Curation Information

Publication
Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals regulon members and insights regarding PvdS function in other pseudomonads.;Swingle B, Thete D, Moll M, Myers CR, Schneider DJ, Cartinhour S;Molecular microbiology 2008 May; 68(4):871-89 [18363796]
TF
PvdS [Q884G0, 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
-

Experimental Process

A conventional promoter trap library screen was used to isolate PvdS-regulated promoters encoded in the DC3000 genome. The lux reporter fusion assays showed that ten of these promoter regions exhibited PvdS-dependent expression. A qRT-PCR assays were used to compare the expression level in cells containing PvdS versus PvdS mutant strain. The results of these assays confirmed PvdS-dependent differential expression in 18 genes. Transcription start sites of several PvdS-dependent genes were mapped by 5'RACE. A PvdS binding motif resembling the motif in promoters recognized by sigma 70-type sigma factors was identified by Gibbs sampling. Site-directed mutagenesis of a putative PvdS binding site confirmed that both the -10 and -35 elements are required for promoter function.

Transcription Factor Binding Sites


TTAATTACTGGCCCTCGCTAATCGTTCTT
TTAATTTTTCGACGTAGCGATACGTTCAA
TCTAAATATTTCCCCGCCAATTCGTTCTT
CTAATTATTTGCAGACGCCATCCGTTCTC
ATAAAAACATGCCAGACCGAGACGTTTAT
CTAAAAATTTTCGCCCGCGCTTCGTTTAA
CTAAATTTTTCGCCCATCCGCTCGTTCTC
CTAAATTTGTCAGCCGGTTTTACGTTCTA
CTAATTTTTCAGCCGCGAAGTACGTTCAA
TTGAATTAATTCTCCCGTCCGTCGTTCTC
CAAAATATTCCTACAGGAATCTCGTTCTC
TTAAATAATCGTTAATCGCTTTCGTTCTC
CTAAATTCCGGCCTGCATTTCTCGTTTAA
TAAATCACTGGAGGCACTCAAACGTTTAT
CTCAAGAAATCAACCACTTGAACGTTTTA
TTAATTACTGGCCCTCGCTAATCGTTCTT
TTAATTTTTCGACGTAGCGATACGTTCAA
TCTAAATATTTCCCCGCCAATTCGTTCTT
CTAATTATTTGCAGACGCCATCCGTTCTC
ATAAAAACATGCCAGACCGAGACGTTTAT
CTAAAAATTTTCGCCCGCGCTTCGTTTAA
CTAAATTTTTCGCCCATCCGCTCGTTCTC
CTAAATTTGTCAGCCGGTTTTACGTTCTA
CTAATTTTTCAGCCGCGAAGTACGTTCAA
TTGAATTAATTCTCCCGTCCGTCGTTCTC
CAAAATATTCCTACAGGAATCTCGTTCTC
TTAAATAATCGTTAATCGCTTTCGTTCTC
CTAAATTCCGGCCTGCATTTCTCGTTTAA
TAAATCACTGGAGGCACTCAAACGTTTAT
CTCAAGAAATCAACCACTTGAACGTTTTA

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
TTAATTACTGGCCCTCGCTAATCGTTCTT azu,
... ... azu PSPTO_4924
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTAATTTTTCGACGTAGCGATACGTTCAA PSPTO_2137,
... ... PSPTO_2137 daT
Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TCTAAATATTTCCCCGCCAATTCGTTCTT PSPTO_2147,
... ... PSPTO_2147 PSPTO_2148 PSPTO_2149 PSPTO_2150
Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
CTAATTATTTGCAGACGCCATCCGTTCTC PSPTO_2134,
... ... PSPTO_2134 PSPTO_2133 pvsA daT PSPTO_2137
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
ATAAAAACATGCCAGACCGAGACGTTTAT PSPTO_3290
... ... PSPTO_3290
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
CTAAAAATTTTCGCCCGCGCTTCGTTTAA PSPTO_2161,
... ... PSPTO_2161 PSPTO_2160 PSPTO_2159 PSPTO_2158
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
CTAAATTTTTCGCCCATCCGCTCGTTCTC PSPTO_2156,
... ... PSPTO_2156 PSPTO_2155 PSPTO_2154 pvdE pvdP
Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
CTAAATTTGTCAGCCGGTTTTACGTTCTA pvdP,
... ... pvdP PSPTO_2156 PSPTO_2155 PSPTO_2154 pvdE
Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
CTAATTTTTCAGCCGCGAAGTACGTTCAA PSPTO_2146,
... ... PSPTO_2146 PSPTO_2145 PSPTO_2144 PSPTO_2143 PSPTO_2142 PSPTO_2141 PSPTO_2140 PSPTO_2139 PSPTO_2138
Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTGAATTAATTCTCCCGTCCGTCGTTCTC PSPTO_0753
... ... PSPTO_0753
Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
CAAAATATTCCTACAGGAATCTCGTTCTC PSPTO_2145,
... ... PSPTO_2145 PSPTO_2144 PSPTO_2143 PSPTO_2142 PSPTO_2141 PSPTO_2140 PSPTO_2139 PSPTO_2138 PSPTO_2146
Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TTAAATAATCGTTAATCGCTTTCGTTCTC PSPTO_2152
... ... PSPTO_2152
Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - Experimental technique details Site directed mutagenesis (ECO:0005667) - activator not specified
CTAAATTCCGGCCTGCATTTCTCGTTTAA PSPTO_2160,
... ... PSPTO_2160 PSPTO_2159 PSPTO_2158 PSPTO_2161
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
TAAATCACTGGAGGCACTCAAACGTTTAT PSPTO_2149,
... ... PSPTO_2149 PSPTO_2148 PSPTO_2150
Experimental technique details Luciferase reporter assay (ECO:0005648) - Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified
CTCAAGAAATCAACCACTTGAACGTTTTA PSPTO_2982,
... ... PSPTO_2982 PSPTO_2983
Experimental technique details Motif-discovery (ECO:0005558) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator not specified