Bacterial genomes are folded and organized into compact yet dynamic structures, called nucleoids. Nucleoid orchestration involves many factors at multiple length scales, such as nucleoid‐associated proteins and liquid–liquid phase separation, and has to be compatible with replication and transcription. Possibly, genome organization plays an intrinsic role in transcription regulation, in addition to classical transcription factors. In this review, we provide arguments supporting this view using the Gram‐positive bacterium Bacillus subtilis as a model. Proteins BsSMC, HBsu and Rok all impact the structure of the B. subtilis chromosome. Particularly for Rok, there is compelling evidence that it combines its structural function with a role as global gene regulator. Many studies describe either function of Rok, but rarely both are addressed at the same time. Here, we review both sides of the coin and integrate them into one model. Rok forms unusually stable DNA–DNA bridges and this ability likely underlies its repressive effect on transcription by either preventing RNA polymerase from binding to DNA or trapping it inside DNA loops. Partner proteins are needed to change or relieve Rok‐mediated gene repression. Lastly, we investigate which features characterize H‐NS‐like proteins, a family that, at present, lacks a clear definition.

中文翻译：

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来自枯草芽孢杆菌的 Rok：桥接基因组结构和转录调控

细菌基因组被折叠并组织成紧凑而动态的结构，称为类核。类核编排涉及多个长度尺度的许多因素，例如类核相关蛋白和液-液相分离，并且必须与复制和转录兼容。除了经典转录因子之外，基因组组织可能在转录调控中发挥着内在作用。在这篇综述中，我们使用革兰氏阳性细菌提供了支持这一观点的论据枯草芽孢杆菌作为模特。蛋白质 BsSMC、HBsu 和 Rok 都会影响枯草芽孢杆菌染色体。特别是对于 Rok 来说，有令人信服的证据表明它将其结构功能与全球基因调节器的作用结合起来。许多研究描述了 Rok 的任一功能，但很少同时讨论这两种功能。在这里，我们回顾了硬币的两面，并将它们集成到一个模型中。 Rok 形成异常稳定的 DNA-DNA 桥，这种能力可能是其通过阻止 RNA 聚合酶与 DNA 结合或将其捕获在 DNA 环内而对转录产生抑制作用的基础。需要伙伴蛋白来改变或缓解 Rok 介导的基因抑制。最后，我们研究了 H-NS 类蛋白的哪些特征，该家族目前缺乏明确的定义。