Fig. 1: Mechanistic model for bacteria response to external perturbations. | Nature Communications

Fig. 1: Mechanistic model for bacteria response to external perturbations.

From: Incoherent feedback from coupled amino acids and ribosome pools generates damped oscillations in growing E. coli

Fig. 1

Global scheme of the regulatory model. The out-of-steady-state dynamics is governed by four main ingredients: A the allocation functions χis, which set the target size for the proteome sectors ϕis B the ppGpp-mediated transcript dynamics (total transcript T and ribosomal transcripts TR), which determine the values of the allocation functions by setting the composition of the transcript pool C the ppGpp dynamics, which reads the translation elongation rate ϵ -determined by the dwelling and translocation time- and regulates the transcript production D the production and consumption of amino acids, ψA, which control ppGpp production by setting the translation speed. The first module on the dynamics of the sector size is derived from ref. 13. Each box contains the equation associated to the illustrated mechanism (described in the main text).

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