Curation Information

Publication
Transcriptional and functional analysis of the Neisseria gonorrhoeae Fur regulon.;Jackson LA, Ducey TF, Day MW, Zaitshik JB, Orvis J, Dyer DW;Journal of bacteriology 2010 Jan; 192(1):77-85 [19854902]
TF
Fur [Q5F961, view regulon]
Reported TF sp.
Neisseria gonorrhoeae FA 1090
Reported site sp.
Neisseria gonorrhoeae FA 1090
Created by
Dinara Sagitova
Curation notes
-
External databases
NCBI GEO (GSE16352) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16352.

Experimental Process

The effect of iron on the global gene expression of FA1090 was determined over a 4-h period by comparing the transcriptional profile of the organism grown under iron-depleted conditions to that for growth under iron-replete conditions. In order to predict the location of potential FB sequences, HMMer and Meta-MEME programs were trained using functional FB seed sequences from organisms whose Fur proteins shared high degrees of identity and conservation with the gonococcal Fur protein and the entire genome FA1090 genome was scanned. To test these in silico FB predictions, an FA1090 genomic library was screened for the ability to titrate gonococcal Fur in an E. coli background using the FURTA.

Transcription Factor Binding Sites


TTAAAATAGAACCATTATC
ATAATGGTAACGATTATT
ATATTGATTATCATT
ATAAATGCAAATAATTATT
AAAAATAGGAACAATTATC
CTTATTGATATTAATTCTT
ATATTAATAATAATTA
AATTAAAACTCATTATCA
GAAAATTACTTTTATTATC
AATAAGAATTATTTTCA
TGTAATGATAATTATTATC
TGATAATAACTATCATTAT
TGATAATAACTATCATTAT
TGATAATCATTA
ATAAACGAAATTTATTATC
ATAAATAATAATTATTATC
AAGAATGATAAGGATTATT
AAATAAGAATCGTTATCA
GCGAACGATAATCATACGC
GCTAATAATAATAATTATC
ATAAATGATAATCTATATC
AAAAATAATAATAATTATT
AAATGATAACCTTTATCA
TTAAAATAGAACCATTATC
ATAATGGTAACGATTATT
ATATTGATTATCATT
ATAAATGCAAATAATTATT
AAAAATAGGAACAATTATC
CTTATTGATATTAATTCTT
ATATTAATAATAATTA
AATTAAAACTCATTATCA
GAAAATTACTTTTATTATC
AATAAGAATTATTTTCA
TGTAATGATAATTATTATC
TGATAATAACTATCATTAT
TGATAATAACTATCATTAT
TGATAATCATTA
ATAAACGAAATTTATTATC
ATAAATAATAATTATTATC
AAGAATGATAAGGATTATT
AAATAAGAATCGTTATCA
GCGAACGATAATCATACGC
GCTAATAATAATAATTATC
ATAAATGATAATCTATATC
AAAAATAATAATAATTATT
AAATGATAACCTTTATCA

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,
... ... NGO0073 NGO0076 NGO0077
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - repressor not specified
ATAATGGTAACGATTATT NGO0108,
... ... NGO0108 NGO0107 NGO0109
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - activator not specified
ATATTGATTATCATT NGO0114,
... ... NGO0114 NGO0113
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - activator not specified
ATAAATGCAAATAATTATT NGO0217,
... ... NGO0217 NGO0216 NGO0215
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - activator not specified
AAAAATAGGAACAATTATC NGO0322
... ... NGO0322
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - activator not specified
CTTATTGATATTAATTCTT NGO0432,
... ... NGO0432 NGO0433
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - repressor not specified
ATATTAATAATAATTA NGO0553
... ... NGO0553
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - activator not specified
AATTAAAACTCATTATCA NGO0554
... ... NGO0554
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - activator not specified
GAAAATTACTTTTATTATC NGO0652,
... ... NGO0652 NGO0653
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - activator not specified
AATAAGAATTATTTTCA NGO0711,
... ... NGO0711 NGO0710
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - repressor not specified
TGTAATGATAATTATTATC NGO0904,
... ... NGO0904 NGO0903 NGO0902 NGO0901 NGO0905 NGO0906
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - repressor not specified
TGATAATAACTATCATTAT NGO1275,
... ... NGO1275 NGO1276
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - activator not specified
TGATAATAACTATCATTAT NGO1276,
... ... NGO1276 NGO1275
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - repressor not specified
TGATAATCATTA NGO1317
... ... NGO1317
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - repressor not specified
ATAAACGAAATTTATTATC NGO1318,
... ... NGO1318 NGO1319 NGO1320 NGO1321 NGO1322 NGO1323
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - activator not specified
ATAAATAATAATTATTATC NGO1430,
... ... NGO1430 NGO1431 NGO1432
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - repressor not specified
AAGAATGATAAGGATTATT NGO1496,
... ... NGO1496 NGO1495
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - activator not specified
AAATAAGAATCGTTATCA NGO1751,
... ... NGO1751 NGO1750 NGO1749 NGO1748 NGO1747
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - repressor not specified
GCGAACGATAATCATACGC NGO1779,
... ... NGO1779 aat NGO1780 NGO1781
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - activator not specified
GCTAATAATAATAATTATC
... ... NGO2003
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - not specified not specified
ATAAATGATAATCTATATC NGO2092
... ... NGO2092
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - activator not specified
AAAAATAATAATAATTATT NGO2093,
... ... NGO2093 groES groEL
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - activator not specified
AAATGATAACCTTTATCA NGO2116,
... ... NGO2116 NGO2117 NGO2118 NGO2119 NGO2120 NGO2121 NGO2122 NGO2123 NGO2124
Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details FURTA (ECO:0005633) - Experimental technique details Machine learning prediction (ECO:0005649) - repressor not specified