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Abstract：
Computational searches for DNA binding sites often utilize consensus sequences. These search models make assumptions that the frequency of a base pair in an alignment relates to the base pair\'s importance in binding and presume that base pairs contribute independently to the overall interaction with the DNA-binding protein. These two assumptions have generally been found to be accurate for DNA binding sites. However, these assumptions are often not satisfied for promoters, which are involved in additional steps in transcription initiation after RNA polymerase has bound to the DNA. To test these assumptions for the flagellar regulatory hierarchy, class 2 and class 3 flagellar promoters were randomly mutagenized in Salmonella. Important positions were then saturated for mutagenesis and compared to scores calculated from the consensus sequence. Double mutants were constructed to determine how mutations combined for each promoter type. Mutations in the binding site for FlhD4C2, the activator of class 2 promoters, better satisfied the assumptions for the binding model than did mutations in the class 3 promoter, which is recognized by the sigma(28) transcription factor. These in vivo results indicate that the activator sites within flagellar promoters can be modeled using simple assumptions, but that the DNA sequences recognized by the flagellar sigma factor require more complex models.
摘要：
DNA结合位点的计算搜索通常利用共有序列。这些搜索模型假设比对中碱基对的频率与碱基对在结合中的重要性相关,并且假设碱基对独立地促成与DNA结合蛋白的整体相互作用。这两种假设通常被发现对于DNA结合位点是准确的。然而,这些假设对于发起人来说往往是不满足的，它们参与RNA聚合酶与DNA结合后转录起始的其他步骤。为了测试鞭毛调节等级的这些假设，在沙门氏菌中随机诱变2类和3类鞭毛启动子。然后使重要位置饱和以进行诱变,并与从共有序列计算的分数进行比较。构建双突变体以确定每种启动子类型的突变如何组合。FlhD4C2结合位点的突变，FlhD4C2是2类启动子的激活剂，比3类启动子中的突变更好地满足结合模型的假设，它被sigma(28)转录因子识别。这些体内结果表明，鞭毛启动子内的激活位点可以使用简单的假设进行建模，但是鞭毛sigma因子识别的DNA序列需要更复杂的模型。
