Theoretical Biology and Bioinformatics, Department of Biology, University of Utrecht, Utrecht, The Netherlands.
PLoS Comput Biol. 2021 Jul 19;17(7):e1009208. doi: 10.1371/journal.pcbi.1009208. eCollection 2021 Jul.
In bacterial cells, protein expression is a highly stochastic process. Gene expression noise moreover propagates through the cell and adds to fluctuations in the cellular growth rate. A common intuition is that, due to their relatively high noise amplitudes, proteins with a low mean expression level are the most important drivers of fluctuations in physiological variables. In this work, we challenge this intuition by considering the effect of natural selection on noise propagation. Mathematically, the contribution of each protein species to the noise in the growth rate depends on two factors: the noise amplitude of the protein's expression level, and the sensitivity of the growth rate to fluctuations in that protein's concentration. We argue that natural selection, while shaping mean abundances to increase the mean growth rate, also affects cellular sensitivities. In the limit in which cells grow optimally fast, the growth rate becomes most sensitive to fluctuations in highly abundant proteins. This causes abundant proteins to overall contribute strongly to the noise in the growth rate, despite their low noise levels. We further explore this result in an experimental data set of protein abundances, and test key assumptions in an evolving, stochastic toy model of cellular growth.
在细菌细胞中,蛋白质表达是一个高度随机的过程。此外,基因表达噪声会在细胞中传播,并增加细胞生长速率的波动。一个常见的直觉是,由于蛋白质的平均表达水平较低,其噪声幅度相对较高,因此它们是生理变量波动的最重要驱动因素。在这项工作中,我们通过考虑自然选择对噪声传播的影响来挑战这一直觉。从数学上讲,每种蛋白质对生长速率噪声的贡献取决于两个因素:蛋白质表达水平的噪声幅度,以及生长速率对该蛋白质浓度波动的敏感性。我们认为,自然选择在塑造平均丰度以增加平均生长速率的同时,也会影响细胞的敏感性。在细胞以最快速度生长的极限情况下,生长速率对高丰度蛋白质的波动最为敏感。这导致丰富的蛋白质尽管噪声水平较低,但总体上对生长速率的噪声有很大的贡献。我们在蛋白质丰度的实验数据集进一步探讨了这一结果,并在细胞生长的进化随机玩具模型中测试了关键假设。