Code for "Coupled ribosome allocation and nutrient sensing lead to oscillatory response in bacterial growth"

Published: 25 October 2023| Version 1 | DOI: 10.17632/w294vd3pgh.1
Contributors:
Rossana Droghetti,

Description

Code used for the simulations employed in the manuscript "Coupled ribosome allocation and nutrient sensing lead to oscillatory response in bacterial growth" In this folder, you can find the simulation of a base model, which can be used to reproduce the oscillatory behavior induced by nutrient shifts. In addition, there is a code for the numerical computation of the steady-state conditions. Abstract: Current theories describing bacterial growth physiology across environments have demonstrated an impressive predictive power, but they are typically phenomenological. Incorporating mechanistic details into these frameworks remains an open challenge that would greatly improve our ability to predict and control bacterial growth in varying environmental conditions. For example, the “Flux Controlled Regulation” (FCR) model is a reference out-of-equilibrium framework that links ribosome allocation to translation efficiency by means of a steady-state assumption. By making use of this assumption, this model does not account for ppGpp-mediated nutrient sensing and transcriptional regulation of ribosomal operons. In this study, we propose a simple model that integrates the FCR framework with a mechanistic description of three key components: (i) the amino-acid pool, (ii) ppGpp sensing of translation elongation rate, and (iii) transcriptional programming of protein allocation strategy by ppGpp-sensitive promoters. Our framework is fully coherent with observed steady-state growth laws and makes testable predictions for unobserved quantities. Furthermore, our theory predicts that under environmental changes the incoherent feedback between sensing and regulation leads to oscillatory relaxation towards new equilibria, a feature observed experimentally but not captured by previous phenomenological models.

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Institutions

Istituto Nazionale di Fisica Nucleare, Universita degli Studi di Milano Dipartimento di Fisica, Fondazione Istituto FIRC di Oncologia Molecolare, Abdus Salam Centro internazionale di fisica teorica

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Computer Simulation

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