Dependence of bacterial chemotaxis on gradient shape and adaptation rate.

Simulation of cellular behavior on multiple scales requires models that are sufficiently detailed to capture central intracellular processes but at the same time enable the simulation of entire cell populations in a computationally cheap way. In this paper we present RapidCell, a hybrid model of che...

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Autores principales:	Nikita Vladimirov, Linda Løvdok, Dirk Lebiedz, Victor Sourjik
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/152a31d2199648e1bf38e4254dbb9e08
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spelling	oai:doaj.org-article:152a31d2199648e1bf38e4254dbb9e082021-11-25T05:41:55ZDependence of bacterial chemotaxis on gradient shape and adaptation rate.1553-734X1553-735810.1371/journal.pcbi.1000242https://doaj.org/article/152a31d2199648e1bf38e4254dbb9e082008-12-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19096502/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Simulation of cellular behavior on multiple scales requires models that are sufficiently detailed to capture central intracellular processes but at the same time enable the simulation of entire cell populations in a computationally cheap way. In this paper we present RapidCell, a hybrid model of chemotactic Escherichia coli that combines the Monod-Wyman-Changeux signal processing by mixed chemoreceptor clusters, the adaptation dynamics described by ordinary differential equations, and a detailed model of cell tumbling. Our model dramatically reduces computational costs and allows the highly efficient simulation of E. coli chemotaxis. We use the model to investigate chemotaxis in different gradients, and suggest a new, constant-activity type of gradient to systematically study chemotactic behavior of virtual bacteria. Using the unique properties of this gradient, we show that optimal chemotaxis is observed in a narrow range of CheA kinase activity, where concentration of the response regulator CheY-P falls into the operating range of flagellar motors. Our simulations also confirm that the CheB phosphorylation feedback improves chemotactic efficiency by shifting the average CheY-P concentration to fit the motor operating range. Our results suggest that in liquid media the variability in adaptation times among cells may be evolutionary favorable to ensure coexistence of subpopulations that will be optimally tactic in different gradients. However, in a porous medium (agar) such variability appears to be less important, because agar structure poses mainly negative selection against subpopulations with low levels of adaptation enzymes. RapidCell is available from the authors upon request.Nikita VladimirovLinda LøvdokDirk LebiedzVictor SourjikPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 4, Iss 12, p e1000242 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Nikita Vladimirov Linda Løvdok Dirk Lebiedz Victor Sourjik Dependence of bacterial chemotaxis on gradient shape and adaptation rate.
description	Simulation of cellular behavior on multiple scales requires models that are sufficiently detailed to capture central intracellular processes but at the same time enable the simulation of entire cell populations in a computationally cheap way. In this paper we present RapidCell, a hybrid model of chemotactic Escherichia coli that combines the Monod-Wyman-Changeux signal processing by mixed chemoreceptor clusters, the adaptation dynamics described by ordinary differential equations, and a detailed model of cell tumbling. Our model dramatically reduces computational costs and allows the highly efficient simulation of E. coli chemotaxis. We use the model to investigate chemotaxis in different gradients, and suggest a new, constant-activity type of gradient to systematically study chemotactic behavior of virtual bacteria. Using the unique properties of this gradient, we show that optimal chemotaxis is observed in a narrow range of CheA kinase activity, where concentration of the response regulator CheY-P falls into the operating range of flagellar motors. Our simulations also confirm that the CheB phosphorylation feedback improves chemotactic efficiency by shifting the average CheY-P concentration to fit the motor operating range. Our results suggest that in liquid media the variability in adaptation times among cells may be evolutionary favorable to ensure coexistence of subpopulations that will be optimally tactic in different gradients. However, in a porous medium (agar) such variability appears to be less important, because agar structure poses mainly negative selection against subpopulations with low levels of adaptation enzymes. RapidCell is available from the authors upon request.
format	article
author	Nikita Vladimirov Linda Løvdok Dirk Lebiedz Victor Sourjik
author_facet	Nikita Vladimirov Linda Løvdok Dirk Lebiedz Victor Sourjik
author_sort	Nikita Vladimirov
title	Dependence of bacterial chemotaxis on gradient shape and adaptation rate.
title_short	Dependence of bacterial chemotaxis on gradient shape and adaptation rate.
title_full	Dependence of bacterial chemotaxis on gradient shape and adaptation rate.
title_fullStr	Dependence of bacterial chemotaxis on gradient shape and adaptation rate.
title_full_unstemmed	Dependence of bacterial chemotaxis on gradient shape and adaptation rate.
title_sort	dependence of bacterial chemotaxis on gradient shape and adaptation rate.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/152a31d2199648e1bf38e4254dbb9e08
work_keys_str_mv	AT nikitavladimirov dependenceofbacterialchemotaxisongradientshapeandadaptationrate AT lindaløvdok dependenceofbacterialchemotaxisongradientshapeandadaptationrate AT dirklebiedz dependenceofbacterialchemotaxisongradientshapeandadaptationrate AT victorsourjik dependenceofbacterialchemotaxisongradientshapeandadaptationrate
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Dependence of bacterial chemotaxis on gradient shape and adaptation rate.

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