细菌类核形成的负相分离方案
Segregative phase separation scenario of the formation of the bacterial nucleoid
摘要：
细菌基因组DNA在一种称为类核的结构中的压缩机制是一个长期存在但仍然有争议的问题。最令人困惑的是，类核只占据细胞的一小部分，尽管它与细胞质的其余部分没有任何膜隔开，并且在细胞外占据的体积大约是细胞的千倍。在这里，通过用粗粒模型进行数值模拟，我们详细说明了这样的猜想，即类核的形成可能是由DNA螺旋和存在于细胞质中的非结合性球状大分子（可能是功能性核糖体）的分层驱动的分离相分离机制引起的。具有球形，哑铃形或八面体几何形状的crowder进行的模拟突出了DNA/DNA，DNA/crowder，和crowder/crowder排斥相互作用的不对称性的DNA压缩的水平的敏感依赖性，从而支持分离相分离的情况。模拟还一致地预测接近干扰阈值的更强的DNA压缩。此外，不同大小的拥挤进行的模拟表明，每个物种的最终密度分布的结果从热力学力和位阻之间的竞争，使更大的拥挤被驱逐选择性地从类核只有在适度的总拥挤浓度。这项工作导致了几个预测，这些预测最终可能会被实验验证。
英文摘要：
The mechanism responsible for the compaction of the genomic DNA of bacteria inside a structure called the nucleoid is a longstanding but still lively debated question. Most puzzling is the fact that the nucleoid occupies only a small fraction of the cell, although it is not separated from the rest of the cytoplasm by any membrane and would occupy a volume about thousand times larger outside from the cell. Here, by performing numerical simulations with coarse-grained models, we elaborate on the conjecture that the formation of the nucleoid may result from a segregative phase separation mechanism driven by the demixing of the DNA coil and non-binding globular macromolecules present in the cytoplasm, presumably functional ribosomes. Simulations performed with crowders having spherical, dumbbell or octahedral geometry highlight the sensitive dependence of the level of DNA compaction on the dissymmetry of DNA/DNA, DNA/crowder, and crowder/crowder repulsive interactions, thereby supporting the segregative phase separation scenario. Simulations also consistently predict much stronger DNA compaction close to the jamming threshold. Moreover, simulations performed with crowders of different sizes suggest that the final density distribution of each species results from the competition between thermodynamic forces and steric hindrance, so that bigger crowders are expelled selectively from the nucleoid only at moderate total crowder concentrations. This work leads to several predictions, which may eventually be tested experimentally.
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