Curation Information

Publication
A high-throughput method to examine protein-nucleotide interactions identifies targets of the bacterial transcriptional regulatory protein fur.;Yu C, Lopez CA, Hu H, Xia Y, Freedman DS, Reddington AP, Daaboul GG, Unl├╝ MS, Genco CA;PloS one 2014; 9(5):e96832 [24811061]
TF
Fur [Q5F5Y9, view regulon]
Reported TF sp.
Neisseria gonorrhoeae F62
Reported site sp.
Neisseria gonorrhoeae FA 1090
Created by
Dinara Sagitova
Curation notes
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Experimental Process

Fur binding motif was identified from previously determined Fur binding sites. This motif was used to search for putative Fur binding sequences throughout the N. gonorrhoeae FA1090 genome. Interferometric Reflectance Imaging Sensor confirmed in vitro binding of Fur to the predicted Fur boxes. EMSAs were performed to further validate two of the newly identified Fur bound probes. qRT-PCR of N. gonorrhoeae wild type, fur mutant, and fur complemented strains identified the role of Fur in transcription of iron-induced genes containing a functional Fur box in their promoter regions.

Transcription Factor Binding Sites


TTAAAATAGAACCATTATC
TATAAAAAAGAGCATTGTT
TATTATATAAATTTTTAGC
TTAATTAACTTTTGTTTTA
TACACTAAGTATCTTATTT
TATAATAAAATCAATTCTT
TTTAAAAAAAATCAATTTT
TGAAAAAAGAATCCATATC
TAATATCAATATATTGATT
ACAAAGAAGTATACTTCTT
CCATACAACTATATTTTTT
AAGAAAAAAGATGATTTTC
TATAAAAAGAAAGTATTTT
TAAAAGAAAACTCATTCTC
TTAAAATAGAACCATTATC
TATAAAAAAGAGCATTGTT
TATTATATAAATTTTTAGC
TTAATTAACTTTTGTTTTA
TACACTAAGTATCTTATTT
TATAATAAAATCAATTCTT
TTTAAAAAAAATCAATTTT
TGAAAAAAGAATCCATATC
TAATATCAATATATTGATT
ACAAAGAAGTATACTTCTT
CCATACAACTATATTTTTT
AAGAAAAAAGATGATTTTC
TATAAAAAGAAAGTATTTT
TAAAAGAAAACTCATTCTC

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
TTAAAATAGAACCATTATC
... ... NGO0073 NGO0076 NGO0077
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified dimer
TATAAAAAAGAGCATTGTT
... ... engB NGO0101
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified dimer
TATTATATAAATTTTTAGC NGO0155,
... ... NGO0155 NGO0156
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TTAATTAACTTTTGTTTTA
... ... pheT ihfA NGO0306
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified dimer
TACACTAAGTATCTTATTT panB,
... ... panB NGO0435 NGO0434 NGO_t09 panC
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
TATAATAAAATCAATTCTT NGO0641,
... ... NGO0641 NGO0640
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer
TTTAAAAAAAATCAATTTT
... ... greA NGO0900
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified dimer
TGAAAAAAGAATCCATATC
... ... hslO NGO1190 NGO1191 NGO1192 NGO1193 argJ NGO1195
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified dimer
TAATATCAATATATTGATT
... ... NGO1283 NGO1282 NGO1284 nusA infB
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified dimer
ACAAAGAAGTATACTTCTT
... ... NGO1419
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified dimer
CCATACAACTATATTTTTT NGO1738,
... ... NGO1738 NGO1737 NGO1736
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - activator dimer
AAGAAAAAAGATGATTTTC
... ... rpsL NGO1844 NGO1843 NGO1842 rpsJ
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified dimer
TATAAAAAGAAAGTATTTT
... ... NGO1948 NGO1947 NGO1946 NGO1945 NGO1944 NGO1943 NGO1949 prfB
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - not specified dimer
TAAAAGAAAACTCATTCTC NGO1957,
... ... NGO1957 NGO1956 NGO1955
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details Interferometric Reflectance Imaging Sensor (ECO:0005645) - Experimental technique details PSSM site search (ECO:0005659) - Experimental technique details qRT-PCR [RNA] (ECO:0001808) - repressor dimer