Erkelens Amanda M, van Erp Bert, Meijer Wilfried J J, Dame Remus T
Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands.
Mol Microbiol. 2025 Feb;123(2):109-123. doi: 10.1111/mmi.15250. Epub 2024 Mar 21.
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.
细菌基因组被折叠并组织成紧凑而动态的结构，称为类核。类核调控涉及多个长度尺度上的许多因素，如类核相关蛋白和液-液相分离，并且必须与复制和转录相兼容。除了经典转录因子外，基因组组织可能在转录调控中发挥内在作用。在本综述中，我们以革兰氏阳性细菌枯草芽孢杆菌为模型，提供支持这一观点的论据。蛋白质BsSMC、HBsu和Rok都会影响枯草芽孢杆菌染色体的结构。特别是对于Rok，有令人信服的证据表明它将其结构功能与作为全局基因调节因子的作用结合在一起。许多研究只描述了Rok的一种功能，但很少同时涉及这两种功能。在这里，我们审视了问题的两面，并将它们整合到一个模型中。Rok形成异常稳定的DNA-DNA桥，这种能力可能是其对转录产生抑制作用的基础，其作用方式要么是阻止RNA聚合酶与DNA结合，要么是将其困在DNA环内。需要伴侣蛋白来改变或解除Rok介导的基因抑制。最后，我们研究了H-NS样蛋白的特征，这是一个目前缺乏明确定义的家族。
