Curation Information

Publication
Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000.;Butcher BG, Bronstein PA, Myers CR, Stodghill PV, Bolton JJ, Markel EJ, Filiatrault MJ, Swingle B, Gaballa A, Helmann JD, Schneider DJ, Cartinhour SW;Journal of bacteriology 2011 Sep; 193(18):4598-611 [21784947]
TF
Fur [Q87WN7, view regulon]
Reported TF sp.
Pseudomonas syringae pv. tomato str. DC3000
Reported site sp.
Pseudomonas syringae pv. tomato str. DC3000
Created by
Elliot White
Curation notes
-
External databases
NCBI GEO (GES13500) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GES13500.

Experimental Process

DNase I footprinting was used to confirm that Fur bound to the sites predicted by MEME in the data generated from a fur ChIP-Seq.This data was cross referenced with a previously published DNA array.

Transcription Factor Binding Sites


ATAGTACAGATTCGTAT
GTAGGAATATTTTGCGT
ACAGGTTTCACTCGCAA
ATGCCTCCCGTTTTCGT
ATGATTGCGGATCTCAG
TCGTTAATCGCTTTCGT
ACCGAAATGACTCGCAA
TTGCAAAGTCTTCTCGT
TCAAGAACCCTTATCGT
ATTCAAATGATTCGCAA
ATAAGAGGGATTATCGT
TCGCGAATGTTTATTAA
TCGACAAGGGTTTTCAT
ATACAACTGATTCTCAT
ACGATATTGATTGTCGT
TTGATAACTGTTCTCAT
CTGGGAATGCTTATCAT
ATGCAAATCTTTCGCAT
ATCATAACGATTCTCAT
ATGAGAATGCTTGTCAA
ATGATATTCATTATCAA
ATGAGAATTAATCTCAA
TTGATAGTGATTCTCAT
ATAGTACAGATTCGTAT
GTAGGAATATTTTGCGT
ACAGGTTTCACTCGCAA
ATGCCTCCCGTTTTCGT
ATGATTGCGGATCTCAG
TCGTTAATCGCTTTCGT
ACCGAAATGACTCGCAA
TTGCAAAGTCTTCTCGT
TCAAGAACCCTTATCGT
ATTCAAATGATTCGCAA
ATAAGAGGGATTATCGT
TCGCGAATGTTTATTAA
TCGACAAGGGTTTTCAT
ATACAACTGATTCTCAT
ACGATATTGATTGTCGT
TTGATAACTGTTCTCAT
CTGGGAATGCTTATCAT
ATGCAAATCTTTCGCAT
ATCATAACGATTCTCAT
ATGAGAATGCTTGTCAA
ATGATATTCATTATCAA
ATGAGAATTAATCTCAA
TTGATAGTGATTCTCAT

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
ATAGTACAGATTCGTAT PSPTO_3294,
... ... PSPTO_3294 PSPTO_3298 PSPTO_3297 PSPTO_3296 pncA hopAH2-2
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
GTAGGAATATTTTGCGT PSPTO_2145, PSPTO_2144, PSPTO_2143, PSPTO_2142, PSPTO_2141, PSPTO_2140, PSPTO_2139, PSPTO_2138,
... ... PSPTO_2145 PSPTO_2144 PSPTO_2143 PSPTO_2142 PSPTO_2141 PSPTO_2140 PSPTO_2139 PSPTO_2138 PSPTO_2146 PSPTO_2134 pvsA daT PSPTO_2137
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
ACAGGTTTCACTCGCAA PSPTO_0426, PSPTO_0425, PSPTO_0424,
... ... PSPTO_0426 PSPTO_0425 PSPTO_0424 ftsY ftsE ftsX rpoH
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
ATGCCTCCCGTTTTCGT cumA, PSPTO_1457,
... ... cumA PSPTO_1457 PSPTO_1455 PSPTO_1458
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
ATGATTGCGGATCTCAG PSPTO_5310,
... ... PSPTO_5310 PSPTO_5667
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
TCGTTAATCGCTTTCGT PSPTO_2152,
... ... PSPTO_2152 PSPTO_2155 PSPTO_2156 pvdE PSPTO_2154
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
ACCGAAATGACTCGCAA PSPTO_1915, PSPTO_1916,
... ... PSPTO_1915 PSPTO_1916 PSPTO_1914 PSPTO_1913 PSPTO_1917
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
TTGCAAAGTCTTCTCGT PSPTO_4368, PSPTO_4369,
... ... PSPTO_4368 PSPTO_4369 PSPTO_4367 PSPTO_4370 inaA PSPTO_4372
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
TCAAGAACCCTTATCGT PSPTO_5658,
... ... PSPTO_5658 PSPTO_3255 PSPTO_3254 PSPTO_3256 PSPTO_3257 PSPTO_3258 PSPTO_3259 PSPTO_3260 PSPTO_3261
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
ATTCAAATGATTCGCAA azu,
... ... azu PSPTO_4924 PSPTO_4925 PSPTO_4926
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
ATAAGAGGGATTATCGT PSPTO_4366,
... ... PSPTO_4366 PSPTO_4367 PSPTO_4368 PSPTO_4369 PSPTO_4370 inaA PSPTO_4372
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
TCGCGAATGTTTATTAA gnd, zwf-2, PSPTO_3120, PSPTO_3119,
... ... gnd zwf-2 PSPTO_3120 PSPTO_3119 alkB PSPTO_3117 PSPTO_3116 PSPTO_3115 PSPTO_3114 PSPTO_3123 PSPTO_3124
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
TCGACAAGGGTTTTCAT PSPTO_0314,
... ... PSPTO_0314 PSPTO_0312 cysA PSPTO_0310 cysT sbp PSPTO_0307 PSPTO_0313
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
ATACAACTGATTCTCAT PSPTO_1284, PSPTO_1283, PSPTO_1282,
... ... PSPTO_1284 PSPTO_1283 PSPTO_1282 PSPTO_1281 PSPTO_1285 PSPTO_1286 gap-1
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
ACGATATTGATTGTCGT PSPTO_4381,
... ... PSPTO_4381 PSPTO_4382 PSPTO_4380 PSPTO_4383 PSPTO_4384
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
TTGATAACTGTTCTCAT PSPTO_3692,
... ... PSPTO_3692 PSPTO_3691 PSPTO_3690 PSPTO_3689
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
CTGGGAATGCTTATCAT PSPTO_3462,
... ... PSPTO_3462 glpQ pssA-2 PSPTO_3464 PSPTO_3465
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
ATGCAAATCTTTCGCAT PSPTO_4366,
... ... PSPTO_4366 PSPTO_4365
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
ATCATAACGATTCTCAT PSPTO_5649,
... ... PSPTO_5649 deoC PSPTO_0974 PSPTO_0975 PSPTO_0976 PSPTO_0977 PSPTO_0978 PSPTO_0979 PSPTO_0980
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
ATGAGAATGCTTGTCAA PSPTO_4159,
... ... PSPTO_4159 rnt PSPTO_4157 PSPTO_4156 argG PSPTO_4154
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
ATGATATTCATTATCAA PSPTO_4462, fumC-2, PSPTO_4460,
... ... PSPTO_4462 fumC-2 PSPTO_4460 sodA PSPTO_4458 ptsH PSPTO_4456 ptsN yfiA rpoN pmbA PSPTO_4464 tldD PSPTO_4466 PSPTO_4467
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
ATGAGAATTAATCTCAA PSPTO_4580,
... ... PSPTO_4580 prfC PSPTO_4581 PSPTO_4582 PSPTO_4583 PSPTO_4584
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer
TTGATAGTGATTCTCAT PSPTO_3574,
... ... PSPTO_3574 PSPTO_3573 PSPTO_3572 PSPTO_3571 PSPTO_3570 PSPTO_3575
Experimental technique details ChIP-Seq (ECO:0006009) - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Motif-discovery (ECO:0005558) - repressor dimer