Curation Information

Publication
Gene repression by the ferric uptake regulator in Pseudomonas aeruginosa: cycle selection of iron-regulated genes.;Ochsner UA, Vasil ML;Proceedings of the National Academy of Sciences of the United States of America 1996 Apr 30; 93(9):4409-14 [8633080]
TF
Fur [Q03456, view regulon]
Reported TF sp.
Pseudomonas aeruginosa PAO1
Reported site sp.
Pseudomonas aeruginosa PAO1
Created by
Erill Lab
Curation notes
-

Experimental Process

A genomic SELEX-like approach was used to identify putative sites. EMSA and DNase footprinting were used to verify bound sites. RNAse protection was used to demonstrate iron induciblity.

Transcription Factor Binding Sites


AAAAACGAGAATTATTCGC
ACGATTGAAAATCATTATC
ACGATTGCTAATCAATCTT
ATAATTGAGAATCGTTATT
CTGAATGAAACCCAATCTT
CTTGATGAGAATTATTATG
GAAAACAATAATCAATCTC
GAAGATGGTAATTAATTGC
GACATTGAGATTCAATGAC
GCAAACGATATTCATCATC
GCCAATGATATTGATTTGC
GGAAATGAGAATCATTATT
GTAATTGACAATCATTATC
GTTATTGAGAATCATTGGC
TAAATTCATAATAATTCTC
TCCAATGCAAATCAATATC
TTTATCGCAACTGATTATC
TTTTATGATAATGATTTTC
AAAAACGAGAATTATTCGC
ACGATTGAAAATCATTATC
ACGATTGCTAATCAATCTT
ATAATTGAGAATCGTTATT
CTGAATGAAACCCAATCTT
CTTGATGAGAATTATTATA
GAAAACAATAATCAATCTC
GAAGATGGTAATTAATTGC
GACATTGAGATTCAATAAC
GCAAACGATATTCATTATC
GCCAATGATATTGATTTGC
GGAAATGAGAATCATTATT
GTAATTGACAATCATTATC
GTTATTGAGAATCATTGGC
TAAATTTATAATAATTCTC
TCCAATGCAAATCAATATC
TTTATCGCAACTGATTATC
TTTTATGATAATGATTTTC

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
AAAAACGAGAATTATTCGC
... ... PA0472 PA0471 fiuA PA0473 PA0474 PA0475 PA0476
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
ACGATTGAAAATCATTATC
... ... PA3410 PA3409 PA3411 PA3412
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
ACGATTGCTAATCAATCTT PA0929,
... ... PA0929 gacS ldhA PA0926 PA0925 PA0924 dinB PA0922.1 PA0930
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
ATAATTGAGAATCGTTATT hemO,
... ... hemO PA0671 PA0670 PA0669 PA0673
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
CTGAATGAAACCCAATCTT PA4634,
... ... PA4634 PA4633 PA4635
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
CTTGATGAGAATTATTATA
... ... fpvI pvdA pvdQ fpvR pvdR pvdT opmQ pvdP
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
GAAAACAATAATCAATCTC
... ... 5000000 PA4471 fumC1 PA4469 sodM PA4467 PA4466 PA4465 ptsN PA4463 rpoN pmbA PA4473 PA4474 PA4475 PA4476 cafA PA4478 mreD mreC mreB
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
GAAGATGGTAATTAATTGC pmpR,
... ... pmpR ruvB ruvA ruvC aspS PA0968 tolQ tolR tolA tolB oprL PA0974 PA0975 PA0976 PA0976.1 PA0977
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
GACATTGAGATTCAATAAC hemO,
... ... hemO PA0671 PA0670 PA0669 PA0673
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
GCAAACGATATTCATTATC nuoA,
... ... nuoA PA2636 PA2635 nuoB nuoD nuoE nuoF nuoG nuoH nuoI nuoJ nuoK nuoL nuoM nuoN PA2650
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
GCCAATGATATTGATTTGC PA4515,
... ... PA4515 PA4514 PA4516 PA4517 PA4518 speC
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
GGAAATGAGAATCATTATT
... ... prrF1 cbpA PA4703 prrF2 PA4705 PA4706 PA4707 phuT PA4709
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
GTAATTGACAATCATTATC pvdS,
... ... pvdS pvdG pvdL PA2427 PA2428
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
GTTATTGAGAATCATTGGC cyoE,
... ... cyoE cyoD cyoC cyoB cyoA PA1322 PA1323 PA1324 PA1324.1 PA1325 ilvA2 PA1327 PA1328 PA1329 PA1330 PA1331
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
TAAATTTATAATAATTCTC
... ... fpvI pvdA pvdQ fpvR pvdR pvdT opmQ pvdP
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
TCCAATGCAAATCAATATC PA4515,
... ... PA4515 PA4514 PA4516 PA4517 PA4518 speC
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
TTTATCGCAACTGATTATC PA4513,
... ... PA4513 PA4514
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified
TTTTATGATAATGATTTTC PA3410,
... ... PA3410 PA3409 PA3411 PA3412
Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Genomic SELEX (ECO:0005634) - Experimental technique details RNAse protection (ECO:0000288) - repressor not specified