Superstability of the yeast cell-cycle dynamics: ensuring causality in the presence of biochemical stochasticity

DOI10.1016/J.JTBI.2006.11.012MaRDI QIDQ2209986zbMATH OpenOpenAlexWikidataFDO

Authors Stefan Braunewell, Stefan Bornholdt

Publication date 5 November 2020

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/q-bio/0605009

zbMATH Keywords

robustnessgene regulatory networkcomputer simulationsBoolean modelsyeast cell cycle

Mathematics Subject Classification ID

Systems biology, networks (92C42) Cell biology (92C37)

Abstract: Gene regulatory dynamics is governed by molecular processes and therefore exhibits an inherent stochasticity. However, for the survival of an organism it is a strict necessity that this intrinsic noise does not prevent robust functioning of the system. It is still an open question how dynamical stability is achieved in biological systems despite the omnipresent fluctuations. In this paper we investigate the cell-cycle of the budding yeast Saccharomyces cerevisiae as an example of a well-studied organism. We study a genetic network model of eleven genes that coordinate the cell-cycle dynamics using a modeling framework which generalizes the concept of discrete threshold dynamics. By allowing for fluctuations in the transcription/translation times, we introduce noise in the model, accounting for the effects of biochemical stochasticity. We study the dynamical attractor of the cell cycle and find a remarkable robustness against fluctuations of this kind. We identify mechanisms that ensure reliability in spite of fluctuations: 'Catcher' states and persistence of activity levels contribute significantly to the stability of the yeast cell cycle despite the inherent stochasticity.

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Cites work

• Robustness and fragility of Boolean models for genetic regulatory networks
• Stability of genetic regulatory networks with time delay
• The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in \textit{Drosophila melanogaster}

Cited in

(9)

• Optimisation of gene expression noise for cellular persistence against lethal events
• Derivation and experimental comparison of cell-division probability densities
• Intrinsic properties of Boolean dynamics in complex networks
• The transition from differential equations to Boolean networks: A case study in simplifying a regulatory network model
• Reliability of regulatory networks and its evolution
• Logical analysis of the budding yeast cell cycle
• Refining network reconstruction based on functional reliability
• Approximating network dynamics: some open problems
• Effects of stochasticity in models of the cell cycle: from quantized cycle times to noise-induced oscillations

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