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Mostert I, Bester R, Burger JT, Maree HJ. Investigating Protein-Protein Interactions Between Grapevine Leafroll-Associated Virus 3 and Vitis vinifera. PHYTOPATHOLOGY 2023; 113:1994-2005. [PMID: 37311734 DOI: 10.1094/phyto-03-23-0107-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Grapevine leafroll disease (GLD) is a globally important disease that affects the metabolic composition and biomass of grapes, leading to a reduction in grape yield and quality of wine produced. Grapevine leafroll-associated virus 3 (GLRaV-3) is the main causal agent for GLD. This study aimed to identify protein-protein interactions between GLRaV-3 and its host. A yeast two-hybrid (Y2H) library was constructed from Vitis vinifera mRNA and screened against GLRaV-3 open reading frames encoding structural proteins and those potentially involved in systemic spread and silencing of host defense mechanisms. Five interacting protein pairs were identified, three of which were demonstrated in planta. The minor coat protein of GLRaV-3 was shown to interact with 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 02, a protein involved in primary carbohydrate metabolism and the biosynthesis of aromatic amino acids. Interactions were also identified between GLRaV-3 p20A and an 18.1-kDa class I small heat shock protein, as well as MAP3K epsilon protein kinase 1. Both proteins are involved in the response of plants to various stressors, including pathogen infections. Two additional proteins, chlorophyll a-b binding protein CP26 and a SMAX1-LIKE 6 protein, were identified as interacting with p20A in yeast but these interactions could not be demonstrated in planta. The findings of this study advance our understanding of the functions of GLRaV-3-encoded proteins and how the interaction between these proteins and those of V. vinifera could lead to GLD.
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Affiliation(s)
- Ilani Mostert
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Rachelle Bester
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
- Citrus Research International, Stellenbosch 7600, South Africa
| | - Johan T Burger
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Hans J Maree
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
- Citrus Research International, Stellenbosch 7600, South Africa
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Kondo H, Sugahara H, Fujita M, Hyodo K, Andika IB, Hisano H, Suzuki N. Discovery and Genome Characterization of a Closterovirus from Wheat Plants with Yellowing Leaf Symptoms in Japan. Pathogens 2023; 12:pathogens12030358. [PMID: 36986280 PMCID: PMC10053543 DOI: 10.3390/pathogens12030358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
Many aphid-borne viruses are important pathogens that affect wheat crops worldwide. An aphid-transmitted closterovirus named wheat yellow leaf virus (WYLV) was found to have infected wheat plants in Japan in the 1970s; however, since then, its viral genome sequence and occurrence in the field have not been investigated. We observed yellowing leaves in the 2018/2019 winter wheat-growing season in an experimental field in Japan where WYLV was detected five decades ago. A virome analysis of those yellow leaf samples lead to the discovery of a closterovirus together with a luteovirus (barley yellow dwarf virus PAV variant IIIa). The complete genomic sequence of this closterovirus, named wheat closterovirus 1 isolate WL19a (WhCV1-WL19a), consisted of 15,452 nucleotides harboring nine open reading frames. Additionally, we identified another WhCV1 isolate, WL20, in a wheat sample from the winter wheat-growing season of 2019/2020. A transmission test indicated that WhCV1-WL20 was able to form typical filamentous particles and transmissible by oat bird-cherry aphid (Rhopalosiphum pad). Sequence and phylogenetic analyses showed that WhCV1 was distantly related to members of the genus Closterovirus (family Closteroviridae), suggesting that the virus represents a novel species in the genus. Furthermore, the characterization of WhCV1-WL19a-derived small RNAs using high-throughput sequencing revealed highly abundant 22-nt-class small RNAs potentially derived from the 3′-terminal end of the WhCV1 negative-strand genomic RNA, indicating that this terminal end of the WhCV1 genome is likely particularly targeted for the synthesis of viral small RNAs in wheat plants. Our results provide further knowledge on closterovirus diversity and pathogenicity and suggest that the impact of WhCV1 on wheat production warrants further investigations.
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Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
- Correspondence: ; Tel./Fax: +81-(86)-434-1232
| | - Hitomi Sugahara
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Miki Fujita
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Kiwamu Hyodo
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Hiroshi Hisano
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources (IPSR), Okayama University, Kurashiki 710-0046, Japan
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Agranovsky AA. Structure and Expression of Large (+)RNA Genomes of Viruses of Higher Eukaryotes. BIOCHEMISTRY (MOSCOW) 2021; 86:248-261. [PMID: 33838627 PMCID: PMC7772802 DOI: 10.1134/s0006297921030020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Viral positive-sense RNA genomes evolve rapidly due to the high mutation rates during replication and RNA recombination, which allowing the viruses to acquire and modify genes for their adaptation. The size of RNA genome is limited by several factors, including low fidelity of RNA polymerases and packaging constraints. However, the 12-kb size limit is exceeded in the two groups of eukaryotic (+)RNA viruses – animal nidoviruses and plant closteroviruses. These virus groups have several traits in common. Their genomes contain 5′-proximal genes that are expressed via ribosomal frameshifting and encode one or two papain-like protease domains, membrane-binding domain(s), methyltransferase, RNA helicase, and RNA polymerase. In addition, some nidoviruses (i.e., coronaviruses) contain replication-associated domains, such as proofreading exonuclease, putative primase, nucleotidyltransferase, and endonuclease. In both nidoviruses and closteroviruses, the 3′-terminal part of the genome contains genes for structural and accessory proteins expressed via a nested set of coterminal subgenomic RNAs. Coronaviruses and closteroviruses have evolved to form flexuous helically symmetrical nucleocapsids as a mean to resolve packaging constraints. Since phylogenetic reconstructions of the RNA polymerase domains indicate only a marginal relationship between the nidoviruses and closteroviruses, their similar properties likely have evolved convergently, along with the increase in the genome size.
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Affiliation(s)
- Alexey A Agranovsky
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
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Fuchs M, Bar-Joseph M, Candresse T, Maree HJ, Martelli GP, Melzer MJ, Menzel W, Minafra A, Sabanadzovic S, Report Consortium ICTV. ICTV Virus Taxonomy Profile: Closteroviridae. J Gen Virol 2020; 101:364-365. [PMID: 32134375 PMCID: PMC7414439 DOI: 10.1099/jgv.0.001397] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 01/30/2020] [Indexed: 01/18/2023] Open
Abstract
Viruses in the family Closteroviridae have a mono-, bi- or tripartite positive-sense RNA genome of 13-19 kb, and non-enveloped, filamentous particles 650-2200 nm long and 12 nm in diameter. They infect plants, mainly dicots, many of which are fruit crops. This is a summary of the ICTV Report on the family Closteroviridae, which is available at ictv.global/report/closteroviridae.
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Affiliation(s)
- Marc Fuchs
- School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | | | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, 33882 Bordeaux, France
| | - Hans J. Maree
- Department of Genetics, Stellenbosh University and Citrus Research International, Stellenbosh, Western Cape, South Africa
| | - Giovanni P. Martelli
- Department of Soil, Plant and Food Sciences, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Michael J. Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawai’i at Manoa, Honolulu, HI 96822, USA
| | - Wulf Menzel
- Leibniz-Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Angelantonio Minafra
- Department of Soil, Plant and Food Sciences, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, MS 39762, USA
| | - ICTV Report Consortium
- School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
- The S. Tolkowsky Laboratory, Bet Dagan 50250, Israel
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, 33882 Bordeaux, France
- Department of Genetics, Stellenbosh University and Citrus Research International, Stellenbosh, Western Cape, South Africa
- Department of Soil, Plant and Food Sciences, Università degli Studi di Bari Aldo Moro, Bari, Italy
- Department of Plant and Environmental Protection Sciences, University of Hawai’i at Manoa, Honolulu, HI 96822, USA
- Leibniz-Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, MS 39762, USA
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Rogozin IB, Agranovsky AA. Nonstructural p26 proteins encoded by the 3'-proximal genes of velariviruses and criniviruses are orthologs. Arch Virol 2020; 165:439-443. [PMID: 31828509 PMCID: PMC6994434 DOI: 10.1007/s00705-019-04491-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/05/2019] [Indexed: 11/28/2022]
Abstract
The 3'-most genes in RNA-2 of the Crinivirus genus members (family Closteroviridae) code for non-structural p26 proteins that share amino acid sequence similarity [Stewart LR, Hwang MS, Falk BW (2009) Virus Res 145:293-299]. In this study, sensitive bioinformatic tools have been used to identify the homologous p26 proteins encoded by the 3' genes in monopartite genomes of the members of Velarivirus, another Closteroviridae genus, and mint vein banding-associated virus, an unassigned member of the family. The p26 proteins showed similarity in their predicted secondary structures, but an amino acid sequence alignment showed no strictly conserved positions, thus indicating a high plasticity of these non-structural proteins. The implications of the sequence analysis for possible functions of the crinivirus and velarivirus p26 proteins are discussed.
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Affiliation(s)
- I B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA
| | - A A Agranovsky
- Faculty of Biology, Moscow State University, Moscow, 119991, Russia.
- Center of Bioengineering, Russian Academy of Sciences, Moscow, Russia.
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Kwon SJ, Jin M, Cho IS, Yoon JY, Choi GS. Identification of rehmannia virus 1, a novel putative member of the genus Closterovirus, from Rehmannia glutinosa. Arch Virol 2018; 163:3383-3388. [PMID: 30191375 DOI: 10.1007/s00705-018-4014-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/10/2018] [Indexed: 11/26/2022]
Abstract
Transcriptome sequencing analysis of a symptomatic Rehmannia glutinosa plant revealed a virome containing two known RNA viruses and one novel virus. In this study, we examined the molecular and biological characteristics of the novel virus. The complete genome of the novel virus is composed of monopartite single-stranded RNA of 15,322 nucleotides with 69% nucleotide sequence identity (with 68% coverage) to tobacco virus 1. Its genome organization is typical of the members of the genus Closterovirus, containing nine putative open reading frames. Molecular and phylogenetic analyses of the genome and encoded protein sequences strongly support that the identified virus is a new species of the genus Closterovirus in the family Closteroviridae. The name rehmannia virus 1 (ReV1) is proposed for this novel virus.
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Affiliation(s)
- Sun-Jung Kwon
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
| | - Meilan Jin
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, 27709, Republic of Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Ju-Yeon Yoon
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Gug-Seoun Choi
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
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Koloniuk I, Thekke-Veetil T, Reynard JS, Mavrič Pleško I, Přibylová J, Brodard J, Kellenberger I, Sarkisova T, Špak J, Lamovšek J, Massart S, Ho T, Postman JD, Tzanetakis IE. Molecular Characterization of Divergent Closterovirus Isolates Infecting Ribes Species. Viruses 2018; 10:E369. [PMID: 30002359 PMCID: PMC6071065 DOI: 10.3390/v10070369] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/06/2018] [Accepted: 07/10/2018] [Indexed: 11/17/2022] Open
Abstract
Five isolates of a new member of the family Closteroviridae, tentatively named blackcurrant leafroll-associated virus 1 (BcLRaV-1), were identified in the currant. The 17-kb-long genome codes for 10 putative proteins. The replication-associated polyprotein has several functional domains, including papain-like proteases, methyltransferase, Zemlya, helicase, and RNA-dependent RNA polymerase. Additional open reading frames code for a small protein predicted to integrate into the host cell wall, a heat-shock protein 70 homolog, a heat-shock protein 90 homolog, two coat proteins, and three proteins of unknown functions. Phylogenetic analysis showed that BcLRaV-1 is related to members of the genus Closterovirus, whereas recombination analysis provided evidence of intraspecies recombination.
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Affiliation(s)
- Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Academy of Sciences of the Czech Republic, v.v.i., Branišovská 31, 370 05 České Budějovice, Czech Republic.
| | - Thanuja Thekke-Veetil
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
| | | | - Irena Mavrič Pleško
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia.
| | - Jaroslava Přibylová
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Academy of Sciences of the Czech Republic, v.v.i., Branišovská 31, 370 05 České Budějovice, Czech Republic.
| | - Justine Brodard
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland.
| | | | - Tatiana Sarkisova
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Academy of Sciences of the Czech Republic, v.v.i., Branišovská 31, 370 05 České Budějovice, Czech Republic.
| | - Josef Špak
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Academy of Sciences of the Czech Republic, v.v.i., Branišovská 31, 370 05 České Budějovice, Czech Republic.
| | - Janja Lamovšek
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia.
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés, 2, 5030 Gembloux, Belgium.
| | - Thien Ho
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
| | - Joseph D Postman
- National Clonal Germplasm Repository, United States Department of Agriculture, Corvallis, OR 97333, USA.
| | - Ioannis E Tzanetakis
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
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Qiao W, Medina V, Falk BW. Inspirations on Virus Replication and Cell-to-Cell Movement from Studies Examining the Cytopathology Induced by Lettuce infectious yellows virus in Plant Cells. FRONTIERS IN PLANT SCIENCE 2017; 8:1672. [PMID: 29021801 PMCID: PMC5623981 DOI: 10.3389/fpls.2017.01672] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 09/12/2017] [Indexed: 05/06/2023]
Abstract
Lettuce infectious yellows virus (LIYV) is the type member of the genus Crinivirus in the family Closteroviridae. Like many other positive-strand RNA viruses, LIYV infections induce a number of cytopathic changes in plant cells, of which the two most characteristic are: Beet yellows virus-type inclusion bodies composed of vesicles derived from cytoplasmic membranes; and conical plasmalemma deposits (PLDs) located at the plasmalemma over plasmodesmata pit fields. The former are not only found in various closterovirus infections, but similar structures are known as 'viral factories' or viroplasms in cells infected with diverse types of animal and plant viruses. These are generally sites of virus replication, virion assembly and in some cases are involved in cell-to-cell transport. By contrast, PLDs induced by the LIYV-encoded P26 non-virion protein are not involved in replication but are speculated to have roles in virus intercellular movement. These deposits often harbor LIYV virions arranged to be perpendicular to the plasma membrane over plasmodesmata, and our recent studies show that P26 is required for LIYV systemic plant infection. The functional mechanism of how LIYV P26 facilitates intercellular movement remains unclear, however, research on other plant viruses provides some insights on the possible ways of viral intercellular movement through targeting and modifying plasmodesmata via interactions between plant cellular components and viral-encoded factors. In summary, beginning with LIYV, we review the studies that have uncovered the biological determinants giving rise to these cytopathological effects and their importance in viral replication, virion assembly and intercellular movement during the plant infection by closteroviruses, and compare these findings with those for other positive-strand RNA viruses.
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Affiliation(s)
- Wenjie Qiao
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Vicente Medina
- Department of Crop and Forest Sciences, University of Lleida, Lleida, Spain
| | - Bryce W. Falk
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
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