Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, UK.
Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK.
Cell Rep. 2020 Jul 21;32(3):107928. doi: 10.1016/j.celrep.2020.107928.
Specific interactions between proteins and DNA are essential to many biological processes. Yet, it remains unclear how the diversification in DNA-binding specificity was brought about, and the mutational paths that led to changes in specificity are unknown. Using a pair of evolutionarily related DNA-binding proteins, each with a different DNA preference (ParB [Partitioning Protein B] and Noc [Nucleoid Occlusion Factor], which both play roles in bacterial chromosome maintenance), we show that specificity is encoded by a set of four residues at the protein-DNA interface. Combining X-ray crystallography and deep mutational scanning of the interface, we suggest that permissive mutations must be introduced before specificity-switching mutations to reprogram specificity and that mutational paths to new specificity do not necessarily involve dual-specificity intermediates. Overall, our results provide insight into the possible evolutionary history of ParB and Noc and, in a broader context, might be useful for understanding the evolution of other classes of DNA-binding proteins.
蛋白质与 DNA 之间的特定相互作用对许多生物过程至关重要。然而，目前尚不清楚 DNA 结合特异性的多样化是如何产生的，也不知道导致特异性变化的突变途径。我们使用一对进化上相关的 DNA 结合蛋白，它们各自具有不同的 DNA 偏好（ParB[分隔蛋白 B]和 Noc[核区封闭因子]，它们在细菌染色体维持中都发挥作用），表明特异性是由蛋白质-DNA 界面上的一组四个残基编码的。结合 X 射线晶体学和界面的深度突变扫描，我们提出，在特异性转换突变之前必须引入允许性突变，以重新编程特异性，并且到新特异性的突变途径不一定涉及双特异性中间体。总的来说，我们的研究结果为 ParB 和 Noc 的可能进化历史提供了一些见解，更广泛地说，可能有助于理解其他类 DNA 结合蛋白的进化。
