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基于细胞内化学动力学简单模型对细菌生长规律的解析推导。

Analytic derivation of bacterial growth laws from a simple model of intracellular chemical dynamics.

作者信息

Pandey Parth Pratim, Jain Sanjay

机构信息

Department of Physics and Astrophysics, University of Delhi, Delhi, 110007, India.

The Simons Center for Systems Biology, Institute of Advanced Study, Princeton, NJ, 08540, USA.

出版信息

Theory Biosci. 2016 Sep;135(3):121-30. doi: 10.1007/s12064-016-0227-9. Epub 2016 May 11.

Abstract

Experiments have found that the growth rate and certain other macroscopic properties of bacterial cells in steady-state cultures depend upon the medium in a surprisingly simple manner; these dependencies are referred to as 'growth laws'. Here we construct a dynamical model of interacting intracellular populations to understand some of the growth laws. The model has only three population variables: an amino acid pool, a pool of enzymes that transport an external nutrient and produce the amino acids, and ribosomes that catalyze their own and the enzymes' production from the amino acids. We assume that the cell allocates its resources between the enzyme sector and the ribosomal sector to maximize its growth rate. We show that the empirical growth laws follow from this assumption and derive analytic expressions for the phenomenological parameters in terms of the more basic model parameters. Interestingly, the maximization of the growth rate of the cell as a whole implies that the cell allocates resources to the enzyme and ribosomal sectors in inverse proportion to their respective 'efficiencies'. The work introduces a mathematical scheme in which the cellular growth rate can be explicitly determined and shows that two large parameters, the number of amino acid residues per enzyme and per ribosome, are useful for making approximations.

摘要

实验发现,稳态培养中细菌细胞的生长速率和某些其他宏观特性以一种惊人的简单方式依赖于培养基;这些依赖性被称为“生长规律”。在这里,我们构建了一个细胞内相互作用群体的动力学模型,以理解一些生长规律。该模型仅有三个群体变量:一个氨基酸库、一组转运外部营养物质并产生氨基酸的酶以及从氨基酸催化自身和酶产生的核糖体。我们假设细胞在酶部分和核糖体部分之间分配其资源,以使其生长速率最大化。我们表明,经验生长规律源于这一假设,并根据更基本的模型参数推导出了现象学参数的解析表达式。有趣的是,整个细胞生长速率的最大化意味着细胞以与其各自“效率”成反比的方式将资源分配到酶和核糖体部分。这项工作引入了一种可以明确确定细胞生长速率的数学方案,并表明两个大参数,即每个酶和每个核糖体的氨基酸残基数,对于进行近似是有用的。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4177/5018264/747dfd57fff3/12064_2016_227_Fig1_HTML.jpg

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