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Carrasco JL, Ambrós S, Gutiérrez PA, Elena SF. Adaptation of turnip mosaic virus to Arabidopsis thaliana involves rewiring of VPg-host proteome interactions. Virus Evol 2024; 10:veae055. [PMID: 39091990 PMCID: PMC11291303 DOI: 10.1093/ve/veae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/23/2024] [Accepted: 07/16/2024] [Indexed: 08/04/2024] Open
Abstract
The outcome of a viral infection depends on a complex interplay between the host physiology and the virus, mediated through numerous protein-protein interactions. In a previous study, we used high-throughput yeast two-hybrid (HT-Y2H) to identify proteins in Arabidopsis thaliana that bind to the proteins encoded by the turnip mosaic virus (TuMV) genome. Furthermore, after experimental evolution of TuMV lineages in plants with mutations in defense-related or proviral genes, most mutations observed in the evolved viruses affected the VPg cistron. Among these mutations, D113G was a convergent mutation selected in many lineages across different plant genotypes, including cpr5-2 with constitutive expression of systemic acquired resistance. In contrast, mutation R118H specifically emerged in the jin1 mutant with affected jasmonate signaling. Using the HT-Y2H system, we analyzed the impact of these two mutations on VPg's interaction with plant proteins. Interestingly, both mutations severely compromised the interaction of VPg with the translation initiation factor eIF(iso)4E, a crucial interactor for potyvirus infection. Moreover, mutation D113G, but not R118H, adversely affected the interaction with RHD1, a zinc-finger homeodomain transcription factor involved in regulating DNA demethylation. Our results suggest that RHD1 enhances plant tolerance to TuMV infection. We also discuss our findings in a broad virus evolution context.
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Affiliation(s)
- José L Carrasco
- Instituto de Biología Integrativa de Sistemas (CSIC—Universitat de València), Catedratico Agustin Escardino 9, Paterna, València 46182, Spain
| | - Silvia Ambrós
- Instituto de Biología Integrativa de Sistemas (CSIC—Universitat de València), Catedratico Agustin Escardino 9, Paterna, València 46182, Spain
| | - Pablo A Gutiérrez
- Laboratorio de Microbiología Industrial, Facultad de Ciencias, Universidad Nacional de Colombia, Carrera 65 Nro. 59A - 110, Medellín, Antioquia 050034, Colombia
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (CSIC—Universitat de València), Catedratico Agustin Escardino 9, Paterna, València 46182, Spain
- The Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, United States
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Wang J, Zhang T, Tu A, Xie H, Hu H, Chen J, Yang J. Genome-Wide Identification and Analysis of APC E3 Ubiquitin Ligase Genes Family in Triticum aestivum. Genes (Basel) 2024; 15:271. [PMID: 38540330 PMCID: PMC10970508 DOI: 10.3390/genes15030271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 06/15/2024] Open
Abstract
E3 ubiquitin ligases play a pivotal role in ubiquitination, a crucial post-translational modification process. Anaphase-promoting complex (APC), a large cullin-RING E3 ubiquitin ligase, regulates the unidirectional progression of the cell cycle by ubiquitinating specific target proteins and triggering plant immune responses. Several E3 ubiquitin ligases have been identified owing to advancements in sequencing and annotation of the wheat genome. However, the types and functions of APC E3 ubiquitin ligases in wheat have not been reported. This study identified 14 members of the APC gene family in the wheat genome and divided them into three subgroups (CCS52B, CCS52A, and CDC20) to better understand their functions. Promoter sequence analysis revealed the presence of several cis-acting elements related to hormone and stress responses in the APC E3 ubiquitin ligases in wheat. All identified APC E3 ubiquitin ligase family members were highly expressed in the leaves, and the expression of most genes was induced by the application of methyl jasmonate (MeJA). In addition, the APC gene family in wheat may play a role in plant defense mechanisms. This study comprehensively analyzes APC genes in wheat, laying the groundwork for future research on the function of APC genes in response to viral infections and expanding our understanding of wheat immunity mechanisms.
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Affiliation(s)
- Jinnan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Tianye Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Aizhu Tu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Haoxin Xie
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Haichao Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.W.); (T.Z.); (A.T.); (H.X.); (H.H.)
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Butkovic A, Ellis TJ, Gonzalez R, Jaegle B, Nordborg M, Elena SF. Genetic basis of Arabidopsis thaliana responses to infection by naïve and adapted isolates of turnip mosaic virus. eLife 2024; 12:RP89749. [PMID: 38240739 PMCID: PMC10945600 DOI: 10.7554/elife.89749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024] Open
Abstract
Plant viruses account for enormous agricultural losses worldwide, and the most effective way to combat them is to identify genetic material conferring plant resistance to these pathogens. Aiming to identify genetic associations with responses to infection, we screened a large panel of Arabidopsis thaliana natural inbred lines for four disease-related traits caused by infection by A. thaliana-naïve and -adapted isolates of the natural pathogen turnip mosaic virus (TuMV). We detected a strong, replicable association in a 1.5 Mb region on chromosome 2 with a 10-fold increase in relative risk of systemic necrosis. The region contains several plausible causal genes as well as abundant structural variation, including an insertion of a Copia transposon into a Toll/interleukin receptor (TIR-NBS-LRR) coding for a gene involved in defense, that could be either a driver or a consequence of the disease-resistance locus. When inoculated with TuMV, loss-of-function mutant plants of this gene exhibited different symptoms than wild-type plants. The direction and severity of symptom differences depended on the adaptation history of the virus. This increase in symptom severity was specific for infections with the adapted isolate. Necrosis-associated alleles are found worldwide, and their distribution is consistent with a trade-off between resistance during viral outbreaks and a cost of resistance otherwise, leading to negative frequency-dependent selection.
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Affiliation(s)
- Anamarija Butkovic
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Científic UVValènciaSpain
| | - Thomas James Ellis
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Doktor-Bohr-GasseViennaAustria
| | - Ruben Gonzalez
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Científic UVValènciaSpain
| | - Benjamin Jaegle
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Doktor-Bohr-GasseViennaAustria
| | - Magnus Nordborg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Doktor-Bohr-GasseViennaAustria
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Científic UVValènciaSpain
- The Santa Fe InstituteSanta FeUnited States
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Melero I, Elena SF, González R. Viral strain-dependent impact of plant developmental stages on the nestedness and modularity of plant-virus interaction matrices. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000943. [PMID: 38021168 PMCID: PMC10667922 DOI: 10.17912/micropub.biology.000943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023]
Abstract
This study examines the specificity of adaptation of lineages of turnip mosaic virus that were experimentally evolved from naïve and preadapted strains to Arabidopsis thaliana plants at various plant developmental stages. We conducted a cross-infection experiment involving three plant developmental stages and assessed the progression of disease and symptoms. We found a significative interaction between the host developmental stage where the virus evolved and the host developmental stage in which the virus was tested. The analysis of the resulting interaction matrices revealed significant nestedness for viruses evolved from the naïve strain, but not for those originating from the preadapted one. Furthermore, there was an absence of modularity across all matrices. Our findings suggest that the past adaptation history of the ancestral strain influences its future evolution, and each plant developmental stage imposes unique selective constraints. The study highlights the complexity of host-parasite interactions and the potential influence of the host's developmental stage on viral adaptation.
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Affiliation(s)
- Izan Melero
- Instituto de Biología Integrativa de Sistemas (CSIC - Universitat de València), Paterna, 46182 València, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (CSIC - Universitat de València), Paterna, 46182 València, Spain
- The Santa Fe Institute, Santa Fe, 87501 NM, USA
| | - Rubén González
- Institut de Biologie de l’École Normale Supérieure-CNRS-INSERM, 75005 Paris, France
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Brine TJ, Viswanathan SB, Murphy AM, Pate AE, Wamonje FO, Carr JP. Investigating the interactions of endornaviruses with each other and with other viruses in common bean, Phaseolus vulgaris. Virol J 2023; 20:216. [PMID: 37737192 PMCID: PMC10515030 DOI: 10.1186/s12985-023-02184-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Plant viruses of the genus Alphaendornavirus are transmitted solely via seed and pollen and generally cause no apparent disease. It has been conjectured that certain plant endornaviruses may confer advantages on their hosts through improved performance (e.g., seed yield) or resilience to abiotic or biotic insult. We recently characterised nine common bean (Phaseolus vulgaris L.) varieties that harboured either Phaseolus vulgaris endornavirus (PvEV1) alone, or PvEV1 in combination with PvEV2 or PvEV1 in combination with PvEV2 and PvEV3. Here, we investigated the interactions of these endornaviruses with each other, and with three infectious pathogenic viruses: cucumber mosaic virus (CMV), bean common mosaic virus (BCMV), and bean common mosaic necrosis virus (BCMNV). RESULTS In lines harbouring PvEV1, PvEV1 and PvEV2, or PvEV1, PvEV2 plus PvEV3, the levels of PvEV1 and PvEV3 RNA were very similar between lines, although there were variations in PvEV2 RNA accumulation. In plants inoculated with infectious viruses, CMV, BCMV and BCMNV levels varied between lines, but this was most likely due to host genotype differences rather than to the presence or absence of endornaviruses. We tested the effects of endornaviruses on seed production and seedborne transmission of infectious pathogenic viruses but found no consistent relationship between the presence of endornaviruses and seed yield or protection from seedborne transmission of infectious pathogenic viruses. CONCLUSIONS It was concluded that endornaviruses do not interfere with each other's accumulation. There appears to be no direct synergy or competition between infectious pathogenic viruses and endornaviruses, however, the effects of host genotype may obscure interactions between endornaviruses and infectious viruses. There is no consistent effect of endornaviruses on seed yield or susceptibility to seedborne transmission of other viruses.
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Affiliation(s)
- Thomas J Brine
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | | | - Alex M Murphy
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Adrienne E Pate
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Francis O Wamonje
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
- Pest and Pathogen Ecology, National Institute of Agricultural Botany, East Malling, ME19 6BJ, UK
| | - John P Carr
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
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Forti LR, Szabo JK, Japyassú HF. Host manipulation by parasites through the lens of Niche Construction Theory. Behav Processes 2023:104907. [PMID: 37352944 DOI: 10.1016/j.beproc.2023.104907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 06/17/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023]
Abstract
The effect of parasites on host behaviour is generally considered an example of the extended phenotype, implying that parasite genes alter host behaviour to benefit the parasite. While the extended phenotype is a valid perspective supported by empirical examples, this approach was proposed from an evolutionary perspective and it does not fully explain all processes that occur at ecological time scales. For instance, the roles of the ontogenetic environment, memory and learning in forming the host phenotype are not explicitly mentioned. Furthermore, the cumulative effect of diverse populations or communities of parasites on host phenotype cannot be attributed to a particular genotype, much less to a particular gene. Building on the idea that the behaviour of a host is the result of a complex process, which certainly goes beyond a specific parasite gene, we use Niche Construction Theory to describe certain systems that are not generally the main focus in the extended phenotype (EP) model. We introduce three niche construction models with corresponding empirical examples that capture the diversity and complexity of host-parasite interactions, providing predictions that simpler models cannot generate. We hope that this novel perspective will inspire further research on the topic, given the impact of ecological factors on both short-, and long-term effects of parasitism.
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Affiliation(s)
- Lucas Rodriguez Forti
- Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, 668 - Campus de Ondina CEP: 40170-115 Salvador - Bahia, Brazil; Departamento de Biociências, Universidade Federal Rural do Semi-Árido, Av. Francisco Mota, 572 - Bairro Costa e Silva, 59625-900, Mossoró - Rio Grande do Norte, Brazil.
| | - Judit K Szabo
- Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, 668 - Campus de Ondina CEP: 40170-115 Salvador - Bahia, Brazil; College of Engineering, IT and Environment, Charles Darwin University, Casuarina, Northern Territory 0909, Australia
| | - Hilton F Japyassú
- Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, 668 - Campus de Ondina CEP: 40170-115 Salvador - Bahia, Brazil; INCT-INTREE: Instituto Nacional de Ciência e Tecnologia para estudos Interdisciplinares e Transdisciplinares em Ecologia e Evolução, Universidade Federal da Bahia
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Nigam D, Muthukrishnan E, Flores-López LF, Nigam M, Wamaitha MJ. Comparative Genome Analysis of Old World and New World TYLCV Reveals a Biasness toward Highly Variable Amino Acids in Coat Protein. PLANTS (BASEL, SWITZERLAND) 2023; 12:1995. [PMID: 37653912 PMCID: PMC10223811 DOI: 10.3390/plants12101995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 09/02/2023]
Abstract
Begomoviruses, belonging to the family Geminiviridae and the genus Begomovirus, are DNA viruses that are transmitted by whitefly Bemisia tabaci (Gennadius) in a circulative persistent manner. They can easily adapt to new hosts and environments due to their wide host range and global distribution. However, the factors responsible for their adaptability and coevolutionary forces are yet to be explored. Among BGVs, TYLCV exhibits the broadest range of hosts. In this study, we have identified variable and coevolving amino acid sites in the proteins of Tomato yellow leaf curl virus (TYLCV) isolates from Old World (African, Indian, Japanese, and Oceania) and New World (Central and Southern America). We focused on mutations in the coat protein (CP), as it is highly variable and interacts with both vectors and host plants. Our observations indicate that some mutations were accumulating in Old World TYLCV isolates due to positive selection, with the S149N mutation being of particular interest. This mutation is associated with TYLCV isolates that have spread in Europe and Asia and is dominant in 78% of TYLCV isolates. On the other hand, the S149T mutation is restricted to isolates from Saudi Arabia. We further explored the implications of these amino acid changes through structural modeling. The results presented in this study suggest that certain hypervariable regions in the genome of TYLCV are conserved and may be important for adapting to different host environments. These regions could contribute to the mutational robustness of the virus, allowing it to persist in different host populations.
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Affiliation(s)
- Deepti Nigam
- Institute for Genomics of Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University (TTU), Lubbock, TX 79409, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA
| | | | - Luis Fernando Flores-López
- Departamento de Biotecnología y Bioquímica, Centro de Investigacióny de Estudios Avanzados de IPN (CINVESTAV) Unidad Irapuato, Irapuato 368224, Mexico
| | - Manisha Nigam
- Department of Biochemistry, Hemvati Nandan Bahuguna Garhwal University, Srinagar 246174, Uttarakhand, India
| | - Mwathi Jane Wamaitha
- Kenya Agricultural and Livestock Research Organization (KALRO), Nairobi P.O. Box 14733-00800, Kenya
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King KC, Hall MD, Wolinska J. Infectious disease ecology and evolution in a changing world. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220002. [PMID: 36744560 PMCID: PMC9900701 DOI: 10.1098/rstb.2022.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 02/07/2023] Open
Affiliation(s)
- Kayla C. King
- Department of Biology, University of Oxford, Oxford OX1 3SZ, UK
| | - Matthew D. Hall
- School of Biological Sciences, Monash University, Melbourne 3800, Australia
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587 Berlin, Germany
- Department of Biology, Chemistry, and Pharmacy, Institute of Biology, Freie Universität Berlin (FU), 14195 Berlin, Germany
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