Quantifying the distribution of protein oligomerization degree reflects cellular information capacity

Ramez Daniel,Ximing Li,Tamir Tuller,Lena Danielli

doi:10.1038/s41598-020-74811-5

Ramez Daniel, Ximing Li + Show 2 more

Open Access

https://doi.org/10.1038/s41598-020-74811-5

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Abstract

The generation of information, energy and biomass in living cells involves integrated processes that optimally evolve into complex and robust cellular networks. Protein homo-oligomerization, which is correlated with cooperativity in biology, is one means of scaling the complexity of protein networks. It can play critical roles in determining the sensitivity of genetic regulatory circuits and metabolic pathways. Therefore, understanding the roles of oligomerization may lead to new approaches of probing biological functions. Here, we analyzed the frequency of protein oligomerization degree in the cell proteome of nine different organisms, and then, we asked whether there are design trade-offs between protein oligomerization, information precision and energy costs of protein synthesis. Our results indicate that there is an upper limit for the degree of protein oligomerization, possibly because of the trade-off between cellular resource limitations and the information precision involved in biochemical reaction networks. These findings can explain the principles of cellular architecture design and provide a quantitative tool to scale synthetic biological systems.

Highlights

The generation of information, energy and biomass in living cells involves integrated processes that optimally evolve into complex and robust cellular networks
Our results indicate that there is an upper limit for protein subunit number, possibly due to the trade-off between the energy cost of protein synthesis and the sensitivity of biochemical reactions
Our analysis showed a common pattern of homo-oligomer frequency for the nine different species (Fig. 1b); the probability of observing proteins with k subunits in the proteome decreased as the value of k increased, and the number of odd subunits tend to be lower than the even subunits

Summary

Introduction

The generation of information, energy and biomass in living cells involves integrated processes that optimally evolve into complex and robust cellular networks. Our results indicate that there is an upper limit for the degree of protein oligomerization, possibly because of the trade-off between cellular resource limitations and the information precision involved in biochemical reaction networks These findings can explain the principles of cellular architecture design and provide a quantitative tool to scale synthetic biological systems. Other biological mechanisms to increase the sensitivity of regulatory c ontrols[24,25], cooperativity is one means of scaling the complexity of cellular networks and improving their sensitivity[18] These improvements in information quality are limited by the energy cost of protein s ynthesis[26], and the balance between them can be achieved via cooperativity and protein oligomerization. It has recently been shown that a high transcription rate decreases stochastic fluctuations in gene expression but increases protein synthesis c osts[27]

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