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Lucioli A, Tavazza R, Baima S, Fatyol K, Burgyan J, Tavazza M. CRISPR-Cas9 Targeting of the eIF4E1 Gene Extends the Potato Virus Y Resistance Spectrum of the Solanum tuberosum L. cv. Desirée. Front Microbiol 2022; 13:873930. [PMID: 35722301 PMCID: PMC9198583 DOI: 10.3389/fmicb.2022.873930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/10/2022] [Indexed: 11/26/2022] Open
Abstract
Translation initiation factors and, in particular, the eIF4E family are the primary source of recessive resistance to potyviruses in many plant species. However, no eIF4E-mediated resistance to this virus genus has been identified in potato (Solanum tuberosum L.) germplasm. As in tomato, the potato eIF4E gene family consists of eIF4E1, its paralog eIF4E2, eIF(iso)4E, and nCBP. In tomato, eIF4E1 knockout (KO) confers resistance to a subset of potyviruses, while the eIF4E1/2 double KO, although conferring a broader spectrum of resistance, leads to plant developmental defects. Here, the tetraploid potato cv. Desirée owning the dominant Ny gene conferring resistance to potato virus Y (PVY) strain O but not NTN was used to evaluate the possibility to expand its PVY resistance spectrum by CRISPR-Cas9-mediated KO of the eIF4E1 susceptibility gene. After a double process of plant protoplast transfection-regeneration, eIF4E1 KO potatoes were obtained. The knockout was specific for the eIF4E1, and no mutations were identified in its eIF4E2 paralog. Expression analysis of the eIF4E family shows that the disruption of the eIF4E1 does not alter the RNA steady-state level of the other family members. The eIF4E1 KO lines challenged with a PVYNTN isolate showed a reduced viral accumulation and amelioration of virus-induced symptoms suggesting that the eIF4E1 gene was required but not essential for its multiplication. Our data show that eIF4E1 editing can be usefully exploited to broaden the PVY resistance spectrum of elite potato cultivars, such as Desirée, by pyramiding eIF4E-mediated recessive resistance.
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Affiliation(s)
- Alessandra Lucioli
- Biotechnology Laboratory, Biotechnology and Agroindustry Division, Department for Sustainability, ENEA, CR Casaccia, Rome, Italy
| | - Raffaela Tavazza
- Biotechnology Laboratory, Biotechnology and Agroindustry Division, Department for Sustainability, ENEA, CR Casaccia, Rome, Italy
| | - Simona Baima
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Rome, Italy
| | - Karoly Fatyol
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Godollo, Hungary
| | - Jozsef Burgyan
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Godollo, Hungary
| | - Mario Tavazza
- Biotechnology Laboratory, Biotechnology and Agroindustry Division, Department for Sustainability, ENEA, CR Casaccia, Rome, Italy
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Udagawa H, Koga K, Shinjo A, Kitashiba H, Takakura Y. Loss-of-function of Nicotiana tabacum L. eukaryotic translation initiation factors eIF4E1-S and eIF(iso)4E-T synergistically confers high-level resistance to both Potato virus Y (PVY) and resistance-breaking PVY. BREEDING SCIENCE 2021; 71:193-200. [PMID: 34377067 PMCID: PMC8329879 DOI: 10.1270/jsbbs.20114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/16/2020] [Indexed: 05/07/2023]
Abstract
The plant eukaryotic translation-initiation factors eIF4E and eIF(iso)4E play key roles in infection by plant RNA viruses, especially potyviruses. Mutations in the genes that encode these factors reduce susceptibility to the viruses. In the amphidiploid plant tobacco (Nicotiana tabacum L.), eIF4E1-S deletion mutants resist Potato virus Y (PVY), but resistance-breaking strains (RB-PVY) have appeared. In an earlier study, we demonstrated that the loss-of-function of eIF(iso)4E-T reduces susceptibility to RB-PVY. Here, we show that simultaneous inhibition of eIF4E1-S and eIF(iso)4E-T synergistically confers enhanced resistance to both PVY and RB-PVY without host growth or development defects. PVY symptoms and accumulation in a tobacco line lacking eIF4E1-S were detected at 14 days post-inoculation (dpi) and RB-PVY symptoms in lines without functional eIF(iso)4E-T were observed at 24 dpi. RB-PVY emerged in a PVY-infected tobacco line lacking eIF4E1-S. In contrast, lines without functional eIF4E1-S and eIF(iso)4E-T were nearly immune to PVY and RB-PVY, and little accumulation of either virus was detected even at 56 dpi. Thus, the lines will be promising for PVY-resistance breeding. This study provides a novel strategy to develop tobacco highly resistant to PVY and RB-PVY, and insights into the mechanisms responsible for high-level resistance.
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Affiliation(s)
- Hisashi Udagawa
- Leaf Tobacco Research Center, Japan Tobacco, Inc., 1900 Idei, Oyama, Tochigi 323-0808, Japan
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Kazuharu Koga
- Leaf Tobacco Research Center, Japan Tobacco, Inc., 1900 Idei, Oyama, Tochigi 323-0808, Japan
| | - Akira Shinjo
- Leaf Tobacco Research Center, Japan Tobacco, Inc., 1900 Idei, Oyama, Tochigi 323-0808, Japan
| | - Hiroyasu Kitashiba
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Yoshimitsu Takakura
- Leaf Tobacco Research Center, Japan Tobacco, Inc., 1900 Idei, Oyama, Tochigi 323-0808, Japan
- Corresponding author (e-mail: )
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Bilal M, Tabassum B, Ali Q, Nasir IA. Down Regulation of Potato Virus Y (PVY) Coat Protein (CP) Expression by Iberis gibraltarica Protein Extract. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721010102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Zhan X, Zhang F, Zhong Z, Chen R, Wang Y, Chang L, Bock R, Nie B, Zhang J. Generation of virus-resistant potato plants by RNA genome targeting. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1814-1822. [PMID: 30803101 PMCID: PMC6686122 DOI: 10.1111/pbi.13102] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 05/07/2023]
Abstract
CRISPR/Cas systems provide bacteria and archaea with molecular immunity against invading phages and foreign plasmids. The class 2 type VI CRISPR/Cas effector Cas13a is an RNA-targeting CRISPR effector that provides protection against RNA phages. Here we report the repurposing of CRISPR/Cas13a to protect potato plants from a eukaryotic virus, Potato virus Y (PVY). Transgenic potato lines expressing Cas13a/sgRNA (small guide RNA) constructs showed suppressed PVY accumulation and disease symptoms. The levels of viral resistance correlated with the expression levels of the Cas13a/sgRNA construct in the plants. Our data further demonstrate that appropriately designed sgRNAs can specifically interfere with multiple PVY strains, while having no effect on unrelated viruses such as PVA or Potato virus S. Our findings provide a novel and highly efficient strategy for engineering crops with resistances to viral diseases.
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Affiliation(s)
- Xiaohui Zhan
- State Key Laboratory of Biocatalysis and Enzyme EngineeringSchool of Life SciencesHubei UniversityWuhanChina
| | - Fengjuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringSchool of Life SciencesHubei UniversityWuhanChina
| | - Ziyang Zhong
- Key Laboratory of Potato Biology and BiotechnologyMinistry of Agriculture and Rural AffairsNational Center for Vegetable Improvement (Central China)Huazhong Agricultural UniversityWuhanChina
| | - Ruhao Chen
- Key Laboratory of Potato Biology and BiotechnologyMinistry of Agriculture and Rural AffairsNational Center for Vegetable Improvement (Central China)Huazhong Agricultural UniversityWuhanChina
| | - Yong Wang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringSchool of Life SciencesHubei UniversityWuhanChina
| | - Ling Chang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringSchool of Life SciencesHubei UniversityWuhanChina
| | - Ralph Bock
- State Key Laboratory of Biocatalysis and Enzyme EngineeringSchool of Life SciencesHubei UniversityWuhanChina
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Bihua Nie
- Key Laboratory of Potato Biology and BiotechnologyMinistry of Agriculture and Rural AffairsNational Center for Vegetable Improvement (Central China)Huazhong Agricultural UniversityWuhanChina
| | - Jiang Zhang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringSchool of Life SciencesHubei UniversityWuhanChina
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Michel V, Julio E, Candresse T, Cotucheau J, Decorps C, Volpatti R, Moury B, Glais L, Jacquot E, de Borne FD, Decroocq V, Gallois J, German-Retana S. A complex eIF4E locus impacts the durability of va resistance to Potato virus Y in tobacco. MOLECULAR PLANT PATHOLOGY 2019; 20:1051-1066. [PMID: 31115167 PMCID: PMC6640182 DOI: 10.1111/mpp.12810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Many recessive resistances against potyviruses are mediated by eukaryotic translation initiation factor 4E (eIF4E). In tobacco, the va resistance gene commonly used to control Potato virus Y (PVY) corresponds to a large deletion affecting the eIF4E-1 gene on chromosome 21. Here, we compared the resistance durability conferred by various types of mutations affecting eIF4E-1 (deletions of various sizes, frameshift or nonsense mutations). The 'large deletion' genotypes displayed the broadest and most durable resistance, whereas frameshift and nonsense mutants displayed a less durable resistance, with rapid and frequent apparition of resistance-breaking variants. In addition, genetic and transcriptomic analyses revealed that resistance durability is strongly impacted by a complex genetic locus on chromosome 14, which contains three other eIF4E genes. One of these, eIF4E-3, is rearranged as a hybrid gene between eIF4E-2 and eIF4E-3 (eIF4E-2-3 ) in the genotypes showing the most durable resistance, while eIF4E-2 is differentially expressed between the tested varieties. RNA-seq and quantitative reverse transcriptase-polymerase chain reaction experiments demonstrated that eIF4E-2 expression level is positively correlated with resistance durability. These results suggest that besides the nature of the mutation affecting eIF4E-1, three factors linked with a complex locus may potentially impact va durability: loss of an integral eIF4E-3, presence of eIF4E-2-3 and overexpression of eIF4E-2. This latter gene might act as a decoy in a non-productive virus-plant interaction, limiting the ability of PVY to evolve towards resistance breaking. Taken together, these results show that va resistance durability can in large part be explained by complex redundancy effects in the eIF4E gene family.
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Affiliation(s)
- Vincent Michel
- UMR 1332 Biologie du Fruit et PathologieINRA, University Bordeaux71 Av. E. BourlauxVillenave d’Ornon Cedex CS 2003233882France
| | - Emilie Julio
- Seita Imperial TobaccoLa Tour24100BergeracFrance
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et PathologieINRA, University Bordeaux71 Av. E. BourlauxVillenave d’Ornon Cedex CS 2003233882France
| | | | | | | | - Benoît Moury
- Unité de Pathologie Végétale, INRA, Centre Recherche PACA, Domaine Saint MauriceMontfavet Cedex CS 60094F84143France
| | - Laurent Glais
- UMR IGEPPINRA, Domaine de la MotteBP 35327Le Rheu Cedex35653France
| | - Emmanuel Jacquot
- INRA‐Cirad‐Supagro Montpellier, UMR BGPIMontpellier Cedex34398France
| | | | - Véronique Decroocq
- UMR 1332 Biologie du Fruit et PathologieINRA, University Bordeaux71 Av. E. BourlauxVillenave d’Ornon Cedex CS 2003233882France
| | - Jean‐Luc Gallois
- INRA‐UR 1052, GAFL Domaine St Maurice – CS 60094Montfavet CedexF‐84143
| | - Sylvie German-Retana
- UMR 1332 Biologie du Fruit et PathologieINRA, University Bordeaux71 Av. E. BourlauxVillenave d’Ornon Cedex CS 2003233882France
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Takakura Y, Udagawa H, Shinjo A, Koga K. Mutation of a Nicotiana tabacum L. eukaryotic translation-initiation factor gene reduces susceptibility to a resistance-breaking strain of Potato virus Y. MOLECULAR PLANT PATHOLOGY 2018; 19:2124-2133. [PMID: 29633509 PMCID: PMC6638035 DOI: 10.1111/mpp.12686] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 03/08/2018] [Accepted: 04/03/2018] [Indexed: 05/23/2023]
Abstract
Eukaryotic translation-initiation factors eIF4E and eIF(iso)4E in plants play key roles in infection by potyviruses and other plant RNA viruses. Mutations in the genes encoding these factors reduce susceptibility to the viruses, and are the basis of several recessive virus resistance genes widely used in plant breeding. Because virus variants occasionally break such resistance, the molecular basis for this process must be elucidated. Although deletion mutants of eIF4E1-S of tobacco (Nicotiana tabacum L.) resist Potato virus Y (PVY; the type member of the genus Potyvirus), resistance-breaking strains of PVY threaten tobacco production worldwide. Here, we used RNA interference technology to knock down tobacco eIF4E2-S and eIF4E2-T genes or eIF(iso)4E-S and eIF(iso)4E-T genes. Transgenic plants with reduced transcript levels of both eIF(iso)4E-S and eIF(iso)4E-T showed reduced susceptibility to a resistance-breaking PVY strain with a K105E mutation in the viral genome-associated protein (VPg). By screening a population of chemically induced mutants of eIF(iso)4E-S and eIF(iso)4E-T, we showed that plants with a nonsense mutation in eIF(iso)4E-T, but not eIF(iso)4E-S, showed reduced susceptibility to the resistance-breaking PVY strain. In a yeast two-hybrid assay, VPg of the resistance-breaking strain, but not wild-type PVY, physically interacted with the eIF(iso)4E-T protein. Thus, eIF4E1-S is required for infection by PVY, but eIF(iso)4E-T is required for infection by the resistance-breaking strain. Our study provides the first evidence for the involvement of a host eukaryotic translation-initiation factor in the infection cycle of a resistance-breaking virus strain. The eIF(iso)4E-T mutants will be useful in tobacco breeding to introduce resistance against resistance-breaking PVY strains.
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Affiliation(s)
- Yoshimitsu Takakura
- Leaf Tobacco Research Center, Japan Tobacco, Inc.1900 Idei, OyamaTochigi 323‐0808Japan
| | - Hisashi Udagawa
- Leaf Tobacco Research Center, Japan Tobacco, Inc.1900 Idei, OyamaTochigi 323‐0808Japan
| | - Akira Shinjo
- Leaf Tobacco Research Center, Japan Tobacco, Inc.1900 Idei, OyamaTochigi 323‐0808Japan
| | - Kazuharu Koga
- Leaf Tobacco Research Center, Japan Tobacco, Inc.1900 Idei, OyamaTochigi 323‐0808Japan
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Michel V, Julio E, Candresse T, Cotucheau J, Decorps C, Volpatti R, Moury B, Glais L, Dorlhac de Borne F, Decroocq V, German-Retana S. NtTPN1: a RPP8-like R gene required for Potato virus Y-induced veinal necrosis in tobacco. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:700-714. [PMID: 29863810 DOI: 10.1111/tpj.13980] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 04/19/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
Potato virus Y (PVY) is one of the most damaging viruses of tobacco. In particular, aggressive necrotic strains (PVYN ) lead to considerable losses in yield. The main source of resistance against PVY is linked to the va locus. However, va-overcoming PVY isolates inducing necrotic symptoms were observed in several countries. In this context, it is important to find va-independent protection strategies. In a previous study, the phenotyping of 162 tobacco varieties revealed 10 accessions that do not carry the va allele and do not exhibit typical PVYN -induced veinal necrosis. Despite the absence of necrotic symptoms, normal viral accumulation in these plants suggests a va-independent mechanism of tolerance to PVYN -induced systemic veinal necrosis. Fine mapping of the genetic determinant(s) was performed in a segregating F2 population. The tolerance trait is inherited as a single recessive gene, and allelism tests demonstrated that eight of the 10 tolerant varieties carry the same determinant. Anchoring the linkage map to the tobacco genome physical map allowed the identification of a RPP8-like R gene, called NtTPN1 (for Nicotiana tabacum Tolerance to PVY-induced Necrosis1), with the same single-nucleotide polymorphism in the eight tolerant accessions. Functional assays using homozygous NtTPN1 EMS mutants confirmed the role of NtTPN1 in the tolerance phenotype. PVYN -induced systemic veinal necrosis in tobacco likely represents an inefficient defense response with hypersensitive response-like characteristics. The identification of NtTPN1 opens breeding options to minimize the impact of emerging and so far uncontrolled va-breaking necrotic PVY isolates.
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Affiliation(s)
- Vincent Michel
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, 71 Av. E. Bourlaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Emilie Julio
- Imperial Tobacco, La Tour, 24100, Bergerac, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, 71 Av. E. Bourlaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | | | | | | | - Benoît Moury
- Pathologie Végétale, INRA, 84140, Montfavet, France
| | - Laurent Glais
- FN3PT/RD3PT, 75008, Paris, France
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, 35650, Le Rheu, France
| | | | - Véronique Decroocq
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, 71 Av. E. Bourlaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Sylvie German-Retana
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, 71 Av. E. Bourlaux, CS 20032, 33882, Villenave d'Ornon Cedex, France
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