热力学不确定性关系约束了细胞信号系统的信息传递。

IF 1.6 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Shreyansh Verma, Vishva Saravanan R, Bhaswar Ghosh
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引用次数: 0

摘要

一般来说,生物系统在非平衡状态下运行,由于非平衡熵的产生,需要持续的能量供应。热力学不确定性关系(TUR)本质上是对给定熵产率的系统所能具有的最小电流波动施加了一个界限。这种波动最终会影响到信噪比,从而对信息传输精度造成上限。在这项研究中,我们利用数学和机器学习方法对酵母在几种应激条件下的实验数据进行了分析,探讨了TUR在一组细胞信号系统的信息传输能力中的作用。细胞信号系统通过激活一组转录因子(TF)来感知环境的变化,这些转录因子通常在细胞核内扩散,从而触发所需基因的转录。然而,与信号传导过程相关的生化途径的固有随机性严重限制了转录因子估计环境输入的准确性。TUR的应用揭示了转录因子的工作原理。我们发现,转录因子(TF)向细胞核的偏扩散激活引发了熵的产生,从而放大了向细胞核的整体TF电流的幅度,并减少了波动。这些结果显著提高了转录因子在TUR约束下进行信息传递的准确性。因此,实验观察与基于TUR的理论模型相结合,证明了热力学波动和熵产生对细胞信息处理的作用。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Thermodynamic uncertainty relation constrains information transmission through cell signaling systems.

Biological systems in general operate out of equilibrium, which brings the requirement for a constant supply of energy due to non-equilibrium entropy production. The thermodynamic uncertainty relation (TUR) essentially imposes a bound on the minimum current fluctuation the system can have given an entropy production rate. The fluctuation eventually impacts the signal-to-noise ratio, imposing an upper bound on the information transmission accuracy. In this study, we explore the role of the TUR on the information transmission capacity of a set of cellular signaling systems using coupled mathematical and machine learning approaches on experimental data in yeast under several stress conditions. Cell signaling systems are involved in sensing changes in the environment by activating a set of transcription factors (TFs), which typically diffuse inside the nucleus to trigger transcription of the required genes. However, the inherent stochasticity of the biochemical pathways severely limits the accuracy of estimating the environmental input by the TFs. The application of TUR reveals a general picture of the working principle of the TFs. We find that the activation followed by biased diffusion of TFs toward the nucleus triggers entropy production, which amplifies the magnitude of the overall TF currents toward the nucleus as well as reducing the fluctuations. These outcomes significantly improve the accuracy of information transmission carried out by the TFs following the bound imposed by TUR, leading to a correlation between accuracy and entropy production. However, TUR only imposes an upper bound on accuracy, and the correlation emerges due to the pathway being operated in the linear response regime. Thus, experimental observations coupled with TUR-based theoretical models demonstrate the role of thermodynamic fluctuation and entropy production on cellular information processing.

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来源期刊
Physical biology
Physical biology 生物-生物物理
CiteScore
4.20
自引率
0.00%
发文量
50
审稿时长
3 months
期刊介绍: Physical Biology publishes articles in the broad interdisciplinary field bridging biology with the physical sciences and engineering. This journal focuses on research in which quantitative approaches – experimental, theoretical and modeling – lead to new insights into biological systems at all scales of space and time, and all levels of organizational complexity. Physical Biology accepts contributions from a wide range of biological sub-fields, including topics such as: molecular biophysics, including single molecule studies, protein-protein and protein-DNA interactions subcellular structures, organelle dynamics, membranes, protein assemblies, chromosome structure intracellular processes, e.g. cytoskeleton dynamics, cellular transport, cell division systems biology, e.g. signaling, gene regulation and metabolic networks cells and their microenvironment, e.g. cell mechanics and motility, chemotaxis, extracellular matrix, biofilms cell-material interactions, e.g. biointerfaces, electrical stimulation and sensing, endocytosis cell-cell interactions, cell aggregates, organoids, tissues and organs developmental dynamics, including pattern formation and morphogenesis physical and evolutionary aspects of disease, e.g. cancer progression, amyloid formation neuronal systems, including information processing by networks, memory and learning population dynamics, ecology, and evolution collective action and emergence of collective phenomena.
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