Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation.
Polarity establishment, the spontaneous generation of asymmetric molecular distributions, is a crucial component of many cellular functions. Saccharomyces cerevisiae (yeast) undergoes directed growth during budding and mating, and is an ideal model organism for studying polarization. In yeast and ma...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2018-03-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1006016 |
| _version_ | 1818584911585476608 |
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| author | Michael Pablo Samuel A Ramirez Timothy C Elston |
| author_facet | Michael Pablo Samuel A Ramirez Timothy C Elston |
| author_sort | Michael Pablo |
| collection | DOAJ |
| description | Polarity establishment, the spontaneous generation of asymmetric molecular distributions, is a crucial component of many cellular functions. Saccharomyces cerevisiae (yeast) undergoes directed growth during budding and mating, and is an ideal model organism for studying polarization. In yeast and many other cell types, the Rho GTPase Cdc42 is the key molecular player in polarity establishment. During yeast polarization, multiple patches of Cdc42 initially form, then resolve into a single front. Because polarization relies on strong positive feedback, it is likely that the amplification of molecular-level fluctuations underlies the generation of multiple nascent patches. In the absence of spatial cues, these fluctuations may be key to driving polarization. Here we used particle-based simulations to investigate the role of stochastic effects in a Turing-type model of yeast polarity establishment. In the model, reactions take place either between two molecules on the membrane, or between a cytosolic and a membrane-bound molecule. Thus, we developed a computational platform that explicitly simulates molecules at and near the cell membrane, and implicitly handles molecules away from the membrane. To evaluate stochastic effects, we compared particle simulations to deterministic reaction-diffusion equation simulations. Defining macroscopic rate constants that are consistent with the microscopic parameters for this system is challenging, because diffusion occurs in two dimensions and particles exchange between the membrane and cytoplasm. We address this problem by empirically estimating macroscopic rate constants from appropriately designed particle-based simulations. Ultimately, we find that stochastic fluctuations speed polarity establishment and permit polarization in parameter regions predicted to be Turing stable. These effects can operate at Cdc42 abundances expected of yeast cells, and promote polarization on timescales consistent with experimental results. To our knowledge, our work represents the first particle-based simulations of a model for yeast polarization that is based on a Turing mechanism. |
| first_indexed | 2024-12-16T08:28:42Z |
| format | Article |
| id | doaj.art-24542db809e4434ea8b075a9d16a6aa7 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-16T08:28:42Z |
| publishDate | 2018-03-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-24542db809e4434ea8b075a9d16a6aa72022-12-21T22:37:56ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582018-03-01143e100601610.1371/journal.pcbi.1006016Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation.Michael PabloSamuel A RamirezTimothy C ElstonPolarity establishment, the spontaneous generation of asymmetric molecular distributions, is a crucial component of many cellular functions. Saccharomyces cerevisiae (yeast) undergoes directed growth during budding and mating, and is an ideal model organism for studying polarization. In yeast and many other cell types, the Rho GTPase Cdc42 is the key molecular player in polarity establishment. During yeast polarization, multiple patches of Cdc42 initially form, then resolve into a single front. Because polarization relies on strong positive feedback, it is likely that the amplification of molecular-level fluctuations underlies the generation of multiple nascent patches. In the absence of spatial cues, these fluctuations may be key to driving polarization. Here we used particle-based simulations to investigate the role of stochastic effects in a Turing-type model of yeast polarity establishment. In the model, reactions take place either between two molecules on the membrane, or between a cytosolic and a membrane-bound molecule. Thus, we developed a computational platform that explicitly simulates molecules at and near the cell membrane, and implicitly handles molecules away from the membrane. To evaluate stochastic effects, we compared particle simulations to deterministic reaction-diffusion equation simulations. Defining macroscopic rate constants that are consistent with the microscopic parameters for this system is challenging, because diffusion occurs in two dimensions and particles exchange between the membrane and cytoplasm. We address this problem by empirically estimating macroscopic rate constants from appropriately designed particle-based simulations. Ultimately, we find that stochastic fluctuations speed polarity establishment and permit polarization in parameter regions predicted to be Turing stable. These effects can operate at Cdc42 abundances expected of yeast cells, and promote polarization on timescales consistent with experimental results. To our knowledge, our work represents the first particle-based simulations of a model for yeast polarization that is based on a Turing mechanism.https://doi.org/10.1371/journal.pcbi.1006016 |
| spellingShingle | Michael Pablo Samuel A Ramirez Timothy C Elston Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation. PLoS Computational Biology |
| title | Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation. |
| title_full | Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation. |
| title_fullStr | Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation. |
| title_full_unstemmed | Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation. |
| title_short | Particle-based simulations of polarity establishment reveal stochastic promotion of Turing pattern formation. |
| title_sort | particle based simulations of polarity establishment reveal stochastic promotion of turing pattern formation |
| url | https://doi.org/10.1371/journal.pcbi.1006016 |
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