Curation Information

Publication
GeneChip expression analysis of the iron starvation response in Pseudomonas aeruginosa: identification of novel pyoverdine biosynthesis genes.;Ochsner UA, Wilderman PJ, Vasil AI, Vasil ML;Molecular microbiology 2002 Sep; 45(5):1277-87 [12207696]
TF
PvdS [G3XCV1, view regulon]
Reported TF sp.
Pseudomonas aeruginosa PAO1
Reported site sp.
Pseudomonas aeruginosa PAO1
Created by
Grace Chandler
Curation notes
-

Experimental Process

Differential expression under low and high iron conditions assessed by DNA array. Expression further assessed by beta-gal assays. PvdS-binding sites in the promoters of differentially expressed genes detected by consensus search.

Transcription Factor Binding Sites


TAAATTTCATTTCCCTGTCCTCGT
TAATTTTCCCGCCGGGCTTTTCGT
TAAATCCGTGCGTCCCTCCTGCGT
TAAATTCGCGGCGGGATGCGACGT
CAAATTTCCGCTGTGATCGTACGT
TAAATTGCAGGCGATGCCGTTCGT
TAAATTTTCCCGCTCCGGCCTCGT
TAATTATTTGCCGTTGTTATCCGT
TAAATACCGGGCATCCTGCTTCGT
TAATTTTCACGATGTGTCGTCCGT
TAAATTTAGCCGCCCTGGCCTCGT
TAAATTTGCCGACGGAAGGAACGT
GAAAGATCCGCCGCGGCGATTCGT
TAAACCGGCCTGGCGCAGCATCGT
TAAAAAATATTTGAACGACTCCGT
TGAATCGTGCCCGGCCAACGGCGT
TGAATGGCCGCTTCGATTCCTCGT
TAAAACCGTCAAGCCTTTATCCGT
TAAATATCCGGATTTTCTTTTCGT
TAAATTTCATTTCCCTGTCCTCGT
TAATTTTCCCGCCGGGCTTTTCGT
TAAATCCGTGCGTCCCTCCTGCGT
TAAATTCGCGGCGGGATGCGACGT
CAAATTTCCGCTGTGATCGTACGT
TAAATTGCAGGCGATGCCGTTCGT
TAAATTTTCCCGCTCCGGCCTCGT
TAATTATTTGCCGTTGTTATCCGT
TAAATACCGGGCATCCTGCTTCGT
TAATTTTCACGATGTGTCGTCCGT
TAAATTTAGCCGCCCTGGCCTCGT
TAAATTTGCCGACGGAAGGAACGT
GAAAGATCCGCCGCGGCGATTCGT
TAAACCGGCCTGGCGCAGCATCGT
TAAAAAATATTTGAACGACTCCGT
TGAATCGTGCCCGGCCAACGGCGT
TGAATGGCCGCTTCGATTCCTCGT
TAAAACCGTCAAGCCTTTATCCGT
TAAATATCCGGATTTTCTTTTCGT

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
TAAATTTCATTTCCCTGTCCTCGT pvdA,
... ... pvdA pvdQ
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAATTTTCCCGCCGGGCTTTTCGT PA2412, PA2411,
... ... PA2412 PA2411 pvdH
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAAATCCGTGCGTCCCTCCTGCGT pvdH,
... ... pvdH PA2412 PA2411
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAAATTCGCGGCGGGATGCGACGT PA2427
... ... PA2427
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
CAAATTTCCGCTGTGATCGTACGT PA2452, PA2451,
... ... PA2452 PA2451 PA2453 PA2454 PA2455 PA2456
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAAATTGCAGGCGATGCCGTTCGT pvdF,
... ... pvdF pvdE fpvA
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAAATTTTCCCGCTCCGGCCTCGT PA2393, pvdN, pvdO,
... ... PA2393 pvdN pvdO pvdP
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAATTATTTGCCGTTGTTATCCGT pvdG, pvdL,
... ... pvdG pvdL pvdS
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAAATACCGGGCATCCTGCTTCGT pvdE,
... ... pvdE pvdF fpvA
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAATTTTCACGATGTGTCGTCCGT PA2402, pvdJ,
... ... PA2402 pvdJ pvdD PA2403 PA2404 PA2405 PA2406 PA2407 PA2408 PA2409 PA2410
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAAATTTAGCCGCCCTGGCCTCGT pvdR, pvdT, opmQ
... ... pvdR pvdT opmQ
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAAATTTGCCGACGGAAGGAACGT pvdP,
... ... pvdP PA2393 pvdN pvdO
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
GAAAGATCCGCCGCGGCGATTCGT PA5150,
... ... PA5150 PA5151
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAAACCGGCCTGGCGCAGCATCGT PA1134,
... ... PA1134 PA1133
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAAAAAATATTTGAACGACTCCGT piv
... ... piv
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TGAATCGTGCCCGGCCAACGGCGT PA0346,
... ... PA0346 PA0345 PA0344 PA0343
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TGAATGGCCGCTTCGATTCCTCGT PA0818,
... ... PA0818 PA0819
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAAAACCGTCAAGCCTTTATCCGT PA4833,
... ... PA4833 PA4832
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified
TAAATATCCGGATTTTCTTTTCGT mvfR,
... ... mvfR nadA
Experimental technique details Beta-gal reporter assay - Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) - activator not specified