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Li Y, Huang X, Zhou G, Ye A, Deng Y, Shi L, Zhang R. Characterization of a novel endornavirus isolated from the phytopathogenic fungus Rhizoctonia solani. Arch Virol 2024; 169:15. [PMID: 38163823 DOI: 10.1007/s00705-023-05915-2] [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: 08/17/2023] [Accepted: 09/19/2023] [Indexed: 01/03/2024]
Abstract
Rhizoctonia solani endornavirus 8 (RsEV8) was isolated from strain XY175 of Rhizoctonia solani AG-1 IA. The full-length genome of RsEV8 is 16,147 nucleotides (nt) in length and contains a single open reading frame that encodes a large polyprotein of 5227 amino acids. The polyprotein contains four conserved domains: viral methyltransferase, putative DEAH box helicase, viral helicase, and RNA-dependent RNA polymerase (RdRp). RsEV8 has a shorter 3'-UTR (58 nt) and a longer 5'-UTR (404 nt). A multiple sequence alignment indicated that the RdRp of RsEV8 possesses eight typical RdRp motifs. According to a BLASTp analysis, RsEV8 shares 39.31% sequence identity with Rhizoctonia cerealis endornavirus-1084-7. Phylogenetic analysis demonstrated that RsEV8 clusters with members of the genus Betaendornavirus.
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Affiliation(s)
- Yangyi Li
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, 430045, Hubei, China
| | - Xingxue Huang
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, 430045, Hubei, China
| | - Guolin Zhou
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, 430045, Hubei, China
| | - Anhua Ye
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, 430045, Hubei, China
| | - Yaohua Deng
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, 430045, Hubei, China
| | - Lingfang Shi
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, 430045, Hubei, China
| | - Runhua Zhang
- Institute of Vegetable Research, Wuhan Academy of Agricultural Sciences, Wuhan, 430045, Hubei, China.
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Sakuta K, Uchida K, Fukuhara T, Komatsu K, Okada R, Moriyama H. Successful full-length genomic cloning and characterization of site-specific nick structures of Phytophthora endornaviruses 2 and 3 in yeast, Saccharomyces cerevisiae. Front Microbiol 2023; 14:1243068. [PMID: 37771702 PMCID: PMC10523305 DOI: 10.3389/fmicb.2023.1243068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
Two endornaviruses, Phytophthora endornavirus 2 (PEV2) and Phytophthora endornavirus 3 (PEV3), have been discovered in pathogens targeting asparagus. In this study, we analyzed the nick structure in the RNA genomes of PEV2 and PEV3 in the host oomycetes. Northern blot hybridization using positive and negative strand-specific RNA probes targeting the 5' and 3' regions of PEV2 and PEV3 RNA genomes revealed approximately 1.0 kilobase (kb) RNA fragments located in the 5' regions of the two genomes. 3' RACE analysis determined that the size of the RNA fragments were 958 nucleotides (nt) for PEV2 and 968 nt for PEV3. We have successfully constructed full-length cDNA clones of the entire RNA genomes of PEV2 and PEV3 using a homologous recombination system in the yeast, Saccharomyces cerevisiae. These full-length cDNA sequences were ligated downstream of a constitutive expression promoter (TDH3) or a galactose-inducing promoter (GAL1) in the shuttle vector to enable the production of the full-length RNA transcripts of PEV2 and PEV3 in yeast cells. Interestingly, a 1.0 kb RNA fragment from the PEV3 positive-strand transcript was also detected with a 5'-region RNA probe, indicating that site-specific cleavage also occurred in yeast cells. Further, when PEV2 or PEV3 mRNA was overexpressed under the GAL1 promoter, yeast cell growth was suppressed. A fusion protein combining EGFP to the N-terminus of the full-length PEV2 ORF or C-terminus of the full-length PEV3 ORF was expressed, and allowed PEV2 and PEV3 ORFs to be successfully visualized in yeast cells. Expression of the fusion protein also revealed presence of heterogeneous bodies in the cells.
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Affiliation(s)
- Kohei Sakuta
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Keiko Uchida
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Toshiyuki Fukuhara
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Ryo Okada
- Horticultural Research Institute, Agricultural Center, Kasama, Ibaraki, Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
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Escalante C, Sela N, Valverde RA. Transcriptome analysis of two near-isogenic lines of bell pepper ( Capsicum annuum) infected with bell pepper endornavirus and pepper mild mottle virus. Front Genet 2023; 14:1182578. [PMID: 37124621 PMCID: PMC10133535 DOI: 10.3389/fgene.2023.1182578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023] Open
Affiliation(s)
- Cesar Escalante
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
- Department of Plant Pathology and Crop Physiology, Louisiana State University, Agricultural Center, Baton Rouge, LA, United States
- *Correspondence: Cesar Escalante,
| | - Noa Sela
- Department of Plant Pathology and Weed Research, The Volcani Center-ARO, Bet-Dagan, Israel
| | - Rodrigo A. Valverde
- Department of Plant Pathology and Crop Physiology, Louisiana State University, Agricultural Center, Baton Rouge, LA, United States
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Solovyev AG, Morozov SY. Uncovering Plant Virus Species Forming Novel Provisional Taxonomic Units Related to the Family Benyviridae. Viruses 2022; 14:v14122680. [PMID: 36560684 PMCID: PMC9781952 DOI: 10.3390/v14122680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 12/05/2022] Open
Abstract
Based on analyses of recent open-source data, this paper describes novel horizons in the diversity and taxonomy of beny-like viruses infecting hosts of the plant kingdom (Plantae or Archaeplastida). First, our data expand the known host range of the family Benyviridae to include red algae. Second, our phylogenetic analysis suggests that the evolution of this virus family may have involved cross-kingdom host change events and gene recombination/exchanges between distant taxa. Third, the identification of gene blocks encoding known movement proteins in beny-like RNA viruses infecting non-vascular plants confirms other evidence that plant virus genomic RNAs may have acquired movement proteins simultaneously or even prior to the evolutionary emergence of the plant vascular system. Fourth, novel data on plant virus diversity highlight that molecular evolution gave rise to numerous provisional species of land-plant-infecting viruses, which encode no known potential movement genetic systems.
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Affiliation(s)
- Andrey G. Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
- Department of Virology, Biological Faculty, Moscow State University, 119234 Moscow, Russia
- All Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Sergey Y. Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
- Department of Virology, Biological Faculty, Moscow State University, 119234 Moscow, Russia
- Correspondence: ; Tel.: +7-(495)-9393198
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Luo X, Jiang D, Xie J, Jia J, Duan J, Cheng J, Fu Y, Chen T, Yu X, Li B, Lin Y. Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum. Viruses 2022; 14:v14030456. [PMID: 35336865 PMCID: PMC8953294 DOI: 10.3390/v14030456] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
Endornaviruses are capsidless linear (+) ssRNA viruses in the family Endornaviridae. In this study, Scelrotinia sclerotiorum endornavirus 11 (SsEV11), a novel endornavirus infecting hypovirulent Sclerotinia sclerotiorum strain XY79, was identified and cloned using virome sequencing analysis and rapid amplification of cDNA ends (RACE) techniques. The full-length genome of SsEV11 is 11906 nt in length with a large ORF, which encodes a large polyprotein of 3928 amino acid residues, containing a viral methyltransferase domain, a cysteine-rich region, a putative DEADc, a viral helicase domain, and an RNA-dependent RNA polymerase (RdRp) 2 domain. The 5’ and 3’ untranslated regions (UTR) are 31 nt and 90 nt, respectively. According to the BLAST result of the nucleotide sequence, SsEV11 shows the highest identity (45%) with Sclerotinia minor endornavirus 1 (SmEV1). Phylogenetic analysis based on amino acid sequence of RdRp demonstrated that SsEV11 clusters to endornavirus and has a close relationship with Betaendornavirus. Phylogenetic analysis based on the sequence of endornaviral RdRp domain indicated that there were three large clusters in the phylogenetic tree. Combining the results of alignment analysis, Cluster I at least has five subclusters including typical members of Alphaendornavirus and many unclassified endornaviruses that isolated from fungi, oomycetes, algae, and insects; Cluster II also has five subclusters including typical members of Betaendornavirus, SsEV11, and other unclassified viruses that infected fungi; Cluster III includes many endorna-like viruses that infect nematodes, mites, and insects. Viruses in Cluster I and Cluster II are close to each other and relatively distant to those in Cluster III. Our study characterized a novel betaendornavirus, SsEV11, infected fungal pathogen S. sclerotiorum, and suggested that notable phylogenetic diverse exists in endornaviruses. In addition, at least, one novel genus, Gammaendornavirus, should be established to accommodate those endorna-like viruses in Cluster III.
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Affiliation(s)
- Xin Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Jichun Jia
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
| | - Jie Duan
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Jiasen Cheng
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Xiao Yu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Bo Li
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Yang Lin
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
- Correspondence:
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Zechmann B, Müller M, Möstl S, Zellnig G. Three-dimensional quantitative imaging of Tobacco mosaic virus and Zucchini yellow mosaic virus induced ultrastructural changes. PROTOPLASMA 2021; 258:1201-1211. [PMID: 33619654 DOI: 10.1007/s00709-021-01626-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
Two-dimensional ultrastructural changes of Tobacco mosaic virus (TMV) and Zucchini yellow mosaic virus (ZYMV) in tobacco and pumpkin plants, respectively, are well studied. To provide 3D data, representative control and infected cells were reconstructed using serial sectioning and transmission electron microscopy. Quantitative data of 3D ultrastructural changes were then extracted from the cytosol and organelles by image analysis. While TMV induced the accumulation of an average of 40 virus inclusion bodies in the cytosol, which covered about 13% of the cell volume, ZYMV caused the accumulation of an average of 1752 cylindrical inclusions in the cytosol, which covered about 2.7% of the total volume of the cell. TMV infection significantly decreased the number and size of mitochondria (- 49 and - 20%) and peroxisomes (- 62 and - 28%) of the reconstructed cell. The reconstructed ZYMV-infected cell contained more (105%) and larger (109%) mitochondria when compared to the control cell. While the reconstructed TMV-infected cell contained larger (20%) and the ZYMV-infected smaller (19%) chloroplasts, both contained less chloroplasts (- 40% for TMV and - 23% for ZYMV). In chloroplasts, the volume of starch and plastoglobules increased (664% and 150% for TMV and 1324% and 1300% for ZYMV) when compared to the control. The latter was correlated with a decrease in the volume of thylakoids in the reconstructed ZYMV-infected cell (- 31%) indicating that degradation products from thylakoids are transported and stored in plastoglobules. Summing up, the data collected in this study give a comprehensive overview of 3D changes induced by TMV and ZYMV in plants.
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Affiliation(s)
- Bernd Zechmann
- Center for Microscopy and Imaging, Baylor University, One Bear Place #97046, Waco, TX, 76798, USA.
| | - Maria Müller
- Institute of Biology, Plant Sciences, University of Graz, NAWI Graz, Schubertstrasse 51, 8010, Graz, Austria
| | - Stefan Möstl
- Institute of Biology, Plant Sciences, University of Graz, NAWI Graz, Schubertstrasse 51, 8010, Graz, Austria
| | - Günther Zellnig
- Institute of Biology, Plant Sciences, University of Graz, NAWI Graz, Schubertstrasse 51, 8010, Graz, Austria
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Complete nucleotide sequence of an alphaendornavirus isolated from common buckwheat (Fagopyrum esculentum). Arch Virol 2021; 166:3483-3486. [PMID: 34608525 DOI: 10.1007/s00705-021-05264-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/20/2021] [Indexed: 12/25/2022]
Abstract
A double-stranded RNA (dsRNA) of approximately 16 kbp was isolated from symptomless common buckwheat (Fagopyrum esculentum) plants. The size of the dsRNA suggested that it was the replicative form of an endornavirus. The dsRNA was sequenced, and it consisted of 15,677 nt, containing a single open reading frame that potentially encoded a polyprotein of 5190 aa. The polyprotein contained conserved domains for a viral methyltransferase, viral RNA helicase 1, MSCRAMM family adhesion SdrC, UDP-glycosyltransferase, and viral RNA-dependent RNA polymerase 2. A site-specific nick in the plus strand was detected near the 5' end of the dsRNA. BLASTp analysis showed that the polyprotein shared the highest identity with the polyprotein of winged bean endornavirus 1. Results of phylogenetic analysis supported placing this novel virus from common buckwheat, which was provisionally named "Fagopyrum esculentum endornavirus 1", in the genus Alphaendornavirus of the family Endornaviridae.
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Herschlag R, Okada R, Alcalá-Briseño RI, de Souto ER, Valverde RA. Identification of a novel endornavirus in Geranium carolinianum and occurrence within three agroecosystems. Virus Res 2020; 288:198116. [PMID: 32795491 DOI: 10.1016/j.virusres.2020.198116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
Abstract
A putative endornavirus was detected in Carolina geranium (Geranium carolinianum) in Louisiana, USA. The virus was provisionally named Geranium carolinianum endornavirus 1 (GcEV1). The viral RNA was sequenced, and it consisted of 14,625 nt containing a single ORF coding a putative polyprotein of 4815 aa with conserved domains for a helicase 1, peptidase C97, glycosyl transferase GTB-type, and RNA-dependent RNA polymerase 2. The 5'end consisted of 130 nt while the 3'end consisted of 54 nt ending in nine cytosine residues. The closest relative to GcEV1 was Phaseolus vulgaris endornavirus 3. In phylogenetic analyses, GcEV1 clustered with members of the genus Alphaendornavirus. GcEV1 was detected in 57 of 60 G. carolinianum plants collected from three distinct agroecosystems. The virus was not detected in eight other species of the genus Geranium. There was no association of a particular phenotypic trait of the host with the presence or absence of the virus. GcEV1 was transmitted at a rate of 100% in seeds of a self-pollinated G. carolinianum plant.
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Affiliation(s)
- Rachel Herschlag
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Ryo Okada
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | | | - Eliezer Rodrigues de Souto
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Rodrigo A Valverde
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, USA.
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