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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. MOLECULAR THERAPY. 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] [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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Abstract
Toxin-antitoxin systems are widespread in bacterial genomes. They are usually composed of two elements: a toxin that inhibits an essential cellular process and an antitoxin that counteracts its cognate toxin. In the past decade, a number of new toxin-antitoxin systems have been described, bringing new growth inhibition mechanisms to light as well as novel modes of antitoxicity. However, recent advances in the field profoundly questioned the role of these systems in bacterial physiology, stress response and antimicrobial persistence. This shifted the paradigm of the functions of toxin-antitoxin systems to roles related to interactions between hosts and their mobile genetic elements, such as viral defence or plasmid stability. In this Review, we summarize the recent progress in understanding the biology and evolution of these small genetic elements, and discuss how genomic conflicts could shape the diversification of toxin-antitoxin systems.
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Huang X, Chen R, Sun M, Peng Y, Pu Q, Yuan Y, Chen G, Dong J, Du F, Cui X, Tang Z. Frame-shifted proteins of a given gene retain the same function. Nucleic Acids Res 2020; 48:4396-4404. [PMID: 32187359 PMCID: PMC7192591 DOI: 10.1093/nar/gkaa169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 01/21/2023] Open
Abstract
Frameshift mutations are generally considered to be lethal because it could result in radical changes of the protein sequence behind. However, the protein of frameshift mutants of a type I toxin (ibsc) was found to be still toxic to bacteria, retaining the similar function as wild-type protein to arrest the cellular growth by impairing the membrane's integrity. Additionally, we have verified that this observation is not an individual event as the same phenomenon had been found in other toxins subsequently. After analyzing the coding sequence of these genes, we proposed a hypothesis to search this kind of hidden gene, through which a dihydrofolate reductase-encoding gene (dfrB3) was found out. Like the wild-type reductase, both +1 and -1 frame-shifted proteins of dfrB3 gene were also proved to catalyze the reduction of dihydrofolate to tetrahydrofolate by using NADPH.
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Affiliation(s)
- Xin Huang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Rong Chen
- Ethnomedicine College, Chengdu University of Traditional Chinese Medicine, Chengdu 610041, P. R. China
| | - Meiling Sun
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Yan Peng
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Qinlin Pu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
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Pu Q, Zhou S, Huang X, Yuan Y, Du F, Dong J, Chen G, Cui X, Tang Z. Intracellular Selection of Theophylline-Sensitive Hammerhead Aptazyme. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:400-408. [PMID: 32244167 PMCID: PMC7118274 DOI: 10.1016/j.omtn.2020.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/14/2020] [Accepted: 03/10/2020] [Indexed: 12/14/2022]
Abstract
Hammerhead ribozyme-based aptazyme (HHAz), inheriting the advantages of small size and high efficiency from the RNA-cleaving ribozyme and the specific recognition ability of aptamers to specific targets, exhibits the huge potential to be a transgene expression regulator. Herein, we report a selection strategy for HHAz by using a toxin protein IbsC as the reporter to offer a positive phenotype, thus realizing an easy-operating, time- and labor-saving selection of HHAz variants with desired properties. Based on this strategy, we obtained a new HHAz (TAP-1), which could react sensitively toward the extracellular regulatory molecule, theophylline, both in prokaryotic and eukaryotic systems. With fluorescent protein reporter, the intracellular switching efficiencies of TAP-1 and other reported theophylline-dependent HHAzs has been quantitatively evaluated, showing that TAP-1 not only exhibits the best downregulating ability at high concentration of theophylline but also maintains high activity with 0.1 mM theophylline, which is a safe concentration in the human body.
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Affiliation(s)
- Qinlin Pu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China; University of Chinese Academy of Sciences, Beijing 10049, P.R. China
| | - Shan Zhou
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China; University of Chinese Academy of Sciences, Beijing 10049, P.R. China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Yi Yuan
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China.
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Huang X, Zhao Y, Pu Q, Liu G, Peng Y, Wang F, Chen G, Sun M, Du F, Dong J, Cui X, Tang Z, Mo X. Intracellular selection of trans-cleaving hammerhead ribozymes. Nucleic Acids Res 2019; 47:2514-2522. [PMID: 30649474 PMCID: PMC6412130 DOI: 10.1093/nar/gkz018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 01/06/2019] [Accepted: 01/08/2019] [Indexed: 02/05/2023] Open
Abstract
Hammerhead ribozyme is the smallest and best characterized catalytic RNA-cleaving ribozyme. It has been reported as potential therapeutic tools to manipulate the expression of target genes. However, most of naturally occurring hammerhead ribozymes process self-cleavage rather than cleave substrate RNA in trans, and its high intracellular activity relies on the tertiary interaction of Loop II and steam I bulge, resulting in decreased performance as applied in gene silencing. We described a direct intracellular selection method to evolve hammerhead variants based on trans-cleavage mode via using a toxin gene as the reporter. And a dual fluorescence proteins system has also been established to quantitatively evaluate the efficiency of selected ribozymes in the cell. Based on this selection strategy, we obtained three mutants with enhanced intracellular cleaving activity compared to wide type hammerhead ribozyme. The best one, TX-2 was revealed to possess better and consistent gene knockdown ability at different positions on diverse targeted mRNA either in prokaryotic or eukaryotic cells than wild-type hammerhead ribozyme. These observations imply the efficiency of the intracellular selection method of the trans-acting ribozyme and the potentials of improved ribozyme variants for research and therapeutic purposes.
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Affiliation(s)
- Xin Huang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Yongyun Zhao
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, P.R. China
| | - Qinlin Pu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Getong Liu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Yan Peng
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Fei Wang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Meiling Sun
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Xianming Mo
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, P.R. China
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Brielle R, Pinel-Marie ML, Felden B. Linking bacterial type I toxins with their actions. Curr Opin Microbiol 2016; 30:114-121. [PMID: 26874964 DOI: 10.1016/j.mib.2016.01.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 01/12/2023]
Abstract
Bacterial type I toxin-antitoxin systems consist of stable toxin-encoding mRNAs whose expression is counteracted by unstable RNA antitoxins. Accumulating evidence suggests that these players belong to broad regulatory networks influencing overall bacterial physiology. The majority of known transmembrane type I toxic peptides have conserved structural characteristics. However, recent studies demonstrated that their mechanisms of toxicity are diverse and complex. To better assess the current state of the art, type I toxins can be grouped into two classes according to their location and mechanisms of action: membrane-associated toxins acting by pore formation and/or by nucleoid condensation; and cytosolic toxins inducing nucleic acid cleavage. This classification will evolve as a result of future investigations.
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Affiliation(s)
- Régine Brielle
- Inserm U835-Upres EA2311, Pharmaceutical Biochemistry Lab, University of Rennes 1, 2 av. du Prof. Léon Bernard, 35000 Rennes, France
| | - Marie-Laure Pinel-Marie
- Inserm U835-Upres EA2311, Pharmaceutical Biochemistry Lab, University of Rennes 1, 2 av. du Prof. Léon Bernard, 35000 Rennes, France.
| | - Brice Felden
- Inserm U835-Upres EA2311, Pharmaceutical Biochemistry Lab, University of Rennes 1, 2 av. du Prof. Léon Bernard, 35000 Rennes, France.
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Barbosa LCB, Garrido SS, Marchetto R. BtoxDB: a comprehensive database of protein structural data on toxin-antitoxin systems. Comput Biol Med 2015; 58:146-53. [PMID: 25656309 DOI: 10.1016/j.compbiomed.2015.01.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 01/11/2015] [Accepted: 01/12/2015] [Indexed: 11/28/2022]
Abstract
PURPOSE Toxin-antitoxin (TA) systems are diverse and abundant genetic modules in prokaryotic cells that are typically formed by two genes encoding a stable toxin and a labile antitoxin. Because TA systems are able to repress growth or kill cells and are considered to be important actors in cell persistence (multidrug resistance without genetic change), these modules are considered potential targets for alternative drug design. In this scenario, structural information for the proteins in these systems is highly valuable. In this report, we describe the development of a web-based system, named BtoxDB, that stores all protein structural data on TA systems. METHODS The BtoxDB database was implemented as a MySQL relational database using PHP scripting language. Web interfaces were developed using HTML, CSS and JavaScript. The data were collected from the PDB, UniProt and Entrez databases. These data were appropriately filtered using specialized literature and our previous knowledge about toxin-antitoxin systems. RESULTS The database provides three modules ("Search", "Browse" and "Statistics") that enable searches, acquisition of contents and access to statistical data. Direct links to matching external databases are also available. CONCLUSIONS The compilation of all protein structural data on TA systems in one platform is highly useful for researchers interested in this content. BtoxDB is publicly available at http://www.gurupi.uft.edu.br/btoxdb.
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Affiliation(s)
- Luiz Carlos Bertucci Barbosa
- UFT - Federal University of Tocantins, Department of Biotechnology, Caixa Postal 66, Gurupi 77402-970, Tocantins, Brazil.
| | - Saulo Santesso Garrido
- UNESP - Universidade Estadual Paulista, Institute of Chemistry, Department of Biochemistry and Technological Chemistry, Araraquara 14800-000, São Paulo, Brazil
| | - Reinaldo Marchetto
- UNESP - Universidade Estadual Paulista, Institute of Chemistry, Department of Biochemistry and Technological Chemistry, Araraquara 14800-000, São Paulo, Brazil
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Wang J, Xu R, Liu A. IRDL cloning: a one-tube, zero-background, easy-to-use, directional cloning method improves throughput in recombinant DNA preparation. PLoS One 2014; 9:e107907. [PMID: 25243603 PMCID: PMC4171505 DOI: 10.1371/journal.pone.0107907] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 08/20/2014] [Indexed: 11/19/2022] Open
Abstract
Rapid and efficient construction of expression vectors and subsequent transformation are basic recombinant methods for the investigation of gene functionality. Although novel cloning methods have recently been developed, many laboratories worldwide continue to use traditional restriction digestion-ligation methods to construct expression vectors owing to financial constraints and the unavailability of appropriate vectors. We describe an improved restriction digestion-ligation (IRDL) cloning method that combines the advantage of directional cloning from double digestion-ligation with that of a low background observed by using a positive selection marker gene ccdB to facilitate digestion and ligation in a single tube. The IRDL cloning overcomes the time-consuming and laborious limits of traditional methods, thereby providing an easy-to-use, low-cost, and one-step strategy for directional cloning of target DNA fragments into an expression vector. As a proof-of-concept example, we developed two yeast vectors to demonstrate the feasibility and the flexibility of the IRDL cloning method. This method would provide an effective and easy-to-use system for gene cloning and functional genomics studies.
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Affiliation(s)
- Jiancai Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, People's Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, People's Republic of China
| | - Ronghua Xu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, People's Republic of China
| | - Aizhong Liu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, People's Republic of China
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Kunming, People's Republic of China
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Tee KL, Wong TS. Polishing the craft of genetic diversity creation in directed evolution. Biotechnol Adv 2013; 31:1707-21. [PMID: 24012599 DOI: 10.1016/j.biotechadv.2013.08.021] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 08/31/2013] [Accepted: 08/31/2013] [Indexed: 12/25/2022]
Abstract
Genetic diversity creation is a core technology in directed evolution where a high quality mutant library is crucial to its success. Owing to its importance, the technology in genetic diversity creation has seen rapid development over the years and its application has diversified into other fields of scientific research. The advances in molecular cloning and mutagenesis since 2008 were reviewed. Specifically, new cloning techniques were classified based on their principles of complementary overhangs, homologous sequences, overlapping PCR and megaprimers and the advantages, drawbacks and performances of these methods were highlighted. New mutagenesis methods developed for random mutagenesis, focused mutagenesis and DNA recombination were surveyed. The technical requirements of these methods and the mutational spectra were compared and discussed with references to commonly used techniques. The trends of mutant library preparation were summarised. Challenges in genetic diversity creation were discussed with emphases on creating "smart" libraries, controlling the mutagenesis spectrum and specific challenges in each group of mutagenesis methods. An outline of the wider applications of genetic diversity creation includes genome engineering, viral evolution, metagenomics and a study of protein functions. The review ends with an outlook for genetic diversity creation and the prospective developments that can have future impact in this field.
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Affiliation(s)
- Kang Lan Tee
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, England, United Kingdom
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