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Cui W, Lin Q, Wu Y, Wang X, Zhang Y, Lin X, Zhang L, Liu X, Han L, Zhou Z. Creation of Architecturally Minimal Transcriptionally Activating Riboswitches Responsive to Theophylline Reveals an Unconventional Design Strategy. ACS Synth Biol 2023; 12:3716-3729. [PMID: 38052004 DOI: 10.1021/acssynbio.3c00519] [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] [Indexed: 12/07/2023]
Abstract
Riboswitches are noncoding RNA switches that are largely utilized in bacteria and play a significant role in synthetic biology. Nonetheless, their natural counterparts possess lengthy sequences and intricate structures, posing challenges for their modular integration into complex gene circuits. Consequently, it is imperative to develop simplified synthetic riboswitches that can be effortlessly incorporated into gene circuits. The conventional approach to generate synthetic riboswitches entails tedious library construction and extensive screening, which frequently yields suboptimal performance. To overcome this obstacle, alternative methods are urgently needed. In this study, we created a novel approach to designing a diverse set of transcription-activating riboswitches that exhibit high performance and broad compatibility. The strategy involved starting with a synthetic theophylline RNA aptamer and designing an expression platform that forms a transcriptional terminator in its inactive state but switches to an antiterminator when it is activated. Several sequences were designed, constructed, and subjected to virtual screening, resulting in the identification of two transcription-activating riboswitches. These riboswitches were then engineered to reduce the basal leakage and increase the activation level through extending the hairpin region using a screened random sequence. These architecturally minimal synthetic riboswitches were highly adapted to different constitutive promoters in a modular manner, generating a differentially responsive output to theophylline. As a proof-of-principle, the synthetic riboswitches were applied to rewire a synthetic quorum-sensing circuit (QSC). The reprogrammed QSC successfully modulated the temporal responsive profile against the activation. This strategy is expected to expand the variety of high-performance riboswitches that are responsive to different ligands, thereby further facilitating the design of complex genetic circuits.
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Affiliation(s)
- Wenjing Cui
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, MOE, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qiao Lin
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yi Wu
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xinran Wang
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuqing Zhang
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xinyu Lin
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Linpei Zhang
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, MOE, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xu Liu
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Laichuang Han
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, MOE, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhemin Zhou
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, MOE, Jiangnan University, Wuxi, Jiangsu 214122, China
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Roy P, Claude JB, Tiwari S, Barulin A, Wenger J. Ultraviolet Nanophotonics Enables Autofluorescence Correlation Spectroscopy on Label-Free Proteins with a Single Tryptophan. NANO LETTERS 2023; 23:497-504. [PMID: 36603115 DOI: 10.1021/acs.nanolett.2c03797] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Using the ultraviolet autofluorescence of tryptophan amino acids offers fascinating perspectives to study single proteins without the drawbacks of fluorescence labeling. However, the low autofluorescence signals have so far limited the UV detection to large proteins containing several tens of tryptophan residues. This limit is not compatible with the vast majority of proteins which contain only a few tryptophans. Here we push the sensitivity of label-free ultraviolet fluorescence correlation spectroscopy (UV-FCS) down to the single tryptophan level. Our results show how the combination of nanophotonic plasmonic antennas, antioxidants, and background reduction techniques can improve the signal-to-background ratio by over an order of magnitude and enable UV-FCS on thermonuclease proteins with a single tryptophan residue. This sensitivity breakthrough unlocks the applicability of UV-FCS technique to a broad library of label-free proteins.
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Affiliation(s)
- Prithu Roy
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, AMUTech, 13013 Marseille, France
| | - Jean-Benoît Claude
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, AMUTech, 13013 Marseille, France
| | - Sunny Tiwari
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, AMUTech, 13013 Marseille, France
| | - Aleksandr Barulin
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, AMUTech, 13013 Marseille, France
| | - Jérôme Wenger
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, AMUTech, 13013 Marseille, France
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Yang Y, Padilla A, de Guillen K, Mammri L, Gracy J, Declerck N, Déméné H. Structural Insights into of the Allosteric Activation of the LicT Antiterminator by PTS-Mediated Phosphorylation. Structure 2020; 28:244-251.e3. [DOI: 10.1016/j.str.2019.10.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/05/2019] [Accepted: 10/24/2019] [Indexed: 10/25/2022]
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