Robust network topologies for temperature-inducible bioswitches
Abstract Background Thermoinducible bioswitches are unique in that the all-or-none switch response is triggered by temperature, which is a global factor that impacts all biochemical reaction processes. To date, temperature-inducible bioswitches rely exclusively on special thermal sensing biomolecule...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2022-05-01
|
| Series: | Journal of Biological Engineering |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13036-022-00290-z |
| _version_ | 1811254165100298240 |
|---|---|
| author | Di Wu Hongli Wang Qi Ouyang |
| author_facet | Di Wu Hongli Wang Qi Ouyang |
| author_sort | Di Wu |
| collection | DOAJ |
| description | Abstract Background Thermoinducible bioswitches are unique in that the all-or-none switch response is triggered by temperature, which is a global factor that impacts all biochemical reaction processes. To date, temperature-inducible bioswitches rely exclusively on special thermal sensing biomolecules of DNA, RNA, proteins and lipids whose conformations are critically temperature dependent. Method This paper extends the traditional thermal switch by utilizing purposely designed network topologies of biomolecular interactions to achieve the switching function. By assuming the general Arrhenius law for biochemical reactions, we explore the full space of all three-node genetic interaction networks to screen topologies capable of thermal bioswitches. Three target bioswitches, i.e., thermal-inducible Off–On, cold-inducible On–Off, and hybrid Off–On-Off double switches, are considered separately. Conclusions We identify the minimal and core network skeletons that are basic and essential for building robust high-performance bioswitches: three Off–On motifs, three On–Off motifs, and an incoherent feedforward motif for an Off–On-Off double switch. Functional topologies are implicitly preferential in choosing parameter values to achieve the target functions. The scenario of the topology-based bioswitch we propose here is an extension of molecule-based bioswitches and would be valuable in aiding the rational design and synthesis of efficient high-performance thermal bioswitches. |
| first_indexed | 2024-04-12T17:03:08Z |
| format | Article |
| id | doaj.art-22e88deeb423493381043bcbe45b0cfc |
| institution | Directory Open Access Journal |
| issn | 1754-1611 |
| language | English |
| last_indexed | 2024-04-12T17:03:08Z |
| publishDate | 2022-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Biological Engineering |
| spelling | doaj.art-22e88deeb423493381043bcbe45b0cfc2022-12-22T03:24:01ZengBMCJournal of Biological Engineering1754-16112022-05-0116111210.1186/s13036-022-00290-zRobust network topologies for temperature-inducible bioswitchesDi Wu0Hongli Wang1Qi Ouyang2The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking UniversityThe State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking UniversityThe State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking UniversityAbstract Background Thermoinducible bioswitches are unique in that the all-or-none switch response is triggered by temperature, which is a global factor that impacts all biochemical reaction processes. To date, temperature-inducible bioswitches rely exclusively on special thermal sensing biomolecules of DNA, RNA, proteins and lipids whose conformations are critically temperature dependent. Method This paper extends the traditional thermal switch by utilizing purposely designed network topologies of biomolecular interactions to achieve the switching function. By assuming the general Arrhenius law for biochemical reactions, we explore the full space of all three-node genetic interaction networks to screen topologies capable of thermal bioswitches. Three target bioswitches, i.e., thermal-inducible Off–On, cold-inducible On–Off, and hybrid Off–On-Off double switches, are considered separately. Conclusions We identify the minimal and core network skeletons that are basic and essential for building robust high-performance bioswitches: three Off–On motifs, three On–Off motifs, and an incoherent feedforward motif for an Off–On-Off double switch. Functional topologies are implicitly preferential in choosing parameter values to achieve the target functions. The scenario of the topology-based bioswitch we propose here is an extension of molecule-based bioswitches and would be valuable in aiding the rational design and synthesis of efficient high-performance thermal bioswitches.https://doi.org/10.1186/s13036-022-00290-zNetwork motifThermoinducible bioswitchGenetic circuits |
| spellingShingle | Di Wu Hongli Wang Qi Ouyang Robust network topologies for temperature-inducible bioswitches Journal of Biological Engineering Network motif Thermoinducible bioswitch Genetic circuits |
| title | Robust network topologies for temperature-inducible bioswitches |
| title_full | Robust network topologies for temperature-inducible bioswitches |
| title_fullStr | Robust network topologies for temperature-inducible bioswitches |
| title_full_unstemmed | Robust network topologies for temperature-inducible bioswitches |
| title_short | Robust network topologies for temperature-inducible bioswitches |
| title_sort | robust network topologies for temperature inducible bioswitches |
| topic | Network motif Thermoinducible bioswitch Genetic circuits |
| url | https://doi.org/10.1186/s13036-022-00290-z |
| work_keys_str_mv | AT diwu robustnetworktopologiesfortemperatureinduciblebioswitches AT hongliwang robustnetworktopologiesfortemperatureinduciblebioswitches AT qiouyang robustnetworktopologiesfortemperatureinduciblebioswitches |