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Gola KK, Patel A, Sen S. Tradeoffs in the design of RNA thermometers. Phys Biol 2024; 21:044001. [PMID: 38949434 DOI: 10.1088/1478-3975/ad5d6b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/01/2024] [Indexed: 07/02/2024]
Abstract
The synthesis of RNA thermometers is aimed at achieving temperature responses with desired thresholds and sensitivities. Although previous works have generated thermometers with a variety of thresholds and sensitivities as well as guidelines for design, possible constraints in the achievable thresholds and sensitivities remain unclear. We addressed this issue using a two-state model and its variants, as well as melt profiles generated from thermodynamic computations. In the two-state model, we found that the threshold was inversely proportional to the sensitivity, in the case of a fixed energy difference between the two states. Notably, this constraint could persist in variations of the two-state model with sequentially unfolding states and branched parallel pathways. Furthermore, the melt profiles generated from a library of thermometers exhibited a similar constraint. These results should inform the design of RNA thermometers as well as other responses that are mediated in a similar fashion.
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Affiliation(s)
- Krishan Kumar Gola
- Department of Electrical Engineering, Indian Institute of Technology Delhi, New Delhi, Delhi 110016, India
| | - Abhilash Patel
- Department of Electrical Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Shaunak Sen
- Department of Electrical Engineering, Indian Institute of Technology Delhi, New Delhi, Delhi 110016, India
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2
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Sharts DM, Almanza MT, Banks AV, Castellanos AM, Hernandez CGO, Lopez ML, Rodriguez D, Tong AY, Segeberg MR, Passalacqua LFM, Abdelsayed MM. Robo-Therm, a pipeline to RNA thermometer discovery and validation. RNA (NEW YORK, N.Y.) 2024; 30:760-769. [PMID: 38565243 PMCID: PMC11182007 DOI: 10.1261/rna.079980.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
RNA thermometers are highly structured noncoding RNAs located in the 5'-untranslated regions (UTRs) of genes that regulate expression by undergoing conformational changes in response to temperature. The discovery of RNA thermometers through bioinformatics is difficult because there is little sequence conservation among their structural elements. Thus, the abundance of these thermosensitive regulatory structures remains unclear. Herein, to advance the discovery and validation of RNA thermometers, we developed Robo-Therm, a pipeline that combines an adaptive and user-friendly in silico motif search with a well-established reporter system. Through our application of Robo-Therm, we discovered two novel RNA thermometers in bacterial and bacteriophage genomes found in the human gut. One of these thermometers is present in the 5'-UTR of a gene that codes for σ 70 RNA polymerase subunit in the bacteria Mediterraneibacter gnavus and Bacteroides pectinophilus, and in the bacteriophage Caudoviricetes, which infects B. pectinophilus The other thermometer is in the 5'-UTR of a tetracycline resistance gene (tetR) in the intestinal bacteria Escherichia coli and Shigella flexneri Our Robo-Therm pipeline can be applied to discover multiple RNA thermometers across various genomes.
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Affiliation(s)
- Davis M Sharts
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Maria T Almanza
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Andrea V Banks
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Alyssa M Castellanos
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | | | - Monica L Lopez
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Daniela Rodriguez
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Alina Y Tong
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Maximilian R Segeberg
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Luiz F M Passalacqua
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael M Abdelsayed
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
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Chung KP, Loiacono FV, Neupert J, Wu M, Bock R. An RNA thermometer in the chloroplast genome of Chlamydomonas facilitates temperature-controlled gene expression. Nucleic Acids Res 2023; 51:11386-11400. [PMID: 37855670 PMCID: PMC10639063 DOI: 10.1093/nar/gkad816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/01/2023] [Accepted: 09/20/2023] [Indexed: 10/20/2023] Open
Abstract
Riboregulators such as riboswitches and RNA thermometers provide simple, protein-independent tools to control gene expression at the post-transcriptional level. In bacteria, RNA thermometers regulate protein synthesis in response to temperature shifts. Thermometers outside of the bacterial world are rare, and in organellar genomes, no RNA thermometers have been identified to date. Here we report the discovery of an RNA thermometer in a chloroplast gene of the unicellular green alga Chlamydomonas reinhardtii. The thermometer, residing in the 5' untranslated region of the psaA messenger RNA forms a hairpin-type secondary structure that masks the Shine-Dalgarno sequence at 25°C. At 40°C, melting of the secondary structure increases accessibility of the Shine-Dalgarno sequence to initiating ribosomes, thus enhancing protein synthesis. By targeted nucleotide substitutions and transfer of the thermometer into Escherichia coli, we show that the secondary structure is necessary and sufficient to confer the thermometer properties. We also demonstrate that the thermometer provides a valuable tool for inducible transgene expression from the Chlamydomonas plastid genome, in that a simple temperature shift of the algal culture can greatly increase recombinant protein yields.
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Affiliation(s)
- Kin Pan Chung
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - F Vanessa Loiacono
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Juliane Neupert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Mengting Wu
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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Sharma P, Mondal K, Kumar S, Tamang S, Najar IN, Das S, Thakur N. RNA thermometers in bacteria: Role in thermoregulation. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - GENE REGULATORY MECHANISMS 2022; 1865:194871. [DOI: 10.1016/j.bbagrm.2022.194871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/09/2022] [Accepted: 08/21/2022] [Indexed: 04/09/2023]
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Chee WKD, Yeoh JW, Dao VL, Poh CL. Thermogenetics: Applications come of age. Biotechnol Adv 2022; 55:107907. [PMID: 35041863 DOI: 10.1016/j.biotechadv.2022.107907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/13/2021] [Accepted: 01/09/2022] [Indexed: 12/20/2022]
Abstract
Temperature is a ubiquitous physical cue that is non-invasive, penetrative and easy to apply. In the growing field of thermogenetics, through beneficial repurposing of natural thermosensing mechanisms, synthetic biology is bringing new opportunities to design and build robust temperature-sensitive (TS) sensors which forms a thermogenetic toolbox of well characterised biological parts. Recent advancements in technological platforms available have expedited the discovery of novel or de novo thermosensors which are increasingly deployed in many practical temperature-dependent biomedical, industrial and biosafety applications. In all, the review aims to convey both the exhilarating recent technological developments underlying the advancement of thermosensors and the exciting opportunities the nascent thermogenetic field holds for biomedical and biotechnology applications.
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Affiliation(s)
- Wai Kit David Chee
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jing Wui Yeoh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Viet Linh Dao
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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