Redefining Escherichia coli σ70 Promoter Elements: -15 Motif as a Complement of the -10 Motif
Redefining Escherichia coli σ70 Promoter Elements: -15 Motif as a Complement of the -10 Motif
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DOI：
10.1128/jb.05947-11
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发表时间：
2011-11-01
影响因子：
3.2
通讯作者：
Djordjevic, Marko
中科院分区：
文献类型：
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作者：
Djordjevic, Marko
σ（70）细菌启动子的经典元件包括-35元件（（-35）TTGACA（-30））、-10元件（（-12）TATAAT（-7））和延伸的-10元件（（-15）TG（-14））。尽管-35元件、延伸的-10元件和-10元件中的最上游碱基（T-12）以双链DNA（dsDNA）形式与sigma（70）相互作用，但-10基序中的下游碱基（（-11）ATAAT（-7））负责sigma（70）-单链DNA（ssDNA）相互作用。为了直接反映这种对应关系，最近提出了将扩展的-10元素扩展为所谓的-15元素（（-15）TGnT（-12））。我在这里研究了所提出的-15元件的序列特异性及其与其他启动子元件的关系。我发现了一个以前未检测到的（-13）G的显着保守性和T-15的高简并性。因此，我将-15元件定义为简并基序，它与-15和-12之间的保守序列一起，允许类似于-35和-10元件来处理该元件。此外，-15元件的强度与-35元件和-10元件的强度呈负相关，而在其他启动子元件之间没有发现这种互补。我发现这个元素有一个明显更强的趋势，以补充参与sigma（70）-ssDNA相互作用的弱-10元素。这一发现与已建立的观点相反，根据该观点，-15元件提供了足够数量的σ（70）-dsDNA相互作用，并表明决定功能性启动子的主要参数是整体启动子强度。
Classical elements of sigma(70) bacterial promoters include the -35 element ((-35)TTGACA(-30)), the -10 element ((-12)TATAAT(-7)), and the extended -10 element ((-15)TG(-14)). Although the -35 element, the extended -10 element, and the upstream-most base in the -10 element (T-12) interact with sigma(70) in double-stranded DNA (dsDNA) form, the downstream bases in the -10 motif ((-11)ATAAT(-7)) are responsible for sigma(70)-single-stranded DNA (ssDNA) interactions. In order to directly reflect this correspondence, an extension of the extended -10 element to a so-called -15 element ((-15)TGnT(-12)) has been recently proposed. I investigated here the sequence specificity of the proposed -15 element and its relationship to other promoter elements. I found a previously undetected significant conservation of (-13)G and a high degeneracy at T-15. I therefore defined the -15 element as a degenerate motif, which, together with the conserved stretch of sequence between -15 and -12, allows treating this element analogously to -35 and -10 elements. Furthermore, the strength of the -15 element inversely correlates with the strengths of the -35 element and -10 element, whereas no such complementation between other promoter elements was found. Despite the direct involvement of -15 element in sigma(70)-dsDNA interactions, I found a significantly stronger tendency of this element to complement weak -10 elements that are involved in sigma(70)-ssDNA interactions. This finding is in contrast to the established view, according to which the -15 element provides a sufficient number of sigma(70)-dsDNA interactions, and suggests that the main parameter determining a functional promoter is the overall promoter strength.