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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.
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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
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Li N, Duan Y, Ye Q, Ma Y, Ma R, Zhao L, Zhu S, Yu F, Qi S, Wang Y. The Arabidopsis eIF4E1 regulates NRT1.1-mediated nitrate signaling at both translational and transcriptional levels. THE NEW PHYTOLOGIST 2023; 240:338-353. [PMID: 37424317 DOI: 10.1111/nph.19129] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/18/2023] [Indexed: 07/11/2023]
Abstract
Identifying new nitrate regulatory genes and illustrating their mechanisms in modulating nitrate signaling are of great significance for achieving the high yield and nitrogen use efficiency (NUE) of crops. Here, we screened a mutant with defects in nitrate response and mapped the mutation to the gene eIF4E1 in Arabidopsis. Our results showed that eIF4E1 regulated nitrate signaling and metabolism. Ribo-seq and polysome profiling analysis revealed that eIF4E1 modulated the amount of some nitrogen (N)-related mRNAs being translated, especially the mRNA of NRT1.1 was reduced in the eif4e1 mutant. RNA-Seq results enriched some N-related genes, supporting that eIF4E1 is involved in nitrate regulation. The genetic analysis indicated that eIF4E1 worked upstream of NRT1.1 in nitrate signaling. In addition, an eIF4E1-interacting protein GEMIN2 was identified and found to be involved in nitrate signaling. Further investigation showed that overexpression of eIF4E1 promoted plant growth and enhanced yield and NUE. These results demonstrate that eIF4E1 regulates nitrate signaling by modulating NRT1.1 at both translational and transcriptional levels, laying the foundation for future research on the regulation of mineral nutrition at the translational level.
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Affiliation(s)
- Na Li
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yawen Duan
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Qing Ye
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yuhan Ma
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Rongjie Ma
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Lufei Zhao
- Agricultural Science and Engineering School, Liaocheng University, Liaocheng, Shandong, 252000, China
| | - Sirui Zhu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan, 410082, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, Hunan, 410082, China
| | - Shengdong Qi
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yong Wang
- College of Life Sciences, National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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Shan H, Chen D, Zhang R, Wang X, Li J, Wang C, Li Y, Huang Y. Relationship between Sugarcane eIF4E Gene and Resistance against Sugarcane Streak Mosaic Virus. PLANTS (BASEL, SWITZERLAND) 2023; 12:2805. [PMID: 37570959 PMCID: PMC10421434 DOI: 10.3390/plants12152805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023]
Abstract
Sugarcane mosaic disease, mainly caused by Sugarcane streak mosaic virus (SCSMV), has serious adverse effects on the yield and quality of sugarcane. Eukaryotic translation initiation factor 4E (eIF4E) is a natural resistance gene in plants. The eIF4E-mediated natural recessive resistance results from non-synonymous mutations of the eIF4E protein. In this study, two sugarcane varieties, CP94-1100 and ROC22, were selected for analysis of their differences in resistance to SCSMV. Four-base missense mutations in the ORF region of eIF4E resulted in different conserved domains. Therefore, the differences in resistance to SCSMV are due to the inherent differences in eIF4E of the sugarcane varieties. The coding regions of eIF4E included 28 SNP loci and no InDel loci, which were affected by negative selection and were relatively conserved. A total of 11 haploids encoded 11 protein sequences. Prediction of the protein spatial structure revealed three non-synonymous mutation sites for amino acids located in the cap pocket of eIF4E; one of these sites existed only in a resistant material (Yuetang 55), whereas the other site existed only in a susceptible material (ROC22), suggesting that these two sites might be related to the resistance to SCSMV. The results provide a strong basis for further analysis of the functional role of eIF4E in regulating mosaic resistance in sugarcane.
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Affiliation(s)
| | | | | | | | | | | | | | - Yingkun Huang
- Sugarcane Research Institute, Yunnan Academy of Agricultural Science, Yunnan Key Laboratory of Sugarcane Genetic Improvement, Kaiyuan 661699, China; (H.S.); (D.C.); (R.Z.); (X.W.); (J.L.); (C.W.); (Y.L.)
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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.
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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.
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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
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Li H, Luo J, Zhang W, Hua L, Li K, Wang J, Xu B, Yang C, Wang G, Rouse MN, Dubcovsky J, Chen S. High-resolution mapping of SrTm4, a recessive resistance gene to wheat stem rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:120. [PMID: 37103626 PMCID: PMC10140103 DOI: 10.1007/s00122-023-04369-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/17/2023] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE The diploid wheat recessive stem rust resistance gene SrTm4 was fine-mapped to a 754-kb region on chromosome arm 2AmL and potential candidate genes were identified. Race Ug99 of Puccinia graminis f. sp. tritici (Pgt), the causal agent of wheat stem (or black) rust is one of the most serious threats to global wheat production. The identification, mapping, and deployment of effective stem rust resistance (Sr) genes are critical to reduce this threat. In this study, we generated SrTm4 monogenic lines and found that this gene confers resistance to North American and Chinese Pgt races. Using a large mapping population (9522 gametes), we mapped SrTm4 within a 0.06 cM interval flanked by marker loci CS4211 and 130K1519, which corresponds to a 1.0-Mb region in the Chinese Spring reference genome v2.1. A physical map of the SrTm4 region was constructed with 11 overlapping BACs from the resistant Triticum monococcum PI 306540. Comparison of the 754-kb physical map with the genomic sequence of Chinese Spring and a discontinuous BAC sequence of DV92 revealed a 593-kb chromosomal inversion in PI 306540. Within the candidate region, we identified an L-type lectin-domain containing receptor kinase (LLK1), which was disrupted by the proximal inversion breakpoint, as a potential candidate gene. Two diagnostic dominant markers were developed to detect the inversion breakpoints. In a survey of T. monococcum accessions, we identified 10 domesticated T. monococcum subsp. monococcum genotypes, mainly from the Balkans, carrying the inversion and showing similar mesothetic resistant infection types against Pgt races. The high-density map and tightly linked molecular markers developed in this study are useful tools to accelerate the deployment of SrTm4-mediated resistance in wheat breeding programs.
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Affiliation(s)
- Hongna Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Jing Luo
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA95616, USA
| | - Lei Hua
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Kun Li
- Department of Plant Sciences, University of California, Davis, CA95616, USA
| | - Jian Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Binyang Xu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chen Yang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guiping Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China
| | - Matthew N Rouse
- US Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory and Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Shisheng Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, 261325, Shandong, China.
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Majumdar A, Sharma A, Belludi R. Natural and Engineered Resistance Mechanisms in Plants against Phytoviruses. Pathogens 2023; 12:pathogens12040619. [PMID: 37111505 PMCID: PMC10143959 DOI: 10.3390/pathogens12040619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Plant viruses, as obligate intracellular parasites, rely exclusively on host machinery to complete their life cycle. Whether a virus is pathogenic or not depends on the balance between the mechanisms used by both plants and viruses during the intense encounter. Antiviral defence mechanisms in plants can be of two types, i.e., natural resistance and engineered resistance. Innate immunity, RNA silencing, translational repression, autophagy-mediated degradation, and resistance to virus movement are the possible natural defence mechanisms against viruses in plants, whereas engineered resistance includes pathogen-derived resistance along with gene editing technologies. The incorporation of various resistance genes through breeding programmes, along with gene editing tools such as CRISPR/Cas technologies, holds great promise in developing virus-resistant plants. In this review, different resistance mechanisms against viruses in plants along with reported resistance genes in major vegetable crops are discussed.
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Affiliation(s)
- Anik Majumdar
- Department of Plant Pathology, College of Agriculture, Punjab Agricultural University, Ludhiana 141004, Punjab, India
| | - Abhishek Sharma
- Department of Vegetable Science, College of Horticulture and Forestry, Punjab Agricultural University, Ludhiana 141004, Punjab, India
| | - Rakesh Belludi
- Department of Plant Pathology, College of Agriculture, Punjab Agricultural University, Ludhiana 141004, Punjab, India
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Fidan H, Calis O, Ari E, Atasayar A, Sarikaya P, Tek MI, Izmirli A, Oz Y, Firat G. Knockout of elF4E using CRISPR/Cas9 for large-scale production of resistant cucumber cultivar against WMV, ZYMV, and PRSV. FRONTIERS IN PLANT SCIENCE 2023; 14:1143813. [PMID: 37008503 PMCID: PMC10064079 DOI: 10.3389/fpls.2023.1143813] [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: 01/13/2023] [Accepted: 02/21/2023] [Indexed: 06/19/2023]
Abstract
CRISPR/Cas9 is one of the most robust technologies for plant breeding enabling precise and efficient modifications in a genome. This technology is being used for the manipulation of target genes in a host to develop resistance against the plant pathogens. Cucumis sativus elF4E is one of the target genes playing a key role in viral infection during interaction with potyvirus viral proteins genome linked (VPg). Nevertheless, the allelic and positional effect of elF4E mutations in C. sativus is to be clarified in elF4E-VPg interaction. In addition, there are entanglements in the massive production of pathogen-resistant cultivars suitable for commercial production using CRISPR/Cas9 technology. Therefore, we targeted different positions of the elF4E in G27 and G247 inbred lines, using specific gRNA1 and gRNA2 for the first and third exons, respectively, and 1,221 transgene-free plants were selected in segregated T1 generation, where 192 G27 and 79 G247 plants had the least mutation at Cas9 cleavage site of gRNA1 or gRNA2. Crossing was performed to see allelic effects of elfF4E mutations in F1 populations, which were homozygous and heterozygous single (elF4E_1DEL or elF4E_3DEL) and double (elF4E_1-3DEL) mutants. Disease symptoms of watermelon mosaic virus (WMV), papaya ringspot virus (PRSV), and zucchini yellow mosaic virus (ZYMV) were evaluated in both non-edited and edited F1 plants, and we did not observe any symptom in homozygous elF4E_1-3DEL and elF4E_1DEL mutants. However, homozygous elF4E_3DEL was positive in reverse transcription polymerase chain reaction (RT-PCR), even if there were no significant symptoms on the inoculated leaves. ELISA and qRT-PCR indicated lower viral accumulation in homozygous elF4E_3DEL than heterozygous and non-edited plants. Regeneration and transformation protocols were also optimized comprehensively for both the genotypes. The average number of shoots/100 explants was determined for both G27 and G247 as 13.6 and 18.0, respectively. We could not detect any distinguishing difference between the non-edited and edited F1 plants for yield and morphology. Our results demonstrate an effective route for mass production of viral resistant cultivars of cucumber to WMV, ZYMV, and PRSV. In this way, the pathogen-resistant cultivars could be generated to reduce the losses caused by these pathogens in cucumber production.
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Affiliation(s)
- Hakan Fidan
- Plant Protection Department Faculty of Agriculture Akdeniz University, Antalya, Türkiye
| | - Ozer Calis
- Plant Protection Department Faculty of Agriculture Akdeniz University, Antalya, Türkiye
| | - Esin Ari
- Agricultural Biotechnology Department, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Aydin Atasayar
- Research and Development Department AD ROSSEN Seeds, Antalya, Türkiye
| | - Pelin Sarikaya
- Plant Protection Department Faculty of Agriculture Akdeniz University, Antalya, Türkiye
- Research and Development Department AD ROSSEN Seeds, Antalya, Türkiye
| | - Mumin Ibrahim Tek
- Plant Protection Department Faculty of Agriculture Akdeniz University, Antalya, Türkiye
| | - Ahmet Izmirli
- Agricultural Biotechnology Department, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Yasemin Oz
- Agricultural Biotechnology Department, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Gulsah Firat
- Research and Development Department AD ROSSEN Seeds, Antalya, Türkiye
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Wei W, Wu X, Garcia A, McCoppin N, Viana JPG, Murad PS, Walker DR, Hartman GL, Domier LL, Hudson ME, Clough SJ. An NBS-LRR protein in the Rpp1 locus negates the dominance of Rpp1-mediated resistance against Phakopsora pachyrhizi in soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:915-933. [PMID: 36424366 DOI: 10.1111/tpj.16038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 11/01/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
The soybean Rpp1 locus confers resistance to Phakopsora pachyrhizi, causal agent of rust, and resistance is usually dominant over susceptibility. However, dominance of Rpp1-mediated resistance is lost when a resistant genotype (Rpp1 or Rpp1b) is crossed with susceptible line TMG06_0011, and the mechanism of this dominant susceptibility (DS) is unknown. Sequencing the Rpp1 region reveals that the TMG06_0011 Rpp1 locus has a single nucleotide-binding site leucine-rich repeat (NBS-LRR) gene (DS-R), whereas resistant PI 594760B (Rpp1b) is similar to PI 200492 (Rpp1) and has three NBS-LRR resistance gene candidates. Evidence that DS-R is the cause of DS was reflected in virus-induced gene silencing of DS-R in Rpp1b/DS-R or Rpp1/DS-R heterozygous plants with resistance partially restored. In heterozygous Rpp1b/DS-R plants, expression of Rpp1b candidate genes was not significantly altered, indicating no effect of DS-R on transcription. Physical interaction of the DS-R protein with candidate Rpp1b resistance proteins was supported by yeast two-hybrid studies and in silico modeling. Thus, we conclude that suppression of resistance most likely does not occur at the transcript level, but instead probably at the protein level, possibly with Rpp1 function inhibited by binding to the DS-R protein. The DS-R gene was found in other soybean lines, with an estimated allele frequency of 6% in a diverse population, and also found in wild soybean (Glycine soja). The identification of a dominant susceptible NBS-LRR gene provides insight into the behavior of NBS-LRR proteins and serves as a reminder to breeders that the dominance of an R gene can be influenced by a susceptibility allele.
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Affiliation(s)
- Wei Wei
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
| | - Xing Wu
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, 260 Whitney Ave # 266, New Haven, CT, 06511, USA
| | - Alexandre Garcia
- Tropical Melhoramento e Genética, LTDA, Rodovia Celso Garcia Cid, Km 87, Cambé, PR, CEP: 86183-600, Brazil
| | - Nancy McCoppin
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit, US Department of Agriculture, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
| | - João Paulo Gomes Viana
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
| | - Praerona S Murad
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
| | - David R Walker
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit, US Department of Agriculture, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
| | - Glen L Hartman
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit, US Department of Agriculture, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit, US Department of Agriculture, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
| | - Matthew E Hudson
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
| | - Steven J Clough
- Department of Crop Sciences, University of Illinois, 1102 S Goodwin Ave, Urbana, IL, 61801, USA
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit, US Department of Agriculture, 1101 W. Peabody Dr, Urbana, IL, 61801, USA
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10
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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.
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Roy A, Sahu PK, Das C, Bhattacharyya S, Raina A, Mondal S. Conventional and new-breeding technologies for improving disease resistance in lentil ( Lens culinaris Medik). FRONTIERS IN PLANT SCIENCE 2023; 13:1001682. [PMID: 36743558 PMCID: PMC9896981 DOI: 10.3389/fpls.2022.1001682] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 12/02/2022] [Indexed: 06/02/2023]
Abstract
Lentil, an important cool season food legume, is a rich source of easily digestible protein, folic acid, bio-available iron, and zinc nutrients. Lentil grows mainly as a sole crop in the winter after harvesting rice in South Asia. However, the annual productivity is low due to its slow growth during the early phase, competitive weed infestation, and disease outbreaks during the crop growth period. Disease resistance breeding has been practiced for a long time to enhance resistance to various diseases. Often the sources of resistance are available in wild crop relatives. Thus, wide hybridization and the ovule rescue technique have helped to introgress the resistance trait into cultivated lentils. Besides hybridization, induced mutagenesis contributed immensely in creating variability for disease tolerance, and several disease-resistant mutant lines have been developed. However, to overcome the limitations of traditional breeding approaches, advancement in molecular marker technologies, and genomics has helped to develop disease-resistant and climate-resilient lentil varieties with more precision and efficiency. This review describes types of diseases, disease screening methods, the role of conventional and new breeding technologies in alleviating disease-incurred damage and progress toward making lentil varieties more resilient to disease outbreaks under the shadow of climate change.
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Affiliation(s)
- Anirban Roy
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur West Bengal, India
- Department of Genetics and Plant Breeding, Ramakrishna Mission Vivekananda Educational & Research Institute (RKMVERI), Ramkrishna Mission Ashrama, Kolkata, India
| | - Parmeshwar K. Sahu
- Department of Genetics and Plant Breeding, College of Agriculture, Indira Gandhi Krishi Viswavidyalaya, Raipur, Chhattisgarh, India
| | - Camellia Das
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur West Bengal, India
| | - Somnath Bhattacharyya
- Department of Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur West Bengal, India
| | - Aamir Raina
- Mutation Breeding Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
- Botany Section, Women’s College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Suvendu Mondal
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, India
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12
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Virus Evolution Faced to Multiple Host Targets: The Potyvirus-Pepper Case Study. Curr Top Microbiol Immunol 2023; 439:121-138. [PMID: 36592244 DOI: 10.1007/978-3-031-15640-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The wealth of variability amongst genes controlling immunity against potyviruses in pepper (Capsicum spp.) has been instrumental in understanding plant-virus co-evolution and major determinants of plant resistance durability. Characterization of the eukaryotic initiation factor 4E1 (eIF4E1), involved in mRNA translation, as the basis of potyvirus resistance in pepper initiated a large body of work that showed that recessive resistance to potyviruses and other single-stranded positive-sense RNA viruses resulted from mutations in eukaryotic initiation factors in many plant crop species. Combining mutations in different eIF4Es in the same pepper genotype had complex effects on the breadth of the resistance spectrum and on resistance durability, revealing a trade-off between these two traits. In addition, combining eIF4E1 mutations with a quantitatively resistant genetic background had a strong positive effect on resistance durability. Analysing the evolutionary forces imposed by pepper genotypes onto virus populations allowed identifying three key factors improving plant resistance durability: the complexity of mutational pathways involved in virus adaptation to the plant resistance, the decrease of competitivity induced by these mutations on the virus and the intensity of genetic drift imposed by plant genotypes on the virus during its infection cycle.
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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.
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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.
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14
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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.
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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
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Lucioli A, Tavazza R, Baima S, Fatyol K, Burgyan J, Tavazza M. CRISPR-Cas9 Targeting of the eIF4E1 Gene Extends the Potato Virus Y Resistance Spectrum of the Solanum tuberosum L. cv. Desirée. Front Microbiol 2022; 13:873930. [PMID: 35722301 PMCID: PMC9198583 DOI: 10.3389/fmicb.2022.873930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/10/2022] [Indexed: 11/26/2022] Open
Abstract
Translation initiation factors and, in particular, the eIF4E family are the primary source of recessive resistance to potyviruses in many plant species. However, no eIF4E-mediated resistance to this virus genus has been identified in potato (Solanum tuberosum L.) germplasm. As in tomato, the potato eIF4E gene family consists of eIF4E1, its paralog eIF4E2, eIF(iso)4E, and nCBP. In tomato, eIF4E1 knockout (KO) confers resistance to a subset of potyviruses, while the eIF4E1/2 double KO, although conferring a broader spectrum of resistance, leads to plant developmental defects. Here, the tetraploid potato cv. Desirée owning the dominant Ny gene conferring resistance to potato virus Y (PVY) strain O but not NTN was used to evaluate the possibility to expand its PVY resistance spectrum by CRISPR-Cas9-mediated KO of the eIF4E1 susceptibility gene. After a double process of plant protoplast transfection-regeneration, eIF4E1 KO potatoes were obtained. The knockout was specific for the eIF4E1, and no mutations were identified in its eIF4E2 paralog. Expression analysis of the eIF4E family shows that the disruption of the eIF4E1 does not alter the RNA steady-state level of the other family members. The eIF4E1 KO lines challenged with a PVYNTN isolate showed a reduced viral accumulation and amelioration of virus-induced symptoms suggesting that the eIF4E1 gene was required but not essential for its multiplication. Our data show that eIF4E1 editing can be usefully exploited to broaden the PVY resistance spectrum of elite potato cultivars, such as Desirée, by pyramiding eIF4E-mediated recessive resistance.
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Affiliation(s)
- Alessandra Lucioli
- Biotechnology Laboratory, Biotechnology and Agroindustry Division, Department for Sustainability, ENEA, CR Casaccia, Rome, Italy
| | - Raffaela Tavazza
- Biotechnology Laboratory, Biotechnology and Agroindustry Division, Department for Sustainability, ENEA, CR Casaccia, Rome, Italy
| | - Simona Baima
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Rome, Italy
| | - Karoly Fatyol
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Godollo, Hungary
| | - Jozsef Burgyan
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Godollo, Hungary
| | - Mario Tavazza
- Biotechnology Laboratory, Biotechnology and Agroindustry Division, Department for Sustainability, ENEA, CR Casaccia, Rome, Italy
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Tomato zonate spot virus induced hypersensitive resistance via an auxin-related pathway in pepper. Gene 2022; 823:146320. [PMID: 35218893 DOI: 10.1016/j.gene.2022.146320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 12/28/2021] [Accepted: 02/11/2022] [Indexed: 11/20/2022]
Abstract
Tomato zonate spotvirus (TZSV) often incurs significant losses in many food and ornamental crops in Yunnan province, China, and the surrounding areas. The pepper (Capsicum chinensePI152225)can develop hypersensitive resistance following infection with TZSV, through an as yet unknown mechanism. The transcriptome dataset showed a total of 45.81 GB of clean data were obtained from six libraries, and the average percentage of the reads mapped to the pepper genome was over 90.00 %. A total of 1403 differentially expressed genes (DEGs) were obtained after TZSV infection, including 825significantly up-regulated genes and 578 down-regulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that most up-regulated DEGs were involved in basal defenses. RT-qPCR, and virus induced gene silencing (VIGS) were used preliminarily to identifyBBC_22506 and BBC_18917, among total of 71 differentially expressed genes (DEGs), that play a key role in mediating the auxin-induced signaling pathway that might take part in hypersensitive response (HR) conferred resistance to viral infection in pepper (PI152225) byTZSV. This is the first study on the mechanism of auxin resistance, involved in defense responses of pepper against viral diseases, which lay the foundation for further study on the pathogenic mechanism of TZSV, as well as the mechanism of resistance to TZSV, in peppers.
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17
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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.
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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
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18
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Helderman TA, Deurhof L, Bertran A, Richard MMS, Kormelink R, Prins M, Joosten MHAJ, van den Burg HA. Members of the ribosomal protein S6 (RPS6) family act as pro-viral factor for tomato spotted wilt orthotospovirus infectivity in Nicotiana benthamiana. MOLECULAR PLANT PATHOLOGY 2022; 23:431-446. [PMID: 34913556 PMCID: PMC8828452 DOI: 10.1111/mpp.13169] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 05/07/2023]
Abstract
To identify host factors for tomato spotted wilt orthotospovirus (TSWV), a virus-induced gene silencing (VIGS) screen using tobacco rattle virus (TRV) was performed on Nicotiana benthamiana for TSWV susceptibility. To rule out any negative effect on the plants' performance due to a double viral infection, the method was optimized to allow screening of hundreds of clones in a standardized fashion. To normalize the results obtained in and between experiments, a set of controls was developed to evaluate in a consist manner both VIGS efficacy and the level of TSWV resistance. Using this method, 4532 random clones of an N. benthamiana cDNA library were tested, resulting in five TRV clones that provided nearly complete resistance against TSWV. Here we report on one of these clones, of which the insert targets a small gene family coding for the ribosomal protein S6 (RPS6) that is part of the 40S ribosomal subunit. This RPS6 family is represented by three gene clades in the genome of Solanaceae family members, which were jointly important for TSWV susceptibility. Interestingly, RPS6 is a known host factor implicated in the replication of different plant RNA viruses, including the negative-stranded TSWV and the positive-stranded potato virus X.
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Affiliation(s)
- Tieme A. Helderman
- Molecular Plant PathologySwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamNetherlands
| | - Laurens Deurhof
- Laboratory of PhytopathologyDepartment of Plant SciencesWageningen UniversityWageningenNetherlands
| | - André Bertran
- Laboratory of VirologyDepartment of Plant SciencesWageningen UniversityWageningenNetherlands
| | - Manon M. S. Richard
- Molecular Plant PathologySwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamNetherlands
| | - Richard Kormelink
- Laboratory of VirologyDepartment of Plant SciencesWageningen UniversityWageningenNetherlands
| | - Marcel Prins
- Molecular Plant PathologySwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamNetherlands
- KeyGene N.V.WageningenNetherlands
| | | | - Harrold A. van den Burg
- Molecular Plant PathologySwammerdam Institute for Life SciencesUniversity of AmsterdamAmsterdamNetherlands
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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.
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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
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20
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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.
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Affiliation(s)
- Vidya R Hinge
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
| | - Rahul L Chavhan
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
| | - Sandeep P Kale
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
| | - Penna Suprasanna
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
| | - Ulhas S Kadam
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
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Lebedeva MV, Nikonova EY, Terentiev AA, Taranov VV, Babakov AV, Nikonov OS. VPg of Potato Virus Y and Potato Cap-Binding eIF4E Factors: Selective Interaction and Its Supposed Mechanism. BIOCHEMISTRY (MOSCOW) 2021; 86:1128-1138. [PMID: 34565316 DOI: 10.1134/s000629792109008x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Potato virus Y (PVY) is one of the most common and harmful plant viruses. Translation of viral RNA starts with the interaction between the plant cap-binding translation initiation factors eIF4E and viral genome-linked protein (VPg) covalently attached to the viral RNA. Disruption of this interaction is one of the natural mechanisms of plant resistance to PVY. The multigene eIF4E family in the potato (Solanum tuberosum L.) genome contains genes for the translation initiation factors eIF4E1, eIF4E2, and eIF(iso)4E. However, which of these factors can be recruited by the PVY, as well as the mechanism of this interaction, remain obscure. Here, we showed that the most common VPg variant from the PVY strain NTN interacts with eIF4E1 and eIF4E2, but not with eIF(iso)4E. Based on the VPg, eIF4E1, and eIF4E2 models and data on the natural polymorphism of VPg amino acid sequence, we suggested that the key role in the recognition of potato cap-binding factors belongs to the R104 residue of VPg. To verify this hypothesis, we created VPg mutants with substitutions at position 104 and examined their ability to interact with potato eIF4E factors. The obtained data were used to build the theoretical model of the VPg-eIF4E2 complex that differs significantly from the earlier models of VPg complexes with eIF4E proteins, but is in a good agreement with the current biochemical data.
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Affiliation(s)
- Marina V Lebedeva
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, 127550, Russia.
| | - Ekaterina Y Nikonova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexey A Terentiev
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region, 142432, Russia.,Scientific and Educational Center in Chernogolovka, Moscow Region State University, Mytishchi, Moscow Region, 141014, Russia.,Faculty of Fundamental Physical and Chemical Engineering, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vasiliy V Taranov
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, 127550, Russia
| | - Alexey V Babakov
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, 127550, Russia
| | - Oleg S Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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22
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Swisher Grimm KD, Porter LD. KASP Markers Reveal Established and Novel Sources of Resistance to Pea Seedborne Mosaic Virus in Pea Genetic Resources. PLANT DISEASE 2021; 105:2503-2508. [PMID: 33487018 DOI: 10.1094/pdis-09-20-1917-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pea seed-borne mosaic virus (PSbMV) is both seedborne and aphid-transmitted and can cause economic losses for pea (Pisum sativum L.) production by reducing yield through decreased seed weight and number. The P1 pathotype is especially virulent, affecting this important vegetable crop across the United States and internationally in regions of West Asia, North Africa, Europe, and Australia. Previously, two kompetitive allele-specific PCR (KASP) genotyping markers (eIF4E resistant 1 and 2) were developed and validated on P. sativum accessions identifying two PSbMV pathotype P1 resistance alleles in the eukaryotic translation initiation factor gene, eIF4E. The current study utilized these novel markers to rapidly evaluate 318 genetic resource accessions maintained as part of the United States Department of Agriculture National Plant Germplasm System's Pea Single Plant Collection (PSPC). The evaluations also included 58 commercial and other plant introduction (PI) lines that were assessed for the two eIF4E resistance alleles. All genotyping results were validated in greenhouse assays by confirmation of observable disease symptoms after inoculations and by enzyme-linked immunosorbent assays. The eIF4E resistant 1 and 2 alleles were found in 18 accessions from the PSPC, five commercial lines, and 14 other PI accessions. A single PSPC accession showed resistance to PSbMV pathotype P1 that is believed to be a novel source of resistance based on sequencing analysis of eIF4E. Sources of resistance were identified in the PSPC and in commercial cultivars that can be introgressed into breeding lines using traditional techniques to reduce the time and cost required to generate germplasm with superior disease-resistant traits.
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Affiliation(s)
- Kylie D Swisher Grimm
- Agricultural Research Service of the United States Department of Agriculture, Temperate Tree Fruit and Vegetable Research Unit, Prosser, WA 99350
| | - Lyndon D Porter
- Agricultural Research Service of the United States Department of Agriculture, Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350
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23
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Toribio R, Muñoz A, Sánchez F, Ponz F, Castellano MM. High overexpression of CERES, a plant regulator of translation, induces different phenotypical defence responses during TuMV infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:256-267. [PMID: 33899980 DOI: 10.1111/tpj.15290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Mutations in the eukaryotic translation initiation factors eIF4E and eIF(iso)4E confer potyvirus resistance in a range of plant hosts. This supports the notion that, in addition to their role in translation of cellular mRNAs, eIF4E isoforms are also essential for the potyvirus cycle. CERES is a plant eIF4E- and eIF(iso)4E-binding protein that, through its binding to the eIF4Es, modulates translation initiation; however, its possible role in potyvirus resistance is unknown. In this article, we analyse if the ectopic expression of AtCERES is able to interfere with turnip mosaic virus replication in plants. Our results demonstrate that, during infection, the ectopic expression of CERES in Nicotiana benthamiana promotes the development of a mosaic phenotype when it is accumulated to moderate levels, but induces veinal necrosis when it is accumulated to higher levels. This necrotic process resembles a hypersensitive response (HR)-like response that occurs with different HR hallmarks. Remarkably, Arabidopsis plants inoculated with a virus clone that promotes high expression of CERES do not show signs of infection. These final phenotypical outcomes are independent of the capacity of CERES to bind to eIF4E. All these data suggest that CERES, most likely due to its leucine-rich repeat nature, could act as a resistance protein, able to promote a range of different defence responses when it is highly overexpressed from viral constructs.
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Affiliation(s)
- René Toribio
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Alfonso Muñoz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
- Departamento de Botánica, Ecología y Fisiología Vegetal, Campus de Rabanales, Edificio Severo Ochoa, Universidad de Córdoba, Córdoba, 14071, Spain
| | - Flora Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Fernando Ponz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - M Mar Castellano
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
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24
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A single resistance factor to solve vineyard degeneration due to grapevine fanleaf virus. Commun Biol 2021; 4:637. [PMID: 34050254 PMCID: PMC8163887 DOI: 10.1038/s42003-021-02164-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/28/2021] [Indexed: 11/08/2022] Open
Abstract
Grapevine fanleaf disease, caused by grapevine fanleaf virus (GFLV), transmitted by the soil-borne nematode Xiphinema index, provokes severe symptoms and economic losses, threatening vineyards worldwide. As no effective solution exists so far to control grapevine fanleaf disease in an environmentally friendly way, we investigated the presence of resistance to GFLV in grapevine genetic resources. We discovered that the Riesling variety displays resistance to GFLV, although it is susceptible to X. index. This resistance is determined by a single recessive factor located on grapevine chromosome 1, which we have named rgflv1. The discovery of rgflv1 paves the way for the first effective and environmentally friendly solution to control grapevine fanleaf disease through the development of new GFLV-resistant grapevine rootstocks, which was hitherto an unthinkable prospect. Moreover, rgflv1 is putatively distinct from the virus susceptibility factors already described in plants.
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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: 1] [Impact Index Per Article: 0.3] [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.
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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
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26
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Selective Interaction of Sugarcane eIF4E with VPgs from Sugarcane Mosaic Pathogens. Viruses 2021; 13:v13030518. [PMID: 33809985 PMCID: PMC8005120 DOI: 10.3390/v13030518] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 03/18/2021] [Accepted: 03/20/2021] [Indexed: 12/25/2022] Open
Abstract
Eukaryotic translation initiation factor 4E (eIF4E) plays a key role in the infection of potyviruses in susceptible plants by interacting with viral genome-linked protein (VPg). Sugarcane (Saccharum spp.) production is threatened by mosaic disease caused by Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV), and Sugarcane streak mosaic virus (SCSMV). In this study, two eIF4Es and their isoform eIF(iso)4E and 4E-binding protein coding genes were cloned from sugarcane cultivar ROC22 and designated SceIF4Ea, SceIF4Eb, SceIF(iso)4E, and ScnCBP, respectively. Real-time quantitative PCR analysis showed different expression profiles of these four genes upon SCMV challenge. A subcellular localization assay showed that SceIF4Ea, SceIF4Eb, SceIF(iso)4E, and ScnCBP were distributed in the nucleus and cytoplasm. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that SceIF4Ea/b and SceIF(iso)4E were selectively employed by different sugarcane mosaic pathogens, i.e., SCMV-VPg interacted with SceIF4Ea/b and SceIF(iso)4E, SrMV-VPg interacted with both SceIF4Eb and SceIF(iso)4E, and SCSMV-VPg interacted only with SceIF(iso)4E. Intriguingly, the BiFC assays, but not the Y2H assays, showed that ScnCBP interacted with the VPgs of SCMV, SrMV, and SCSMV. Competitive interaction assays showed that SCMV-VPg, SrMV-VPg, and SCMV-VPg did not compete with each other to interact with SceIF(iso)4E, and SceIF(iso)4E competed with SceIF4Eb to interact with SrMV-VPg but not SCMV-VPg. This study sheds light on the molecular mechanism of sugarcane mosaic pathogen infection of sugarcane plants and benefits sugarcane breeding against the sugarcane mosaic disease.
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Zafirov D, Giovinazzo N, Bastet A, Gallois J. When a knockout is an Achilles' heel: Resistance to one potyvirus species triggers hypersusceptibility to another one in Arabidopsis thaliana. MOLECULAR PLANT PATHOLOGY 2021; 22:334-347. [PMID: 33377260 PMCID: PMC7865081 DOI: 10.1111/mpp.13031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/03/2020] [Accepted: 12/01/2020] [Indexed: 05/04/2023]
Abstract
The translation initiation factors 4E are a small family of major susceptibility factors to potyviruses. It has been suggested that knocking out these genes could provide genetic resistance in crops when natural resistance alleles, which encode functional eIF4E proteins, are not available. Here, using the well-characterized Arabidopsis thaliana-potyvirus pathosystem, we evaluate the resistance spectrum of plants knocked out for eIF4E1, the susceptibility factor to clover yellow vein virus (ClYVV). We show that besides resistance to ClYVV, the eIF4E1 loss of function is associated with hypersusceptibility to turnip mosaic virus (TuMV), a potyvirus known to rely on the paralog host factor eIFiso4E. On TuMV infection, plants knocked out for eIF4E1 display striking developmental defects such as early senescence and primordia development stoppage. This phenotype is coupled with a strong TuMV overaccumulation throughout the plant, while remarkably the levels of the viral target eIFiso4E remain uninfluenced. Our data suggest that this hypersusceptibility cannot be explained by virus evolution leading to a gain of TuMV aggressiveness. Furthermore, we report that a functional eIF4E1 resistance allele engineered by CRISPR/Cas9 base-editing technology successfully circumvents the increase of TuMV susceptibility conditioned by eIF4E1 disruption. These findings in Arabidopsis add to several previous findings in crops suggesting that resistance based on knocking out eIF4E factors should be avoided in plant breeding, as it could also expose the plant to the severe threat of potyviruses able to recruit alternative eIF4E copies. At the same time, it provides a simple model that can help understanding of the homeostasis among eIF4E proteins in the plant cell and what makes them available to potyviruses.
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28
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Torrance L, Talianksy ME. Potato Virus Y Emergence and Evolution from the Andes of South America to Become a Major Destructive Pathogen of Potato and Other Solanaceous Crops Worldwide. Viruses 2020; 12:v12121430. [PMID: 33322703 PMCID: PMC7764287 DOI: 10.3390/v12121430] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/04/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023] Open
Abstract
The potato was introduced to Europe from the Andes of South America in the 16th century, and today it is grown worldwide; it is a nutritious staple food eaten by millions and underpins food security in many countries. Unknowingly, potato virus Y (PVY) was also introduced through trade in infected potato tubers, and it has become the most important viral pathogen of potato. Phylogenetic analysis has revealed the spread and emergence of strains of PVY, including strains causing economically important diseases in tobacco, tomato and pepper, and that the virus continues to evolve with the relatively recent emergence of new damaging recombinant strains. High-throughput, next-generation sequencing platforms provide powerful tools for detection, identification and surveillance of new PVY strains. Aphid vectors of PVY are expected to increase in incidence and abundance in a warmer climate, which will increase the risk of virus spread. Wider deployment of crop cultivars carrying virus resistance will be an important means of defence against infection. New cutting-edge biotechnological tools such as CRISPR and SIGS offer a means for rapid engineering of resistance in established cultivars. We conclude that in future, human activities and ingenuity should be brought to bear to control PVY and the emergence of new strains in key crops by increased focus on host resistance and factors driving virus evolution and spread.
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Affiliation(s)
- Lesley Torrance
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK;
- The School of Biology, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK
- Correspondence:
| | - Michael E. Talianksy
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK;
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
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29
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Urquidi-Camacho RA, Lokdarshi A, von Arnim AG. Translational gene regulation in plants: A green new deal. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1597. [PMID: 32367681 PMCID: PMC9258721 DOI: 10.1002/wrna.1597] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 01/09/2023]
Abstract
The molecular machinery for protein synthesis is profoundly similar between plants and other eukaryotes. Mechanisms of translational gene regulation are embedded into the broader network of RNA-level processes including RNA quality control and RNA turnover. However, over eons of their separate history, plants acquired new components, dropped others, and generally evolved an alternate way of making the parts list of protein synthesis work. Research over the past 5 years has unveiled how plants utilize translational control to defend themselves against viruses, regulate translation in response to metabolites, and reversibly adjust translation to a wide variety of environmental parameters. Moreover, during seed and pollen development plants make use of RNA granules and other translational controls to underpin developmental transitions between quiescent and metabolically active stages. The economics of resource allocation over the daily light-dark cycle also include controls over cellular protein synthesis. Important new insights into translational control on cytosolic ribosomes continue to emerge from studies of translational control mechanisms in viruses. Finally, sketches of coherent signaling pathways that connect external stimuli with a translational response are emerging, anchored in part around TOR and GCN2 kinase signaling networks. These again reveal some mechanisms that are familiar and others that are different from other eukaryotes, motivating deeper studies on translational control in plants. This article is categorized under: Translation > Translation Regulation RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Ricardo A. Urquidi-Camacho
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996
| | - Ansul Lokdarshi
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Albrecht G von Arnim
- Department of Biochemistry & Cellular and Molecular Biology and UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
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30
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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.
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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
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31
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Parisi M, Alioto D, Tripodi P. Overview of Biotic Stresses in Pepper ( Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics. Int J Mol Sci 2020; 21:E2587. [PMID: 32276403 PMCID: PMC7177692 DOI: 10.3390/ijms21072587] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 12/16/2022] Open
Abstract
Pepper (Capsicum spp.) is one of the major vegetable crops grown worldwide largely appreciated for its economic importance and nutritional value. This crop belongs to the large Solanaceae family, which, among more than 90 genera and 2500 species of flowering plants, includes commercially important vegetables such as tomato and eggplant. The genus includes over 30 species, five of which (C. annuum, C. frutescens, C. chinense, C. baccatum, and C. pubescens) are domesticated and mainly grown for consumption as food and for non-food purposes (e.g., cosmetics). The main challenges for vegetable crop improvement are linked to the sustainable development of agriculture, food security, the growing consumers' demand for food. Furthermore, demographic trends and changes to climate require more efficient use of plant genetic resources in breeding programs. Increases in pepper consumption have been observed in the past 20 years, and for maintaining this trend, the development of new resistant and high yielding varieties is demanded. The range of pathogens afflicting peppers is very broad and includes fungi, viruses, bacteria, and insects. In this context, the large number of accessions of domesticated and wild species stored in the world seed banks represents a valuable resource for breeding in order to transfer traits related to resistance mechanisms to various biotic stresses. In the present review, we report comprehensive information on sources of resistance to a broad range of pathogens in pepper, revisiting the classical genetic studies and showing the contribution of genomics for the understanding of the molecular basis of resistance.
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Affiliation(s)
- Mario Parisi
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, Italy;
| | - Daniela Alioto
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055 Portici, Naples, Italy;
| | - Pasquale Tripodi
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, Italy;
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32
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Gao L, Luo J, Ding X, Wang T, Hu T, Song P, Zhai R, Zhang H, Zhang K, Li K, Zhi H. Soybean RNA interference lines silenced for eIF4E show broad potyvirus resistance. MOLECULAR PLANT PATHOLOGY 2020; 21:303-317. [PMID: 31860775 PMCID: PMC7036369 DOI: 10.1111/mpp.12897] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 05/27/2023]
Abstract
Soybean mosaic virus (SMV), a potyvirus, is the most prevalent and destructive viral pathogen in soybean-planting regions of China. Moreover, other potyviruses, including bean common mosaic virus (BCMV) and watermelon mosaic virus (WMV), also threaten soybean farming. The eukaryotic translation initiation factor 4E (eIF4E) plays a critical role in controlling resistance/susceptibility to potyviruses in plants. In the present study, much higher SMV-induced eIF4E1 expression levels were detected in a susceptible soybean cultivar when compared with a resistant cultivar, suggesting the involvement of eIF4E1 in the response to SMV by the susceptible cultivar. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that soybean eIF4E1 interacted with SMV VPg in the nucleus and with SMV NIa-Pro/NIb in the cytoplasm, revealing the involvement of VPg, NIa-Pro, and NIb in SMV infection and multiplication. Furthermore, transgenic soybeans silenced for eIF4E were produced using an RNA interference approach. Through monitoring for viral symptoms and viral titers, robust and broad-spectrum resistance was confirmed against five SMV strains (SC3/7/15/18 and SMV-R), BCMV, and WMV in the transgenic plants. Our findings represent fresh insights for investigating the mechanism underlying eIF4E-mediated resistance in soybean and also suggest an effective alternative for breeding soybean with broad-spectrum viral resistance.
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Affiliation(s)
- Le Gao
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
- College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jinyan Luo
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Xueni Ding
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Tao Wang
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
- Institute of Cereal and Oil CropsHandan Academy of Agricultural SciencesHandanChina
| | - Ting Hu
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Puwen Song
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Rui Zhai
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Hongyun Zhang
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Kai Zhang
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Kai Li
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Haijian Zhi
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
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Branham SE, Patrick Wechter W, Ling KS, Chanda B, Massey L, Zhao G, Guner N, Bello M, Kabelka E, Fei Z, Levi A. QTL mapping of resistance to Fusarium oxysporum f. sp. niveum race 2 and Papaya ringspot virus in Citrullus amarus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:677-687. [PMID: 31822938 DOI: 10.1007/s00122-019-03500-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
A Citrullus amarus mapping population segregating for resistance to Fusarium oxysporum f. sp. niveum race 2 and Papaya ringspot virus was used to identify novel QTL, important for the improvement in watermelon disease resistance. Multiple disease screens of the USDA Citrullus spp. germplasm collection have highlighted the value of Citrullus amarus (citron melon or wild watermelon) as a resource for enhancing modern watermelon cultivars (Citrullus lanatus) with resistance to a broad range of fungal, bacterial and viral diseases of watermelon. We have generated a genetic population of C. amarus segregating for resistance to two important watermelon diseases: Fusarium wilt (caused by the fungus Fusarium oxysporum f. sp. niveum; Fon race 2) and Papaya ringspot virus-watermelon strain (PRSV-W). QTL mapping of Fon race 2 resistance identified seven significant QTLs, with the major QTL representing a novel genetic source of resistance and an opportunity for gene pyramiding. A single QTL was associated with resistance to PRSV-W, which adhered to expectations of a prior study indicating a single-gene recessive inheritance in watermelon. The resistance loci identified here provide valuable genetic resources for introgression into cultivated watermelon for the improvement in disease resistance.
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Affiliation(s)
- Sandra E Branham
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA
- Coastal Research and Education Center, Clemson University, 2700 Savannah Highway, Charleston, SC, 29414, USA
| | - W Patrick Wechter
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA
| | - Kai-Shu Ling
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA
| | - Bidisha Chanda
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA
| | - Laura Massey
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA
| | - Guangwei Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Hanghai East Road, Zhengzhou, 450009, China
| | - Nihat Guner
- Sakata Seed America, 20900 State Road 82, Fort Myers, FL, 33913, USA
| | - Marco Bello
- Sakata Seed America, 20900 State Road 82, Fort Myers, FL, 33913, USA
| | - Eileen Kabelka
- Sakata Seed America, 18095 Serene Drive, Morgan Hill, CA, 95037, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY, 14853, USA
- Robert W. Holley Center for Agriculture and Health, U.S. Department of Agriculture, Agricultural Research Service, Ithaca, NY, 14853, USA
| | - Amnon Levi
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA.
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Taninaka Y, Nakahara KS, Hagiwara-Komoda Y. Intracellular proliferation of clover yellow vein virus is unaffected by the recessive resistance gene cyv1 of Pisum sativum. Microbiol Immunol 2020; 64:76-82. [PMID: 31687790 DOI: 10.1111/1348-0421.12755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/24/2019] [Accepted: 11/01/2019] [Indexed: 11/30/2022]
Abstract
The pea cyv1 gene is a yet-to-be-identified recessive resistance gene that inhibits the infection of clover yellow vein virus (ClYVV). Previous studies confirmed that the cell-to-cell movement of ClYVV is inhibited in cyv1-carrying pea plants; however, the effect of cyv1 on viral replication remains unknown. In this study, we developed a new pea protoplast transfection method to investigate ClYVV propagation at the single-cell level. Using this method, we revealed that ClYVV accumulates to similar levels in both ClYVV-susceptible and cyv1-carrying pea protoplasts. Thus, the cyv1-mediated resistance would not suppress intracellular ClYVV replication.
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Affiliation(s)
- Yosuke Taninaka
- Department of Sustainable Agriculture, College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Ebetsu, Japan
| | - Kenji S Nakahara
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yuka Hagiwara-Komoda
- Department of Sustainable Agriculture, College of Agriculture, Food and Environment Sciences, Rakuno Gakuen University, Ebetsu, Japan
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[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.
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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.
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Affiliation(s)
- H. Peter van Esse
- 2Blades Foundation1630 Chicago AvenueEvanstonIL 60201USA
- The Sainsbury LaboratoryUniversity of East AngliaNorwich Research ParkNR4 7UHUK
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De Mori G, Falchi R, Testolin R, Bassi D, Savazzini F, Dondini L, Tartarini S, Palmisano F, Minafra A, Spadotto A, Scalabrin S, Geuna F. Resistance to Sharka in Apricot: Comparison of Phase-Reconstructed Resistant and Susceptible Haplotypes of 'Lito' Chromosome 1 and Analysis of Candidate Genes. FRONTIERS IN PLANT SCIENCE 2019; 10:1576. [PMID: 31867032 PMCID: PMC6905379 DOI: 10.3389/fpls.2019.01576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
Sharka, a common disease among most stone fruit crops, is caused by the Plum Pox Virus (PPV). Resistant genotypes have been found in apricot (Prunus armeniaca L.), one of which-the cultivar 'Lito' heterozygous for the resistance-has been used to map a major quantitative trait locus (QTL) on linkage group 1, following a pseudo-test-cross mating design with 231 individuals. In addition, 19 SNP markers were selected from among the hundreds previously developed, which allowed the region to be limited to 236 kb on chromosome 1. A 'Lito' bacterial artificial chromosome (BAC) library was produced, screened with markers of the region, and positive BAC clones were sequenced. Resistant (R) and susceptible (S) haplotypes were assembled independently. To refine the assembly, the whole genome of 'Lito' was sequenced to high coverage (98×) using PacBio technology, enabling the development of a detailed assembly of the region that was able to predict and annotate the genes in the QTL region. The selected cultivar 'Lito' allowed not only to discriminate structural variants between the two haplotypic regions but also to distinguish specific allele expression, contributing towards mining the PPVres locus. In light of these findings, genes previously indicated (i.e., MATHd genes) to have a possible role in PPV resistance were further analyzed, and new candidates were discussed. Although the results are not conclusive, the accurate and independent assembly of R and S haplotypes of 'Lito' is a valuable resource to predict and test alternative transcription and regulation mechanisms underpinning PPV resistance.
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Affiliation(s)
- Gloria De Mori
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Rachele Falchi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Raffaele Testolin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy
| | - Federica Savazzini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Francesco Palmisano
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Locorotondo, Italy
| | - Angelantonio Minafra
- National Research Council, Institute for Sustainable Plant Protection, Bari, Italy
| | | | - Simone Scalabrin
- IGA Technology Services, Science and Technology Park, ZIU, Udine, Italy
| | - Filippo Geuna
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, Milan, Italy
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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.
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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
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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.
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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
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Michel V, Julio E, Candresse T, Cotucheau J, Decorps C, Volpatti R, Moury B, Glais L, Jacquot E, de Borne FD, Decroocq V, Gallois J, German-Retana S. A complex eIF4E locus impacts the durability of va resistance to Potato virus Y in tobacco. MOLECULAR PLANT PATHOLOGY 2019; 20:1051-1066. [PMID: 31115167 PMCID: PMC6640182 DOI: 10.1111/mpp.12810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Many recessive resistances against potyviruses are mediated by eukaryotic translation initiation factor 4E (eIF4E). In tobacco, the va resistance gene commonly used to control Potato virus Y (PVY) corresponds to a large deletion affecting the eIF4E-1 gene on chromosome 21. Here, we compared the resistance durability conferred by various types of mutations affecting eIF4E-1 (deletions of various sizes, frameshift or nonsense mutations). The 'large deletion' genotypes displayed the broadest and most durable resistance, whereas frameshift and nonsense mutants displayed a less durable resistance, with rapid and frequent apparition of resistance-breaking variants. In addition, genetic and transcriptomic analyses revealed that resistance durability is strongly impacted by a complex genetic locus on chromosome 14, which contains three other eIF4E genes. One of these, eIF4E-3, is rearranged as a hybrid gene between eIF4E-2 and eIF4E-3 (eIF4E-2-3 ) in the genotypes showing the most durable resistance, while eIF4E-2 is differentially expressed between the tested varieties. RNA-seq and quantitative reverse transcriptase-polymerase chain reaction experiments demonstrated that eIF4E-2 expression level is positively correlated with resistance durability. These results suggest that besides the nature of the mutation affecting eIF4E-1, three factors linked with a complex locus may potentially impact va durability: loss of an integral eIF4E-3, presence of eIF4E-2-3 and overexpression of eIF4E-2. This latter gene might act as a decoy in a non-productive virus-plant interaction, limiting the ability of PVY to evolve towards resistance breaking. Taken together, these results show that va resistance durability can in large part be explained by complex redundancy effects in the eIF4E gene family.
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Affiliation(s)
- Vincent Michel
- UMR 1332 Biologie du Fruit et PathologieINRA, University Bordeaux71 Av. E. BourlauxVillenave d’Ornon Cedex CS 2003233882France
| | - Emilie Julio
- Seita Imperial TobaccoLa Tour24100BergeracFrance
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et PathologieINRA, University Bordeaux71 Av. E. BourlauxVillenave d’Ornon Cedex CS 2003233882France
| | | | | | | | - Benoît Moury
- Unité de Pathologie Végétale, INRA, Centre Recherche PACA, Domaine Saint MauriceMontfavet Cedex CS 60094F84143France
| | - Laurent Glais
- UMR IGEPPINRA, Domaine de la MotteBP 35327Le Rheu Cedex35653France
| | - Emmanuel Jacquot
- INRA‐Cirad‐Supagro Montpellier, UMR BGPIMontpellier Cedex34398France
| | | | - Véronique Decroocq
- UMR 1332 Biologie du Fruit et PathologieINRA, University Bordeaux71 Av. E. BourlauxVillenave d’Ornon Cedex CS 2003233882France
| | - Jean‐Luc Gallois
- INRA‐UR 1052, GAFL Domaine St Maurice – CS 60094Montfavet CedexF‐84143
| | - Sylvie German-Retana
- UMR 1332 Biologie du Fruit et PathologieINRA, University Bordeaux71 Av. E. BourlauxVillenave d’Ornon Cedex CS 2003233882France
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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.
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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
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Schmitt-Keichinger C. Manipulating Cellular Factors to Combat Viruses: A Case Study From the Plant Eukaryotic Translation Initiation Factors eIF4. Front Microbiol 2019; 10:17. [PMID: 30804892 PMCID: PMC6370628 DOI: 10.3389/fmicb.2019.00017] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/09/2019] [Indexed: 12/20/2022] Open
Abstract
Genes conferring resistance to plant viruses fall in two categories; the dominant genes that mostly code for proteins with a nucleotide binding site and leucine rich repeats (NBS-LRR), and that directly or indirectly, recognize viral avirulence factors (Avr), and the recessive genes. The latter provide a so-called recessive resistance. They represent roughly half of the known resistance genes and are alleles of genes that play an important role in the virus life cycle. Conversely, all cellular genes critical for the viral infection virtually represent recessive resistance genes. Based on the well-documented case of recessive resistance mediated by eukaryotic translation initiation factors of the 4E/4G family, this review is intended to summarize the possible approaches to control viruses via their host interactors. Classically, resistant crops have been developed through introgression of natural variants of the susceptibility factor from compatible relatives or by random mutagenesis and screening. Transgenic methods have also been applied to engineer improved crops by overexpressing the translation factor either in its natural form or after directed mutagenesis. More recently, innovative approaches like silencing or genome editing have proven their great potential in model and crop plants. The advantages and limits of these different strategies are discussed. This example illustrates the need to identify and characterize more host factors involved in virus multiplication and to assess their application potential in the control of viral diseases.
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Role of the Genetic Background in Resistance to Plant Viruses. Int J Mol Sci 2018; 19:ijms19102856. [PMID: 30241370 PMCID: PMC6213453 DOI: 10.3390/ijms19102856] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 01/03/2023] Open
Abstract
In view of major economic problems caused by viruses, the development of genetically resistant crops is critical for breeders but remains limited by the evolution of resistance-breaking virus mutants. During the plant breeding process, the introgression of traits from Crop Wild Relatives results in a dramatic change of the genetic background that can alter the resistance efficiency or durability. Here, we conducted a meta-analysis on 19 Quantitative Trait Locus (QTL) studies of resistance to viruses in plants. Frequent epistatic effects between resistance genes indicate that a large part of the resistance phenotype, conferred by a given QTL, depends on the genetic background. We next reviewed the different resistance mechanisms in plants to survey at which stage the genetic background could impact resistance or durability. We propose that the genetic background may impair effector-triggered dominant resistances at several stages by tinkering the NB-LRR (Nucleotide Binding-Leucine-Rich Repeats) response pathway. In contrast, effects on recessive resistances by loss-of-susceptibility-such as eIF4E-based resistances-are more likely to rely on gene redundancy among the multigene family of host susceptibility factors. Finally, we show how the genetic background is likely to shape the evolution of resistance-breaking isolates and propose how to take this into account in order to breed plants with increased resistance durability to viruses.
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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.
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Garcia-Ruiz H. Susceptibility Genes to Plant Viruses. Viruses 2018; 10:E484. [PMID: 30201857 PMCID: PMC6164914 DOI: 10.3390/v10090484] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/28/2018] [Accepted: 09/07/2018] [Indexed: 12/26/2022] Open
Abstract
Plant viruses use cellular factors and resources to replicate and move. Plants respond to viral infection by several mechanisms, including innate immunity, autophagy, and gene silencing, that viruses must evade or suppress. Thus, the establishment of infection is genetically determined by the availability of host factors necessary for virus replication and movement and by the balance between plant defense and viral suppression of defense responses. Host factors may have antiviral or proviral activities. Proviral factors condition susceptibility to viruses by participating in processes essential to the virus. Here, we review current advances in the identification and characterization of host factors that condition susceptibility to plant viruses. Host factors with proviral activity have been identified for all parts of the virus infection cycle: viral RNA translation, viral replication complex formation, accumulation or activity of virus replication proteins, virus movement, and virion assembly. These factors could be targets of gene editing to engineer resistance to plant viruses.
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Affiliation(s)
- Hernan Garcia-Ruiz
- Nebraska Center for Virology, Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68503, USA.
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Choi S, Lee JH, Kang WH, Kim J, Huy HN, Park SW, Son EH, Kwon JK, Kang BC. Identification of Cucumber mosaic resistance 2 ( cmr2) That Confers Resistance to a New Cucumber mosaic virus Isolate P1 (CMV-P1) in Pepper ( Capsicum spp.). FRONTIERS IN PLANT SCIENCE 2018; 9:1106. [PMID: 30186289 PMCID: PMC6110927 DOI: 10.3389/fpls.2018.01106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/09/2018] [Indexed: 05/09/2023]
Abstract
Cucumber mosaic virus (CMV) is one of the most devastating phytopathogens of Capsicum. The single dominant resistance gene, Cucumber mosaic resistant 1 (Cmr1), that confers resistance to the CMV isolate P0 has been overcome by a new isolate (CMV-P1) after being deployed in pepper (Capsicum annuum) breeding for over 20 years. A recently identified Indian C. annuum cultivar, "Lam32," displays resistance to CMV-P1. In this study, we show that the resistance in "Lam32" is controlled by a single recessive gene, CMV resistance gene 2 (cmr2). We found that cmr2 conferred resistance to CMV strains including CMV-Korean, CMV-Fny, and CMV-P1, indicating that cmr2 provides a broad-spectrum type of resistance. We utilized two molecular mapping approaches to determine the chromosomal location of cmr2. Bulked segregant analysis (BSA) using amplified fragment-length polymorphism (AFLP) (BSA-AFLP) revealed one marker, cmvAFLP, located 16 cM from cmr2. BSA using the Affymetrix pepper array (BSA-Affy) identified a single-nucleotide polymorphism (SNP) marker (Affy4) located 2.3 cM from cmr2 on chromosome 8. We further screened a pepper germplasm collection of 4,197 accessions for additional CMV-P1 resistance sources and found that some accessions contained equivalent levels of resistance to that of "Lam32." Inheritance and allelism tests demonstrated that all the resistance sources examined contained cmr2. Our result thus provide genetic and molecular evidence that cmr2 is a single recessive gene that confers to pepper an unprecedented resistance to the dangerous new isolate CMV-P1 that had overcome Cmr1.
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Affiliation(s)
- Seula Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Joung-Ho Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Won-Hee Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Joonyup Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hoang N. Huy
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Sung-Woo Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Eun-Ho Son
- RDA-Genebank Information Center, Jeonju, South Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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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.
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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
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Venkatesh J, An J, Kang WH, Jahn M, Kang BC. Fine Mapping of the Dominant Potyvirus Resistance Gene Pvr7 Reveals a Relationship with Pvr4 in Capsicum annuum. PHYTOPATHOLOGY 2018; 108:142-148. [PMID: 28945517 DOI: 10.1094/phyto-07-17-0231-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Pepper mottle virus (PepMoV) is the most common potyvirus infection of pepper plants and causes significant yield losses. The Pvr7 gene from Capsicum chinense PI159236 and the Pvr4 gene from C. annuum CM334 both have been reported to confer dominant resistance to PepMoV. The Pvr7 locus conferring resistance to PepMoV in C. annuum '9093' was previously mapped to chromosome 10. To develop a high-resolution map of the Pvr7 locus in 9093, we constructed an intraspecific F2 mapping population consisting of 916 individuals by crossing PepMoV-resistant C. annuum '9093' and the PepMoV-susceptible C. annuum 'Jeju'. To delimit the Pvr7 target region, single-nucleotide polymorphism (SNP) markers derived from the Pvr4 region were used for genotyping the F2 population. Molecular mapping delimited the Pvr7 locus to a physical interval of 258 kb, which was the same region as Pvr4 on chromosome 10. Three SNP markers derived from Pvr4 mapping perfectly cosegregated with PepMoV resistance. Sequencing analyses of the Pvr7 flanking markers and the Pvr4-specific gene indicated that Pvr7 and Pvr4 are the same gene. Resistance spectrum analysis of 9093 against pepper potyviruses showed that 9093 has a resistance spectrum similar to that of cultivar CM334. These combined results demonstrate that, unlike previously thought, the dominant PepMoV resistance in 9093 could be derived from C. annuum 'CM334', and that Pvr4 and Pvr7 should be considered as the same locus.
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Affiliation(s)
- Jelli Venkatesh
- First, second, third, and fifth authors: Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea; and fourth author: Department of Agronomy, College of Agriculture and Life Sciences, University of Wisconsin-Madison
| | - Jeongtak An
- First, second, third, and fifth authors: Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea; and fourth author: Department of Agronomy, College of Agriculture and Life Sciences, University of Wisconsin-Madison
| | - Won-Hee Kang
- First, second, third, and fifth authors: Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea; and fourth author: Department of Agronomy, College of Agriculture and Life Sciences, University of Wisconsin-Madison
| | - Molly Jahn
- First, second, third, and fifth authors: Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea; and fourth author: Department of Agronomy, College of Agriculture and Life Sciences, University of Wisconsin-Madison
| | - Byoung-Cheorl Kang
- First, second, third, and fifth authors: Department of Plant Science and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea; and fourth author: Department of Agronomy, College of Agriculture and Life Sciences, University of Wisconsin-Madison
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Reyes MI, Flores‐Vergara MA, Guerra‐Peraza O, Rajabu C, Desai J, Hiromoto‐Ruiz YH, Ndunguru J, Hanley‐Bowdoin L, Kjemtrup S, Ascencio‐Ibáñez JT, Robertson D. A VIGS screen identifies immunity in the Arabidopsis Pla-1 accession to viruses in two different genera of the Geminiviridae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:796-807. [PMID: 28901681 PMCID: PMC5725698 DOI: 10.1111/tpj.13716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/01/2017] [Accepted: 09/06/2017] [Indexed: 05/21/2023]
Abstract
Geminiviruses are DNA viruses that cause severe crop losses in different parts of the world, and there is a need for genetic sources of resistance to help combat them. Arabidopsis has been used as a source for virus-resistant genes that derive from alterations in essential host factors. We used a virus-induced gene silencing (VIGS) vector derived from the geminivirus Cabbage leaf curl virus (CaLCuV) to assess natural variation in virus-host interactions in 190 Arabidopsis accessions. Silencing of CH-42, encoding a protein needed to make chlorophyll, was used as a visible marker to discriminate asymptomatic accessions from those showing resistance. There was a wide range in symptom severity and extent of silencing in different accessions, but two correlations could be made. Lines with severe symptoms uniformly lacked extensive VIGS, and lines that showed attenuated symptoms over time (recovery) showed a concomitant increase in the extent of VIGS. One accession, Pla-1, lacked both symptoms and silencing, and was immune to wild-type infectious clones corresponding to CaLCuV or Beet curly top virus (BCTV), which are classified in different genera in the Geminiviridae. It also showed resistance to the agronomically important Tomato yellow leaf curl virus (TYLCV). Quantitative trait locus mapping of a Pla-1 X Col-0 F2 population was used to detect a major peak on chromosome 1, which is designated gip-1 (geminivirus immunity Pla-1-1). The recessive nature of resistance to CaLCuV and the lack of obvious candidate genes near the gip-1 locus suggest that a novel resistance gene(s) confers immunity.
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Affiliation(s)
- Maria Ines Reyes
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Miguel A. Flores‐Vergara
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
- Paradigm GeneticsResearch Triangle ParkNCUSA
| | - Orlene Guerra‐Peraza
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
- Present address:
Citrus Research and Education CenterUniversity of FloridaLake AlfredFL33850USA
| | - Cyprian Rajabu
- Mikocheni Agricultural Research InstituteDar es SalaamTanzania
| | - Jigar Desai
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNCUSA
| | | | - Joseph Ndunguru
- Mikocheni Agricultural Research InstituteDar es SalaamTanzania
| | - Linda Hanley‐Bowdoin
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Susanne Kjemtrup
- Paradigm GeneticsResearch Triangle ParkNCUSA
- Present address:
Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Jose T. Ascencio‐Ibáñez
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNCUSA
| | - Dominique Robertson
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
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50
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Gal-On A, Fuchs M, Gray S. Generation of novel resistance genes using mutation and targeted gene editing. Curr Opin Virol 2017; 26:98-103. [DOI: 10.1016/j.coviro.2017.07.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 01/10/2023]
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