Limit cycles in models of circular gene networks regulated by negative feedback loops
Abstract Background The regulatory feedback loops that present in structural and functional organization of molecular-genetic systems and the phenomenon of the regulatory signal delay, a time period between the moment of signal reception and its implementation, provide natural conditions for complic...
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| Format: | Article |
| Language: | English |
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BMC
2020-09-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-020-03598-z |
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| author | Vitaly A. Likhoshvai Vladimir P. Golubyatnikov Tamara M. Khlebodarova |
| author_facet | Vitaly A. Likhoshvai Vladimir P. Golubyatnikov Tamara M. Khlebodarova |
| author_sort | Vitaly A. Likhoshvai |
| collection | DOAJ |
| description | Abstract Background The regulatory feedback loops that present in structural and functional organization of molecular-genetic systems and the phenomenon of the regulatory signal delay, a time period between the moment of signal reception and its implementation, provide natural conditions for complicated dynamic regimes in these systems. The delay phenomenon at the intracellular level is a consequence of the matrix principle of data transmission, implemented through the rather complex processes of transcription and translation.However, the rules of the influence of system structure on system dynamics are not clearly understood. Knowledge of these rules is particularly important for construction of synthetic gene networks with predetermined properties. Results We study dynamical properties of models of simplest circular gene networks regulated by negative feedback mechanisms. We have shown existence and stability of oscillating trajectories (cycles) in these models. Two algorithms of construction and localization of these cycles have been proposed. For one of these models, we have solved an inverse problem of parameters identification. Conclusions The modeling results demonstrate that non-stationary dynamics in the models of circular gene networks with negative feedback loops is achieved by a high degree of non-linearity of the mechanism of the autorepressor influence on its own expression, by the presence of regulatory signal delay, the value of which must exceed a certain critical value, and transcription/translation should be initiated from a sufficiently strong promoter/Shine-Dalgarno site. We believe that the identified patterns are key elements of the oscillating construction design. |
| first_indexed | 2024-12-21T09:37:54Z |
| format | Article |
| id | doaj.art-89363eb1dc274465aef7f4001b3749ca |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-21T09:37:54Z |
| publishDate | 2020-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-89363eb1dc274465aef7f4001b3749ca2022-12-21T19:08:35ZengBMCBMC Bioinformatics1471-21052020-09-0121S1111510.1186/s12859-020-03598-zLimit cycles in models of circular gene networks regulated by negative feedback loopsVitaly A. Likhoshvai0Vladimir P. Golubyatnikov1Tamara M. Khlebodarova2Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch RASLaboratory of Inverse Problems of Mathematical Physics, Sobolev Institute of Mathematics Siberian Branch RASDepartment of Systems Biology, Institute of Cytology and Genetics, Siberian Branch RASAbstract Background The regulatory feedback loops that present in structural and functional organization of molecular-genetic systems and the phenomenon of the regulatory signal delay, a time period between the moment of signal reception and its implementation, provide natural conditions for complicated dynamic regimes in these systems. The delay phenomenon at the intracellular level is a consequence of the matrix principle of data transmission, implemented through the rather complex processes of transcription and translation.However, the rules of the influence of system structure on system dynamics are not clearly understood. Knowledge of these rules is particularly important for construction of synthetic gene networks with predetermined properties. Results We study dynamical properties of models of simplest circular gene networks regulated by negative feedback mechanisms. We have shown existence and stability of oscillating trajectories (cycles) in these models. Two algorithms of construction and localization of these cycles have been proposed. For one of these models, we have solved an inverse problem of parameters identification. Conclusions The modeling results demonstrate that non-stationary dynamics in the models of circular gene networks with negative feedback loops is achieved by a high degree of non-linearity of the mechanism of the autorepressor influence on its own expression, by the presence of regulatory signal delay, the value of which must exceed a certain critical value, and transcription/translation should be initiated from a sufficiently strong promoter/Shine-Dalgarno site. We believe that the identified patterns are key elements of the oscillating construction design.http://link.springer.com/article/10.1186/s12859-020-03598-zMathematical modelingCircular gene networksDelay argument equationsFeedback loops regulationAutorepressorCycles |
| spellingShingle | Vitaly A. Likhoshvai Vladimir P. Golubyatnikov Tamara M. Khlebodarova Limit cycles in models of circular gene networks regulated by negative feedback loops BMC Bioinformatics Mathematical modeling Circular gene networks Delay argument equations Feedback loops regulation Autorepressor Cycles |
| title | Limit cycles in models of circular gene networks regulated by negative feedback loops |
| title_full | Limit cycles in models of circular gene networks regulated by negative feedback loops |
| title_fullStr | Limit cycles in models of circular gene networks regulated by negative feedback loops |
| title_full_unstemmed | Limit cycles in models of circular gene networks regulated by negative feedback loops |
| title_short | Limit cycles in models of circular gene networks regulated by negative feedback loops |
| title_sort | limit cycles in models of circular gene networks regulated by negative feedback loops |
| topic | Mathematical modeling Circular gene networks Delay argument equations Feedback loops regulation Autorepressor Cycles |
| url | http://link.springer.com/article/10.1186/s12859-020-03598-z |
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