Tartaglia L A, Gimeno C J, Storz G, Ames B N
Division of Biochemistry and Molecular Biology, University of California, Berkeley 94720.
J Biol Chem. 1992 Jan 25;267(3):2038-45.
The Escherichia coli OxyR protein, a regulator of hydrogen peroxide-inducible genes, is a potent stimulator of transcription in its oxidized form but not in its reduced form. OxyR protein purified in its oxidized form was found to bind four of its non-homologous, functional DNA-binding sites with over 10(6)-fold higher affinity than random DNA sequences. A similarly high DNA binding specificity was observed for the reduced (transcriptionally inactive) form of OxyR, consistent with a model in which the OxyR protein is bound to its recognition sequences even in the absence of an oxidative stress. Alignment of five functional OxyR-binding sites revealed a marked lack of perfectly conserved positions, yet an unusually high number of degenerate homologies (positions at which only two of the four possible base pairs are represented). Methylation interference assays on two OxyR-binding sites showed that OxyR contacts its recognition sequences predominantly at positions of degenerate homology. These results suggest that the OxyR protein specifically recognizes seemingly dissimilar sequences through the use of a multidegenerate recognition code. The chemical basis for a plausible degenerate recognition system is discussed.
大肠杆菌OxyR蛋白是过氧化氢诱导基因的调节因子，其氧化形式是转录的有效刺激剂，而还原形式则不是。发现以氧化形式纯化的OxyR蛋白与其四个非同源功能性DNA结合位点结合，其亲和力比随机DNA序列高10^6倍以上。对于OxyR的还原（转录无活性）形式，也观察到了类似的高DNA结合特异性，这与即使在没有氧化应激的情况下OxyR蛋白也与其识别序列结合的模型一致。五个功能性OxyR结合位点的比对显示，明显缺乏完全保守的位置，但存在异常高数量的简并同源性（四个可能碱基对中只有两个出现的位置）。对两个OxyR结合位点的甲基化干扰试验表明，OxyR主要在简并同源性位置与其识别序列接触。这些结果表明，OxyR蛋白通过使用多重简并识别密码特异性识别看似不同的序列。本文还讨论了一个合理的简并识别系统的化学基础。
