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Discovery of Fur binding site clusters in Escherichia coli by information theory models.

Chen Z, Lewis KA, Shultzaberger RK, Lyakhov IG, Zheng M, Doan B, Storz G, Schneider TD - Nucleic Acids Res. (2007)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: National Cancer Institute at Frederick, Center for Cancer Research Nanobiology Program, Basic Research Program, SAIC-Frederick, Inc., Frederick, MD 21702-1201, USA.

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.

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Different Fur binding models to interpret the Fur box.
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Figure 6: Different Fur binding models to interpret the Fur box.

Mentions: Several other consensus-based Fur binding site models have been proposed to interpret a 19-bp consensus ‘Fur box’ (Figure 6) (65). Within these, two earlier models, the classical model and hexamer model (5,7,37,54), interpreted the ‘Fur box’ as a single recognition unit of a Fur dimer. Later, Lavrrar and McIntosh suggested that a 13-bp inverted repeat (6-1-6) is the minimal unit recognized by a single Fur dimer, and that two overlapping ‘6-1-6’ motifs correspond to the Fur box, which is required for high-affinity binding of Fur (55,58). Baichoo and Helmann reinterpreted the Fur box as two overlapping 7-1-7 inverted repeats with a 6-bp spacing, and suggested that a 7-1-7 site, but not 6-1-6, represents the minimal recognition unit of Fur (40). Baichoo and Helmann also demonstrated that high-affinity binding by Fur can happen on a single-dimer binding site, i.e. an inverted 7-1-7 site.Figure 6.


Discovery of Fur binding site clusters in Escherichia coli by information theory models.

Chen Z, Lewis KA, Shultzaberger RK, Lyakhov IG, Zheng M, Doan B, Storz G, Schneider TD - Nucleic Acids Res. (2007)

Different Fur binding models to interpret the Fur box.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2189734&req=5

Figure 6: Different Fur binding models to interpret the Fur box.
Mentions: Several other consensus-based Fur binding site models have been proposed to interpret a 19-bp consensus ‘Fur box’ (Figure 6) (65). Within these, two earlier models, the classical model and hexamer model (5,7,37,54), interpreted the ‘Fur box’ as a single recognition unit of a Fur dimer. Later, Lavrrar and McIntosh suggested that a 13-bp inverted repeat (6-1-6) is the minimal unit recognized by a single Fur dimer, and that two overlapping ‘6-1-6’ motifs correspond to the Fur box, which is required for high-affinity binding of Fur (55,58). Baichoo and Helmann reinterpreted the Fur box as two overlapping 7-1-7 inverted repeats with a 6-bp spacing, and suggested that a 7-1-7 site, but not 6-1-6, represents the minimal recognition unit of Fur (40). Baichoo and Helmann also demonstrated that high-affinity binding by Fur can happen on a single-dimer binding site, i.e. an inverted 7-1-7 site.Figure 6.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: National Cancer Institute at Frederick, Center for Cancer Research Nanobiology Program, Basic Research Program, SAIC-Frederick, Inc., Frederick, MD 21702-1201, USA.

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.

Show MeSH
Related in: MedlinePlus