The allocation of resources during bacterial growth is strongly related to the availability of ribosomes and RNA polymerase molecules. Here, coarse-grained models offer a promising start due to their simple structure and the limited number of kinetic parameters. Based on published data sets for proteome and mRNA data in Escherichia coli, and together with mass balance equations describing gene expression, we are able to calculate the number of active molecules (that is, the number of ribosomes that are currently translating nascent and mature mRNA, as well as the number of RNA polymerase molecules on the DNA). This information is a prerequisite for meaningful coarse-grained models. In our approach, the cellular compartment is structured into a cytosolic region and a nucleoid region, and the processes of transcription and translation are assigned accordingly. The theoretical study reveals a quadratic relationship between the number of active ribosomes and the growth rate μ. While the overall available number of ribosomes follows the linear “bacterial growth law”, the approach allows us to determine the growth limit for the chosen experimental environment (minimal medium, only one C source). The new approach is in good agreement with published experimental data, and, with a simple rule of thumb can be applied to other cellular systems.

细菌生长过程中的资源分配与核糖体和 RNA 聚合酶分子的可用性密切相关。在这里，粗粒度模型由于其简单的结构和有限数量的动力学参数提供了一个有希望的开端。基于已发表的大肠杆菌蛋白质组和 mRNA 数据集，结合描述基因表达的质量平衡方程，我们能够计算活性分子的数量（即当前翻译新生和成熟 mRNA 的核糖体数量，以及 DNA 上 RNA 聚合酶分子的数量）。此信息是有意义的粗粒度模型的先决条件。在我们的方法中，细胞区室被构造成一个细胞质区域和一个类核区域，转录和翻译的过程也相应地进行了分配。理论研究揭示了活性核糖体数量与生长速率μ之间的二次关系. 虽然核糖体的总体可用数量遵循线性“细菌生长规律”，但该方法允许我们确定所选实验环境（最低培养基，只有一个 C 源）的生长极限。新方法与已发表的实验数据非常吻合，并且可以根据简单的经验法则应用于其他蜂窝系统。