Department of Chemistry, University of Wisconsin, Madison, Wisconsin, USA.
Biophys J. 2011 Jun 8;100(11):2605-13. doi: 10.1016/j.bpj.2011.04.030.
In Escherichia coli, ribosomes concentrate near the cylindrical wall and at the endcaps, whereas the chromosomal DNA segregates in the more centrally located nucleoid. A simple statistical model recovers the observed ribosome-nucleoid segregation remarkably well. Plectonemic DNA is represented as a hyperbranched hard-sphere polymer, and multiple ribosomes that simultaneously translate the same mRNA strand (polysomes) are represented as freely jointed chains of hard spheres. There are no attractive interactions between particles, only excluded-volume effects. At realistic DNA and ribosome concentrations, segregation arises primarily from two effects: the DNA polymer avoids walls to maximize conformational entropy, and the polysomes occupy the empty space near the walls to maximize translational entropy. In this complex system, maximizing total entropy results in spatial organization of the components. Due to coupling of mRNA to DNA through RNA polymerase, the same entropic effects should favor the placement of highly expressed genes at the interface between the nucleoid and the ribosome-rich periphery. Such a placement would enable efficient cotranscriptional translation and facile transertion of membrane proteins into the cytoplasmic membrane. Finally, in the model, monofunctional DNA polymer beads representing the tips of plectonemes preferentially locate near the cylindrical wall. This suggests that initiation of transcription may occur preferentially near the ribosome-rich periphery.
在大肠杆菌中，核糖体集中在圆柱形壁附近和端帽处，而染色体 DNA 则在更居中的核区分离。一个简单的统计模型很好地恢复了观察到的核糖体-核区分离。扭结 DNA 表示为超支化硬球聚合物，同时翻译同一 mRNA 链（多核糖体）的多个核糖体表示为硬球的自由连接链。颗粒之间没有吸引力相互作用，只有排斥体积效应。在现实的 DNA 和核糖体浓度下，分离主要来自两个效应：DNA 聚合物避免壁以最大化构象熵，而多核糖体占据壁附近的空空间以最大化翻译熵。在这个复杂的系统中，最大化总熵导致组件的空间组织。由于 RNA 聚合酶通过 RNA 将 mRNA 与 DNA 偶联，相同的熵效应应该有利于将高表达基因放置在核区和富含核糖体的外围之间的界面处。这种放置方式将能够有效地进行共转录翻译，并使膜蛋白容易转位到细胞质膜中。最后，在该模型中，代表扭结尖端的单功能 DNA 聚合物珠优先定位在圆柱形壁附近。这表明转录的起始可能优先发生在富含核糖体的外围附近。
