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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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Comparison of M9 Fur models of three bacterial species. Experimentally proven Fur binding sites from E. coli (A), P. aeruginosa (B) and B. subtilis (C) were used to build the models for these three bacteria. The marked region from −7 to +7 in each logo indicates the 7-1-7 model that was proposed by Baichoo and Helmann (40).
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Figure 4: Comparison of M9 Fur models of three bacterial species. Experimentally proven Fur binding sites from E. coli (A), P. aeruginosa (B) and B. subtilis (C) were used to build the models for these three bacteria. The marked region from −7 to +7 in each logo indicates the 7-1-7 model that was proposed by Baichoo and Helmann (40).

Mentions: To strengthen our model, we added the 13 confirmed sites to the 11 previously footprinted sites (Figure 4A). As with the 11 sites, multiple alignment of the 24 sites using different window sizes also gave three classes of alignments, M12, M9 and M6 (Supplementary Figure S4). When these models were tested against the same set of sequences as that used to test the 11-site models (Table 1, Supplementary Figure S3), similar, but cleaner results were obtained, i.e. the weak walkers that were not counted previously become weaker (some are even below 0 bits), but the strong walkers still have similar Ri values (Supplementary Figure S5). This confirms that our counting of major walkers predicted by the initial 11-site models was reasonable.Figure 4.


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)

Comparison of M9 Fur models of three bacterial species. Experimentally proven Fur binding sites from E. coli (A), P. aeruginosa (B) and B. subtilis (C) were used to build the models for these three bacteria. The marked region from −7 to +7 in each logo indicates the 7-1-7 model that was proposed by Baichoo and Helmann (40).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: Comparison of M9 Fur models of three bacterial species. Experimentally proven Fur binding sites from E. coli (A), P. aeruginosa (B) and B. subtilis (C) were used to build the models for these three bacteria. The marked region from −7 to +7 in each logo indicates the 7-1-7 model that was proposed by Baichoo and Helmann (40).
Mentions: To strengthen our model, we added the 13 confirmed sites to the 11 previously footprinted sites (Figure 4A). As with the 11 sites, multiple alignment of the 24 sites using different window sizes also gave three classes of alignments, M12, M9 and M6 (Supplementary Figure S4). When these models were tested against the same set of sequences as that used to test the 11-site models (Table 1, Supplementary Figure S3), similar, but cleaner results were obtained, i.e. the weak walkers that were not counted previously become weaker (some are even below 0 bits), but the strong walkers still have similar Ri values (Supplementary Figure S5). This confirms that our counting of major walkers predicted by the initial 11-site models was reasonable.Figure 4.

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