1
|
Yang Z, Li G, Zhang Y, Li F, Zhou T, Ye J, Wang X, Zhang X, Sun Z, Tao X, Wu M, Wu J, Li Y. Crop antiviral defense: Past and future perspective. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2680-3. [PMID: 39190125 DOI: 10.1007/s11427-024-2680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/09/2024] [Indexed: 08/28/2024]
Abstract
Viral pathogens not only threaten the health and life of humans and animals but also cause enormous crop yield losses and contribute to global food insecurity. To defend against viral pathogens, plants have evolved an intricate immune system to perceive and cope with such attacks. Although most of the fundamental studies were carried out in model plants, more recent research in crops has provided new insights into the antiviral strategies employed by crop plants. We summarize recent advances in understanding the biological roles of cellular receptors, RNA silencing, RNA decay, hormone signaling, autophagy, and ubiquitination in manipulating crop host-mediated antiviral responses. The potential functions of circular RNAs, the rhizosphere microbiome, and the foliar microbiome of crops in plant-virus interactions will be fascinating research directions in the future. These findings will be beneficial for the development of modern crop improvement strategies.
Collapse
Affiliation(s)
- Zhirui Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Guangyao Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tao Zhou
- State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Jian Ye
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianbing Wang
- State Key Laboratory of Plant Environmental Resilience, Frontiers Science Center for Molecular Design Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100049, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Xiaorong Tao
- Department of Plant Pathology, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ming Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianguo Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yi Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| |
Collapse
|
2
|
Sun P, Han X, Milne RJ, Li G. Trans-crop applications of atypical R genes for multipathogen resistance. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00122-5. [PMID: 38811244 DOI: 10.1016/j.tplants.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/31/2024]
Abstract
Genetic resistance to plant diseases is essential for global food security. Significant progress has been achieved for plant disease-resistance (R) genes comprising nucleotide-binding domain, leucine-rich repeat-containing receptors (NLRs), and membrane-localized receptor-like kinases or proteins (RLKs/RLPs), which we refer to as typical R genes. However, there is a knowledge gap in how non-receptor-type or atypical R genes contribute to plant immunity. Here, we summarize resources and technologies facilitating the study of atypical R genes, examine diverse atypical R proteins for broad-spectrum resistance, and outline potential approaches for trans-crop applications of atypical R genes. Studies of atypical R genes are important for a holistic understanding of plant immunity and the development of novel strategies in disease control and crop improvement.
Collapse
Affiliation(s)
- Peng Sun
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinyu Han
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ricky J Milne
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia.
| | - Guotian Li
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, The Center of Crop Nanobiotechnology, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
3
|
Lebedeva M, Nikonova E, Babakov A, Kolesnikova V, Razhina O, Zlobin N, Taranov V, Nikonov O. Interaction of Solanum tuberosum L. translation initiation factors eIF4E with potato virus Y VPg: Apprehend and avoid. Biochimie 2024; 219:1-11. [PMID: 37562705 DOI: 10.1016/j.biochi.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
Potato virus Y (PVY) is one of the most dangerous agricultural pathogens that causes substantial harm to vegetative propagated crops, such as potatoes (Solanum tuberosum L.). A necessary condition for PVY infection is an interaction between the plant cap-binding translation initiation factors eIF4E and a viral protein VPg, which mimics the cap-structure. In this study, we identified the point mutations in potato eIF4E1 and eIF4E2 that disrupt VPg binding while preserving the functional activity. For the structural interpretation of the obtained results, molecular models of all the studied forms of eIF4E1 and eIF4E2 were constructed and analyzed via molecular dynamics. The results of molecular dynamics simulations corresponds to the biochemical results and suggests that the β1β2 loop plays a key role in the stabilization of both eIF4E-cap and eIF4E-VPg complexes.
Collapse
Affiliation(s)
- Marina Lebedeva
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, 127550, Moscow, Russia.
| | - Ekaterina Nikonova
- Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
| | - Alexey Babakov
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, 127550, Moscow, Russia
| | - Victoria Kolesnikova
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, 127550, Moscow, Russia; Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
| | - Oksana Razhina
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, 127550, Moscow, Russia
| | - Nikolay Zlobin
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, 127550, Moscow, Russia
| | - Vasiliy Taranov
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, 127550, Moscow, Russia
| | - Oleg Nikonov
- Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
| |
Collapse
|
4
|
Shahriari Z, Su X, Zheng K, Zhang Z. Advances and Prospects of Virus-Resistant Breeding in Tomatoes. Int J Mol Sci 2023; 24:15448. [PMID: 37895127 PMCID: PMC10607384 DOI: 10.3390/ijms242015448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Plant viruses are the main pathogens which cause significant quality and yield losses in tomato crops. The important viruses that infect tomatoes worldwide belong to five genera: Begomovirus, Orthotospovirus, Tobamovirus, Potyvirus, and Crinivirus. Tomato resistance genes against viruses, including Ty gene resistance against begomoviruses, Sw gene resistance against orthotospoviruses, Tm gene resistance against tobamoviruses, and Pot 1 gene resistance against potyviruses, have been identified from wild germplasm and introduced into cultivated cultivars via hybrid breeding. However, these resistance genes mainly exhibit qualitative resistance mediated by single genes, which cannot protect against virus mutations, recombination, mixed-infection, or emerging viruses, thus posing a great challenge to tomato antiviral breeding. Based on the epidemic characteristics of tomato viruses, we propose that future studies on tomato virus resistance breeding should focus on rapidly, safely, and efficiently creating broad-spectrum germplasm materials resistant to multiple viruses. Accordingly, we summarized and analyzed the advantages and characteristics of the three tomato antiviral breeding strategies, including marker-assisted selection (MAS)-based hybrid breeding, RNA interference (RNAi)-based transgenic breeding, and CRISPR/Cas-based gene editing. Finally, we highlighted the challenges and provided suggestions for improving tomato antiviral breeding in the future using the three breeding strategies.
Collapse
Affiliation(s)
- Zolfaghar Shahriari
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
- Crop and Horticultural Science Research Department, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Shiraz 617-71555, Iran
| | - Xiaoxia Su
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
| | - Kuanyu Zheng
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
| | - Zhongkai Zhang
- Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, Yunnan Seed Laboratory, 2238# Beijing Rd, Panlong District, Kunming 650205, China; (Z.S.); (X.S.)
| |
Collapse
|
5
|
Gebhardt C. A physical map of traits of agronomic importance based on potato and tomato genome sequences. Front Genet 2023; 14:1197206. [PMID: 37564870 PMCID: PMC10411547 DOI: 10.3389/fgene.2023.1197206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/30/2023] [Indexed: 08/12/2023] Open
Abstract
Potato, tomato, pepper, and eggplant are worldwide important crop and vegetable species of the Solanaceae family. Molecular linkage maps of these plants have been constructed and used to map qualitative and quantitative traits of agronomic importance. This research has been undertaken with the vision to identify the molecular basis of agronomic characters on the one hand, and on the other hand, to assist the selection of improved varieties in breeding programs by providing DNA-based markers that are diagnostic for specific agronomic characters. Since 2011, whole genome sequences of tomato and potato became available in public databases. They were used to combine the results of several hundred mapping and map-based cloning studies of phenotypic characters between 1988 and 2022 in physical maps of the twelve tomato and potato chromosomes. The traits evaluated were qualitative and quantitative resistance to pathogenic oomycetes, fungi, bacteria, viruses, nematodes, and insects. Furthermore, quantitative trait loci for yield and sugar content of tomato fruits and potato tubers and maturity or earliness were physically mapped. Cloned genes for pathogen resistance, a few genes underlying quantitative trait loci for yield, sugar content, and maturity, and several hundred candidate genes for these traits were included in the physical maps. The comparison between the physical chromosome maps revealed, in addition to known intrachromosomal inversions, several additional inversions and translocations between the otherwise highly collinear tomato and potato genomes. The integration of the positional information from independent mapping studies revealed the colocalization of qualitative and quantitative loci for resistance to different types of pathogens, called resistance hotspots, suggesting a similar molecular basis. Synteny between potato and tomato with respect to genomic positions of quantitative trait loci was frequently observed, indicating eventual similarity between the underlying genes.
Collapse
|
6
|
Kuroiwa K, Danilo B, Perrot L, Thenault C, Veillet F, Delacote F, Duchateau P, Nogué F, Mazier M, Gallois J. An iterative gene-editing strategy broadens eIF4E1 genetic diversity in Solanum lycopersicum and generates resistance to multiple potyvirus isolates. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:918-930. [PMID: 36715107 PMCID: PMC10106848 DOI: 10.1111/pbi.14003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/09/2022] [Accepted: 12/17/2022] [Indexed: 05/04/2023]
Abstract
Resistance to potyviruses in plants has been largely provided by the selection of natural variant alleles of eukaryotic translation initiation factors (eIF) 4E in many crops. However, the sources of such variability for breeding can be limited for certain crop species, while new virus isolates continue to emerge. Different methods of mutagenesis have been applied to inactivate the eIF4E genes to generate virus resistance, but with limited success due to the physiological importance of translation factors and their redundancy. Here, we employed genome editing approaches at the base level to induce non-synonymous mutations in the eIF4E1 gene and create genetic diversity in cherry tomato (Solanum lycopersicum var. cerasiforme). We sequentially edited the genomic sequences coding for two regions of eIF4E1 protein, located around the cap-binding pocket and known to be important for susceptibility to potyviruses. We show that the editing of only one of the two regions, by gene knock-in and base editing, respectively, is not sufficient to provide resistance. However, combining amino acid mutations in both regions resulted in resistance to multiple potyviruses without affecting the functionality in translation initiation. Meanwhile, we report that extensive base editing in exonic region can alter RNA splicing pattern, resulting in gene knockout. Altogether our work demonstrates that precision editing allows to design plant factors based on the knowledge on evolutionarily selected alleles and enlarge the gene pool to potentially provide advantageous phenotypes such as pathogen resistance.
Collapse
Affiliation(s)
| | | | - Laura Perrot
- Toulouse Biotechnology Institute, Université de ToulouseToulouseFrance
| | | | - Florian Veillet
- INRAE, Agrocampus OuestUniversité de Rennes, IGEPPPloudanielFrance
| | | | | | - Fabien Nogué
- Université Paris‐Saclay, INRAE, AgroParisTech, Institut Jean‐Pierre Bourgin (IJPB)VersaillesFrance
| | | | | |
Collapse
|
7
|
Zlobin N, Taranov V. Plant eIF4E isoforms as factors of susceptibility and resistance to potyviruses. FRONTIERS IN PLANT SCIENCE 2023; 14:1041868. [PMID: 36844044 PMCID: PMC9950400 DOI: 10.3389/fpls.2023.1041868] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Potyviruses are the largest group of plant-infecting RNA viruses that affect a wide range of crop plants. Plant resistance genes against potyviruses are often recessive and encode translation initiation factors eIF4E. The inability of potyviruses to use plant eIF4E factors leads to the development of resistance through a loss-of-susceptibility mechanism. Plants have a small family of eIF4E genes that encode several isoforms with distinct but overlapping functions in cell metabolism. Potyviruses use distinct eIF4E isoforms as susceptibility factors in different plants. The role of different members of the plant eIF4E family in the interaction with a given potyvirus could differ drastically. An interplay exists between different members of the eIF4E family in the context of plant-potyvirus interactions, allowing different eIF4E isoforms to modulate each other's availability as susceptibility factors for the virus. In this review, possible molecular mechanisms underlying this interaction are discussed, and approaches to identify the eIF4E isoform that plays a major role in the plant-potyvirus interaction are suggested. The final section of the review discusses how knowledge about the interaction between different eIF4E isoforms can be used to develop plants with durable resistance to potyviruses.
Collapse
|
8
|
Tatineni S, Hein GL. Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies. PHYTOPATHOLOGY 2023; 113:117-141. [PMID: 36095333 DOI: 10.1094/phyto-05-22-0167-rvw] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.
Collapse
Affiliation(s)
- Satyanarayana Tatineni
- U.S. Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Gary L Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583
| |
Collapse
|
9
|
Tsai WA, Brosnan CA, Mitter N, Dietzgen RG. Perspectives on plant virus diseases in a climate change scenario of elevated temperatures. STRESS BIOLOGY 2022; 2:37. [PMID: 37676437 PMCID: PMC10442010 DOI: 10.1007/s44154-022-00058-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/15/2022] [Indexed: 09/08/2023]
Abstract
Global food production is at risk from many abiotic and biotic stresses and can be affected by multiple stresses simultaneously. Virus diseases damage cultivated plants and decrease the marketable quality of produce. Importantly, the progression of virus diseases is strongly affected by changing climate conditions. Among climate-changing variables, temperature increase is viewed as an important factor that affects virus epidemics, which may in turn require more efficient disease management. In this review, we discuss the effect of elevated temperature on virus epidemics at both macro- and micro-climatic levels. This includes the temperature effects on virus spread both within and between host plants. Furthermore, we focus on the involvement of molecular mechanisms associated with temperature effects on plant defence to viruses in both susceptible and resistant plants. Considering various mechanisms proposed in different pathosystems, we also offer a view of the possible opportunities provided by RNA -based technologies for virus control at elevated temperatures. Recently, the potential of these technologies for topical field applications has been strengthened through a combination of genetically modified (GM)-free delivery nanoplatforms. This approach represents a promising and important climate-resilient substitute to conventional strategies for managing plant virus diseases under global warming scenarios. In this context, we discuss the knowledge gaps in the research of temperature effects on plant-virus interactions and limitations of RNA-based emerging technologies, which should be addressed in future studies.
Collapse
Affiliation(s)
- Wei-An Tsai
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Christopher A Brosnan
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Neena Mitter
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Ralf G Dietzgen
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| |
Collapse
|
10
|
Genome-Wide Identification and Expression Analysis of eIF Family Genes from Brassica rapa in Response to TuMV Resistance. PLANTS 2022; 11:plants11172248. [PMID: 36079630 PMCID: PMC9460045 DOI: 10.3390/plants11172248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/13/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022]
Abstract
Brassica rapa is one of the most important leafy vegetables worldwide, and has a long history of cultivation. However, it has not been possible to completely control the damage of turnip mosaic virus (TuMV), a serious virus in B. rapa, to production. In this study, the genome-wide identification and expression detection of eIF family genes from B. rapa in response to TuMV resistance were analyzed, including the identification of eIF family genes, chromosomal distribution, three-dimensional (3D) structure and sequence logo analyses, and the expression characterization as well as differential metabolite analysis of eIF family genes in resistant/susceptible lines, which may further prove the whole-genome tripling (WGT) event in B. rapa evolution and provide evidence for the functional redundancy and functional loss of multicopy eIF genes in evolution. A qRT-PCR analysis revealed that the relative expressions of eIF genes in a susceptible line (80461) were higher than those in a resistant line (80124), which may prove that, when TuMV infects host plants, the eIF genes can combine with the virus mRNA 5′ end cap structure and promote the initiation of virus mRNA translation in the susceptible B. rapa line. In addition, the metabolite substances were detected, the differences in metabolites between disease-resistant and disease-susceptible plants were mainly manifested by altered compounds such as flavonoids, jasmonic acid, salicylic acid, ketones, esters, etc., which inferred that the different metabolite regulations of eIF family genes and reveal the resistance mechanisms of eIF genes against TuMV in brassica crops. This study may lay a new theoretical foundation for revealing eIF family gene resistance to TuMV in B. rapa, as well as advancing our understanding of virus–host interactions.
Collapse
|
11
|
Chen R, Yang M, Tu Z, Xie F, Chen J, Luo T, Hu X, Nie B, He C. Eukaryotic translation initiation factor 4E family member nCBP facilitates the accumulation of TGB-encoding viruses by recognizing the viral coat protein in potato and tobacco. FRONTIERS IN PLANT SCIENCE 2022; 13:946873. [PMID: 36003826 PMCID: PMC9393630 DOI: 10.3389/fpls.2022.946873] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Due to their limited coding capacity, plant viruses have to depend on various host factors for successful infection of the host. Loss of function of these host factors will result in recessively inherited resistance, and therefore, these host factors are also described as susceptibility genes or recessive resistance genes. Most of the identified recessive resistance genes are members of the eukaryotic translation initiation factors 4E family (eIF4E) and its isoforms. Recently, an eIF4E-type gene, novel cap-binding protein (nCBP), was reported to be associated with the infection of several viruses encoding triple gene block proteins (TGBps) in Arabidopsis. Here, we, for the first time, report that the knockdown of nCBP in potato (StnCBP) compromises the accumulation of potato virus S (PVS) but not that of potato virus M (PVM) and potato virus X (PVX), which are three potato viruses encoding TGBps. Further assays demonstrated that StnCBP interacts with the coat proteins (CPs) of PVS and PVM but not with that of PVX, and substitution of PVS CP in the PVS infectious clone by PVM CP recovered the virus infection in StnCBP-silenced transgenic plants, suggesting that the recognition of PVS CP is crucial for StnCBP-mediated recessive resistance to PVS. Moreover, the knockdown of nCBP in Nicotiana benthamiana (NbnCBP) by virus-induced gene silencing suppressed PVX accumulation but not PVM, while NbnCBP interacted with the CPs of both PVX and PVM. Our results indicate that the nCBP orthologues in potato and tobacco have conserved function as in Arabidopsis in terms of recessive resistance against TGB-encoding viruses, and the interaction between nCBP and the CP of TGB-encoding virus is necessary but not sufficient to determine the function of nCBP as a susceptibility gene.
Collapse
Affiliation(s)
- Ruhao Chen
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, Hunan Agricultural University, Changsha, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Manhua Yang
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Zhen Tu
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Fangru Xie
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jiaru Chen
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Tao Luo
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Xinxi Hu
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, Hunan Agricultural University, Changsha, China
| | - Bihua Nie
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Changzheng He
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, Hunan Agricultural University, Changsha, China
| |
Collapse
|
12
|
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: 12] [Impact Index Per Article: 6.0] [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.
Collapse
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
| |
Collapse
|
13
|
Kuroiwa K, Thenault C, Nogué F, Perrot L, Mazier M, Gallois JL. CRISPR-based knock-out of eIF4E2 in a cherry tomato background successfully recapitulates resistance to pepper veinal mottle virus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 316:111160. [PMID: 35151441 DOI: 10.1016/j.plantsci.2021.111160] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/22/2021] [Accepted: 12/17/2021] [Indexed: 05/15/2023]
Abstract
The host susceptibility factors are important targets to develop genetic resistances in crops. Genome editing tools offer exciting prospects to develop resistances based on these susceptibility factors, directly in the cultivar of choice. Translation initiation factors 4E have long been known to be a susceptibility factor to the main genus of Potyviridae, potyviruses, but the inactivation of the eIF4E2 gene has only recently been shown to provide resistance to some isolates of pepper veinal mottle virus (PVMV) in big-fruit tomato plants. Here, using CRISPR-Cas9-NG, we show how eIF4E2 can be targeted and inactivated in cherry tomato plants. Three independent knockout alleles caused by indel in the first exon of eIF4E2, resulted in the complete absence of the eIF4E2 protein. All three lines displayed a narrow resistance spectrum to potyvirus, similar to the one described earlier for an eIF4E2 EMS mutant of M82, a big-fruit tomato cultivar; the plants were fully resistant to PVMV-Ca31, partially to PVMV-IC and were fully susceptible to two isolates of PVY assayed: N605 and LYE84. These results show how easily a resistance based on eIF4E2 can be transferred across tomato cultivar, but also confirm that gene redundancy can narrow the resistances based on eIF4E knockout.
Collapse
Affiliation(s)
| | | | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Laura Perrot
- Toulouse Biotechnology Institute, Université de Toulouse, 135 avenue de Rangueil, 31077 Toulouse CEDEX 04, France
| | | | | |
Collapse
|
14
|
Chen R, Tu Z, He C, Nie X, Li K, Fei S, Song B, Nie B, Xie C. Susceptibility factor StEXA1 interacts with StnCBP to facilitate potato virus Y accumulation through the stress granule-dependent RNA regulatory pathway in potato. HORTICULTURE RESEARCH 2022; 9:uhac159. [PMID: 36204208 PMCID: PMC9531334 DOI: 10.1093/hr/uhac159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 07/22/2022] [Accepted: 07/06/2022] [Indexed: 06/16/2023]
Abstract
Plant viruses recruit multiple host factors for translation, replication, and movement in the infection process. The loss-of-function mutation of the susceptibility genes will lead to the loss of susceptibility to viruses, which is referred to as 'recessive resistance'. Essential for potexvirus Accumulation 1 (EXA1) has been identified as a susceptibility gene required for potexvirus, lolavirus, and bacterial and oomycete pathogens. In this study, EXA1 knockdown in potato (StEXA1) was found to confer novel resistance to potato virus Y (PVY, potyvirus) in a strain-specific manner. It significantly compromised PVYO accumulation but not PVYN:O and PVYNTN. Further analysis revealed that StEXA1 is associated with the HC-Pro of PVY through a member of eIF4Es (StnCBP). HC-ProO and HC-ProN, two HC-Pro proteins from PVYO and PVYN, exhibited strong and weak interactions with StnCBP, respectively, due to their different spatial conformation. Moreover, the accumulation of PVYO was mainly dependent on the stress granules (SGs) induced by StEXA1 and StnCBP, whereas PVYN:O and PVYNTN could induce SGs by HC-ProN independently through an unknown mechanism. These results could explain why StEXA1 or StnCBP knockdown conferred resistance to PVYO but not to PVYN:O and PVYNTN. In summary, our results for the first time demonstrate that EXA1 can act as a susceptibility gene for PVY infection. Finally, a hypothetical model was proposed for understanding the mechanism by which StEXA1 interacts with StnCBP to facilitate PVY accumulation in potato through the SG-dependent RNA regulatory pathway.
Collapse
Affiliation(s)
- Ruhao Chen
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, Hunan Agricultural University, Changsha, 410128, China
| | - Zhen Tu
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Changzheng He
- ERC for Germplasm Innovation and New Variety Breeding of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, Hunan Agricultural University, Changsha, 410128, China
| | - Xianzhou Nie
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, New Brunswick, E3B 4Z7,
Canada
| | - Kun Li
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sitian Fei
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Botao Song
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Conghua Xie
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Key Laboratory of Horticultural Plant Biology (HZAU), Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|
15
|
Hinge VR, Chavhan RL, Kale SP, Suprasanna P, Kadam US. Engineering Resistance Against Viruses in Field Crops Using CRISPR- Cas9. Curr Genomics 2021; 22:214-231. [PMID: 34975291 PMCID: PMC8640848 DOI: 10.2174/1389202922666210412102214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/29/2021] [Accepted: 02/24/2021] [Indexed: 12/26/2022] Open
Abstract
Food security is threatened by various biotic stresses that affect the growth and production of agricultural crops. Viral diseases have become a serious concern for crop plants as they incur huge yield losses. The enhancement of host resistance against plant viruses is a priority for the effective management of plant viral diseases. However, in the present context of the climate change scenario, plant viruses are rapidly evolving, resulting in the loss of the host resistance mechanism. Advances in genome editing techniques, such as CRISPR-Cas9 [clustered regularly interspaced palindromic repeats-CRISPR-associated 9], have been recognized as promising tools for the development of plant virus resistance. CRISPR-Cas9 genome editing tool is widely preferred due to high target specificity, simplicity, efficiency, and reproducibility. CRISPR-Cas9 based virus resistance in plants has been successfully achieved by gene targeting and cleaving the viral genome or altering the plant genome to enhance plant innate immunity. In this article, we have described the CRISPR-Cas9 system, mechanism of plant immunity against viruses and highlighted the use of the CRISPR-Cas9 system to engineer virus resistance in plants. We also discussed prospects and challenges on the use of CRISPR-Cas9-mediated plant virus resistance in crop improvement.
Collapse
Affiliation(s)
| | | | | | | | - Ulhas S. Kadam
- Address correspondenceto this author at the Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany; E-mail: ,
‡Present Address: Division of Life Sciences, Plant Molecular Biology and Biotechnology Research Center, Gyenongsang National University, Jinju-si, Republic of Korea; E-mail:
| |
Collapse
|
16
|
Pepper Mottle Virus and Its Host Interactions: Current State of Knowledge. Viruses 2021; 13:v13101930. [PMID: 34696360 PMCID: PMC8539092 DOI: 10.3390/v13101930] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 01/08/2023] Open
Abstract
Pepper mottle virus (PepMoV) is a destructive pathogen that infects various solanaceous plants, including pepper, bell pepper, potato, and tomato. In this review, we summarize what is known about the molecular characteristics of PepMoV and its interactions with host plants. Comparisons of symptom variations caused by PepMoV isolates in plant hosts indicates a possible relationship between symptom development and genetic variation. Researchers have investigated the PepMoV–plant pathosystem to identify effective and durable genes that confer resistance to the pathogen. As a result, several recessive pvr or dominant Pvr resistance genes that confer resistance to PepMoV in pepper have been characterized. On the other hand, the molecular mechanisms underlying the interaction between these resistance genes and PepMoV-encoded genes remain largely unknown. Our understanding of the molecular interactions between PepMoV and host plants should be increased by reverse genetic approaches and comprehensive transcriptomic analyses of both the virus and the host genes.
Collapse
|
17
|
Anuradha C, Selvarajan R, Jebasingh T, Sankara Naynar P. Evidence of viral genome linked protein of banana bract mosaic virus interaction with translational eukaryotic initiation factor 4E of plantain cv. Nendran based on yeast two hybrid system study. Virusdisease 2021; 32:123-130. [PMID: 33969156 DOI: 10.1007/s13337-021-00672-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 01/27/2023] Open
Abstract
Banana bract mosaic virus (BBrMV), belongs to the genus Potyvirus and it is an important viral pathogen of bananas and plantains. The eukaryotic translation initiation factor, eIF4E, and its isoform play key roles during the virus infection in plants, particularly Potyvirus. The present study was undertaken to determine the role of BBrMV-viral protein genome-linked (VPg) in virus infectivity by analyzing the interaction with the eukaryotic translation initiation factor eIF4E through yeast two-hybrid system. The results suggest that plantain cv. Nendran eIF4E plays an essential role in the initiation of the translation of capped mRNAs and its association with VPg would point to a role of the viral protein in the translation of the virus and may potentially contribute to BBrMV resistance.
Collapse
Affiliation(s)
- Chelliah Anuradha
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli, Tamil Nadu India
| | - R Selvarajan
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli, Tamil Nadu India
| | - T Jebasingh
- Department of Plant Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu India
| | - P Sankara Naynar
- Department of Plant Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu India
| |
Collapse
|
18
|
Li G, Zhang S, Li F, Zhang H, Zhang S, Zhao J, Sun R. Variability in the Viral Protein Linked to the Genome of Turnip Mosaic Virus Influences Interactions with eIF(iso)4Es in Brassica rapa. THE PLANT PATHOLOGY JOURNAL 2021; 37:47-56. [PMID: 33551696 PMCID: PMC7847760 DOI: 10.5423/ppj.oa.07.2020.0125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/26/2020] [Accepted: 12/31/2020] [Indexed: 06/12/2023]
Abstract
Plants protect against viruses through passive and active resistance mechanisms, and in most cases characterized thus far, natural recessive resistance to potyviruses has been mapped to mutations in the eukaryotic initiation factor eIF4E or eIF(iso)4E genes. Five eIF4E copies and three eIF(iso)4E copies were detected in Brassica rapa. The eIF4E and eIF(iso)4E genes could interact with turnip mosaic virus (TuMV) viral protein linked to the genome (VPg) to initiate virus translation. From the yeast two-hybrid system (Y2H) and bimolecular fluorescence complementation (BiFC) assays, the TuMV-CHN2/CHN3 VPgs could not interact with BraA.eIF4E.a/c or BraA.eIF(iso)4E.c, but they could interact with BraA.eIF(iso)4E.a in B. rapa. Further analysis indicated that the amino acid substitution L186F (nt T556C) in TuMV-UK1 VPg was important for the interaction networks between the TuMV VPg and eIF(iso)4E proteins. An interaction model of the BraA. eIF(iso)4E protein with TuMV VPg was constructed to infer the effect of the significant amino acids on the interaction of TuMV VPgs-eIF(iso)4Es, particularly whether the L186F in TuMV-UK1 VPg could change the structure of the TuMV-UK1 VPg protein, which may terminate the interaction of the BraA.eIF(iso)4E and TuMV VPg protein. This study provides new insights into the interactions between plant viruses and translation initiation factors to reveal the working of key amino acids.
Collapse
Affiliation(s)
- Guoliang Li
- State Key Laboratory of North China Crop Improvement and Regulation, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 0008, China
| | - Shifan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 0008, China
| | - Fei Li
- State Key Laboratory of North China Crop Improvement and Regulation, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 0008, China
| | - Hui Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 0008, China
| | - Shujiang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 0008, China
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Department of Horticulture, Hebei Agricultural University, Baoding 071001, China
| | - Rifei Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 0008, China
| |
Collapse
|
19
|
Atarashi H, Jayasinghe WH, Kwon J, Kim H, Taninaka Y, Igarashi M, Ito K, Yamada T, Masuta C, Nakahara KS. Artificially Edited Alleles of the Eukaryotic Translation Initiation Factor 4E1 Gene Differentially Reduce Susceptibility to Cucumber Mosaic Virus and Potato Virus Y in Tomato. Front Microbiol 2020; 11:564310. [PMID: 33362728 PMCID: PMC7758215 DOI: 10.3389/fmicb.2020.564310] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/11/2020] [Indexed: 01/27/2023] Open
Abstract
Eukaryotic translation initiation factors, including eIF4E, are susceptibility factors for viral infection in host plants. Mutation and double-stranded RNA-mediated silencing of tomato eIF4E genes can confer resistance to viruses, particularly members of the Potyvirus genus. Here, we artificially mutated the eIF4E1 gene on chromosome 3 of a commercial cultivar of tomato (Solanum lycopersicum L.) by using CRISPR/Cas9. We obtained three alleles, comprising two deletions of three and nine nucleotides (3DEL and 9DEL) and a single nucleotide insertion (1INS), near regions that encode amino acid residues important for binding to the mRNA 5' cap structure and to eIF4G. Plants homozygous for these alleles were termed 3DEL, 9DEL, and 1INS plants, respectively. In accordance with previous studies, inoculation tests with potato virus Y (PVY; type member of the genus Potyvirus) yielded a significant reduction in susceptibility to the N strain (PVYN), but not to the ordinary strain (PVYO), in 1INS plants. 9DEL among three artificial alleles had a deleterious effect on infection by cucumber mosaic virus (CMV, type member of the genus Cucumovirus). When CMV was mechanically inoculated into tomato plants and viral coat accumulation was measured in the non-inoculated upper leaves, the level of viral coat protein was significantly lower in the 9DEL plants than in the parental cultivar. Tissue blotting of microperforated inoculated leaves of the 9DEL plants revealed significantly fewer infection foci compared with those of the parental cultivar, suggesting that 9DEL negatively affects the initial steps of infection with CMV in a mechanically inoculated leaf. In laboratory tests, viral aphid transmission from an infected susceptible plant to 9DEL plants was reduced compared with the parental control. Although many pathogen resistance genes have been discovered in tomato and its wild relatives, no CMV resistance genes have been used in practice. RNA silencing of eIF4E expression has previously been reported to not affect susceptibility to CMV in tomato. Our findings suggest that artificial gene editing can introduce additional resistance to that achieved with mutagenesis breeding, and that edited eIF4E alleles confer an alternative way to manage CMV in tomato fields.
Collapse
Affiliation(s)
- Hiroki Atarashi
- Research and Development Division, Kikkoman Corporation, Noda, Chiba, Japan
| | - Wikum Harshana Jayasinghe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.,Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - Joon Kwon
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hangil Kim
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yosuke Taninaka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Manabu Igarashi
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Kotaro Ito
- Research and Development Division, Kikkoman Corporation, Noda, Chiba, Japan
| | - Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Chikara Masuta
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kenji S Nakahara
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| |
Collapse
|
20
|
Aphid Transmission of Potyvirus: The Largest Plant-Infecting RNA Virus Genus. Viruses 2020; 12:v12070773. [PMID: 32708998 PMCID: PMC7411817 DOI: 10.3390/v12070773] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/12/2020] [Accepted: 07/15/2020] [Indexed: 12/15/2022] Open
Abstract
Potyviruses are the largest group of plant infecting RNA viruses that cause significant losses in a wide range of crops across the globe. The majority of viruses in the genus Potyvirus are transmitted by aphids in a non-persistent, non-circulative manner and have been extensively studied vis-à-vis their structure, taxonomy, evolution, diagnosis, transmission, and molecular interactions with hosts. This comprehensive review exclusively discusses potyviruses and their transmission by aphid vectors, specifically in the light of several virus, aphid and plant factors, and how their interplay influences potyviral binding in aphids, aphid behavior and fitness, host plant biochemistry, virus epidemics, and transmission bottlenecks. We present the heatmap of the global distribution of potyvirus species, variation in the potyviral coat protein gene, and top aphid vectors of potyviruses. Lastly, we examine how the fundamental understanding of these multi-partite interactions through multi-omics approaches is already contributing to, and can have future implications for, devising effective and sustainable management strategies against aphid-transmitted potyviruses to global agriculture.
Collapse
|
21
|
Swisher Grimm KD, Porter LD. Development and Validation of KASP Markers for the Identification of Pea seedborne mosaic virus Pathotype P1 Resistance in Pisum sativum. PLANT DISEASE 2020; 104:1824-1830. [PMID: 32272026 DOI: 10.1094/pdis-09-19-1920-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
As pesticides have become heavily relied on for management of insect pests vectoring economically important pathogens of vegetable crops, development of pathogen-resistant germplasm remains a promising alternative to reduce or eliminate costly and timely chemical inputs. Molecular markers can be used to rapidly identify resistant genotypes to aid breeders in advancing germplasm. This study developed two kompetitive allele-specific PCR (KASP) genotyping markers for rapid screening of Pisum sativum genotypes for resistance to Pea seedborne mosaic virus pathotype P1 (PSbMV-P1), the most economically devastating strain worldwide. The KASP markers differentiate two eIF4E PSbMV-P1-resistant allelic variants from susceptible eIF4E variants. A single nucleotide polymorphism (Resistant 1) and a 3-basepair deletion (Resistant 2) present in either of the two resistant alleles were used for marker design. Forty-four P. sativum lines previously characterized for resistance to PSbMV were inoculated with PSbMV-P1 in a greenhouse, observed for visual symptoms, assayed for virus susceptibility by enzyme-linked immunosorbent assay (ELISA), and genotyped by KASP marker analysis. The KASP markers were 100% accurate in characterizing PSbMV-P1-susceptible and PSbMV-P1-resistant genotypes when correlated with the ELISA results. The Resistant 1 marker also correlated with resistance to PSbMV pathotypes P2 and P4 completely, making this marker a new advanced tool for P. sativum breeding programs.
Collapse
Affiliation(s)
- Kylie D Swisher Grimm
- Temperate Tree Fruit and Vegetable Research Unit, U.S. Department of Agriculture Agricultural Research Service, Prosser, WA 99350
| | - Lyndon D Porter
- Grain Legume Genetics and Physiology Research Unit, U.S. Department of Agriculture Agricultural Research Service, Prosser, WA 99350
| |
Collapse
|
22
|
Yoon YJ, Venkatesh J, Lee JH, Kim J, Lee HE, Kim DS, Kang BC. Genome Editing of eIF4E1 in Tomato Confers Resistance to Pepper Mottle Virus. FRONTIERS IN PLANT SCIENCE 2020. [PMID: 32849681 DOI: 10.3398/fpls.2020.01098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Many of the recessive virus-resistance genes in plants encode eukaryotic translation initiation factors (eIFs), including eIF4E, eIF4G, and related proteins. Notably, eIF4E and its isoform eIF(iso)4E are pivotal for viral infection and act as recessive resistance genes against various potyviruses in a wide range of plants. In this study, we used Clustered Regularly Interspaced Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated targeted mutagenesis to test whether novel sequence-specific mutations at eIF4E1 in Solanum lycopersicum (tomato) cv. Micro-Tom could confer enhanced resistance to potyviruses. This approach produced heritable homozygous mutations in the transgene-free E1 generation. Sequence analysis of eIF4E1 from E0 transgenic plants expressing Cas9 and eIF4E-sgRNA transcripts identified chimeric deletions ranging from 11 to 43 bp. Genotype analysis of the eIF4E1-edited lines in E0, E1, and E2 transgenic tomato plants showed that the mutations were transmitted to subsequent generations. When homozygous mutant lines were tested for resistance to potyviruses, they exhibited no resistance to tobacco etch virus (TEV). Notably, however, several mutant lines showed no accumulation of viral particles upon infection with pepper mottle virus (PepMoV). These results indicate that site-specific mutation of tomato eIF4E1 successfully conferred enhanced resistance to PepMoV. Thus, this study demonstrates the feasibility of the use of CRISPR/Cas9 approach to accelerate breeding for trait improvement in tomato plants.
Collapse
Affiliation(s)
- Yoo-Joung Yoon
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jelli Venkatesh
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Joung-Ho Lee
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jinhee Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, RDA, Jeonju-si, South Korea
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, RDA, Jeonju-si, South Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, RDA, Jeonju-si, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| |
Collapse
|
23
|
[Recessive resistance to plant viruses by the deficiency of eukaryotic translation initiation factor genes.]. Uirusu 2020; 70:61-68. [PMID: 33967115 DOI: 10.2222/jsv.70.61] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Plant viruses, obligate parasitic pathogens, utilize a variety of host plant factors in the process of their infection due to the limited number of genes encoded in their own genomes. The genes encoding these host factors are called susceptibility genes because they are responsible for the susceptibility of plants to viruses. Plants lacking or having mutations in a susceptibility gene essential for the infection of a virus acquire resistance to the virus. Such resistance trait is called recessive resistance because of the recessive inherited characteristics. Recessive resistance is reported to account for about half of the plant viral resistance loci mapped in known cultivated crops. Eukaryotic translation initiation factor (eIF) 4E family genes are well-known susceptibility genes. Although there are many reports about eIF4E-mediated recessive resistance to plant viruses, the mechanistic insight of the resistance is still limited. Here we review focusing on studies that have elucidated the mechanism of eIF4E-mediated recessive resistance.
Collapse
|
24
|
van Esse HP, Reuber TL, van der Does D. Genetic modification to improve disease resistance in crops. THE NEW PHYTOLOGIST 2020; 225:70-86. [PMID: 31135961 PMCID: PMC6916320 DOI: 10.1111/nph.15967] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/08/2019] [Indexed: 05/19/2023]
Abstract
Plant pathogens are a significant challenge in agriculture despite our best efforts to combat them. One of the most effective and sustainable ways to manage plant pathogens is to use genetic modification (GM) and genome editing, expanding the breeder's toolkit. For use in the field, these solutions must be efficacious, with no negative effect on plant agronomy, and deployed thoughtfully. They must also not introduce a potential allergen or toxin. Expensive regulation of biotech crops is prohibitive for local solutions. With 11-30% average global yield losses and greater local impacts, tackling plant pathogens is an ethical imperative. We need to increase world food production by at least 60% using the same amount of land, by 2050. The time to act is now and we cannot afford to ignore the new solutions that GM provides to manage plant pathogens.
Collapse
Affiliation(s)
- H. Peter van Esse
- 2Blades Foundation1630 Chicago AvenueEvanstonIL 60201USA
- The Sainsbury LaboratoryUniversity of East AngliaNorwich Research ParkNR4 7UHUK
| | | | | |
Collapse
|
25
|
Yoon YJ, Venkatesh J, Lee JH, Kim J, Lee HE, Kim DS, Kang BC. Genome Editing of eIF4E1 in Tomato Confers Resistance to Pepper Mottle Virus. FRONTIERS IN PLANT SCIENCE 2020; 11:1098. [PMID: 32849681 PMCID: PMC7396686 DOI: 10.3389/fpls.2020.01098] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/03/2020] [Indexed: 05/07/2023]
Abstract
Many of the recessive virus-resistance genes in plants encode eukaryotic translation initiation factors (eIFs), including eIF4E, eIF4G, and related proteins. Notably, eIF4E and its isoform eIF(iso)4E are pivotal for viral infection and act as recessive resistance genes against various potyviruses in a wide range of plants. In this study, we used Clustered Regularly Interspaced Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated targeted mutagenesis to test whether novel sequence-specific mutations at eIF4E1 in Solanum lycopersicum (tomato) cv. Micro-Tom could confer enhanced resistance to potyviruses. This approach produced heritable homozygous mutations in the transgene-free E1 generation. Sequence analysis of eIF4E1 from E0 transgenic plants expressing Cas9 and eIF4E-sgRNA transcripts identified chimeric deletions ranging from 11 to 43 bp. Genotype analysis of the eIF4E1-edited lines in E0, E1, and E2 transgenic tomato plants showed that the mutations were transmitted to subsequent generations. When homozygous mutant lines were tested for resistance to potyviruses, they exhibited no resistance to tobacco etch virus (TEV). Notably, however, several mutant lines showed no accumulation of viral particles upon infection with pepper mottle virus (PepMoV). These results indicate that site-specific mutation of tomato eIF4E1 successfully conferred enhanced resistance to PepMoV. Thus, this study demonstrates the feasibility of the use of CRISPR/Cas9 approach to accelerate breeding for trait improvement in tomato plants.
Collapse
Affiliation(s)
- Yoo-Joung Yoon
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jelli Venkatesh
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Joung-Ho Lee
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jinhee Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, RDA, Jeonju-si, South Korea
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, RDA, Jeonju-si, South Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, RDA, Jeonju-si, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- *Correspondence: Byoung-Cheorl Kang,
| |
Collapse
|
26
|
Rubio J, Sánchez E, Tricon D, Montes C, Eyquard JP, Chague A, Aguirre C, Prieto H, Decroocq V. Silencing of one copy of the translation initiation factor eIFiso4G in Japanese plum (Prunus salicina) impacts susceptibility to Plum pox virus (PPV) and small RNA production. BMC PLANT BIOLOGY 2019; 19:440. [PMID: 31640557 PMCID: PMC6806492 DOI: 10.1186/s12870-019-2047-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 09/20/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND In plants, host factors encoded by susceptibility (S) genes are indispensable for viral infection. Resistance is achieved through the impairment or the absence of those susceptibility factors. Many S genes have been cloned from model and crop species and a majority of them are coding for members of the eukaryotic translation initiation complex, mainly eIF4E, eIF4G and their isoforms. The aim of this study was to investigate the role of those translation initiation factors in susceptibility of stone fruit species to sharka, a viral disease due to Plum pox virus (PPV). RESULTS For this purpose, hairpin-inducing silencing constructs based on Prunus persica orthologs were used to generate Prunus salicina (Japanese plum) 4E and 4G silenced plants by Agrobacterium tumefaciens-mediated transformation and challenged with PPV. While down-regulated eIFiso4E transgenic Japanese plums were not regenerated in our conditions, eIFiso4G11-, but not the eIFiso4G10-, silenced plants displayed durable and stable resistance to PPV. We also investigated the alteration of the si- and mi-RNA profiles in transgenic and wild-type Japanese plums upon PPV infection and confirmed that the newly generated small interfering (si) RNAs, which are derived from the engineered inverted repeat construct, are the major contributor of resistance to sharka. CONCLUSIONS Our results indicate that S gene function of the translation initiation complex isoform is conserved in Prunus species. We discuss the possibilities of using RNAi silencing or loss-of-function mutations of the different isoforms of proteins involved in this complex to breed for resistance to sharka in fruit trees.
Collapse
Affiliation(s)
- Julia Rubio
- Biotechnology Laboratory, La Platina Station, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, La Pintana, Santiago Chile
- Agronomical Sciences Doctoral Program, Campus Sur, University of Chile, Santa Rosa 11315, La Pintana, Santiago Chile
- Present address: Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Providencia, Chile
| | - Evelyn Sánchez
- Biotechnology Laboratory, La Platina Station, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, La Pintana, Santiago Chile
- Present address: Integrative Genomics Doctoral Program, Universidad Mayor, Camino La Pirámide 575, Huechuraba, Santiago Chile
| | - David Tricon
- INRA, UMR 1332 BFP, Equipe de virologie, 71 Avenue Edouard Bourlaux, 33883 Villenave d’Ornon, France
- Université de Bordeaux, UMR 1332 BFP, CS20032, 33883 Villenave d’Ornon, France
| | - Christian Montes
- Biotechnology Laboratory, La Platina Station, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, La Pintana, Santiago Chile
- Present address: Genetics and Genomics Doctoral Program, Iowa State University, 2437 Pammel Drive, Ames, IA 50011–1079 USA
| | - Jean-Philippe Eyquard
- INRA, UMR 1332 BFP, Equipe de virologie, 71 Avenue Edouard Bourlaux, 33883 Villenave d’Ornon, France
- Université de Bordeaux, UMR 1332 BFP, CS20032, 33883 Villenave d’Ornon, France
| | - Aurélie Chague
- INRA, UMR 1332 BFP, Equipe de virologie, 71 Avenue Edouard Bourlaux, 33883 Villenave d’Ornon, France
- Université de Bordeaux, UMR 1332 BFP, CS20032, 33883 Villenave d’Ornon, France
| | - Carlos Aguirre
- Biotechnology Laboratory, La Platina Station, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, La Pintana, Santiago Chile
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Station, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, La Pintana, Santiago Chile
| | - Véronique Decroocq
- INRA, UMR 1332 BFP, Equipe de virologie, 71 Avenue Edouard Bourlaux, 33883 Villenave d’Ornon, France
- Université de Bordeaux, UMR 1332 BFP, CS20032, 33883 Villenave d’Ornon, France
| |
Collapse
|
27
|
Knock-out mutation of eukaryotic initiation factor 4E2 (eIF4E2) confers resistance to pepper veinal mottle virus in tomato. Virology 2019; 539:11-17. [PMID: 31622792 DOI: 10.1016/j.virol.2019.09.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 11/23/2022]
Abstract
Translation initiation factors 4E (eIF4E) are the main source of resistance to potyvirus. We systematically assessed tomato single and double knock-out (KO) mutants of members of the eIF4E-coding gene family for resistance to Pepper veinal mottle virus (PVMV), a major constraint to tomato production. We show that the KO mutant of eIF4E2 has partial resistance to PVMV isolate IC, with plants harboring weak symptoms and low virus loads at the systemic level. The causal effect of eIF4E2 loss-of-function on resistance was confirmed on a progeny segregating for the KO mutation. The eIF4E2 KO mutant was resistant to six of the eight PVMV isolates tested and no resistance to other potyviruses was observed. This is the first evidence that mutation of eIF4E2 is in itself conferring resistance to a potyvirus and 3D protein modelling suggests that the eIF4E2 gene could be converted into a functional resistance allele.
Collapse
|
28
|
Bastet A, Zafirov D, Giovinazzo N, Guyon‐Debast A, Nogué F, Robaglia C, Gallois J. Mimicking natural polymorphism in eIF4E by CRISPR-Cas9 base editing is associated with resistance to potyviruses. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1736-1750. [PMID: 30784179 PMCID: PMC6686125 DOI: 10.1111/pbi.13096] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 05/08/2023]
Abstract
In many crop species, natural variation in eIF4E proteins confers resistance to potyviruses. Gene editing offers new opportunities to transfer genetic resistance to crops that seem to lack natural eIF4E alleles. However, because eIF4E are physiologically important proteins, any introduced modification for virus resistance must not bring adverse phenotype effects. In this study, we assessed the role of amino acid substitutions encoded by a Pisum sativum eIF4E virus-resistance allele (W69L, T80D S81D, S84A, G114R and N176K) by introducing them independently into the Arabidopsis thaliana eIF4E1 gene, a susceptibility factor to the Clover yellow vein virus (ClYVV). Results show that most mutations were sufficient to prevent ClYVV accumulation in plants without affecting plant growth. In addition, two of these engineered resistance alleles can be combined with a loss-of-function eIFiso4E to expand the resistance spectrum to other potyviruses. Finally, we use CRISPR-nCas9-cytidine deaminase technology to convert the Arabidopsis eIF4E1 susceptibility allele into a resistance allele by introducing the N176K mutation with a single-point mutation through C-to-G base editing to generate resistant plants. This study shows how combining knowledge on pathogen susceptibility factors with precise genome-editing technologies offers a feasible solution for engineering transgene-free genetic resistance in plants, even across species barriers.
Collapse
Affiliation(s)
- Anna Bastet
- GAFLINRAMontfavetFrance
- Laboratoire de Génétique et Biophysique des PlantesCEACNRSBIAMAix Marseille UniversityMarseilleFrance
| | - Delyan Zafirov
- GAFLINRAMontfavetFrance
- Laboratoire de Génétique et Biophysique des PlantesCEACNRSBIAMAix Marseille UniversityMarseilleFrance
| | | | - Anouchka Guyon‐Debast
- Institut Jean‐Pierre BourginINRAAgroParisTechCNRSUniversité Paris‐SaclayVersaillesFrance
| | - Fabien Nogué
- Institut Jean‐Pierre BourginINRAAgroParisTechCNRSUniversité Paris‐SaclayVersaillesFrance
| | - Christophe Robaglia
- Laboratoire de Génétique et Biophysique des PlantesCEACNRSBIAMAix Marseille UniversityMarseilleFrance
| | | |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Miras M, Juárez M, Aranda MA. Resistance to the Emerging Moroccan Watermelon Mosaic Virus in Squash. PHYTOPATHOLOGY 2019; 109:895-903. [PMID: 30620690 DOI: 10.1094/phyto-10-18-0395-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Moroccan watermelon mosaic virus (MWMV) represents an emerging threat to cucurbit production in the Mediterranean Basin. We sequenced the near complete genome of MWMV-SQ10_1.1, a cloned Spanish isolate. MWMV-SQ10_1.1 has the typical potyvirus genomic structure, and phylogenetic analysis showed that it shared a common ancestor with other Mediterranean MWMV isolates. We used MWMV SQ10_1.1 to inoculate plants in a collection of commercial squash cultivars, including some described as potyvirus resistant. All inoculated plants from all cultivars showed severe infection symptoms. Twenty-four Cucurbita spp. accessions were then tested for their susceptibility to MWMV-SQ10_1.1. Plants of the C. ecuadorensis PI 432441 accession showed no symptoms and their enzyme-linked immunosorbent assay readings were similar to uninfected controls. Progeny analysis of F1 and F2 populations suggested that two recessive genes control PI 432441 resistance to MWMV. We hypothesized that this resistance could be associated with alleles of genes encoding the eukaryotic translation initiation factor 4E (eIF4E), particularly after determination of its recessive nature. A multiple sequence alignment including the two eIF4E ortholog sequences from PI 432441 (CeeIF4E1 and CeeIF4E2) identified three amino acid substitutions in CeeIF4E1 and two amino acid substitutions in CeeIF4E2 potentially involved in potyvirus resistance. Polymerase chain reaction markers for CeeIF4E1 and CeeIF4E2 were developed and used to genotype 156 F2 individuals already phenotyped; this analysis did not support an association of either CeeIF4E2 or CeeIF4E1 with MWMV resistance.
Collapse
Affiliation(s)
- Manuel Miras
- 1 Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, 30100 Espinardo, Murcia, Spain; and
| | - Miguel Juárez
- 2 Escuela Politécnica Superior de Orihuela, Universidad Miguel Hernández de Elche, 03312 Orihuela, Alicante, Spain
| | - Miguel A Aranda
- 1 Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas, 30100 Espinardo, Murcia, Spain; and
| |
Collapse
|
31
|
Variability in eukaryotic initiation factor iso4E in Brassica rapa influences interactions with the viral protein linked to the genome of Turnip mosaic virus. Sci Rep 2018; 8:13588. [PMID: 30206242 PMCID: PMC6134127 DOI: 10.1038/s41598-018-31739-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/21/2018] [Indexed: 12/22/2022] Open
Abstract
Plant potyviruses require eukaryotic translation initiation factors (eIFs) such as eIF4E and eIF(iso)4E to replicate and spread. When Turnip mosaic virus (TuMV) infects a host plant, its viral protein linked to the genome (VPg) needs to interact with eIF4E or eIF(iso)4E to initiate translation. TuMV utilizes BraA.eIF4E.a, BraA.eIF4E.c, BraA.eIF(iso)4E.a, and BraA.eIF(iso)4E.c of Brassica rapa to initiate translation in Arabidopsis thaliana. In this study, the BraA.eIF4E.a, BraA.eIF4E.c, BraA.eIF(iso)4E.a, and BraA.eIF(iso)4E.c genes were cloned and sequenced from eight B. rapa lines, namely, two BraA.eIF4E.a alleles, four BraA.eIF4E.c alleles, four BraA.eIF(iso)4E.a alleles, and two BraA.eIF(iso)4E.c alleles. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) analyses indicated that TuMV VPg could not interact with eIF4E, but only with eIF(iso)4E of B. rapa. In addition, the VPgs of the different TuMV isolates interacted with various eIF(iso)4E copies in B. rapa. In particular, TuMV-UK1/CDN1 VPg only interacted with BraA.eIF(iso)4E.c, not with BraA.eIF(iso)4E.a. Some single nucleotide polymorphisms (SNPs) were identified that may have affected the interaction between eIF(iso)4E and VPg such as the SNP T106C in BraA.eIF(iso)4E.c and the SNP A154C in VPg. Furthermore, a three-dimensional structural model of the BraA.eIF(iso)4E.c-1 protein was constructed to identify the specific conformation of the variable amino acids from BraA.eIF(iso)4E.c. The 36th amino acid in BraA.eIF(iso)4E.c is highly conserved and may play an important role in establishing protein structural stability. The findings of the present study may lay the foundation for future investigations on the co-evolution of TuMV and eIF(iso)4E.
Collapse
|
32
|
Wang Y, Jiang J, Zhao L, Zhou R, Yu W, Zhao T. Application of Whole Genome Resequencing in Mapping of a Tomato Yellow Leaf Curl Virus Resistance Gene. Sci Rep 2018; 8:9592. [PMID: 29941914 PMCID: PMC6018388 DOI: 10.1038/s41598-018-27925-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/12/2018] [Indexed: 01/23/2023] Open
Abstract
Tomato yellow leaf curl virus (TYLCV) has significantly impacted the tomato industry around the world, and the use of insecticides and insect nets have not effectively controlled the spread of this pathogen. The tomato line AVTO1227 is highly resistant to TYLCV. In this study, F2 and BC1 populations derived from AVTO1227 and the susceptible line Money maker were used to assess the genetic mechanism underlying TYLCV resistance. We have identified a recessive TYLCV resistance gene, hereby designated as ty-5, which is linked to SlNACI. Genomic DNA pools from resistant and susceptible groups were constructed, and their genomes were resequenced. The ty-5 gene was identified on an interval encompassing the genomic positions 2.22 Mb to 3.19 Mb on tomato chromosome 4. Genotyping using linkage markers further mapped ty-5 within the interval between markers ty5-25 and ty5-29, where only the pelota gene is located. Consequently, pelota was considered as the candidate gene corresponding to ty-5. Two nucleotide transversions within the promoter region and one transversion in exon region of the pelota gene were detected in the parental lines. However, the relative transcript levels of pelota did not significantly differ among the three tomato lines, regardless of TYLCV infection. This study will facilitate marker-assisted breeding for resistance to TYLCV and lay a foundation for the research of the resistance mechanism of ty-5 in tomato.
Collapse
Affiliation(s)
- Yinlei Wang
- Institute of Vegetable Crop, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China
- Laboratory for Genetic Improvement of High Efficiency Horticultural Crops in Jiangsu province, Jiangsu, Nanjing, China
| | - Jing Jiang
- Institute of Vegetable Crop, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China
- Laboratory for Genetic Improvement of High Efficiency Horticultural Crops in Jiangsu province, Jiangsu, Nanjing, China
| | - Liping Zhao
- Institute of Vegetable Crop, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China
- Laboratory for Genetic Improvement of High Efficiency Horticultural Crops in Jiangsu province, Jiangsu, Nanjing, China
| | - Rong Zhou
- Institute of Vegetable Crop, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China
- Laboratory for Genetic Improvement of High Efficiency Horticultural Crops in Jiangsu province, Jiangsu, Nanjing, China
| | - Wengui Yu
- Institute of Vegetable Crop, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China
- Laboratory for Genetic Improvement of High Efficiency Horticultural Crops in Jiangsu province, Jiangsu, Nanjing, China
| | - Tongmin Zhao
- Institute of Vegetable Crop, Jiangsu Academy of Agricultural Science, Nanjing, Jiangsu, China.
- Laboratory for Genetic Improvement of High Efficiency Horticultural Crops in Jiangsu province, Jiangsu, Nanjing, China.
| |
Collapse
|
33
|
Bastet A, Lederer B, Giovinazzo N, Arnoux X, German‐Retana S, Reinbold C, Brault V, Garcia D, Djennane S, Gersch S, Lemaire O, Robaglia C, Gallois J. Trans-species synthetic gene design allows resistance pyramiding and broad-spectrum engineering of virus resistance in plants. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1569-1581. [PMID: 29504210 PMCID: PMC6097130 DOI: 10.1111/pbi.12896] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/10/2018] [Accepted: 01/28/2018] [Indexed: 05/19/2023]
Abstract
To infect plants, viruses rely heavily on their host's machinery. Plant genetic resistances based on host factor modifications can be found among existing natural variability and are widely used for some but not all crops. While biotechnology can supply for the lack of natural resistance alleles, new strategies need to be developed to increase resistance spectra and durability without impairing plant development. Here, we assess how the targeted allele modification of the Arabidopsis thaliana translation initiation factor eIF4E1 can lead to broad and efficient resistance to the major group of potyviruses. A synthetic Arabidopsis thaliana eIF4E1 allele was designed by introducing multiple amino acid changes associated with resistance to potyvirus in naturally occurring Pisum sativum alleles. This new allele encodes a functional protein while maintaining plant resistance to a potyvirus isolate that usually hijacks eIF4E1. Due to its biological functionality, this synthetic allele allows, at no developmental cost, the pyramiding of resistances to potyviruses that selectively use the two major translation initiation factors, eIF4E1 or its isoform eIFiso4E. Moreover, this combination extends the resistance spectrum to potyvirus isolates for which no efficient resistance has so far been found, including resistance-breaking isolates and an unrelated virus belonging to the Luteoviridae family. This study is a proof-of-concept for the efficiency of gene engineering combined with knowledge of natural variation to generate trans-species virus resistance at no developmental cost to the plant. This has implications for breeding of crops with broad-spectrum and high durability resistance using recent genome editing techniques.
Collapse
Affiliation(s)
- Anna Bastet
- GAFLINRAMontfavetFrance
- Aix Marseille UniversityUMR 7265 Biologie Végétale et Microbiologie EnvironnementalesLaboratoire de Génétique et Biophysique des PlantesMarseilleFrance
- CNRSUMR 7265 Biologie Végétale et Microbiologie EnvironnementalesMarseilleFrance
- CEABioscience and Biotechnology Institute of Aix‐MarseilleMarseilleFrance
| | | | | | - Xavier Arnoux
- UMR 1332 Biologie du Fruit et PathologieINRAUniv. BordeauxVillenave d'OrnonFrance
| | - Sylvie German‐Retana
- UMR 1332 Biologie du Fruit et PathologieINRAUniv. BordeauxVillenave d'OrnonFrance
| | - Catherine Reinbold
- Université de StrasbourgINRAUMR‐A 1131Santé de la Vigne et Qualité du VinColmarFrance
| | - Véronique Brault
- Université de StrasbourgINRAUMR‐A 1131Santé de la Vigne et Qualité du VinColmarFrance
| | - Damien Garcia
- Centre National de la Recherche ScientifiqueInstitut de Biologie Moléculaire des Plantes (IBMP)UPR 2357StrasbourgFrance
| | - Samia Djennane
- Université de StrasbourgINRAUMR‐A 1131Santé de la Vigne et Qualité du VinColmarFrance
| | - Sophie Gersch
- Université de StrasbourgINRAUMR‐A 1131Santé de la Vigne et Qualité du VinColmarFrance
| | - Olivier Lemaire
- Université de StrasbourgINRAUMR‐A 1131Santé de la Vigne et Qualité du VinColmarFrance
| | - Christophe Robaglia
- Aix Marseille UniversityUMR 7265 Biologie Végétale et Microbiologie EnvironnementalesLaboratoire de Génétique et Biophysique des PlantesMarseilleFrance
- CNRSUMR 7265 Biologie Végétale et Microbiologie EnvironnementalesMarseilleFrance
- CEABioscience and Biotechnology Institute of Aix‐MarseilleMarseilleFrance
| | | |
Collapse
|
34
|
Which Plant Proteins Are Involved in Antiviral Defense? Review on In Vivo and In Vitro Activities of Selected Plant Proteins against Viruses. Int J Mol Sci 2017; 18:ijms18112300. [PMID: 29104238 PMCID: PMC5713270 DOI: 10.3390/ijms18112300] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/24/2017] [Accepted: 10/27/2017] [Indexed: 11/23/2022] Open
Abstract
Plants have evolved a variety of defense mechanisms to tackle virus attack. Endogenous plant proteins can function as virus suppressors. Different types of proteins mediate defense responses against plant viruses. Pathogenesis-related (PR) proteins are activated upon pathogen infections or in different stress situations and their production is one of many components in plant defense. Ribosome-inactivating proteins (RIPs) suppress translation by enzymatically damaging ribosomes and they have been found to have antiviral activity. RNA-binding proteins (RBPs) bind to target RNAs via specialized RNA-binding domain and can directly or indirectly function in plant defense system against RNA viruses. Proteins involved in silencing machinery, namely Dicer-like (DCL) proteins, Argonaute (AGO) proteins, and RNA-dependent RNA polymerases (RDRs) confer innate antiviral defense in plants as they are able to degrade foreign RNA of viral origin. This review aims to provide a comprehensive and up-to-date picture of plant proteins participating in antiviral defense. As a result we discuss proteins conferring plant antiviral resistance and their potential future applications in different fields of life including agriculture and medicine.
Collapse
|
35
|
Amuge T, Berger DK, Katari MS, Myburg AA, Goldman SL, Ferguson ME. A time series transcriptome analysis of cassava (Manihot esculenta Crantz) varieties challenged with Ugandan cassava brown streak virus. Sci Rep 2017; 7:9747. [PMID: 28852026 PMCID: PMC5575035 DOI: 10.1038/s41598-017-09617-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 07/21/2017] [Indexed: 12/13/2022] Open
Abstract
A time-course transcriptome analysis of two cassava varieties that are either resistant or susceptible to cassava brown streak disease (CBSD) was conducted using RNASeq, after graft inoculation with Ugandan cassava brown streak virus (UCBSV). From approximately 1.92 billion short reads, the largest number of differentially expressed genes (DEGs) was obtained in the resistant (Namikonga) variety at 2 days after grafting (dag) (3887 DEGs) and 5 dag (4911 DEGs). At the same time points, several defense response genes (encoding LRR-containing, NBARC-containing, pathogenesis-related, late embryogenesis abundant, selected transcription factors, chaperones, and heat shock proteins) were highly expressed in Namikonga. Also, defense-related GO terms of 'translational elongation', 'translation factor activity', 'ribosomal subunit' and 'phosphorelay signal transduction', were overrepresented in Namikonga at these time points. More reads corresponding to UCBSV sequences were recovered from the susceptible variety (Albert) (733 and 1660 read counts per million (cpm)) at 45 dag and 54 dag compared to Namikonga (10 and 117 cpm respectively). These findings suggest that Namikonga's resistance involves restriction of multiplication of UCBSV within the host. These findings can be used with other sources of evidence to identify candidate genes and biomarkers that would contribute substantially to knowledge-based resistance breeding.
Collapse
Affiliation(s)
- T Amuge
- National Crops Resources Research Institute (NaCRRI), Namulonge, Uganda
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - D K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - M S Katari
- Center for Genomics and Systems Biology, New York University, New York, USA
| | - A A Myburg
- Genetics Department, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - S L Goldman
- Center for Genomics and Systems Biology, New York University, New York, USA
| | - M E Ferguson
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya.
| |
Collapse
|
36
|
Bastet A, Robaglia C, Gallois JL. eIF4E Resistance: Natural Variation Should Guide Gene Editing. TRENDS IN PLANT SCIENCE 2017; 22:411-419. [PMID: 28258958 DOI: 10.1016/j.tplants.2017.01.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/20/2017] [Accepted: 01/31/2017] [Indexed: 05/19/2023]
Abstract
eIF4E translation initiation factors have emerged as major susceptibility factors for RNA viruses. Natural eIF4E-based resistance alleles are found in many species and are mostly variants that maintain the translation function of the protein. eIF4E genes represent major targets for engineering viral resistance, and gene-editing technologies can be used to make up for the lack of natural resistance alleles in some crops, often by knocking out eIF4E susceptibility factors. However, we report here how redundancy among eIF4E genes can restrict the efficient use of knockout alleles in breeding. We therefore discuss how gene-editing technologies can be used to design de novo functional alleles, using knowledge about the natural evolution of eIF4E genes in different species, to drive resistance to viruses without affecting plant physiology.
Collapse
Affiliation(s)
- Anna Bastet
- GAFL, INRA, 84140, Montfavet, France; Aix Marseille University, Biologie Végétale et Microbiologie Environnementales UMR 7265, Laboratoire de Génétique et Biophysique des Plantes, Marseille F-13009, France; CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Marseille F-13009, France; CEA, Bioscience and Biotechnology Institute of Aix-Marseille, Marseille F-13009, France
| | - Christophe Robaglia
- Aix Marseille University, Biologie Végétale et Microbiologie Environnementales UMR 7265, Laboratoire de Génétique et Biophysique des Plantes, Marseille F-13009, France; CNRS, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Marseille F-13009, France; CEA, Bioscience and Biotechnology Institute of Aix-Marseille, Marseille F-13009, France
| | | |
Collapse
|
37
|
Machado JPB, Calil IP, Santos AA, Fontes EPB. Translational control in plant antiviral immunity. Genet Mol Biol 2017; 40:292-304. [PMID: 28199446 PMCID: PMC5452134 DOI: 10.1590/1678-4685-gmb-2016-0092] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/27/2016] [Indexed: 01/11/2023] Open
Abstract
Due to the limited coding capacity of viral genomes, plant viruses depend extensively on the host cell machinery to support the viral life cycle and, thereby, interact with a large number of host proteins during infection. Within this context, as plant viruses do not harbor translation-required components, they have developed several strategies to subvert the host protein synthesis machinery to produce rapidly and efficiently the viral proteins. As a countermeasure against infection, plants have evolved defense mechanisms that impair viral infections. Among them, the host-mediated translational suppression has been characterized as an efficient mean to restrict infection. To specifically suppress translation of viral mRNAs, plants can deploy susceptible recessive resistance genes, which encode translation initiation factors from the eIF4E and eIF4G family and are required for viral mRNA translation and multiplication. Additionally, recent evidence has demonstrated that, alternatively to the cleavage of viral RNA targets, host cells can suppress viral protein translation to silence viral RNA. Finally, a novel strategy of plant antiviral defense based on suppression of host global translation, which is mediated by the transmembrane immune receptor NIK1 (nuclear shuttle protein (NSP)-Interacting Kinase1), is discussed in this review.
Collapse
Affiliation(s)
- João Paulo B Machado
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Iara P Calil
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Anésia A Santos
- Department of General Biology, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Elizabeth P B Fontes
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| |
Collapse
|
38
|
Miras M, Miller WA, Truniger V, Aranda MA. Non-canonical Translation in Plant RNA Viruses. FRONTIERS IN PLANT SCIENCE 2017; 8:494. [PMID: 28428795 PMCID: PMC5382211 DOI: 10.3389/fpls.2017.00494] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/21/2017] [Indexed: 05/03/2023]
Abstract
Viral protein synthesis is completely dependent upon the host cell's translational machinery. Canonical translation of host mRNAs depends on structural elements such as the 5' cap structure and/or the 3' poly(A) tail of the mRNAs. Although many viral mRNAs are devoid of one or both of these structures, they can still translate efficiently using non-canonical mechanisms. Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs. We highlight how these elements may interact with host translation factors and speculate on their contribution for achieving translational control. We also describe other translation strategies used by plant viruses to optimize the usage of the coding capacity of their very compact genomes, including leaky scanning initiation, ribosomal frameshifting and stop-codon readthrough. Finally, future research perspectives on the unusual translational strategies of +ssRNA viruses are discussed, including parallelisms between viral and host mRNAs mechanisms of translation, particularly for host mRNAs which are translated under stress conditions.
Collapse
Affiliation(s)
- Manuel Miras
- Centro de Edafología y Biología Aplicada del Segura - CSICMurcia, Spain
| | - W. Allen Miller
- Department of Plant Pathology and Microbiology, Iowa State UniversityAmes, IA, USA
| | - Verónica Truniger
- Centro de Edafología y Biología Aplicada del Segura - CSICMurcia, Spain
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura - CSICMurcia, Spain
- *Correspondence: Miguel A. Aranda
| |
Collapse
|
39
|
Hashimoto M, Neriya Y, Yamaji Y, Namba S. Recessive Resistance to Plant Viruses: Potential Resistance Genes Beyond Translation Initiation Factors. Front Microbiol 2016; 7:1695. [PMID: 27833593 PMCID: PMC5080351 DOI: 10.3389/fmicb.2016.01695] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/11/2016] [Indexed: 12/13/2022] Open
Abstract
The ability of plant viruses to propagate their genomes in host cells depends on many host factors. In the absence of an agrochemical that specifically targets plant viral infection cycles, one of the most effective methods for controlling viral diseases in plants is taking advantage of the host plant’s resistance machinery. Recessive resistance is conferred by a recessive gene mutation that encodes a host factor critical for viral infection. It is a branch of the resistance machinery and, as an inherited characteristic, is very durable. Moreover, recessive resistance may be acquired by a deficiency in a negative regulator of plant defense responses, possibly due to the autoactivation of defense signaling. Eukaryotic translation initiation factor (eIF) 4E and eIF4G and their isoforms are the most widely exploited recessive resistance genes in several crop species, and they are effective against a subset of viral species. However, the establishment of efficient, recessive resistance-type antiviral control strategies against a wider range of plant viral diseases requires genetic resources other than eIF4Es. In this review, we focus on recent advances related to antiviral recessive resistance genes evaluated in model plants and several crop species. We also address the roles of next-generation sequencing and genome editing technologies in improving plant genetic resources for recessive resistance-based antiviral breeding in various crop species.
Collapse
Affiliation(s)
- Masayoshi Hashimoto
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo Tokyo, Japan
| | - Yutaro Neriya
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo Tokyo, Japan
| | - Yasuyuki Yamaji
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo Tokyo, Japan
| | - Shigetou Namba
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo Tokyo, Japan
| |
Collapse
|
40
|
Hashimoto M, Neriya Y, Keima T, Iwabuchi N, Koinuma H, Hagiwara-Komoda Y, Ishikawa K, Himeno M, Maejima K, Yamaji Y, Namba S. EXA1, a GYF domain protein, is responsible for loss-of-susceptibility to plantago asiatica mosaic virus in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:120-131. [PMID: 27402258 DOI: 10.1111/tpj.13265] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 06/24/2016] [Accepted: 07/06/2016] [Indexed: 06/06/2023]
Abstract
One of the plant host resistance machineries to viruses is attributed to recessive alleles of genes encoding critical host factors for virus infection. This type of resistance, also referred to as recessive resistance, is useful for revealing plant-virus interactions and for breeding antivirus resistance in crop plants. Therefore, it is important to identify a novel host factor responsible for robust recessive resistance to plant viruses. Here, we identified a mutant from an ethylmethane sulfonate (EMS)-mutagenized Arabidopsis population which confers resistance to plantago asiatica mosaic virus (PlAMV, genus Potexvirus). Based on map-based cloning and single nucleotide polymorphism analysis, we identified a premature termination codon in a functionally unknown gene containing a GYF domain, which binds to proline-rich sequences in eukaryotes. Complementation analyses and robust resistance to PlAMV in a T-DNA mutant demonstrated that this gene, named Essential for poteXvirus Accumulation 1 (EXA1), is indispensable for PlAMV infection. EXA1 contains a GYF domain and a conserved motif for interaction with eukaryotic translation initiation factor 4E (eIF4E), and is highly conserved among monocot and dicot species. Analysis using qRT-PCR and immunoblotting revealed that EXA1 was expressed in all tissues, and was not transcriptionally responsive to PlAMV infection in Arabidopsis plants. Moreover, accumulation of PlAMV and a PlAMV-derived replicon was drastically diminished in the initially infected cells by the EXA1 deficiency. Accumulation of two other potexviruses also decreased in exa1-1 mutant plants. Our results provided a functional annotation to GYF domain-containing proteins by revealing the function of the highly conserved EXA1 gene in plant-virus interactions.
Collapse
Affiliation(s)
- Masayoshi Hashimoto
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yutaro Neriya
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takuya Keima
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Nozomu Iwabuchi
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hiroaki Koinuma
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuka Hagiwara-Komoda
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kazuya Ishikawa
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Misako Himeno
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kensaku Maejima
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuyuki Yamaji
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shigetou Namba
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| |
Collapse
|
41
|
Pyott DE, Sheehan E, Molnar A. Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants. MOLECULAR PLANT PATHOLOGY 2016; 17:1276-88. [PMID: 27103354 PMCID: PMC5026172 DOI: 10.1111/mpp.12417] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Members of the eukaryotic translation initiation factor (eIF) gene family, including eIF4E and its paralogue eIF(iso)4E, have previously been identified as recessive resistance alleles against various potyviruses in a range of different hosts. However, the identification and introgression of these alleles into important crop species is often limited. In this study, we utilise CRISPR/Cas9 technology to introduce sequence-specific deleterious point mutations at the eIF(iso)4E locus in Arabidopsis thaliana to successfully engineer complete resistance to Turnip mosaic virus (TuMV), a major pathogen in field-grown vegetable crops. By segregating the induced mutation from the CRISPR/Cas9 transgene, we outline a framework for the production of heritable, homozygous mutations in the transgene-free T2 generation in self-pollinating species. Analysis of dry weights and flowering times for four independent T3 lines revealed no differences from wild-type plants under standard growth conditions, suggesting that homozygous mutations in eIF(iso)4E do not affect plant vigour. Thus, the established CRISPR/Cas9 technology provides a new approach for the generation of Potyvirus resistance alleles in important crops without the use of persistent transgenes.
Collapse
Affiliation(s)
- Douglas E Pyott
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Emma Sheehan
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Attila Molnar
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3JR, UK.
| |
Collapse
|
42
|
Li H, Kondo H, Kühne T, Shirako Y. Barley Yellow Mosaic Virus VPg Is the Determinant Protein for Breaking eIF4E-Mediated Recessive Resistance in Barley Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:1449. [PMID: 27746794 PMCID: PMC5043020 DOI: 10.3389/fpls.2016.01449] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 09/12/2016] [Indexed: 05/25/2023]
Abstract
In this study, we investigated the barley yellow mosaic virus (BaYMV, genus Bymovirus) factor(s) responsible for breaking eIF4E-mediated recessive resistance genes (rym4/5/6) in barley. Genome mapping analysis using chimeric infectious cDNA clones between rym5-breaking (JT10) and rym5-non-breaking (JK05) isolates indicated that genome-linked viral protein (VPg) is the determinant protein for breaking the rym5 resistance. Likewise, VPg is also responsible for overcoming the resistances of rym4 and rym6 alleles. Mutational analysis identified that amino acids Ser-118, Thr-120, and His-142 in JT10 VPg are the most critical residues for overcoming rym5 resistance in protoplasts. Moreover, the rym5-non-breaking JK05 could accumulate in the rym5 protoplasts when eIF4E derived from a susceptible barley cultivar was expressed from the viral genome. Thus, the compatibility between VPg and host eIF4E determines the ability of BaYMV to infect barley plants.
Collapse
Affiliation(s)
- Huangai Li
- Graduate School of Agricultural and Life Sciences, The University of TokyoTokyo, Japan
- Asian Natural Environmental Science Center, The University of TokyoTokyo, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama UniversityKurashiki, Japan
| | - Thomas Kühne
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-InstitutQuedlinburg, Germany
| | - Yukio Shirako
- Asian Natural Environmental Science Center, The University of TokyoTokyo, Japan
| |
Collapse
|
43
|
Lebaron C, Rosado A, Sauvage C, Gauffier C, German-Retana S, Moury B, Gallois JL. A new eIF4E1 allele characterized by RNAseq data mining is associated with resistance to potato virus Y in tomato albeit with a low durability. J Gen Virol 2016; 97:3063-3072. [PMID: 27655175 DOI: 10.1099/jgv.0.000609] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Allele mining on susceptibility factors offers opportunities to find new sources of resistance among crop wild relatives for breeding purposes. As a proof of concept, we used available RNAseq data to investigate polymorphisms among the four tomato genes encoding translation initiation factors [eIF4E1 and eIF4E2, eIFiso4E and the related gene new cap-binding protein(nCBP)] to look for new potential resistance alleles to potyviruses. By analysing polymorphism among RNAseq data obtained for 20 tomato accessions, 10 belonging to the cultivated type Solanum lycopersicum and 10 belonging to the closest related wild species Solanum pimpinellifolium, we isolated one new eIF4E1 allele, in the S. pimpinellifolium LA0411 accession, which encodes a potential new resistance allele, mainly due to a polymorphism associated with an amino acid change within eIF4E1 region II. We confirmed that this new allele, pot12, is indeed associated with resistance to potato virus Y, although with a restricted resistance spectrum and a very low durability potential. This suggests that mutations occurring in eIF4E region II only may not be sufficient to provide efficient and durable resistance in plants. However, our study emphasizes the opportunity brought by RNAseq data to mine for new resistance alleles. Moreover, this approach could be extended to seek for putative new resistance alleles by screening for variant forms of susceptibility genes encoding plant host proteins known to interact with viral proteins.
Collapse
Affiliation(s)
| | | | | | | | | | - Benoît Moury
- Pathologie Végétale, INRA, 84140 Montfavet, France
| | | |
Collapse
|
44
|
Tatineni S, Wosula EN, Bartels M, Hein GL, Graybosch RA. Temperature-Dependent Wsm1 and Wsm2 Gene-Specific Blockage of Viral Long-Distance Transport Provides Resistance to Wheat streak mosaic virus and Triticum mosaic virus in Wheat. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:724-738. [PMID: 27551888 DOI: 10.1094/mpmi-06-16-0110-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are economically important viral pathogens of wheat. Wheat cvs. Mace, carrying the Wsm1 gene, is resistant to WSMV and TriMV, and Snowmass, with Wsm2, is resistant to WSMV. Viral resistance in both cultivars is temperature sensitive and is effective at 18°C or below but not at higher temperatures. The underlying mechanisms of viral resistance of Wsm1 and Wsm2, nonallelic single dominant genes, are not known. In this study, we found that fluorescent protein-tagged WSMV and TriMV elicited foci that were approximately similar in number and size at 18 and 24°C, on inoculated leaves of resistant and susceptible wheat cultivars. These data suggest that resistant wheat cultivars at 18°C facilitated efficient cell-to-cell movement. Additionally, WSMV and TriMV efficiently replicated in inoculated leaves of resistant wheat cultivars at 18°C but failed to establish systemic infection, suggesting that Wsm1- and Wsm2-mediated resistance debilitated viral long-distance transport. Furthermore, we found that neither virus was able to enter the leaf sheaths of inoculated leaves or crowns of resistant wheat cultivars at 18°C but both were able to do so at 24°C. Thus, wheat cvs. Mace and Snowmass provide resistance at the long-distance movement stage by specifically blocking virus entry into the vasculature. Taken together, these data suggest that both Wsm1 and Wsm2 genes similarly confer virus resistance by temperature-dependent impairment of viral long-distance movement.
Collapse
Affiliation(s)
- Satyanarayana Tatineni
- 1 United States Department of Agriculture-Agricultural Research Service (USDA-ARS) and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | | | - Melissa Bartels
- 1 United States Department of Agriculture-Agricultural Research Service (USDA-ARS) and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, U.S.A
| | - Gary L Hein
- 2 Department of Entomology, University of Nebraska-Lincoln; and
| | - Robert A Graybosch
- 3 USDA-ARS and Department of Agronomy and Horticulture, University of Nebraska-Lincoln
| |
Collapse
|
45
|
Gauffier C, Lebaron C, Moretti A, Constant C, Moquet F, Bonnet G, Caranta C, Gallois JL. A TILLING approach to generate broad-spectrum resistance to potyviruses in tomato is hampered by eIF4E gene redundancy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:717-29. [PMID: 26850324 DOI: 10.1111/tpj.13136] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/22/2016] [Accepted: 02/01/2016] [Indexed: 05/23/2023]
Abstract
Genetic resistance to pathogens is important for sustainable maintenance of crop yields. Recent biotechnologies offer alternative approaches to generate resistant plants by compensating for the lack of natural resistance. Tomato (Solanum lycopersicum) and related species offer a model in which natural and TILLING-induced potyvirus resistance alleles may be compared. For resistance based on translation initiation factor eIF4E1, we confirm that the natural allele Sh-eIF4E1(PI24)-pot1, isolated from the wild tomato species Solanum habrochaites, is associated with a wide spectrum of resistance to both potato virus Y and tobacco etch virus isolates. In contrast, a null allele of the same gene, isolated through a TILLING strategy in cultivated tomato S. lycopersicum, is associated with a much narrower resistance spectrum. Introgressing the null allele into S. habrochaites did not extend its resistance spectrum, indicating that the genetic background is not responsible for the broad resistance. Instead, the different types of eIF4E1 mutations affect the levels of eIF4E2 differently, suggesting that eIF4E2 is also involved in potyvirus resistance. Indeed, combining two null mutations affecting eIF4E1 and eIF4E2 re-establishes a wide resistance spectrum in cultivated tomato, but to the detriment of plant development. These results highlight redundancy effects within the eIF4E gene family, where regulation of expression alters susceptibility or resistance to potyviruses. For crop improvement, using loss-of-function alleles to generate resistance may be counter-productive if they narrow the resistance spectrum and limit growth. It may be more effective to use alleles encoding functional variants similar to those found in natural diversity.
Collapse
Affiliation(s)
- Camille Gauffier
- INRA-UR 1052, GAFL Domaine St Maurice, CS 60094, F-84143, Montfavet, France
| | - Caroline Lebaron
- INRA-UR 1052, GAFL Domaine St Maurice, CS 60094, F-84143, Montfavet, France
| | - André Moretti
- INRA-UR 1052, GAFL Domaine St Maurice, CS 60094, F-84143, Montfavet, France
| | - Carole Constant
- Sakata Vegetables Europe, Domaine de Sablas Rue du Moulin, F-30620, Uchaud, France
| | - Frédéric Moquet
- Gautier Semences, Route d'Avignon, F-13630, Eyragues, France
| | - Grégori Bonnet
- Syngenta, 346 Route des Pasquiers, F-84260, Sarrians, France
| | - Carole Caranta
- INRA-UR 1052, GAFL Domaine St Maurice, CS 60094, F-84143, Montfavet, France
| | - Jean-Luc Gallois
- INRA-UR 1052, GAFL Domaine St Maurice, CS 60094, F-84143, Montfavet, France
| |
Collapse
|
46
|
|
47
|
Plant Translation Factors and Virus Resistance. Viruses 2015; 7:3392-419. [PMID: 26114476 PMCID: PMC4517107 DOI: 10.3390/v7072778] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 02/06/2023] Open
Abstract
Plant viruses recruit cellular translation factors not only to translate their viral RNAs but also to regulate their replication and potentiate their local and systemic movement. Because of the virus dependence on cellular translation factors, it is perhaps not surprising that many natural plant recessive resistance genes have been mapped to mutations of translation initiation factors eIF4E and eIF4G or their isoforms, eIFiso4E and eIFiso4G. The partial functional redundancy of these isoforms allows specific mutation or knock-down of one isoform to provide virus resistance without hindering the general health of the plant. New possible targets for antiviral strategies have also been identified following the characterization of other plant translation factors (eIF4A-like helicases, eIF3, eEF1A and eEF1B) that specifically interact with viral RNAs and proteins and regulate various aspects of the infection cycle. Emerging evidence that translation repression operates as an alternative antiviral RNA silencing mechanism is also discussed. Understanding the mechanisms that control the development of natural viral resistance and the emergence of virulent isolates in response to these plant defense responses will provide the basis for the selection of new sources of resistance and for the intelligent design of engineered resistance that is broad-spectrum and durable.
Collapse
|
48
|
Galvez LC, Banerjee J, Pinar H, Mitra A. Engineered plant virus resistance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 228:11-25. [PMID: 25438782 DOI: 10.1016/j.plantsci.2014.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 07/16/2014] [Accepted: 07/18/2014] [Indexed: 06/04/2023]
Abstract
Virus diseases are among the key limiting factors that cause significant yield loss and continuously threaten crop production. Resistant cultivars coupled with pesticide application are commonly used to circumvent these threats. One of the limitations of the reliance on resistant cultivars is the inevitable breakdown of resistance due to the multitude of variable virus populations. Similarly, chemical applications to control virus transmitting insect vectors are costly to the farmers, cause adverse health and environmental consequences, and often result in the emergence of resistant vector strains. Thus, exploiting strategies that provide durable and broad-spectrum resistance over diverse environments are of paramount importance. The development of plant gene transfer systems has allowed for the introgression of alien genes into plant genomes for novel disease control strategies, thus providing a mechanism for broadening the genetic resources available to plant breeders. Genetic engineering offers various options for introducing transgenic virus resistance into crop plants to provide a wide range of resistance to viral pathogens. This review examines the current strategies of developing virus resistant transgenic plants.
Collapse
Affiliation(s)
- Leny C Galvez
- Department of Plant Pathology, University of Nebarska, Lincoln, NE 68583-0722, USA
| | - Joydeep Banerjee
- Department of Plant Pathology, University of Nebarska, Lincoln, NE 68583-0722, USA
| | - Hasan Pinar
- Department of Plant Pathology, University of Nebarska, Lincoln, NE 68583-0722, USA
| | - Amitava Mitra
- Department of Plant Pathology, University of Nebarska, Lincoln, NE 68583-0722, USA.
| |
Collapse
|
49
|
Kim J, Kang WH, Hwang J, Yang HB, Dosun K, Oh CS, Kang BC. Transgenic Brassica rapa plants over-expressing eIF(iso)4E variants show broad-spectrum Turnip mosaic virus (TuMV) resistance. MOLECULAR PLANT PATHOLOGY 2014; 15:615-26. [PMID: 24417952 PMCID: PMC6638765 DOI: 10.1111/mpp.12120] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The protein-protein interaction between VPg (viral protein genome-linked) of potyviruses and eIF4E (eukaryotic initiation factor 4E) or eIF(iso)4E of their host plants is a critical step in determining viral virulence. In this study, we evaluated the approach of engineering broad-spectrum resistance in Chinese cabbage (Brassica rapa) to Turnip mosaic virus (TuMV), which is one of the most important potyviruses, by a systematic knowledge-based approach to interrupt the interaction between TuMV VPg and B. rapa eIF(iso)4E. The seven amino acids in the cap-binding pocket of eIF(iso)4E were selected on the basis of other previous results and comparison of protein models of cap-binding pockets, and mutated. Yeast two-hybrid assay and co-immunoprecipitation analysis demonstrated that W95L, K150L and W95L/K150E amino acid mutations of B. rapa eIF(iso)4E interrupted its interaction with TuMV VPg. All eIF(iso)4E mutants were able to complement an eIF4E-knockout yeast strain, indicating that the mutated eIF(iso)4E proteins retained their function as a translational initiation factor. To determine whether these mutations could confer resistance, eIF(iso)4E W95L, W95L/K150E and eIF(iso)4E wild-type were over-expressed in a susceptible Chinese cabbage cultivar. Evaluation of the TuMV resistance of T1 and T2 transformants demonstrated that the over-expression of the eIF(iso)4E mutant forms can confer resistance to multiple TuMV strains. These data demonstrate the utility of knowledge-based approaches for the engineering of broad-spectrum resistance in Chinese cabbage.
Collapse
Affiliation(s)
- Jinhee Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea
| | | | | | | | | | | | | |
Collapse
|
50
|
Interaction patterns between potato virus Y and eIF4E-mediated recessive resistance in the Solanaceae. J Virol 2014; 88:9799-807. [PMID: 24942572 DOI: 10.1128/jvi.00930-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The structural pattern of infectivity matrices, which contains infection data resulting from inoculations of a set of hosts by a set of parasites, is a key parameter for our understanding of biological interactions and their evolution. This pattern determines the evolution of parasite pathogenicity and host resistance, the spatiotemporal distribution of host and parasite genotypes, and the efficiency of disease control strategies. Two major patterns have been proposed for plant-virus genotype infectivity matrices. In the gene-for-gene model, infectivity matrices show a nested pattern, where the host ranges of specialist virus genotypes are subsets of the host ranges of less specialized viruses. In contrast, in the matching-allele (MA) model, each virus genotype is specialized to infect one (or a small set of) host genotype(s). The corresponding infectivity matrix shows a modular pattern where infection is frequent for plants and viruses belonging to the same module but rare for those belonging to different modules. We analyzed the structure of infectivity matrices between Potato virus Y (PVY) and plant genotypes in the family Solanaceae carrying different eukaryotic initiation factor 4E (eIF4E)-coding alleles conferring recessive resistance. Whereas this system corresponds mechanistically to an MA model, the expected modular pattern was rejected based on our experimental data. This was mostly because PVY mutations involved in adaptation to a particular plant genotype displayed frequent pleiotropic effects, conferring simultaneously an adaptation to additional plant genotypes with different eIF4E alleles. Such effects should be taken into account for the design of strategies of sustainable control of PVY through plant varietal mixtures or rotations. IMPORTANCE The interaction pattern between host and virus genotypes has important consequences on their respective evolution and on issues regarding the application of disease control strategies. We found that the structure of the interaction between Potato virus Y (PVY) variants and host plants in the family Solanaceae departs significantly from the current model of interaction considered for these organisms because of frequent pleiotropic effects of virus mutations. These mutational effects allow the virus to expand rapidly its range of host plant genotypes, make it very difficult to predict the effects of mutations in PVY infectivity factors, and raise concerns about strategies of sustainable management of plant genetic resistance to viruses.
Collapse
|