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Perez-Quintero AL, Szurek B. A Decade Decoded: Spies and Hackers in the History of TAL Effectors Research. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:459-481. [PMID: 31387457 DOI: 10.1146/annurev-phyto-082718-100026] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Transcription activator-like effectors (TALEs) from the genus Xanthomonas are proteins with the remarkable ability to directly bind the promoters of genes in the plant host to induce their expression, which often helps bacterial colonization. Metaphorically, TALEs act as spies that infiltrate the plant disguised as high-ranking civilians (transcription factors) to trick the plant into activating weak points that allow an invasion. Current knowledge of how TALEs operate allows researchers to predict their activity (counterespionage) and exploit their function, engineering them to do our bidding (a Manchurian agent). This has been possible thanks particularly to the discovery of their DNA binding mechanism, which obeys specific amino acid-DNA correspondences (the TALE code). Here, we review the history of how researchers discovered the way these proteins work and what has changed in the ten years since the discovery of the code. Recommended music for reading this review can be found in the Supplemental Material.
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Affiliation(s)
- Alvaro L Perez-Quintero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523-1177, USA;
- IRD, CIRAD, Université Montpellier, IPME, 34000 Montpellier, France;
| | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, 34000 Montpellier, France;
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Ma Y, Wang M, Li W, Zhang Z, Zhang X, Tan T, Zhang XE, Cui Z. Live cell imaging of single genomic loci with quantum dot-labeled TALEs. Nat Commun 2017; 8:15318. [PMID: 28480886 PMCID: PMC5424152 DOI: 10.1038/ncomms15318] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 03/10/2017] [Indexed: 12/22/2022] Open
Abstract
Single genomic loci are often related to specific cellular functions, genetic diseases, or pathogenic infections. Visualization of single genomic loci in live human cells is currently of great interest, yet it remains challenging. Here, we describe a strategy for live cell imaging of single genomic loci by combining transcription activator-like effectors (TALEs) with a quantum dot labelling technique. We design and select a pair of TALEs that specifically target HIV-1 proviral DNA sequences, and use bioorthogonal ligation reactions to label them with different colour quantum dots (QDs). These QD-labelled TALEs are able to enter the cell nucleus to provide fluorescent signals to identify single gene loci. Based on the co-localization of the pair of different coloured QD-labelled TALEs, we determine and map single-copy HIV-1 provirus loci in human chromosomes in live host cells.
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Affiliation(s)
- Yingxin Ma
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China.,Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mingxiu Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Wei Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhiping Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xiaowei Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Tianwei Tan
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xian-En Zhang
- CAS Center for Biological Macromolecules, National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
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Hu H, Zhang H, Wang S, Ding M, An H, Hou Y, Yang X, Wei W, Sun Y, Tang C. Live visualization of genomic loci with BiFC-TALE. Sci Rep 2017; 7:40192. [PMID: 28074901 PMCID: PMC5225478 DOI: 10.1038/srep40192] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 12/02/2016] [Indexed: 11/08/2022] Open
Abstract
Tracking the dynamics of genomic loci is important for understanding the mechanisms of fundamental intracellular processes. However, fluorescent labeling and imaging of such loci in live cells have been challenging. One of the major reasons is the low signal-to-background ratio (SBR) of images mainly caused by the background fluorescence from diffuse full-length fluorescent proteins (FPs) in the living nucleus, hampering the application of live cell genomic labeling methods. Here, combining bimolecular fluorescence complementation (BiFC) and transcription activator-like effector (TALE) technologies, we developed a novel method for labeling genomic loci (BiFC-TALE), which largely reduces the background fluorescence level. Using BiFC-TALE, we demonstrated a significantly improved SBR by imaging telomeres and centromeres in living cells in comparison with the methods using full-length FP.
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Affiliation(s)
- Huan Hu
- School of Life Sciences, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Hongmin Zhang
- School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, People’s Republic of China
| | - Sheng Wang
- School of Life Sciences, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
| | - Miao Ding
- School of Life Sciences, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
| | - Hui An
- School of Life Sciences, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Yingping Hou
- School of Life Sciences, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
| | - Xiaojing Yang
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Wensheng Wei
- School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, People’s Republic of China
| | - Yujie Sun
- School of Life Sciences, Peking University, Beijing 100871, China
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system, a versatile RNA-guided DNA targeting platform, has been revolutionizing our ability to modify, manipulate, and visualize the human genome, which greatly advances both biological research and therapeutics development. Here, we review the current development of CRISPR/Cas9 technologies for gene editing, transcription regulation, genome imaging, and epigenetic modification. We discuss the broad application of this system to the study of functional genomics, especially genome-wide genetic screening, and to therapeutics development, including establishing disease models, correcting defective genetic mutations, and treating diseases.
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Affiliation(s)
- Xin Xiong
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158; ,
| | - Meng Chen
- Department of Bioengineering, Stanford University, Stanford, California 94305; ,
- Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305
- ChEM-H, Stanford University, Stanford, California 94305
- Gladstone Institute of Cardiovascular Disease, San Francisco, California 94158;
| | - Wendell A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158; ,
| | - Dehua Zhao
- Department of Bioengineering, Stanford University, Stanford, California 94305; ,
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, California 94305; ,
- Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305
- ChEM-H, Stanford University, Stanford, California 94305
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Shao S, Zhang W, Hu H, Xue B, Qin J, Sun C, Sun Y, Wei W, Sun Y. Long-term dual-color tracking of genomic loci by modified sgRNAs of the CRISPR/Cas9 system. Nucleic Acids Res 2016; 44:e86. [PMID: 26850639 PMCID: PMC4872083 DOI: 10.1093/nar/gkw066] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 01/17/2016] [Accepted: 01/25/2016] [Indexed: 12/13/2022] Open
Abstract
Visualization of chromosomal dynamics is important for understanding many fundamental intra-nuclear processes. Efficient and reliable live-cell multicolor labeling of chromosomal loci can realize this goal. However, the current methods are constrained mainly by insufficient labeling throughput, efficiency, flexibility as well as photostability. Here we have developed a new approach to realize dual-color chromosomal loci imaging based on a modified single-guide RNA (sgRNA) of the CRISPR/Cas9 system. The modification of sgRNA was optimized by structure-guided engineering of the original sgRNA, consisting of RNA aptamer insertions that bind fluorescent protein-tagged effectors. By labeling and tracking telomeres, centromeres and genomic loci, we demonstrate that the new approach is easy to implement and enables robust dual-color imaging of genomic elements. Importantly, our data also indicate that the fast exchange rate of RNA aptamer binding effectors makes our sgRNA-based labeling method much more tolerant to photobleaching than the Cas9-based labeling method. This is crucial for continuous, long-term tracking of chromosomal dynamics. Lastly, as our method is complementary to other live-cell genomic labeling systems, it is therefore possible to combine them into a plentiful palette for the study of native chromatin organization and genome ultrastructure dynamics in living cells.
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Affiliation(s)
- Shipeng Shao
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Weiwei Zhang
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Huan Hu
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Jinshan Qin
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Chaoying Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yuao Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Wensheng Wei
- Biodynamic Optical Imaging Center (BIOPIC), Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
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Tanaka A, Fukuoka Y, Morimoto Y, Honjo T, Koda D, Goto M, Maruyama T. Cancer cell death induced by the intracellular self-assembly of an enzyme-responsive supramolecular gelator. J Am Chem Soc 2015; 137:770-5. [PMID: 25521540 DOI: 10.1021/ja510156v] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report cancer cell death initiated by the intracellular molecular self-assembly of a peptide lipid, which was derived from a gelator precursor. The gelator precursor was designed to form nanofibers via molecular self-assembly, after cleavage by a cancer-related enzyme (matrix metalloproteinase-7, MMP-7), leading to hydrogelation. The gelator precursor exhibited remarkable cytotoxicity to five different cancer cell lines, while the precursor exhibited low cytotoxicity to normal cells. Cancer cells secrete excessive amounts of MMP-7, which converted the precursor into a supramolecular gelator prior to its uptake by the cells. Once inside the cells, the supramolecular gelator formed a gel via molecular self-assembly, exerting vital stress on the cancer cells. The present study thus describes a new drug where molecular self-assembly acts as the mechanism of cytotoxicity.
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Affiliation(s)
- Akiko Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University , 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan
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