Pugatch Rami
Simons Center for Systems Biology, School of Natural Sciences, Institute for Advanced Study, Princeton, NJ 08540
Proc Natl Acad Sci U S A. 2015 Feb 24;112(8):2611-6. doi: 10.1073/pnas.1418738112. Epub 2015 Feb 9.
Bacterial self-replication is a complex process composed of many de novo synthesis steps catalyzed by a myriad of molecular processing units, e.g., the transcription-translation machinery, metabolic enzymes, and the replisome. Successful completion of all production tasks requires a schedule-a temporal assignment of each of the production tasks to its respective processing units that respects ordering and resource constraints. Most intracellular growth processes are well characterized. However, the manner in which they are coordinated under the control of a scheduling policy is not well understood. When fast replication is favored, a schedule that minimizes the completion time is desirable. However, if resources are scarce, it is typically computationally hard to find such a schedule, in the worst case. Here, we show that optimal scheduling naturally emerges in cellular self-replication. Optimal doubling time is obtained by maintaining a sufficiently large inventory of intermediate metabolites and processing units required for self-replication and additionally requiring that these processing units be "greedy," i.e., not idle if they can perform a production task. We calculate the distribution of doubling times of such optimally scheduled self-replicating factories, and find it has a universal form-log-Frechet, not sensitive to many microscopic details. Analyzing two recent datasets of Escherichia coli growing in a stationary medium, we find excellent agreement between the observed doubling-time distribution and the predicted universal distribution, suggesting E. coli is optimally scheduling its replication. Greedy scheduling appears as a simple generic route to optimal scheduling when speed is the optimization criterion. Other criteria such as efficiency require more elaborate scheduling policies and tighter regulation.
细菌的自我复制是一个复杂的过程,由许多从头合成步骤组成,这些步骤由无数分子加工单元催化,例如转录-翻译机器、代谢酶和复制体。成功完成所有生产任务需要一个时间表——将每个生产任务按时间分配到各自的加工单元,同时要考虑顺序和资源限制。大多数细胞内生长过程都有很好的特征描述。然而,它们在调度策略控制下的协调方式却尚未得到很好的理解。当倾向于快速复制时,一个能使完成时间最小化的时间表是理想的。然而,如果资源稀缺,在最坏的情况下,找到这样的时间表通常在计算上是困难的。在这里,我们表明最优调度在细胞自我复制中自然出现。通过维持足够大量的自我复制所需的中间代谢物和加工单元库存,并额外要求这些加工单元是“贪婪的”,即如果它们能执行生产任务就不闲置,可获得最优的倍增时间。我们计算了这种最优调度的自我复制工厂倍增时间的分布,发现它具有一种通用形式——对数弗雷歇分布,对许多微观细节不敏感。分析最近两个大肠杆菌在固定培养基中生长的数据集,我们发现观察到的倍增时间分布与预测的通用分布之间有很好的一致性,这表明大肠杆菌正在对其复制进行最优调度。当速度是优化标准时,贪婪调度似乎是实现最优调度的一条简单通用途径。其他标准,如效率,则需要更精细的调度策略和更严格的调控。