Discovery of Fur binding site clusters in Escherichia coli by information theory models.
Discovery of Fur binding site clusters in Escherichia coli by information theory models.
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DOI：
10.1093/nar/gkm631
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发表时间：
2007
影响因子：
14.9
通讯作者：
Schneider TD
中科院分区：
文献类型：
--
作者：
Chen Z;Lewis KA;Shultzaberger RK;Lyakhov IG;Zheng M;Doan B;Storz G;Schneider TD
Fur是抑制细菌铁吸收系统的DNA结合蛋白。十一足迹大肠杆菌毛皮结合位点被用来创建一个初始的信息理论模型的毛皮结合，然后通过添加13个实验证实的网站进行改进。当在所有可用的足迹序列上扫描改进的模型时，序列步行者（sequence walkers）（预测结合位点的视觉识别）经常出现在适合足迹的簇中（约83%覆盖率）。这表明该模型可以准确地预测Fur结合。在这些簇中，个体步行者与它们的邻居正好相隔3或6个碱基，这与毛皮二聚体结合在DNA螺旋的不同表面上的模型一致。当E.对大肠杆菌全基因组进行了扫描，发现了363个独特的簇，其中包括所有已知的与铁代谢有关的皮毛抑制基因。相比之下，只有少数已知的毛皮激活基因预测毛皮结合位点在其启动子。这些观察结果表明，Fur是直接阻遏物或间接激活物。铜绿假单胞菌和枯草芽孢杆菌Fur模型与E. coli Fur模型，表明Fur-DNA识别机制可能是保守的，即使是远亲细菌。
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 (∼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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影响因子：
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作者：
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