Effects of spatial heterogeneity on bacterial genetic circuits
Intracellular spatial heterogeneity is frequently observed in bacteria, where the chromosome occupies part of the cell's volume and a circuit's DNA often localizes within the cell. How this heterogeneity affects core processes and genetic circuits is still poorly understood. In fact, commo...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2021
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| Online Access: | https://hdl.handle.net/1721.1/138532 |
| _version_ | 1811087697559683072 |
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| author | Barajas, Carlos Del Vecchio, Domitilla |
| author2 | Massachusetts Institute of Technology. Department of Mechanical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Mechanical Engineering Barajas, Carlos Del Vecchio, Domitilla |
| author_sort | Barajas, Carlos |
| collection | MIT |
| description | Intracellular spatial heterogeneity is frequently observed in bacteria, where the chromosome occupies part of the cell's volume and a circuit's DNA often localizes within the cell. How this heterogeneity affects core processes and genetic circuits is still poorly understood. In fact, commonly used ordinary differential equation (ODE) models of genetic circuits assume a well-mixed ensemble of molecules and, as such, do not capture spatial aspects. Reaction-diffusion partial differential equation (PDE) models have been only occasionally used since they are difficult to integrate and do not provide mechanistic understanding of the effects of spatial heterogeneity. In this paper, we derive a reduced ODE model that captures spatial effects, yet has the same dimension as commonly used well-mixed models. In particular, the only difference with respect to a well-mixed ODE model is that the association rate constant of binding reactions is multiplied by a coefficient, which we refer to as the binding correction factor (BCF). The BCF depends on the size of interacting molecules and on their location when fixed in space and it is equal to unity in a well-mixed ODE model. The BCF can be used to investigate how spatial heterogeneity affects the behavior of core processes and genetic circuits. Specifically, our reduced model indicates that transcription and its regulation are more effective for genes located at the cell poles than for genes located on the chromosome. The extent of these effects depends on the value of the BCF, which we found to be close to unity. For translation, the value of the BCF is always greater than unity, it increases with mRNA size, and, with biologically relevant parameters, is substantially larger than unity. Our model has broad validity, has the same dimension as a well-mixed model, yet it incorporates spatial heterogeneity. This simple-to-use model can be used to both analyze and design genetic circuits while accounting for spatial intracellular effects. |
| first_indexed | 2024-09-23T13:50:35Z |
| format | Article |
| id | mit-1721.1/138532 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T13:50:35Z |
| publishDate | 2021 |
| publisher | Public Library of Science (PLoS) |
| record_format | dspace |
| spelling | mit-1721.1/1385322023-04-10T18:46:39Z Effects of spatial heterogeneity on bacterial genetic circuits Barajas, Carlos Del Vecchio, Domitilla Massachusetts Institute of Technology. Department of Mechanical Engineering Intracellular spatial heterogeneity is frequently observed in bacteria, where the chromosome occupies part of the cell's volume and a circuit's DNA often localizes within the cell. How this heterogeneity affects core processes and genetic circuits is still poorly understood. In fact, commonly used ordinary differential equation (ODE) models of genetic circuits assume a well-mixed ensemble of molecules and, as such, do not capture spatial aspects. Reaction-diffusion partial differential equation (PDE) models have been only occasionally used since they are difficult to integrate and do not provide mechanistic understanding of the effects of spatial heterogeneity. In this paper, we derive a reduced ODE model that captures spatial effects, yet has the same dimension as commonly used well-mixed models. In particular, the only difference with respect to a well-mixed ODE model is that the association rate constant of binding reactions is multiplied by a coefficient, which we refer to as the binding correction factor (BCF). The BCF depends on the size of interacting molecules and on their location when fixed in space and it is equal to unity in a well-mixed ODE model. The BCF can be used to investigate how spatial heterogeneity affects the behavior of core processes and genetic circuits. Specifically, our reduced model indicates that transcription and its regulation are more effective for genes located at the cell poles than for genes located on the chromosome. The extent of these effects depends on the value of the BCF, which we found to be close to unity. For translation, the value of the BCF is always greater than unity, it increases with mRNA size, and, with biologically relevant parameters, is substantially larger than unity. Our model has broad validity, has the same dimension as a well-mixed model, yet it incorporates spatial heterogeneity. This simple-to-use model can be used to both analyze and design genetic circuits while accounting for spatial intracellular effects. 2021-12-17T17:13:34Z 2021-12-17T17:13:34Z 2020 2021-12-17T17:09:23Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/138532 Barajas, Carlos and Del Vecchio, Domitilla. 2020. "Effects of spatial heterogeneity on bacterial genetic circuits." PLoS Computational Biology, 16 (9). en 10.1371/JOURNAL.PCBI.1008159 PLoS Computational Biology Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Public Library of Science (PLoS) PLoS |
| spellingShingle | Barajas, Carlos Del Vecchio, Domitilla Effects of spatial heterogeneity on bacterial genetic circuits |
| title | Effects of spatial heterogeneity on bacterial genetic circuits |
| title_full | Effects of spatial heterogeneity on bacterial genetic circuits |
| title_fullStr | Effects of spatial heterogeneity on bacterial genetic circuits |
| title_full_unstemmed | Effects of spatial heterogeneity on bacterial genetic circuits |
| title_short | Effects of spatial heterogeneity on bacterial genetic circuits |
| title_sort | effects of spatial heterogeneity on bacterial genetic circuits |
| url | https://hdl.handle.net/1721.1/138532 |
| work_keys_str_mv | AT barajascarlos effectsofspatialheterogeneityonbacterialgeneticcircuits AT delvecchiodomitilla effectsofspatialheterogeneityonbacterialgeneticcircuits |