Curation Information

Publication
The Fur repressor controls transcription of iron-activated and -repressed genes in Helicobacter pylori.;Delany I, Spohn G, Rappuoli R, Scarlato V;Molecular microbiology 2001 Dec; 42(5):1297-309 [11886560]
TF
Fur [B5Z6G7, view regulon]
Reported TF sp.
Helicobacter pylori G27
Reported site sp.
Helicobacter pylori G27
Created by
Matthew Coveyou
Curation notes
-

Experimental Process

A gene of interest was identified by SDS-PAGE of cell lysates from wild-type and fur-mutant cells, which indicated a protein (identified as pfr) was highly up-regulated in the fur mutant. Primer extension identified the transcription start site and demonstrated 30x pfr transcription in the fur mutant compared to the wild type, suggesting fur represses pfr. Further, in iron-variable assays, increased iron was shown to increase pfr transcript, and decreased iron reduced pfr transcript, though the fur mutant showed no response to changes in iron concentration. DNAse I protection demonstrated specific binding in the presence of a non-specific competitor, and revealed three putative binding sites displaying a “unique repeated pattern of dual binding sites flanking a hypersensitive site.” Additional protection assays of iron-variable cells showed fur-Fe2+ complex has reduced affinity for the pfr binding sites. The sites were aligned with each other and the Fur box of E. coli, and showed limited conservation.

Transcription Factor Binding Sites


GTTGTCCCATAATTATAGCATAAATGATAATGAAAAAGTA
ATTTTATCATAAAAATCTATTTAATGAGAATTAGGTAAA
GTTGTCCCATAATTATAGCATAAATGATAATGAAAAAGTA
ATTTTATCATAAAAATCTATTTAATGAGAATTAGGTAAA

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
GTTGTCCCATAATTATAGCATAAATGATAATGAAAAAGTA HPG27_615,
... ... HPG27_615 HPG27_614 HPG27_613 HPG27_616 HPG27_617 HPG27_618 HPG27_619 gatB HPG27_621 HPG27_622 HPG27_623 rnc HPG27_625 HPG27_626 HPG27_627 HPG27_628 HPG27_629 HPG27_630
Experimental technique details 2D PAGE (ECO:0005614) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) - repressor not specified
ATTTTATCATAAAAATCTATTTAATGAGAATTAGGTAAA HPG27_615,
... ... HPG27_615 HPG27_614 HPG27_613 HPG27_616 HPG27_617 HPG27_618 HPG27_619 gatB HPG27_621 HPG27_622 HPG27_623 rnc HPG27_625 HPG27_626 HPG27_627 HPG27_628 HPG27_629 HPG27_630
Experimental technique details 2D PAGE (ECO:0005614) - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details Multiple sequence alignment (MSA) (ECO:0005556) - Experimental technique details Primer Extension assay (ECO:0005657) - repressor not specified