Equation-free analysis of two-component system signalling model reveals the emergence of co-existing phenotypes in the absence of multistationarity.
Phenotypic differences of genetically identical cells under the same environmental conditions have been attributed to the inherent stochasticity of biochemical processes. Various mechanisms have been suggested, including the existence of alternative steady states in regulatory networks that are reac...
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002396&type=printable |
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| author | Rebecca B Hoyle Daniele Avitabile Andrzej M Kierzek |
| author_facet | Rebecca B Hoyle Daniele Avitabile Andrzej M Kierzek |
| author_sort | Rebecca B Hoyle |
| collection | DOAJ |
| description | Phenotypic differences of genetically identical cells under the same environmental conditions have been attributed to the inherent stochasticity of biochemical processes. Various mechanisms have been suggested, including the existence of alternative steady states in regulatory networks that are reached by means of stochastic fluctuations, long transient excursions from a stable state to an unstable excited state, and the switching on and off of a reaction network according to the availability of a constituent chemical species. Here we analyse a detailed stochastic kinetic model of two-component system signalling in bacteria, and show that alternative phenotypes emerge in the absence of these features. We perform a bifurcation analysis of deterministic reaction rate equations derived from the model, and find that they cannot reproduce the whole range of qualitative responses to external signals demonstrated by direct stochastic simulations. In particular, the mixed mode, where stochastic switching and a graded response are seen simultaneously, is absent. However, probabilistic and equation-free analyses of the stochastic model that calculate stationary states for the mean of an ensemble of stochastic trajectories reveal that slow transcription of either response regulator or histidine kinase leads to the coexistence of an approximate basal solution and a graded response that combine to produce the mixed mode, thus establishing its essential stochastic nature. The same techniques also show that stochasticity results in the observation of an all-or-none bistable response over a much wider range of external signals than would be expected on deterministic grounds. Thus we demonstrate the application of numerical equation-free methods to a detailed biochemical reaction network model, and show that it can provide new insight into the role of stochasticity in the emergence of phenotypic diversity. |
| format | Article |
| id | doaj-art-45a0b052f82f4ad88391d3cef329c41e |
| institution | OA Journals |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS Computational Biology |
| spelling | doaj-art-45a0b052f82f4ad88391d3cef329c41e2025-08-20T02:34:09ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582012-01-0186e100239610.1371/journal.pcbi.1002396Equation-free analysis of two-component system signalling model reveals the emergence of co-existing phenotypes in the absence of multistationarity.Rebecca B HoyleDaniele AvitabileAndrzej M KierzekPhenotypic differences of genetically identical cells under the same environmental conditions have been attributed to the inherent stochasticity of biochemical processes. Various mechanisms have been suggested, including the existence of alternative steady states in regulatory networks that are reached by means of stochastic fluctuations, long transient excursions from a stable state to an unstable excited state, and the switching on and off of a reaction network according to the availability of a constituent chemical species. Here we analyse a detailed stochastic kinetic model of two-component system signalling in bacteria, and show that alternative phenotypes emerge in the absence of these features. We perform a bifurcation analysis of deterministic reaction rate equations derived from the model, and find that they cannot reproduce the whole range of qualitative responses to external signals demonstrated by direct stochastic simulations. In particular, the mixed mode, where stochastic switching and a graded response are seen simultaneously, is absent. However, probabilistic and equation-free analyses of the stochastic model that calculate stationary states for the mean of an ensemble of stochastic trajectories reveal that slow transcription of either response regulator or histidine kinase leads to the coexistence of an approximate basal solution and a graded response that combine to produce the mixed mode, thus establishing its essential stochastic nature. The same techniques also show that stochasticity results in the observation of an all-or-none bistable response over a much wider range of external signals than would be expected on deterministic grounds. Thus we demonstrate the application of numerical equation-free methods to a detailed biochemical reaction network model, and show that it can provide new insight into the role of stochasticity in the emergence of phenotypic diversity.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002396&type=printable |
| spellingShingle | Rebecca B Hoyle Daniele Avitabile Andrzej M Kierzek Equation-free analysis of two-component system signalling model reveals the emergence of co-existing phenotypes in the absence of multistationarity. PLoS Computational Biology |
| title | Equation-free analysis of two-component system signalling model reveals the emergence of co-existing phenotypes in the absence of multistationarity. |
| title_full | Equation-free analysis of two-component system signalling model reveals the emergence of co-existing phenotypes in the absence of multistationarity. |
| title_fullStr | Equation-free analysis of two-component system signalling model reveals the emergence of co-existing phenotypes in the absence of multistationarity. |
| title_full_unstemmed | Equation-free analysis of two-component system signalling model reveals the emergence of co-existing phenotypes in the absence of multistationarity. |
| title_short | Equation-free analysis of two-component system signalling model reveals the emergence of co-existing phenotypes in the absence of multistationarity. |
| title_sort | equation free analysis of two component system signalling model reveals the emergence of co existing phenotypes in the absence of multistationarity |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002396&type=printable |
| work_keys_str_mv | AT rebeccabhoyle equationfreeanalysisoftwocomponentsystemsignallingmodelrevealstheemergenceofcoexistingphenotypesintheabsenceofmultistationarity AT danieleavitabile equationfreeanalysisoftwocomponentsystemsignallingmodelrevealstheemergenceofcoexistingphenotypesintheabsenceofmultistationarity AT andrzejmkierzek equationfreeanalysisoftwocomponentsystemsignallingmodelrevealstheemergenceofcoexistingphenotypesintheabsenceofmultistationarity |