Abstract Bacterial genomes have been shown to be partitioned into several kilobases long chromosomal domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbors. Both in vivo and in vitro experiments have been performed to question the nature of the topological barriers at play, leading to several predictions on possible molecular actors. Here, we address the question of topological barriers using polymer models of supercoiled DNA chains that are constrained such as to mimic the action of predicted molecular actors. More specifically, we determine under which conditions DNA-bridging proteins may act as topological barriers. To this end, we developed a coarse-grained bead-and-spring model and investigated its properties through Brownian dynamics simulations. As a result, we find that DNA-bridging proteins must exert rather strong constraints on their binding sites: they must block the diffusion of the excess of twist through the two binding sites on the DNA molecule and, simultaneously, prevent the rotation of one DNA segment relative to the other one. Importantly, not all DNA-bridging proteins satisfy this second condition. For example, single bridges formed by proteins that bind DNA non-specifically, like H-NS dimers, are expected to fail with this respect. Our findings might also explain, in the case of specific DNA-bridging proteins like LacI, why multiple bridges are required to create stable independent topological domains. Strikingly, when the relative rotation of the DNA segments is not prevented, relaxation results in complex intrication of the two domains. Moreover, while the value of the torsional stress in each domain may vary, their differential is preserved. Our work also predicts that nucleoid associated proteins known to wrap DNA must form higher protein-DNA complexes to efficiently work as topological barriers.

中文翻译：

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对 DNA 桥接蛋白作为细菌基因组拓扑屏障的要求

摘要 细菌基因组已被证明被划分为数千碱基长的染色体域，这些域在拓扑上彼此独立，这意味着一个域中 DNA 超螺旋的变化不会传播到邻居。已经进行了体内和体外实验以质疑正在发挥作用的拓扑障碍的性质，从而对可能的分子参与者进行了一些预测。在这里，我们使用受约束的超螺旋 DNA 链的聚合物模型来解决拓扑障碍的问题，例如模拟预测分子参与者的行为。更具体地说，我们确定在哪些条件下 DNA 桥接蛋白可以充当拓扑屏障。为此，我们开发了一个粗粒度的珠子和弹簧模型，并通过布朗动力学模拟研究了它的特性。结果，我们发现 DNA 桥接蛋白必须对其结合位点施加相当强的约束：它们必须阻止过量扭曲通过 DNA 分子上的两个结合位点扩散，同时阻止一个 DNA 的旋转段相对于另一段。重要的是，并非所有 DNA 桥接蛋白都满足第二个条件。例如，由非特异性结合 DNA 的蛋白质形成的单桥，如 H-NS 二聚体，预计会在这方面失败。我们的发现还可以解释，在特定 DNA 桥接蛋白（如 LacI）的情况下，为什么需要多个桥来创建稳定的独立拓扑域。引人注目的是，当不阻止 DNA 片段的相对旋转时，松弛会导致两个域的复杂错综复杂。而且，虽然每个域中的扭转应力值可能会有所不同，但它们的差异仍然存在。我们的工作还预测，已知包裹 DNA 的类核蛋白必须形成更高的蛋白质-DNA 复合物才能有效地作为拓扑屏障。