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...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-09-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-98570-z |
| _version_ | 1819203185425776640 |
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| author | Kosmas Kosmidis Marc-Thorsten Hütt |
| author_facet | Kosmas Kosmidis Marc-Thorsten Hütt |
| author_sort | Kosmas Kosmidis |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-23T04:15:54Z |
| format | Article |
| id | doaj.art-5189648266a84352a4241c933f499484 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-23T04:15:54Z |
| publishDate | 2021-09-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-5189648266a84352a4241c933f4994842022-12-21T18:00:22ZengNature PortfolioScientific Reports2045-23222021-09-0111111210.1038/s41598-021-98570-zA minimal model for gene expression dynamics of bacterial type II toxin–antitoxin systemsKosmas Kosmidis0Marc-Thorsten Hütt1Physics Department, Aristotle University of ThessalonikiDepartment of Life Sciences and Chemistry, Jacobs University BremenAbstract 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.https://doi.org/10.1038/s41598-021-98570-z |
| spellingShingle | Kosmas Kosmidis Marc-Thorsten Hütt A minimal model for gene expression dynamics of bacterial type II toxin–antitoxin systems Scientific Reports |
| title | 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_short | 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 |
| url | https://doi.org/10.1038/s41598-021-98570-z |
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