DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis.
DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis.
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DOI：
10.1371/journal.pone.0150189
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Johnson RC
中科院分区：
文献类型：
--
作者：
Hancock SP;Stella S;Cascio D;Johnson RC
丰富的Fis类核蛋白以高亲和力选择性地结合不相关的DNA序列以调节不同的DNA反应。Fis主要通过DNA骨架接触结合DNA，并通过阅读DNA序列的构象特性（最显著的是固有小沟宽度）选择靶位点。高亲和力结合需要取决于DNA序列而变化的Fis-stabilized DNA构象变化。为了更好地理解高亲和力位点识别的分子基础，我们分析了核心Fis结合位点内和侧翼的DNA序列对结合亲和力和DNA结构的影响。在结合位点的非接触中心或在大沟界面内的变化中含有可变序列的Fis-DNA复合物的X射线晶体结构表明，DNA可以不对称地适应Fis二聚体表面。我们发现，嘧啶嘌呤碱基步骤的存在和位置内的大沟接口影响本地DNA弯曲和小沟压缩，以调节亲和力和寿命的Fis-DNA复合物。侧翼的核心结合位点的序列也调节复杂的亲和力，寿命，以及局部和全球的Fis-induced DNA弯曲的程度。特别是，G直接上游的15 bp的核心序列抑制结合和弯曲，和A-区间内的侧翼碱基对增加复杂的寿命和全球DNA曲率。两者合计，我们的观察结果支持修订后的DNA基序指定高亲和力的Fis结合，并突出显示了Fis结合的DNA可以采用的构象范围。个别Fis-DNA复合物的亲和力和DNA构象很可能是针对其特定的生物功能。
The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequences in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. The affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.