expression by RhpR. Promoter deletion analysis indicated the presence of an RhprR-dependent promoter element in the -170 to -120 region in the rhpR promoter. rhpR transcriptional start site was identified by 5'RACE reaction. Site-directed mutagenesis of the putative RhpR binding site in conjunction with rhpR-luc reporter assay showed that the IR element in the rhpR promoter is important in regulating the promoter activity. Also, it was shown that the 6 bp length of the spacer is required for the activity of the IR element. Additionally, the DC3000 genome was searched for the IR sequence with upto one mismatch. The RhpR-dependent expression of the genes identified by this search was confirmed using RNA blotting, ChIP, and qRT-PCR.

Transcription Factor Binding Sites


GTATCCGTATCGATAC
GTATCAACCTGGGTAC
GTATCGCGCCGCTTAC
GTATCGCCGCTGCTAC
GTATCACCCCGGACAC
GTAACACAGACGATAC
GTATCCGTATCGATAC
GTATCAACCTGGGTAC
GTATCGCGCCGCTTAC
GTATCGCCGCTGCTAC
GTATCACCCCGGACAC
GTAACACAGACGATAC

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
GTATCCGTATCGATAC PSPTO_2223,
... ... PSPTO_2223 PSPTO_2222 PSPTO_2224
Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details Site directed mutagenesis (ECO:0005667) - Experimental technique details Visual sequence inspection (nan) - activator dimer
GTATCAACCTGGGTAC PSPTO_2767
... ... PSPTO_2767
Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
GTATCGCGCCGCTTAC PSPTO_2036,
... ... PSPTO_2036 folE-2 PSPTO_2034
Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
GTATCGCCGCTGCTAC PSPTO_3477,
... ... PSPTO_3477 PSPTO_3478
Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
GTATCACCCCGGACAC PSPTO_0536,
... ... PSPTO_0536 tRNA-Met-1 PSPTO_0535
Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
GTAACACAGACGATAC PSPTO_0897,
... ... PSPTO_0897 PSPTO_0898
Experimental technique details ChIP-PCR (ECO:0005620) - Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Northern blot (ECO:0005653) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer