1
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Makino K, Sugiyama I, Asanuma H, Kashida H. Kinetics of Strand Displacement Reaction with Acyclic Artificial Nucleic Acids. Angew Chem Int Ed Engl 2024; 63:e202319864. [PMID: 38840525 DOI: 10.1002/anie.202319864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/15/2024] [Accepted: 06/05/2024] [Indexed: 06/07/2024]
Abstract
Toehold-mediated strand displacement (TMSD) reaction, one of the DNA nanotechnologies, has great potential as s biological programmable platform in the cellular environment. Various artificial nucleic acids have been developed to improve stability and affinity for biological applications. However, the lack of understanding of the kinetics of TMSD reaction among artificial nucleic acids has limited their applications. We herein systematically characterized the kinetics of TMSD reactions with acyclic xeno nucleic acids (XNAs): serinol nucleic acid (SNA), acyclic D-threoninol nucleic acid (D-aTNA), and acyclic L-threoninol nucleic acid (L-aTNA). We found that the strand displacement reactions by D-aTNA and by L-aTNA were highly dependent on temperature. D-aTNA and L-aTNA systems were orthogonal to each other, and chirality of the input can be switched by using SNA as an interface. We also applied TMSD reactions of XNAs to a seesaw gate amplification system which utilizes the orthogonality. This work will contribute to the developments of thermoresponsive and bioorthogonal nucleic acid circuits.
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Affiliation(s)
- Koki Makino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Itsumi Sugiyama
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
| | - Hiromu Kashida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8603, Japan
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2
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Kang H, Park D, Kim J. Logical regulation of endogenous gene expression using programmable, multi-input processing CRISPR guide RNAs. Nucleic Acids Res 2024; 52:8595-8608. [PMID: 38943344 DOI: 10.1093/nar/gkae549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 07/01/2024] Open
Abstract
The CRISPR-Cas system provides a versatile RNA-guided approach for a broad range of applications. Thanks to advances in RNA synthetic biology, the engineering of guide RNAs (gRNAs) has enabled the conditional control of the CRISPR-Cas system. However, achieving precise regulation of the CRISPR-Cas system for efficient modulation of internal metabolic processes remains challenging. In this work, we developed a robust dCas9 regulator with engineered conditional gRNAs to enable tight control of endogenous genes. Our conditional gRNAs in Escherichia coli can control gene expression upon specific interaction with trigger RNAs with a dynamic range as high as 130-fold, evaluating up to a three-input logic A OR (B AND C). The conditional gRNA-mediated targeting of endogenous metabolic genes, lacZ, malT and poxB, caused differential regulation of growth in Escherichia coli via metabolic flux control. Further, conditional gRNAs could regulate essential cytoskeleton genes, ftsZ and mreB, to control cell filamentation and division. Finally, three types of two-input logic gates could be applied for the conditional control of ftsZ regulation, resulting in morphological changes. The successful operation and application of conditional gRNAs based on programmable RNA interactions suggests that our system could be compatible with other Cas-effectors and implemented in other host organisms.
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Affiliation(s)
- Hansol Kang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Dongwon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
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3
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Zhou Y, Sheng P, Li J, Li Y, Xie M, Green AA. Conditional RNA interference in mammalian cells via RNA transactivation. Nat Commun 2024; 15:6855. [PMID: 39127751 PMCID: PMC11316766 DOI: 10.1038/s41467-024-50600-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 07/15/2024] [Indexed: 08/12/2024] Open
Abstract
RNA interference (RNAi) is a powerful tool for sequence-specific gene knockdown in therapeutic and research applications. However, spatiotemporal control of RNAi is required to decrease nonspecific targeting, potential toxicity, and allow targeting of essential genes. Herein we describe a class of de-novo-designed RNA switches that enable sequence-specific regulation of RNAi in mammalian cells. Using cis-repressing RNA elements, we engineer RNA devices that only initiate microRNA biogenesis when binding with cognate trigger RNAs. We demonstrate that this conditional RNAi system, termed Orthogonal RNA Interference induced by Trigger RNA (ORIENTR), provides up to 14-fold increases in artificial miRNA biogenesis upon activation in orthogonal libraries. We show that integration of ORIENTR triggers with dCas13d enhances dynamic range to up to 31-fold. We further demonstrate that ORIENTR can be applied to detect endogenous RNA signals and to conditionally knockdown endogenous genes, thus enabling regulatory possibilities including cell-type-specific RNAi and rewiring of transcriptional networks via RNA profile.
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Affiliation(s)
- Yu Zhou
- UF Center for NeuroGenetics (CNG), Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology (MGM), University of Florida, Gainesville, FL, USA
| | - Peike Sheng
- UF Center for NeuroGenetics (CNG), Gainesville, FL, USA
- Department of Biochemistry and Molecular Biology, College of Medicine (COM), University of Florida, Gainesville, FL, USA
- UF Health Cancer Center, Gainesville, FL, USA
| | - Jiayi Li
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Yudan Li
- Biological Design Center, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Mingyi Xie
- UF Center for NeuroGenetics (CNG), Gainesville, FL, USA.
- Department of Biochemistry and Molecular Biology, College of Medicine (COM), University of Florida, Gainesville, FL, USA.
- UF Health Cancer Center, Gainesville, FL, USA.
| | - Alexander A Green
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, Boston, MA, USA.
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4
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Kim J, Seo M, Lim Y, Kim J. START: A Versatile Platform for Bacterial Ligand Sensing with Programmable Performances. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402029. [PMID: 39075726 DOI: 10.1002/advs.202402029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/31/2024] [Indexed: 07/31/2024]
Abstract
Recognition of signaling molecules for coordinated regulation of target genes is a fundamental process for biological systems. Cells often rely on transcription factors to accomplish these intricate tasks, yet the subtle conformational changes of protein structures, coupled with the complexity of intertwined protein interaction networks, pose challenges for repurposing these for bioengineering applications. This study introduces a novel platform for ligand-responsive gene regulation, termed START (Synthetic Trans-Acting Riboswitch with Triggering RNA). Inspired by the bacterial ligand sensing system, riboswitch, and the synthetic gene regulator, toehold switch, the START platform enables the implementation of synthetic biosensors for various ligands. Rational sequence design with targeted domain optimization yields high-performance STARTs with a dynamic range up to 67.29-fold and a tunable ligand sensitivity, providing a simple and intuitive strategy for sensor engineering. The START platform also exhibits modularity and composability to allow flexible genetic circuit construction, enabling seamless implementation of OR, AND, and NOT Boolean logic gates for multiple ligand inputs. The START design principle is capable of broadening the suite of synthetic biosensors for diverse chemical and protein ligands, providing a novel riboregulator chassis for synthetic biology and bioengineering applications.
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Affiliation(s)
- Jeongwon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Minchae Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Yelin Lim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, South Korea
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5
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Yan Z, Eshed A, Tang AA, Arevalos NR, Ticktin ZM, Chaudhary S, Ma D, McCutcheon G, Li Y, Wu K, Saha S, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Collins JJ, Yin P, Green AA. Rapid, Multiplexed, and Enzyme-Free Nucleic Acid Detection Using Programmable Aptamer-Based RNA Switches. Chem 2024; 10:2220-2244. [PMID: 39036067 PMCID: PMC11259118 DOI: 10.1016/j.chempr.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Rapid, simple, and low-cost diagnostic technologies are crucial tools for combatting infectious disease. We describe a class of aptamer-based RNA switches or aptaswitches that recognize target nucleic acid molecules and initiate folding of a reporter aptamer. Aptaswitches can detect virtually any sequence and provide an intense fluorescent readout without intervening enzymes, generating signals in as little as 5 minutes and enabling detection by eye with minimal equipment. Aptaswitches can be used to regulate folding of seven fluorogenic aptamers, providing a general means of controlling aptamers and an array of multiplexable reporter colors. Coupling isothermal amplification reactions with aptaswitches, we reach sensitivities down to 1 RNA copy/μL in one-pot reactions. Application of multiplexed all-in-one reactions against RNA from clinical saliva samples yields an overall accuracy of 96.67% for detection of SARS-CoV-2 in 30 minutes. Aptaswitches are thus versatile tools for nucleic acid detection that are readily integrated into rapid diagnostic assays.
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Affiliation(s)
- Zhaoqing Yan
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Amit Eshed
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Anli A. Tang
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Nery R. Arevalos
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Zachary M. Ticktin
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Soma Chaudhary
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Griffin McCutcheon
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yudan Li
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Kaiyue Wu
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Sanchari Saha
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | | | | | | | - James J. Collins
- Department of Biological Engineering, Massachusetts
Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT,
Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA,
USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School,
Boston, MA, USA
| | - Alexander A. Green
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
- Lead contact
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6
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Wu RY, Wu CQ, Xie F, Xing X, Xu L. Building RNA-Mediated Artificial Signaling Pathways between Endogenous Genes. Acc Chem Res 2024; 57:1777-1789. [PMID: 38872074 DOI: 10.1021/acs.accounts.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
ConspectusSophisticated genetic networks play a pivotal role in orchestrating cellular responses through intricate signaling pathways across diverse environmental conditions. Beyond the inherent complexity of natural cellular signaling networks, the construction of artificial signaling pathways (ASPs) introduces a vast array of possibilities for reshaping cellular responses, enabling programmable control of living organisms. ASPs can be integrated with existing cellular networks and redirect output responses as desired, allowing seamless communication and coordination with other cellular processes, thereby achieving designable transduction within cells. Among diversified ASPs, establishing connections between originally independent endogenous genes is of particular significance in modifying the genetic networks, so that cells can be endowed with new capabilities to sense and deal with abnormal factors related to differentiated gene expression (i.e., solve the issues of the aberrant gene expression induced by either external or internal stimuli). In a typical scenario, the two genes X and Y in the cell are originally expressed independently. After the introduction of an ASP, changes in the expression of gene X may exert a designed impact on gene Y, subsequently inducing the cellular response related to gene Y. If X represents a disease signal and Y serves as a therapeutic module, the introduction of the ASP empowers cells with a new spontaneous defense system to handle potential risks, which holds great potential for both fundamental and translational studies.In this Account, we primarily review our endeavors in the construction of RNA-mediated ASPs between endogenous genes that can respond to differentiated RNA expression. In contrast to other molecules that may be restricted to specific pathways, synthetic RNA circuits can be easily utilized and expanded as a general platform for constructing ASPs with a high degree of programmability and tunability for diversified functionalities through predictable Watson-Crick base pairing. We first provide an overview of recent advancements in RNA-based genetic circuits, encompassing but not limited to utilization of RNA toehold switches, siRNA and CRISPR systems. Despite notable progress, most reported RNA circuits have to contain at least one exogenous RNA X as input or one engineered RNA Y as a target, which is not suitable for establishing endogenous gene connections. While exogenous RNAs can be engineered and controlled as desired, constructing a general and efficient platform for manipulation of naturally occurring RNAs poses a formidable challenge, especially for the mammalian system. With a focus on this goal, we are devoted to developing efficient strategies to manipulate cell responses by establishing RNA-mediated ASPs between endogenous genes, particularly in mammalian cells. Our step-by-step progress in engineering customized cell signaling circuits, from bacterial cells to mammalian cells, from gene expression regulation to phenotype control, and from small RNA to long mRNA of low abundance and more complex secondary structures, is systematically described. Finally, future perspectives and potential applications of these RNA-mediated ASPs between endogenous genes are also discussed.
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Affiliation(s)
- Ruo-Yue Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Chao-Qun Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Fan Xie
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiwen Xing
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510006, China
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7
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Jiang G, Gao Y, Zhou N, Wang B. CRISPR-powered RNA sensing in vivo. Trends Biotechnol 2024:S0167-7799(24)00094-5. [PMID: 38734565 DOI: 10.1016/j.tibtech.2024.04.002] [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: 01/25/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 05/13/2024]
Abstract
RNA sensing in vivo evaluates past or ongoing endogenous RNA disturbances, which is crucial for identifying cell types and states and diagnosing diseases. Recently, the CRISPR-driven genetic circuits have offered promising solutions to burgeoning challenges in RNA sensing. This review delves into the cutting-edge developments of CRISPR-powered RNA sensors in vivo, reclassifying these RNA sensors into four categories based on their working mechanisms, including programmable reassembly of split single-guide RNA (sgRNA), RNA-triggered RNA processing and protein cleavage, miRNA-triggered RNA interference (RNAi), and strand displacement reactions. Then, we discuss the advantages and challenges of existing methodologies in diverse application scenarios and anticipate and analyze obstacles and opportunities in forthcoming practical implementations.
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Affiliation(s)
- Guo Jiang
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, Zhejiang, China
| | - Yuanli Gao
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, Zhejiang, China; School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK
| | - Nan Zhou
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, Zhejiang, China
| | - Baojun Wang
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310058, Zhejiang, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, Zhejiang, China.
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8
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Koksaldi I, Park D, Atilla A, Kang H, Kim J, Seker UOS. RNA-Based Sensor Systems for Affordable Diagnostics in the Age of Pandemics. ACS Synth Biol 2024; 13:1026-1037. [PMID: 38588603 PMCID: PMC11036506 DOI: 10.1021/acssynbio.3c00698] [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: 11/21/2023] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024]
Abstract
In the era of the COVID-19 pandemic, the significance of point-of-care (POC) diagnostic tools has become increasingly vital, driven by the need for quick and precise virus identification. RNA-based sensors, particularly toehold sensors, have emerged as promising candidates for POC detection systems due to their selectivity and sensitivity. Toehold sensors operate by employing an RNA switch that changes the conformation when it binds to a target RNA molecule, resulting in a detectable signal. This review focuses on the development and deployment of RNA-based sensors for POC viral RNA detection with a particular emphasis on toehold sensors. The benefits and limits of toehold sensors are explored, and obstacles and future directions for improving their performance within POC detection systems are presented. The use of RNA-based sensors as a technology for rapid and sensitive detection of viral RNA holds great potential for effectively managing (dealing/coping) with present and future pandemics in resource-constrained settings.
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Affiliation(s)
- Ilkay
Cisil Koksaldi
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center (UNAM), Bilkent
University, Ankara 06800, Turkey
| | - Dongwon Park
- Department
of Life Sciences, Pohang University of Science
and Technology, Pohang 37673, South Korea
| | - Abdurahman Atilla
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center (UNAM), Bilkent
University, Ankara 06800, Turkey
| | - Hansol Kang
- Department
of Life Sciences, Pohang University of Science
and Technology, Pohang 37673, South Korea
| | - Jongmin Kim
- Department
of Life Sciences, Pohang University of Science
and Technology, Pohang 37673, South Korea
| | - Urartu Ozgur Safak Seker
- UNAM
− Institute of Materials Science and Nanotechnology, National
Nanotechnology Research Center (UNAM), Bilkent
University, Ankara 06800, Turkey
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9
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Wu CQ, Wu RY, Zhang QL, Wang LL, Wang Y, Dai C, Zhang CX, Xu L. Harnessing Catalytic RNA Circuits for Construction of Artificial Signaling Pathways in Mammalian Cells. Angew Chem Int Ed Engl 2024; 63:e202319309. [PMID: 38298112 DOI: 10.1002/anie.202319309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/21/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024]
Abstract
Engineering of genetic networks with artificial signaling pathways (ASPs) can reprogram cellular responses and phenotypes under different circumstances for a variety of diagnostic and therapeutic purposes. However, construction of ASPs between originally independent endogenous genes in mammalian cells is highly challenging. Here we report an amplifiable RNA circuit that can theoretically build regulatory connections between any endogenous genes in mammalian cells. We harness the system of catalytic hairpin assembly with combination of controllable CRISPR-Cas9 function to transduce the signals from distinct messenger RNA expression of trigger genes into manipulation of target genes. Through introduction of these RNA-based genetic circuits, mammalian cells are endowed with autonomous capabilities to sense the changes of RNA expression either induced by ligand stimuli or from various cell types and control the cellular responses and fates via apoptosis-related ASPs. Our design provides a generalized platform for construction of ASPs inside the genetic networks of mammalian cells based on differentiated RNA expression.
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Affiliation(s)
- Chao-Qun Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ruo-Yue Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiu-Long Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
- School of Pharmacy and Medical Technology, Key Laboratory of Pharmaceutical Analysis and Laboratory Medicine of Fujian Province, Putian University, Putian, 351100, China
| | - Liang-Liang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Chu Dai
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Chen-Xi Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
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10
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Vallina NS, McRae EKS, Geary C, Andersen ES. An RNA origami robot that traps and releases a fluorescent aptamer. SCIENCE ADVANCES 2024; 10:eadk1250. [PMID: 38507482 PMCID: PMC10954211 DOI: 10.1126/sciadv.adk1250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
RNA nanotechnology aims to use RNA as a programmable material to create self-assembling nanodevices for application in medicine and synthetic biology. The main challenge is to develop advanced RNA robotic devices that both sense, compute, and actuate to obtain enhanced control over molecular processes. Here, we use the RNA origami method to prototype an RNA robotic device, named the "Traptamer," that mechanically traps the fluorescent aptamer, iSpinach. The Traptamer is shown to sense two RNA key strands, acts as a Boolean AND gate, and reversibly controls the fluorescence of the iSpinach aptamer. Cryo-electron microscopy of the closed Traptamer structure at 5.45-angstrom resolution reveals the mechanical mode of distortion of the iSpinach motif. Our study suggests a general approach to distorting RNA motifs and a path forward to build sophisticated RNA machines that through sensing, computing, and actuation modules can be used to precisely control RNA functionalities in cellular systems.
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Affiliation(s)
| | - Ewan K. S. McRae
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, 6670 Bertner Ave, R10-117, Houston, TX 77030, USA
| | - Cody Geary
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Ebbe S. Andersen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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11
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Buson F, Gao Y, Wang B. Genetic Parts and Enabling Tools for Biocircuit Design. ACS Synth Biol 2024; 13:697-713. [PMID: 38427821 DOI: 10.1021/acssynbio.3c00691] [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: 03/03/2024]
Abstract
Synthetic biology aims to engineer biological systems for customized tasks through the bottom-up assembly of fundamental building blocks, which requires high-quality libraries of reliable, modular, and standardized genetic parts. To establish sets of parts that work well together, synthetic biologists created standardized part libraries in which every component is analyzed in the same metrics and context. Here we present a state-of-the-art review of the currently available part libraries for designing biocircuits and their gene expression regulation paradigms at transcriptional, translational, and post-translational levels in Escherichia coli. We discuss the necessary facets to integrate these parts into complex devices and systems along with the current efforts to catalogue and standardize measurement data. To better display the range of available parts and to facilitate part selection in synthetic biology workflows, we established biopartsDB, a curated database of well-characterized and useful genetic part and device libraries with detailed quantitative data validated by the published literature.
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Affiliation(s)
- Felipe Buson
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, U.K
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310058, China
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12
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Lv Y, Chang J, Zhang W, Dong H, Chen S, Wang X, Zhao A, Zhang S, Alam MA, Wang S, Du C, Xu J, Wang W, Xu P. Improving Microbial Cell Factory Performance by Engineering SAM Availability. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3846-3871. [PMID: 38372640 DOI: 10.1021/acs.jafc.3c09561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Methylated natural products are widely spread in nature. S-Adenosyl-l-methionine (SAM) is the secondary abundant cofactor and the primary methyl donor, which confer natural products with structural and functional diversification. The increasing demand for SAM-dependent natural products (SdNPs) has motivated the development of microbial cell factories (MCFs) for sustainable and efficient SdNP production. Insufficient and unsustainable SAM availability hinders the improvement of SdNP MCF performance. From the perspective of developing MCF, this review summarized recent understanding of de novo SAM biosynthesis and its regulatory mechanism. SAM is just the methyl mediator but not the original methyl source. Effective and sustainable methyl source supply is critical for efficient SdNP production. We compared and discussed the innate and relatively less explored alternative methyl sources and identified the one involving cheap one-carbon compound as more promising. The SAM biosynthesis is synergistically regulated on multilevels and is tightly connected with ATP and NAD(P)H pools. We also covered the recent advancement of metabolic engineering in improving intracellular SAM availability and SdNP production. Dynamic regulation is a promising strategy to achieve accurate and dynamic fine-tuning of intracellular SAM pool size. Finally, we discussed the design and engineering constraints underlying construction of SAM-responsive genetic circuits and envisioned their future applications in developing SdNP MCFs.
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Affiliation(s)
- Yongkun Lv
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Jinmian Chang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Weiping Zhang
- Bloomage Biotechnology Corporation Limited, 678 Tianchen Street, Jinan, Shandong 250101, China
| | - Hanyu Dong
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Song Chen
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Xian Wang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Anqi Zhao
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou, 450001, China
| | - Shen Zhang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Md Asraful Alam
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Shilei Wang
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Chaojun Du
- Nanyang Research Institute of Zhengzhou University, Nanyang Institute of Technology, No. 80 Changjiang Road, Nanyang 473004, China
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
- National Key Laboratory of Biobased Transportation Fuel Technology, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Weigao Wang
- Department of Chemical Engineering, Stanford University, 443 Via Ortega, Palo Alto, California 94305, United States
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong 515063, China
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13
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Gao Y, Wang L, Wang B. Customizing cellular signal processing by synthetic multi-level regulatory circuits. Nat Commun 2023; 14:8415. [PMID: 38110405 PMCID: PMC10728147 DOI: 10.1038/s41467-023-44256-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
As synthetic biology permeates society, the signal processing circuits in engineered living systems must be customized to meet practical demands. Towards this mission, novel regulatory mechanisms and genetic circuits with unprecedented complexity have been implemented over the past decade. These regulatory mechanisms, such as transcription and translation control, could be integrated into hybrid circuits termed "multi-level circuits". The multi-level circuit design will tremendously benefit the current genetic circuit design paradigm, from modifying basic circuit dynamics to facilitating real-world applications, unleashing our capabilities to customize cellular signal processing and address global challenges through synthetic biology.
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Affiliation(s)
- Yuanli Gao
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058, China
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Lei Wang
- Center of Synthetic Biology and Integrated Bioengineering & School of Engineering, Westlake University, Hangzhou, 310030, China.
| | - Baojun Wang
- College of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310058, China.
- Research Center for Biological Computation, Zhejiang Lab, Hangzhou, 311100, China.
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14
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Franco RAL, Brenner G, Zocca VFB, de Paiva GB, Lima RN, Rech EL, Amaral DT, Lins MRCR, Pedrolli DB. Signal Amplification for Cell-Free Biosensors, an Analog-to-Digital Converter. ACS Synth Biol 2023; 12:2819-2826. [PMID: 37792474 DOI: 10.1021/acssynbio.3c00227] [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: 10/06/2023]
Abstract
Toehold switches are biosensors useful for the detection of endogenous and environmental RNAs. They have been successfully engineered to detect virus RNAs in cell-free gene expression reactions. Their inherent sequence programmability makes engineering a fast and predictable process. Despite improvements in the design, toehold switches suffer from leaky translation in the OFF state, which compromises the fold change and sensitivity of the biosensor. To address this, we constructed and tested signal amplification circuits for three toehold switches triggered by Dengue and SARS-CoV-2 RNAs and an artificial RNA. The serine integrase circuit efficiently contained leakage, boosted the expression fold change from OFF to ON, and decreased the detection limit of the switches by 3-4 orders of magnitude. Ultimately, the integrase circuit converted the analog switches' signals into digital-like output. The circuit is broadly useful for biosensors and eliminates the hard work of designing and testing multiple switches to find the best possible performer.
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Affiliation(s)
- Rafael A L Franco
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau km1, 14800-903 Araraquara, Brazil
| | - Gabriel Brenner
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau km1, 14800-903 Araraquara, Brazil
| | - Vitória F B Zocca
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau km1, 14800-903 Araraquara, Brazil
| | - Gabriela B de Paiva
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau km1, 14800-903 Araraquara, Brazil
| | - Rayane N Lima
- Embrapa Genetic Resources and Biotechnology, National Institute of Science and Technology - Synthetic Biology, 70770-917 Brasília, Brazil
| | - Elibio L Rech
- Embrapa Genetic Resources and Biotechnology, National Institute of Science and Technology - Synthetic Biology, 70770-917 Brasília, Brazil
| | - Danilo T Amaral
- Federal University of ABC (UFABC), Center for Natural and Human Sciences, Campus Santo André, Avenida dos Estados 5001, 09210-580 Santo André, Brazil
| | - Milca R C R Lins
- Federal University of ABC (UFABC), Center for Natural and Human Sciences, Campus Santo André, Avenida dos Estados 5001, 09210-580 Santo André, Brazil
| | - Danielle B Pedrolli
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess Engineering and Biotechnology, Rodovia Araraquara-Jau km1, 14800-903 Araraquara, Brazil
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15
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Tang L, Tian Z, Cheng J, Zhang Y, Song Y, Liu Y, Wang J, Zhang P, Ke Y, Simmel FC, Song J. Circular single-stranded DNA as switchable vector for gene expression in mammalian cells. Nat Commun 2023; 14:6665. [PMID: 37863879 PMCID: PMC10589306 DOI: 10.1038/s41467-023-42437-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
Synthetic gene networks in mammalian cells are currently limited to either protein-based transcription factors or RNA-based regulators. Here, we demonstrate a regulatory approach based on circular single-stranded DNA (Css DNA), which can be used as an efficient expression vector with switchable activity, enabling gene regulation in mammalian cells. The Css DNA is transformed into its double-stranded form via DNA replication and used as vectors encoding a variety of different proteins in a wide range of cell lines as well as in mice. The rich repository of DNA nanotechnology allows to use sort single-stranded DNA effectors to fold Css DNA into DNA nanostructures of different complexity, leading the gene expression to programmable inhibition and subsequently re-activation via toehold-mediated strand displacement. The regulatory strategy from Css DNA can thus expand the molecular toolbox for the realization of synthetic regulatory networks with potential applications in genetic diagnosis and gene therapy.
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Affiliation(s)
- Linlin Tang
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Zhijin Tian
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
- Department of Chemistry, University of Science & Technology of China, 230026, Hefei, Anhui, China
| | - Jin Cheng
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Yijing Zhang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
- School of Life Sciences, Tianjin University, 300072, Tianjin, China
| | - Yongxiu Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Yan Liu
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Jinghao Wang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
- Department of Chemistry, University of Science & Technology of China, 230026, Hefei, Anhui, China
| | - Pengfei Zhang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA.
| | | | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 200240, Shanghai, China.
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, 310022, Hangzhou, Zhejiang, China.
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16
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Zhu J, Wang B, Zhang Y, Wei T, Gao T. Living electrochemical biosensing: Engineered electroactive bacteria for biosensor development and the emerging trends. Biosens Bioelectron 2023; 237:115480. [PMID: 37379794 DOI: 10.1016/j.bios.2023.115480] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Bioelectrical interfaces made of living electroactive bacteria (EAB) provide a unique opportunity to bridge biotic and abiotic systems, enabling the reprogramming of electrochemical biosensing. To develop these biosensors, principles from synthetic biology and electrode materials are being combined to engineer EAB as dynamic and responsive transducers with emerging, programmable functionalities. This review discusses the bioengineering of EAB to design active sensing parts and electrically connective interfaces on electrodes, which can be applied to construct smart electrochemical biosensors. In detail, by revisiting the electron transfer mechanism of electroactive microorganisms, engineering strategies of EAB cells for biotargets recognition, sensing circuit construction, and electrical signal routing, engineered EAB have demonstrated impressive capabilities in designing active sensing elements and developing electrically conductive interfaces on electrodes. Thus, integration of engineered EAB into electrochemical biosensors presents a promising avenue for advancing bioelectronics research. These hybridized systems equipped with engineered EAB can promote the field of electrochemical biosensing, with applications in environmental monitoring, health monitoring, green manufacturing, and other analytical fields. Finally, this review considers the prospects and challenges of the development of EAB-based electrochemical biosensors, identifying potential future applications.
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Affiliation(s)
- Jin Zhu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China
| | - Baoguo Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China
| | - Yixin Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China
| | - Tianxiang Wei
- School of Environment, Nanjing Normal University, Nanjing, 210023, PR China
| | - Tao Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, PR China.
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17
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Velazquez Sanchez AK, Klopprogge B, Zimmermann KH, Ignatova Z. Tailored Synthetic sRNAs Dynamically Tune Multilayer Genetic Circuits. ACS Synth Biol 2023; 12:2524-2535. [PMID: 37595156 DOI: 10.1021/acssynbio.2c00614] [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: 08/20/2023]
Abstract
Predictable and controllable tuning of genetic circuits to regulate gene expression, including modulation of existing circuits or constructs without the need for redesign or rebuilding, is a persistent challenge in synthetic biology. Here, we propose rationally designed new small RNAs (sRNAs) that dynamically modulate gene expression of genetic circuits with a broad range (high, medium, and low) of repression. We designed multiple multilayer genetic circuits in which the variable effector element is a transcription factor (TF) controlling downstream the production of a reporter protein. The sRNAs target TFs instead of a reporter gene, and harnessing the intrinsic RNA-interference pathway in E. coli allowed for a wide range of expression modulation of the reporter protein, including the most difficult to achieve dynamic switch to an OFF state. The synthetic sRNAs are expressed independently of the circuit(s), thus allowing for repression without modifying the circuit itself. Our work provides a frame for achieving independent modulation of gene expression and dynamic and modular control of the multilayer genetic circuits by only including an independent control circuit expressing synthetic sRNAs, without altering the structure of existing genetic circuits.
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Affiliation(s)
- Ana K Velazquez Sanchez
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Bjarne Klopprogge
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
| | - Karl-Heinz Zimmermann
- Algebraic Engineering, Institute of Embedded Systems, Hamburg University of Technology, 21073 Hamburg, Germany
| | - Zoya Ignatova
- Biochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany
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18
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Liu B, Samaniego CC, Bennett MR, Franco E, Chappell J. A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria. Nat Commun 2023; 14:5268. [PMID: 37644054 PMCID: PMC10465534 DOI: 10.1038/s41467-023-40785-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/10/2023] [Indexed: 08/31/2023] Open
Abstract
A lack of composable and tunable gene regulators has hindered efforts to engineer non-model bacteria and consortia. Toward addressing this, we explore the broad-host potential of small transcription activating RNA (STAR) and propose a design strategy to achieve tunable gene control. First, we demonstrate that STARs optimized for E. coli function across different Gram-negative species and can actuate using phage RNA polymerase, suggesting that RNA systems acting at the level of transcription are portable. Second, we explore an RNA design strategy that uses arrays of tandem and transcriptionally fused RNA regulators to precisely alter regulator concentration from 1 to 8 copies. This provides a simple means to predictably tune output gain across species and does not require access to large regulatory part libraries. Finally, we show RNA arrays can be used to achieve tunable cascading and multiplexing circuits across species, analogous to the motifs used in artificial neural networks.
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Affiliation(s)
- Baiyang Liu
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Christian Cuba Samaniego
- Department of Mechanical and Aerospace Engineering, Bioengineering, Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Matthew R Bennett
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, Bioengineering, Molecular Biology Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - James Chappell
- Department of Biosciences, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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19
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Wang WJ, Lin J, Wu CQ, Luo AL, Xing X, Xu L. Establishing artificial gene connections through RNA displacement-assembly-controlled CRISPR/Cas9 function. Nucleic Acids Res 2023; 51:7691-7703. [PMID: 37395400 PMCID: PMC10415155 DOI: 10.1093/nar/gkad558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 07/04/2023] Open
Abstract
Construction of synthetic circuits that can reprogram genetic networks and signal pathways is a long-term goal for manipulation of biosystems. However, it is still highly challenging to build artificial genetic communications among endogenous RNA species due to their sequence independence and structural diversities. Here we report an RNA-based synthetic circuit that can establish regulatory linkages between expression of endogenous genes in both Escherichiacoli and mammalian cells. This design employs a displacement-assembly approach to modulate the activity of guide RNA for function control of CRISPR/Cas9. Our experiments demonstrate the great effectiveness of this RNA circuit for building artificial connections between expression of originally unrelated genes. Both exogenous and naturally occurring RNAs, including small/microRNAs and long mRNAs, are capable of controlling expression of another endogenous gene through this approach. Moreover, an artificial signal pathway inside mammalian cells is also successfully established to control cell apoptosis through our designed synthetic circuit. This study provides a general strategy for constructing synthetic RNA circuits, which can introduce artificial connections into the genetic networks of mammalian cells and alter the cellular phenotypes.
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Affiliation(s)
- Wei-Jia Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jiao Lin
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chao-Qun Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ai-Ling Luo
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiwen Xing
- Department of Biotechnology, College of Life Science and Technology, Jinan University Institution, Guangzhou 510632, China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
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20
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Riley AT, Robson JM, Green AA. Generative and predictive neural networks for the design of functional RNA molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549043. [PMID: 37503279 PMCID: PMC10370010 DOI: 10.1101/2023.07.14.549043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
RNA is a remarkably versatile molecule that has been engineered for applications in therapeutics, diagnostics, and in vivo information-processing systems. However, the complex relationship between the sequence and structural properties of an RNA molecule and its ability to perform specific functions often necessitates extensive experimental screening of candidate sequences. Here we present a generalized neural network architecture that utilizes the sequence and structure of RNA molecules (SANDSTORM) to inform functional predictions. We demonstrate that this approach achieves state-of-the-art performance across several distinct RNA prediction tasks, while learning interpretable abstractions of RNA secondary structure. We paired these predictive models with generative adversarial RNA design networks (GARDN), allowing the generative modelling of novel mRNA 5' untranslated regions and toehold switch riboregulators exhibiting a predetermined fitness. This approach enabled the design of novel toehold switches with a 43-fold increase in experimentally characterized dynamic range compared to those designed using classic thermodynamic algorithms. SANDSTORM and GARDN thus represent powerful new predictive and generative tools for the development of diagnostic and therapeutic RNA molecules with improved function.
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Affiliation(s)
- Aidan T. Riley
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - James M. Robson
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Alexander A. Green
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA 02215, USA
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21
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Schaffter SW, Wintenberg ME, Murphy TM, Strychalski EA. Design Approaches to Expand the Toolkit for Building Cotranscriptionally Encoded RNA Strand Displacement Circuits. ACS Synth Biol 2023; 12:1546-1561. [PMID: 37134273 DOI: 10.1021/acssynbio.3c00079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cotranscriptionally encoded RNA strand displacement (ctRSD) circuits are an emerging tool for programmable molecular computation, with potential applications spanning in vitro diagnostics to continuous computation inside living cells. In ctRSD circuits, RNA strand displacement components are continuously produced together via transcription. These RNA components can be rationally programmed through base pairing interactions to execute logic and signaling cascades. However, the small number of ctRSD components characterized to date limits circuit size and capabilities. Here, we characterize over 200 ctRSD gate sequences, exploring different input, output, and toehold sequences and changes to other design parameters, including domain lengths, ribozyme sequences, and the order in which gate strands are transcribed. This characterization provides a library of sequence domains for engineering ctRSD components, i.e., a toolkit, enabling circuits with up to 4-fold more inputs than previously possible. We also identify specific failure modes and systematically develop design approaches that reduce the likelihood of failure across different gate sequences. Lastly, we show the ctRSD gate design is robust to changes in transcriptional encoding, opening a broad design space for applications in more complex environments. Together, these results deliver an expanded toolkit and design approaches for building ctRSD circuits that will dramatically extend capabilities and potential applications.
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Affiliation(s)
- Samuel W Schaffter
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Molly E Wintenberg
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Terence M Murphy
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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22
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Jiang K, Koob J, Chen XD, Krajeski RN, Zhang Y, Volf V, Zhou W, Sgrizzi SR, Villiger L, Gootenberg JS, Chen F, Abudayyeh OO. Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR. Nat Biotechnol 2023; 41:698-707. [PMID: 36302988 DOI: 10.1038/s41587-022-01534-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Programmable approaches to sense and respond to the presence of specific RNAs in biological systems have broad applications in research, diagnostics, and therapeutics. Here we engineer a programmable RNA-sensing technology, reprogrammable ADAR sensors (RADARS), which harnesses RNA editing by adenosine deaminases acting on RNA (ADAR) to gate translation of a cargo protein by the presence of endogenous RNA transcripts. Introduction of a stop codon in a guide upstream of the cargo makes translation contingent on binding of an endogenous transcript to the guide, leading to ADAR editing of the stop codon and allowing translational readthrough. Through systematic sensor engineering, we achieve 277 fold improvement in sensor activation and engineer RADARS with diverse cargo proteins, including luciferases, fluorescent proteins, recombinases, and caspases, enabling detection sensitivity on endogenous transcripts expressed at levels as low as 13 transcripts per million. We show that RADARS are functional as either expressed DNA or synthetic mRNA and with either exogenous or endogenous ADAR. We apply RADARS in multiple contexts, including tracking transcriptional states, RNA-sensing-induced cell death, cell-type identification, and control of synthetic mRNA translation.
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Affiliation(s)
- Kaiyi Jiang
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeremy Koob
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Xi Dawn Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Systems, Synthetic, and Quantitative Biology Program, Harvard Medical School, Boston, MA, USA
| | - Rohan N Krajeski
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yifan Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Verena Volf
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Wenyuan Zhou
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Samantha R Sgrizzi
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lukas Villiger
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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23
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Yarra SS, Ashok G, Mohan U. "Toehold Switches; a foothold for Synthetic Biology". Biotechnol Bioeng 2023; 120:932-952. [PMID: 36527224 DOI: 10.1002/bit.28309] [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: 02/18/2022] [Revised: 08/24/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Toehold switches are de novo designed riboregulators that contain two RNA components interacting through linear-linear RNA interactions, regulating the gene expression. These are highly versatile, exhibit excellent orthogonality, wide dynamic range, and are highly programmable, so can be used for various applications in synthetic biology. In this review, we summarized and discussed the design characteristics and benefits of toehold switch riboregulators over conventional riboregulators. We also discussed applications and recent advancements of toehold switch riboregulators in various fields like gene editing, DNA nanotechnology, translational repression, and diagnostics (detection of microRNAs and some pathogens). Toehold switches, therefore, furnished advancement in synthetic biology applications in various fields with their prominent features.
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Affiliation(s)
- Sai Sumanjali Yarra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research (NIPER) Kolkata, Kolkata, West Bengal, India
| | - Ganapathy Ashok
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research (NIPER) Kolkata, Kolkata, West Bengal, India
| | - Utpal Mohan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research (NIPER) Kolkata, Kolkata, West Bengal, India
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24
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McSweeney MA, Zhang Y, Styczynski MP. Short Activators and Repressors of RNA Toehold Switches. ACS Synth Biol 2023; 12:681-688. [PMID: 36802167 PMCID: PMC10028691 DOI: 10.1021/acssynbio.2c00641] [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: 02/23/2023]
Abstract
RNA toehold switches are a widely used class of molecule to detect specific RNA "trigger" sequences, but their design, intended function, and characterization to date leave it unclear whether they can function properly with triggers shorter than 36 nucleotides. Here, we explore the feasibility of using standard toehold switches with 23-nucleotide truncated triggers. We assess the crosstalk of different triggers with significant homology and identify a highly sensitive trigger region where just one mutation from the consensus trigger sequence can reduce switch activation by 98.6%. However, we also find that triggers with as many as seven mutations outside of this region can still lead to 5-fold induction of the switch. We also present a new approach using 18- to 22-nucleotide triggers as translational repressors for toehold switches and assess the off-target regulation for this strategy as well. The development and characterization of these strategies could help enable applications like microRNA sensors, where well-characterized crosstalk between sensors and detection of short target sequences are critical.
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Affiliation(s)
- Megan A McSweeney
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yan Zhang
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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25
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Montagud-Martínez R, Márquez-Costa R, Rodrigo G. Programmable regulation of translation by harnessing the CRISPR-Cas13 system. Chem Commun (Camb) 2023; 59:2616-2619. [PMID: 36757178 DOI: 10.1039/d3cc00058c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The ability to control protein expression at both the transcriptional and post-transcriptional levels is instrumental for the cell to integrate multiple molecular signals and then reach high operational sophistication. Although challenging, fully artificial regulations at different levels are required for boosting systems and synthetic biology. Here, we report the development of a novel framework to regulate translation by repurposing the CRISPR-Cas13 immune system, which uses an RNA-guided ribonuclease. By exploiting a cell-free expression system for prototyping gene regulatory structures, our results demonstrate that CRISPR-dCas13a ribonucleoproteins (d means catalytically dead) can be programmed to repress or activate translation initiation. The performance assessment of the engineered systems also revealed guide RNA design principles. Moreover, we show that the system can work in vivo. This development complements the ability to regulate transcription with other CRISPR-Cas systems and offers potential applications.
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Affiliation(s)
- Roser Montagud-Martínez
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
| | - Rosa Márquez-Costa
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC - University of Valencia, 46980, Paterna, Spain.
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26
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Liu B, Samaniego CC, Bennett MR, Franco E, Chappell J. A portable regulatory RNA array design enables tunable and complex regulation across diverse bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529951. [PMID: 36865180 PMCID: PMC9980294 DOI: 10.1101/2023.02.24.529951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
A lack of composable and tunable gene regulators has hindered efforts to engineer non-model bacteria and consortia. To address this, we explore the broad-host potential of small transcription activating RNA (STAR) and propose a novel design strategy to achieve tunable gene control. First, we demonstrate that STARs optimized for E. coli function across different Gram-negative species and can actuate using phage RNA polymerase, suggesting that RNA systems acting at the level of transcription are portable. Second, we explore a novel RNA design strategy that uses arrays of tandem and transcriptionally fused RNA regulators to precisely alter regulator concentration from 1 to 8 copies. This provides a simple means to predictably tune output gain across species and does not require access to large regulatory part libraries. Finally, we show RNA arrays can be used to achieve tunable cascading and multiplexing circuits across species, analogous to the motifs used in artificial neural networks.
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Affiliation(s)
- Baiyang Liu
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - Christian Cuba Samaniego
- Department of Mechanical and Aerospace Engineering, Bioengineering, and Molecular Biology Institute, University of California at Los Angeles, CA, USA
| | - Matthew R. Bennett
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, Bioengineering, and Molecular Biology Institute, University of California at Los Angeles, CA, USA
| | - James Chappell
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
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27
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Han YH, Kim G, Seo SW. Programmable synthetic biology tools for developing microbial cell factories. Curr Opin Biotechnol 2023; 79:102874. [PMID: 36610368 DOI: 10.1016/j.copbio.2022.102874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/24/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023]
Abstract
Microbial conversion to generate value-added chemicals from diverse biomass is one of the keystones of energy biotechnology. Programmable synthetic biology tools offer versatile, standardized options for developing microbial cell factories. These tools thus can be reprogrammed in a user-defined manner for flexible wiring of stimuli and response, highly efficient genome engineering, and extensive perturbation of metabolic flux and genetic circuits. They also can be modularly assembled to construct elaborate and unprecedented biological systems with unique features. This review highlights recent advances in programmable synthetic biology tools based on biosensors, CRISPR-Cas, and RNA devices for developing microbial cell factories that have the potential to be utilized for energy biotechnology.
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Affiliation(s)
- Yong Hee Han
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Giho Kim
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul 08826, Republic of Korea
| | - Sang Woo Seo
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul 08826, Republic of Korea; Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Bio-MAX Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
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28
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Wang T, Hellmer H, Simmel FC. Genetic switches based on nucleic acid strand displacement. Curr Opin Biotechnol 2023; 79:102867. [PMID: 36535150 DOI: 10.1016/j.copbio.2022.102867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022]
Abstract
Toehold-mediated strand displacement (TMSD) is an isothermal switching process that enables the sequence-programmable and reversible conversion of DNA or RNA strands between single- and double-stranded conformations or other secondary structures. TMSD processes have already found widespread application in DNA nanotechnology, where they are used to drive DNA-based molecular devices or for the realization of synthetic biochemical computing circuits. Recently, researchers have started to employ TMSD also for the control of RNA-based gene regulatory processes in vivo, in particular in the context of synthetic riboregulators and conditional guide RNAs for CRISPR/Cas. Here, we provide a review over recent developments in this emerging field and discuss the opportunities and challenges for such systems in in vivo applications.
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Affiliation(s)
- Tianhe Wang
- Physics of Synthetic Biological Systems - E14, Physics Department and ZNN, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Henning Hellmer
- Physics of Synthetic Biological Systems - E14, Physics Department and ZNN, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
| | - Friedrich C Simmel
- Physics of Synthetic Biological Systems - E14, Physics Department and ZNN, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany.
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Using CIVT-SELEX to Select Aptamers as Genetic Parts to Regulate Gene Circuits in a Cell-Free System. Int J Mol Sci 2023; 24:ijms24032833. [PMID: 36769156 PMCID: PMC9917220 DOI: 10.3390/ijms24032833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
The complexity of genetic circuits has not seen a significant increase over the last decades, even with the rapid development of synthetic biology tools. One of the bottlenecks is the limited number of orthogonal transcription factor-operator pairs. Researchers have tried to use aptamer-ligand pairs as genetic parts to regulate transcription. However, most aptamers selected using traditional methods cannot be directly applied in gene circuits for transcriptional regulation. To that end, we report a new method called CIVT-SELEX to select DNA aptamers that can not only bind to macromolecule ligands but also undergo significant conformational changes, thus affecting transcription. The single-stranded DNA library with affinity to our example ligand human thrombin protein is first selected and enriched. Then, these ssDNAs are inserted into a genetic circuit and tested in the in vitro transcription screening to obtain the ones with significant inhibitory effects on downstream gene transcription when thrombins are present. These aptamer-thrombin pairs can inhibit the transcription of downstream genes, demonstrating the feasibility and robustness of their use as genetic parts in both linear DNAs and plasmids. We believe that this method can be applied to select aptamers of any target ligands and vastly expand the genetic part library for transcriptional regulation.
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30
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Simmel FC. Nucleic acid strand displacement - from DNA nanotechnology to translational regulation. RNA Biol 2023; 20:154-163. [PMID: 37095744 PMCID: PMC10132225 DOI: 10.1080/15476286.2023.2204565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Nucleic acid strand displacement reactions involve the competition of two or more DNA or RNA strands of similar sequence for binding to a complementary strand, and facilitate the isothermal replacement of an incumbent strand by an invader. The process can be biased by augmenting the duplex comprising the incumbent with a single-stranded extension, which can act as a toehold for a complementary invader. The toehold gives the invader a thermodynamic advantage over the incumbent, and can be programmed as a unique label to activate a specific strand displacement process. Toehold-mediated strand displacement processes have been extensively utilized for the operation of DNA-based molecular machines and devices as well as for the design of DNA-based chemical reaction networks. More recently, principles developed initially in the context of DNA nanotechnology have been applied for the de novo design of gene regulatory switches that can operate inside living cells. The article specifically focuses on the design of RNA-based translational regulators termed toehold switches. Toehold switches utilize toehold-mediated strand invasion to either activate or repress translation of an mRNA in response to the binding of a trigger RNA molecule. The basic operation principles of toehold switches will be discussed as well as their applications in sensing and biocomputing. Finally, strategies for their optimization will be described as well as challenges for their operation in vivo.
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Affiliation(s)
- Friedrich C Simmel
- TU Munich, School of Natural Sciences, Department of Bioscience, Garching, Germany
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31
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Moškon M, Pušnik Ž, Stanovnik L, Zimic N, Mraz M. A computational design of a programmable biological processor. Biosystems 2022; 221:104778. [PMID: 36099979 DOI: 10.1016/j.biosystems.2022.104778] [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: 06/02/2022] [Revised: 08/02/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
Basic synthetic information processing structures, such as logic gates, oscillators and flip-flops, have already been implemented in living organisms. Current implementations of these structures have yet to be extended to more complex processing structures that would constitute a biological computer. We make a step forward towards the construction of a biological computer. We describe a model-based computational design of a biological processor that uses transcription and translation resources of the host cell to perform its operations. The proposed processor is composed of an instruction memory containing a biological program, a program counter that is used to address this memory, and a biological oscillator that triggers the execution of the next instruction in the memory. We additionally describe the implementation of a biological compiler that compiles a sequence of human-readable instructions into ordinary differential equation-based models, which can be used to simulate and analyse the dynamics of the processor. The proposed implementation presents the first programmable biological processor that exploits cellular resources to execute the specified instructions. We demonstrate the application of the described processor on a set of simple yet scalable biological programs. Biological descriptions of these programs can be produced manually or automatically using the provided compiler.
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Affiliation(s)
- Miha Moškon
- University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, Ljubljana, SI-1000, Slovenia.
| | - Žiga Pušnik
- University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, Ljubljana, SI-1000, Slovenia
| | - Lidija Stanovnik
- University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, Ljubljana, SI-1000, Slovenia
| | - Nikolaj Zimic
- University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, Ljubljana, SI-1000, Slovenia
| | - Miha Mraz
- University of Ljubljana, Faculty of Computer and Information Science, Večna pot 113, Ljubljana, SI-1000, Slovenia
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32
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Toehold-mediated biosensors: Types, mechanisms and biosensing strategies. Biosens Bioelectron 2022; 220:114922. [DOI: 10.1016/j.bios.2022.114922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
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33
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Yin G, Peng A, Zhang L, Wang Y, Du G, Chen J, Kang Z. Design of artificial small regulatory trans-RNA for gene knockdown in Bacillus subtilis. Synth Syst Biotechnol 2022; 8:61-68. [DOI: 10.1016/j.synbio.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
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34
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Dai Z, Xie X, Gao Z, Li Q. DNA‐PAINT Super‐Resolution Imaging for Characterization of Nucleic Acid Nanostructures. Chempluschem 2022; 87:e202200127. [DOI: 10.1002/cplu.202200127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/12/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Zheze Dai
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Xiaodong Xie
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering 200240 Shanghai CHINA
| | - Zhaoshuai Gao
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering 200240 Shanghai CHINA
| | - Qian Li
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering Dongchuan Road 800中国 200240 Shanghai CHINA
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35
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Liu XH, Li BR, Ying ZM, Tang LJ, Wang F, Jiang JH. Small-Molecule-Mediated Split-Aptamer Assembly for Inducible CRISPR-dCas9 Transcription Activation. ACS Chem Biol 2022; 17:1769-1777. [PMID: 35700146 DOI: 10.1021/acschembio.2c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inducible CRISPR-dCas9 transcription system has become a powerful tool for transcription regulation and sensing. Here, we develop a new concept of small-molecule-mediated split-aptamer assembly for inducible CRISPR-dCas9 transcription activation, allowing quantitative detection and imaging of S-adenosyl methionine (SAM) in live cells. This inducible transcription system is designed by integrating one fragment of a split SAM aptamer to guide RNA (gRNA) and the other to MS2 arrays. SAM-mediated reassembly of the split fragments recruits an MCP-fused transcription activator to the gRNA-dCas9 complex, activating the expression of a near-infrared fluorescent protein for imaging. We demonstrate that this inducible transcription system achieves quantitative detection of SAM with high sensitivity in live cells. Our system shows that methionine adenosyltransferase 1A (MAT1A) and MAT2A can both catalyze SAM production in live cells and the SAM levels in cancer cells can be increased via upregulation of MAT1A mRNA by epigenetic inhibitors. This split-aptamer assembly strategy could afford a new approach for controlling the CRISPR-dCas9 system, enabling conditional transcription regulation in response to endogenous metabolites in live cells.
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Affiliation(s)
- Xiao-Han Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Bang-Rui Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Zhan-Ming Ying
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Li-Juan Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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36
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Ryan J, Hong S, Foo M, Kim J, Tang X. Model-Based Investigation of the Relationship between Regulation Level and Pulse Property of I1-FFL Gene Circuits. ACS Synth Biol 2022; 11:2417-2428. [PMID: 35729788 PMCID: PMC9295143 DOI: 10.1021/acssynbio.2c00109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Mathematical models are powerful tools in guiding the construction of synthetic biological circuits, given their capability of accurately capturing and predicting circuit dynamics. Recent innovations in RNA technology have enabled the development of a variety of new tools for regulating gene expression at both the transcription and translation levels. However, the effects of different regulation levels on the circuit dynamics remain largely unexplored. In this study, we focus on the type 1 incoherent feed-forward loop (I1-FFL) gene circuit with four different variations (TX, TL, HY-1, HY-2), to investigate how regulation at the transcription and translation levels affect the circuit dynamics. We develop a mechanistic model for each of the four circuits and deploy sensitivity analysis to investigate the circuits' dynamics in terms of pulse generation. Based on the analysis, we observe that the repression regulation mechanism dominates the characteristics of the pulse as compared to the activation regulation mechanism and find that the I1-FFL with transcription repression has a higher chance of generating a pulse meeting the desired criteria. The experimental results in Escherichia coli also confirm our findings from the computational analysis. We expect our findings to facilitate future experimental construction of gene circuits with insights on the selection of appropriate transcription and translation regulation tools.
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Affiliation(s)
- Jordan Ryan
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Seongho Hong
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Mathias Foo
- School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Xun Tang
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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37
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Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria. J Mol Biol 2022; 434:167689. [PMID: 35717997 DOI: 10.1016/j.jmb.2022.167689] [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: 03/11/2022] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 01/24/2023]
Abstract
RNA switches are versatile tools in synthetic biology for sensing and regulation applications. The discoveries of RNA-mediated translational and transcriptional control have facilitated the development of complexde novodesigns of RNA switches. Specifically, RNA toehold-mediated switches, in which binding to the toehold sensing domain controls the transition between switch states via strand displacement, have been extensively adapted for coupling systems responses to specifictrans-RNA inputs. This review highlights some of the challenges associated with applying these switches for native RNA detectionin vivo, including transferability between organisms. The applicability and design considerations of toehold-mediated switches are discussed by highlighting twelve recently developed switch designs. This review finishes with future perspectives to address current gaps in the field, particularly regarding the power of structural prediction algorithms for improved in vivo functionality of RNA switches.
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38
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Nguyen MTA, Pothoulakis G, Andersen ES. Synthetic Translational Regulation by Protein-Binding RNA Origami Scaffolds. ACS Synth Biol 2022; 11:1710-1718. [PMID: 35438978 PMCID: PMC9127956 DOI: 10.1021/acssynbio.1c00608] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rational design approaches for the regulation of gene expression are expanding the synthetic biology toolbox. However, only a few tools for regulating gene expression at the translational level have been developed. Here, we devise an approach for translational regulation using the MS2 and PP7 aptamer and coat-protein pairs in Escherichia coli. The aptamers are used as operators in transcription units that encode proteins fused to their cognate coat proteins, which leads to self-repression. RNA origami scaffolds that contain up to four aptamers serve as an alternate binder to activate translation. With this system, we demonstrate that the increase in expression of a reporter protein is dependent on both the concentration and number of aptamers on RNA origami scaffolds. We also demonstrate regulation of multiple proteins using a single MS2 coat protein fusion and apply this method to regulate the relative expression of enzymes of the branched pathway for deoxyviolacein biosynthesis.
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Affiliation(s)
| | | | - Ebbe S. Andersen
- Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus C, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
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39
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Falgenhauer E, Mückl A, Schwarz-Schilling M, Simmel FC. Transcriptional Interference in Toehold Switch-Based RNA Circuits. ACS Synth Biol 2022; 11:1735-1745. [PMID: 35412304 DOI: 10.1021/acssynbio.1c00486] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gene regulation based on regulatory RNA is an important mechanism in cells and is increasingly used for regulatory circuits in synthetic biology. Toehold switches are rationally designed post-transcriptional riboregulators placed in the 5' untranslated region of mRNA molecules. In the inactive state of a toehold switch, the ribosome-binding site is inaccessible to the ribosome. In the presence of a trigger RNA molecule, protein production is turned on. Using antisense RNA against trigger molecules (antitrigger RNA), gene expression can also be switched off again. We here study the utility of antisense transcription in this context, which enables a particularly compact circuit design. Our circuits utilize two inducible promoters that separately regulate trigger and antitrigger transcription, whereas their cognate toehold switch, regulating the expression of a reporter protein, is transcribed from a constitutive promoter. We explore various design options for the arrangement of the promoters and demonstrate that the resulting dynamic behavior is influenced by transcriptional interference (TI) effects depending on the promoter distance. Our experimental results are consistent with previous findings that enhanced local RNA polymerase concentrations due to active promoters in close proximity lead to an increase in transcriptional activity of the strongest promoter in the circuits. We observed that the range of this effect is larger when the participating promoters are stronger. Based on this insight, we combined two promoter arrangements for the realization of a genetic circuit comprised of two toehold switches, two triggers, and two antitriggers that function as a two-input two-output logic gate.
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Affiliation(s)
- Elisabeth Falgenhauer
- Physics Department - E14 and ZNN/WSI, TU Munich, Am Coulombwall 4a, 85748 Garching, Germany
| | - Andrea Mückl
- Physics Department - E14 and ZNN/WSI, TU Munich, Am Coulombwall 4a, 85748 Garching, Germany
| | | | - Friedrich C. Simmel
- Physics Department - E14 and ZNN/WSI, TU Munich, Am Coulombwall 4a, 85748 Garching, Germany
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40
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Wang T, Simmel FC. Riboswitch-inspired toehold riboregulators for gene regulation in Escherichia coli. Nucleic Acids Res 2022; 50:4784-4798. [PMID: 35446427 PMCID: PMC9071393 DOI: 10.1093/nar/gkac275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
Regulatory RNA molecules have been widely investigated as components for synthetic gene circuits, complementing the use of protein-based transcription factors. Among the potential advantages of RNA-based gene regulators are their comparatively simple design, sequence-programmability, orthogonality, and their relatively low metabolic burden. In this work, we developed a set of riboswitch-inspired riboregulators in Escherichia coli that combine the concept of toehold-mediated strand displacement (TMSD) with the switching principles of naturally occurring transcriptional and translational riboswitches. Specifically, for translational activation and repression, we sequestered anti-anti-RBS or anti-RBS sequences, respectively, inside the loop of a stable hairpin domain, which is equipped with a single-stranded toehold region at its 5' end and is followed by regulated sequences on its 3' side. A trigger RNA binding to the toehold region can invade the hairpin, inducing a structural rearrangement that results in translational activation or deactivation. We also demonstrate that TMSD can be applied in the context of transcriptional regulation by switching RNA secondary structure involved in Rho-dependent termination. Our designs expand the repertoire of available synthetic riboregulators by a set of RNA switches with no sequence limitation, which should prove useful for the development of robust genetic sensors and circuits.
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Affiliation(s)
- Tianhe Wang
- Physics of Synthetic Biological Systems – E14, Physics Department and ZNN, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
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41
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Cellular Computational Logic Using Toehold Switches. Int J Mol Sci 2022; 23:ijms23084265. [PMID: 35457085 PMCID: PMC9033136 DOI: 10.3390/ijms23084265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/09/2022] [Accepted: 04/10/2022] [Indexed: 11/16/2022] Open
Abstract
The development of computational logic that carries programmable and predictable features is one of the key requirements for next-generation synthetic biological devices. Despite considerable progress, the construction of synthetic biological arithmetic logic units presents numerous challenges. In this paper, utilizing the unique advantages of RNA molecules in building complex logic circuits in the cellular environment, we demonstrate the RNA-only bitwise logical operation of XOR gates and basic arithmetic operations, including a half adder, a half subtractor, and a Feynman gate, in Escherichia coli. Specifically, de-novo-designed riboregulators, known as toehold switches, were concatenated to enhance the functionality of an OR gate, and a previously utilized antisense RNA strategy was further optimized to construct orthogonal NIMPLY gates. These optimized synthetic logic gates were able to be seamlessly integrated to achieve final arithmetic operations on small molecule inputs in cells. Toehold-switch-based ribocomputing devices may provide a fundamental basis for synthetic RNA-based arithmetic logic units or higher-order systems in cells.
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42
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Hong KQ, Zhang J, Jin B, Chen T, Wang ZW. Development and characterization of a glycine biosensor system for fine-tuned metabolic regulation in Escherichia coli. Microb Cell Fact 2022; 21:56. [PMID: 35392910 PMCID: PMC8991567 DOI: 10.1186/s12934-022-01779-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
Background In vivo biosensors have a wide range of applications, ranging from the detection of metabolites to the regulation of metabolic networks, providing versatile tools for synthetic biology and metabolic engineering. However, in view of the vast array of metabolite molecules, the existing number and performance of biosensors is far from sufficient, limiting their potential applications in metabolic engineering. Therefore, we developed the synthetic glycine-ON and -OFF riboswitches for metabolic regulation and directed evolution of enzyme in Escherichia coli. Results The results showed that a synthetic glycine-OFF riboswitch (glyOFF6) and an increased-detection-range synthetic glycine-ON riboswitch (glyON14) were successfully screened from a library based on the Bacillus subtilis glycine riboswitch using fluorescence-activated cell sorting (FACS) and tetA-based dual genetic selection. The two synthetic glycine riboswitches were successfully used in tunable regulation of lactate synthesis, dynamic regulation of serine synthesis and directed evolution of alanine-glyoxylate aminotransferase in Escherichia coli, respectively. Mutants AGXT22 and AGXT26 of alanine-glyoxylate aminotransferase with an increase of 58% and 73% enzyme activity were obtained by using a high-throughput screening platform based on the synthetic glycine-OFF riboswitch, and successfully used to increase the 5-aminolevulinic acid yield of engineered Escherichia coli. Conclusions A synthetic glycine-OFF riboswitch and an increased-detection-range synthetic glycine-ON riboswitch were successfully designed and screened. The developed riboswitches showed broad application in tunable regulation, dynamic regulation and directed evolution of enzyme in E. coli. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01779-4.
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Affiliation(s)
- Kun-Qiang Hong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China.,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Jing Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China.,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Biao Jin
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China.,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Tao Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China.,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Zhi-Wen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China. .,Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China.
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43
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Zhao EM, Mao AS, de Puig H, Zhang K, Tippens ND, Tan X, Ran FA, Han I, Nguyen PQ, Chory EJ, Hua TY, Ramesh P, Thompson DB, Oh CY, Zigon ES, English MA, Collins JJ. RNA-responsive elements for eukaryotic translational control. Nat Biotechnol 2022; 40:539-545. [PMID: 34711989 DOI: 10.1038/s41587-021-01068-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 08/20/2021] [Indexed: 02/07/2023]
Abstract
The ability to control translation of endogenous or exogenous RNAs in eukaryotic cells would facilitate a variety of biotechnological applications. Current strategies are limited by low fold changes in transgene output and the size of trigger RNAs (trRNAs). Here we introduce eukaryotic toehold switches (eToeholds) as modular riboregulators. eToeholds contain internal ribosome entry site sequences and form inhibitory loops in the absence of a specific trRNA. When the trRNA is present, eToeholds anneal to it, disrupting the inhibitory loops and allowing translation. Through optimization of RNA annealing, we achieved up to 16-fold induction of transgene expression in mammalian cells. We demonstrate that eToeholds can discriminate among viral infection status, presence or absence of gene expression and cell types based on the presence of exogenous or endogenous RNA transcripts.
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Affiliation(s)
- Evan M Zhao
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Angelo S Mao
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helena de Puig
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kehan Zhang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nathaniel D Tippens
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xiao Tan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - F Ann Ran
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Isaac Han
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Peter Q Nguyen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Emma J Chory
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tiffany Y Hua
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Pradeep Ramesh
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - David B Thompson
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Crystal Yuri Oh
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Eric S Zigon
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Max A English
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. .,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA, USA.
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44
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Dykstra PB, Kaplan M, Smolke CD. Engineering synthetic RNA devices for cell control. Nat Rev Genet 2022; 23:215-228. [PMID: 34983970 PMCID: PMC9554294 DOI: 10.1038/s41576-021-00436-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 12/16/2022]
Abstract
The versatility of RNA in sensing and interacting with small molecules, proteins and other nucleic acids while encoding genetic instructions for protein translation makes it a powerful substrate for engineering biological systems. RNA devices integrate cellular information sensing, processing and actuation of specific signals into defined functions and have yielded programmable biological systems and novel therapeutics of increasing sophistication. However, challenges centred on expanding the range of analytes that can be sensed and adding new mechanisms of action have hindered the full realization of the field's promise. Here, we describe recent advances that address these limitations and point to a significant maturation of synthetic RNA-based devices.
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Affiliation(s)
- Peter B. Dykstra
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Matias Kaplan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Christina D. Smolke
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,
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45
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Multi-arm RNA junctions encoding molecular logic unconstrained by input sequence for versatile cell-free diagnostics. Nat Biomed Eng 2022; 6:298-309. [PMID: 35288660 PMCID: PMC8940621 DOI: 10.1038/s41551-022-00857-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 02/07/2022] [Indexed: 12/12/2022]
Abstract
Applications of RNA-based molecular logic have been hampered by sequence constraints imposed on the input and output of the circuits. Here we show that the sequence constraints can be substantially reduced by appropriately encoded multi-arm junctions of single-stranded RNA structures. To conditionally activate RNA translation, we integrated multi-arm junctions, self-assembled upstream of a regulated gene and designed to unfold sequentially in response to different RNA inputs, with motifs of loop-initiated RNA activators that function independently of the sequence of the input RNAs and that reduce interference with the output gene. We used the integrated RNA system and sequence-independent input RNAs to execute two-input and three-input OR and AND logic in Escherichia coli, and designed paper-based cell-free colourimetric assays that accurately identified two human immunodeficiency virus (HIV) subtypes (by executing OR logic) in amplified synthetic HIV RNA as well as severe acute respiratory syndrome coronavirus-2 (via two-input AND logic) in amplified RNA from saliva samples. The sequence-independent molecular logic enabled by the integration of multi-arm junction RNAs with motifs for loop-initiated RNA activators may be broadly applicable in biotechnology.
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46
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Hunt JP, Zhao EL, Free TJ, Soltani M, Warr CA, Benedict AB, Takahashi MK, Griffitts JS, Pitt WG, Bundy BC. Towards detection of SARS-CoV-2 RNA in human saliva: A paper-based cell-free toehold switch biosensor with a visual bioluminescent output. N Biotechnol 2022; 66:53-60. [PMID: 34555549 PMCID: PMC8452453 DOI: 10.1016/j.nbt.2021.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 11/30/2022]
Abstract
The COVID-19 pandemic has illustrated the global demand for rapid, low-cost, widely distributable and point-of-care nucleic acid diagnostic technologies. Such technologies could help disrupt transmission, sustain economies and preserve health and lives during widespread infection. In contrast, conventional nucleic acid diagnostic procedures require trained personnel, complex laboratories, expensive equipment, and protracted processing times. In this work, lyophilized cell-free protein synthesis (CFPS) and toehold switch riboregulators are employed to develop a promising paper-based nucleic acid diagnostic platform activated simply by the addition of saliva. First, to facilitate distribution and deployment, an economical paper support matrix is identified and a mass-producible test cassette designed with integral saliva sample receptacles. Next, CFPS is optimized in the presence of saliva using murine RNase inhibitor. Finally, original toehold switch riboregulators are engineered to express the bioluminescent reporter NanoLuc in response to SARS-CoV-2 RNA sequences present in saliva samples. The biosensor generates a visible signal in as few as seven minutes following administration of 15 μL saliva enriched with high concentrations of SARS-CoV-2 RNA sequences. The estimated cost of this test is less than 0.50 USD, which could make this platform readily accessible to both the developed and developing world. While additional research is needed to decrease the limit of detection, this work represents important progress toward developing a diagnostic technology that is rapid, low-cost, distributable and deployable at the point-of-care by a layperson.
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Affiliation(s)
- J Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Emily Long Zhao
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Tyler J Free
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Mehran Soltani
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Chandler A Warr
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Alex B Benedict
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Melissa K Takahashi
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - Joel S Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - William G Pitt
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA.
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47
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Hong S, Park D, Chaudhary S, McCutcheon G, Green AA, Kim J. Design of RNA-Based Translational Repressors. Methods Mol Biol 2022; 2518:49-64. [PMID: 35666438 DOI: 10.1007/978-1-0716-2421-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The toehold switch is an RNA-based riboregulator that activates translation in response to a cognate trigger RNA and provides high ON/OFF ratios, excellent orthogonality, and logic capabilities. Riboregulators that provide the inverse function - turning off translation in response to a trigger RNA - are also versatile tools for sensing and efficiently implementing logic gates such as NAND or NOR. Toehold and three-way junction (3WJ) repressors are two de novo designed translational repressors devised to provide NOT functions with an easily programmable and intuitive structural design. Toehold and 3WJ repressors repress translation upon binding to cognate trigger RNAs by forming strong hairpin and three-way junction structures, respectively. These two translational repressors can be incorporated into multi-input NAND and NOR gates. This chapter provides methods for designing these translational repressors and protocols for in vivo characterization in E. coli.
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Affiliation(s)
- Seongho Hong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea
| | - Dongwon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea
| | - Soma Chaudhary
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute, and the School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Griffin McCutcheon
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute, and the School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Alexander A Green
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute, and the School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
| | - Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, South Korea.
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48
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Liu B, Chappell J. Computational Design of Small Transcription Activating RNAs (STARs). Methods Mol Biol 2022; 2518:87-97. [PMID: 35666440 DOI: 10.1007/978-1-0716-2421-0_5] [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: 06/15/2023]
Abstract
A major goal of synthetic biology has been to develop libraries of versatile genetic regulators that enable the precise control of gene expression. In recent years, the creation of novel RNA design motifs has allowed for the bottom-up, computational design of large libraries of high-performing and orthogonal RNA regulator systems. One example of this is Small Transcription Activating RNAs (STARs), which function through the conditional formation of terminator hairpins to activate the transcription of targeted genes. STARs have found broad utility for creating synthetic gene circuits, engineering metabolic pathways, and creating new types of diagnostics. Here we describe the method to computationally design, build, and characterize STAR regulators.
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Affiliation(s)
- Baiyang Liu
- Graduate Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - James Chappell
- Department of BioSciences, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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49
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Chen C, Wu Q, Ke Q, Wang T, Zhang Y, Wei F, Wang X, Liu G. Implementation of novel boolean logic gates for IMPLICATION and XOR functions using riboregulators. Bioengineered 2022; 13:1235-1248. [PMID: 34983299 PMCID: PMC8805959 DOI: 10.1080/21655979.2021.2020493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
To date, several different types of synthetic genetic switches, including riboregulators, riboswitches, and toehold switches, have been developed to construct AND, OR, NOT, NAND, NOR, and NOT IMPLICATION (NIMP) gates. The logic gate can integrate multiple input signals following a set of algorithms and generate a response only if strictly defined conditions are met. However, there are still some logic gates that have not been implemented but are necessary to build complex genetic circuits. Here, based on the toehold switches and three-way-junction (3WJ) repressors, we designed two novel biological Boolean logic gates of IMPLICATION (IMP) and XOR. Subsequently, the outputs of these two logic gates were characterized by fluorescence analysis, indicating that they can achieve the truth tables of logical gates. Furthermore, the fluorescence intensity under the logical TRUE condition was significantly higher than under the logical FALSE condition, suggesting the high dynamic range of the ON/OFF ratios. Because of the programmability of synthetic RNA switches, the constructed RNA logic gates could serve as elementary units to build a versatile and powerful platform for translational regulation and RNA-based biological computation.
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Affiliation(s)
- Chaoxin Chen
- The iGEM Laboratory of OUC-China, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qi Wu
- The iGEM Laboratory of OUC-China, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qingying Ke
- The iGEM Laboratory of OUC-China, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ting Wang
- The iGEM Laboratory of OUC-China, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yifan Zhang
- The iGEM Laboratory of OUC-China, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Feiwen Wei
- The iGEM Laboratory of OUC-China, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaolong Wang
- The iGEM Laboratory of OUC-China, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Guanglei Liu
- The iGEM Laboratory of OUC-China, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
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50
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Wu K, Green AA. Detection of Norovirus Using Paper-Based Cell-Free Systems. Methods Mol Biol 2022; 2433:375-390. [PMID: 34985757 DOI: 10.1007/978-1-0716-1998-8_23] [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: 06/14/2023]
Abstract
Norovirus infections are the leading cause of foodborne illness and human gastroenteritis, afflicting hundreds of millions of people each year. Molecular assays with the capacity to detect norovirus without expensive equipment and with high sensitivity and specificity represent useful tools to track and contain future outbreaks. Here we describe how norovirus can be detected in low-cost paper-based cell-free reactions. These assays combine freeze-dried, thermostable cell-free transcription-translation reactions with toehold switch riboregulators designed to target the norovirus genome, enabling convenient colorimetric assay readouts. Coupling cell-free reactions with synbody-based viral enrichment and isothermal amplification enables detection of norovirus from clinical samples down to concentrations as low as 270 zM. These diagnostic tests are promising assays for confronting norovirus outbreaks and can be adapted to a variety of other human pathogens.
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Affiliation(s)
- Kaiyue Wu
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology and Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
| | - Alexander A Green
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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