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Abstract
One of the most prominent features of genetically encoded biosensors (GEBs) is their evolvability-the ability to invent new sensory functions using mutations. Among the GEBs, the transcription factor-based biosensors (TF-biosensors) is the focus of this review. We also discuss how this class of sensors can be highly evolvable and how we can exploit it. With an established platform for directed evolution, researchers can create, or evolve, new TF-biosensors. Directed evolution experiments have revealed the TF-biosensors' evolvability, which is based partially on their characteristic physicochemical properties.
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Affiliation(s)
- Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Yuki Kimura
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, Chiba University
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Tominaga M, Nozaki K, Umeno D, Ishii J, Kondo A. Robust and flexible platform for directed evolution of yeast genetic switches. Nat Commun 2021; 12:1846. [PMID: 33758180 PMCID: PMC7988172 DOI: 10.1038/s41467-021-22134-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/26/2021] [Indexed: 01/31/2023] Open
Abstract
A wide repertoire of genetic switches has accelerated prokaryotic synthetic biology, while eukaryotic synthetic biology has lagged in the model organism Saccharomyces cerevisiae. Eukaryotic genetic switches are larger and more complex than prokaryotic ones, complicating the rational design and evolution of them. Here, we present a robust workflow for the creation and evolution of yeast genetic switches. The selector system was designed so that both ON- and OFF-state selection of genetic switches is completed solely by liquid handling, and it enabled parallel screen/selection of different motifs with different selection conditions. Because selection threshold of both ON- and OFF-state selection can be flexibly tuned, the desired selection conditions can be rapidly pinned down for individual directed evolution experiments without a prior knowledge either on the library population. The system's utility was demonstrated using 20 independent directed evolution experiments, yielding genetic switches with elevated inducer sensitivities, inverted switching behaviours, sensory functions, and improved signal-to-noise ratio (>100-fold induction). The resulting yeast genetic switches were readily integrated, in a plug-and-play manner, into an AND-gated carotenoid biosynthesis pathway.
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Affiliation(s)
- Masahiro Tominaga
- grid.31432.370000 0001 1092 3077Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Kenta Nozaki
- grid.31432.370000 0001 1092 3077Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Daisuke Umeno
- grid.136304.30000 0004 0370 1101Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, Chiba, Japan
| | - Jun Ishii
- grid.31432.370000 0001 1092 3077Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan ,grid.31432.370000 0001 1092 3077Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Akihiko Kondo
- grid.31432.370000 0001 1092 3077Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan ,grid.31432.370000 0001 1092 3077Engineering Biology Research Center, Kobe University, Kobe, Japan ,grid.31432.370000 0001 1092 3077Department of Chemical Science and Engineering, Faculty of Engineering, Kobe University, Kobe, Japan ,grid.7597.c0000000094465255Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
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Improvement of the dP-nucleoside-mediated herpes simplex virus thymidine kinase negative-selection system by manipulating dP metabolism genes. J Biosci Bioeng 2020; 130:121-127. [PMID: 32229092 DOI: 10.1016/j.jbiosc.2020.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/14/2020] [Accepted: 03/03/2020] [Indexed: 11/21/2022]
Abstract
A variety of positive/negative selection systems have been exploited as genome engineering tools and screening platforms for genetic switches. While numerous positive-selection systems are available, only a handful of negative-selection systems are useful for such applications. We previously reported a powerful negative-selection system using herpes simplex virus thymidine kinase (HsvTK) and the mutagenic nucleoside analog 6-(β-d-2-deoxyribofuranosyl)-3,4-dihydro-8H-pyrimido [4,5-c][1,2] oxazin-7-one (dP). Upon addition of 1000 nM dP, cells expressing HsvTK quickly die, with unprecedented efficacy. However, this selection procedure elevates the spontaneous mutation rate of the host cells by 10-fold due to the mutagenic nature of dP. To decrease the operative concentration of dP required for negative selection, we systematically created the strains of Escherichia coli either by removing or overexpressing genes involved in DNA/RNA metabolism. We found that over-expression of NupC and NupG (nucleoside uptake-related inner membrane transporters), Tsx (outer membrane transporter), NdK (nucleotide kinase) sensitized E. coli cells to dP. Simultaneous overexpression of these three genes (ndk-nupC-tsx) significantly improved the dP-sensitivity of E. coli, lowering the necessary operative concentration of dP for negative selection by 10-fold. This enabled robust and selective elimination of strains harboring chromosomally-encoded hsvtk simply by adding as low as 100 nM dP, which causes only a modest increase in the spontaneous mutation frequency as compared to the cells without hsvtk.
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Kimura Y, Kawai-Noma S, Saito K, Umeno D. Directed Evolution of the Stringency of the LuxR Vibrio fischeri Quorum Sensor without OFF-State Selection. ACS Synth Biol 2020; 9:567-575. [PMID: 31999435 DOI: 10.1021/acssynbio.9b00444] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Stringency (low leak) is one of the most important specifications required for genetic circuits and induction systems, but it is challenging to evolve without sacrificing the maximum output level. This problem also comes from the absence of truly tunable negative selection methods. This paper reports that stringently switching variants can sometimes emerge with surprising frequency upon mutations. We randomly mutated the previously generated leaky variants of LuxR, the quorum-sensing transcription activator from Vibrio fischeri, to restore the stringency. We found as much as 10-20% of the entire population exhibited significantly improved signal-to-noise ratios compared with their parents. This indicated that these mutants arose by the loss of folding capability by accumulating destabilizing mutations, not by introducing rare adaptive mutations, thereby becoming AHL-dependent folders. Only four rounds of mutagenesis and ON-state selection resulted in the domination of the entire population by the improved variants with low leak, without direct selection pressure for stringency. With this surprising frequency, conversion into the "ligand-addicted folders" should be one of the prevailing modes of evolving stringency both in the laboratory and in nature, and the workflow described here provides a rapid and versatile method of improving the signal-to-noise ratio of various genetic switches.
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Affiliation(s)
- Yuki Kimura
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
| | - Shigeko Kawai-Noma
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33, Yayoi-Cho, Inage-ku, Chiba 263-8522, Japan
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Kimura Y, Umeno D. Directed evolution of transcriptional switches using dual-selector systems. Methods Enzymol 2020; 644:191-207. [DOI: 10.1016/bs.mie.2020.04.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Jang S, Jang S, Yang J, Seo SW, Jung GY. RNA-based dynamic genetic controllers: development strategies and applications. Curr Opin Biotechnol 2017; 53:1-11. [PMID: 29132120 PMCID: PMC7126020 DOI: 10.1016/j.copbio.2017.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/11/2017] [Accepted: 10/16/2017] [Indexed: 12/25/2022]
Abstract
Unique properties of RNA lead to the development of RNA-based dynamic genetic controllers. Natural riboswitches are re-engineered to detect new molecules. RNA-based regulatory mechanisms are exploited to construct novel dynamic RNA controllers. Computational methods and in vitro–in vivo selection enable de novo design of dynamic RNA controllers. Dynamic RNA controllers are utilized for metabolic engineering and synthetic biology.
Dynamic regulation of gene expression in response to various molecules is crucial for both basic science and practical applications. RNA is considered an attractive material for creating dynamic genetic controllers because of its specific binding to ligands, structural flexibility, programmability, and small size. Here, we review recent advances in strategies for developing RNA-based dynamic controllers and applications. First, we describe studies that re-engineered natural riboswitches to generate new dynamic controllers. Next, we summarize RNA-based regulatory mechanisms that have been exploited to build novel artificial dynamic controllers. We also discuss computational methods and high-throughput selection approaches for de novo design of dynamic RNA controllers. Finally, we explain applications of dynamic RNA controllers for metabolic engineering and synthetic biology.
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Affiliation(s)
- Sungho Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sungyeon Jang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jina Yang
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1, Gwanak-ro, Gwanak-Gu, Seoul 08826, Republic of Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Institute of Chemical Process, Seoul National University, 1, Gwanak-ro, Gwanak-Gu, Seoul 08826, Republic of Korea.
| | - Gyoo Yeol Jung
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea.
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Saeki K, Tominaga M, Kawai-Noma S, Saito K, Umeno D. Rapid Diversification of BetI-Based Transcriptional Switches for the Control of Biosynthetic Pathways and Genetic Circuits. ACS Synth Biol 2016; 5:1201-1210. [PMID: 26991155 DOI: 10.1021/acssynbio.5b00230] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synthetic biologists are in need of genetic switches, or inducible sensor/promoter systems, that can be reliably integrated in multiple contexts. Using a liquid-based selection method, we systematically engineered the choline-inducible transcription factor BetI, yielding various choline-inducible and choline-repressive promoter systems with various input-output characteristics. In addition to having high stringency and a high maximum induction level, they underwent a graded and single-peaked response to choline. Taking advantage of these features, we demonstrated the utility of these systems for controlling the carotenoid biosynthetic pathway and for constructing two-input logic gates. Additionally, we demonstrated the rapidity, throughput, robustness, and cost-effectiveness of our selection method, which facilitates the conversion of natural genetic controlling systems into systems that are designed for various synthetic biology applications.
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Affiliation(s)
- Kazuya Saeki
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Masahiro Tominaga
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Shigeko Kawai-Noma
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Kyoichi Saito
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
| | - Daisuke Umeno
- Department
of Applied Chemistry and Biotechnology, Faculty of Engineering, Chiba University, 1-33 Yayoi-Cyo, Inage-ku, Chiba 263-8522, Japan
- Precursory Research
for Embryonic Science and Technology (PRESTO), Japan Science and Technology
Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Hoffmann SA, Kruse SM, Arndt KM. Long-range transcriptional interference in E. coli used to construct a dual positive selection system for genetic switches. Nucleic Acids Res 2016; 44:e95. [PMID: 26932362 PMCID: PMC4889929 DOI: 10.1093/nar/gkw125] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 02/21/2016] [Indexed: 11/29/2022] Open
Abstract
We have investigated transcriptional interference between convergent genes in E. coli and demonstrate substantial interference for inter-promoter distances of as far as 3 kb. Interference can be elicited by both strong σ70 dependent and T7 promoters. In the presented design, a strong promoter driving gene expression of a ‘forward’ gene interferes with the expression of a ‘reverse’ gene by a weak promoter. This arrangement allows inversely correlated gene expression without requiring further regulatory components. Thus, modulation of the activity of the strong promoter alters expression of both the forward and the reverse gene. We used this design to develop a dual selection system for conditional operator site binding, allowing positive selection both for binding and for non-binding to DNA. This study demonstrates the utility of this novel system using the Lac repressor as a model protein for conditional DNA binding, and spectinomycin and chloramphenicol resistance genes as positive selection markers in liquid culture. Randomized LacI libraries were created and subjected to subsequent dual selection, but mispairing IPTG and selection cues in respect to the wild-type LacI response, allowing the isolation of a LacI variant with a reversed IPTG response within three rounds of library generation and dual selection.
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Affiliation(s)
- Stefan A Hoffmann
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Sabrina M Kruse
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Katja M Arndt
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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