A minimal model for gene expression dynamics of bacterial type II toxin–antitoxin systems

Abstract Toxin–antitoxin (TA) modules are part of most bacteria’s regulatory machinery for stress responses and general aspects of their physiology. Due to the interplay of a long-lived toxin with a short-lived antitoxin, TA modules have also become systems of interest for mathematical modelling. He...

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Autores principales:	Kosmas Kosmidis, Marc-Thorsten Hütt
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5189648266a84352a4241c933f499484
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spelling	oai:doaj.org-article:5189648266a84352a4241c933f4994842021-12-02T17:37:12ZA minimal model for gene expression dynamics of bacterial type II toxin–antitoxin systems10.1038/s41598-021-98570-z2045-2322https://doaj.org/article/5189648266a84352a4241c933f4994842021-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-98570-zhttps://doaj.org/toc/2045-2322Abstract Toxin–antitoxin (TA) modules are part of most bacteria’s regulatory machinery for stress responses and general aspects of their physiology. Due to the interplay of a long-lived toxin with a short-lived antitoxin, TA modules have also become systems of interest for mathematical modelling. Here we resort to previous modelling efforts and extract from these a minimal model of type II TA system dynamics on a timescale of hours, which can be used to describe time courses derived from gene expression data of TA pairs. We show that this model provides a good quantitative description of TA dynamics for the 11 TA pairs under investigation here, while simpler models do not. Our study brings together aspects of Biophysics with its focus on mathematical modelling and Computational Systems Biology with its focus on the quantitative interpretation of ’omics’ data. This mechanistic model serves as a generic transformation of time course information into kinetic parameters. The resulting parameter vector can, in turn, be mechanistically interpreted. We expect that TA pairs with similar mechanisms are characterized by similar vectors of kinetic parameters, allowing us to hypothesize on the mode of action for TA pairs still under discussion.Kosmas KosmidisMarc-Thorsten HüttNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Kosmas Kosmidis Marc-Thorsten Hütt A minimal model for gene expression dynamics of bacterial type II toxin–antitoxin systems
description	Abstract Toxin–antitoxin (TA) modules are part of most bacteria’s regulatory machinery for stress responses and general aspects of their physiology. Due to the interplay of a long-lived toxin with a short-lived antitoxin, TA modules have also become systems of interest for mathematical modelling. Here we resort to previous modelling efforts and extract from these a minimal model of type II TA system dynamics on a timescale of hours, which can be used to describe time courses derived from gene expression data of TA pairs. We show that this model provides a good quantitative description of TA dynamics for the 11 TA pairs under investigation here, while simpler models do not. Our study brings together aspects of Biophysics with its focus on mathematical modelling and Computational Systems Biology with its focus on the quantitative interpretation of ’omics’ data. This mechanistic model serves as a generic transformation of time course information into kinetic parameters. The resulting parameter vector can, in turn, be mechanistically interpreted. We expect that TA pairs with similar mechanisms are characterized by similar vectors of kinetic parameters, allowing us to hypothesize on the mode of action for TA pairs still under discussion.
format	article
author	Kosmas Kosmidis Marc-Thorsten Hütt
author_facet	Kosmas Kosmidis Marc-Thorsten Hütt
author_sort	Kosmas Kosmidis
title	A minimal model for gene expression dynamics of bacterial type II toxin–antitoxin systems
title_short	A minimal model for gene expression dynamics of bacterial type II toxin–antitoxin systems
title_full	A minimal model for gene expression dynamics of bacterial type II toxin–antitoxin systems
title_fullStr	A minimal model for gene expression dynamics of bacterial type II toxin–antitoxin systems
title_full_unstemmed	A minimal model for gene expression dynamics of bacterial type II toxin–antitoxin systems
title_sort	minimal model for gene expression dynamics of bacterial type ii toxin–antitoxin systems
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/5189648266a84352a4241c933f499484
work_keys_str_mv	AT kosmaskosmidis aminimalmodelforgeneexpressiondynamicsofbacterialtypeiitoxinantitoxinsystems AT marcthorstenhutt aminimalmodelforgeneexpressiondynamicsofbacterialtypeiitoxinantitoxinsystems AT kosmaskosmidis minimalmodelforgeneexpressiondynamicsofbacterialtypeiitoxinantitoxinsystems AT marcthorstenhutt minimalmodelforgeneexpressiondynamicsofbacterialtypeiitoxinantitoxinsystems
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A minimal model for gene expression dynamics of bacterial type II toxin–antitoxin systems

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