1
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Su GM, Chu LW, Chien CC, Liao PS, Chiu YC, Chang CH, Chu TH, Li CH, Wu CS, Wang JF, Cheng YS, Chang CH, Cheng CP. Tomato NADPH oxidase SlWfi1 interacts with the effector protein RipBJ of Ralstonia solanacearum to mediate host defence. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39132878 DOI: 10.1111/pce.15086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/30/2024] [Accepted: 07/31/2024] [Indexed: 08/13/2024]
Abstract
Reactive oxygen species (ROS) play a crucial role in regulating numerous functions in organisms. Among the key regulators of ROS production are NADPH oxidases, primarily referred to as respiratory burst oxidase homologues (RBOHs). However, our understanding of whether and how pathogens directly target RBOHs has been limited. In this study, we revealed that the effector protein RipBJ, originating from the phytopathogenic bacterium Ralstonia solanacearum, was present in low- to medium-virulence strains but absent in high-virulence strains. Functional genetic assays demonstrated that the expression of ripBJ led to a reduction in bacterial infection. In the plant, RipBJ expression triggered plant cell death and the accumulation of H2O2, while also enhancing host defence against R. solanacearum by modulating multiple defence signalling pathways. Through protein interaction and functional studies, we demonstrated that RipBJ was associated with the plant's plasma membrane and interacted with the tomato RBOH known as SlWfi1, which contributed positively to RipBJ's effects on plants. Importantly, SlWfi1 expression was induced during the early stages following R. solanacearum infection and played a key role in defence against this bacterium. This research uncovers the plant RBOH as an interacting target of a pathogen's effector, providing valuable insights into the mechanisms of plant defence.
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Affiliation(s)
- Guan-Ming Su
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Li-Wen Chu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chih-Cheng Chien
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
- Institute of Ecology and Evolutionary Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Pei-Shan Liao
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yu-Chuan Chiu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chi-Hsin Chang
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Tai-Hsiang Chu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chien-Hui Li
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chien-Sheng Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Jaw-Fen Wang
- Bacteriology Unit, AVRDC-The World Vegetable Center, Tainan, Taiwan
| | - Yi-Sheng Cheng
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
- Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Chuan-Hsin Chang
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
| | - Chiu-Ping Cheng
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
- Department of Life Science, College of Life Science, National Taiwan University, Taipei, Taiwan
- Global Agriculture Technology and Genomic Science Master Program, International College, National Taiwan University, Taipei, Taiwan
- Master Program for Plant Medicine, College of Bio-Resources & Agriculture, National Taiwan University, Taipei, Taiwan
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2
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Singh C, Kumar R, Sehgal H, Bhati S, Singhal T, Gayacharan, Nimmy MS, Yadav R, Gupta SK, Abdallah NA, Hamwieh A, Kumar R. Unclasping potentials of genomics and gene editing in chickpea to fight climate change and global hunger threat. Front Genet 2023; 14:1085024. [PMID: 37144131 PMCID: PMC10153629 DOI: 10.3389/fgene.2023.1085024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/24/2023] [Indexed: 09/09/2023] Open
Abstract
Genomics and genome editing promise enormous opportunities for crop improvement and elementary research. Precise modification in the specific targeted location of a genome has profited over the unplanned insertional events which are generally accomplished employing unadventurous means of genetic modifications. The advent of new genome editing procedures viz; zinc finger nucleases (ZFNs), homing endonucleases, transcription activator like effector nucleases (TALENs), Base Editors (BEs), and Primer Editors (PEs) enable molecular scientists to modulate gene expressions or create novel genes with high precision and efficiency. However, all these techniques are exorbitant and tedious since their prerequisites are difficult processes that necessitate protein engineering. Contrary to first generation genome modifying methods, CRISPR/Cas9 is simple to construct, and clones can hypothetically target several locations in the genome with different guide RNAs. Following the model of the application in crop with the help of the CRISPR/Cas9 module, various customized Cas9 cassettes have been cast off to advance mark discrimination and diminish random cuts. The present study discusses the progression in genome editing apparatuses, and their applications in chickpea crop development, scientific limitations, and future perspectives for biofortifying cytokinin dehydrogenase, nitrate reductase, superoxide dismutase to induce drought resistance, heat tolerance and higher yield in chickpea to encounter global climate change, hunger and nutritional threats.
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Affiliation(s)
- Charul Singh
- USBT, Guru Govind Singh Indraprastha University, Delhi, India
| | - Ramesh Kumar
- Department of Biochemistry, University of Allahabad Prayagraj, Prayagraj, India
| | - Hansa Sehgal
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani, India
| | - Sharmista Bhati
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Tripti Singhal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Gayacharan
- Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - M. S. Nimmy
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | | | | | - Aladdin Hamwieh
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Cairo, Egypt
| | - Rajendra Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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3
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Zhang B, Han X, Yuan W, Zhang H. TALEs as double-edged swords in plant-pathogen interactions: Progress, challenges, and perspectives. PLANT COMMUNICATIONS 2022; 3:100318. [PMID: 35576155 PMCID: PMC9251431 DOI: 10.1016/j.xplc.2022.100318] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 03/08/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
Xanthomonas species colonize many host plants and cause huge losses worldwide. Transcription activator-like effectors (TALEs) are secreted by Xanthomonas and translocated into host cells to manipulate the expression of target genes, especially by Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola, which cause bacterial blight and bacterial leaf streak, respectively, in rice. In this review, we summarize the progress of studies on the interaction between Xanthomonas and hosts, covering both rice and other plants. TALEs are not only key factors that make plants susceptible but are also essential components of plant resistance. Characterization of TALEs and TALE-like proteins has improved our understanding of TALE evolution and promoted the development of gene editing tools. In addition, the interactions between TALEs and hosts have also provided strategies and possibilities for genetic engineering in crop improvement.
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Affiliation(s)
- Biaoming Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiaoyuan Han
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Wenya Yuan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Haitao Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
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4
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Janowski M, Milewska M, Zare P, Pękowska A. Chromatin Alterations in Neurological Disorders and Strategies of (Epi)Genome Rescue. Pharmaceuticals (Basel) 2021; 14:765. [PMID: 34451862 PMCID: PMC8399958 DOI: 10.3390/ph14080765] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/26/2022] Open
Abstract
Neurological disorders (NDs) comprise a heterogeneous group of conditions that affect the function of the nervous system. Often incurable, NDs have profound and detrimental consequences on the affected individuals' lives. NDs have complex etiologies but commonly feature altered gene expression and dysfunctions of the essential chromatin-modifying factors. Hence, compounds that target DNA and histone modification pathways, the so-called epidrugs, constitute promising tools to treat NDs. Yet, targeting the entire epigenome might reveal insufficient to modify a chosen gene expression or even unnecessary and detrimental to the patients' health. New technologies hold a promise to expand the clinical toolkit in the fight against NDs. (Epi)genome engineering using designer nucleases, including CRISPR-Cas9 and TALENs, can potentially help restore the correct gene expression patterns by targeting a defined gene or pathway, both genetically and epigenetically, with minimal off-target activity. Here, we review the implication of epigenetic machinery in NDs. We outline syndromes caused by mutations in chromatin-modifying enzymes and discuss the functional consequences of mutations in regulatory DNA in NDs. We review the approaches that allow modifying the (epi)genome, including tools based on TALENs and CRISPR-Cas9 technologies, and we highlight how these new strategies could potentially change clinical practices in the treatment of NDs.
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Affiliation(s)
| | | | | | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur Street, 02-093 Warsaw, Poland; (M.J.); (M.M.); (P.Z.)
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5
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Arnesen JA, Hoof JB, Kildegaard HF, Borodina I. Genome Editing of Eukarya. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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6
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CRISPR-Cas9 system: A genome-editing tool with endless possibilities. J Biotechnol 2020; 319:36-53. [DOI: 10.1016/j.jbiotec.2020.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/30/2020] [Accepted: 05/14/2020] [Indexed: 12/27/2022]
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7
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Xue J, Lu Z, Liu W, Wang S, Lu D, Wang X, He X. The genetic arms race between plant and Xanthomonas: lessons learned from TALE biology. SCIENCE CHINA-LIFE SCIENCES 2020; 64:51-65. [PMID: 32661897 DOI: 10.1007/s11427-020-1699-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/29/2020] [Indexed: 10/23/2022]
Abstract
The pathogenic bacterial genus Xanthomonas infects a wide variety of host plants and causes devastating diseases in many crops. Transcription activator-like effectors (TALEs) are important virulence factors secreted by Xanthomonas with the ability to directly bind to the promoters of target genes in plant hosts and activate their expression, which often facilitates the proliferation of pathogens. Understanding how plants cope with TALEs will provide mechanistic insights into crop breeding for Xanthomonas defense. Over the past 30 years, numerous studies have revealed the modes of action of TALEs in plant cells and plant defense strategies to overcome TALE attack. Based on these findings, new technologies were adopted for disease management to optimize crop production. In this article, we will review the most recent advances in the evolutionary arms race between plant resistance and TALEs from Xanthomonas, with a specific focus on TALE applications in the development of novel breeding strategies for durable and broad-spectrum resistance.
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Affiliation(s)
- Jiao Xue
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Zhanhua Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Wei Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Shiguang Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Dongbai Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Xiaofei Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China
| | - Xiuying He
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, 510640, China.
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8
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Luo F, Qin G, Xia T, Fang X. Single-Molecule Imaging of Protein Interactions and Dynamics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2020; 13:337-361. [PMID: 32228033 DOI: 10.1146/annurev-anchem-091619-094308] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Live-cell single-molecule fluorescence imaging has become a powerful analytical tool to investigate cellular processes that are not accessible to conventional biochemical approaches. This has greatly enriched our understanding of the behaviors of single biomolecules in their native environments and their roles in cellular events. Here, we review recent advances in fluorescence-based single-molecule bioimaging of proteins in living cells. We begin with practical considerations of the design of single-molecule fluorescence imaging experiments such as the choice of imaging modalities, fluorescent probes, and labeling methods. We then describe analytical observables from single-molecule data and the associated molecular parameters along with examples of live-cell single-molecule studies. Lastly, we discuss computational algorithms developed for single-molecule data analysis.
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Affiliation(s)
- Fang Luo
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gege Qin
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tie Xia
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohong Fang
- Beijing National Research Center for Molecular Sciences, CAS Key Laboratory of Molecule Nanostructure and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China;
- Department of Chemistry, University of the Chinese Academy of Sciences, Beijing 100049, China
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9
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Jeon H, Kim W, Kim B, Lee S, Jayaraman J, Jung G, Choi S, Sohn KH, Segonzac C. Ralstonia solanacearum Type III Effectors with Predicted Nuclear Localization Signal Localize to Various Cell Compartments and Modulate Immune Responses in Nicotiana spp. THE PLANT PATHOLOGY JOURNAL 2020; 36:43-53. [PMID: 32089660 PMCID: PMC7012579 DOI: 10.5423/ppj.oa.08.2019.0227] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 05/11/2023]
Abstract
Ralstonia solanacearum (Rso) is a causal agent of bacterial wilt in Solanaceae crops worldwide including Republic of Korea. Rso virulence predominantly relies on type III secreted effectors (T3Es). However, only a handful of Rso T3Es have been characterized. In this study, we investigated subcellular localization of and manipulation of plant immunity by 8 Rso T3Es predicted to harbor a nuclear localization signal (NLS). While 2 of these T3Es elicited cell death in both Nicotiana benthamiana and N. tabacum, only one was dependent on suppressor of G2 allele of skp1 (SGT1), a molecular chaperone of nucleotide-binding and leucine-rich repeat immune receptors. We also identified T3Es that differentially regulate flg22-induced reactive oxygen species production and gene expression. Interestingly, several of the NLS-containing T3Es translationally fused with yellow fluorescent protein accumulated in subcellular compartments other than the cell nucleus. Our findings bring new clues to decipher Rso T3E function in planta.
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Affiliation(s)
- Hyelim Jeon
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Wanhui Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
- Plant Immunity Research Center, Seoul National University, Seoul 08826,
Korea
| | - Boyoung Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Sookyeong Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Jay Jayaraman
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
- New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Auckland 1025,
New Zealand
| | - Gayoung Jung
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Sera Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Kee Hoon Sohn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673,
Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang 37673,
Korea
| | - Cécile Segonzac
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
- Plant Immunity Research Center, Seoul National University, Seoul 08826,
Korea
- Corresponding author: Phone) +82-2-880-2229, FAX) +82-2-873-2056, E-mail)
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10
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Sedeek KEM, Mahas A, Mahfouz M. Plant Genome Engineering for Targeted Improvement of Crop Traits. FRONTIERS IN PLANT SCIENCE 2019; 10:114. [PMID: 30809237 PMCID: PMC6379297 DOI: 10.3389/fpls.2019.00114] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/23/2019] [Indexed: 05/18/2023]
Abstract
To improve food security, plant biology research aims to improve crop yield and tolerance to biotic and abiotic stress, as well as increasing the nutrient contents of food. Conventional breeding systems have allowed breeders to produce improved varieties of many crops; for example, hybrid grain crops show dramatic improvements in yield. However, many challenges remain and emerging technologies have the potential to address many of these challenges. For example, site-specific nucleases such as TALENs and CRISPR/Cas systems, which enable high-efficiency genome engineering across eukaryotic species, have revolutionized biological research and its applications in crop plants. These nucleases have been used in diverse plant species to generate a wide variety of site-specific genome modifications through strategies that include targeted mutagenesis and editing for various agricultural biotechnology applications. Moreover, CRISPR/Cas genome-wide screens make it possible to discover novel traits, expand the range of traits, and accelerate trait development in target crops that are key for food security. Here, we discuss the development and use of various site-specific nuclease systems for different plant genome-engineering applications. We highlight the existing opportunities to harness these technologies for targeted improvement of traits to enhance crop productivity and resilience to climate change. These cutting-edge genome-editing technologies are thus poised to reshape the future of agriculture and food security.
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Affiliation(s)
| | | | - Magdy Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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11
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Bastedo DP, Lo T, Laflamme B, Desveaux D, Guttman DS. Diversity and Evolution of Type III Secreted Effectors: A Case Study of Three Families. Curr Top Microbiol Immunol 2019; 427:201-230. [DOI: 10.1007/82_2019_165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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12
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Barnes SN, Wram CL, Mitchum MG, Baum TJ. The plant-parasitic cyst nematode effector GLAND4 is a DNA-binding protein. MOLECULAR PLANT PATHOLOGY 2018; 19:2263-2276. [PMID: 29719112 PMCID: PMC6637993 DOI: 10.1111/mpp.12697] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/23/2018] [Accepted: 04/30/2018] [Indexed: 05/24/2023]
Abstract
Cyst nematodes are plant pathogens that infect a wide range of economically important crops. One parasitic mechanism employed by cyst nematodes is the production and in planta delivery of effector proteins to modify plant cells and suppress defences to favour parasitism. This study focuses on GLAND4, an effector of Heterodera glycines and H. schachtii, the soybean and sugar beet cyst nematodes, respectively. We show that GLAND4 is recognized by the plant cellular machinery and is transported to the plant nucleus, an organelle for which little is known about plant nematode effector functions. We show that GLAND4 has DNA-binding ability and represses reporter gene expression in a plant transcriptional assay. One DNA fragment that binds to GLAND4 is localized in an Arabidopsis chromosomal region associated with the promoters of two lipid transfer protein genes (LTP). These LTPs have known defence functions and are down-regulated in the nematode feeding site. When expressed in Arabidopsis, the presence of GLAND4 causes the down-regulation of the two LTP genes in question, which is also associated with increased susceptibility to the plant-pathogenic bacterium Pseudomonas syringae. Furthermore, overexpression of one of the LTP genes reduces plant susceptibility to H. schachtii and P. syringae, confirming that LTP repression probably suppresses plant defences. This study makes GLAND4 one of a small subset of characterized plant nematode nuclear effectors and identifies GLAND4 as the first DNA-binding, plant-parasitic nematode effector.
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Affiliation(s)
- Stacey N. Barnes
- Plant Pathology & Microbiology DepartmentIowa State UniversityAmesIA 50011USA
| | - Catherine L. Wram
- Plant Pathology & Microbiology DepartmentIowa State UniversityAmesIA 50011USA
- Present address:
Department of Botany and Plant PathologyOregon State UniversityCorvallisOR 97330USA
| | - Melissa G. Mitchum
- Division of Plant Sciences and Bond Life Sciences CenterUniversity of MissouriColumbiaMO 65211USA
| | - Thomas J. Baum
- Plant Pathology & Microbiology DepartmentIowa State UniversityAmesIA 50011USA
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13
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Abstract
Programmable nucleases including zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein have tremendous potential biological and therapeutic applications as novel genome editing tools. These nucleases enable precise modification of the gene of interest by disruption, insertion, or correction. The application of genome editing technology to pluripotent stem cells or hematopoietic stem cells has the potential to remarkably advance the contribution of this technology to life sciences. Specifically, disease models can be generated and effective therapeutics can be developed with great efficiency and speed. Here we review the characteristics and mechanisms of each programmable nuclease. In addition, we review the applications of these nucleases to stem cells for disease therapies and summarize key studies of interest.
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Affiliation(s)
- Minjung Song
- Department of Food Biotechnology, College of Medical and Life Science, Silla University, Busan, South Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea. .,College of Medicine, Hanyang University, Seoul, South Korea.
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14
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Khan M, Seto D, Subramaniam R, Desveaux D. Oh, the places they'll go! A survey of phytopathogen effectors and their host targets. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:651-663. [PMID: 29160935 DOI: 10.1111/tpj.13780] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/03/2017] [Accepted: 11/07/2017] [Indexed: 05/09/2023]
Abstract
Phytopathogens translocate effector proteins into plant cells where they sabotage the host cellular machinery to promote infection. An individual pathogen can translocate numerous distinct effectors during the infection process to target an array of host macromolecules (proteins, metabolites, DNA, etc.) and manipulate them using a variety of enzymatic activities. In this review, we have surveyed the literature for effector targets and curated them to convey the range of functions carried out by phytopathogenic proteins inside host cells. In particular, we have curated the locations of effector targets, as well as their biological and molecular functions and compared these properties across diverse phytopathogens. This analysis validates previous observations about effector functions (e.g. immunosuppression), and also highlights some interesting features regarding effector specificity as well as functional diversification of phytopathogen virulence strategies.
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Affiliation(s)
- Madiha Khan
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Derek Seto
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Rajagopal Subramaniam
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada, KW Neatby bldg, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
| | - Darrell Desveaux
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
- Centre for the Analysis of Genome Function and Evolution, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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15
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Büttner D. Behind the lines-actions of bacterial type III effector proteins in plant cells. FEMS Microbiol Rev 2018; 40:894-937. [PMID: 28201715 PMCID: PMC5091034 DOI: 10.1093/femsre/fuw026] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/31/2016] [Accepted: 07/03/2016] [Indexed: 01/30/2023] Open
Abstract
Pathogenicity of most Gram-negative plant-pathogenic bacteria depends on the type III secretion (T3S) system, which translocates bacterial effector proteins into plant cells. Type III effectors modulate plant cellular pathways to the benefit of the pathogen and promote bacterial multiplication. One major virulence function of type III effectors is the suppression of plant innate immunity, which is triggered upon recognition of pathogen-derived molecular patterns by plant receptor proteins. Type III effectors also interfere with additional plant cellular processes including proteasome-dependent protein degradation, phytohormone signaling, the formation of the cytoskeleton, vesicle transport and gene expression. This review summarizes our current knowledge on the molecular functions of type III effector proteins with known plant target molecules. Furthermore, plant defense strategies for the detection of effector protein activities or effector-triggered alterations in plant targets are discussed.
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Affiliation(s)
- Daniela Büttner
- Genetics Department, Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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16
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Perycz M, Krwawicz J, Bochtler M. A TALE-inspired computational screen for proteins that contain approximate tandem repeats. PLoS One 2017; 12:e0179173. [PMID: 28617832 PMCID: PMC5472282 DOI: 10.1371/journal.pone.0179173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/24/2017] [Indexed: 11/18/2022] Open
Abstract
TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs. Candidate proteins were scored according to their propensity for nuclear localization, secondary structure, repeat sequence complexity, as well as covariation and predicted structural proximity of variable residues. Biological context was tentatively inferred from co-occurrence of other domains and interactome predictions. Approximate repeats with TALE-like features that merit experimental characterization were found in a protein of chestnut blight fungus, a eukaryotic plant pathogen.
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Affiliation(s)
- Malgorzata Perycz
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Joanna Krwawicz
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Matthias Bochtler
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
- International Institute of Molecular and Cell Biology in Warsaw, Poland
- * E-mail:
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17
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Zaidi SSEA, Tashkandi M, Mahfouz MM. Engineering Molecular Immunity Against Plant Viruses. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:167-186. [PMID: 28712496 DOI: 10.1016/bs.pmbts.2017.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genomic engineering has been used to precisely alter eukaryotic genomes at the single-base level for targeted gene editing, replacement, fusion, and mutagenesis, and plant viruses such as Tobacco rattle virus have been developed into efficient vectors for delivering genome-engineering reagents. In addition to altering the host genome, these methods can target pathogens to engineer molecular immunity. Indeed, recent studies have shown that clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) systems that target the genomes of DNA viruses can interfere with viral activity and limit viral symptoms in planta, demonstrating the utility of this system for engineering molecular immunity in plants. CRISPR/Cas9 can efficiently target single and multiple viral infections and confer plant immunity. Here, we discuss the use of site-specific nucleases to engineer molecular immunity against DNA and RNA viruses in plants. We also explore how to address the potential challenges encountered when producing plants with engineered resistance to single and mixed viral infections.
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Affiliation(s)
- Syed Shan-E-Ali Zaidi
- Laboratory for Genome Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia; National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Manal Tashkandi
- Laboratory for Genome Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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18
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Genome editing: the road of CRISPR/Cas9 from bench to clinic. Exp Mol Med 2016; 48:e265. [PMID: 27741224 PMCID: PMC5099421 DOI: 10.1038/emm.2016.111] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/14/2016] [Accepted: 05/24/2016] [Indexed: 12/17/2022] Open
Abstract
Molecular scissors engineered for site-specific modification of the genome hold great promise for effective functional analyses of genes, genomes and epigenomes and could improve our understanding of the molecular underpinnings of disease states and facilitate novel therapeutic applications. Several platforms for molecular scissors that enable targeted genome engineering have been developed, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and, most recently, clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated-9 (Cas9). The CRISPR/Cas9 system's simplicity, facile engineering and amenability to multiplexing make it the system of choice for many applications. CRISPR/Cas9 has been used to generate disease models to study genetic diseases. Improvements are urgently needed for various aspects of the CRISPR/Cas9 system, including the system's precision, delivery and control over the outcome of the repair process. Here, we discuss the current status of genome engineering and its implications for the future of biological research and gene therapy.
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19
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Xu S, Cao S, Zou B, Yue Y, Gu C, Chen X, Wang P, Dong X, Xiang Z, Li K, Zhu M, Zhao Q, Zhou G. An alternative novel tool for DNA editing without target sequence limitation: the structure-guided nuclease. Genome Biol 2016; 17:186. [PMID: 27634179 PMCID: PMC5025552 DOI: 10.1186/s13059-016-1038-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/05/2016] [Indexed: 01/31/2023] Open
Abstract
Engineered endonucleases are a powerful tool for editing DNA. However, sequence preferences may limit their application. We engineer a structure-guided endonuclease (SGN) composed of flap endonuclease-1 (FEN-1), which recognizes the 3′ flap structure, and the cleavage domain of Fok I (Fn1), which cleaves DNA strands. The SGN recognizes the target DNA on the basis of the 3′ flap structure formed between the target and the guide DNA (gDNA) and cut the target through its Fn1 dimerization. Our results show that the SGN, guided by a pair of gDNAs, cleaves transgenic reporter gene and endogenous genes in zebrafish embryonic genome.
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Affiliation(s)
- Shu Xu
- Department of Pharmacology, Jinling Hospital, School of Medicine, Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, People's Republic of China
| | - Shasha Cao
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Bingjie Zou
- Department of Pharmacology, Jinling Hospital, School of Medicine, Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, People's Republic of China
| | - Yunyun Yue
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Chun Gu
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Xin Chen
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Pei Wang
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Xiaohua Dong
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China
| | - Zheng Xiang
- Department of Pharmacology, Jinling Hospital, School of Medicine, Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, People's Republic of China
| | - Kai Li
- College of Pharmaceutical Science, Soochow University, No. 199, Renai Road, Suzhou, 215123, People's Republic of China
| | - Minsheng Zhu
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China.
| | - Qingshun Zhao
- MOE Key Laboratory of Model Animal for Disease Study, State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou High-tech Development Zone, Nanjing, 210061, People's Republic of China.
| | - Guohua Zhou
- Department of Pharmacology, Jinling Hospital, School of Medicine, Nanjing University, No. 305 Zhongshan East Road, Nanjing, 210002, People's Republic of China.
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20
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Piatek A, Mahfouz MM. Targeted genome regulation via synthetic programmable transcriptional regulators. Crit Rev Biotechnol 2016; 37:429-440. [DOI: 10.3109/07388551.2016.1165180] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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21
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Schandry N, de Lange O, Prior P, Lahaye T. TALE-Like Effectors Are an Ancestral Feature of the Ralstonia solanacearum Species Complex and Converge in DNA Targeting Specificity. FRONTIERS IN PLANT SCIENCE 2016; 7:1225. [PMID: 27582755 PMCID: PMC4987410 DOI: 10.3389/fpls.2016.01225] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/02/2016] [Indexed: 05/19/2023]
Abstract
Ralstonia solanacearum, a species complex of bacterial plant pathogens divided into four monophyletic phylotypes, causes plant diseases in tropical climates around the world. Some strains exhibit a broad host range on solanaceous hosts, while others are highly host-specific as for example some banana-pathogenic strains. Previous studies showed that transcription activator-like (TAL) effectors from Ralstonia, termed RipTALs, are capable of activating reporter genes in planta, if these are preceded by a matching effector binding element (EBE). RipTALs target DNA via their central repeat domain (CRD), where one repeat pairs with one DNA-base of the given EBE. The repeat variable diresidue dictates base repeat specificity in a predictable fashion, known as the TALE code. In this work, we analyze RipTALs across all phylotypes of the Ralstonia solanacearum species complex. We find that RipTALs are prevalent in phylotypes I and IV but absent from most phylotype III and II strains (10/12, 8/14, 1/24, and 1/5 strains contained a RipTAL, respectively). RipTALs originating from strains of the same phylotype show high levels of sequence similarity (>98%) in the N-terminal and C-terminal regions, while RipTALs isolated from different phylotypes show 47-91% sequence similarity in those regions, giving rise to four RipTAL classes. We show that, despite sequence divergence, the base preference for guanine, mediated by the N-terminal region, is conserved across RipTALs of all classes. Using the number and order of repeats found in the CRD, we functionally sub-classify RipTALs, introduce a new simple nomenclature, and predict matching EBEs for all seven distinct RipTALs identified. We experimentally study RipTAL EBEs and uncover that some RipTALs are able to target the EBEs of other RipTALs, referred to as cross-reactivity. In particular, RipTALs from strains with a broad host range on solanaceous hosts cross-react on each other's EBEs. Investigation of sequence divergence between RipTAL repeats allows for a reconstruction of repeat array biogenesis, for example through slipped strand mispairing or gene conversion. Using these studies we show how RipTALs of broad host range strains evolved convergently toward a shared target sequence. Finally, we discuss the differences between TALE-likes of plant pathogens in the context of disease ecology.
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Affiliation(s)
- Niklas Schandry
- Center for Plant Molecular Biology, University of TübingenTübingen, Germany
| | - Orlando de Lange
- Center for Plant Molecular Biology, University of TübingenTübingen, Germany
| | - Philippe Prior
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de Coopération Internationale en Recherche Agronomique pour le Développement – Institut National de la Recherche AgronomiqueSaint-Pierre, France
| | - Thomas Lahaye
- Center for Plant Molecular Biology, University of TübingenTübingen, Germany
- *Correspondence: Thomas Lahaye,
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Abstract
The development of a facile genome engineering technology based on transcription activator-like effector nucleases (TALENs) has led to significant advances in diverse areas of science and medicine. In this review, we provide a broad overview of the development of TALENs and the use of this technology in basic science, biotechnology, and biomedical applications. This includes the discovery of DNA recognition by TALEs, engineering new TALE proteins to diverse targets, general advances in nuclease-based editing strategies, and challenges that are specific to various applications of the TALEN technology. We review examples of applying TALENs for studying gene function and regulation, generating disease models, and developing gene therapies. The current status of genome editing and future directions for other uses of these technologies are also discussed.
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Affiliation(s)
- David G Ousterout
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Room 136 Hudson Hall, Box 90281, Durham, NC, 27708-0281, USA. .,Center for Genomic and Computational Biology, Duke University, Durham, NC, 27708, USA. .,Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC, 27710, USA.
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23
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Abstract
Transcription activator-like effectors (TALEs) are proteins with a unique DNA-binding domain that confers both a predictable and programmable specificity. The DNA-binding domain consists typically of 34-amino acid near-identical repeats. The repeats form a right-handed superhelical structure that wraps around the DNA double helix and exposes the variable amino acids at position 13 of each repeat to the sense strand DNA bases. Each repeat binds one base in a highly specific, non-overlapping, and comma-free fashion. Although TALE specificities are encoded in a simple way, sophisticated rules can be taken into account to build highly efficient DNA-binding modules for biotechnological use.
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24
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de Lange O, Wolf C, Thiel P, Krüger J, Kleusch C, Kohlbacher O, Lahaye T. DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats. Nucleic Acids Res 2015; 43:10065-10080. [PMID: 26481363 DOI: 10.1093/nar.gkv1053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/14/2015] [Indexed: 05/28/2023] Open
Abstract
Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats.
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Affiliation(s)
- Orlando de Lange
- Department of General Genetics, Centre for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Christina Wolf
- Department of General Genetics, Centre for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Philipp Thiel
- Department of Computer Science and Centre for Bioinformatics, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Jens Krüger
- Department of Computer Science and Centre for Bioinformatics, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | | | - Oliver Kohlbacher
- Department of Computer Science and Centre for Bioinformatics, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany Quantitative Biology Centre and Faculty of Medicine, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Thomas Lahaye
- Department of General Genetics, Centre for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, Tuebingen, Baden-Wuerttemberg, 72076, Germany
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25
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de Lange O, Wolf C, Thiel P, Krüger J, Kleusch C, Kohlbacher O, Lahaye T. DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats. Nucleic Acids Res 2015; 43:10065-80. [PMID: 26481363 PMCID: PMC4787788 DOI: 10.1093/nar/gkv1053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/14/2015] [Indexed: 12/24/2022] Open
Abstract
Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats.
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Affiliation(s)
- Orlando de Lange
- Department of General Genetics, Centre for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Christina Wolf
- Department of General Genetics, Centre for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Philipp Thiel
- Department of Computer Science and Centre for Bioinformatics, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Jens Krüger
- Department of Computer Science and Centre for Bioinformatics, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | | | - Oliver Kohlbacher
- Department of Computer Science and Centre for Bioinformatics, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany Quantitative Biology Centre and Faculty of Medicine, University of Tuebingen, Sand 14, Tuebingen, Baden-Wuerttemberg, 72076, Germany
| | - Thomas Lahaye
- Department of General Genetics, Centre for Plant Molecular Biology, University of Tuebingen, Auf der Morgenstelle 32, Tuebingen, Baden-Wuerttemberg, 72076, Germany
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26
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Bogdanove AJ, Booher NJ. Online Tools for TALEN Design. Methods Mol Biol 2015; 1338:43-7. [PMID: 26443212 DOI: 10.1007/978-1-4939-2932-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Transcription activator-like effector nucleases (TALENs) can be exquisitely specific and highly effective genome editing reagents. Specificity and efficacy depend however on good design for minimal off-targeting and strong binding. Several online tools are accessible to aid in this process. Here, we tabulate those tools, noting their functions and key features.
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Affiliation(s)
- Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science, Ithaca, NY, 14853, USA.
| | - Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science, Ithaca, NY, 14853, USA
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27
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Aouida M, Eid A, Ali Z, Cradick T, Lee C, Deshmukh H, Atef A, AbuSamra D, Gadhoum SZ, Merzaban J, Bao G, Mahfouz M. Efficient fdCas9 Synthetic Endonuclease with Improved Specificity for Precise Genome Engineering. PLoS One 2015; 10:e0133373. [PMID: 26225561 PMCID: PMC4520497 DOI: 10.1371/journal.pone.0133373] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 06/25/2015] [Indexed: 12/26/2022] Open
Abstract
The Cas9 endonuclease is used for genome editing applications in diverse eukaryotic species. A high frequency of off-target activity has been reported in many cell types, limiting its applications to genome engineering, especially in genomic medicine. Here, we generated a synthetic chimeric protein between the catalytic domain of the FokI endonuclease and the catalytically inactive Cas9 protein (fdCas9). A pair of guide RNAs (gRNAs) that bind to sense and antisense strands with a defined spacer sequence range can be used to form a catalytically active dimeric fdCas9 protein and generate double-strand breaks (DSBs) within the spacer sequence. Our data demonstrate an improved catalytic activity of the fdCas9 endonuclease, with a spacer range of 15-39 nucleotides, on surrogate reporters and genomic targets. Furthermore, we observed no detectable fdCas9 activity at known Cas9 off-target sites. Taken together, our data suggest that the fdCas9 endonuclease variant is a superior platform for genome editing applications in eukaryotic systems including mammalian cells.
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Affiliation(s)
- Mustapha Aouida
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Thomas Cradick
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, United States of America
| | - Ciaran Lee
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, United States of America
| | - Harshavardhan Deshmukh
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, United States of America
| | - Ahmed Atef
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
| | - Dina AbuSamra
- Laboratory of Cell Signaling and Migration, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Samah Zeineb Gadhoum
- Laboratory of Cell Signaling and Migration, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Jasmeen Merzaban
- Laboratory of Cell Signaling and Migration, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
| | - Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, United States of America
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955–6900, Kingdom of Saudi Arabia
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28
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Abstract
Human pluripotent stem cells provide a versatile platform for regenerative studies, drug testing and disease modeling. That the expression of only four transcription factors, Oct4, Klf4, Sox2 and c-Myc (OKSM), is sufficient for generation of induced pluripotent stem cells (iPSCs) from differentiated somatic cells has revolutionized the field and also highlighted the importance of OKSM as targets for genome editing. A number of novel genome-editing systems have been developed recently. In this review, we focus on successful applications of several such systems for generation of iPSCs. In particular, we discuss genome-editing systems based on zinc-finger fusion proteins (ZFs), transcription activator-like effectors (TALEs) and an RNA-guided DNA-specific nuclease, Cas9, derived from the bacterial defense system against viruses that utilizes clustered regularly interspaced short palindromic repeats (CRISPR).
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29
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Ali Z, Abul-faraj A, Piatek M, Mahfouz MM. Activity and specificity of TRV-mediated gene editing in plants. PLANT SIGNALING & BEHAVIOR 2015; 10:e1044191. [PMID: 26039254 PMCID: PMC4883890 DOI: 10.1080/15592324.2015.1044191] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 05/05/2023]
Abstract
Plant trait engineering requires efficient targeted genome-editing technologies. Clustered regularly interspaced palindromic repeats (CRISPRs)/ CRISPR associated (Cas) type II system is used for targeted genome-editing applications across eukaryotic species including plants. Delivery of genome engineering reagents and recovery of mutants remain challenging tasks for in planta applications. Recently, we reported the development of Tobacco rattle virus (TRV)-mediated genome editing in Nicotiana benthamiana. TRV infects the growing points and possesses small genome size; which facilitate cloning, multiplexing, and agroinfections. Here, we report on the persistent activity and specificity of the TRV-mediated CRISPR/Cas9 system for targeted modification of the Nicotiana benthamiana genome. Our data reveal the persistence of the TRV- mediated Cas9 activity for up to 30 d post-agroinefection. Further, our data indicate that TRV-mediated genome editing exhibited no off-target activities at potential off-targets indicating the precision of the system for plant genome engineering. Taken together, our data establish the feasibility and exciting possibilities of using virus-mediated CRISPR/Cas9 for targeted engineering of plant genomes.
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Affiliation(s)
- Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, King Abdullah University of Science and Technology; Thuwal, Kingdom of Saudi Arabia
| | - Aala Abul-faraj
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, King Abdullah University of Science and Technology; Thuwal, Kingdom of Saudi Arabia
| | - Marek Piatek
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, King Abdullah University of Science and Technology; Thuwal, Kingdom of Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, King Abdullah University of Science and Technology; Thuwal, Kingdom of Saudi Arabia
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30
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Piatek A, Ali Z, Baazim H, Li L, Abulfaraj A, Al-Shareef S, Aouida M, Mahfouz MM. RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:578-89. [PMID: 25400128 DOI: 10.1111/pbi.12284] [Citation(s) in RCA: 210] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/19/2014] [Accepted: 09/21/2014] [Indexed: 05/20/2023]
Abstract
Targeted genomic regulation is a powerful approach to accelerate trait discovery and development in agricultural biotechnology. Bacteria and archaea use clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) regulatory systems for adaptive molecular immunity against foreign nucleic acids introduced by invading phages and conjugative plasmids. The type II CRISPR/Cas system has been adapted for genome editing in many cell types and organisms. A recent study used the catalytically inactive Cas9 (dCas9) protein combined with guide-RNAs (gRNAs) as a DNA-targeting platform to modulate gene expression in bacterial, yeast, and human cells. Here, we modified this DNA-targeting platform for targeted transcriptional regulation in planta by developing chimeric dCas9-based transcriptional activators and repressors. To generate transcriptional activators, we fused the dCas9 C-terminus with the activation domains of EDLL and TAL effectors. To generate a transcriptional repressor, we fused the dCas9 C-terminus with the SRDX repression domain. Our data demonstrate that dCas9 fusion with the EDLL activation domain (dCas9:EDLL) and the TAL activation domain (dCas9:TAD), guided by gRNAs complementary to selected promoter elements, induce strong transcriptional activation on Bs3::uidA targets in plant cells. Further, the dCas9:SRDX-mediated transcriptional repression of an endogenous gene. Thus, our results suggest that the synthetic transcriptional repressor (dCas9:SRDX) and activators (dCas9:EDLL and dCas9:TAD) can be used as endogenous transcription factors to repress or activate transcription of an endogenous genomic target. Our data indicate that the CRISPR/dCas9 DNA-targeting platform can be used in plants as a functional genomics tool and for biotechnological applications.
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Affiliation(s)
- Agnieszka Piatek
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Transcription activator-like effector nucleases mediated metabolic engineering for enhanced fatty acids production in Saccharomyces cerevisiae. J Biosci Bioeng 2015; 120:364-71. [PMID: 25907574 DOI: 10.1016/j.jbiosc.2015.02.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 02/12/2015] [Accepted: 02/24/2015] [Indexed: 01/01/2023]
Abstract
Targeted engineering of microbial genomes holds much promise for diverse biotechnological applications. Transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/Cas9 systems are capable of efficiently editing microbial genomes, including that of Saccharomyces cerevisiae. Here, we demonstrate the use of TALENs to edit the genome of S. cerevisiae with the aim of inducing the overproduction of fatty acids. Heterodimeric TALENs were designed to simultaneously edit the FAA1 and FAA4 genes encoding acyl-CoA synthetases in S. cerevisiae. Functional yeast double knockouts generated using these TALENs over-produce large amounts of free fatty acids into the cell. This study demonstrates the use of TALENs for targeted engineering of yeast and demonstrates that this technology can be used to stimulate the enhanced production of free fatty acids, which are potential substrates for biofuel production. This proof-of-principle study extends the utility of TALENs as excellent genome editing tools and highlights their potential use for metabolic engineering of yeast and other organisms, such as microalgae and plants, for biofuel production.
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Mesarich CH, Bowen JK, Hamiaux C, Templeton MD. Repeat-containing protein effectors of plant-associated organisms. FRONTIERS IN PLANT SCIENCE 2015; 6:872. [PMID: 26557126 PMCID: PMC4617103 DOI: 10.3389/fpls.2015.00872] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/01/2015] [Indexed: 05/10/2023]
Abstract
Many plant-associated organisms, including microbes, nematodes, and insects, deliver effector proteins into the apoplast, vascular tissue, or cell cytoplasm of their prospective hosts. These effectors function to promote colonization, typically by altering host physiology or by modulating host immune responses. The same effectors however, can also trigger host immunity in the presence of cognate host immune receptor proteins, and thus prevent colonization. To circumvent effector-triggered immunity, or to further enhance host colonization, plant-associated organisms often rely on adaptive effector evolution. In recent years, it has become increasingly apparent that several effectors of plant-associated organisms are repeat-containing proteins (RCPs) that carry tandem or non-tandem arrays of an amino acid sequence or structural motif. In this review, we highlight the diverse roles that these repeat domains play in RCP effector function. We also draw attention to the potential role of these repeat domains in adaptive evolution with regards to RCP effector function and the evasion of effector-triggered immunity. The aim of this review is to increase the profile of RCP effectors from plant-associated organisms.
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Affiliation(s)
- Carl H. Mesarich
- School of Biological Sciences, The University of AucklandAuckland, New Zealand
- Host–Microbe Interactions, Bioprotection, The New Zealand Institute for Plant & Food Research LtdAuckland, New Zealand
- *Correspondence: Carl H. Mesarich
| | - Joanna K. Bowen
- Host–Microbe Interactions, Bioprotection, The New Zealand Institute for Plant & Food Research LtdAuckland, New Zealand
| | - Cyril Hamiaux
- Human Responses, The New Zealand Institute for Plant & Food Research LimitedAuckland, New Zealand
| | - Matthew D. Templeton
- School of Biological Sciences, The University of AucklandAuckland, New Zealand
- Host–Microbe Interactions, Bioprotection, The New Zealand Institute for Plant & Food Research LtdAuckland, New Zealand
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A Ralstonia solanacearum type III effector directs the production of the plant signal metabolite trehalose-6-phosphate. mBio 2014; 5:mBio.02065-14. [PMID: 25538193 PMCID: PMC4278537 DOI: 10.1128/mbio.02065-14] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The plant pathogen Ralstonia solanacearum possesses two genes encoding a trehalose-6-phosphate synthase (TPS), an enzyme of the trehalose biosynthetic pathway. One of these genes, named ripTPS, was found to encode a protein with an additional N-terminal domain which directs its translocation into host plant cells through the type 3 secretion system. RipTPS is a conserved effector in the R. solanacearum species complex, and homologues were also detected in other bacterial plant pathogens. Functional analysis of RipTPS demonstrated that this type 3 effector synthesizes trehalose-6-phosphate and identified residues essential for this enzymatic activity. Although trehalose-6-phosphate is a key signal molecule in plants that regulates sugar status and carbon assimilation, the disruption of ripTPS did not alter the virulence of R. solanacearum on plants. However, heterologous expression assays showed that this effector specifically elicits a hypersensitive-like response on tobacco that is independent of its enzymatic activity and is triggered by the C-terminal half of the protein. Recognition of this effector by the plant immune system is suggestive of a role during the infectious process. Ralstonia solanacearum, the causal agent of bacterial wilt disease, infects more than two hundred plant species, including economically important crops. The type III secretion system plays a major role in the pathogenicity of this bacterium, and approximately 70 effector proteins have been shown to be translocated into host plant cells. This study provides the first description of a type III effector endowed with a trehalose-6-phosphate synthase enzymatic activity and illustrates a new mechanism by which the bacteria may manipulate the plant metabolism upon infection. In recent years, trehalose-6-phosphate has emerged as an essential signal molecule in plants, connecting plant metabolism and development. The finding that a bacterial pathogen could induce the production of trehalose-6-phosphate in plant cells further highlights the importance of this metabolite in multiple aspects of the molecular physiology of plants.
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Moore R, Chandrahas A, Bleris L. Transcription activator-like effectors: a toolkit for synthetic biology. ACS Synth Biol 2014; 3:708-16. [PMID: 24933470 PMCID: PMC4210167 DOI: 10.1021/sb400137b] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Transcription
activator-like effectors (TALEs) are proteins secreted
by Xanthomonas bacteria to aid the infection of plant
species. TALEs assist infections by binding to specific DNA sequences
and activating the expression of host genes. Recent results show that
TALE proteins consist of a central repeat domain, which determines
the DNA targeting specificity and can be rapidly synthesized de novo. Considering the highly modular nature of TALEs,
their versatility, and the ease of constructing these proteins, this
technology can have important implications for synthetic biology applications.
Here, we review developments in the area with a particular focus on
modifications for custom and controllable gene regulation.
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Affiliation(s)
- Richard Moore
- Bioengineering
Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080 United States
- Center
for Systems Biology, The University of Texas at Dallas, 800 West Campbell
Road, Richardson, Texas 75080 United States
| | - Anita Chandrahas
- Bioengineering
Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080 United States
- Center
for Systems Biology, The University of Texas at Dallas, 800 West Campbell
Road, Richardson, Texas 75080 United States
| | - Leonidas Bleris
- Bioengineering
Department, The University of Texas at Dallas, 800 West Campbell Road, Richardson, Texas 75080 United States
- Electrical
Engineering Department, The University of Texas at Dallas, 800
West Campbell Road, Richardson, Texas 75080 United States
- Center
for Systems Biology, The University of Texas at Dallas, 800 West Campbell
Road, Richardson, Texas 75080 United States
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Mahfouz MM, Piatek A, Stewart CN. Genome engineering via TALENs and CRISPR/Cas9 systems: challenges and perspectives. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1006-14. [PMID: 25250853 DOI: 10.1111/pbi.12256] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 08/07/2014] [Accepted: 08/14/2014] [Indexed: 05/07/2023]
Abstract
The ability to precisely modify genome sequence and regulate gene expression patterns in a site-specific manner holds much promise in plant biotechnology. Genome-engineering technologies that enable such highly specific and efficient modification are advancing with unprecedented pace. Transcription activator-like effectors (TALEs) provide customizable DNA-binding modules designed to bind to any sequence of interest. Thus, TALEs have been used as a DNA targeting module fused to functional domains for a variety of targeted genomic and epigenomic modifications. TALE nucleases (TALENs) have been used with much success across eukaryotic species to edit genomes. Recently, clustered regularly interspaced palindromic repeats (CRISPRs) that are used as guide RNAs for Cas9 nuclease-specific digestion has been introduced as a highly efficient DNA-targeting platform for genome editing and regulation. Here, we review the discovery, development and limitations of TALENs and CRIPSR/Cas9 systems as genome-engineering platforms in plants. We discuss the current questions, potential improvements and the development of the next-generation genome-editing platforms with an emphasis on producing designer plants to address the needs of agriculture and basic plant biology.
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Affiliation(s)
- Magdy M Mahfouz
- Division of Biological Sciences & Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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36
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Scott JNF, Kupinski AP, Boyes J. Targeted genome regulation and modification using transcription activator-like effectors. FEBS J 2014; 281:4583-97. [DOI: 10.1111/febs.12973] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 08/07/2014] [Accepted: 08/13/2014] [Indexed: 11/30/2022]
Affiliation(s)
- James N. F. Scott
- School of Molecular and Cellular Biology; Faculty of Biological Sciences; University of Leeds; UK
| | - Adam P. Kupinski
- School of Molecular and Cellular Biology; Faculty of Biological Sciences; University of Leeds; UK
| | - Joan Boyes
- School of Molecular and Cellular Biology; Faculty of Biological Sciences; University of Leeds; UK
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37
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Booher NJ, Bogdanove AJ. Tools for TAL effector design and target prediction. Methods 2014; 69:121-7. [PMID: 24981075 PMCID: PMC4175064 DOI: 10.1016/j.ymeth.2014.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 06/11/2014] [Accepted: 06/13/2014] [Indexed: 10/25/2022] Open
Abstract
TAL effectors are transcription factors injected into plant cells by pathogenic bacteria during infection. They find their specific DNA targets via a string of contiguous, structural repeats that individually recognize single nucleotides (with some degeneracy) by virtue of polymorphisms at residue 13. The number of repeats and sequence of the amino acids at position 13 determine the nucleotide sequence of the DNA target. Due to this modularity, TAL effectors are readily engineered and have been used alone or as molecular fusions for targeted gene activation, gene repression, chromatin modification, chromatin tagging, and most broadly, for genome editing as TAL effector nucleases (TALENs). Several moderate and high-throughput cloning methods are in place for assembling TAL effector-based genetic constructs. Targeting is complicated to an extent by a general requirement for thymine to precede the DNA target, a requirement of TALENs to bind paired opposing sites separated by a defined range of distances, differential contributions of different repeat types to overall affinity, and a polarity to mismatch tolerance. Several computational tools are available online to aid in design and the identification of candidate off-target binding sites, as well as assembly and implementation. These tools vary in their approaches, capabilities, and relative utility for different types of TAL effector applications. Accuracy of off-target prediction is not well characterized yet for any of the tools and will require a better understanding of the qualitative and quantitative variation in the nucleotide preferences of individual repeats.
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Affiliation(s)
- Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology, 334 Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology, 334 Plant Science, Cornell University, Ithaca, NY 14853, USA.
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Deslandes L, Genin S. Opening the Ralstonia solanacearum type III effector tool box: insights into host cell subversion mechanisms. CURRENT OPINION IN PLANT BIOLOGY 2014; 20:110-7. [PMID: 24880553 DOI: 10.1016/j.pbi.2014.05.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/23/2014] [Accepted: 05/01/2014] [Indexed: 05/19/2023]
Abstract
Effectors delivered to host cells by the Type III secretion system are essential to Ralstonia solanacearum pathogenicity, as in several other plant pathogenic bacteria. The establishment of exhaustive effector repertoires in multiple R. solanacearum strains drew a first picture of the evolutionary dynamics of the pathogen effector suites. Effector repertoires are diversified, with a core of 20-30 effectors present in most of the strains and the obtention of mutants lacking one or more effector genes revealed the functional overlap among this effector network. Recent functional studies have provided insights into the ability of single effectors to manipulate the host proteasome, elicit cell death, trigger the expression of plant genes, and/or display biochemical activities on plant protein targets.
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Affiliation(s)
- Laurent Deslandes
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan F-31326, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan F-31326, France
| | - Stephane Genin
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan F-31326, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan F-31326, France.
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Abstract
Genome editing is the practice of making predetermined and precise changes to a genome by controlling the location of DNA DSBs (double-strand breaks) and manipulating the cell's repair mechanisms. This technology results from harnessing natural processes that have taken decades and multiple lines of inquiry to understand. Through many false starts and iterative technology advances, the goal of genome editing is just now falling under the control of human hands as a routine and broadly applicable method. The present review attempts to define the technique and capture the discovery process while following its evolution from meganucleases and zinc finger nucleases to the current state of the art: TALEN (transcription-activator-like effector nuclease) technology. We also discuss factors that influence success, technical challenges and future prospects of this quickly evolving area of study and application.
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40
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Abstract
Xanthomonas phytopathogenic bacteria produce unique transcription activator-like effector (TALE) proteins that recognize and activate specific plant promoters through a set of tandem repeats. A unique TALE-DNA-binding code uses two polymorphic amino acids in each repeat to mediate recognition of specific nucleotides. The order of repeats determines effector’s specificity toward the cognate nucleotide sequence of the sense DNA strand. Artificially designed TALE-DNA-binding domains fused to nuclease or activation and repressor domains provide an outstanding toolbox for targeted gene editing and gene regulation in research, biotechnology and gene therapy. Gene editing with custom-designed TALE nucleases (TALENs) extends the repertoire of targeted genome modifications across a broad spectrum of organisms ranging from plants and insect to mammals.
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Kuhn H, Panstruga R. Introduction to a Virtual Special Issue on phytopathogen effector proteins. THE NEW PHYTOLOGIST 2014; 202:727-730. [PMID: 24716512 DOI: 10.1111/nph.12804] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Affiliation(s)
- Hannah Kuhn
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Aachen, Germany
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Aachen, Germany
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Abstract
Programmable nucleases - including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and RNA-guided engineered nucleases (RGENs) derived from the bacterial clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) system - enable targeted genetic modifications in cultured cells, as well as in whole animals and plants. The value of these enzymes in research, medicine and biotechnology arises from their ability to induce site-specific DNA cleavage in the genome, the repair (through endogenous mechanisms) of which allows high-precision genome editing. However, these nucleases differ in several respects, including their composition, targetable sites, specificities and mutation signatures, among other characteristics. Knowledge of nuclease-specific features, as well as of their pros and cons, is essential for researchers to choose the most appropriate tool for a range of applications.
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Affiliation(s)
- Hyongbum Kim
- Graduate School of Biomedical Science and Engineering, and College of Medicine, Hanyang University, Wangsimni-ro 222, Sungdong-gu, Seoul 133-791, South Korea
| | - Jin-Soo Kim
- 1] Center for Genome Engineering, Institute for Basic Science, Gwanak-ro 1, Gwanak-gu, Seoul 151-747, South Korea. [2] Department of Chemistry, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 151-747, South Korea
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43
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A TAL effector repeat architecture for frameshift binding. Nat Commun 2014; 5:3447. [PMID: 24614980 DOI: 10.1038/ncomms4447] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 02/13/2014] [Indexed: 11/08/2022] Open
Abstract
Transcription activator-like effectors (TALEs) are important Xanthomonas virulence factors that bind DNA via a unique tandem 34-amino-acid repeat domain to induce expression of plant genes. So far, TALE repeats are described to bind as a consecutive array to a consecutive DNA sequence, in which each repeat independently recognizes a single DNA base. This modular protein architecture enables the design of any desired DNA-binding specificity for biotechnology applications. Here we report that natural TALE repeats of unusual amino-acid sequence length break the strict one repeat-to-one base pair binding mode and introduce a local flexibility to TALE-DNA binding. This flexibility allows TALEs and TALE nucleases to recognize target sequence variants with single nucleotide deletions. The flexibility also allows TALEs to activate transcription at allelic promoters that otherwise confer resistance to the host plant.
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Activities and specificities of homodimeric TALENs in Saccharomyces cerevisiae. Curr Genet 2013; 60:61-74. [PMID: 24081604 DOI: 10.1007/s00294-013-0412-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 08/19/2013] [Accepted: 09/19/2013] [Indexed: 12/20/2022]
Abstract
The development of highly efficient genome engineering reagents is of paramount importance to launch the next wave of biotechnology. TAL effectors have been developed as an adaptable DNA binding scaffold that can be engineered to bind to any user-defined sequence. Thus, TAL-based DNA binding modules have been used to generate chimeric proteins for a variety of targeted genome modifications across eukaryotic species. For example, TAL effectors fused to the catalytic domain of FokI endonuclease (TALENs) were used to generate site-specific double strand breaks (DSBs), the repair of which can be harnessed to dictate user-desired, genome-editing outcomes. To cleave DNA, FokI endonuclease must dimerize which can be achieved using a pair of TALENs that bind to the DNA targeted in a tail-to-tail orientation with proper spacing allowing the dimer formation. Because TALENs binding to DNA are dependent on their repeat sequences and nucleotides binding specificities, homodimers and heterodimers binding can be formed. In the present study, we used several TALEN monomers with increased repeats binding degeneracy to allow homodimer formation at increased number of genomic loci. We assessed their binding specificities and genome modification activities. Our results indicate that homodimeric TALENs could be used to modify the yeast genome in a site-specific manner and their binding to the promoter regions might modulate the expression of target genes. Taken together, our data indicate that homodimeric TALENs could be used to achieve different engineering possibilities of biotechnological applications and that their transcriptional modulations need to be considered when analyzing their phenotypic effects.
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Peeters N, Guidot A, Vailleau F, Valls M. Ralstonia solanacearum, a widespread bacterial plant pathogen in the post-genomic era. MOLECULAR PLANT PATHOLOGY 2013; 14:651-62. [PMID: 23718203 PMCID: PMC6638647 DOI: 10.1111/mpp.12038] [Citation(s) in RCA: 194] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
UNLABELLED Ralstonia solanacearum is a soil-borne bacterium causing the widespread disease known as bacterial wilt. Ralstonia solanacearum is also the causal agent of Moko disease of banana and brown rot of potato. Since the last R. solanacearum pathogen profile was published 10 years ago, studies concerning this plant pathogen have taken a genomic and post-genomic direction. This was pioneered by the first sequenced and annotated genome for a major plant bacterial pathogen and followed by many more genomes in subsequent years. All molecular features studied now have a genomic flavour. In the future, this will help in connecting the classical field of pathology and diversity studies with the gene content of specific strains. In this review, we summarize the recent research on this bacterial pathogen, including strain classification, host range, pathogenicity determinants, regulation of virulence genes, type III effector repertoire, effector-triggered immunity, plant signalling in response to R. solanacearum, as well as a review of different new pathosystems. TAXONOMY Bacteria; Proteobacteria; β subdivision; Ralstonia group; genus Ralstonia. DISEASE SYMPTOMS Ralstonia solanacearum is the agent of bacterial wilt of plants, characterized by a sudden wilt of the whole plant. Typically, stem cross-sections will ooze a slimy bacterial exudate. In the case of Moko disease of banana and brown rot of potato, there is also visible bacterial colonization of banana fruit and potato tuber. DISEASE CONTROL As a soil-borne pathogen, infected fields can rarely be reused, even after rotation with nonhost plants. The disease is controlled by the use of resistant and tolerant plant cultivars. The prevention of spread of the disease has been achieved, in some instances, by the application of strict prophylactic sanitation practices. USEFUL WEBSITES Stock centre: International Centre for Microbial Resources-French Collection for Plant-associated Bacteria CIRM-CFBP, IRHS UMR 1345 INRA-ACO-UA, 42 rue Georges Morel, 49070 Beaucouzé Cedex, France, http://www.angers-nantes.inra.fr/cfbp/. Ralstonia Genome browser: https://iant.toulouse.inra.fr/R.solanacearum. GMI1000 insertion mutant library: https://iant.toulouse.inra.fr/R.solanacearumGMI1000/GenomicResources. MaGe Genome Browser: https://www.genoscope.cns.fr/agc/microscope/mage/viewer.php?
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Affiliation(s)
- Nemo Peeters
- INRA UMR441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), 24 chemin de Borde Rouge-Auzeville CS 52627, 31326, Castanet Tolosan Cedex, France
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46
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Doyle EL, Stoddard BL, Voytas DF, Bogdanove AJ. TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins. Trends Cell Biol 2013; 23:390-8. [PMID: 23707478 PMCID: PMC3729746 DOI: 10.1016/j.tcb.2013.04.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 12/19/2022]
Abstract
Transcription activator-like (TAL) effectors are transcription factors injected into plant cells by pathogenic bacteria of the genus Xanthomonas. They function as virulence factors by activating host genes important for disease, or as avirulence factors by turning on genes that provide resistance. DNA-binding specificity is encoded by polymorphic repeats in each protein that correspond one-to-one with different nucleotides. This code has facilitated target identification and opened new avenues for engineering disease resistance. It has also enabled TAL effector customization for targeted gene control, genome editing, and other applications. This article reviews the structural basis for TAL effector-DNA specificity, the impact of the TAL effector-DNA code on plant pathology and engineered resistance, and recent accomplishments and future challenges in TAL effector-based DNA targeting.
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Affiliation(s)
- Erin L. Doyle
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey Hall, Ames, IA 50011
| | - Barry L. Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. A3-025, Seattle WA 98109
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, 321 Church Street SE, University of Minnesota, Minneapolis, MN 55455
| | - Adam J. Bogdanove
- Department of Plant Pathology and Microbiology, Iowa State University, 351 Bessey Hall, Ames, IA 50011
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, 334 Plant Science, Ithaca NY 14853
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47
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Schornack S, Moscou MJ, Ward ER, Horvath DM. Engineering plant disease resistance based on TAL effectors. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:383-406. [PMID: 23725472 DOI: 10.1146/annurev-phyto-082712-102255] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Transcription activator-like (TAL) effectors are encoded by plant-pathogenic bacteria and induce expression of plant host genes. TAL effectors bind DNA on the basis of a unique code that specifies binding of amino acid residues in repeat units to particular DNA bases in a one-to-one correspondence. This code can be used to predict binding sites of natural TAL effectors and to design novel synthetic DNA-binding domains for targeted genome manipulation. Natural mechanisms of resistance in plants against TAL effector-containing pathogens have given insights into new strategies for disease control.
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Affiliation(s)
- Sebastian Schornack
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, United Kingdom
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