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Protein degradation sets the fraction of active ribosomes at vanishing growth

Growing cells adopt common basic strategies to achieve optimal resource allocation under limited resource availability. Our current understanding of such “growth laws” neglects degradation, assuming that it occurs slowly compared to the cell cycle duration. Here we argue that this assumption cannot...

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Detalles Bibliográficos
Autores principales: Calabrese, Ludovico, Grilli, Jacopo, Osella, Matteo, Kempes, Christopher P., Lagomarsino, Marco Cosentino, Ciandrini, Luca
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9098079/
https://www.ncbi.nlm.nih.gov/pubmed/35500024
http://dx.doi.org/10.1371/journal.pcbi.1010059
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author Calabrese, Ludovico
Grilli, Jacopo
Osella, Matteo
Kempes, Christopher P.
Lagomarsino, Marco Cosentino
Ciandrini, Luca
author_facet Calabrese, Ludovico
Grilli, Jacopo
Osella, Matteo
Kempes, Christopher P.
Lagomarsino, Marco Cosentino
Ciandrini, Luca
author_sort Calabrese, Ludovico
collection PubMed
description Growing cells adopt common basic strategies to achieve optimal resource allocation under limited resource availability. Our current understanding of such “growth laws” neglects degradation, assuming that it occurs slowly compared to the cell cycle duration. Here we argue that this assumption cannot hold at slow growth, leading to important consequences. We propose a simple framework showing that at slow growth protein degradation is balanced by a fraction of “maintenance” ribosomes. Consequently, active ribosomes do not drop to zero at vanishing growth, but as growth rate diminishes, an increasing fraction of active ribosomes performs maintenance. Through a detailed analysis of compiled data, we show that the predictions of this model agree with data from E. coli and S. cerevisiae. Intriguingly, we also find that protein degradation increases at slow growth, which we interpret as a consequence of active waste management and/or recycling. Our results highlight protein turnover as an underrated factor for our understanding of growth laws across kingdoms.
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spelling pubmed-90980792022-05-13 Protein degradation sets the fraction of active ribosomes at vanishing growth Calabrese, Ludovico Grilli, Jacopo Osella, Matteo Kempes, Christopher P. Lagomarsino, Marco Cosentino Ciandrini, Luca PLoS Comput Biol Research Article Growing cells adopt common basic strategies to achieve optimal resource allocation under limited resource availability. Our current understanding of such “growth laws” neglects degradation, assuming that it occurs slowly compared to the cell cycle duration. Here we argue that this assumption cannot hold at slow growth, leading to important consequences. We propose a simple framework showing that at slow growth protein degradation is balanced by a fraction of “maintenance” ribosomes. Consequently, active ribosomes do not drop to zero at vanishing growth, but as growth rate diminishes, an increasing fraction of active ribosomes performs maintenance. Through a detailed analysis of compiled data, we show that the predictions of this model agree with data from E. coli and S. cerevisiae. Intriguingly, we also find that protein degradation increases at slow growth, which we interpret as a consequence of active waste management and/or recycling. Our results highlight protein turnover as an underrated factor for our understanding of growth laws across kingdoms. Public Library of Science 2022-05-02 /pmc/articles/PMC9098079/ /pubmed/35500024 http://dx.doi.org/10.1371/journal.pcbi.1010059 Text en © 2022 Calabrese et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Calabrese, Ludovico
Grilli, Jacopo
Osella, Matteo
Kempes, Christopher P.
Lagomarsino, Marco Cosentino
Ciandrini, Luca
Protein degradation sets the fraction of active ribosomes at vanishing growth
title Protein degradation sets the fraction of active ribosomes at vanishing growth
title_full Protein degradation sets the fraction of active ribosomes at vanishing growth
title_fullStr Protein degradation sets the fraction of active ribosomes at vanishing growth
title_full_unstemmed Protein degradation sets the fraction of active ribosomes at vanishing growth
title_short Protein degradation sets the fraction of active ribosomes at vanishing growth
title_sort protein degradation sets the fraction of active ribosomes at vanishing growth
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9098079/
https://www.ncbi.nlm.nih.gov/pubmed/35500024
http://dx.doi.org/10.1371/journal.pcbi.1010059
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