In all growth conditions, ribosomes translate mRNA while it is being synthesized. The segregation of the chromosomal DNA from the majority of the ribosomes is puzzling from a biochemical perspective. Although in a few cases the molecular mechanisms underlying this organization are understood ( 11), many important examples lack an explanation at present. Many proteins and even some lipids are known to have specific addresses in the cell ( 2,9,10). In rapidly growing Escherichia coli and Bacillus subtilis, the ribosomes strongly concentrate in the cytoplasmic periphery, including the two poles (i.e., outside the nucleoid) ( 6–8). The chromosomal DNA is condensed into a central region called the nucleoid ( 3), and specific DNA loci adopt specific locations during the cell cycle ( 4,5). This suggests that initiation of transcription may occur preferentially near the ribosome-rich periphery.ĭespite its lack of organelles, the bacterial cytoplasm exhibits a high degree of spatial organization ( 1,2). Finally, in the model, monofunctional DNA polymer beads representing the tips of plectonemes preferentially locate near the cylindrical wall. Such a placement would enable efficient cotranscriptional translation and facile transertion of membrane proteins into the cytoplasmic membrane. 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. In this complex system, maximizing total entropy results in spatial organization of the components. 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. There are no attractive interactions between particles, only excluded-volume effects. 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.

A simple statistical model recovers the observed ribosome-nucleoid segregation remarkably well. In Escherichia coli, ribosomes concentrate near the cylindrical wall and at the endcaps, whereas the chromosomal DNA segregates in the more centrally located nucleoid.

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