Han Kook, Kim Kwang-Sun, Bak Geunu, Park Hongmarn, Lee Younghoon
Department of Chemistry, KAIST, Daejeon 305-701 and Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Korea.
Nucleic Acids Res. 2010 Sep;38(17):5851-66. doi: 10.1093/nar/gkq292. Epub 2010 May 7.
Five Sib antitoxin RNAs, members of a family of cis-encoded small regulatory RNAs (sRNAs) in Escherichia coli, repress their target mRNAs, which encode Ibs toxins. This target repression occurs only between cognate sRNA-mRNA pairs with an exception of ibsA. We performed co-transformation assays to assess the ability of SibC derivatives to repress ibsC expression, thereby revealing the regions of SibC that are essential for ibsC mRNA recognition. SibC has two target recognition domains, TRD1 and TRD2, which function independently. The target site for TRD1 is located within the ORF of ibsC, whereas the target site for TRD2 is located in the translational initiation region. The TRD1 sequence is sufficient to repress ibsC expression. In contrast, TRD2 requires a specific structure in addition to the recognition sequence. An in vitro structural probing analysis showed that the initial interactions at these two recognition sites allowed base-pairing to progress into the flanking sequences. Displacement of the TRD1 and TRD2 domains of SibC by the corresponding domains of SibD changed the target specificity of SibC from ibsC to ibsD, suggesting that these two elements modulate the cognate target recognition of each Sib RNA by discriminating among non-cognate ibs mRNAs.
五种Sib抗毒素RNA是大肠杆菌中顺式编码的小调节RNA（sRNA）家族的成员，它们抑制其靶标mRNA，这些mRNA编码Ibs毒素。这种靶标抑制仅发生在同源sRNA-mRNA对之间，ibsA除外。我们进行了共转化试验，以评估SibC衍生物抑制ibsC表达的能力，从而揭示SibC中对ibsC mRNA识别至关重要的区域。SibC有两个靶标识别结构域，TRD1和TRD2，它们独立发挥作用。TRD1的靶位点位于ibsC的开放阅读框内，而TRD2的靶位点位于翻译起始区域。TRD1序列足以抑制ibsC表达。相比之下，TRD2除了识别序列外还需要特定的结构。体外结构探测分析表明，这两个识别位点的初始相互作用允许碱基配对延伸到侧翼序列。SibD的相应结构域取代SibC的TRD1和TRD2结构域，将SibC的靶标特异性从ibsC改变为ibsD，这表明这两个元件通过区分非同源ibs mRNA来调节每个Sib RNA的同源靶标识别。
