1
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Zhou J, Wang J, Chen F, Zhuang Z, Chen M, Yang Y, Luo X, Tang C, Zhou X, Chi Y, Wang J, He Y, Zhang K, Zou Q. Improved USER cloning for TALE assembly and its application to base editing. PLoS One 2023; 18:e0289509. [PMID: 37540669 PMCID: PMC10403120 DOI: 10.1371/journal.pone.0289509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/19/2023] [Indexed: 08/06/2023] Open
Abstract
Transcription activator-like effectors (TALEs) have been widely used for genome editing, transcriptional regulation, and locus-specific DNA imaging. However, TALEs are difficult to handle in routine laboratories because of their complexity and the considerable time consumed in TALE construction. Here, we described a simple and rapid TALE assembly method based on uracil-specific excision reagent (USER) cloning. Polymerase chain reaction was amplified with TALE trimer templates and deoxyuridine-containing primers. The products were treated with USER at 37°C for 30 min, followed by the treatment of T4 DNA Ligase at 16°C for 30 min. The TALE trimer unit could be rejoined hierarchically to form complete TALE expression vectors with high efficiency. This method was adopted to construct TALE-deaminases, which were used in combination with Cas9 nickases to generate efficient C-to-T or A-to-G base editing while eliminating predictable DNA off-target effects. This improved USER assembly is a simple, rapid, and laboratory-friendly TALE construction technique that will be valuable for DNA targeting.
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Affiliation(s)
- Jizeng Zhou
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Jiaowei Wang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Fangbing Chen
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhenpeng Zhuang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Min Chen
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yang Yang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
| | - Xian Luo
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Chengcheng Tang
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Xiaoqing Zhou
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yue Chi
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Jinling Wang
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Yu He
- National Drug Clinical Trial Institution, Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Kun Zhang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, China
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
| | - Qingjian Zou
- Guangdong Provincial Key Laboratory of Large Animal models for Biomedicine, South China Institute of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, China
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2
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Teper D, White FF, Wang N. The Dynamic Transcription Activator-Like Effector Family of Xanthomonas. PHYTOPATHOLOGY 2023; 113:651-666. [PMID: 36449529 DOI: 10.1094/phyto-10-22-0365-kd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Transcription activator-like effectors (TALEs) are bacterial proteins that are injected into the eukaryotic nucleus to act as transcriptional factors and function as key virulence factors of the phytopathogen Xanthomonas. TALEs are translocated into plant host cells via the type III secretion system and induce the expression of host susceptibility (S) genes to facilitate disease. The unique modular DNA binding domains of TALEs comprise an array of nearly identical direct repeats that enable binding to DNA targets based on the recognition of a single nucleotide target per repeat. The very nature of TALE structure and function permits the proliferation of TALE genes and evolutionary adaptations in the host to counter TALE function, making the TALE-host interaction the most dynamic story in effector biology. The TALE genes appear to be a relatively young effector gene family, with a presence in all virulent members of some species and absent in others. Genome sequencing has revealed many TALE genes throughout the xanthomonads, and relatively few have been associated with a cognate S gene. Several species, including Xanthomonas oryzae pv. oryzae and X. citri pv. citri, have near absolute requirement for TALE gene function, while the genes appear to be just now entering the disease interactions with new fitness contributions to the pathogens of tomato and pepper among others. Deciphering the simple and effective DNA binding mechanism also has led to the development of DNA manipulation tools in fields of gene editing and transgenic research. In the three decades since their discovery, TALE research remains at the forefront of the study of bacterial evolution, plant-pathogen interactions, and synthetic biology. We also discuss critical questions that remain to be addressed regarding TALEs.
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Affiliation(s)
- Doron Teper
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Frank F White
- Department of Plant Pathology, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Gainesville, FL, U.S.A
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, U.S.A
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3
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Abstract
Transcription activator-like effector (TALE) nuclease (TALEN) is the second-generation genome editing tool consisting of TALE protein containing customizable DNA-binding repeats and nuclease domain of FokI enzyme. Each DNA-binding repeat recognizes one base of double-strand DNA, and functional TALEN can be created by a simple modular assembly of these repeats. To easily and efficiently assemble the highly repetitive DNA-binding repeat arrays, various construction systems such as Golden Gate assembly, serial ligation, and ligation-independent cloning have been reported. In this chapter, we summarize the updated situation of these systems and publicly available reagents and protocols, enabling optimal selection of best suited systems for every researcher who wants to utilize TALENs in various research fields.
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Affiliation(s)
- Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.
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4
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Villalobos-López MA, Arroyo-Becerra A, Quintero-Jiménez A, Iturriaga G. Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops. Int J Mol Sci 2022; 23:12053. [PMID: 36233352 PMCID: PMC9570234 DOI: 10.3390/ijms231912053] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/02/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops are not tolerant to extreme climatic environments. The aim in the near future, in a world with hunger and an increasing population, is to breed and/or engineer crops to tolerate abiotic stress with a higher yield. Some crop varieties display a certain degree of tolerance, which has been exploited by plant breeders to develop varieties that thrive under stress conditions. Moreover, a long list of genes involved in abiotic stress tolerance have been identified and characterized by molecular techniques and overexpressed individually in plant transformation experiments. Nevertheless, stress tolerance phenotypes are polygenetic traits, which current genomic tools are dissecting to exploit their use by accelerating genetic introgression using molecular markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe plant mechanisms to sense and tolerate adverse climate conditions and examine and discuss classic and new molecular tools to select and improve abiotic stress tolerance in major crops.
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Affiliation(s)
- Miguel Angel Villalobos-López
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Ex-Hacienda San Juan Molino Carretera Estatal Km 1.5, Santa Inés-Tecuexcomac-Tepetitla 90700, Tlaxcala, Mexico
| | - Analilia Arroyo-Becerra
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Ex-Hacienda San Juan Molino Carretera Estatal Km 1.5, Santa Inés-Tecuexcomac-Tepetitla 90700, Tlaxcala, Mexico
| | - Anareli Quintero-Jiménez
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México/I.T. Roque, Km. 8 Carretera Celaya-Juventino Rosas, Roque, Celaya 38110, Guanajato, Mexico
| | - Gabriel Iturriaga
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México/I.T. Roque, Km. 8 Carretera Celaya-Juventino Rosas, Roque, Celaya 38110, Guanajato, Mexico
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5
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Cheng L, Zhou X, Zheng Y, Tang C, Liu Y, Zheng S, Liu Y, Zhou J, Li C, Chen M, Lai L, Zou Q. Simple and Rapid Assembly of TALE Modules Based on the Degeneracy of the Codons and Trimer Repeats. Genes (Basel) 2021; 12:genes12111761. [PMID: 34828367 PMCID: PMC8621181 DOI: 10.3390/genes12111761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/15/2022] Open
Abstract
Transcription activator-like effectors (TALEs) have been effectively used for targeted genome editing, transcriptional regulation, epigenetic modification, and locus-specific DNA imaging. However, with the advent of the clustered regularly interspaced short palindromic repeat/Cas9 system, an easy-to-use tool with the same function as TALEs, TALEs have recently been abandoned because of their complexity, time consumption, and difficult handling in common labs. Here, we described a degenerated codon-based TALE assembly system for simple, rapid, and efficient TALE assembly. TALE trimers with nonrepetitive DNA sequences were amplified by PCR and sequentially assembled via Gibson assembly. Our method is cost-effective, requires only commonly used basic molecular biology reagents, and takes only 2 h from target sequence analysis to completion. This simple, rapid, and lab-friendly TALE assembly method will restore the value of TALEs in DNA targeting.
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Affiliation(s)
- Lingyin Cheng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (L.C.); (X.Z.); (Y.Z.); (C.T.); (Y.L.); (S.Z.); (C.L.); (M.C.)
| | - Xiaoqing Zhou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (L.C.); (X.Z.); (Y.Z.); (C.T.); (Y.L.); (S.Z.); (C.L.); (M.C.)
| | - Yuling Zheng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (L.C.); (X.Z.); (Y.Z.); (C.T.); (Y.L.); (S.Z.); (C.L.); (M.C.)
| | - Chengcheng Tang
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (L.C.); (X.Z.); (Y.Z.); (C.T.); (Y.L.); (S.Z.); (C.L.); (M.C.)
| | - Yu Liu
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (L.C.); (X.Z.); (Y.Z.); (C.T.); (Y.L.); (S.Z.); (C.L.); (M.C.)
| | - Shuwen Zheng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (L.C.); (X.Z.); (Y.Z.); (C.T.); (Y.L.); (S.Z.); (C.L.); (M.C.)
| | - Yang Liu
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China;
| | - Jizeng Zhou
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510643, China;
| | - Chuan Li
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (L.C.); (X.Z.); (Y.Z.); (C.T.); (Y.L.); (S.Z.); (C.L.); (M.C.)
| | - Min Chen
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (L.C.); (X.Z.); (Y.Z.); (C.T.); (Y.L.); (S.Z.); (C.L.); (M.C.)
| | - Liangxue Lai
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (L.C.); (X.Z.); (Y.Z.); (C.T.); (Y.L.); (S.Z.); (C.L.); (M.C.)
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China;
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510643, China;
- Correspondence: (L.L.); (Q.Z.)
| | - Qingjian Zou
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; (L.C.); (X.Z.); (Y.Z.); (C.T.); (Y.L.); (S.Z.); (C.L.); (M.C.)
- Correspondence: (L.L.); (Q.Z.)
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6
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Di Blasi R, Zouein A, Ellis T, Ceroni F. Genetic Toolkits to Design and Build Mammalian Synthetic Systems. Trends Biotechnol 2021; 39:1004-1018. [PMID: 33526300 DOI: 10.1016/j.tibtech.2020.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 11/17/2022]
Abstract
Construction of DNA-encoded programs is central to synthetic biology and the chosen method often determines the time required to design and build constructs for testing. Here, we describe and summarise key features of the available toolkits for DNA construction for mammalian cells. We compare the different cloning strategies based on their complexity and the time needed to generate constructs of different sizes, and we reflect on why Golden Gate toolkits now dominate due to their modular design. We look forward to future advances, including accessory packs for cloning toolkits that can facilitate editing, orthogonality, advanced regulation, and integration into synthetic chromosome construction.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Annalise Zouein
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK; Department of Bioengineering, Imperial College London, South Kensington Campus, London, UK
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK; Department of Bioengineering, Imperial College London, South Kensington Campus, London, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK.
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7
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Xie SS, Qiu XY, Zhu LY, Zhu CS, Liu CY, Wu XM, Zhu L, Zhang DY. Assembly of TALE-based DNA scaffold for the enhancement of exogenous multi-enzymatic pathway. J Biotechnol 2019; 296:69-74. [DOI: 10.1016/j.jbiotec.2019.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/11/2019] [Accepted: 03/14/2019] [Indexed: 10/27/2022]
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8
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Heiderscheit EA, Eguchi A, Spurgat MC, Ansari AZ. Reprogramming cell fate with artificial transcription factors. FEBS Lett 2018; 592:888-900. [PMID: 29389011 DOI: 10.1002/1873-3468.12993] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/15/2018] [Accepted: 01/24/2018] [Indexed: 01/10/2023]
Abstract
Transcription factors (TFs) reprogram cell states by exerting control over gene regulatory networks and the epigenetic landscape of a cell. Artificial transcription factors (ATFs) are designer regulatory proteins comprised of modular units that can be customized to overcome challenges faced by natural TFs in establishing and maintaining desired cell states. Decades of research on DNA-binding proteins and synthetic molecules has provided a molecular toolkit for ATF design and the construction of genome-scale libraries of ATFs capable of phenotypic manipulation and reprogramming of cell states. Here, we compare the unique strengths and limitations of different ATF platforms, highlight the advantages of cooperative assembly, and present the potential of ATF libraries in revealing gene regulatory networks that govern cell fate choices.
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Affiliation(s)
- Evan A Heiderscheit
- Department of Biochemistry, University of Wisconsin - Madison, WI, USA.,The Genome Center of Wisconsin, University of Wisconsin - Madison, WI, USA
| | - Asuka Eguchi
- Department of Biochemistry, University of Wisconsin - Madison, WI, USA.,The Genome Center of Wisconsin, University of Wisconsin - Madison, WI, USA
| | - Mackenzie C Spurgat
- Department of Biochemistry, University of Wisconsin - Madison, WI, USA.,The Genome Center of Wisconsin, University of Wisconsin - Madison, WI, USA
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin - Madison, WI, USA.,The Genome Center of Wisconsin, University of Wisconsin - Madison, WI, USA
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9
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Gogolok S, Köber U, Pollard SM. STAR: A Simple TAL Effector Assembly Reaction Using Isothermal Assembly. Methods Mol Biol 2018; 1772:477-490. [PMID: 29754248 DOI: 10.1007/978-1-4939-7795-6_29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Transcription activator-like effectors (TALEs) contain programmable DNA-binding domains that can be fused to various effectors to manipulate genetic sequences or transcriptional state. However, the construction of plasmids encoding the modular DNA-binding domain remains challenging due to their repetitive nature. Here, we describe methods for a simple TALE assembly reaction (STAR) that uses a 68-part plasmid library to create TALEs binding to 17 bp target sequences. Manual production of many tens of TALEs can be achieved using a simple 8 h protocol, with full length sequence-verified plasmids available within a few days. This simple tale assembly reaction (STAR) provides a convenient method for generating tens to hundreds of TALENs or TALE-TFs without the need for large plasmid libraries or expensive liquid handling.
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Affiliation(s)
- Sabine Gogolok
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Ute Köber
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK.
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10
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Machens F, Balazadeh S, Mueller-Roeber B, Messerschmidt K. Synthetic Promoters and Transcription Factors for Heterologous Protein Expression in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2017; 5:63. [PMID: 29098147 PMCID: PMC5653697 DOI: 10.3389/fbioe.2017.00063] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/29/2017] [Indexed: 12/19/2022] Open
Abstract
Orthogonal systems for heterologous protein expression as well as for the engineering of synthetic gene regulatory circuits in hosts like Saccharomyces cerevisiae depend on synthetic transcription factors (synTFs) and corresponding cis-regulatory binding sites. We have constructed and characterized a set of synTFs based on either transcription activator-like effectors or CRISPR/Cas9, and corresponding small synthetic promoters (synPs) with minimal sequence identity to the host’s endogenous promoters. The resulting collection of functional synTF/synP pairs confers very low background expression under uninduced conditions, while expression output upon induction of the various synTFs covers a wide range and reaches induction factors of up to 400. The broad spectrum of expression strengths that is achieved will be useful for various experimental setups, e.g., the transcriptional balancing of expression levels within heterologous pathways or the construction of artificial regulatory networks. Furthermore, our analyses reveal simple rules that enable the tuning of synTF expression output, thereby allowing easy modification of a given synTF/synP pair. This will make it easier for researchers to construct tailored transcriptional control systems.
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Affiliation(s)
- Fabian Machens
- University of Potsdam, Cell2Fab Research Unit, Potsdam, Germany
| | - Salma Balazadeh
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Department Molecular Biology, University of Potsdam, Potsdam, Germany
| | - Bernd Mueller-Roeber
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Department Molecular Biology, University of Potsdam, Potsdam, Germany
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11
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Lo CL, Choudhury SR, Irudayaraj J, Zhou FC. Epigenetic Editing of Ascl1 Gene in Neural Stem Cells by Optogenetics. Sci Rep 2017; 7:42047. [PMID: 28181538 PMCID: PMC5299429 DOI: 10.1038/srep42047] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 01/09/2017] [Indexed: 11/09/2022] Open
Abstract
Enzymes involved in epigenetic processes such as methyltransferases or demethylases are becoming highly utilized for their persistent DNA or histone modifying efficacy. Herein, we have developed an optogenetic toolbox fused to the catalytic domain (CD) of DNA-methyltransferase3A (DNMT3A-CD) or Ten-Eleven Dioxygenase-1 (TET1-CD) for loci-specific alteration of the methylation state at the promoter of Ascl1 (Mash1), a candidate proneuron gene. Optogenetical protein pairs, CRY2 linked to DNMT3A-CD or TET1-CD and CIB1 fused to a Transcription Activator-Like Element (TALE) locating an Ascl1 promoter region, were designed for site specific epigenetic editing. A differentially methylated region at the Ascl1 promoter, isolated from murine dorsal root ganglion (hypermethylated) and striated cells (hypomethylated), was targeted with these optogenetic-epigenetic constructs. Optimized blue-light illumination triggered the co-localization of TALE constructs with DNMT3A-CD or TET1-CD fusion proteins at the targeted site of the Ascl1 promoter. We found that this spatiotemporal association of the fusion proteins selectively alters the methylation state and also regulates gene activity. This proof of concept developed herein holds immense promise for the ability to regulate gene activity via epigenetic modulation with spatiotemporal precision.
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Affiliation(s)
- Chiao-Ling Lo
- Department of Anatomy &Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Samrat Roy Choudhury
- Bindley Bioscience Center, Department of Agricultural &Biological Engineering, Purdue University, West Lafayette, IN, USA
| | - Joseph Irudayaraj
- Bindley Bioscience Center, Department of Agricultural &Biological Engineering, Purdue University, West Lafayette, IN, USA
| | - Feng C Zhou
- Department of Anatomy &Cell Biology, Indiana University School of Medicine, Indianapolis, IN, USA.,Stark Institute of Neuroscience Research, Indiana University School of Medicine, Indianapolis, IN, USA
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12
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Abstract
Transcription activator-like effector (TALE) nuclease (TALEN) is the second-generation genome editing tool consisting of TALE protein containing customizable DNA-binding repeats and nuclease domain of FokI enzyme. Each DNA-binding repeat recognizes one base of double-strand DNA, and functional TALEN can be created by a simple modular assembly of these repeats. To easily and efficiently assemble the highly repetitive DNA-binding repeat arrays, various construction systems such as Golden Gate assembly, serial ligation, and ligation-independent cloning have been reported. In this chapter, we summarize the current situation of these systems and publically available reagents and protocols, enabling optimal selection of best suited systems for every researcher who wants to utilize TALENs in various research fields.
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Affiliation(s)
- Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
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