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Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth

Inside prokaryotic cells, passive translational diffusion typically limits the rates with which cytoplasmic proteins can reach their locations. Diffusion is thus fundamental to most cellular processes, but the understanding of protein mobility in the highly crowded and non-homogeneous environment of...

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Autores principales: Bellotto, Nicola, Agudo-Canalejo, Jaime, Colin, Remy, Golestanian, Ramin, Malengo, Gabriele, Sourjik, Victor
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9810338/
https://www.ncbi.nlm.nih.gov/pubmed/36468683
http://dx.doi.org/10.7554/eLife.82654
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author Bellotto, Nicola
Agudo-Canalejo, Jaime
Colin, Remy
Golestanian, Ramin
Malengo, Gabriele
Sourjik, Victor
author_facet Bellotto, Nicola
Agudo-Canalejo, Jaime
Colin, Remy
Golestanian, Ramin
Malengo, Gabriele
Sourjik, Victor
author_sort Bellotto, Nicola
collection PubMed
description Inside prokaryotic cells, passive translational diffusion typically limits the rates with which cytoplasmic proteins can reach their locations. Diffusion is thus fundamental to most cellular processes, but the understanding of protein mobility in the highly crowded and non-homogeneous environment of a bacterial cell is still limited. Here, we investigated the mobility of a large set of proteins in the cytoplasm of Escherichia coli, by employing fluorescence correlation spectroscopy (FCS) combined with simulations and theoretical modeling. We conclude that cytoplasmic protein mobility could be well described by Brownian diffusion in the confined geometry of the bacterial cell and at the high viscosity imposed by macromolecular crowding. We observed similar size dependence of protein diffusion for the majority of tested proteins, whether native or foreign to E. coli. For the faster-diffusing proteins, this size dependence is well consistent with the Stokes-Einstein relation once taking into account the specific dumbbell shape of protein fusions. Pronounced subdiffusion and hindered mobility are only observed for proteins with extensive interactions within the cytoplasm. Finally, while protein diffusion becomes markedly faster in actively growing cells, at high temperature, or upon treatment with rifampicin, and slower at high osmolarity, all of these perturbations affect proteins of different sizes in the same proportions, which could thus be described as changes of a well-defined cytoplasmic viscosity.
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spelling pubmed-98103382023-01-04 Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth Bellotto, Nicola Agudo-Canalejo, Jaime Colin, Remy Golestanian, Ramin Malengo, Gabriele Sourjik, Victor eLife Cell Biology Inside prokaryotic cells, passive translational diffusion typically limits the rates with which cytoplasmic proteins can reach their locations. Diffusion is thus fundamental to most cellular processes, but the understanding of protein mobility in the highly crowded and non-homogeneous environment of a bacterial cell is still limited. Here, we investigated the mobility of a large set of proteins in the cytoplasm of Escherichia coli, by employing fluorescence correlation spectroscopy (FCS) combined with simulations and theoretical modeling. We conclude that cytoplasmic protein mobility could be well described by Brownian diffusion in the confined geometry of the bacterial cell and at the high viscosity imposed by macromolecular crowding. We observed similar size dependence of protein diffusion for the majority of tested proteins, whether native or foreign to E. coli. For the faster-diffusing proteins, this size dependence is well consistent with the Stokes-Einstein relation once taking into account the specific dumbbell shape of protein fusions. Pronounced subdiffusion and hindered mobility are only observed for proteins with extensive interactions within the cytoplasm. Finally, while protein diffusion becomes markedly faster in actively growing cells, at high temperature, or upon treatment with rifampicin, and slower at high osmolarity, all of these perturbations affect proteins of different sizes in the same proportions, which could thus be described as changes of a well-defined cytoplasmic viscosity. eLife Sciences Publications, Ltd 2022-12-05 /pmc/articles/PMC9810338/ /pubmed/36468683 http://dx.doi.org/10.7554/eLife.82654 Text en © 2022, Bellotto et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Cell Biology
Bellotto, Nicola
Agudo-Canalejo, Jaime
Colin, Remy
Golestanian, Ramin
Malengo, Gabriele
Sourjik, Victor
Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth
title Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth
title_full Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth
title_fullStr Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth
title_full_unstemmed Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth
title_short Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth
title_sort dependence of diffusion in escherichia coli cytoplasm on protein size, environmental conditions, and cell growth
topic Cell Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9810338/
https://www.ncbi.nlm.nih.gov/pubmed/36468683
http://dx.doi.org/10.7554/eLife.82654
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