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Tamisier L, Fabre F, Szadkowski M, Chateau L, Nemouchi G, Girardot G, Millot P, Palloix A, Moury B. Within-plant genetic drift to control virus adaptation to host resistance genes. PLoS Pathog 2024; 20:e1012424. [PMID: 39102439 PMCID: PMC11326801 DOI: 10.1371/journal.ppat.1012424] [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: 08/04/2023] [Revised: 08/15/2024] [Accepted: 07/01/2024] [Indexed: 08/07/2024] Open
Abstract
Manipulating evolutionary forces imposed by hosts on pathogens like genetic drift and selection could avoid the emergence of virulent pathogens. For instance, increasing genetic drift could decrease the risk of pathogen adaptation through the random fixation of deleterious mutations or the elimination of favorable ones in the pathogen population. However, no experimental proof of this approach is available for a plant-pathogen system. We studied the impact of pepper (Capsicum annuum) lines carrying the same major resistance gene but contrasted genetic backgrounds on the evolution of Potato virus Y (PVY). The pepper lines were chosen for the contrasted levels of genetic drift (inversely related to Ne, the effective population size) they exert on PVY populations, as well as for their contrasted resistance efficiency (inversely related to the initial replicative fitness, Wi, of PVY in these lines). Experimental evolution was performed by serially passaging 64 PVY populations every month on six contrasted pepper lines during seven months. These PVY populations exhibited highly divergent evolutionary trajectories, ranging from viral extinctions to replicative fitness gains. The sequencing of the PVY VPg cistron, where adaptive mutations are likely to occur, allowed linking these replicative fitness gains to parallel adaptive nonsynonymous mutations. Evolutionary trajectories were well explained by the genetic drift imposed by the host. More specifically, Ne, Wi and their synergistic interaction played a major role in the fate of PVY populations. When Ne was low (i.e. strong genetic drift), the final PVY replicative fitness remained close to the initial replicative fitness, whereas when Ne was high (i.e. low genetic drift), the final PVY replicative fitness was high independently of the replicative fitness of the initially inoculated virus. We show that combining a high resistance efficiency (low Wi) and a strong genetic drift (low Ne) is the best solution to increase resistance durability, that is, to avoid virus adaptation on the long term.
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Affiliation(s)
- Lucie Tamisier
- INRAE, Pathologie Végétale, F-84140 Montfavet, France
- INRAE, Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
| | | | - Marion Szadkowski
- INRAE, Pathologie Végétale, F-84140 Montfavet, France
- INRAE, Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
| | - Lola Chateau
- INRAE, Pathologie Végétale, F-84140 Montfavet, France
| | - Ghislaine Nemouchi
- INRAE, Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
| | | | | | - Alain Palloix
- INRAE, Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
| | - Benoît Moury
- INRAE, Pathologie Végétale, F-84140 Montfavet, France
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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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3
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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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4
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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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Moury B, Michon T, Simon V, Palloix A. A Single Nonsynonymous Substitution in the RNA-Dependent RNA Polymerase of Potato virus Y Allows the Simultaneous Breakdown of Two Different Forms of Antiviral Resistance in Capsicum annuum. Viruses 2023; 15:v15051081. [PMID: 37243167 DOI: 10.3390/v15051081] [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: 04/03/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
The dominant Pvr4 gene in pepper (Capsicum annuum) confers resistance to members of six potyvirus species, all of which belong to the Potato virus Y (PVY) phylogenetic group. The corresponding avirulence factor in the PVY genome is the NIb cistron (i.e., RNA-dependent RNA polymerase). Here, we describe a new source of potyvirus resistance in the Guatemalan accession C. annuum cv. PM949. PM949 is resistant to members of at least three potyvirus species, a subset of those controlled by Pvr4. The F1 progeny between PM949 and the susceptible cultivar Yolo Wonder was susceptible to PVY, indicating that the resistance is recessive. The segregation ratio between resistant and susceptible plants observed in the F2 progeny matched preferably with resistance being determined by two unlinked recessive genes independently conferring resistance to PVY. Inoculations by grafting resulted in the selection of PVY mutants breaking PM949 resistance and, less efficiently, Pvr4-mediated resistance. The codon substitution E472K in the NIb cistron of PVY, which was shown previously to be sufficient to break Pvr4 resistance, was also sufficient to break PM949 resistance, a rare example of cross-pathogenicity effect. In contrast, the other selected NIb mutants showed specific infectivity in PM949 or Pvr4 plants. Comparison of Pvr4 and PM949 resistance, which share the same target in PVY, provides interesting insights into the determinants of resistance durability.
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Affiliation(s)
- Benoît Moury
- INRAE, Pathologie Végétale, 84140 Montfavet, France
| | - Thierry Michon
- UMR Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, CS 20032, 33882 Villenave d'Ornon, France
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6
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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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7
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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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8
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Pechar GS, Donaire L, Gosalvez B, García‐Almodovar C, Sánchez‐Pina MA, Truniger V, Aranda MA. Editing melon eIF4E associates with virus resistance and male sterility. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2006-2022. [PMID: 35778883 PMCID: PMC9491454 DOI: 10.1111/pbi.13885] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/19/2022] [Accepted: 06/23/2022] [Indexed: 05/20/2023]
Abstract
The cap-binding protein eIF4E, through its interaction with eIF4G, constitutes the core of the eIF4F complex, which plays a key role in the circularization of mRNAs and their subsequent cap-dependent translation. In addition to its fundamental role in mRNA translation initiation, other functions have been described or suggested for eIF4E, including acting as a proviral factor and participating in sexual development. We used CRISPR/Cas9 genome editing to generate melon eif4e knockout mutant lines. Editing worked efficiently in melon, as we obtained transformed plants with a single-nucleotide deletion in homozygosis in the first eIF4E exon already in a T0 generation. Edited and non-transgenic plants of a segregating F2 generation were inoculated with Moroccan watermelon mosaic virus (MWMV); homozygous mutant plants showed virus resistance, while heterozygous and non-mutant plants were infected, in agreement with our previous results with plants silenced in eIF4E. Interestingly, all homozygous edited plants of the T0 and F2 generations showed a male sterility phenotype, while crossing with wild-type plants restored fertility, displaying a perfect correlation between the segregation of the male sterility phenotype and the segregation of the eif4e mutation. Morphological comparative analysis of melon male flowers along consecutive developmental stages showed postmeiotic abnormal development for both microsporocytes and tapetum, with clear differences in the timing of tapetum degradation in the mutant versus wild-type. An RNA-Seq analysis identified critical genes in pollen development that were down-regulated in flowers of eif4e/eif4e plants, and suggested that eIF4E-specific mRNA translation initiation is a limiting factor for male gametes formation in melon.
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Affiliation(s)
- Giuliano S. Pechar
- Department of Stress Biology and Plant PathologyCentro de Edafología y Biología Aplicada del Segura (CEBAS)‐CSICMurciaSpain
| | - Livia Donaire
- Department of Stress Biology and Plant PathologyCentro de Edafología y Biología Aplicada del Segura (CEBAS)‐CSICMurciaSpain
| | - Blanca Gosalvez
- Department of Stress Biology and Plant PathologyCentro de Edafología y Biología Aplicada del Segura (CEBAS)‐CSICMurciaSpain
| | - Carlos García‐Almodovar
- Department of Stress Biology and Plant PathologyCentro de Edafología y Biología Aplicada del Segura (CEBAS)‐CSICMurciaSpain
| | - María Amelia Sánchez‐Pina
- Department of Stress Biology and Plant PathologyCentro de Edafología y Biología Aplicada del Segura (CEBAS)‐CSICMurciaSpain
| | - Verónica Truniger
- Department of Stress Biology and Plant PathologyCentro de Edafología y Biología Aplicada del Segura (CEBAS)‐CSICMurciaSpain
| | - Miguel A. Aranda
- Department of Stress Biology and Plant PathologyCentro de Edafología y Biología Aplicada del Segura (CEBAS)‐CSICMurciaSpain
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Jiang C, Lei M, Luan H, Pan Y, Zhang L, Zhou S, Cai Y, Xu X, Shen H, Xu R, Feng Z, Zhang J, Yang P. Genomic and Pathogenic Diversity of Barley Yellow Mosaic Virus and Barley Mild Mosaic Virus Isolates in Fields of China and Their Compatibility with Resistance Genes of Cultivated Barley. PLANT DISEASE 2022; 106:2201-2210. [PMID: 35077235 DOI: 10.1094/pdis-11-21-2473-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plant viruses transmitted by the soilborne plasmodiophorid Polymyxa graminis constantly threaten global production of cereal crops. Although the yellow mosaic virus disease of barley has been known to be present for a long time in China, the understanding of the diversity of the viral pathogens and their interactions with host resistance remains limited. In this study, we conducted a nationwide survey of P. graminis and the barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV) it transmits, followed by genomic and pathogenic diversity analyses of both viruses. BaYMV and BaMMV were found exclusively in the region downstream of the Yangtze River, despite the national distribution of its transmission vector P. graminis. Analysis of the genomic variations of BaYMV and BaMMV revealed an elevated rate of nonsynonymous substitutions in the viral genome-linked protein (VPg), in which most substitutions were located in its interaction surface with the host eukaryotic translation initiation factor 4E (eIF4E). VPg sequence diversity was associated with the divergence in virus pathogenicity that was identified through multiple field trials. The majority of the resistance genes, including the widely applied rym4 and rym5 (alleles of eIF4E), as well as the combination of rym1/11 and rym5, are not sufficient to protect cultivated barley against viruses in China. Collectively, these results provide insights into virulence specificity and interaction mode with host resistance in cultivated barley, which has significant implications in breeding for the broad-spectrum resistance barley varieties.
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Affiliation(s)
- Congcong Jiang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Miaomiao Lei
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Haiye Luan
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng 224002, China
| | - Yuhan Pan
- College of Agronomy, Yangzhou University, Yangzhou 225009, China
| | - Li Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shenghui Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yu Cai
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiao Xu
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng 224002, China
| | - Huiquan Shen
- Institute of Agricultural Science in Jiangsu Coastal Areas, Yancheng 224002, China
| | - Rugen Xu
- College of Agronomy, Yangzhou University, Yangzhou 225009, China
| | - Zongyun Feng
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ping Yang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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10
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Noureen A, Khan MZ, Amin I, Zainab T, Mansoor S. CRISPR/Cas9-Mediated Targeting of Susceptibility Factor eIF4E-Enhanced Resistance Against Potato Virus Y. Front Genet 2022; 13:922019. [PMID: 35910230 PMCID: PMC9326172 DOI: 10.3389/fgene.2022.922019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
Potato (Solanum tuberosum L.) is an important staple food around the world, and potato virus Y (PVY) is a major constraint for potato production. The VPg protein of PVY interacts with the translation initiation factor eIF4E of the host that works as a susceptibility factor during infection. The interaction between eIF4E and VPg was disrupted by CRISPR/Cas9. The homozygous conserved region of eIF4E of the potato variety “Kruda” was mutated by CRISPR/Cas9. Tracking of insertion, deletion, and conversion events was performed by Sanger sequencing with ∼15% editing efficiency. Truncated and mutated eIF4E proteins were unable to interact with VPg, and the virus was not able to exploit the host machinery for replication and systemic spreading. Mutated eIF4E lines showed enhanced resistance to PVYO strain. DAS-ELISA and RT-PCR were used for validation of the observed resistance. PVY resistance in tetraploid lines via CRISPR/Cas9 provides a route to develop novel resistant potato cultivars.
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Affiliation(s)
- Azka Noureen
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
- University Institute of Biochemistry and Biotechnology (UIBB), Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Zuhaib Khan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Tayyaba Zainab
- University Institute of Biochemistry and Biotechnology (UIBB), Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
- National Centre of Industrial Biotechnology (NCIB), Pir Mehr Ali Shah-Arid Agriculture University, Rawalpindi, Pakistan
- *Correspondence: Tayyaba Zainab, ; Shahid Mansoor,
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
- *Correspondence: Tayyaba Zainab, ; Shahid Mansoor,
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11
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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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12
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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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13
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Veillet F, Durand M, Kroj T, Cesari S, Gallois JL. Precision Breeding Made Real with CRISPR: Illustration through Genetic Resistance to Pathogens. PLANT COMMUNICATIONS 2020; 1:100102. [PMID: 33367260 PMCID: PMC7747970 DOI: 10.1016/j.xplc.2020.100102] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 05/10/2023]
Abstract
Since its discovery as a bacterial adaptive immune system and its development for genome editing in eukaryotes, the CRISPR technology has revolutionized plant research and precision crop breeding. The CRISPR toolbox holds great promise in the production of crops with genetic disease resistance to increase agriculture resilience and reduce chemical crop protection with a strong impact on the environment and public health. In this review, we provide an extensive overview on recent breakthroughs in CRISPR technology, including the newly developed prime editing system that allows precision gene editing in plants. We present how each CRISPR tool can be selected for optimal use in accordance with its specific strengths and limitations, and illustrate how the CRISPR toolbox can foster the development of genetically pathogen-resistant crops for sustainable agriculture.
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Affiliation(s)
- Florian Veillet
- IGEPP, INRAE, Institut Agro, Univ Rennes, Ploudaniel 29260, France
- Germicopa Breeding, Kerguivarch, Chateauneuf Du Faou 29520, France
- INRAE, BGPI, Biology and Genetics of Plant-Pathogen Interactions, Campus International de Baillarguet, Montpellier, France
| | - Mickael Durand
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles 78000, France
| | - Thomas Kroj
- INRAE, BGPI, Biology and Genetics of Plant-Pathogen Interactions, Campus International de Baillarguet, Montpellier, France
| | - Stella Cesari
- INRAE, BGPI, Biology and Genetics of Plant-Pathogen Interactions, Campus International de Baillarguet, Montpellier, France
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14
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Walter J, Barra A, Charon J, Tavert-Roudet G, Michon T. Spectroscopic Investigation of the Kinetic Mechanism Involved in the Association of Potyviral VPg with the Host Plant Translation Initiation Factor eIF4E. Int J Mol Sci 2020; 21:ijms21165618. [PMID: 32764527 PMCID: PMC7460627 DOI: 10.3390/ijms21165618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022] Open
Abstract
The infectious cycle of potyviruses requires the formation of a complex between the viral genome-linked protein VPg and the host eukaryotic translation initiation factor 4E, eIF4E. Mutations associated with plant resistance to potyviruses were previously mapped at the eIF4E surface, while on the virus side, mutations leading to plant resistance breaking were identified within the VPg. In the present study, fluorescence spectroscopy was used to probe the contribution of the VPg intrinsically disordered region bearing amino acids determinant of the resistance breaking, to the VPg–eIF4E binding mechanism. Synthetic peptides encompassing the VPg88–120 central region were found to tightly bind to eIF4E. Fluorescence energy transfer experiments show that, upon binding to eIF4E, the N and C termini of the VPg88–111 fragment move closer to one another, at a distance compatible with a α-helix folding. When the VPg112–120 region, which contains amino acids associated with resistance breakdown, is appended to VPg88–111, the complex formation with eIF4E switches from a single-step to a two-step kinetic model. This study revisits a recent investigation of the VPg–eIF4E complex by specifying the contribution of the VPg central helix and its appended disordered region to VPg association with eIF4E.
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Affiliation(s)
- Jocelyne Walter
- INRAE, Biologie du Fruit et Pathologie, University of Bordeaux, UMR 1332, F-33140 Villenave d’Ornon, France; (J.W.); (A.B.); (G.T.-R.)
| | - Amandine Barra
- INRAE, Biologie du Fruit et Pathologie, University of Bordeaux, UMR 1332, F-33140 Villenave d’Ornon, France; (J.W.); (A.B.); (G.T.-R.)
| | - Justine Charon
- Faculty of Sciences, University of Sydney, Charles Perkins Center D17, Camperdown Campus, Sydney, NSW 2006, Australia;
| | - Geneviève Tavert-Roudet
- INRAE, Biologie du Fruit et Pathologie, University of Bordeaux, UMR 1332, F-33140 Villenave d’Ornon, France; (J.W.); (A.B.); (G.T.-R.)
| | - Thierry Michon
- INRAE, Biologie du Fruit et Pathologie, University of Bordeaux, UMR 1332, F-33140 Villenave d’Ornon, France; (J.W.); (A.B.); (G.T.-R.)
- Correspondence: ; Tel.: +33-(0)-557-12-23-91
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15
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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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16
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Saha S, Mäkinen K. Insights into the Functions of eIF4E-Biding Motif of VPg in Potato Virus A Infection. Viruses 2020; 12:E197. [PMID: 32053987 PMCID: PMC7077193 DOI: 10.3390/v12020197] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022] Open
Abstract
The interaction between the viral protein genome-linked (VPg) and eukaryotic initiation factor 4E (eIF4E) or eIF(iso)4E of the host plays a crucial role in potyvirus infection. The VPg of potato virus A (PVA) contains the Tyr-X-X-X-X-Leu-phi (YXXXLΦ) binding motif for eIF(iso)4E. In order to investigate its role in PVA infection, we substituted the conserved tyrosine and leucine residues of the motif with alanine residues in the infectious cDNA of PVA (PVAVPgmut). PVAVPgmut RNA replicated in infiltrated leaves, but RNA accumulation remained low. Systemic infection occurred only if a reversion to wild type PVA occurred. VPg was able to stabilize PVA RNA and enhance the expression of Renilla luciferase (3'RLUC) from the 3' end of the PVA genome. VPgmut could not support either PVA RNA stabilization or enhanced 3'RLUC expression. The RNA silencing suppressor helper-component proteinase (HCPro) is responsible for the formation of PVA-induced RNA granules (PGs) during infection. While VPgmut increased the number of PG-like foci, the percentage of PVA RNA co-localization with PGs was reduced from 86% to 20%. A testable hypothesis for future studies based on these results is that the binding of eIF(iso)4E to PVA VPg via the YXXXLΦ motif is required for PVA RNA stabilization, as well as the transfer to the RNA silencing suppression pathway and, further, to polysomes for viral protein synthesis.
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Affiliation(s)
| | - Kristiina Mäkinen
- Department of Microbiology and Viikki Plant Science Centre, University of Helsinki, 00014 Helsinki, Finland;
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17
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Gutierrez Sanchez PA, Babujee L, Jaramillo Mesa H, Arcibal E, Gannon M, Halterman D, Jahn M, Jiang J, Rakotondrafara AM. Overexpression of a modified eIF4E regulates potato virus Y resistance at the transcriptional level in potato. BMC Genomics 2020; 21:18. [PMID: 31906869 PMCID: PMC6945410 DOI: 10.1186/s12864-019-6423-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/22/2019] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Potato virus Y (PVY) is a major pathogen of potatoes with major impact on global agricultural production. Resistance to PVY can be achieved by engineering potatoes to express a recessive, resistant allele of eukaryotic translation initiation factor eIF4E, a host dependency factor essential to PVY replication. Here we analyzed transcriptome changes in eIF4E over-expressing potatoes to shed light on the mechanism underpinning eIF4E-mediated recessive PVY resistance. RESULTS As anticipated, modified eIF4E-expressing potatoes demonstrated a high level of resistance, eIF4E expression, and an unexpected suppression of the susceptible allele transcript, likely explaining the bulk of the potent antiviral phenotype. In resistant plants, we also detected marked upregulation of genes involved in cell stress responses. CONCLUSIONS Our results reveal a previously unanticipated second layer of signaling attributable to eIF4E regulatory control, and potentially relevant to establishment of a broader, more systematic antiviral host defense.
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Affiliation(s)
- Pablo A Gutierrez Sanchez
- Laboratorio de Microbiología Industrial, Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellín, Calle 59 A N 63-20, Medellín, Colombia
| | - Lavanya Babujee
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA
| | - Helena Jaramillo Mesa
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA
| | - Erica Arcibal
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA
| | - Megan Gannon
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA
| | - Dennis Halterman
- U.S. Department of Agriculture-Agricultural Research Service, Madison, WI, 53726, USA
| | - Molly Jahn
- Department of Agronomy, University of Wisconsin-Madison, Moore Hall, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Aurélie M Rakotondrafara
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI, 53706, USA.
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18
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Ala-Poikela M, Rajamäki ML, Valkonen JP. A Novel Interaction Network Used by Potyviruses in Virus-Host Interactions at the Protein Level. Viruses 2019; 11:E1158. [PMID: 31847316 PMCID: PMC6950583 DOI: 10.3390/v11121158] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 12/30/2022] Open
Abstract
Host proteins that are central to infection of potyviruses (genus Potyvirus; family Potyviridae) include the eukaryotic translation initiation factors eIF4E and eIF(iso)4E. The potyviral genome-linked protein (VPg) and the helper component proteinase (HCpro) interact with each other and with eIF4E and eIF(iso)4E and proteins are involved in the same functions during viral infection. VPg interacts with eIF4E/eIF(iso)4E via the 7-methylguanosine cap-binding region, whereas HCpro interacts with eIF4E/eIF(iso)4E via the 4E-binding motif YXXXXLΦ, similar to the motif in eIF4G. In this study, HCpro and VPg were found to interact in the nucleus, nucleolus, and cytoplasm in cells infected with the potyvirus potato virus A (PVA). In the cytoplasm, interactions between HCpro and VPg occurred in punctate bodies not associated with viral replication vesicles. In addition to HCpro, the 4E-binding motif was recognized in VPg of PVA. Mutations in the 4E-binding motif of VPg from PVA weakened interactions with eIF4E and heavily reduced PVA virulence. Furthermore, mutations in the 4G-binding domain of eIF4E reduced interactions with VPg and abolished interactions with HCpro. Thus, HCpro and VPg can both interact with eIF4E using the 4E-binding motif. Our results suggest a novel interaction network used by potyviruses to interact with host plants via translation initiation factors.
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Affiliation(s)
| | - Minna-Liisa Rajamäki
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, FI-00014 Helsinki, Finland;
| | - Jari P.T. Valkonen
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, FI-00014 Helsinki, Finland;
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19
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Structural studies of the eIF4E-VPg complex reveal a direct competition for capped RNA: Implications for translation. Proc Natl Acad Sci U S A 2019; 116:24056-24065. [PMID: 31712417 DOI: 10.1073/pnas.1904752116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Viruses have transformed our understanding of mammalian RNA processing, including facilitating the discovery of the methyl-7-guanosine (m7G) cap on the 5' end of RNAs. The m7G cap is required for RNAs to bind the eukaryotic translation initiation factor eIF4E and associate with the translation machinery across plant and animal kingdoms. The potyvirus-derived viral genome-linked protein (VPg) is covalently bound to the 5' end of viral genomic RNA (gRNA) and associates with host eIF4E for successful infection. Divergent models to explain these observations proposed either an unknown mode of eIF4E engagement or a competition of VPg for the m7G cap-binding site. To dissect these possibilities, we resolved the structure of VPg, revealing a previously unknown 3-dimensional (3D) fold, and characterized the VPg-eIF4E complex using NMR and biophysical techniques. VPg directly bound the cap-binding site of eIF4E and competed for m7G cap analog binding. In human cells, VPg inhibited eIF4E-dependent RNA export, translation, and oncogenic transformation. Moreover, VPg formed trimeric complexes with eIF4E-eIF4G, eIF4E bound VPg-luciferase RNA conjugates, and these VPg-RNA conjugates were templates for translation. Informatic analyses revealed structural similarities between VPg and the human kinesin EG5. Consistently, EG5 directly bound eIF4E in a similar manner to VPg, demonstrating that this form of engagement is relevant beyond potyviruses. In all, we revealed an unprecedented modality for control and engagement of eIF4E and show that VPg-RNA conjugates functionally engage eIF4E. As such, potyvirus VPg provides a unique model system to interrogate eIF4E.
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20
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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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21
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Kim IH, Ju HK, Gong J, Han JY, Seo EY, Cho SW, Hu WX, Choi SR, Lim YP, Domier LL, Hammond J, Lim HS. A Turnip Mosaic Virus Determinant of Systemic Necrosis in Nicotiana benthamiana and a Novel Resistance-Breaking Determinant in Chinese Cabbage Identified from Chimeric Infectious Clones. PHYTOPATHOLOGY 2019; 109:1638-1647. [PMID: 31044662 DOI: 10.1094/phyto-08-18-0323-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Infectious clones of Korean turnip mosaic virus (TuMV) isolates KIH1 and HJY1 share 88.1% genomic nucleotides and 96.4% polyprotein amino acid identity, and they induce systemic necrosis or mild mosaic, respectively, in Nicotiana benthamiana. Chimeric constructs between these isolates exchanged the 5', central, and 3' domains of KIH1 (K) and HJY1 (H), where the order of the letters indicates the origin of these domains. KIH1 and chimeras KHH and KKH induced systemic necrosis, whereas HJY1 and chimeras HHK, HKK, and HKH induced mild symptoms, indicating the determinant of necrosis to be within the 5' 3.9 kb of KIH1; amino acid identities of the included P1, Helper component protease, P3, 6K1, and cylindrical inclusion N-terminal domain were 90.06, 98.91, 93.80, 100, and 100%, respectively. Expression of P1 or P3 from a potato virus X vector yielded symptom differences only between P3 of KIH1 and HJY1, implicating a role for P3 in necrosis in N. benthamiana. Chimera KKH infected Brassica rapa var. pekinensis 'Norang', which was resistant to both KIH1 and HJY1, indicating that two separate TuMV determinants are required to overcome the resistance. Ability of diverse TuMV isolates, chimeras, and recombinants to overcome resistance in breeding lines may allow identification of novel resistance genes.
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Affiliation(s)
- Ik-Hyun Kim
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Hye-Kyoung Ju
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Junsu Gong
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Jae-Yeong Han
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Eun-Young Seo
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Sang-Won Cho
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Wen-Xing Hu
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
| | - Su Ryun Choi
- Department of Horticulture, Chungnam National University, Daejeon, South Korea
| | - Yong Pyo Lim
- Department of Horticulture, Chungnam National University, Daejeon, South Korea
| | - Leslie L Domier
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, U.S.A
| | - John Hammond
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, U.S. Department of Agriculture-Agriculture Research Service, Beltsville, MD, U.S.A
| | - Hyoun-Sub Lim
- Department of Applied Biology, Chungnam National University, Daejeon, South Korea
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22
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Mao Y, Sun X, Shen J, Gao F, Qiu G, Wang T, Nie X, Zhang W, Gao Y, Bai Y. Molecular Evolutionary Analysis of Potato Virus Y Infecting Potato Based on the VPg Gene. Front Microbiol 2019; 10:1708. [PMID: 31402905 PMCID: PMC6676787 DOI: 10.3389/fmicb.2019.01708] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/10/2019] [Indexed: 11/21/2022] Open
Abstract
Potato virus Y (PVY) is an important plant pathogen infecting solanaceous crops, causing significant losses to global potato and tobacco production. Some aspects of the plant pathology and molecular biology of PVY have been studied intensively, but the evolutionary dynamics of this virus are poorly understood. Here, we performed a comprehensive set of rigorous evolutionary analyses using 177 nucleotide sequences of the viral genome linked protein (VPg) gene, which interacts with the plant eukaryotic translation initiation factor 4E (eIF4E). Our Bayesian analysis reveals that the VPg gene of PVY has been evolving at a rate of 5.60 × 10–4 subs/site/year (95% credibility interval 3.35 × 10–4–8.17 × 10–4), which is equivalent to those of other plant-infecting RNA viruses. We identified different evolutionary constraints on the two clades of PVY, clade N and clade O, whose diverge time were estimated at the year 1861 CE (95% credibility interval 1750–1948 CE). We also found that genetic variations were correlated with geographic regions, suggesting that the evolution of this pathogen is strongly affected by geographical associated factors. Taken together, the results of our study have potential implications for the control strategies of PVY.
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Affiliation(s)
- Yanzhi Mao
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xuhong Sun
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jianguo Shen
- Inspection and Quarantine Technology Center, Fujian Exit-Entry, Inspection and Quarantine Bureau, Fuzhou, China
| | - Fangluan Gao
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guangwei Qiu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Teng Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xianzhou Nie
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Wei Zhang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yanling Gao
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yanju Bai
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
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Walter J, Barra A, Doublet B, Céré N, Charon J, Michon T. Hydrodynamic Behavior of the Intrinsically Disordered Potyvirus Protein VPg, of the Translation Initiation Factor eIF4E and of their Binary Complex. Int J Mol Sci 2019; 20:E1794. [PMID: 30978975 PMCID: PMC6479716 DOI: 10.3390/ijms20071794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 01/12/2023] Open
Abstract
Protein intrinsic disorder is involved in many biological processes and good experimental models are valuable to investigate its functions. The potyvirus genome-linked protein, VPg, displays many features of an intrinsically disordered protein. The virus cycle requires the formation of a complex between VPg and eIF4E, one of the host translation initiation factors. An in-depth characterization of the hydrodynamic properties of VPg, eIF4E, and of their binary complex VPg-eIF4E was carried out. Two complementary experimental approaches, size-exclusion chromatography and fluorescence anisotropy, which is more resolving and revealed especially suitable when protein concentration is the limiting factor, allowed to estimate monomers compaction upon complex formation. VPg possesses a high degree of hydration which is in agreement with its classification as a partially folded protein in between a molten and pre-molten globule. The natively disordered first 46 amino acids of eIF4E contribute to modulate the protein hydrodynamic properties. The addition of an N-ter His tag decreased the conformational entropy of this intrinsically disordered region. A comparative study between the two tagged and untagged proteins revealed the His tag contribution to proteins hydrodynamic behavior.
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Affiliation(s)
- Jocelyne Walter
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS 20032, 33140 Villenave d'Ornon, France.
| | - Amandine Barra
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS 20032, 33140 Villenave d'Ornon, France.
| | - Bénédicte Doublet
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS 20032, 33140 Villenave d'Ornon, France.
| | - Nicolas Céré
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS 20032, 33140 Villenave d'Ornon, France.
| | - Justine Charon
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS 20032, 33140 Villenave d'Ornon, France.
| | - Thierry Michon
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS 20032, 33140 Villenave d'Ornon, France.
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Walter J, Charon J, Hu Y, Lachat J, Leger T, Lafforgue G, Barra A, Michon T. Comparative analysis of mutational robustness of the intrinsically disordered viral protein VPg and of its interactor eIF4E. PLoS One 2019; 14:e0211725. [PMID: 30763345 PMCID: PMC6375565 DOI: 10.1371/journal.pone.0211725] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/20/2019] [Indexed: 01/02/2023] Open
Abstract
Conformational intrinsic disorder is a feature present in many virus proteins. Intrinsically disordered regions (IDRs) have weaker structural requirement than ordered regions and mutations in IDRs could have a lower impact on the virus fitness. This could favor its exploration of adaptive solutions. The potyviral protein VPg contains IDRs with determinants for adaptation to its host plant. To experimentally assess whether IDRs are more resistant to mutations than ordered regions, the biologically relevant interaction between mutant libraries of both VPg and the eukaryotic translation initiation factor 4E (eIF4E) and their respective wild type partner was examined using yeast two hybrid assay. Our data shows that VPg is significantly more robust to mutations than eIF4E and as such belongs to a particular class of intrinsically disordered proteins. This result is discussed from the standpoint of IDRs involvement in the virus adaptive processes.
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Affiliation(s)
- Jocelyne Walter
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
- * E-mail: (JW); (TM)
| | - Justine Charon
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
- School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Yihua Hu
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
| | - Joy Lachat
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
| | - Thomas Leger
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
| | - Guillaume Lafforgue
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
| | - Amandine Barra
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
| | - Thierry Michon
- UMR Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, CS, Villenave d’Ornon, France
- * E-mail: (JW); (TM)
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Langner T, Kamoun S, Belhaj K. CRISPR Crops: Plant Genome Editing Toward Disease Resistance. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:479-512. [PMID: 29975607 DOI: 10.1146/annurev-phyto-080417-050158] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Genome editing by sequence-specific nucleases (SSNs) has revolutionized biology by enabling targeted modifications of genomes. Although routine plant genome editing emerged only a few years ago, we are already witnessing the first applications to improve disease resistance. In particular, CRISPR-Cas9 has democratized the use of genome editing in plants thanks to the ease and robustness of this method. Here, we review the recent developments in plant genome editing and its application to enhancing disease resistance against plant pathogens. In the future, bioedited disease resistant crops will become a standard tool in plant breeding.
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Affiliation(s)
- Thorsten Langner
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
| | - Khaoula Belhaj
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, United Kingdom;
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26
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Hajimorad MR, Domier LL, Tolin SA, Whitham SA, Saghai Maroof MA. Soybean mosaic virus: a successful potyvirus with a wide distribution but restricted natural host range. MOLECULAR PLANT PATHOLOGY 2018; 19:1563-1579. [PMID: 29134790 PMCID: PMC6638002 DOI: 10.1111/mpp.12644] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/18/2017] [Accepted: 11/07/2017] [Indexed: 05/12/2023]
Abstract
TAXONOMY Soybean mosaic virus (SMV) is a species within the genus Potyvirus, family Potyviridae, which includes almost one-quarter of all known plant RNA viruses affecting agriculturally important plants. The Potyvirus genus is the largest of all genera of plant RNA viruses with 160 species. PARTICLE The filamentous particles of SMV, typical of potyviruses, are about 7500 Å long and 120 Å in diameter with a central hole of about 15 Å in diameter. Coat protein residues are arranged in helices of about 34 Å pitch having slightly less than nine subunits per turn. GENOME The SMV genome consists of a single-stranded, positive-sense, polyadenylated RNA of approximately 9.6 kb with a virus-encoded protein (VPg) linked at the 5' terminus. The genomic RNA contains a single large open reading frame (ORF). The polypeptide produced from the large ORF is processed proteolytically by three viral-encoded proteinases to yield about 10 functional proteins. A small ORF, partially overlapping the P3 cistron, pipo, is encoded as a fusion protein in the N-terminus of P3 (P3N + PIPO). BIOLOGICAL PROPERTIES SMV's host range is restricted mostly to two plant species of a single genus: Glycine max (cultivated soybean) and G. soja (wild soybean). SMV is transmitted by aphids non-persistently and by seeds. The variability of SMV is recognized by reactions on cultivars with dominant resistance (R) genes. Recessive resistance genes are not known. GEOGRAPHICAL DISTRIBUTION AND ECONOMIC IMPORTANCE As a consequence of its seed transmissibility, SMV is present in all soybean-growing areas of the world. SMV infections can reduce significantly seed quantity and quality (e.g. mottled seed coats, reduced seed size and viability, and altered chemical composition). CONTROL The most effective means of managing losses from SMV are the planting of virus-free seeds and cultivars containing single or multiple R genes. KEY ATTRACTIONS The interactions of SMV with soybean genotypes containing different dominant R genes and an understanding of the functional role(s) of SMV-encoded proteins in virulence, transmission and pathogenicity have been investigated intensively. The SMV-soybean pathosystem has become an excellent model for the examination of the genetics and genomics of a uniquely complex gene-for-gene resistance model in a crop of worldwide importance.
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Affiliation(s)
- M. R. Hajimorad
- Department of Entomology and Plant PathologyThe University of TennesseeKnoxvilleTN 37996USA
| | - L. L. Domier
- United States Department of Agriculture‐Agricultural Research Service and Department of Crop SciencesUniversity of IllinoisUrbanaIL 61801USA
| | - S. A. Tolin
- Department of Plant Pathology, Physiology and Weed ScienceVirginia TechBlacksburgVA 24061USA
| | - S. A. Whitham
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA 50011USA
| | - M. A. Saghai Maroof
- Department of Crop and Soil Environmental SciencesVirginia TechBlacksburgVA 24061USA
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Rolland M, Villemot J, Marais A, Theil S, Faure C, Cadot V, Valade R, Vitry C, Rabenstein F, Candresse T. Classical and next generation sequencing approaches unravel Bymovirus diversity in barley crops in France. PLoS One 2017; 12:e0188495. [PMID: 29182661 PMCID: PMC5705140 DOI: 10.1371/journal.pone.0188495] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 11/08/2017] [Indexed: 11/18/2022] Open
Abstract
Despite the generalized use of cultivars carrying the rym4 resistance gene, the impact of viral mosaic diseases on winter barleys increased in recent years in France. This change could reflect i) an increased prevalence of the rym4 resistance-breaking pathotype of Barley yellow mosaic virus Y (BaYMV-2), ii) the emergence of rym4 resistance-breaking pathotypes of Barley mild mosaic virus (BaMMV) or iii) the emergence of other viruses. A study was undertaken to determine the distribution and diversity of viruses causing yellow mosaic disease. A collection of 241 symptomatic leaf samples from susceptible, rym4 and rym5 varieties was gathered from 117 sites. The viruses present in all samples were identified by specific RT-PCR assays and, for selected samples, by double-stranded RNA next-generation sequencing (NGS). The results show that BaYMV-2 is responsible for the symptoms observed in varieties carrying the resistance gene rym4. In susceptible varieties, both BaYMV-1 and BaYMV-2 were detected, together with BaMMV. Phylogenetic analyses indicate that the rym4 resistance-breaking ability independently evolved in multiple genetic backgrounds. Parallel analyses revealed a similar scenario of multiple independent emergence events in BaMMV for rym5 resistance-breaking, likely involving multiple amino acid positions in the viral-linked genome protein. NGS analyses and classical techniques provided highly convergent results, highlighting and validating the power of NGS approaches for diagnostics and viral population characterization.
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Affiliation(s)
- Mathieu Rolland
- Groupe d'Etude et de contrôle des Variétés Et des Semences, Beaucouzé, France
| | - Julie Villemot
- Groupe d'Etude et de contrôle des Variétés Et des Semences, Beaucouzé, France
| | - Armelle Marais
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d’Ornon, France
| | - Sébastien Theil
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d’Ornon, France
| | - Chantal Faure
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d’Ornon, France
| | - Valérie Cadot
- Groupe d'Etude et de contrôle des Variétés Et des Semences, Beaucouzé, France
| | - Romain Valade
- ARVALIS–Institut du végétal, Thiverval-Grignon, France
| | - Cindy Vitry
- ARVALIS–Institut du végétal, Thiverval-Grignon, France
| | | | - Thierry Candresse
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d’Ornon, France
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Charon J, Theil S, Nicaise V, Michon T. Protein intrinsic disorder within the Potyvirus genus: from proteome-wide analysis to functional annotation. MOLECULAR BIOSYSTEMS 2016; 12:634-52. [PMID: 26699268 DOI: 10.1039/c5mb00677e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Within proteins, intrinsically disordered regions (IDRs) are devoid of stable secondary and tertiary structures under physiological conditions and rather exist as dynamic ensembles of inter-converting conformers. Although ubiquitous in all domains of life, the intrinsic disorder content is highly variable in viral genomes. Over the years, functional annotations of disordered regions at the scale of the whole proteome have been conducted for several animal viruses. But to date, similar studies applied to plant viruses are still missing. Based on disorder prediction tools combined with annotation programs and evolutionary studies, we analyzed the intrinsic disorder content in Potyvirus, using a 10-species dataset representative of this genus diversity. In this paper, we revealed that: (i) the Potyvirus proteome displays high disorder content, (ii) disorder is conserved during Potyvirus evolution, suggesting a functional advantage of IDRs, (iii) IDRs evolve faster than ordered regions, and (iv) IDRs may be associated with major biological functions required for the Potyvirus cycle. Notably, the proteins P1, Coat protein (CP) and Viral genome-linked protein (VPg) display a high content of conserved disorder, enriched in specific motifs mimicking eukaryotic functional modules and suggesting strategies of host machinery hijacking. In these three proteins, IDRs are particularly conserved despite their high amino acid polymorphism, indicating a link to adaptive processes. Through this comprehensive study, we further investigate the biological relevance of intrinsic disorder in Potyvirus biology and we propose a functional annotation of potyviral proteome IDRs.
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Affiliation(s)
- Justine Charon
- UMR Biologie du Fruit et Pathologie, INRA, Villenave d'Ornon cedex, France. and UMR Biologie du Fruit et Pathologie, Université de Bordeaux, Villenave d'Ornon cedex, France
| | - Sébastien Theil
- UMR Biologie du Fruit et Pathologie, INRA, Villenave d'Ornon cedex, France. and UMR Biologie du Fruit et Pathologie, Université de Bordeaux, Villenave d'Ornon cedex, France
| | - Valérie Nicaise
- UMR Biologie du Fruit et Pathologie, INRA, Villenave d'Ornon cedex, France. and UMR Biologie du Fruit et Pathologie, Université de Bordeaux, Villenave d'Ornon cedex, France
| | - Thierry Michon
- UMR Biologie du Fruit et Pathologie, INRA, Villenave d'Ornon cedex, France. and UMR Biologie du Fruit et Pathologie, Université de Bordeaux, Villenave d'Ornon cedex, France
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29
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Poulicard N, Pacios LF, Gallois JL, Piñero D, García-Arenal F. Human Management of a Wild Plant Modulates the Evolutionary Dynamics of a Gene Determining Recessive Resistance to Virus Infection. PLoS Genet 2016; 12:e1006214. [PMID: 27490800 PMCID: PMC4973933 DOI: 10.1371/journal.pgen.1006214] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 07/01/2016] [Indexed: 02/07/2023] Open
Abstract
This work analyses the genetic variation and evolutionary patterns of recessive resistance loci involved in matching-allele (MA) host-pathogen interactions, focusing on the pvr2 resistance gene to potyviruses of the wild pepper Capsicum annuum glabriusculum (chiltepin). Chiltepin grows in a variety of wild habitats in Mexico, and its cultivation in home gardens started about 25 years ago. Potyvirus infection of Capsicum plants requires the physical interaction of the viral VPg with the pvr2 product, the translation initiation factor eIF4E1. Mutations impairing this interaction result in resistance, according to the MA model. The diversity of pvr2/eIF4E1 in wild and cultivated chiltepin populations from six biogeographical provinces in Mexico was analysed in 109 full-length coding sequences from 97 plants. Eleven alleles were found, and their interaction with potyvirus VPg in yeast-two-hybrid assays, plus infection assays of plants, identified six resistance alleles. Mapping resistance mutations on a pvr2/eIF4E1 model structure showed that most were around the cap-binding pocket and strongly altered its surface electrostatic potential, suggesting resistance-associated costs due to functional constraints. The pvr2/eIF4E1 phylogeny established that susceptibility was ancestral and resistance was derived. The spatial structure of pvr2/eIF4E1 diversity differed from that of neutral markers, but no evidence of selection for resistance was found in wild populations. In contrast, the resistance alleles were much more frequent, and positive selection stronger, in cultivated chiltepin populations, where diversification of pvr2/eIF4E1 was higher. This analysis of the genetic variation of a recessive resistance gene involved in MA host-pathogen interactions in populations of a wild plant show that evolutionary patterns differ according to the plant habitat, wild or cultivated. It also demonstrates that human management of the plant population has profound effects on the diversity and the evolution of the resistance gene, resulting in the selection of resistance alleles.
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Affiliation(s)
- Nils Poulicard
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Luis Fernández Pacios
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Campus de Montegancedo, Pozuelo de Alarcón (Madrid) and Departamento de Sistemas y Recursos Naturales, E.T.S.I. Montes, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Jean-Luc Gallois
- Institut National de Recherche Agronomique (INRA), UR1052, Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, México, D.F., México
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
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30
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Hillung J, Cuevas JM, Elena SF. Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0292. [PMID: 26150658 DOI: 10.1098/rstb.2014.0292] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The existence of genetic variation for resistance in host populations is assumed to be essential to the spread of an emerging virus. Models predict that the rate of spread slows down with the increasing frequency and higher diversity of resistance alleles in the host population. We have been using the experimental pathosystem Arabidopsis thaliana-tobacco etch potyvirus (TEV) to explore the interplay between genetic variation in host's susceptibility and virus diversity. We have recently shown that TEV populations evolving in A. thaliana ecotypes that differ in susceptibility to infection gained within-host fitness, virulence and infectivity in a manner compatible with a gene-for-gene model of host-parasite interactions: hard-to-infect ecotypes were infected by generalist viruses, whereas easy-to-infect ecotypes were infected by every virus. We characterized the genomes of the evolved viruses and found cases of host-driven convergent mutations. To gain further insights in the mechanistic basis of this gene-for-gene model, we have generated all viral mutations individually as well as in specific combinations and tested their within-host fitness effects across ecotypes. Most of these mutations were deleterious or neutral in their local ecotype and only a very reduced number had a host-specific beneficial effect. We conclude that most of the mutations fixed during the evolution experiment were so by drift or by selective sweeps along with the selected driver mutation. In addition, we evaluated the ruggedness of the underlying adaptive fitness landscape and found that mutational effects were mostly multiplicative, with few cases of significant epistasis.
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Affiliation(s)
- Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain
| | - José M Cuevas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain The Santa Fe Institute, Santa Fe, NM 87501, USA
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31
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Plant Translation Factors and Virus Resistance. Viruses 2015; 7:3392-419. [PMID: 26114476 PMCID: PMC4517107 DOI: 10.3390/v7072778] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 02/06/2023] Open
Abstract
Plant viruses recruit cellular translation factors not only to translate their viral RNAs but also to regulate their replication and potentiate their local and systemic movement. Because of the virus dependence on cellular translation factors, it is perhaps not surprising that many natural plant recessive resistance genes have been mapped to mutations of translation initiation factors eIF4E and eIF4G or their isoforms, eIFiso4E and eIFiso4G. The partial functional redundancy of these isoforms allows specific mutation or knock-down of one isoform to provide virus resistance without hindering the general health of the plant. New possible targets for antiviral strategies have also been identified following the characterization of other plant translation factors (eIF4A-like helicases, eIF3, eEF1A and eEF1B) that specifically interact with viral RNAs and proteins and regulate various aspects of the infection cycle. Emerging evidence that translation repression operates as an alternative antiviral RNA silencing mechanism is also discussed. Understanding the mechanisms that control the development of natural viral resistance and the emergence of virulent isolates in response to these plant defense responses will provide the basis for the selection of new sources of resistance and for the intelligent design of engineered resistance that is broad-spectrum and durable.
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32
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Browning KS, Bailey-Serres J. Mechanism of cytoplasmic mRNA translation. THE ARABIDOPSIS BOOK 2015; 13:e0176. [PMID: 26019692 PMCID: PMC4441251 DOI: 10.1199/tab.0176] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein synthesis is a fundamental process in gene expression that depends upon the abundance and accessibility of the mRNA transcript as well as the activity of many protein and RNA-protein complexes. Here we focus on the intricate mechanics of mRNA translation in the cytoplasm of higher plants. This chapter includes an inventory of the plant translational apparatus and a detailed review of the translational processes of initiation, elongation, and termination. The majority of mechanistic studies of cytoplasmic translation have been carried out in yeast and mammalian systems. The factors and mechanisms of translation are for the most part conserved across eukaryotes; however, some distinctions are known to exist in plants. A comprehensive understanding of the complex translational apparatus and its regulation in plants is warranted, as the modulation of protein production is critical to development, environmental plasticity and biomass yield in diverse ecosystems and agricultural settings.
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Affiliation(s)
- Karen S. Browning
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin TX 78712-0165
- Both authors contributed equally to this work
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California, Riverside, CA, 92521 USA
- Both authors contributed equally to this work
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Abstract
Potyvirus is the largest genus of plant viruses causing significant losses in a wide range of crops. Potyviruses are aphid transmitted in a nonpersistent manner and some of them are also seed transmitted. As important pathogens, potyviruses are much more studied than other plant viruses belonging to other genera and their study covers many aspects of plant virology, such as functional characterization of viral proteins, molecular interaction with hosts and vectors, structure, taxonomy, evolution, epidemiology, and diagnosis. Biotechnological applications of potyviruses are also being explored. During this last decade, substantial advances have been made in the understanding of the molecular biology of these viruses and the functions of their various proteins. After a general presentation on the family Potyviridae and the potyviral proteins, we present an update of the knowledge on potyvirus multiplication, movement, and transmission and on potyvirus/plant compatible interactions including pathogenicity and symptom determinants. We end the review providing information on biotechnological applications of potyviruses.
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Interaction patterns between potato virus Y and eIF4E-mediated recessive resistance in the Solanaceae. J Virol 2014; 88:9799-807. [PMID: 24942572 DOI: 10.1128/jvi.00930-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The structural pattern of infectivity matrices, which contains infection data resulting from inoculations of a set of hosts by a set of parasites, is a key parameter for our understanding of biological interactions and their evolution. This pattern determines the evolution of parasite pathogenicity and host resistance, the spatiotemporal distribution of host and parasite genotypes, and the efficiency of disease control strategies. Two major patterns have been proposed for plant-virus genotype infectivity matrices. In the gene-for-gene model, infectivity matrices show a nested pattern, where the host ranges of specialist virus genotypes are subsets of the host ranges of less specialized viruses. In contrast, in the matching-allele (MA) model, each virus genotype is specialized to infect one (or a small set of) host genotype(s). The corresponding infectivity matrix shows a modular pattern where infection is frequent for plants and viruses belonging to the same module but rare for those belonging to different modules. We analyzed the structure of infectivity matrices between Potato virus Y (PVY) and plant genotypes in the family Solanaceae carrying different eukaryotic initiation factor 4E (eIF4E)-coding alleles conferring recessive resistance. Whereas this system corresponds mechanistically to an MA model, the expected modular pattern was rejected based on our experimental data. This was mostly because PVY mutations involved in adaptation to a particular plant genotype displayed frequent pleiotropic effects, conferring simultaneously an adaptation to additional plant genotypes with different eIF4E alleles. Such effects should be taken into account for the design of strategies of sustainable control of PVY through plant varietal mixtures or rotations. IMPORTANCE The interaction pattern between host and virus genotypes has important consequences on their respective evolution and on issues regarding the application of disease control strategies. We found that the structure of the interaction between Potato virus Y (PVY) variants and host plants in the family Solanaceae departs significantly from the current model of interaction considered for these organisms because of frequent pleiotropic effects of virus mutations. These mutational effects allow the virus to expand rapidly its range of host plant genotypes, make it very difficult to predict the effects of mutations in PVY infectivity factors, and raise concerns about strategies of sustainable management of plant genetic resistance to viruses.
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Abstract
To confer resistance against pathogens and pests in plants, typically dominant resistance genes are deployed. However, because resistance is based on recognition of a single pathogen-derived molecular pattern, these narrow-spectrum genes are usually readily overcome. Disease arises from a compatible interaction between plant and pathogen. Hence, altering a plant gene that critically facilitates compatibility could provide a more broad-spectrum and durable type of resistance. Here, such susceptibility (S) genes are reviewed with a focus on the mechanisms underlying loss of compatibility. We distinguish three groups of S genes acting during different stages of infection: early pathogen establishment, modulation of host defenses, and pathogen sustenance. The many examples reviewed here show that S genes have the potential to be used in resistance breeding. However, because S genes have a function other than being a compatibility factor for the pathogen, the side effects caused by their mutation demands a one-by-one assessment of their usefulness for application.
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