Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor
Abstract The ability to independently control the expression of different genes is important for quantitative biology. Using budding yeast, we characterize GAL1pr, GALL, MET3pr, CUP1pr, PHO5pr, tetOpr, terminator-tetOpr, Z3EV, blue-light inducible optogenetic systems El222-LIP, El222-GLIP, and red-l...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-06-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-38959-8 |
| _version_ | 1797789694783651840 |
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| author | Vojislav Gligorovski Ahmad Sadeghi Sahand Jamal Rahi |
| author_facet | Vojislav Gligorovski Ahmad Sadeghi Sahand Jamal Rahi |
| author_sort | Vojislav Gligorovski |
| collection | DOAJ |
| description | Abstract The ability to independently control the expression of different genes is important for quantitative biology. Using budding yeast, we characterize GAL1pr, GALL, MET3pr, CUP1pr, PHO5pr, tetOpr, terminator-tetOpr, Z3EV, blue-light inducible optogenetic systems El222-LIP, El222-GLIP, and red-light inducible PhyB-PIF3. We report kinetic parameters, noise scaling, impact on growth, and the fundamental leakiness of each system using an intuitive unit, maxGAL1. We uncover disadvantages of widely used tools, e.g., nonmonotonic activity of MET3pr and GALL, slow off kinetics of the doxycycline- and estradiol-inducible systems tetOpr and Z3EV, and high variability of PHO5pr and red-light activated PhyB-PIF3 system. We introduce two previously uncharacterized systems: strongLOV, a more light-sensitive El222 mutant, and ARG3pr, which is induced in the absence of arginine or presence of methionine. To demonstrate fine control over gene circuits, we experimentally tune the time between cell cycle Start and mitosis, artificially simulating near-wild-type timing. All strains, constructs, code, and data ( https://promoter-benchmark.epfl.ch/ ) are made available. |
| first_indexed | 2024-03-13T01:54:19Z |
| format | Article |
| id | doaj.art-430780b579ae410e94839a761ea12158 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-13T01:54:19Z |
| publishDate | 2023-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-430780b579ae410e94839a761ea121582023-07-02T11:19:47ZengNature PortfolioNature Communications2041-17232023-06-0114111810.1038/s41467-023-38959-8Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factorVojislav Gligorovski0Ahmad Sadeghi1Sahand Jamal Rahi2Laboratory of the Physics of Biological Systems, Institute of Physics, École polytechnique fédérale de Lausanne (EPFL)Laboratory of the Physics of Biological Systems, Institute of Physics, École polytechnique fédérale de Lausanne (EPFL)Laboratory of the Physics of Biological Systems, Institute of Physics, École polytechnique fédérale de Lausanne (EPFL)Abstract The ability to independently control the expression of different genes is important for quantitative biology. Using budding yeast, we characterize GAL1pr, GALL, MET3pr, CUP1pr, PHO5pr, tetOpr, terminator-tetOpr, Z3EV, blue-light inducible optogenetic systems El222-LIP, El222-GLIP, and red-light inducible PhyB-PIF3. We report kinetic parameters, noise scaling, impact on growth, and the fundamental leakiness of each system using an intuitive unit, maxGAL1. We uncover disadvantages of widely used tools, e.g., nonmonotonic activity of MET3pr and GALL, slow off kinetics of the doxycycline- and estradiol-inducible systems tetOpr and Z3EV, and high variability of PHO5pr and red-light activated PhyB-PIF3 system. We introduce two previously uncharacterized systems: strongLOV, a more light-sensitive El222 mutant, and ARG3pr, which is induced in the absence of arginine or presence of methionine. To demonstrate fine control over gene circuits, we experimentally tune the time between cell cycle Start and mitosis, artificially simulating near-wild-type timing. All strains, constructs, code, and data ( https://promoter-benchmark.epfl.ch/ ) are made available.https://doi.org/10.1038/s41467-023-38959-8 |
| spellingShingle | Vojislav Gligorovski Ahmad Sadeghi Sahand Jamal Rahi Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor Nature Communications |
| title | Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor |
| title_full | Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor |
| title_fullStr | Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor |
| title_full_unstemmed | Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor |
| title_short | Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor |
| title_sort | multidimensional characterization of inducible promoters and a highly light sensitive lov transcription factor |
| url | https://doi.org/10.1038/s41467-023-38959-8 |
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