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Ng BW, Kaukonen MK, McClements ME, Shamsnajafabadi H, MacLaren RE, Cehajic-Kapetanovic J. Genetic therapies and potential therapeutic applications of CRISPR activators in the eye. Prog Retin Eye Res 2024:101289. [PMID: 39127142 DOI: 10.1016/j.preteyeres.2024.101289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Conventional gene therapy involving supplementation only treats loss-of-function diseases and is limited by viral packaging sizes, precluding therapy of large genes. The discovery of CRISPR/Cas has led to a paradigm shift in the field of genetic therapy, with the promise of precise gene editing, thus broadening the range of diseases that can be treated. The initial uses of CRISPR/Cas have focused mainly on gene editing or silencing of abnormal variants via utilising Cas endonuclease to trigger the target cell endogenous non-homologous end joining. Subsequently, the technology has evolved to modify the Cas enzyme and even its guide RNA, leading to more efficient editing tools in the form of base and prime editing. Further advancements of this CRISPR/Cas technology itself have expanded its functional repertoire from targeted editing to programmable transactivation, shifting the therapeutic focus to precise endogenous gene activation or upregulation with the potential for epigenetic modifications. In vivo experiments using this platform have demonstrated the potential of CRISPR-activators (CRISPRa) to treat various loss-of-function diseases, as well as in regenerative medicine, highlighting their versatility to overcome limitations associated with conventional strategies. This review summarises the molecular mechanisms of CRISPRa platforms, the current applications of this technology in vivo, and discusses potential solutions to translational hurdles for this therapy, with a focus on ophthalmic diseases.
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Affiliation(s)
- Benjamin Wj Ng
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Maria K Kaukonen
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Michelle E McClements
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Hoda Shamsnajafabadi
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Robert E MacLaren
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Jasmina Cehajic-Kapetanovic
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
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2
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Anny CA, Nouaille S, Fauré R, Schulz C, Spriet C, Huvent I, Biot C, Lefebvre T. A Step-by-Step Guide for the Production of Recombinant Fluorescent TAT-HA-Tagged Proteins and their Transduction into Mammalian Cells. Curr Protoc 2024; 4:e1016. [PMID: 38511507 DOI: 10.1002/cpz1.1016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Investigating the function of target proteins for functional prospection or therapeutic applications typically requires the production and purification of recombinant proteins. The fusion of these proteins with tag peptides and fluorescently derived proteins allows the monitoring of candidate proteins using SDS-PAGE coupled with western blotting and fluorescent microscopy, respectively. However, protein engineering poses a significant challenge for many researchers. In this protocol, we describe step-by-step the engineering of a recombinant protein with various tags: TAT-HA (trans-activator of transduction-hemagglutinin), 6×His and EGFP (enhanced green fluorescent protein) or mCherry. Fusion proteins are produced in E. coli BL21(DE3) cells and purified by immobilized metal affinity chromatography (IMAC) using a Ni-nitrilotriacetic acid (NTA) column. Then, tagged recombinant proteins are introduced into cultured animal cells by using the penetrating peptide TAT-HA. Here, we present a thorough protocol providing a detailed guide encompassing every critical step from plasmid DNA molecular assembly to protein expression and subsequent purification and outlines the conditions necessary for protein transduction technology into animal cells in a comprehensive manner. We believe that this protocol will be a valuable resource for researchers seeking an exhaustive, step-by-step guide for the successful production and purification of recombinant proteins and their entry by transduction within living cells. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: DNA cloning, molecular assembly strategies, and protein production Basic Protocol 2: Protein purification Basic Protocol 3: Protein transduction in mammalian cells.
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Affiliation(s)
| | | | - Régis Fauré
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Céline Schulz
- Université de Lille, CNRS, UMR 8576 - UGSF, Lille, France
| | - Corentin Spriet
- Université de Lille, CNRS, UMR 8576 - UGSF, Lille, France
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | | | | | - Tony Lefebvre
- Université de Lille, CNRS, UMR 8576 - UGSF, Lille, France
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3
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Erkes A, Grove RP, Žarković M, Krautwurst S, Koebnik R, Morgan RD, Wilson GG, Hölzer M, Marz M, Boch J, Grau J. Assembling highly repetitive Xanthomonas TALomes using Oxford Nanopore sequencing. BMC Genomics 2023; 24:151. [PMID: 36973643 PMCID: PMC10045945 DOI: 10.1186/s12864-023-09228-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome. The DNA-binding domain of TALEs is comprised of highly conserved repeats and TALE genes often occur in gene clusters, which precludes the assembly of TALE-carrying Xanthomonas genomes based on standard sequencing approaches. RESULTS Here, we report the successful assembly of the 5 Mbp genomes of five Xanthomonas strains from Oxford Nanopore Technologies (ONT) sequencing data. For one of these strains, Xanthomonas oryzae pv. oryzae (Xoo) PXO35, we illustrate why Illumina short reads and longer PacBio reads are insufficient to fully resolve the genome. While ONT reads are perfectly suited to yield highly contiguous genomes, they suffer from a specific error profile within homopolymers. To still yield complete and correct TALomes from ONT assemblies, we present a computational correction pipeline specifically tailored to TALE genes, which yields at least comparable accuracy as Illumina-based polishing. We further systematically assess the ONT-based pipeline for its multiplexing capacity and find that, combined with computational correction, the complete TALome of Xoo PXO35 could have been reconstructed from less than 20,000 ONT reads. CONCLUSIONS Our results indicate that multiplexed ONT sequencing combined with a computational correction of TALE genes constitutes a highly capable tool for characterizing the TALomes of huge collections of Xanthomonas strains in the future.
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany
| | - René P Grove
- Department of Plant Biotechnology, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Milena Žarković
- Bioinformatics/High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Sebastian Krautwurst
- Bioinformatics/High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34090, Montpellier, France
| | | | | | - Martin Hölzer
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, 13353, Berlin, Germany
| | - Manja Marz
- Bioinformatics/High-Throughput Analysis, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, 30419, Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany.
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4
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Wu LB, Eom JS, Isoda R, Li C, Char SN, Luo D, Schepler-Luu V, Nakamura M, Yang B, Frommer WB. OsSWEET11b, a potential sixth leaf blight susceptibility gene involved in sugar transport-dependent male fertility. THE NEW PHYTOLOGIST 2022; 234:975-989. [PMID: 35211968 DOI: 10.1111/nph.18054] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
SWEETs play important roles in intercellular sugar transport. Induction of SWEET sugar transporters by Transcription Activator-Like effectors (TALe) of Xanthomonas ssp. is key for virulence in rice, cassava and cotton. We identified OsSWEET11b with roles in male fertility and potential bacterial blight (BB) susceptibility in rice. While single ossweet11a or 11b mutants were fertile, double mutants were sterile. As clade III SWEETs can transport gibberellin (GA), a key hormone for spikelet fertility, sterility and BB susceptibility might be explained by GA transport deficiencies. However, in contrast with the Arabidopsis homologues, OsSWEET11b did not mediate detectable GA transport. Fertility and susceptibility therefore are likely to depend on sucrose transport activity. Ectopic induction of OsSWEET11b by designer TALe enabled TALe-free Xanthomonas oryzae pv. oryzae (Xoo) to cause disease, identifying OsSWEET11b as a potential BB susceptibility gene and demonstrating that the induction of host sucrose uniporter activity is key to virulence of Xoo. Notably, only three of six clade III SWEETs are targeted by known Xoo strains from Asia and Africa. The identification of OsSWEET11b is relevant for fertility and for protecting rice against emerging Xoo strains that target OsSWEET11b.
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Affiliation(s)
- Lin-Bo Wu
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
- Department of Agronomy and Crop Physiology, Institute for Agronomy and Plant Breeding I, Justus-Liebig University Giessen, Giessen, 35392, Germany
| | - Joon-Seob Eom
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Reika Isoda
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Chenhao Li
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Si Nian Char
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Dangping Luo
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Van Schepler-Luu
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Masayoshi Nakamura
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Bing Yang
- Division of Plant Science and Technology, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Wolf B Frommer
- Institute for Molecular Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
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5
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Zárate‐Chaves CA, Gómez de la Cruz D, Verdier V, López CE, Bernal A, Szurek B. Cassava diseases caused by Xanthomonas phaseoli pv. manihotis and Xanthomonas cassavae. MOLECULAR PLANT PATHOLOGY 2021; 22:1520-1537. [PMID: 34227737 PMCID: PMC8578842 DOI: 10.1111/mpp.13094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 05/27/2023]
Abstract
Xanthomonas phaseoli pv. manihotis (Xpm) and X. cassavae (Xc) are two bacterial pathogens attacking cassava. Cassava bacterial blight (CBB) is a systemic disease caused by Xpm, which might have dramatic effects on plant growth and crop production. Cassava bacterial necrosis is a nonvascular disease caused by Xc with foliar symptoms similar to CBB, but its impacts on the plant vigour and the crop are limited. In this review, we describe the epidemiology and ecology of the two pathogens, the impacts and management of the diseases, and the main research achievements for each pathosystem. Because Xc data are sparse, our main focus is on Xpm and CBB.
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Affiliation(s)
| | | | - Valérie Verdier
- PHIMUniversité MontpellierCIRADINRAeIRDInstitut AgroMontpellierFrance
| | - Camilo E. López
- Manihot Biotec, Departamento de BiologíaUniversidad Nacional de ColombiaBogotáColombia
| | - Adriana Bernal
- Laboratorio de Interacciones Moleculares de Microorganismos AgrícolasDepartamento de Ciencias BásicasUniversidad de los AndesBogotáColombia
| | - Boris Szurek
- PHIMUniversité MontpellierCIRADINRAeIRDInstitut AgroMontpellierFrance
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6
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Zou L, Zhang C, Li Y, Yang X, Wang Y, Yan Y, Yang R, Huang M, Haq F, Yang C, Chen G. An improved, versatile and efficient modular plasmid assembly system for expression analyses of genes in Xanthomonas oryzae. MOLECULAR PLANT PATHOLOGY 2021; 22:480-492. [PMID: 33486879 PMCID: PMC7938625 DOI: 10.1111/mpp.13033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/02/2020] [Accepted: 12/10/2020] [Indexed: 06/12/2023]
Abstract
Xanthomonas oryzae pathovars oryzae (Xoo) and oryzicola (Xoc) infect rice, causing bacterial blight and bacterial leaf streak, respectively, which are two economically important bacterial diseases in paddy fields. The interactions of Xoo and Xoc with rice can be used as models for studying fundamental aspects of bacterial pathogenesis and host tissue specificity. However, an improved vector system for gene expression analysis is desired for Xoo and Xoc because some broad host range vectors that can replicate stably in X. oryzae pathovars are low-copy number plasmids. To overcome this limitation, we developed a modular plasmid assembly system to transfer the functional DNA modules from the entry vectors into the pHM1-derived backbone vectors on a high-copy number basis. We demonstrated the feasibility of our vector system for protein detection, and quantification of virulence gene expression under laboratory conditions and in association with host rice and nonhost tobacco cells. This system also allows execution of a mutant complementation equivalent to the single-copy chromosomal integration system and tracing of pathogens in rice leaf. Based on this assembly system, we constructed a series of protein expression and promoter-probe vectors suitable for classical double restriction enzyme cloning. These vector systems enable cloning of all genes or promoters of interest from Xoo and Xoc strains. Our modular assembly system represents a versatile and highly efficient toolkit for gene expression analysis that will accelerate studies on interactions of X. oryzae with rice.
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Affiliation(s)
- Lifang Zou
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of ChinaShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
| | - Cuiping Zhang
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yilang Li
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xiaofei Yang
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yanyan Wang
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Yichao Yan
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ruihuan Yang
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Mengsang Huang
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Fazal Haq
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Ching‐Hong Yang
- Department of Biological SciencesUniversity of WisconsinMilwaukeeWisconsinUSA
| | - Gongyou Chen
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of ChinaShanghai Jiao Tong UniversityShanghaiChina
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences & BiotechnologyShanghai Jiao Tong UniversityShanghaiChina
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7
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Webster J, Bogema D, Chapman TA. Comparative Genomics of Xanthomonas citri pv. citri A* Pathotype Reveals Three Distinct Clades with Varying Plasmid Distribution. Microorganisms 2020; 8:microorganisms8121947. [PMID: 33302542 PMCID: PMC7764509 DOI: 10.3390/microorganisms8121947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 11/23/2022] Open
Abstract
Citrus bacterial canker (CBC) is an important disease of citrus cultivars worldwide that causes blister-like lesions on host plants and leads to more severe symptoms such as plant defoliation and premature fruit drop. The causative agent, Xanthomonas citri pv. citri, exists as three pathotypes—A, A*, and Aw—which differ in their host range and elicited host response. To date, comparative analyses have been hampered by the lack of closed genomes for the A* pathotype. In this study, we sequenced and assembled six CBC isolates of pathotype A* using second- and third-generation sequencing technologies to produce complete, closed assemblies. Analysis of these genomes and reference A, A*, and Aw sequences revealed genetic groups within the A* pathotype. Investigation of accessory genomes revealed virulence factors, including type IV secretion systems and heavy metal resistance genes, differentiating the genetic groups. Genomic comparisons of closed genome assemblies also provided plasmid distribution information for the three genetic groups of A*. The genomes presented here complement existing closed genomes of A and Aw pathotypes that are publicly available and open opportunities to investigate the evolution of X. citri pv. citri and the virulence factors that contribute to this serious pathogen.
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8
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Oliva R, Ji C, Atienza-Grande G, Huguet-Tapia JC, Perez-Quintero A, Li T, Eom JS, Li C, Nguyen H, Liu B, Auguy F, Sciallano C, Luu VT, Dossa GS, Cunnac S, Schmidt SM, Slamet-Loedin IH, Vera Cruz C, Szurek B, Frommer WB, White FF, Yang B. Broad-spectrum resistance to bacterial blight in rice using genome editing. Nat Biotechnol 2019; 37:1344-1350. [PMID: 31659337 PMCID: PMC6831514 DOI: 10.1038/s41587-019-0267-z] [Citation(s) in RCA: 305] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/28/2019] [Indexed: 02/01/2023]
Abstract
Bacterial blight of rice is an important disease in Asia and Africa. The pathogen, Xanthomonas oryzae pv. oryzae (Xoo), secretes one or more of six known transcription-activator-like effectors (TALes) that bind specific promoter sequences and induce, at minimum, one of the three host sucrose transporter genes SWEET11, SWEET13 and SWEET14, the expression of which is required for disease susceptibility. We used CRISPR-Cas9-mediated genome editing to introduce mutations in all three SWEET gene promoters. Editing was further informed by sequence analyses of TALe genes in 63 Xoo strains, which revealed multiple TALe variants for SWEET13 alleles. Mutations were also created in SWEET14, which is also targeted by two TALes from an African Xoo lineage. A total of five promoter mutations were simultaneously introduced into the rice line Kitaake and the elite mega varieties IR64 and Ciherang-Sub1. Paddy trials showed that genome-edited SWEET promoters endow rice lines with robust, broad-spectrum resistance.
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Affiliation(s)
- Ricardo Oliva
- International Rice Research Institute, Metro Manila, Philippines.
| | - Chonghui Ji
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Genelou Atienza-Grande
- International Rice Research Institute, Metro Manila, Philippines
- College of Agriculture and Food Science, University of the Philippines Los Baños, Los Baños, Philippines
| | | | - Alvaro Perez-Quintero
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Ting Li
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Joon-Seob Eom
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf and Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Chenhao Li
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Hanna Nguyen
- International Rice Research Institute, Metro Manila, Philippines
| | - Bo Liu
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Florence Auguy
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | | | - Van T Luu
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf and Max Planck Institute for Plant Breeding Research, Köln, Germany
| | | | | | - Sarah M Schmidt
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf and Max Planck Institute for Plant Breeding Research, Köln, Germany
| | | | | | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | - Wolf B Frommer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf and Max Planck Institute for Plant Breeding Research, Köln, Germany.
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Aichi, Japan.
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
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9
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Eom JS, Luo D, Atienza-Grande G, Yang J, Ji C, Thi Luu V, Huguet-Tapia JC, Char SN, Liu B, Nguyen H, Schmidt SM, Szurek B, Vera Cruz C, White FF, Oliva R, Yang B, Frommer WB. Diagnostic kit for rice blight resistance. Nat Biotechnol 2019; 37:1372-1379. [PMID: 31659338 PMCID: PMC6831515 DOI: 10.1038/s41587-019-0268-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/28/2019] [Indexed: 11/09/2022]
Abstract
Blight-resistant rice lines are the most effective solution for bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo). Key resistance mechanisms involve SWEET genes as susceptibility factors. Bacterial transcription activator-like (TAL) effectors bind to effector-binding elements (EBEs) in SWEET gene promoters and induce SWEET genes. EBE variants that cannot be recognized by TAL effectors abrogate induction, causing resistance. Here we describe a diagnostic kit to enable analysis of bacterial blight in the field and identification of suitable resistant lines. Specifically, we include a SWEET promoter database, RT–PCR primers for detecting SWEET induction, engineered reporter rice lines to visualize SWEET protein accumulation and knock-out rice lines to identify virulence mechanisms in bacterial isolates. We also developed CRISPR–Cas9 genome-edited Kitaake rice to evaluate the efficacy of EBE mutations in resistance, software to predict the optimal resistance gene set for a specific geographic region, and two resistant ‘mega’ rice lines that will empower farmers to plant lines that are most likely to resist rice blight. Strategic deployment of blight-resistant rice lines is enabled by a molecular diagnostic kit.
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Affiliation(s)
- Joon-Seob Eom
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dangping Luo
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Genelou Atienza-Grande
- International Rice Research Institute, Metro Manila, Philippines.,College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
| | - Jungil Yang
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Chonghui Ji
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Van Thi Luu
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Si Nian Char
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Bo Liu
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Hanna Nguyen
- International Rice Research Institute, Metro Manila, Philippines
| | - Sarah Maria Schmidt
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | | | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Ricardo Oliva
- International Rice Research Institute, Metro Manila, Philippines
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA. .,Donald Danforth Plant Science Center, St. Louis, MO, USA.
| | - Wolf B Frommer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany. .,Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Aichi, Japan.
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