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Khalili M, Candresse T, Faure C, Brans Y, Marais A. Complete genome sequences of three Prunus-infecting nepoviruses: apricot latent ringspot virus, myrobalan latent ringspot virus, and a novel virus from smooth stone peach (Prunus mira Koehne). Arch Virol 2024; 169:168. [PMID: 39020218 DOI: 10.1007/s00705-024-06091-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/05/2024] [Indexed: 07/19/2024]
Abstract
The complete genome sequences of two poorly studied Prunus-infecting nepoviruses, apricot latent ringspot virus (ALRSV) and myrobalan latent ringspot virus (MLRSV) were determined, confirming that they are members of subgroup C. Serological, biological, and molecular data, in particular a low level (58.8%) of amino acid sequence identity in the coat protein, suggest that ALRSV and MLRSV should be considered taxonomically distinct. In addition, data mining of public RNASeq data from wild and ornamental Prunus identified two contigs representing the nearly complete genome of a new subgroup A nepovirus from a smooth stone peach (Prunus mira) dataset (SRR8369794) from the Himalayas, for which the name "Prunus mira virus A" is proposed.
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Affiliation(s)
- M Khalili
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
- INRAE, ISVV, Univ. Bordeaux, UMR EGFV, 33140, Villenave d'Ornon Cedex, France
| | - T Candresse
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - C Faure
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France
| | - Y Brans
- Laboratoire de Virologie et de Biologie Moléculaire, CTIFL, 24130, Prigonrieux, France
| | - A Marais
- INRAE, Univ. Bordeaux, UMR BFP, 33140, Villenave d'Ornon, France.
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2
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Sidharthan VK, Reddy V, Kiran G, Rajeswari V, Baranwal VK, Kumar MK, Kumar KS. Probing of plant transcriptomes reveals the hidden genetic diversity of the family Secoviridae. Arch Virol 2024; 169:150. [PMID: 38898334 DOI: 10.1007/s00705-024-06076-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 05/07/2024] [Indexed: 06/21/2024]
Abstract
Secoviruses are single-stranded RNA viruses that infect plants. In the present study, we identified 61 putative novel secoviral genomes in various plant species by mining publicly available plant transcriptome data. These viral sequences represent the genomes of 13 monopartite and 48 bipartite secovirids. The genome sequences of 52 secovirids were coding-complete, and nine were partial. Except for small open reading frames (ORFs) determined in waikaviral genomes and RNA2 of torradoviruses, all of the recovered genomes/genome segments contained a large ORF encoding a polyprotein. Based on genome organization and phylogeny, all but three of the novel secoviruses were assigned to different genera. The genome organization of two identified waika-like viruses resembled that of the recently identified waika-like virus Triticum aestivum secovirus. Phylogenetic analysis revealed a pattern of host-virus co-evolution in a few waika- and waika-like viruses and increased phylogenetic diversity of nepoviruses. The study provides a basis for further investigation of the biological properties of these novel secoviruses.
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Affiliation(s)
- V Kavi Sidharthan
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India.
| | - Vijayprakash Reddy
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India
| | - G Kiran
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India
| | - V Rajeswari
- School of Agricultural Sciences, Malla Reddy University, Hyderabad, India
| | - V K Baranwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - M Kiran Kumar
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India
| | - K Sudheer Kumar
- Division of Genetics and Tree Improvement, ICFRE-Institute of Forest Biodiversity, Hyderabad, India
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3
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Sanfaçon H, Skern T. AlphaFold modeling of nepovirus 3C-like proteinases provides new insights into their diverse substrate specificities. Virology 2024; 590:109956. [PMID: 38052140 DOI: 10.1016/j.virol.2023.109956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/10/2023] [Accepted: 11/24/2023] [Indexed: 12/07/2023]
Abstract
The majority of picornaviral 3C proteinases (3Cpro) cleavage sites possess glutamine at the P1 position. Plant nepovirus 3C-like proteinases (3CLpro) show however much broader specificity, cleaving not only after glutamine, but also after several basic and hydrophobic residues. To investigate this difference, we employed AlphaFold to generate structural models of twelve selected 3CLpro, representing six substrate specificities. Generally, we observed favorable correlations between the architecture and charge of nepovirus proteinase S1 subsites and their ability to accept or restrict larger residues. The models identified a conserved aspartate residue close to the P1 residue in the S1 subsites of all nepovirus proteinases examined, consistent with the observed strong bias against negatively-charged residues at the P1 position of nepovirus cleavage sites. Finally, a cramped S4 subsite along with the presence of two unique histidine and serine residues explains the strict requirement of the grapevine fanleaf virus proteinase for serine at the P4 position.
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Affiliation(s)
- Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, V0H 1Z0, Summerland, BC, Canada.
| | - Tim Skern
- Department of Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, A-1030, Vienna, Austria.
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Roy BG, Choi J, Fuchs MF. Predictive Modeling of Proteins Encoded by a Plant Virus Sheds a New Light on Their Structure and Inherent Multifunctionality. Biomolecules 2024; 14:62. [PMID: 38254661 PMCID: PMC10813169 DOI: 10.3390/biom14010062] [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: 11/29/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Plant virus genomes encode proteins that are involved in replication, encapsidation, cell-to-cell, and long-distance movement, avoidance of host detection, counter-defense, and transmission from host to host, among other functions. Even though the multifunctionality of plant viral proteins is well documented, contemporary functional repertoires of individual proteins are incomplete. However, these can be enhanced by modeling tools. Here, predictive modeling of proteins encoded by the two genomic RNAs, i.e., RNA1 and RNA2, of grapevine fanleaf virus (GFLV) and their satellite RNAs by a suite of protein prediction software confirmed not only previously validated functions (suppressor of RNA silencing [VSR], viral genome-linked protein [VPg], protease [Pro], symptom determinant [Sd], homing protein [HP], movement protein [MP], coat protein [CP], and transmission determinant [Td]) and previously identified putative functions (helicase [Hel] and RNA-dependent RNA polymerase [Pol]), but also predicted novel functions with varying levels of confidence. These include a T3/T7-like RNA polymerase domain for protein 1AVSR, a short-chain reductase for protein 1BHel/VSR, a parathyroid hormone family domain for protein 1EPol/Sd, overlapping domains of unknown function and an ABC transporter domain for protein 2BMP, and DNA topoisomerase domains, transcription factor FBXO25 domain, or DNA Pol subunit cdc27 domain for the satellite RNA protein. Structural predictions for proteins 2AHP/Sd, 2BMP, and 3A? had low confidence, while predictions for proteins 1AVSR, 1BHel*/VSR, 1CVPg, 1DPro, 1EPol*/Sd, and 2CCP/Td retained higher confidence in at least one prediction. This research provided new insights into the structure and functions of GFLV proteins and their satellite protein. Future work is needed to validate these findings.
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Affiliation(s)
- Brandon G. Roy
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 15 Castle Creek Drive, Geneva, NY 14456, USA; (J.C.); (M.F.F.)
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Elbeaino T, Ben Slimen A, Belgacem I, Mnari-Hattab M, Spanò R, Digiaro M, Abdelkhalek A. Identification, Sequencing, and Molecular Analysis of RNA2 of Artichoke Italian Latent Virus Isolates from Known Hosts and a New Host Plant Species. Viruses 2023; 15:2170. [PMID: 38005847 PMCID: PMC10675341 DOI: 10.3390/v15112170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Despite its first description in 1977 and numerous reports of its presence in various plant species in many countries, the molecular information available in GenBank for artichoke Italian latent virus (AILV) is still limited to a single complete genome sequence (RNA1 and 2) of a grapevine isolate (AILV-V) and a partial portion of the RNA2 sequence from an isolate of unknown origin and host. Here, we report the results of molecular analyses conducted on the RNA2 of some AILV isolates, sequenced for the first time in this study, together with the first-time identification of AILV in a new host plant species, namely chard (Beta vulgaris subsp. vulgaris), associated with vein clearing and mottling symptoms on leaves. The different AILV isolates sequenced were from artichoke (AILV-C), gladiolus (AILV-G), Sonchus (AILV-S), and chard (AILV-B). At the molecular level, the sequencing results of the RNA2 segments showed that AILV-C, AILV-G, AILV-S, and AILV-B had a length of 4629 nt (excluding the 3' terminal polyA tail), which is one nt shorter than that of the AILV-V reported in GenBank. A comparison of the RNA2 coding region sequences of all the isolates showed that AILV-V was the most divergent isolate, with the lowest sequence identities of 83.2% at the nucleotide level and 84.7% at the amino acid level. Putative intra-species sequence recombination sites were predicted among the AILV isolates, mainly involving the genomes of AILV-V, AILV-C, and AILV-B. This study adds insights into the variability of AILV and the occurrence of recombination that may condition plant infection.
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Affiliation(s)
- Toufic Elbeaino
- Istituto Agronomico Mediterraneo of Bari, Via Ceglie 9, 70010 Valenzano, Italy; (A.B.S.); (I.B.); (M.D.)
| | - Amani Ben Slimen
- Istituto Agronomico Mediterraneo of Bari, Via Ceglie 9, 70010 Valenzano, Italy; (A.B.S.); (I.B.); (M.D.)
| | - Imen Belgacem
- Istituto Agronomico Mediterraneo of Bari, Via Ceglie 9, 70010 Valenzano, Italy; (A.B.S.); (I.B.); (M.D.)
| | - Monia Mnari-Hattab
- Laboratoire de Biotechnologie Appliquée à l’Agriculture, INRA Tunisie, Université de Carthage, Rue Hedi Karray, Tunis 1004, Tunisia
| | - Roberta Spanò
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari, Via G. Amendola, 165/A, 70126 Bari, Italy;
| | - Michele Digiaro
- Istituto Agronomico Mediterraneo of Bari, Via Ceglie 9, 70010 Valenzano, Italy; (A.B.S.); (I.B.); (M.D.)
| | - Ahmed Abdelkhalek
- Plant Protection and Biomolecular Diagnosis Department, ALCRI, City of Scientific Research and Technological Applications, New Borg El Arab City 21934, Egypt;
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Choi J, Pakbaz S, Yepes LM, Cieniewicz EJ, Schmitt-Keichinger C, Labarile R, Minutillo SA, Heck M, Hua J, Fuchs M. Grapevine Fanleaf Virus RNA1-Encoded Proteins 1A and 1B Hel Suppress RNA Silencing. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:558-571. [PMID: 36998121 DOI: 10.1094/mpmi-01-23-0008-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Grapevine fanleaf virus (GFLV) (genus Nepovirus, family Secoviridae) causes fanleaf degeneration, one of the most damaging viral diseases of grapevines. Despite substantial advances at deciphering GFLV-host interactions, how this virus overcomes the host antiviral pathways of RNA silencing is poorly understood. In this study, we identified viral suppressors of RNA silencing (VSRs) encoded by GFLV, using fluorescence assays, and tested their capacity at modifying host gene expression in transgenic Nicotiana benthamiana expressing the enhanced green fluorescent protein gene (EGFP). Results revealed that GFLV RNA1-encoded protein 1A, for which a function had yet to be assigned, and protein 1BHel, a putative helicase, reverse systemic RNA silencing either individually or as a fused form (1ABHel) predicted as an intermediary product of RNA1 polyprotein proteolytic processing. The GFLV VSRs differentially altered the expression of plant host genes involved in RNA silencing, as shown by reverse transcription-quantitative PCR. In a co-infiltration assay with an EGFP hairpin construct, protein 1A upregulated NbDCL2, NbDCL4, and NbRDR6, and proteins 1BHel and 1A+1BHel upregulated NbDCL2, NbDCL4, NbAGO1, NbAGO2, and NbRDR6, while protein 1ABHel upregulated NbAGO1 and NbRDR6. In a reversal of systemic silencing assay, protein 1A upregulated NbDCL2 and NbAGO2 and protein 1ABHel upregulated NbDCL2, NbDCL4, and NbAGO1. This is the first report of VSRs encoded by a nepovirus RNA1 and of two VSRs that act either individually or as a predicted fused form to counteract the systemic antiviral host defense, suggesting that GFLV might devise a unique counterdefense strategy to interfere with various steps of the plant antiviral RNA silencing pathways during infection. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jiyeong Choi
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Samira Pakbaz
- Plant Pathology Department, Faculty of Agriculture and Natural Resources, Lorestan University, Khorramabad, Iran
| | - Luz Marcela Yepes
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
| | - Elizabeth Jeannette Cieniewicz
- Deparment of Plant and Environmental Sciences, College of Agriculture, Forestry, and Life Sciences, Clemson University, Clemson, SC 29634, U.S.A
| | - Corinne Schmitt-Keichinger
- CNRS, IBMP UPR 2357, Université de Strasbourg, 67000 Strasbourg, France
- INRAE, SVQV UMR 1131, Université de Strasbourg, 68000 Colmar, France
| | - Rossella Labarile
- National Research Council (CNR), Institute of Chemical-Physical Processes, Via Amendola 165/A, 70126 Bari, Italy
| | - Serena Anna Minutillo
- International Center for Advanced Mediterranean Agronomic Studies - Institute of Bari (CIHEAM-Bari), 70010 Valenzano, Italy
| | - Michelle Heck
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
- Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, U.S.A
| | - Jian Hua
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Marc Fuchs
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY 14456, U.S.A
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Joly AC, Garcia S, Hily JM, Koechler S, Demangeat G, Garcia D, Vigne E, Lemaire O, Zuber H, Gagliardi D. An extensive survey of phytoviral RNA 3' uridylation identifies extreme variations and virus-specific patterns. PLANT PHYSIOLOGY 2023; 193:271-290. [PMID: 37177985 PMCID: PMC10469402 DOI: 10.1093/plphys/kiad278] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/30/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023]
Abstract
Viral RNAs can be uridylated in eukaryotic hosts. However, our knowledge of uridylation patterns and roles remains rudimentary for phytoviruses. Here, we report global 3' terminal RNA uridylation profiles for representatives of the main families of positive single-stranded RNA phytoviruses. We detected uridylation in all 47 viral RNAs investigated here, revealing its prevalence. Yet, uridylation levels of viral RNAs varied from 0.2% to 90%. Unexpectedly, most poly(A) tails of grapevine fanleaf virus (GFLV) RNAs, including encapsidated tails, were strictly monouridylated, which corresponds to an unidentified type of viral genomic RNA extremity. This monouridylation appears beneficial for GFLV because it became dominant when plants were infected with nonuridylated GFLV transcripts. We found that GFLV RNA monouridylation is independent of the known terminal uridylyltransferases (TUTases) HEN1 SUPPRESSOR 1 (HESO1) and UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) in Arabidopsis (Arabidopsis thaliana). By contrast, both TUTases can uridylate other viral RNAs like turnip crinkle virus (TCV) and turnip mosaic virus (TuMV) RNAs. Interestingly, TCV and TuMV degradation intermediates were differentially uridylated by HESO1 and URT1. Although the lack of both TUTases did not prevent viral infection, we detected degradation intermediates of TCV RNA at higher levels in an Arabidopsis heso1 urt1 mutant, suggesting that uridylation participates in clearing viral RNA. Collectively, our work unveils an extreme diversity of uridylation patterns across phytoviruses and constitutes a valuable resource to further decipher pro- and antiviral roles of uridylation.
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Affiliation(s)
- Anne Caroline Joly
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67084, France
| | - Shahinez Garcia
- UMR Santé de la Vigne et Qualité du Vin, INRAE, Université de Strasbourg, Colmar 68000, France
| | - Jean-Michel Hily
- UMR Santé de la Vigne et Qualité du Vin, INRAE, Université de Strasbourg, Colmar 68000, France
- Institut Français de la Vigne et du Vin, Le Grau-Du-Roi 30240, France
| | - Sandrine Koechler
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67084, France
| | - Gérard Demangeat
- UMR Santé de la Vigne et Qualité du Vin, INRAE, Université de Strasbourg, Colmar 68000, France
| | - Damien Garcia
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67084, France
| | - Emmanuelle Vigne
- UMR Santé de la Vigne et Qualité du Vin, INRAE, Université de Strasbourg, Colmar 68000, France
| | - Olivier Lemaire
- UMR Santé de la Vigne et Qualité du Vin, INRAE, Université de Strasbourg, Colmar 68000, France
| | - Hélène Zuber
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67084, France
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg 67084, France
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Fuchs M, Hily JM, Petrzik K, Sanfaçon H, Thompson JR, van der Vlugt R, Wetzel T, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Secoviridae 2022. J Gen Virol 2022; 103. [PMID: 36748634 DOI: 10.1099/jgv.0.001807] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Members of the family Secoviridae are non-enveloped plant viruses with mono- or bipartite linear positive-sense ssRNA genomes with a combined genome of 9 to 13.7 kb and icosahedral particles 25-30 nm in diameter. They are related to picornaviruses and are members of the order Picornavirales. Genera in the family are distinguished by the host range, vector, genomic features and phylogeny of the member viruses. Most members infect dicotyledonous plants, and many cause serious disease epidemics. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) report on the family Secoviridae, which is available at ictv.global/report/secoviridae.
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Affiliation(s)
- Marc Fuchs
- School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Jean-Michel Hily
- Institut Français de la Vigne et du Vin, 30240 Le Grau du Roi, France
| | - Karel Petrzik
- Institute of Plant Molecular Biology, 370 05 České Budějovice, Czech Republic
| | | | | | | | - Thierry Wetzel
- DLR Rheinpfalz, Neustadt an der Weinstrasse 67435, Germany
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