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Sanfaçon H. Re-examination of nepovirus polyprotein cleavage sites highlights the diverse specificities and evolutionary relationships of nepovirus 3C-like proteases. Arch Virol 2022; 167:2529-2543. [PMID: 36042138 PMCID: PMC9741568 DOI: 10.1007/s00705-022-05564-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/30/2022] [Indexed: 12/14/2022]
Abstract
Plant-infecting viruses of the genus Nepovirus (subfamily Comovirinae, family Secoviridae, order Picornavirales) are bipartite positive-strand RNA viruses with each genomic RNA encoding a single large polyprotein. The RNA1-encoded 3C-like protease cleaves the RNA1 polyprotein at five sites and the RNA2 polyprotein at two or three sites, depending on the nepovirus. The specificity of nepovirus 3C-like proteases is notoriously diverse, making the prediction of cleavage sites difficult. In this study, the position of nepovirus cleavage sites was systematically re-evaluated using alignments of the RNA1 and RNA2 polyproteins, phylogenetic relationships of the proteases, and sequence logos to examine specific preferences for the P6 to P1' positions of the cleavage sites. Based on these analyses, the positions of previously elusive cleavage sites, notably the 2a-MP cleavage sites of subgroup B nepoviruses, are now proposed. Distinct nepovirus protease clades were identified, each with different cleavage site specificities, mostly determined by the nature of the amino acid at the P1 and P1' positions of the cleavage sites, as well as the P2 and P4 positions. The results will assist the prediction of cleavage sites for new nepoviruses and help refine the taxonomy of nepoviruses. An improved understanding of the specificity of nepovirus 3C-like proteases can also be used to investigate the cleavage of plant proteins by nepovirus proteases and to understand their adaptation to a broad range of hosts.
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Affiliation(s)
- Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, V0H1Z0, Summerland, BC, Canada.
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Osterbaan LJ, Hoyle V, Curtis M, DeBlasio S, Rivera KD, Heck M, Fuchs M. Identification of protein interactions of grapevine fanleaf virus RNA-dependent RNA polymerase during infection of Nicotiana benthamiana by affinity purification and tandem mass spectrometry. J Gen Virol 2021; 102:001607. [PMID: 34043500 PMCID: PMC8295916 DOI: 10.1099/jgv.0.001607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/07/2021] [Indexed: 11/24/2022] Open
Abstract
The RNA-dependent RNA polymerase (1EPol) is involved in replication of grapevine fanleaf virus (GFLV, Nepovirus, Secoviridae) and causes vein clearing symptoms in Nicotiana benthamiana. Information on protein 1EPol interaction with other viral and host proteins is scarce. To study protein 1EPol biology, three GFLV infectious clones, i.e. GHu (a symptomatic wild-type strain), GHu-1EK802G (an asymptomatic GHu mutant) and F13 (an asymptomatic wild-type strain), were engineered with protein 1EPol fused to a V5 epitope tag at the C-terminus. Following Agrobacterium tumefaciens-mediated delivery of GFLV clones in N. benthamiana and protein extraction at seven dpi, when optimal 1EPol:V5 accumulation was detected, two viral and six plant putative interaction partners of V5-tagged protein 1EPol were identified for the three GFLV clones by affinity purification and tandem mass spectrometry. This study provides insights into the protein interactome of 1EPol during GFLV systemic infection in N. benthamiana and lays the foundation for validation work.
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Affiliation(s)
- Larissa J. Osterbaan
- Cornell University, Plant Pathology and Plant Microbe-Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Geneva, NY 14456, USA
- Present address: Department of Biology, Utica College, Utica, NY 13502, USA
| | - Victoria Hoyle
- Cornell University, Plant Pathology and Plant Microbe-Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Geneva, NY 14456, USA
| | - Michelle Curtis
- Cornell University, Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Ithaca, NY 14853, USA
| | - Stacy DeBlasio
- Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Keith D. Rivera
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Present address: The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Michelle Heck
- Cornell University, Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Ithaca, NY 14853, USA
- Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Marc Fuchs
- Cornell University, Plant Pathology and Plant Microbe-Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Geneva, NY 14456, USA
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Fuchs M, Schmitt-Keichinger C, Sanfaçon H. A Renaissance in Nepovirus Research Provides New Insights Into Their Molecular Interface With Hosts and Vectors. Adv Virus Res 2016; 97:61-105. [PMID: 28057260 DOI: 10.1016/bs.aivir.2016.08.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nepoviruses supplied seminal landmarks to the historical trail of plant virology. Among the first agriculturally relevant viruses recognized in the late 1920s and among the first plant viruses officially classified in the early 1970s, nepoviruses also comprise the first species for which a soil-borne ectoparasitic nematode vector was identified. Early research on nepoviruses shed light on the genome structure and expression, biological properties of the two genomic RNAs, and mode of transmission. In recent years, research on nepoviruses enjoyed an extraordinary renaissance. This resurgence provided new insights into the molecular interface between viruses and their plant hosts, and between viruses and dagger nematode vectors to advance our understanding of some of the major steps of the infectious cycle. Here we examine these recent findings, highlight ongoing work, and offer some perspectives for future research.
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Affiliation(s)
- M Fuchs
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, United States.
| | - C Schmitt-Keichinger
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
| | - H Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada
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Characterization of a Non-Canonical Signal Peptidase Cleavage Site in a Replication Protein from Tomato Ringspot Virus. PLoS One 2016; 11:e0162223. [PMID: 27589230 PMCID: PMC5010249 DOI: 10.1371/journal.pone.0162223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/18/2016] [Indexed: 11/19/2022] Open
Abstract
The NTB-VPg polyprotein from tomato ringspot virus is an integral membrane replication protein associated with endoplasmic reticulum membranes. A signal peptidase (SPase) cleavage was previously detected in the C-terminal region of NTB-VPg downstream of a 14 amino acid (aa)-long hydrophobic region (termed TM2). However, the exact location of the cleavage site was not determined. Using in vitro translation assays, we show that the SPase cleavage site is conserved in the NTB-VPg protein from various ToRSV isolates, although the rate of cleavage varies from one isolate to another. Systematic site-directed mutagenesis of the NTB-VPg SPase cleavage sites of two ToRSV isolates allowed the identification of sequences that affect cleavage efficiency. We also present evidence that SPase cleavage in the ToRSV-Rasp2 isolate occurs within a GAAGG sequence likely after the AAG (GAAG/G). Mutation of a downstream MAAV sequence to AAAV resulted in SPase cleavage at both the natural GAAG/G and the mutated AAA/V sequences. Given that there is a distance of seven aa between the two cleavage sites, this indicates that there is flexibility in the positioning of the cleavage sites relative to the inner surface of the membrane and the SPase active site. SPase cleavage sites are typically located 3–7 aa downstream of the hydrophobic region. However, the NTB-VPg GAAG/G cleavage site is located 17 aa downstream of the TM2 hydrophobic region, highlighting unusual features of the NTB-VPg SPase cleavage site. A putative 11 aa-long amphipathic helix was identified immediately downstream of the TM2 region and five aa upstream of the GAAG/G cleavage site. Based on these results, we present an updated topology model in which the hydrophobic and amphipathic domains form a long tilted helix or a bent helix in the membrane lipid bilayer, with the downstream cleavage site(s) oriented parallel to the membrane inner surface.
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Symptom recovery in virus-infected plants: Revisiting the role of RNA silencing mechanisms. Virology 2015; 479-480:167-79. [DOI: 10.1016/j.virol.2015.01.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/02/2015] [Accepted: 01/08/2015] [Indexed: 01/11/2023]
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Vigne E, Gottula J, Schmitt-Keichinger C, Komar V, Ackerer L, Belval L, Rakotomalala L, Lemaire O, Ritzenthaler C, Fuchs M. A strain-specific segment of the RNA-dependent RNA polymerase of grapevine fanleaf virus determines symptoms in Nicotiana species. J Gen Virol 2013; 94:2803-2813. [PMID: 24088345 DOI: 10.1099/vir.0.057646-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Factors involved in symptom expression of viruses from the genus Nepovirus in the family Secoviridae such as grapevine fanleaf virus (GFLV) are poorly characterized. To identify symptom determinants encoded by GFLV, infectious cDNA clones of RNA1 and RNA2 of strain GHu were developed and used alongside existing infectious cDNA clones of strain F13 in a reverse genetics approach. In vitro transcripts of homologous combinations of RNA1 and RNA2 induced systemic infection in Nicotiana benthamiana and Nicotiana clevelandii with identical phenotypes to WT virus strains, i.e. vein clearing and chlorotic spots on N. benthamiana and N. clevelandii for GHu, respectively, and lack of symptoms on both hosts for F13. The use of assorted transcripts mapped symptom determinants on RNA1 of GFLV strain GHu, in particular within the distal 408 nt of the RNA-dependent RNA polymerase (1E(Pol)), as shown by RNA1 transcripts for which coding regions or fragments derived thereof were swapped. Semi-quantitative analyses indicated no significant differences in virus titre between symptomatic and asymptomatic plants infected with various recombinants. Also, unlike the nepovirus tomato ringspot virus, no apparent proteolytic cleavage of GFLV protein 1E(Pol) was detected upon virus infection or transient expression in N. benthamiana. In addition, GFLV protein 1E(Pol) failed to suppress silencing of EGFP in transgenic N. benthamiana expressing EGFP or to enhance GFP expression in patch assays in WT N. benthamiana. Together, our results suggest the existence of strain-specific functional domains, including a symptom determinant module, on the RNA-dependent RNA polymerase of GFLV.
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Affiliation(s)
- Emmanuelle Vigne
- Université de Strasbourg, UMR 1131 'Santé de la Vigne et Qualité du Vin', 68021 Colmar, France
- INRA, UMR 1131 'Santé de la Vigne et Qualité du Vin', 68021 Colmar, France
| | - John Gottula
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, USA
| | - Corinne Schmitt-Keichinger
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Véronique Komar
- Université de Strasbourg, UMR 1131 'Santé de la Vigne et Qualité du Vin', 68021 Colmar, France
- INRA, UMR 1131 'Santé de la Vigne et Qualité du Vin', 68021 Colmar, France
| | - Léa Ackerer
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Lorène Belval
- Université de Strasbourg, UMR 1131 'Santé de la Vigne et Qualité du Vin', 68021 Colmar, France
- INRA, UMR 1131 'Santé de la Vigne et Qualité du Vin', 68021 Colmar, France
| | - Lalaina Rakotomalala
- Université de Strasbourg, UMR 1131 'Santé de la Vigne et Qualité du Vin', 68021 Colmar, France
- INRA, UMR 1131 'Santé de la Vigne et Qualité du Vin', 68021 Colmar, France
| | - Olivier Lemaire
- Université de Strasbourg, UMR 1131 'Santé de la Vigne et Qualité du Vin', 68021 Colmar, France
- INRA, UMR 1131 'Santé de la Vigne et Qualité du Vin', 68021 Colmar, France
| | - Christophe Ritzenthaler
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Marc Fuchs
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, USA
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Jiang J, Laliberté JF. The genome-linked protein VPg of plant viruses-a protein with many partners. Curr Opin Virol 2011; 1:347-54. [PMID: 22440836 DOI: 10.1016/j.coviro.2011.09.010] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 09/23/2011] [Accepted: 09/26/2011] [Indexed: 12/19/2022]
Abstract
For some plant positive-sense RNA viruses, a protein known as VPg (short for virus protein, genome linked) is covalently linked to the 5' end of the viral RNA. The VPg is an intrinsically disordered protein, and this property would confer an ability to bind several proteins. Accordingly, the potyvirus VPg interacts with many proteins, notably host factors involved in protein synthesis within viral replication factories or within the nucleus. The number of protein partners, the clustering of the various interactions centering around it, the biological importance for some of these interactions (e.g. VPg-eIF4E) and the intrinsically disordered state of the protein are all elements that support the notion that VPg is a hub protein that controls many processes leading to virus production and spread.
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Affiliation(s)
- Jun Jiang
- Institut National de la Recherche Scientifique, Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, Canada H7V 1B7
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Wetzel T, Chisholm J, Bassler A, Sanfaçon H. Characterization of proteinase cleavage sites in the N-terminal region of the RNA1-encoded polyprotein from Arabis mosaic virus (subgroup A nepovirus). Virology 2008; 375:159-69. [DOI: 10.1016/j.virol.2008.01.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 12/20/2007] [Accepted: 01/30/2008] [Indexed: 11/25/2022]
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