How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome.
How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome.
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细菌异种沉默子rok如何区分其常驻基因组中的外来DNA和自身DNA
DOI：
10.1093/nar/gky836
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发表时间：
2018-11-02
影响因子：
14.9
通讯作者：
Xia B
中科院分区：
文献类型：
--
作者：
Duan B;Ding P;Hughes TR;Navarre WW;Liu J;Xia B
细菌异种沉默子通过识别和抑制通过水平基因转移获得的外源基因的表达在细菌进化中发挥重要作用，从而缓冲其错误表达的潜在适应性后果。在这里，详细的DNA结合特性的Rok，在枯草芽孢杆菌的异种沉默，研究了使用蛋白质结合芯片，并确定其C-末端DNA结合结构域的溶液结构与DNA的复合物。Rok的C端结构域具有典型的翼状螺旋结构，具有不同于其他翼状螺旋蛋白或异种沉默子的新型DNA识别机制。Rok通过α3螺旋N端的N154、T156和W1翼区的R174与碱基形成氢键结合DNA小沟，并由4个赖氨酸残基与DNA骨架磷酸基团静电相互作用辅助。这些结构特征赋予Rok对含有AACTA、TACTA和柔性多TpA步骤的DNA序列的偏好，而刚性A-片段是不利的。相应地，含有Rok的芽孢杆菌属基因组富含A区，并且显示出AACTA和TACTA的显著代表性不足，AACTA和TACTA在Rok结合区中显著富集。这些观察结果表明，异种沉默蛋白和它的居民基因组可能已经协同进化。
Bacterial xenogeneic silencers play important roles in bacterial evolution by recognizing and inhibiting expression from foreign genes acquired through horizontal gene transfer, thereby buffering against potential fitness consequences of their misregulated expression. Here, the detailed DNA binding properties of Rok, a xenogeneic silencer in Bacillus subtilis, was studied using protein binding microarray, and the solution structure of its C-terminal DNA binding domain was determined in complex with DNA. The C-terminal domain of Rok adopts a typical winged helix fold, with a novel DNA recognition mechanism different from other winged helix proteins or xenogeneic silencers. Rok binds the DNA minor groove by forming hydrogen bonds to bases through N154, T156 at the N-terminal of α3 helix and R174 of wing W1, assisted by four lysine residues interacting electrostatically with DNA backbone phosphate groups. These structural features endow Rok with preference towards DNA sequences harboring AACTA, TACTA, and flexible multiple TpA steps, while rigid A-tracts are disfavored. Correspondingly, the Bacillus genomes containing Rok are rich in A-tracts and show a dramatic underrepresentation of AACTA and TACTA, which are significantly enriched in Rok binding regions. These observations suggest that the xenogeneic silencing protein and its resident genome may have evolved cooperatively.
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PCG2 识别 DNA 的结构基础揭示了翼状螺旋-转角-螺旋结构域的新型 DNA 结合模式。
影响因子：
14.9
作者：
Liu J;Huang J;Zhao Y;Liu H;Wang D;Yang J;Zhao W;Taylor IA;Peng YL
通讯作者：
Peng YL
DOI：
10.1073/pnas.0913551107
发表时间：
2010-03-16
影响因子：
11.1
作者：
Gordon, Blair R. G.;Li, Yifei;Liu, Jun
通讯作者：
Liu, Jun
影响因子：
46.9
作者：
Berger, Michael F.;Philippakis, Anthony A.;Bulyk, Martha L.
通讯作者：
Bulyk, Martha L.
影响因子：
5.7
作者：
Blanco, AG;Sola, M;Coll, M
通讯作者：
Coll, M
影响因子：
14.9
作者：
Blanchet C;Pasi M;Zakrzewska K;Lavery R
通讯作者：
Lavery R