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Zhou S, Chen M, Yuan Y, Xu Y, Pu Q, Ai X, Liu S, Du F, Huang X, Dong J, Cui X, Tang Z. Trans-acting aptazyme for conditional gene knockdown in eukaryotic cells. Mol Ther Nucleic Acids 2023; 33:367-375. [PMID: 37547296 PMCID: PMC10400872 DOI: 10.1016/j.omtn.2023.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Trans-acting hammerhead ribozyme inherits the advantages of being the smallest and best-characterized RNA-cleaving ribozyme, offering high modularity and the ability to cleave any desired sequence without the aid of any protein, as long as the target sequence contains a cleavage site. However, achieving precise control over the trans-acting hammerhead ribozyme would enable safer and more accurate regulation of gene expression. Herein, we described an intracellular selection of hammerhead aptazyme that contains a theophylline aptamer on stem II based on toxin protein IbsC. Based on the intracellular selection, we obtained three new cis-acting hammerhead aptazymes. Moreover, the corresponding trans-acting aptazymes could be efficiently induced by theophylline to knock down different targeted genes in eukaryotic cells. Notably, the best one, T195, exhibited a ligand-dependent and dose-dependent response to theophylline, and the cleavage efficiency could be enhanced by incorporating multiplex aptazymes.
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Affiliation(s)
- Shan Zhou
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Meiyi Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Yan Xu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Qinlin Pu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Xilei Ai
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Shuai Liu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
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2
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Abstract
RNA viral vectors that replicate without DNA intermediates are attractive platforms for manipulation of cells for biomedical and veterinary applications because they have minimal risk of chromosomal integration. Vesicular stomatitis virus (VSV) vectors are among the most well-studied RNA viral vectors due to their low pathogenicity to humans and ability to express transgenes at high levels for weeks to months. However, their applications have been mostly limited to oncolytic and vaccine vectors due to their cytopathogenicity. We discovered two mutations in the VSV vector that synergistically confer improved stability in mouse embryonic stem cells (ESCs) with markedly lower cytopathic effects. We also demonstrated chemical regulation of transgene expression through embedded riboswitches. The ESCs infected with the mutant vector were shown to maintain pluripotency. This new vector sets the stage for precise regulation of gene expression in ESCs to produce a variety of differentiated cells without chromosomal alteration.
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Affiliation(s)
- Narae Kim
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
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3
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Svehlova K, Lukšan O, Jakubec M, Curtis EA. Supernova: A Deoxyribozyme that Catalyzes a Chemiluminescent Reaction. Angew Chem Int Ed Engl 2021; 61:e202109347. [PMID: 34559935 PMCID: PMC9298802 DOI: 10.1002/anie.202109347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/17/2021] [Indexed: 11/10/2022]
Abstract
Functional DNA molecules are useful components in nanotechnology and synthetic biology. To expand the toolkit of functional DNA parts, in this study we used artificial evolution to identify a glowing deoxyribozyme called Supernova. This deoxyribozyme transfers a phosphate from a 1,2-dioxetane substrate to its 5' hydroxyl group, which triggers a chemiluminescent reaction and a flash of blue light. An engineered version of Supernova is only catalytically active in the presence of an oligonucleotide complementary to its 3' end, demonstrating that light production can be coupled to ligand binding. We anticipate that Supernova will be useful in a wide variety of applications, including as a signaling component in allosterically regulated sensors and in logic gates of molecular computers.
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Affiliation(s)
- Katerina Svehlova
- Institute of Organic Chemistry and Biochemistry ASCR, Prague, Czech Republic.,Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Ondřej Lukšan
- Institute of Organic Chemistry and Biochemistry ASCR, Prague, Czech Republic
| | - Martin Jakubec
- Institute of Organic Chemistry and Biochemistry ASCR, Prague, Czech Republic.,Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Edward A Curtis
- Institute of Organic Chemistry and Biochemistry ASCR, Prague, Czech Republic
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4
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Mustafina K, Nomura Y, Rotrattanadumrong R, Yokobayashi Y. Circularly-Permuted Pistol Ribozyme: A Synthetic Ribozyme Scaffold for Mammalian Riboswitches. ACS Synth Biol 2021; 10:2040-2048. [PMID: 34374523 DOI: 10.1021/acssynbio.1c00213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A small molecule-responsive self-cleaving ribozyme (aptazyme) embedded in the untranslated region of an mRNA functions as a riboswitch that allows chemical regulation of gene expression in mammalian cells. Aptazymes are engineered by fusing a self-cleaving ribozyme with an RNA aptamer that recognizes a small molecule so that the ribozyme is either activated or inhibited in the presence of the small molecule. However, the variety of aptamers, ribozymes, and aptazyme design strategies suitable for mammalian riboswitch applications is still limited. This work focuses on a new ribozyme scaffold for engineering aptazymes and riboswitches that function in mammalian cells. We investigated circularly permuted variants of the pistol ribozyme class (CPP) as a synthetic ribozyme scaffold for mammalian riboswitch applications. Through semirational design and high-throughput screening, we designed guanine and tetracycline activated riboswitches based on three distinct aptazyme architectures, resulting in riboswitches with ON/OFF ratios as high as 8.6. Our work adds CPP to the limited ribozyme scaffold toolbox for mammalian synthetic biology applications and highlights the opportunities in exploring ribozymes beyond natural motifs.
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Affiliation(s)
- Kamila Mustafina
- Nucleic Acid Chemistry and Engineering Unit Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 904 0495, Japan
| | - Yoko Nomura
- Nucleic Acid Chemistry and Engineering Unit Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 904 0495, Japan
| | - Rachapun Rotrattanadumrong
- Nucleic Acid Chemistry and Engineering Unit Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 904 0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit Okinawa Institute of Science and Technology Graduate University Onna, Okinawa 904 0495, Japan
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5
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Krüger A, de Jesus Santos AP, de Sá V, Ulrich H, Wrenger C. Aptamer Applications in Emerging Viral Diseases. Pharmaceuticals (Basel) 2021; 14:ph14070622. [PMID: 34203242 PMCID: PMC8308861 DOI: 10.3390/ph14070622] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers are single-stranded DNA or RNA molecules which are submitted to a process denominated SELEX. SELEX uses reiterative screening of a random oligonucleotide library to identify high-affinity binders to a chosen target, which may be a peptide, protein, or entire cells or viral particles. Aptamers can rival antibodies in target recognition, and benefit from their non-proteic nature, ease of modification, increased stability, and pharmacokinetic properties. This turns them into ideal candidates for diagnostic as well as therapeutic applications. Here, we review the recent accomplishments in the development of aptamers targeting emerging viral diseases, with emphasis on recent findings of aptamers binding to coronaviruses. We focus on aptamer development for diagnosis, including biosensors, in addition to aptamer modifications for stabilization in body fluids and tissue penetration. Such aptamers are aimed at in vivo diagnosis and treatment, such as quantification of viral load and blocking host cell invasion, virus assembly, or replication, respectively. Although there are currently no in vivo applications of aptamers in combating viral diseases, such strategies are promising for therapy development in the future.
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Affiliation(s)
- Arne Krüger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000-SP, Brazil;
| | - Ana Paula de Jesus Santos
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-900-SP, Brazil; (A.P.d.J.S.); (V.d.S.)
| | - Vanessa de Sá
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-900-SP, Brazil; (A.P.d.J.S.); (V.d.S.)
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo 05508-900-SP, Brazil; (A.P.d.J.S.); (V.d.S.)
- Correspondence: (H.U.); (C.W.)
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000-SP, Brazil;
- Correspondence: (H.U.); (C.W.)
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6
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Tickner ZJ, Farzan M. Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors. Pharmaceuticals (Basel) 2021; 14:ph14060554. [PMID: 34200913 PMCID: PMC8230432 DOI: 10.3390/ph14060554] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
Vectors developed from adeno-associated virus (AAV) are powerful tools for in vivo transgene delivery in both humans and animal models, and several AAV-delivered gene therapies are currently approved for clinical use. However, AAV-mediated gene therapy still faces several challenges, including limited vector packaging capacity and the need for a safe, effective method for controlling transgene expression during and after delivery. Riboswitches, RNA elements which control gene expression in response to ligand binding, are attractive candidates for regulating expression of AAV-delivered transgene therapeutics because of their small genomic footprints and non-immunogenicity compared to protein-based expression control systems. In addition, the ligand-sensing aptamer domains of many riboswitches can be exchanged in a modular fashion to allow regulation by a variety of small molecules, proteins, and oligonucleotides. Riboswitches have been used to regulate AAV-delivered transgene therapeutics in animal models, and recently developed screening and selection methods allow rapid isolation of riboswitches with novel ligands and improved performance in mammalian cells. This review discusses the advantages of riboswitches in the context of AAV-delivered gene therapy, the subsets of riboswitch mechanisms which have been shown to function in human cells and animal models, recent progress in riboswitch isolation and optimization, and several examples of AAV-delivered therapeutic systems which might be improved by riboswitch regulation.
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Affiliation(s)
- Zachary J. Tickner
- Department of Immunology and Microbiology, the Scripps Research Institute, Jupiter, FL 33458, USA;
- Correspondence:
| | - Michael Farzan
- Department of Immunology and Microbiology, the Scripps Research Institute, Jupiter, FL 33458, USA;
- Emmune, Inc., Jupiter, FL 33458, USA
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7
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Zhuang C, Zhuang C, Zhou Q, Huang X, Gui Y, Lai Y, Yang S. Engineered CRISPR/Cas13d Sensing hTERT Selectively Inhibits the Progression of Bladder Cancer In Vitro. Front Mol Biosci 2021; 8:646412. [PMID: 33816560 PMCID: PMC8017217 DOI: 10.3389/fmolb.2021.646412] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Aptazyme and CRISPR/Cas gene editing system were widely used for regulating gene expression in various diseases, including cancer. This work aimed to reconstruct CRISPR/Cas13d tool for sensing hTERT exclusively based on the new device OFF-switch hTERT aptazyme that was inserted into the 3’ UTR of the Cas13d. In bladder cancer cells, hTERT ligand bound to aptamer in OFF-switch hTERT aptazyme to inhibit the degradation of Cas13d. Results showed that engineered CRISPR/Cas13d sensing hTERT suppressed cell proliferation, migration, invasion and induced cell apoptosis in bladder cancer 5637 and T24 cells without affecting normal HFF cells. In short, we constructed engineered CRISPR/Cas13d sensing hTERT selectively inhibited the progression of bladder cancer cells significantly. It may serve as a promising specifically effective therapy for bladder cancer cells.
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Affiliation(s)
- Chengle Zhuang
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Changshui Zhuang
- Department of Urology, Union Shenzhen Hospital, Huazhong University of Science and Technology, Shenzhen, China
| | - Qun Zhou
- Department of Urology, the Affiliated Nanhua Hospital of University of South China, Hengyang, China
| | - Xueting Huang
- Department of Nephrorheumatology, Shenzhen Yantian District People's Hospital, Shenzhen, China
| | - Yaoting Gui
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yongqing Lai
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Shangqi Yang
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, China
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8
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Abstract
Self-cleaving ribozymes engineered to be activated or inhibited by a small molecule binding to an RNA aptamer inserted within a ribozyme (aptazymes) have proven to be useful for controlling gene expression in living cells. In mammalian cells, an aptazyme embedded in the 5' or 3' untranslated region of an mRNA functions as a synthetic riboswitch to chemically regulate gene expression. However, the variety of aptazyme architectures and the ribozyme scaffolds that have been used for mammalian riboswitches has been limited. In particular, fewer synthetic riboswitches that activate gene expression in response to a small molecule (ON-switches) in mammalian cells have been reported compared to OFF-switches. In this work, we developed mammalian riboswitches that function as guanine-activated ON-switches based on a novel aptazyme architecture in which an aptamer and a ribozyme are fused in tandem. The riboswitch performance was optimized by fine-tuning the stability of a critical stem that controls the ribozyme structure and function, yielding switches with ON/OFF ratios greater than 6.0. Our new aptazyme architecture expands the RNA device toolbox for controlling gene expression in mammalian cells.
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Affiliation(s)
- Kamila Mustafina
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| | - Keisuke Fukunaga
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
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9
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Abstract
Synthetic riboswitches based on small molecule-responsive self-cleaving ribozymes (aptazymes) embedded in the untranslated regions (UTRs) allow chemical control of gene expression in mammalian cells. In this work, we used a guanine-responsive aptazyme to control transgene expression from a replication-incompetent vesicular stomatitis virus (VSV) vector. VSV is a nonsegmented, negative-sense, cytoplasmic RNA virus that replicates without DNA intermediates, and its applications for vaccines and oncolytic viral therapy are being explored. By inserting the guanine-activated ribozyme in the 3' UTRs of viral genes and transgenes, GFP expression from the VSV vector in mammalian cells was repressed by as much as 26.8-fold in the presence of guanine. Furthermore, we demonstrated reversible regulation of a transgene (secreted NanoLuc) by adding and withdrawing guanine from the medium over the course of 12 days. In summary, our riboswitch-controlled VSV vector allows robust, long-term, and reversible regulation of gene expression in mammalian cells without the risk of undesirable genomic integration.
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Affiliation(s)
- Kei Takahashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
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10
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Miao S, Yang T, Cui W, Zhou Z. [Construction and application of theophylline-activated RNA switches in the regulation of expression of recombinant proteins in Bacillus subtilis]. Sheng Wu Gong Cheng Xue Bao 2019; 35:1478-1490. [PMID: 31441619 DOI: 10.13345/j.cjb.190037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacillus subtilis can be widely used as an important microorganism for metabolic engineering and recombinant proteins expression in industrial biotechnology and synthetic biology. However, it is difficult to make accurate regulation of exogenous gene by biological tools in B. subtilis, which limits the application of B. subtilis in synthetic biology. The purpose of this study is to develop regulatory tools for precise control of gene expression by using non-coding RNAs, by which the activation of heterologous gene could be achieved without the auxiliary protein factors. We constructed the synthetic riboswitch E and aptazyme AZ using the theophylline aptamer. Six different native promoters from B. subtilis were functionally adapted with the E and AZ to fabricate an array of novel regulatory elements activated by theophylline. Then, we determined the performance of these elements using green fluorescence protein as reporter, and then further verified using red fluorescence protein and pullulanase as cargo proteins. Results showed that the same kind of RNA elements with different promoters showed different levels of efficiency. Promoter PsigW and E combination (sigWE) had the highest induction rate in B. subtilis. Compared with the control group, it can produce the induction rate of 16.8. Promoter PrpoB and AZ combination (rpoBAZ) showed the highest induction rate of 6.2. SigWE mediated mCherry induction rate was 9.2, and P43E mediated pullulanase induction rate was 32.8, in which enzyme activity reached 81 U/mL. This study confirmed that GFP, mCherry and pullulan can all be regulated by riboswitch and aptazyme, but there were differences between different combinations of promoters with RNA regulators.
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Affiliation(s)
- Shengnan Miao
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Tingyao Yang
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology (MOE), School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
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11
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Hajiahmadi Z, Movahedi A, Wei H, Li D, Orooji Y, Ruan H, Zhuge Q. Strategies to Increase On-Target and Reduce Off-Target Effects of the CRISPR/Cas9 System in Plants. Int J Mol Sci 2019; 20:E3719. [PMID: 31366028 PMCID: PMC6696359 DOI: 10.3390/ijms20153719] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/21/2019] [Accepted: 07/27/2019] [Indexed: 12/20/2022] Open
Abstract
The CRISPR/Cas9 system (clustered regularly interspaced short palindromic repeat-associated protein 9) is a powerful genome-editing tool in animals, plants, and humans. This system has some advantages, such as a high on-target mutation rate (targeting efficiency), less cost, simplicity, and high-efficiency multiplex loci editing, over conventional genome editing tools, including meganucleases, transcription activator-like effector nucleases (TALENs), and zinc finger nucleases (ZFNs). One of the crucial shortcomings of this system is unwanted mutations at off-target sites. We summarize and discuss different approaches, such as dCas9 and Cas9 paired nickase, to decrease the off-target effects in plants. According to studies, the most effective method to reduce unintended mutations is the use of ligand-dependent ribozymes called aptazymes. The single guide RNA (sgRNA)/ligand-dependent aptazyme strategy has helped researchers avoid unwanted mutations in human cells and can be used in plants as an alternative method to dramatically decrease the frequency of off-target mutations. We hope our concept provides a new, simple, and fast gene transformation and genome-editing approach, with advantages including reduced time and energy consumption, the avoidance of unwanted mutations, increased frequency of on-target changes, and no need for external forces or expensive equipment.
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Affiliation(s)
- Zahra Hajiahmadi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
- Department of Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht 4199613776, Iran
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China.
| | - Hui Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Dawei Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Yasin Orooji
- College of Materials Science and Engineering, Nanjing Forestry University, No. 159, Longpan Road, Nanjing 210037, China
| | - Honghua Ruan
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
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12
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Stifel J, Spöring M, Hartig JS. Expanding the toolbox of synthetic riboswitches with guanine-dependent aptazymes. Synth Biol (Oxf) 2019; 4:ysy022. [PMID: 32995528 PMCID: PMC7445771 DOI: 10.1093/synbio/ysy022] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/04/2018] [Accepted: 12/06/2018] [Indexed: 12/18/2022] Open
Abstract
Artificial riboswitches based on ribozymes serve as versatile tools for ligand-dependent gene expression regulation. Advantages of these so-called aptazymes are their modular architecture and the comparably little coding space they require. A variety of aptamer-ribozyme combinations were constructed in the past 20 years and the resulting aptazymes were applied in diverse contexts in prokaryotic and eukaryotic systems. Most in vivo functional aptazymes are OFF-switches, while ON-switches are more advantageous regarding potential applications in e.g. gene therapy vectors. We developed new ON-switching aptazymes in the model organism Escherichia coli and in mammalian cell culture using the intensely studied guanine-sensing xpt aptamer. Utilizing a high-throughput screening based on fluorescence-activated cell sorting in bacteria we identified up to 9.2-fold ON-switches and OFF-switches with a dynamic range up to 32.7-fold. For constructing ON-switches in HeLa cells, we used a rational design approach based on existing tetracycline-sensitive ON-switches. We discovered that communication modules responding to tetracycline are also functional in the context of guanine aptazymes, demonstrating a high degree of modularity. Here, guanine-responsive ON-switches with a four-fold dynamic range were designed. Summarizing, we introduce a series of novel guanine-dependent ribozyme switches operative in bacteria and human cell culture that significantly broaden the existing toolbox.
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Affiliation(s)
- Julia Stifel
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - Maike Spöring
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - Jörg Steffen Hartig
- Department of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
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13
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Abstract
Chemically regulated self-cleaving ribozymes, or aptazymes, are emerging as a promising class of genetic devices that allow dynamic control of gene expression in synthetic biology. However, further expansion of the limited repertoire of ribozymes and aptamers, and development of new strategies to couple the RNA elements to engineer functional aptazymes are highly desirable for synthetic biology applications. Here, we report aptazymes based on the recently identified self-cleaving pistol ribozyme class using a guanine aptamer as the molecular sensing element. Two aptazyme architectures were studied by constructing and assaying 17 728 mutants by deep sequencing. Although one of the architectures did not yield functional aptazymes, a novel aptazyme design in which the aptamer and the ribozyme were placed in tandem yielded a number of guanine-inhibited ribozymes. Detailed analysis of the extensive sequence-function data suggests a mechanism that involves a competition between two mutually exclusive RNA structures reminiscent of natural bacterial riboswitches.
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Affiliation(s)
- Shungo Kobori
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| | - Kei Takahashi
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan
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14
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Zhong G, Wang H, Bailey CC, Gao G, Farzan M. Rational design of aptazyme riboswitches for efficient control of gene expression in mammalian cells. eLife 2016; 5. [PMID: 27805569 PMCID: PMC5130294 DOI: 10.7554/elife.18858] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/01/2016] [Indexed: 12/21/2022] Open
Abstract
Efforts to control mammalian gene expression with ligand-responsive riboswitches have been hindered by lack of a general method for generating efficient switches in mammalian systems. Here we describe a rational-design approach that enables rapid development of efficient cis-acting aptazyme riboswitches. We identified communication-module characteristics associated with aptazyme functionality through analysis of a 32-aptazyme test panel. We then developed a scoring system that predicts an aptazymes’s activity by integrating three characteristics of communication-module bases: hydrogen bonding, base stacking, and distance to the enzymatic core. We validated the power and generality of this approach by designing aptazymes responsive to three distinct ligands, each with markedly wider dynamic ranges than any previously reported. These aptayzmes efficiently regulated adeno-associated virus (AAV)-vectored transgene expression in cultured mammalian cells and mice, highlighting one application of these broadly usable regulatory switches. Our approach enables efficient, protein-independent control of gene expression by a range of small molecules. DOI:http://dx.doi.org/10.7554/eLife.18858.001
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Affiliation(s)
- Guocai Zhong
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, Jupiter, United States
| | - Haimin Wang
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, Jupiter, United States
| | - Charles C Bailey
- Department of Molecular and Comparative Pathology, Johns Hopkins School of Medicine, Baltimore, United States
| | - Guangping Gao
- Gene Therapy Center, University of Massachusetts Medical School, Worcester, United States
| | - Michael Farzan
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, Jupiter, United States
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15
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Abstract
A system was developed to detect the self-replication of an RNA enzyme in real time. The enzyme is an RNA ligase that undergoes exponential amplification at a constant temperature and can be made to operate in a ligand-dependent manner. The real-time system is based on a fluorimetric readout that directly couples the ligation event to an increase in florescence signal that can be monitored using standard instrumentation. The real-time system can also operate entirely with l-RNA, which is not susceptible to degradation by ribonucleases that are present in biological samples. The system is analogous to real-time PCR, but with the potential to detect small molecules, proteins, and other targets that can be recognized by a suitable aptamer. The ligand-dependent self-replication of RNA has potential applications in molecular diagnostics and biosensing that benefit from the rapid, precise, and real-time detection of various target molecules.
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16
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Kobori S, Ichihashi N, Kazuta Y, Matsuura T, Yomo T. Kinetic analysis of aptazyme-regulated gene expression in a cell-free translation system: modeling of ligand-dependent and -independent expression. RNA 2012; 18:1458-1465. [PMID: 22733807 PMCID: PMC3404367 DOI: 10.1261/rna.032748.112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 05/26/2012] [Indexed: 06/01/2023]
Abstract
Aptazymes are useful as RNA-based switches of gene expression responsive to several types of compounds. One of the most important properties of the switching ability is the signal/noise (S/N) ratio, i.e., the ratio of gene expression in the presence of ligand to that in the absence of ligand. The present study was performed to gain a quantitative understanding of how the aptazyme S/N ratio is determined by factors involved in gene expression, such as transcription, RNA self-cleavage, RNA degradation, protein translation, and their ligand dependencies. We performed switching of gene expression using two on-switch aptazymes with different properties in a cell-free translation system, and constructed a kinetic model that quantitatively describes the dynamics of RNA and protein species involved in switching. Both theoretical and experimental analyses consistently demonstrated that factors determining both the absolute value and the dynamics of the S/N ratio are highly dependent on the routes of translation in the absence of ligand: translation from the ligand-independently cleaved RNA or leaky translation from the noncleaved RNA. The model obtained here is useful to assess the factors that restrict the S/N ratio and to improve aptazymes more efficiently.
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Affiliation(s)
- Shungo Kobori
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Norikazu Ichihashi
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka 565-0871, Japan
| | - Yasuaki Kazuta
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka 565-0871, Japan
| | - Tomoaki Matsuura
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka 565-0871, Japan
- Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Tetsuya Yomo
- Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
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17
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Abstract
The hairpin ribozyme can catalyze the cleavage of RNA substrates by employing its conformational flexibility. To form a catalytic complex, the two domains A and B of the hairpin-ribozyme complex must interact with one another in a folding step called docking. We have constructed hairpin ribozyme variants harboring an aptamer sequence that can be allosterically induced by flavin mononucleotide (FMN). Domains A and B are separated by distinct bridge sequences that communicate the formation of the FMN-aptamer complex to domains A and B, facilitating their docking. In the presence of a short oligonucleotide that is complementary to the aptamer, catalytic activity of the ribozyme is completely abolished, due to the formation of an extended conformer that cannot perform catalysis. However, in the presence of the small molecule effector FMN, the inhibitory effect of the oligonucleotide is competitively neutralized and the ribozyme is activated 150-fold. We thus have established a new principle for the regulation of ribozyme catalysis in which two regulatory factors (an oligonucleotide and a small molecule) that switch the ribozyme's activity in opposite directions compete for the same binding site in the aptamer domain.
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18
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Robertson MP, Knudsen SM, Ellington AD. In vitro selection of ribozymes dependent on peptides for activity. RNA 2004; 10:114-27. [PMID: 14681590 PMCID: PMC1370523 DOI: 10.1261/rna.5900204] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2003] [Accepted: 09/22/2003] [Indexed: 05/20/2023]
Abstract
A peptide-dependent ribozyme ligase (aptazyme ligase) has been selected from a random sequence population based on the small L1 ligase. The aptazyme ligase is activated > 18,000-fold by its cognate peptide effector, the HIV-1 Rev arginine-rich motif (ARM), and specifically recognizes the Rev ARM relative to other peptides containing arginine-rich motifs. Moreover, the aptazyme ligase can preferentially recognize the Rev ARM in the context of the full-length HIV-1 Rev protein. The only cross-reactivity exhibited by the aptazyme is toward the Tat ARM. Reselection of peptide- and protein-dependent aptazymes from a partially randomized population yielded aptazymes that could readily discriminate against the Tat ARM. These results have important implications for the development of aptazymes that can be used in arrays for the detection and quantitation of multiple cellular proteins (proteome arrays).
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MESH Headings
- Amino Acid Motifs
- Arginine/metabolism
- Base Sequence
- Binding Sites
- Gene Products, rev/metabolism
- Gene Products, tat/metabolism
- HIV-1/genetics
- HIV-1/metabolism
- Humans
- In Vitro Techniques
- Ligases/chemical synthesis
- Ligases/genetics
- Ligases/metabolism
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Mutation
- Nucleic Acid Conformation
- Peptide Fragments/genetics
- Peptide Fragments/metabolism
- RNA, Catalytic/chemical synthesis
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Viral
- Selection, Genetic
- Sequence Homology, Nucleic Acid
- Substrate Specificity
- rev Gene Products, Human Immunodeficiency Virus
- tat Gene Products, Human Immunodeficiency Virus
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19
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Abstract
Switches and sensors play important roles in our everyday lives. The chemical properties of RNA make it amenable for use as a switch or sensor, both artificially and in nature. This review focuses on recent advances in artificial RNA switches and sensors. Researchers have been applying classical biochemical principles such as allostery in elegant ways that are influencing the development of biosensors and other applications. Particular attention is given here to allosteric ribozymes (aptazymes) that are regulated by small organic molecules, by proteins, or by oligonucleotides. Also discussed are ribozymes whose activities are controlled by various nonallosteric strategies.
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Affiliation(s)
- Scott K Silverman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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