Differentiating the roles of proteins and polysomes in nucleoid size homeostasis in Escherichia coli
Differentiating the roles of proteins and polysomes in nucleoid size homeostasis in Escherichia coli
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DOI：
10.1016/j.bpj.2023.11.010
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发表时间：
2024-06-04
影响因子：
3.4
通讯作者：
Mannik，Jaan
中科院分区：
文献类型：
--
作者：
Chang，Mu-Hung;Lavrentovich，Maxim O.;Mannik，Jaan
细菌胞质内部的一个定义特征是一个独特的无膜细胞器，即含有染色体DNA的类核。虽然越来越多的实验证据表明，大分子拥挤是类核形成的主要机制，但仍不清楚哪些拥挤控制类核体积。通常认为多聚核糖体起主导作用，然而胞质溶胶中可溶性蛋白质的体积分数与多聚核糖体的体积分数相当。在这里，我们开发了一个基于自由能的细菌细胞的胞质内部模型，以区分多聚核糖体和胞质蛋白质在类核体积控制中的贡献。模型的参数由已有的实验数据确定。我们发现，虽然多核糖体建立的存在的类核作为一个独特的阶段，蛋白质控制的类核体积在生理相关的条件。我们的模型解释了实验结果inEscherichia coli，在渗透压休克测量的类核压实曲线不依赖于细胞的生长速率和解离的多聚核糖体在缓慢的生长速率不会导致显着的类核扩张，而类核相消失在最快的增长速度。此外，该模型预测了通过其线性尺寸从类核相中排除拥挤物的交叉：在30-50 nm的交叉以下，类核相中拥挤物的浓度作为拥挤物直径的函数线性降低，而在交叉尺寸以上指数降低。我们的工作指出了细菌细胞通过反馈维持类核大小和蛋白质浓度稳态的可能性，其中蛋白质浓度控制类核尺寸，类核尺寸控制蛋白质合成速率。
A defining feature of the bacterial cytosolic interior is a distinct membrane-less organelle, the nucleoid, that contains the chromosomal DNA. Although increasing experimental evidence indicates that macromolecular crowding is the dominant mechanism for nucleoid formation, it has remained unclear which crowders control nucleoid volume. It is commonly assumed that polyribosomes play a dominant role, yet the volume fraction of soluble proteins in the cytosol is comparable with that of polyribosomes. Here, we develop a free energy-based model for the cytosolic interior of a bacterial cell to distinguish contributions arising from polyribosomes and cytosolic proteins in nucleoid volume control. The parameters of the model are determined from the existing experimental data. We show that, while the polysomes establish the existence of the nucleoid as a distinct phase, the proteins control the nucleoid volume in physiologically relevant conditions. Our model explains experimental findings inEscherichia colithat the nucleoid compaction curves in osmotic shock measurements do not depend on cell growth rate and that dissociation of polysomes in slow growth rates does not lead to significant nucleoid expansion, while the nucleoid phase disappears in fastest growth rates. Furthermore, the model predicts a cross-over in the exclusion of crowders by their linear dimensions from the nucleoid phase: below the cross-over of 30–50 nm, the concentration of crowders in the nucleoid phase decreases linearly as a function of the crowder diameter, while decreasing exponentially above the cross-over size. Our work points to the possibility that bacterial cells maintain nucleoid size and protein concentration homeostasis via feedback in which protein concentration controls nucleoid dimensions and the nucleoid dimensions control protein synthesis rate.