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Khalifa ME, MacDiarmid RM. Molecular Characterization of Two Totiviruses from the Commensal Yeast Geotrichum candidum. Viruses 2023; 15:2150. [PMID: 38005831 PMCID: PMC10674808 DOI: 10.3390/v15112150] [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: 09/13/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
Mycoviruses can infect many of the major taxa of fungi including yeasts. Mycoviruses in the yeast fungus Geotrichum candidum are not well studied with only three G. candidum-associated viral species characterized to date, all of which belong to the Totiviridae genus Totivirus. In this study, we report the molecular characteristics of another two totiviruses co-infecting isolate Gc6 of G. candidum. The two totiviruses were tentatively named Geotrichum candidum totivirus 2 isolate Gc6 (GcTV2-Gc6) and Geotrichum candidum totivirus 4 isolate Gc6 (GcTV4-Gc6). Both viruses have the typical genome organization of totiviruses comprising two ORFs encoding capsid protein (CP) and RNA-dependent RNA polymerase (RdRp) at the N and C termini, respectively. The genomes of GcTV2-Gc6 and GcTV4-Gc6 are 4592 and 4530 bp long, respectively. Both viruses contain the-frameshifting elements and their proteins could be expressed as a single fusion protein. GcTV2-Gc6 is closely related to a totivirus isolated from the same host whereas GcTV4-Gc6 is related to insect-associated totiviruses. The phylogenetic analysis indicated that GcTV2-Gc6 and GcTV4-Gc6 belong to two different sister clades, I-A and I-B, respectively. It is interesting that all viruses identified from G. candidum belong to the genus Totivirus; however, this might be due to the lack of research reporting the characterization of mycoviruses from this fungal host. It is possible that the RNA interference (RNAi) mechanism cannot actively suppress totivirus accumulation in G. candidum Gc6.
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Affiliation(s)
- Mahmoud E. Khalifa
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta 34517, Egypt;
| | - Robin M. MacDiarmid
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1025, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
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Wen Y, Qu J, Zhang H, Yang Y, Huang R, Deng J, Zhang J, Xiao Y, Li J, Zhang M, Wang G, Zhai L. Identification and Characterization of a Novel Hypovirus from the Phytopathogenic Fungus Botryosphaeria dothidea. Viruses 2023; 15:2059. [PMID: 37896836 PMCID: PMC10611357 DOI: 10.3390/v15102059] [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: 08/22/2023] [Revised: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Many mycoviruses have been accurately and successfully identified in plant pathogenic fungus Botryosphaeria dothidea. This study discovered three mycoviruses from a B. dothidea strain SXD111 using high-throughput sequencing technology. A novel hypovirus was tentatively named Botryosphaeria dothidea hypovirus 1 (BdHV1/SXD111). The other two were known viruses, which we named Botryosphaeria dothidea polymycovirus 1 strain SXD111 (BdPmV1/SXD111) and Botryosphaeria dothidea partitivirus 1 strain SXD111 (BdPV1/SXD111). The genome of BdHV1/SXD111 is 11,128 nucleotides long, excluding the poly (A) tail. A papain-like cysteine protease (Pro), a UDP-glucose/sterol glucosyltransferase (UGT), an RNA-dependent RNA polyprotein (RdRp), and a helicase (Hel) were detected in the polyprotein of BdHV1/SXD111. Phylogenetic analysis showed that BdHV1/SXD111 was clustered with betahypovirus and separated from members of the other genera in the family Hypoviridae. The BdPmV1/SXD111 genome comprised five dsRNA segments with 2396, 2232, 1967, 1131, and 1060 bp lengths. Additionally, BdPV1/SXD111 harbored three dsRNA segments with 1823, 1623, and 557 bp lengths. Furthermore, the smallest dsRNA was a novel satellite component of BdPV1/SXD111. BdHV1/SXD111 could be transmitted through conidia and hyphae contact, whereas it likely has no apparent impact on the morphologies and virulence of the host fungus. Thus, this study is the first report of a betahypovirus isolated from the fungus B. dothidea. Importantly, our results significantly enhance the diversity of the B. dothidea viruses.
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Affiliation(s)
- Yongqi Wen
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Jinyue Qu
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Honglin Zhang
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Yi Yang
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Rui Huang
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Jili Deng
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Jiayu Zhang
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Yanping Xiao
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Jiali Li
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Meixin Zhang
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Lifeng Zhai
- College of Life Science and Biotechnology, Yangtze Normal University, Chongqing 408100, China; (Y.W.); (J.Q.); (H.Z.); (Y.Y.); (R.H.); (J.D.); (J.Z.); (Y.X.); (J.L.); (M.Z.)
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Pagnoni S, Oufensou S, Balmas V, Bulgari D, Gobbi E, Forgia M, Migheli Q, Turina M. A collection of Trichoderma isolates from natural environments in Sardinia reveals a complex virome that includes negative-sense fungal viruses with unprecedented genome organizations. Virus Evol 2023; 9:vead042. [PMID: 37692893 PMCID: PMC10491862 DOI: 10.1093/ve/vead042] [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: 04/14/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 09/12/2023] Open
Abstract
Trichoderma genus includes soil-inhabiting fungi that provide important ecosystem services in their interaction with plants and other fungi, as well as biocontrol of fungal plant diseases. A collection of Trichoderma isolates from Sardinia has been previously characterized, but here we selected 113 isolates, representatives of the collection, and characterized their viral components. We carried out high-throughput sequencing of ribosome-depleted total RNA following a bioinformatics pipeline that detects virus-derived RNA-directed RNA polymerases (RdRps) and other conserved viral protein sequences. This pipeline detected seventeen viral RdRps with two of them corresponding to viruses already detected in other regions of the world and the remaining fifteen representing isolates of new putative virus species. Surprisingly, eight of them are from new negative-sense RNA viruses, a first in the genus Trichoderma. Among them is a cogu-like virus, closely related to plant-infecting viruses. Regarding the positive-sense viruses, we report the presence of an 'ormycovirus' belonging to a recently characterized group of bisegmented single-stranded RNA viruses with uncertain phylogenetic assignment. Finally, for the first time, we report a bisegmented member of Mononegavirales which infects fungi. The proteins encoded by the second genomic RNA of this virus were used to re-evaluate several viruses in the Penicillimonavirus and Plasmopamonavirus genera, here shown to be bisegmented and encoding a conserved polypeptide that has structural conservation with the nucleocapsid domain of rhabdoviruses.
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Affiliation(s)
- Saul Pagnoni
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, via Celoria 2, Milan 20133, Italy
| | - Safa Oufensou
- Department of Agricultural Sciences and NRD—Desertification Research Center, University of Sassari, Viale Italia 39a, Sassari, Sardegna 07100, Italy
| | - Virgilio Balmas
- Department of Agricultural Sciences and NRD—Desertification Research Center, University of Sassari, Viale Italia 39a, Sassari, Sardegna 07100, Italy
| | - Daniela Bulgari
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, Brescia 25123, Italy
| | - Emanuela Gobbi
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, Brescia 25123, Italy
| | - Marco Forgia
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce, 73, Torino 10135, Italy
| | - Quirico Migheli
- Department of Agricultural Sciences and NRD—Desertification Research Center, University of Sassari, Viale Italia 39a, Sassari, Sardegna 07100, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection, National Research Council of Italy, Strada delle Cacce, 73, Torino 10135, Italy
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Jiang Y, Yang B, Liu X, Tian X, Wang Q, Wang B, Zhang Q, Yu W, Qi X, Jiang Y, Hsiang T. A Satellite dsRNA Attenuates the Induction of Helper Virus-Mediated Symptoms in Aspergillus flavus. Front Microbiol 2022; 13:895844. [PMID: 35711767 PMCID: PMC9195127 DOI: 10.3389/fmicb.2022.895844] [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: 03/14/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Aspergillus flavus is an important fungal pathogen of animals and plants. Previously, we reported a novel partitivirus, Aspergillus flavus partitivirus 1 (AfPV1), infecting A. flavus. In this study, we obtained a small double-stranded (ds) RNA segment (734 bp), which is a satellite RNA of the helper virus, AfPV1. The presence of AfPV1 altered the colony morphology, decreased the number of conidiophores, created significantly larger vacuoles, and caused more sensitivity to osmotic, oxidative, and UV stresses in A. flavus, but the small RNA segment could attenuate the above symptoms caused by the helper virus AfPV1 in A. flavus. Moreover, AfPV1 infection reduced the pathogenicity of A. flavus in corn (Zea mays), honeycomb moth (Galleria mellonella), mice (Mus musculus), and the adhesion of conidia to host epithelial cells, and increased conidial death by macrophages. However, the small RNA segment could also attenuate the above symptoms caused by the helper virus AfPV1 in A. flavus, perhaps by reducing the genomic accumulation of the helper virus AfPV1 in A. flavus. We used this model to investigate transcriptional genes regulated by AfPV1 and the small RNA segment in A. flavus, and their role in generating different phenotypes. We found that the pathways of the genes regulated by AfPV1 in its host were similar to those of retroviral viruses. Therefore, some pathways may be of benefit to non-retroviral viral integration or endogenization into the genomes of its host. Moreover, some potential antiviral substances were also found in A. flavus using this system.
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Affiliation(s)
- Yinhui Jiang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Bi Yang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Xiang Liu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Xun Tian
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Qinrong Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Bi Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Qifang Zhang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Wenfeng Yu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Yanping Jiang
- Department of Dermatology, The Affiliated Hospital, Guizhou Medical University, Guiyang, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
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5
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Petrzik K. Evolutionary forces at work in partitiviruses. Virus Genes 2019; 55:563-573. [PMID: 31230256 DOI: 10.1007/s11262-019-01680-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023]
Abstract
The family Partitiviridae consists of dsRNA viruses with genome separated into two segments and encoding replicase and capsid protein only. We examined the nucleotide diversity expressed as the ratio dN/dS of nonsynonymous and synonymous substitutions, which has been calculated for 12 representative viruses of all five genera of partitiviruses. We can state that strong purifying selection works on both the RdRp and CP genes and propose that putative positive selection occurs also on the RdRp genes in two viruses. Among the 95 evaluated viruses, wherein both segments had been sequenced, 8 viruses in betapartitiviruses and 9 in alphapartitiviruses were identified as reassortment candidates because they differ extremely in their CP identity even as they are related in terms of RdRp. Furthermore, there are indications that reassortants are present among isolates of different viruses.
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Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic.
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Hyder R, Piri T, Hantula J, Nuorteva H, Vainio EJ. Distribution of Viruses Inhabiting Heterobasidion annosum in a Pine-Dominated Forest Plot in Southern Finland. MICROBIAL ECOLOGY 2018; 75:622-630. [PMID: 28779297 DOI: 10.1007/s00248-017-1027-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
We investigated the diversity and spatial distribution of viruses infecting strains of the root rot fungus Heterobasidion annosum collected from pine stumps at a heavily infected forest site. Four different partitiviruses were detected in 14 H. annosum isolates at the study site, constituting approximately 29% of all Heterobasidion isolates investigated (N = 48). Two of the viruses detected were new partitiviruses designated here as Heterobasidion partitivirus 16 (HetPV16) and HetPV20, and two were previously known partitiviruses: HetPV7 and HetPV13. The two new partitiviruses found, HetPV16-an1 and HetPV20-an1, shared ~70% RdRp nucleotide sequence identity with the alphapartitivirus Rosellinia necatrix partitivirus 2, and less than 40% identity with known viruses of Heterobasidion spp. HetPV7-an1 was closely similar to HetPV7-pa1 isolated earlier from Heterobasidion parviporum, supporting the view of conspecific virus pools in different Heterobasidion species. Three fungal isolates were found to be co-infected with two different partitivirus strains (HetPV7-an1 and HetPV13-an2 or HetPV16-an1 and HetPV20-an1). Different isolates representing each host clone had variable virus compositions, and virus strains occurring in more than one host clone showed minor sequence variations between clones.
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Affiliation(s)
- Rafiqul Hyder
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland.
| | - Tuula Piri
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Jarkko Hantula
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Heikki Nuorteva
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Eeva J Vainio
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland
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Hrabáková L, Grum-Grzhimaylo AA, Koloniuk I, Debets AJM, Sarkisova T, Petrzik K. The alkalophilic fungus Sodiomyces alkalinus hosts beta- and gammapartitiviruses together with a new fusarivirus. PLoS One 2017; 12:e0187799. [PMID: 29186149 PMCID: PMC5706713 DOI: 10.1371/journal.pone.0187799] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 10/26/2017] [Indexed: 11/18/2022] Open
Abstract
Mixed infection by three dsRNA viruses, a novel betapartitivirus, a gammapartitivirus, and a novel fusarivirus, has been identified in four isolates of the obligate alkalophilic fungus Sodiomyces alkalinus. The first, Sodiomyces alkalinus partitivirus 1 (SaPV1), is placed within the genus Betapartitivirus and is related to Ustilaginoidea virens partitivirus 2. The taxonomic position of the second virus is less clear as it shares high (85%) amino acid sequence identity but significantly low (77%) nucleotide sequence identity of the capsid protein with Colletotrichum truncatum partitivirus 1. The third, the novel Sodiomyces alkalinus fusarivirus 1 (SaFV1), is related to Fusarium poae fusarivirus 1. All the viruses show efficient vertical transmission through asexual and sexual spores. These novel coexisting viruses do not evoke apparent phenotypic alteration to their fungal host. This is the first description of a viral infection in an alkalophilic fungus.
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Affiliation(s)
- Lenka Hrabáková
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | | | - Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | | | - Tatiana Sarkisova
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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Sequence determination of a satellite RNA isolated from Aspergillus foetidus. Arch Virol 2015; 160:883-5. [PMID: 25613164 DOI: 10.1007/s00705-015-2338-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/10/2015] [Indexed: 10/24/2022]
Abstract
Aspergillus foetidus virus (AfV) has at least two distinct particle types, designated as AfV-fast (F) and AfV-slow (S). AfV-S includes AfV-S1, a victorivirus; AfV-S2, an unclassified satellite RNA; and AfV-S3, a previously uncharacterized dsRNA element. Here, we describe the complete sequence of AfV-S3, which is a short non-coding RNA with no known homologs. AfV-S3 is predicted to form an extended secondary structure, shares a 5' terminus with AfV-S2, and is a satellite RNA possibly dependent on both AfV-S1 and AfV-S2. This work concludes the sequencing of the A. foetidus virome.
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Jurvansuu J, Kashif M, Vaario L, Vainio E, Hantula J. Partitiviruses of a fungal forest pathogen have species-specific quantities of genome segments and transcripts. Virology 2014; 462-463:25-33. [DOI: 10.1016/j.virol.2014.05.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 04/12/2014] [Accepted: 05/20/2014] [Indexed: 11/16/2022]
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Wang L, Jiang J, Wang Y, Hong N, Zhang F, Xu W, Wang G. Hypovirulence of the phytopathogenic fungus Botryosphaeria dothidea: association with a coinfecting chrysovirus and a partitivirus. J Virol 2014; 88:7517-27. [PMID: 24760881 PMCID: PMC4054428 DOI: 10.1128/jvi.00538-14] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 04/08/2014] [Indexed: 12/13/2022] Open
Abstract
UNLABELLED Botryosphaeria dothidea is an important pathogenic fungus causing fruit rot, leaf and stem ring spots and dieback, stem canker, stem death or stool mortality, and decline of pear trees. Seven double-stranded RNAs (dsRNAs; dsRNAs 1 to 7 with sizes of 3,654, 2,773, 2,597, 2,574, 1,823, 1,623, and 511 bp, respectively) were identified in an isolate of B. dothidea exhibiting attenuated growth and virulence and a sectoring phenotype. Characterization of the dsRNAs revealed that they belong to two dsRNA mycoviruses. The four largest dsRNAs (dsRNAs 1 to 4) are the genomic components of a novel member of the family Chrysoviridae (tentatively designated Botryosphaeria dothidea chrysovirus 1 [BdCV1]), a view supported by the morphology of the virions and phylogenetic analysis of the putative RNA-dependent RNA polymerases (RdRps). Two other dsRNAs (dsRNAs 5 and 6) are the genomic components of a novel member of the family Partitiviridae (tentatively designated Botryosphaeria dothidea partitivirus 1 [BdPV1]), which is placed in a clade distinct from other established partitivirus genera on the basis of the phylogenetic analysis of its RdRp. The smallest dsRNA, dsRNA7, seems to be a noncoding satellite RNA of BdPV1 on the basis of the conservation of its terminal sequences in BdPV1 genomic segments and its cosegregation with BdPV1 after horizontal transmission. This is the first report of a chrysovirus and a partitivirus infecting B. dothidea and of a chrysovirus associated with the hypovirulence of a phytopathogenic fungus. IMPORTANCE Our studies identified and characterized two novel mycoviruses, Botryosphaeria dothidea chrysovirus 1 (BdCV1) and Botryosphaeria dothidea partitivirus 1 (BdPV1), associated with the hypovirulence of an important fungus pathogenic to fruit trees. This is the first report of a chrysovirus and a partitivirus infecting B. dothidea and of a chrysovirus associated with the hypovirulence of a phytopathogenic fungus. BdCV1 appears to be a good candidate for the biological control of the serious disease induced by B. dothidea. Additionally, BdPV1 is placed in a clade distinct from the established genera. The BdCV1 capsid has two major structural proteins, and the capsid is distinct from that made up by a single polypeptide of the typical chrysoviruses. BdPV1 is the second partitivirus in which the putative capsid protein shares no significant identity with any mycovirus protein. A small accompanying dsRNA that is presumed to be a noncoding satellite RNA of BdPV1 is the first of its kind reported for a partitivirus.
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Affiliation(s)
- LiPing Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, People's Republic of China College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China National Indoor Conservation Center of Virus-Free Germplasms of Fruit Crops, Wuhan, Hubei, People's Republic of China Lab of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, People's Republic of China
| | - JingJing Jiang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, People's Republic of China College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China National Indoor Conservation Center of Virus-Free Germplasms of Fruit Crops, Wuhan, Hubei, People's Republic of China Lab of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, People's Republic of China
| | - YanFen Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, People's Republic of China College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China National Indoor Conservation Center of Virus-Free Germplasms of Fruit Crops, Wuhan, Hubei, People's Republic of China Lab of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, People's Republic of China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, People's Republic of China College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China National Indoor Conservation Center of Virus-Free Germplasms of Fruit Crops, Wuhan, Hubei, People's Republic of China Lab of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, People's Republic of China
| | - Fangpeng Zhang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, People's Republic of China College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China National Indoor Conservation Center of Virus-Free Germplasms of Fruit Crops, Wuhan, Hubei, People's Republic of China Lab of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, People's Republic of China
| | - WenXing Xu
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, People's Republic of China College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China National Indoor Conservation Center of Virus-Free Germplasms of Fruit Crops, Wuhan, Hubei, People's Republic of China Lab of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, People's Republic of China
| | - GuoPing Wang
- State Key Laboratory of Agricultural Microbiology, Wuhan, Hubei, People's Republic of China College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China National Indoor Conservation Center of Virus-Free Germplasms of Fruit Crops, Wuhan, Hubei, People's Republic of China Lab of Key Lab of Plant Pathology of Hubei Province, Wuhan, Hubei, People's Republic of China
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Abstract
Partitiviruses constitute one of the nine currently recognized families of viruses with encapsidated, double-stranded (ds)RNA genomes. The partitivirus genome is bisegmented, and each genome segment is packaged inside a separate viral capsid. Different partitiviruses infect plants, fungi, or protozoa. Recent studies have shed light on the three-dimensional structures of the virions of three representative fungal partitiviruses. These structures include a number of distinctive features, allowing informative comparisons with the structures of dsRNA viruses from other families. The results and comparisons suggest several new conclusions about the functions, assembly, and evolution of these viruses.
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Baeza M, Bravo N, Sanhueza M, Flores O, Villarreal P, Cifuentes V. Molecular characterization of totiviruses in Xanthophyllomyces dendrorhous. Virol J 2012; 9:140. [PMID: 22838956 PMCID: PMC3561658 DOI: 10.1186/1743-422x-9-140] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 07/17/2012] [Indexed: 12/12/2022] Open
Abstract
Background Occurrence of extrachromosomal dsRNA elements has been described in the red-yeast Xanthophyllomyces dendrorhous, with numbers and sizes that are highly variable among strains with different geographical origin. The studies concerning to the encapsidation in viral-like particles and dsRNA-curing have suggested that some dsRNAs are helper viruses, while others are satellite viruses. However, the nucleotide sequences and functions of these dsRNAs are still unknown. In this work, the nucleotide sequences of four dsRNAs of the strain UCD 67–385 of X. dendrorhous were determined, and their identities and genome structures are proposed. Based on this molecular data, the dsRNAs of different strains of X. dendrorhous were analyzed. Results The complete sequences of L1, L2, S1 and S2 dsRNAs of X. dendrorhous UCD 67–385 were determined, finding two sequences for L1 dsRNA (L1A and L1B). Several ORFs were uncovered in both S1 and S2 dsRNAs, but no homologies were found for any of them when compared to the database. Instead, two ORFs were identified in each L1A, L1B and L2 dsRNAs, whose deduced amino acid sequences were homologous with a major capsid protein (5’-ORF) and a RNA-dependent RNA polymerase (3’-ORF) belonging to the Totiviridae family. The genome structures of these dsRNAs are characteristic of Totiviruses, with two overlapped ORFs (the 3’-ORF in the −1 frame with respect to the 5’-ORF), with a slippery site and a pseudoknot in the overlapped regions. These structures are essential for the synthesis of the viral polymerase as a fusion protein with the viral capsid protein through −1 ribosomal frameshifting. In the RNase protection analysis, all the dsRNAs in the four analyzed X. dendrorhous strains were protected from enzymatic digestion. The RT-PCR analysis revealed that, similar to strain UCD 67–385, the L1A and L1B dsRNAs coexist in the strains VKM Y-2059, UCD 67–202 and VKM Y-2786. Furthermore, determinations of the relative amounts of L1 dsRNAs using two-step RT-qPCR revealed a 40-fold increment of the ratio L1A/L1B in the S2 dsRNA-cured strain compared to its parental strain. Conclusions Three totiviruses, named as XdV-L1A, XdV-L1B and XdV-L2, were identified in the strain UCD 67–385 of X. dendrorhous. The viruses XdV-L1A and XdV-L1B were also found in other three X. dendrorhous strains. Our results suggest that the smaller dsRNAs (named XdRm-S1 and XdRm-S2) of strain UCD 67–385 are satellite viruses, and particularly that XdRm-S2 is a satellite of XdV-L1A.
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Affiliation(s)
- Marcelo Baeza
- Departamento de Ciencias Ecológicas, Laboratorio de Genética, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile.
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13
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Tang J, Pan J, Havens WM, Ochoa WF, Guu TSY, Ghabrial SA, Nibert ML, Tao YJ, Baker TS. Backbone trace of partitivirus capsid protein from electron cryomicroscopy and homology modeling. Biophys J 2010; 99:685-94. [PMID: 20643089 DOI: 10.1016/j.bpj.2010.04.058] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 04/23/2010] [Accepted: 04/26/2010] [Indexed: 11/28/2022] Open
Abstract
Most dsRNA viruses have a genome-enclosing capsid that comprises 120 copies of a single coat protein (CP). These 120 CP subunits are arranged as asymmetrical dimers that surround the icosahedral fivefold axes, forming pentamers of dimers that are thought to be assembly intermediates. This scheme is violated, however, in recent structures of two dsRNA viruses, a fungal virus from family Partitiviridae and a rabbit virus from family Picobirnaviridae, both of which have 120 CP subunits organized as dimers of quasisymmetrical dimers. In this study, we report the CP backbone trace of a second fungal partitivirus, determined in this case by electron cryomicroscopy and homology modeling. This virus also exhibits quasisymmetrical CP dimers that are connected by prominent surface arches and stabilized by domain swapping between the two CP subunits. The CP fold is dominated by alpha-helices, although beta-strands mediate several important contacts. A dimer-of-dimers assembly intermediate is again implicated. The disordered N-terminal tail of each CP subunit protrudes into the particle interior and likely interacts with the genome during packaging and/or transcription. These results broaden our understanding of conserved and variable aspects of partitivirus structure and reflect the growing use of electron cryomicroscopy for atomic modeling of protein folds.
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Affiliation(s)
- Jinghua Tang
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92037, USA
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14
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Tang J, Ochoa WF, Li H, Havens WM, Nibert ML, Ghabrial SA, Baker TS. Structure of Fusarium poae virus 1 shows conserved and variable elements of partitivirus capsids and evolutionary relationships to picobirnavirus. J Struct Biol 2010; 172:363-71. [PMID: 20599510 DOI: 10.1016/j.jsb.2010.06.022] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/17/2010] [Accepted: 06/26/2010] [Indexed: 11/30/2022]
Abstract
Filamentous fungus Fusarium poae is a worldwide cause of the economically important disease Fusarium head blight of cereal grains. The fungus is itself commonly infected with a bisegmented dsRNA virus from the family Partitiviridae. For this study, we determined the structure of partitivirus Fusarium poae virus 1 (FpV1) to a resolution of 5.6Å or better by electron cryomicroscopy and three-dimensional image reconstruction. The main structural features of FpV1 are consistent with those of two other fungal partitiviruses for which high-resolution structures have been recently reported. These shared features include a 120-subunit T=1 capsid comprising 60 quasisymmetrical capsid protein dimers with both shell and protruding domains. Distinguishing features are evident throughout the FpV1 capsid, however, consistent with its more massive subunits and its greater phylogenetic divergence relative to the other two structurally characterized partitiviruses. These results broaden our understanding of conserved and variable elements of fungal partitivirus structure, as well as that of vertebrate picobirnavirus, and support the suggestion that a phylogenetic subcluster of partitiviruses closely related to FpV1 should constitute a separate taxonomic genus.
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Affiliation(s)
- Jinghua Tang
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093, USA
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15
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Evolutionary capture of viral and plasmid DNA by yeast nuclear chromosomes. EUKARYOTIC CELL 2009; 8:1521-31. [PMID: 19666779 DOI: 10.1128/ec.00110-09] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A 10-kb region of the nuclear genome of the yeast Vanderwaltozyma polyspora contains an unusual cluster of five pseudogenes homologous to five different genes from yeast killer viruses, killer plasmids, the 2microm plasmid, and a Penicillium virus. By further database searches, we show that this phenomenon is not unique to V. polyspora but that about 40% of the sequenced genomes of Saccharomycotina species contain integrated copies of genes from DNA plasmids or RNA viruses. We propose the name NUPAVs (nuclear sequences of plasmid and viral origin) for these objects, by analogy to NUMTs (nuclear copies of mitochondrial DNA) and NUPTs (nuclear copies of plastid DNA, in plants) of organellar origin. Although most of the NUPAVs are pseudogenes, one intact and active gene that was formed in this way is the KHS1 chromosomal killer locus of Saccharomyces cerevisiae. We show that KHS1 is a NUPAV related to M2 killer virus double-stranded RNA. Many NUPAVs are located beside tRNA genes, and some contain sequences from a mixture of different extrachromosomal sources. We propose that NUPAVs are sequences that were captured by the nuclear genome during the repair of double-strand breaks that occurred during evolution and that some of their properties may be explained by repeated breakage at fragile chromosomal sites.
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16
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Atomic structure reveals the unique capsid organization of a dsRNA virus. Proc Natl Acad Sci U S A 2009; 106:4225-30. [PMID: 19246376 DOI: 10.1073/pnas.0812071106] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
For most dsRNA viruses, the genome-enclosing capsid comprises 120 copies of a single capsid protein (CP) organized into 60 icosahedrally equivalent dimers, generally identified as 2 nonsymmetricallyinteracting CP molecules with extensive lateral contacts. The crystal structure of a partitivirus, Penicillium stoloniferum virus F (PsV-F), reveals a different organization, in which the CP dimer is related by almost-perfect local 2-fold symmetry, forms prominent surface arches, and includes extensive structure swapping between the 2 subunits. An electron cryomicroscopy map of PsV-F shows that the disordered N terminus of each CP molecule interacts with the dsRNA genome and probably participates in its packaging or transcription. Intact PsV-F particles mediate semiconservative transcription, and transcripts are likely to exit through negatively charged channels at the icosahedral 5-fold axes. Other findings suggest that the PsV-F capsid is assembled from dimers of CP dimers, with an arrangement similar to flavivirus E glycoproteins.
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17
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Pearson MN, Beever RE, Boine B, Arthur K. Mycoviruses of filamentous fungi and their relevance to plant pathology. MOLECULAR PLANT PATHOLOGY 2009; 10:115-28. [PMID: 19161358 PMCID: PMC6640375 DOI: 10.1111/j.1364-3703.2008.00503.x] [Citation(s) in RCA: 314] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Mycoviruses (fungal viruses) are reviewed with emphasis on plant pathogenic fungi. Based on the presence of virus-like particles and unencapsidated dsRNAs, mycoviruses are common in all major fungal groups. Over 80 mycovirus species have been officially recognized from ten virus families, but a paucity of nucleic acid sequence data makes assignment of many reported mycoviruses difficult. Although most of the particle types recognized to date are isometric, a variety of morphologies have been found and, additionally, many apparently unencapsidated dsRNAs have been reported. Until recently, most characterized mycoviruses have dsRNA genomes, but ssRNA mycoviruses now constitute about one-third of the total. Two hypotheses for the origin of mycoviruses of plant pathogens are discussed: the first that they are of unknown but ancient origin and have coevolved along with their hosts, the second that they have relatively recently moved from a fungal plant host into the fungus. Although mycoviruses are typically readily transmitted through asexual spores, transmission through sexual spores varies with the host fungus. Evidence for natural horizontal transmission has been found. Typically, mycoviruses are apparently symptomless (cryptic) but beneficial effects on the host fungus have been reported. Of more practical interest to plant pathologists are those viruses that confer a hypovirulent phenotype, and the scope for using such viruses as biocontrol agents is reviewed. New tools are being developed based on host genome studies that will help to address the intellectual challenge of understanding the fungal-virus interactions and the practical challenge of manipulating this relationship to develop novel biocontrol agents for important plant pathogens.
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Affiliation(s)
- Michael N Pearson
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
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18
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Genomic characterization of a novel partitivirus infecting Aspergillus ochraceus. Virus Genes 2008; 37:322-7. [DOI: 10.1007/s11262-008-0265-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Accepted: 07/17/2008] [Indexed: 11/25/2022]
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19
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Ochoa WF, Havens WM, Sinkovits RS, Nibert ML, Ghabrial SA, Baker TS. Partitivirus structure reveals a 120-subunit, helix-rich capsid with distinctive surface arches formed by quasisymmetric coat-protein dimers. Structure 2008; 16:776-86. [PMID: 18462682 DOI: 10.1016/j.str.2008.02.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Revised: 02/07/2008] [Accepted: 02/09/2008] [Indexed: 11/30/2022]
Abstract
Two distinct partitiviruses, Penicillium stoloniferum viruses S and F, can be isolated from the fungus Penicillium stoloniferum. The bisegmented dsRNA genomes of these viruses are separately packaged in icosahedral capsids containing 120 coat-protein subunits. We used transmission electron cryomicroscopy and three-dimensional image reconstruction to determine the structure of Penicillium stoloniferum virus S at 7.3 A resolution. The capsid, approximately 350 A in outer diameter, contains 12 pentons, each of which is topped by five arched protrusions. Each of these protrusions is, in turn, formed by a quasisymmetric dimer of coat protein, for a total of 60 such dimers per particle. The density map shows numerous tubular features, characteristic of alpha helices and consistent with secondary structure predictions for the coat protein. This three-dimensional structure of a virus from the family Partitiviridae exhibits both similarities to and differences from the so-called "T = 2" capsids of other dsRNA viruses.
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Affiliation(s)
- Wendy F Ochoa
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0378, USA
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20
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Blawid R, Stephan D, Maiss E. Molecular characterization and detection of Vicia cryptic virus in different Vicia faba cultivars. Arch Virol 2007; 152:1477-88. [PMID: 17533556 DOI: 10.1007/s00705-007-0966-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 03/06/2007] [Indexed: 10/23/2022]
Abstract
After extraction of double-stranded (ds) RNAs from Vicia faba, dsRNA1 and dsRNA2 of Vicia cryptic virus (VCV), a member of the genus Alphacryptovirus (family Partitiviridae), were detected in six out of seven different cultivars by agarose gel electrophoresis. In attempts to sequence the complete VCV genome, the dsRNA1 and dsRNA2 sequences from a total of five different V. faba cultivars were determined. Analysis of these sequences indicated that V. faba cultivars contain almost indistinguishable VCV sequences. The larger dsRNA1 was 2012 bp in length and contained a major open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp). The smaller dsRNA2 was 1779 bp in length and comprised a single ORF on its plus-strand encoding the coat protein (CP). The sequences of the dsRNA1 and dsRNA2 ORFs shared highest amino acid sequence identities (84 and 56%, respectively) with the corresponding gene products of the alphacryptovirus white clover cryptic virus 1 (WCCV-1). The 5'-terminal untranslated regions of dsRNA1 and dsRNA2 of VCV were highly conserved and were strikingly similar to the corresponding regions of WCCV-1. RdRp amino acid sequence alignments revealed conserved motifs, which correlate with the phylogenetic clustering of the family Partitiviridae.
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Affiliation(s)
- R Blawid
- Faculty of Natural Sciences, Institute of Plant Diseases and Plant Protection, Leibniz Universität Hannover, Hannover, Germany
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21
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Kim JW, Choi EY, Kim YT. Intergeneric relationship between the Aspergillus ochraceous virus F and the Penicillium stoloniferum virus S. Virus Res 2006; 120:212-5. [PMID: 16725223 DOI: 10.1016/j.virusres.2006.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Revised: 04/04/2006] [Accepted: 04/10/2006] [Indexed: 11/18/2022]
Abstract
It was reported that the "slow" component (PsV-S) of Penicillium stoloniferum virus complex also occurred in a second genus, Aspergillus ochraceous. The responsible virus for this intergeneric occurrence was considered to be the "fast" component (AoV-F) of A. ochraceous virus complex. In this investigation, AoV dsRNA 1, that was previously shown to cross-hybridize with PsV-S dsRNA, has been cloned. It was 1754 bp in length and contained one open reading frame of 539 amino acids (p63), had the same genome organization as PsV-S dsRNA S1 and also had the conserved sequence motif of the PsV-S dsRNAs (5'-GCGCAAAA-3') at the 5' terminus. A BLAST search indicated that p63 was a putative dsRNA-dependent RNA polymerase (RdRp), had 81% of sequence homology to members of the genus Partitivirus, and grouped together with PsV-S in phylogenetic analysis. But immunoblot analysis showed that the capsid protein (P3) of AoV-F virus component did not reacted against PsV-S antiserum. These evidences suggest that the cross serological relationship between AoV-F and PsV-S previously observed may have been due to the RdRps of the respective viruses rather than between their respective capsid proteins as was assumed in 1985.
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Affiliation(s)
- Jong Wook Kim
- Department of Biochemistry, College of Medicine, Inha University, Incheon 402-751, South Korea.
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22
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Chen L, Chen JS, Zhang H, Chen SN. Complete nucleotide sequences of three dsRNA segments from Raphanus sativus-root cv. Yipinghong with leaf yellow edge symptoms. Arch Virol 2006; 151:2077-83. [PMID: 16639633 DOI: 10.1007/s00705-006-0765-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Accepted: 03/09/2006] [Indexed: 10/24/2022]
Abstract
The two minor dsRNA bands, previously detected in symptomatic leaves of Raphanus sativus-root cv. Yidianhong [corrected] were subjected to further analysis. cDNA cloning and sequencing revealed that the smaller of the two dsRNA bands is actually a doublet consisting of two co-migrating dsRNA segments and the resulting three segments were designated as RasR 3, RasR 4, and RasR 5. RasR 3 was 1717 bp in length and potentially encoded a protein of about 55.3 kDa, containing all of the six conserved motifs shared by the RNA dependent RNA polymerases of members of the family Partitiviridae. RasR 4 and RasR 5, which co-migrated in the 5% polyacrylamide gel, were 1521 and 1485 bp in length and each encoded a putative protein of unknown function. Their molecular masses, as calculated from the deduced amino acid, were 38.2 and 38.8 kDa, respectively. The 5' UTRs of all three segments shared regions of high sequence similarities, but were distinct from those of the RasR 1 and RasR 2. Taken together, these results along with those described in the previous report, suggest that more than one partitivirus was co-infecting radish leaves.
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Affiliation(s)
- L Chen
- Institute of Bioengineering, Zhejiang Sci-Tech University, Hangzhou, China
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23
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Chen L, Chen JS, Liu L, Yu X, Yu S, Fu TZ, Liu WH. Complete nucleotide sequences and genome characterization of double-stranded RNA 1 and RNA 2 in the Raphanus sativus-root cv. Yipinghong. Arch Virol 2005; 151:849-59. [PMID: 16369860 DOI: 10.1007/s00705-005-0685-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Accepted: 10/28/2005] [Indexed: 11/30/2022]
Abstract
Four distinct double-stranded (ds) RNA bands were extracted from leaves of Raphanus sativus-root cv. Yidianhong [corrected] with yellowing at the leaf edge in China. Purified viral particles of 28-30 nm in diameter contained dsRNA segments with the same number and mobility as these extracted directly from radish leaves. The two major dsRNA segments, namely RasR 1 and RasR 2, were 1866 and 1791 bp in length, respectively. Computer analysis predicted that they both contained a single open reading frame (ORF) on their plus-stranded RNA, putatively encoding a RNA dependent RNA polymerase and a capsid protein similar to that encoded by members of the family Partitiviridae. In addition, both RasR 1 and RasR 2 were highly conserved at the 5' untranslated regions (UTR) and had an adenosine-uracil rich stretch at the 3' UTR, with an identical terminal motif (5'-AAAAUAAAACC-3'). Taken together, these results suggest that the two major dsRNA segments constitute the genome of a partitivirus infecting radish.
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Affiliation(s)
- L Chen
- College of Life Sciences, Zhejiang University, Hangzhou, PR China
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