PMID:17921503

Citation	Chen, Z, Lewis, KA, Shultzaberger, RK, Lyakhov, IG, Zheng, M, Doan, B, Storz, G and Schneider, TD (2007) Discovery of Fur binding site clusters in Escherichia coli by information theory models. Nucleic Acids Res. 35:6762-77
Abstract	Fur is a DNA binding protein that represses bacterial iron uptake systems. Eleven footprinted Escherichia coli Fur binding sites were used to create an initial information theory model of Fur binding, which was then refined by adding 13 experimentally confirmed sites. When the refined model was scanned across all available footprinted sequences, sequence walkers, which are visual depictions of predicted binding sites, frequently appeared in clusters that fit the footprints ( approximately 83% coverage). This indicated that the model can accurately predict Fur binding. Within the clusters, individual walkers were separated from their neighbors by exactly 3 or 6 bases, consistent with models in which Fur dimers bind on different faces of the DNA helix. When the E. coli genome was scanned, we found 363 unique clusters, which includes all known Fur-repressed genes that are involved in iron metabolism. In contrast, only a few of the known Fur-activated genes have predicted Fur binding sites at their promoters. These observations suggest that Fur is either a direct repressor or an indirect activator. The Pseudomonas aeruginosa and Bacillus subtilis Fur models are highly similar to the E. coli Fur model, suggesting that the Fur-DNA recognition mechanism may be conserved for even distantly related bacteria.
Links	PubMed PMC2189734 Online version:10.1093/nar/gkm631
Keywords	Bacillus subtilis/metabolism; Bacterial Proteins/chemistry; Bacterial Proteins/metabolism; Base Sequence; Binding Sites; DNA Footprinting; Escherichia coli/genetics; Escherichia coli/metabolism; Models, Biological; Pseudomonas aeruginosa/metabolism; Repressor Proteins/chemistry; Repressor Proteins/metabolism
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
ECOLI:FUR	enables	GO:0043565: sequence-specific DNA binding	ECO:0001807: electrophoretic mobility shift assay evidence used in manual assertion		F		Seeded From UniProt	complete
ECOLI:FUR	part_of	GO:0032993: protein-DNA complex	ECO:0001807: electrophoretic mobility shift assay evidence used in manual assertion		C		Seeded From UniProt	complete

References

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