Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins
Structural Mechanisms of Cooperative DNA Binding by Bacterial Single-Stranded DNA-Binding Proteins
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DOI：
10.1016/j.jmb.2018.11.019
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发表时间：
2019-01-18
影响因子：
5.6
通讯作者：
Keck, James L.
中科院分区：
文献类型：
--
作者：
Dubiel, Katarzyna;Myers, Angela R.;Keck, James L.
细菌编码同源寡聚单链 (ss) DNA 结合蛋白 (SSB)，这些蛋白包被并保护在基因组维持反应期间形成的 ssDNA 中间体。典型的大肠杆菌 SSB 四聚体可以使用多种模式结合 ssDNA，这些模式的不同之处在于每个四聚体结合的碱基数量和结合协同性的大小。由于连接 ssDNA 上相邻 SSB 蛋白的界面可用的结构信息有限，我们对 SSB 协同结合 ssDNA 的机制的理解受到了阻碍。在这里，我们展示了与 ssDNA 结合的枯草芽孢杆菌 SsbA 的晶体结构。该结构解析了通过 ssDNA“桥”连接在一起的 SsbA 四聚体，并确定了一个称为“桥接口”的界面，该界面通过 ssDNA 结合位点附近的进化保守表面连接相邻的 SSB 四聚体。具有改变的桥接界面残基的大肠杆菌 SSB 变体结合 ssDNA 时，协同性降低，并且 DNA 结合模式的分布发生改变。与野生型 SSB 相比，这些变体也更容易被 RecA 从 ssDNA 中取代。尽管存在这些生化差异，每种变体都能够补充大肠杆菌中 ssb 基因的缺失。我们的数据共同提出了一个模型，其中桥界面有助于协同 ssDNA 结合和 SSB 功能，但细胞中可以容忍桥界面的不稳定。 (C) 2018 Elsevier Ltd. 保留所有权利。
Bacteria encode homooligomeric single-stranded (ss) DNA-binding proteins (SSBs) that coat and protect ssDNA intermediates formed during genome maintenance reactions. The prototypical Escherichia coli SSB tetramer can bind ssDNA using multiple modes that differ by the number of bases bound per tetramer and the magnitude of the binding cooperativity. Our understanding of the mechanisms underlying cooperative ssDNA binding by SSBs has been hampered by the limited amount of structural information available for interfaces that link adjacent SSB proteins on ssDNA. Here we present a crystal structure of Bacillus subtilis SsbA bound to ssDNA. The structure resolves SsbA tetramers joined together by a ssDNA "bridge" and identifies an interface, termed the "bridge interface," that links adjacent SSB tetramers through an evolutionarily conserved surface near the ssDNA-binding site. E. coli SSB variants with altered bridge interface residues bind ssDNA with reduced cooperativity and with an altered distribution of DNA binding modes. These variants are also more readily displaced from ssDNA by RecA than wild-type SSB. In spite of these biochemical differences, each variant is able to complement deletion of the ssb gene in E. coli. Together our data suggest a model in which the bridge interface contributes to cooperative ssDNA binding and SSB function but that destabilization of the bridge interface is tolerated in cells. (C) 2018 Elsevier Ltd. All rights reserved.