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Hai D, Li J, Lan S, Wu T, Li Y, Cheng J, Fu Y, Lin Y, Jiang D, Wang M, Xie J. Discovery and Evolution of Six Positive-Sense RNA Viruses Co-infecting the Hypovirulent Strain SCH733 of Sclerotinia sclerotiorum. PHYTOPATHOLOGY 2022; 112:2449-2461. [PMID: 35793152 DOI: 10.1094/phyto-05-22-0148-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Sclerotinia sclerotiorum is a well-known phytopathogenic fungus with a wide host range. Identifying novel mycoviruses in phytopathogenic fungi is necessary to develop novel strategies for plant health protection and contribute to understanding the origin of viruses. Six new mycoviruses with positive single-stranded RNA genomes co-infecting the hypovirulent strain SCH733 of S. sclerotiorum were identified using a metatranscriptomic approach, and their complete genome sequences were molecularly determined. These mycoviruses belong to the following five families: Narnaviridae, Mitoviridae, Deltaflexviridae, Botourmiaviridae, and Ambiguiviridae. Three of these mycoviruses belong to existing International Committee on Taxonomy of Viruses (ICTV)-recognized species. Two of these newly identified mycoviruses have unique genomic features that are significantly different from those of all known mycoviruses. Phylogenetic analysis revealed that these six mycoviruses included close as well as distant relatives of known mycoviruses, thereby providing new insight into virus evolution and classification. Mycovirus horizontal transmission and elimination experiments revealed that Sclerotinia sclerotiorum narnavirus 5 is associated with hypovirulence of S. sclerotiorum, although we have not shown that it is independently responsible for the hypovirulence phenotype. This study broadens the diversity of known mycoviruses infecting S. sclerotiorum and provides a clue toward limiting hypovirulence in S. sclerotiorum.
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Affiliation(s)
- Du Hai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jincang Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Shangsong Lan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Tun Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Ying Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Minghong Wang
- Hubei Key Laboratory of Biological Resources Protection and Utilization, College of Forestry and Horticulture, Hubei Minzu University, Enshi, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Three-Layered Complex Interactions among Capsidless (+)ssRNA Yadokariviruses, dsRNA Viruses, and a Fungus. mBio 2022; 13:e0168522. [PMID: 36040032 PMCID: PMC9600902 DOI: 10.1128/mbio.01685-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have previously discovered a virus neo-lifestyle exhibited by a capsidless positive-sense (+), single-stranded (ss) RNA virus YkV1 (family Yadokariviridae) and an unrelated double-stranded (ds) RNA virus YnV1 (proposed family "Yadonushiviridae") in a phytopathogenic ascomycete, Rosellinia necatrix. YkV1 has been proposed to replicate in the capsid provided by YnV1 as if it were a dsRNA virus and enhance YnV1 replication in return. Recently, viruses related to YkV1 (yadokariviruses) have been isolated from diverse ascomycetous fungi. However, it remains obscure whether such viruses generally show the YkV1-like lifestyle. Here, we identified partner viruses for three distinct yadokariviruses, YkV3, YkV4a, and YkV4b, isolated from R. necatrix that were coinfected with multiple dsRNA viruses phylogenetically distantly related to YnV1. We first established transformants of R. necatrix carrying single yadokarivirus cDNAs and fused them with infectants by single partner candidate dsRNA viruses. Consequently, YkV3 and YkV4s replicated only in the presence of RnMBV3 (family Megabirnaviridae) and RnMTV1 (proposed family "Megatotiviridae"), respectively. The partners were mutually interchangeable between the two YkV4 strains and three RnMTV1 strains but not between other combinations involving YkV1 or YkV3. In contrast to YkV1 enhancing YnV1 accumulation, YkV4s reduced RnMTV1 accumulation to different degrees according to strains. Interestingly, YkV4 rescued the host R. necatrix from impaired growth induced by RnMTV1. YkV3 exerted no apparent effect on its partner (RnMBV3) or host fungus. Overall, we revealed that while yadokariviruses generally require partner dsRNA viruses for replication, each yadokarivirus partners with a different dsRNA virus species in the three diverse families and shows a distinct symbiotic relation in a fungus. IMPORTANCE A capsidless (+)ssRNA virus YkV1 (family Yadokariviridae) highjacks the capsid of an unrelated dsRNA virus YnV1 (proposed family "Yadonushiviridae") in a phytopathogenic ascomycete, while YkV1 trans-enhances YnV1 replication. Herein, we identified the dsRNA virus partners of three yadokariviruses (YkV3, YkV4a, and YkV4b) with genome organization different from YkV1 as being different from YnV1 at the suborder level. Their partners were mutually interchangeable between the two YkV4 strains and three strains of the partner virus RnMTV1 (proposed family "Megatotiviridae") but not between other combinations involving YkV1 or YkV3. Unlike YkV1, YkV4s reduced RnMTV1 accumulation and rescued the host fungus from impaired growth induced by RnMTV1. YkV3 exerted no apparent effect on its partner (RnMBV3, family Megabirnaviridae) or host fungus. These revealed that while each yadokarivirus has a species-specific partnership with a dsRNA virus, yadokariviruses collectively partner extremely diverse dsRNA viruses and show three-layered complex mutualistic/antagonistic interactions in a fungus.
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De Miccolis Angelini RM, Raguseo C, Rotolo C, Gerin D, Faretra F, Pollastro S. The Mycovirome in a Worldwide Collection of the Brown Rot Fungus Monilinia fructicola. J Fungi (Basel) 2022; 8:jof8050481. [PMID: 35628739 PMCID: PMC9147972 DOI: 10.3390/jof8050481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
The fungus Monilinia fructicola is responsible for brown rot on stone and pome fruit and causes heavy yield losses both pre- and post-harvest. Several mycoviruses are known to infect fungal plant pathogens. In this study, a metagenomic approach was applied to obtain a comprehensive characterization of the mycovirome in a worldwide collection of 58 M. fructicola strains. Deep sequencing of double-stranded (ds)RNA extracts revealed a great abundance and variety of mycoviruses. A total of 32 phylogenetically distinct positive-sense (+) single-stranded (ss)RNA viruses were identified. They included twelve mitoviruses, one in the proposed family Splipalmiviridae, and twelve botourmiaviruses (phylum Lenarviricota), eleven of which were novel viral species; two hypoviruses, three in the proposed family Fusariviridae, and one barnavirus (phylum Pisuviricota); as well as one novel beny-like virus (phylum Kitrinoviricota), the first one identified in Ascomycetes. A partial sequence of a new putative ssDNA mycovirus related to viruses within the Parvoviridae family was detected in a M. fructicola isolate from Serbia. The availability of genomic sequences of mycoviruses will serve as a solid basis for further research aimed at deepening the knowledge on virus–host and virus–virus interactions and to explore their potential as biocontrol agents against brown rot disease.
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Molecular characterization of a novel victorivirus infecting Corynespora cassiicola. Arch Virol 2022; 167:1365-1368. [DOI: 10.1007/s00705-022-05394-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/12/2022] [Indexed: 12/20/2022]
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Sato Y, Shahi S, Telengech P, Hisano S, Cornejo C, Rigling D, Kondo H, Suzuki N. A new tetra-segmented splipalmivirus with divided RdRP domains from Cryphonectria naterciae, a fungus found on chestnut and cork oak trees in Europe. Virus Res 2022; 307:198606. [PMID: 34688782 DOI: 10.1016/j.virusres.2021.198606] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 01/01/2023]
Abstract
Positive-sense (+), single-stranded (ss) RNA viruses with divided RNA-dependent RNA polymerase (RdRP) domains have been reported from diverse filamentous ascomycetes since 2020. These viruses are termed splipalmiviruses or polynarnaviruses and have been characterized largely at the sequence level, but ill-defined biologically. Cryphonectria naterciae, from which only one virus has been reported, is an ascomycetous fungus potentially plant-pathogenic to chestnut and oak trees. We molecularly characterized multiple viruses in a single Portuguese isolate (C0614) of C. naterciae, taking a metatranscriptomic and conventional double-stranded RNA approach. Among them are a novel splipalmivirus (Cryphonectria naterciae splipalmivirus 1, CnSpV1) and a novel fusagravirus (Cryphonectria naterciae fusagravirus 1, CnFGV1). This study focused on the former virus. CnSpV1 has a tetra-segmented, (+)ssRNA genome (RNA1 to RNA4). As observed for other splipalmiviruses reported in 2020 and 2021, the RdRP domain is separately encoded by RNA1 (motifs F, A and B) and RNA2 (motifs C and D). A hypothetical protein encoded by the 5'-proximal open reading frame of RNA3 shows similarity to a counterpart conserved in some splipalmiviruses. The other RNA3-encoded protein and RNA4-encoded protein show no similarity with known proteins in a blastp search. The tetra-segment nature was confirmed by the conserved terminal sequences of the four CnSpV1 segments (RNA1 to RNA4) and their 100% coexistence in over 100 single conidial isolates tested. The experimental introduction of CnSpV1 along with CnFGV1 into a virus free strain C0754 of C. naterciae vegetatively incompatible with C0614 resulted in no phenotypic alteration, suggesting asymptomatic infection. The protoplast fusion assay indicates a considerably narrow host range of CnSpV1, restricted to the species C. naterciae and C. carpinicola. This study contributes to better understanding of the molecular and biological properties of this unique group of viruses.
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Affiliation(s)
- Yukiyo Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Sabitree Shahi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Paul Telengech
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Sakae Hisano
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Carolina Cornejo
- Swiss Federal Research Institute WSL, Forest Health & Biotic Interactions, Zuercherstrasse 111, CH-8903 Birmensdorf
| | - Daniel Rigling
- Swiss Federal Research Institute WSL, Forest Health & Biotic Interactions, Zuercherstrasse 111, CH-8903 Birmensdorf
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan.
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Crucitti D, Chiapello M, Oliva D, Forgia M, Turina M, Carimi F, La Bella F, Pacifico D. Identification and Molecular Characterization of Novel Mycoviruses in Saccharomyces and Non- Saccharomyces Yeasts of Oenological Interest. Viruses 2021; 14:v14010052. [PMID: 35062256 PMCID: PMC8778689 DOI: 10.3390/v14010052] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/18/2021] [Accepted: 12/24/2021] [Indexed: 11/16/2022] Open
Abstract
Wine yeasts can be natural hosts for dsRNA, ssRNA viruses and retrotransposon elements. In this study, high-throughput RNA sequencing combined with bioinformatic analyses unveiled the virome associated to 16 Saccharomyces cerevisiae and 8 non-Saccharomyces strains of oenological interest. Results showed the presence of six viruses and two satellite dsRNAs from four different families, two of which-Partitiviridae and Mitoviridae-were not reported before in yeasts, as well as two ORFan contigs of viral origin. According to phylogenetic analysis, four new putative mycoviruses distributed in Totivirus, Cryspovirus, and Mitovirus genera were identified. The majority of commercial S. cerevisiae strains were confirmed to be the host for helper L-A type totiviruses and satellite M dsRNAs associated with the killer phenotype, both in single and mixed infections with L-BC totiviruses, and two viral sequences belonging to a new cryspovirus putative species discovered here for the first time. Moreover, single infection by a narnavirus 20S-related sequence was also found in one S. cerevisiae strain. Considering the non-Saccharomyces yeasts, Starmerella bacillaris hosted four RNAs of viral origin-two clustering in Totivirus and Mitovirus genera, and two ORFans with putative satellite behavior. This study confirmed the infection of wine yeasts by viruses associated with useful technological characteristics and demonstrated the presence of complex mixed infections with unpredictable biological effects.
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Affiliation(s)
- Dalila Crucitti
- Dipartimento di Scienze Bio-Agroalimentari, Istituto di Bioscienze e BioRisorse (IBBR), C.N.R., Corso Calatafimi 414, 90129 Palermo, Italy; (F.C.); (F.L.B.)
- Correspondence: (D.C.); (D.P.); Tel.: +39-091-657-4578 (D.C.)
| | - Marco Chiapello
- Dipartimento di Scienze Bio-Agroalimentari, Istituto per la Protezione Sostenibile delle Piante (IPSP), C.N.R., Strada delle Cacce, 73, 10135 Torino, Italy; (M.C.); (M.F.); (M.T.)
| | - Daniele Oliva
- Istituto Regionale del Vino e dell’Olio (IRVO), Via Libertà 66, 90143 Palermo, Italy;
| | - Marco Forgia
- Dipartimento di Scienze Bio-Agroalimentari, Istituto per la Protezione Sostenibile delle Piante (IPSP), C.N.R., Strada delle Cacce, 73, 10135 Torino, Italy; (M.C.); (M.F.); (M.T.)
| | - Massimo Turina
- Dipartimento di Scienze Bio-Agroalimentari, Istituto per la Protezione Sostenibile delle Piante (IPSP), C.N.R., Strada delle Cacce, 73, 10135 Torino, Italy; (M.C.); (M.F.); (M.T.)
| | - Francesco Carimi
- Dipartimento di Scienze Bio-Agroalimentari, Istituto di Bioscienze e BioRisorse (IBBR), C.N.R., Corso Calatafimi 414, 90129 Palermo, Italy; (F.C.); (F.L.B.)
| | - Francesca La Bella
- Dipartimento di Scienze Bio-Agroalimentari, Istituto di Bioscienze e BioRisorse (IBBR), C.N.R., Corso Calatafimi 414, 90129 Palermo, Italy; (F.C.); (F.L.B.)
| | - Davide Pacifico
- Dipartimento di Scienze Bio-Agroalimentari, Istituto di Bioscienze e BioRisorse (IBBR), C.N.R., Corso Calatafimi 414, 90129 Palermo, Italy; (F.C.); (F.L.B.)
- Correspondence: (D.C.); (D.P.); Tel.: +39-091-657-4578 (D.C.)
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Yang M, Xu W, Zhou X, Yang Z, Wang Y, Xiao F, Guo Y, Hong N, Wang G. Discovery and Characterization of a Novel Bipartite Botrexvirus From the Phytopathogenic Fungus Botryosphaeria dothidea. Front Microbiol 2021; 12:696125. [PMID: 34276630 PMCID: PMC8280476 DOI: 10.3389/fmicb.2021.696125] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 05/31/2021] [Indexed: 11/15/2022] Open
Abstract
In this study, we describe a novel positive, single-stranded (+ss) RNA mycovirus, named Botryosphaeria dothidea botrexvirus 1 (BdBV1), from a phytopathogenic fungus Botryosphaeria dothidea showing abnormal morphology and attenuated virulence. BdBV1 is phylogenetically related to Botrytis virus X (BotVX) and is the second potential member of the proposed genus Botrexvirus in the family Alphaflexiviridae. However, it differs from the monopartite BotVX in that BdBV1 possesses a bipartite genome comprised of two ssRNA segments (RNA1 and RNA2 with lengths of 5,035 and 1,063 nt, respectively). BdBV1 RNA1 and RNA2 encode putative RNA-dependent RNA polymerase (RdRp) and coat protein (CP) genes, which share significant identity with corresponding genes in both fungal and plant viruses. Moreover, open reading frames (ORFs) 2-4 of BdBV1 RNA1 shared no detectable identity with any known viral proteins. Immunosorbent electron microscopy (ISEM) analysis using an antibody against the virus CP generated in vitro revealed that BdBV1 is encapsidated in filamentous particles. A comparison of the biological effects of BdBV1 infection on symptoms and growth in isogenic lines of virus-free and virus-infected B. dothidea revealed that BdBV1 is probably involved in reduced growth and virulence of the host fungus. This study describes and characterizes a novel bipartite botrexvirus, which is closely related to uni- and multi-partite fungal and plant viruses and contributes useful information to a better understanding of virus evolution.
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Affiliation(s)
- Mengmeng Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Wenxing Xu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Xiaoqi Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zuokun Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanxiang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Feng Xiao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yashuang Guo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
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Zhu JZ, Guo J, Hu Z, Zhang XT, Li XG, Zhong J. A Novel Partitivirus That Confer Hypovirulence to the Plant Pathogenic Fungus Colletotrichum liriopes. Front Microbiol 2021; 12:653809. [PMID: 34248869 PMCID: PMC8262616 DOI: 10.3389/fmicb.2021.653809] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/14/2021] [Indexed: 12/20/2022] Open
Abstract
Here, we report a novel double-stranded RNA virus designated Colletotrichum liriopes partitivirus 1 (ClPV1) from the plant pathogenic fungus C. liriopes. ClPV1 genome has two double stranded RNAs (dsRNAs), named as dsRNA 1 and dsRNA 2, which in the lengths of 1,807 and 1,706 bp, respectively. The dsRNA 1 and dsRNA 2 encoded proteins showing significant amino acid (aa) sequence identity to the RNA-dependent RNA polymerase (RdRp) and coat protein (CP) of partitiviruses, respectively. Phylogenetic analysis using the aa sequences of RdRp and CP indicated that ClPV1 was grouped to members of the putative Epsilonpartitivirus genus in the Partitiviridae family. Spherical viral particles in approximately 35 nm in diameter and packaging the ClPV1 genome were isolated. Virus elimination and virus transfection with purified viral particles, and biological comparison revealed that ClPV1 could reduce the virulence and conidia production of C. liriopes. To the best of our knowledge, this is the first report of mycovirus in C. liriopes fungus.
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Affiliation(s)
- Jun Zi Zhu
- Hunan Engineering Research Center of Agricultural Pest Early Warning and Control, Hunan Agricultural University, Changsha, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Jun Guo
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Zhao Hu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Xu Tong Zhang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Xiao Gang Li
- Hunan Engineering Research Center of Agricultural Pest Early Warning and Control, Hunan Agricultural University, Changsha, China.,Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
| | - Jie Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, China
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Cryo-electron Microscopy Structure, Assembly, and Mechanics Show Morphogenesis and Evolution of Human Picobirnavirus. J Virol 2020; 94:JVI.01542-20. [PMID: 32938763 DOI: 10.1128/jvi.01542-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/08/2020] [Indexed: 12/17/2022] Open
Abstract
Despite their diversity, most double-stranded-RNA (dsRNA) viruses share a specialized T=1 capsid built from dimers of a single protein that provides a platform for genome transcription and replication. This ubiquitous capsid remains structurally undisturbed throughout the viral cycle, isolating the genome to avoid triggering host defense mechanisms. Human picobirnavirus (hPBV) is a dsRNA virus frequently associated with gastroenteritis, although its pathogenicity is yet undefined. Here, we report the cryo-electron microscopy (cryo-EM) structure of hPBV at 2.6-Å resolution. The capsid protein (CP) is arranged in a single-shelled, ∼380-Å-diameter T=1 capsid with a rough outer surface similar to that of dsRNA mycoviruses. The hPBV capsid is built of 60 quasisymmetric CP dimers (A and B) stabilized by domain swapping, and only the CP-A N-terminal basic region interacts with the packaged nucleic acids. hPBV CP has an α-helical domain with a fold similar to that of fungal partitivirus CP, with many domain insertions in its C-terminal half. In contrast to dsRNA mycoviruses, hPBV has an extracellular life cycle phase like complex reoviruses, which indicates that its own CP probably participates in cell entry. Using an in vitro reversible assembly/disassembly system of hPBV, we isolated tetramers as possible assembly intermediates. We used atomic force microscopy to characterize the biophysical properties of hPBV capsids with different cargos (host nucleic acids or proteins) and found that the CP N-terminal segment not only is involved in nucleic acid interaction/packaging but also modulates the mechanical behavior of the capsid in conjunction with the cargo.IMPORTANCE Despite intensive study, human virus sampling is still sparse, especially for viruses that cause mild or asymptomatic disease. Human picobirnavirus (hPBV) is a double-stranded-RNA virus, broadly dispersed in the human population, but its pathogenicity is uncertain. Here, we report the hPBV structure derived from cryo-electron microscopy (cryo-EM) and reconstruction methods using three capsid protein variants (of different lengths and N-terminal amino acid compositions) that assemble as virus-like particles with distinct properties. The hPBV near-atomic structure reveals a quasisymmetric dimer as the structural subunit and tetramers as possible assembly intermediates that coassemble with nucleic acids. Our structural studies and atomic force microscopy analyses indicate that hPBV capsids are potentially excellent nanocages for gene therapy and targeted drug delivery in humans.
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Honda S, Eusebio-Cope A, Miyashita S, Yokoyama A, Aulia A, Shahi S, Kondo H, Suzuki N. Establishment of Neurospora crassa as a model organism for fungal virology. Nat Commun 2020; 11:5627. [PMID: 33159072 PMCID: PMC7648066 DOI: 10.1038/s41467-020-19355-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/08/2020] [Indexed: 01/07/2023] Open
Abstract
The filamentous fungus Neurospora crassa is used as a model organism for genetics, developmental biology and molecular biology. Remarkably, it is not known to host or to be susceptible to infection with any viruses. Here, we identify diverse RNA viruses in N. crassa and other Neurospora species, and show that N. crassa supports the replication of these viruses as well as some viruses from other fungi. Several encapsidated double-stranded RNA viruses and capsid-less positive-sense single-stranded RNA viruses can be experimentally introduced into N. crassa protoplasts or spheroplasts. This allowed us to examine viral replication and RNAi-mediated antiviral responses in this organism. We show that viral infection upregulates the transcription of RNAi components, and that Dicer proteins (DCL-1, DCL-2) and an Argonaute (QDE-2) participate in suppression of viral replication. Our study thus establishes N. crassa as a model system for the study of host-virus interactions. The fungus Neurospora crassa is a model organism for the study of various biological processes, but it is not known to be infected by any viruses. Here, Honda et al. identify RNA viruses that infect N. crassa and examine viral replication and RNAi-mediated antiviral responses, thus establishing this fungus as a model for the study of host-virus interactions.
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Affiliation(s)
- Shinji Honda
- Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan
| | - Ana Eusebio-Cope
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Shuhei Miyashita
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza- Aoba, Sendai, 980-0845, Japan
| | - Ayumi Yokoyama
- Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan
| | - Annisa Aulia
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Sabitree Shahi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan.
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11
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Jacquat AG, Theumer MG, Cañizares MC, Debat HJ, Iglesias J, García Pedrajas MD, Dambolena JS. A Survey of Mycoviral Infection in Fusarium spp. Isolated from Maize and Sorghum in Argentina Identifies the First Mycovirus from Fusarium verticillioides. Viruses 2020; 12:v12101161. [PMID: 33066620 PMCID: PMC7602464 DOI: 10.3390/v12101161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 12/30/2022] Open
Abstract
Mycoviruses appear to be widespread in Fusarium species worldwide. The aim of this work was to identify mycoviral infections in Fusarium spp., isolated from maize and sorghum grown in Argentina, and to estimate their potential effects on the pathogenicity and toxigenesis of the host fungus towards maize. Mycoviruses were identified in 2 out of 105 isolates analyzed; Fusarium verticillioides strain Sec505 and Fusarium andiyazi strain 162. They were characterized as members of the genus Mitovirus by high-throughput sequencing and sequence analysis. The F. verticillioides mitovirus was a novel mycovirus whereas the F. andiyazi mitovirus was found to be a new strain of a previously identified mitovirus. We have named these mitoviruses, Fusarium verticillioides mitovirus 1 (FvMV1) and Fusarium andiyazi mitovirus 1 strain 162 (FaMV1-162). To our knowledge, FvMV1 is the first mycovirus reported as naturally infecting F. verticillioides, the major causal agent of ear rot and fumonisin producer in corn. Both mitoviruses exhibited 100% vertical transmission rate to microconidia. The Fa162 strain infected with FaMV1-162 did not show phenotypic alterations. In contract, F. verticillioides Sec505 infected with FvMV1 showed increased virulence as well as microconidia and fumonisin-B1 production, compared with two uninfected strains. These results suggest that FvMV1 could have a role in modulating F. verticillioides pathogenicity and toxin production worth further exploring.
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Affiliation(s)
- Andrés Gustavo Jacquat
- Facultad de Ciencias Exactas Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba (UNC), Córdoba 5000, Argentina;
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Vélez Sarsfield 1611, Córdoba X5016GCA, Argentina
| | - Martín Gustavo Theumer
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas (FCQ), Universidad Nacional de Córdoba (UNC), Córdoba 5000, Argentina;
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Haya de la Torre y Medina Allende—Ciudad Universitaria, Córdoba X5000HUA, Argentina
| | - María Carmen Cañizares
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM—UMA—CSIC), Estación Experimental “La Mayora”, Avenida Dr. Wienberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
| | - Humberto Julio Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5.5, Córdoba X5020ICA, Argentina;
| | - Juliana Iglesias
- Estación Experimental Pergamino, (EEA) INTA Pergamino, Universidad Nacional Noroeste (UNNOBA), Pergamino (Buenos Aires) B2700, Argentina;
| | - María Dolores García Pedrajas
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM—UMA—CSIC), Estación Experimental “La Mayora”, Avenida Dr. Wienberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
- Correspondence: (M.D.G.P.); (J.S.D.)
| | - José Sebastián Dambolena
- Facultad de Ciencias Exactas Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba (UNC), Córdoba 5000, Argentina;
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Vélez Sarsfield 1611, Córdoba X5016GCA, Argentina
- Correspondence: (M.D.G.P.); (J.S.D.)
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12
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Mata CP, Rodríguez JM, Suzuki N, Castón JR. Structure and assembly of double-stranded RNA mycoviruses. Adv Virus Res 2020; 108:213-247. [PMID: 33837717 DOI: 10.1016/bs.aivir.2020.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycoviruses are a diverse group that includes ssRNA, dsRNA, and ssDNA viruses, with or without a protein capsid, as well as with a complex envelope. Most mycoviruses are transmitted by cytoplasmic interchange and are thought to lack an extracellular phase in their infection cycle. Structural analysis has focused on dsRNA mycoviruses, which usually package their genome in a 120-subunit T=1 icosahedral capsid, with a capsid protein (CP) dimer as the asymmetric unit. The atomic structure is available for four dsRNA mycovirus from different families: Saccharomyces cerevisiae virus L-A (ScV-L-A), Penicillium chrysogenum virus (PcV), Penicillium stoloniferum virus F (PsV-F), and Rosellinia necatrix quadrivirus 1 (RnQV1). Their capsids show structural variations of the same framework, with asymmetric or symmetric CP dimers respectively for ScV-L-A and PsV-F, dimers of similar domains of a single CP for PcV, or of two different proteins for RnQV1. The CP dimer is the building block, and assembly proceeds through dimers of dimers or pentamers of dimers, in which the genome is packed as ssRNA by interaction with CP and/or viral polymerase. These capsids remain structurally undisturbed throughout the viral cycle. The T=1 capsid participates in RNA synthesis, organizing the viral polymerase (1-2 copies) and a single loosely packaged genome segment. It also acts as a molecular sieve, to allow the passage of viral transcripts and nucleotides, but to prevent triggering of host defense mechanisms. Due to the close mycovirus-host relationship, CP evolved to allocate peptide insertions with enzyme activity, as reflected in a rough outer capsid surface.
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Affiliation(s)
- Carlos P Mata
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Javier M Rodríguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
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13
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Chen Y, Su JE, Qin XY, Fan ZY, Zhang XH, Yu Q, Xia ZY, Zou CM, Zhao GK, Lin ZL. A novel putative betapartitivirus isolated from the plant-pathogenic fungus Rhizoctonia solani. Arch Virol 2020; 165:1697-1701. [PMID: 32405824 DOI: 10.1007/s00705-020-04598-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/24/2020] [Indexed: 10/24/2022]
Abstract
In this study, we describe the genome sequence of a novel double-stranded RNA (dsRNA) mycovirus, designated as "Rhizoctonia solani partitivirus 15" (RsPV15), from the phytopathogenic fungus Rhizoctonia solani. RsPV15 consists of two genomic double-stranded RNA segments, dsRNA-1 and dsRNA-2, which are 2433 bp and 2350 bp long, respectively. Each of the dsRNA segments contains a single open reading frame, encoding the putative RNA-dependent RNA polymerase and coat protein, respectively. Homology searches and phylogenetic analysis suggested that RsPV15 is a new member of the genus Betapartitivirus within the family Partitiviridae.
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Affiliation(s)
- Yi Chen
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Jia En Su
- Research center of Yunnan Aromatic Tobacco Company, Dali, 671000, Yunnan, China
| | - Xi Yun Qin
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Zhi Yong Fan
- Research center of Yunnan Aromatic Tobacco Company, Dali, 671000, Yunnan, China
| | - Xiao Hai Zhang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Qing Yu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Zhen Yuan Xia
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Cong Ming Zou
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Gao Kun Zhao
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China.
| | - Zhong Long Lin
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China.
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14
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Translation of the long-term fundamental studies on viral DNA packaging motors into nanotechnology and nanomedicine. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1103-1129. [DOI: 10.1007/s11427-020-1752-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023]
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15
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Hu Z, Guo J, Da Gao B, Zhong J. A novel mycovirus isolated from the plant-pathogenic fungus Alternaria dianthicola. Arch Virol 2020; 165:2105-2109. [DOI: 10.1007/s00705-020-04700-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/14/2020] [Indexed: 11/27/2022]
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16
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Sato Y, Shamsi W, Jamal A, Bhatti MF, Kondo H, Suzuki N. Hadaka Virus 1: a Capsidless Eleven-Segmented Positive-Sense Single-Stranded RNA Virus from a Phytopathogenic Fungus, Fusarium oxysporum. mBio 2020; 11:e00450-20. [PMID: 32457242 PMCID: PMC7251205 DOI: 10.1128/mbio.00450-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/28/2020] [Indexed: 12/16/2022] Open
Abstract
The search for viruses infecting fungi, or mycoviruses, has extended our knowledge about the diversity of RNA viruses, as exemplified by the discovery of polymycoviruses, a phylogenetic group of multisegmented RNA viruses with unusual forms. The genomic RNAs of known polymycoviruses, which show a phylogenetic affinity for animal positive-sense single-stranded RNA [(+)RNA] viruses such as caliciviruses, are comprised of four conserved segments with an additional zero to four segments. The double-stranded form of polymycovirus genomic RNA is assumed to be associated with a virally encoded protein (proline-alanine-serine-rich protein [PASrp]) in either of two manners: a capsidless colloidal form or a filamentous encapsidated form. Detailed molecular characterizations of polymycoviruses, however, have been conducted for only a few strains. Here, a novel polymyco-related virus named Hadaka virus 1 (HadV1), from the phytopathogenic fungus Fusarium oxysporum, was characterized. The genomic RNA of HadV1 consisted of an 11-segmented positive-sense RNA with highly conserved terminal nucleotide sequences. HadV1 shared the three conserved segments with known polymycoviruses but lacked the PASrp-encoding segment. Unlike the known polymycoviruses and encapsidated viruses, HadV1 was not pelleted by conventional ultracentrifugation, possibly due to the lack of PASrp. This result implied that HadV1 exists only as a soluble form with naked RNA. Nevertheless, the 11 genomic segments of HadV1 have been stably maintained through host subculturing and conidiation. Taken together, the results of this study revealed a virus with a potential novel virus lifestyle, carrying many genomic segments without typical capsids or PASrp-associated forms.IMPORTANCE Fungi collectively host various RNA viruses. Examples include encapsidated double-stranded RNA (dsRNA) viruses with diverse numbers of genomic segments (from 1 to 12) and capsidless viruses with nonsegmented (+)RNA genomes. Recently, viruses with unusual intermediate features of an infectious entity between encapsidated dsRNA viruses and capsidless (+)RNA viruses were found. They are called polymycoviruses, which typically have four to eight dsRNA genomic segments associated with one of the virus-encoded proteins and are phylogenetically distantly related to animal (+)RNA caliciviruses. Here, we identified a novel virus phylogenetically related to polymycoviruses, from the phytopathogenic fungus Fusarium oxysporum The virus, termed Hadaka virus 1 (HadV1), has 11 (+)RNA genomic segments, the largest number in known (+)RNA viruses. Nevertheless, HadV1 lacked a typical structural protein of polymycoviruses and was not pelleted by standard ultracentrifugation, implying an unusual capsidless nature of HadV1. This study reveals a potential novel lifestyle of multisegmented RNA viruses.
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Affiliation(s)
- Yukiyo Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Wajeeha Shamsi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, Pakistan
| | - Atif Jamal
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, Pakistan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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17
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Li P, Wang S, Zhang L, Qiu D, Zhou X, Guo L. A tripartite ssDNA mycovirus from a plant pathogenic fungus is infectious as cloned DNA and purified virions. SCIENCE ADVANCES 2020; 6:eaay9634. [PMID: 32284975 PMCID: PMC7138691 DOI: 10.1126/sciadv.aay9634] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/09/2020] [Indexed: 05/27/2023]
Abstract
Here, we describe a tripartite circular single-stranded (ss) DNA mycovirus, named Fusarium graminearum gemytripvirus 1 (FgGMTV1). The genome of FgGMTV1 comprises three circular ssDNA segments (DNA-A, DNA-B, and DNA-C). Sequence alignments and phylogenetic analyses showed that FgGMTV1 is nested within the family Genomoviridae. We also constructed the first infectious DNA clones of a DNA mycovirus. Our results show that DNA-A and DNA-B are mutually interdependent for their replication and are associated with severely reduced colony growth and hypovirulence. DNA-C relies on DNA-A and DNA-B for replication and is necessary for the recovery of abnormal fungal phenotypes. DNA-C also enhances the accumulation of viral DNA in infected fungi and permits stable colonization and easy transmission via conidia. This is the first multipartite DNA virus isolated from a fungus. Our phylogenetic analyses also suggest that the multipartite genome of FgGMTV1 may have evolved from a monopartite genome of an ancient genomovirus.
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18
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Characterization of three novel betapartitiviruses co-infecting the phytopathogenic fungus Rhizoctonia solani. Virus Res 2019; 270:197649. [DOI: 10.1016/j.virusres.2019.197649] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/29/2019] [Accepted: 07/01/2019] [Indexed: 11/17/2022]
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19
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Hitch TCA, Edwards JE, Gilbert RA. Metatranscriptomics reveals mycoviral populations in the ovine rumen. FEMS Microbiol Lett 2019; 366:5533320. [DOI: 10.1093/femsle/fnz161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/16/2019] [Indexed: 12/26/2022] Open
Abstract
ABSTRACT
The rumen is known to contain DNA-based viruses, although it is not known whether RNA-based viruses that infect fungi (mycoviruses) are also present. Analysis of publicly available rumen metatranscriptome sequence data from sheep rumen samples (n = 20) was used to assess whether RNA-based viruses exist within the ovine rumen. A total of 2466 unique RNA viral contigs were identified that had homology to nine viral families. The Partitiviridae was the most consistently observed mycoviral family. High variation in the abundance of each detected mycovirus suggests that rumen mycoviral populations vary greatly between individual sheep. Functional analysis of the genes within the assembled mycoviral contigs suggests that the mycoviruses detected had simple genomes, often only carrying the machinery required for replication. The fungal population of the ovine rumen was also assessed using metagenomics data from the same samples, and was consistently dominated by the phyla Ascomycota and Basidomycota. The strictly anaerobic phyla Neocallimastigomycota were also present in all samples but at a low abundance. This preliminary investigation has provided clear evidence that mycoviruses with RNA genomes exist in the rumen, with further in-depth studies now required to characterise this mycoviral community and determine its role in the rumen.
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Affiliation(s)
- Thomas C A Hitch
- Institute of Biological, Environmental and Rural Sciences, Penglais Campus, Aberystwyth University, Aberystwyth, UK
- Institute of Medical Microbiology, RWTH Aachen University Hospital, Aachen, Germany
| | - Joan E Edwards
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Rosalind A Gilbert
- Department of Agriculture and Fisheries, Brisbane, Australia
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
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20
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Shamsi W, Sato Y, Jamal A, Shahi S, Kondo H, Suzuki N, Bhatti MF. Molecular and biological characterization of a novel botybirnavirus identified from a Pakistani isolate of Alternaria alternata. Virus Res 2019; 263:119-128. [DOI: 10.1016/j.virusres.2019.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 11/15/2022]
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21
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The 13th International Double-Stranded RNA Virus Symposium, Houffalize, Belgium, 24 to 28 September 2018. J Virol 2019; 93:JVI.01964-18. [PMID: 30723139 DOI: 10.1128/jvi.01964-18] [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: 11/02/2018] [Accepted: 11/20/2018] [Indexed: 11/20/2022] Open
Abstract
The triennial International Double-Stranded RNA Virus Symposium, this year organized by J. Matthijnssens, J. S. L. Parker, P. Danthi, and P. Van Damme in Belgium, gathered over 200 scientists to discuss novel observations and hypotheses in the field. The keynote lecture on functional interactions of bacteria and viruses in the gut microbiome was presented by Julie Pfeiffer. Workshops were held on viral diversity, molecular epidemiology, molecular virology, immunity and pathogenesis, virus structure, the viral use and abuse of cellular pathways, and applied double-stranded RNA (dsRNA) virology. The establishment of a plasmid only-based reverse genetics system for rotaviruses by several Japanese research groups in 2017 has now been reproduced by various other research groups and was discussed in detail. The visualization of dsRNA virus replication steps in living cells received much attention. Mechanisms of the cellular innate immune response to virus infection and of viral pathogenesis were explored. Knowledge of the gut microbiome's influence on specific immune responses has increased rapidly, also due to the availability of relevant animal models of virus infection. The method of cryo-electron microscopic (cryo-EM) tomography has elucidated various asymmetric structures in viral particles. The use of orthoreoviruses for oncolytic virotherapy was critically assessed. The application of llama-derived single chain nanobodies for passive immunotherapy was considered attractive. In a satellite symposium the introduction, impact and further developments of rotavirus vaccines were reviewed. The Jean Cohen Lecturer of this meeting was Harry B. Greenberg, who presented aspects of his research on rotaviruses over a period of more than 40 years. He was also interviewed at the meeting by Vincent Racaniello for the 513th session of This Week in Virology.
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22
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Shah UA, Kotta-Loizou I, Fitt BDL, Coutts RHA. Identification, Molecular Characterization, and Biology of a Novel Quadrivirus Infecting the Phytopathogenic Fungus Leptosphaeria biglobosa. Viruses 2018; 11:E9. [PMID: 30585188 PMCID: PMC6356713 DOI: 10.3390/v11010009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 12/20/2018] [Accepted: 12/22/2018] [Indexed: 01/18/2023] Open
Abstract
Here we report the molecular characterisation of a novel dsRNA virus isolated from the filamentous, plant pathogenic fungus Leptosphaeria biglobosa and known to cause significant alterations to fungal pigmentation and growth and to result in hypervirulence, as illustrated by comparisons between virus-infected and -cured isogenic fungal strains. The virus forms isometric particles approximately 40⁻45 nm in diameter and has a quadripartite dsRNA genome structure with size ranges of 4.9 to 4 kbp, each possessing a single ORF. Sequence analysis of the putative proteins encoded by dsRNAs 1⁻4, termed P1⁻P4, respectively, revealed modest similarities to the amino acid sequences of equivalent proteins predicted from the nucleotide sequences of known and suspected members of the family Quadriviridae and for that reason the virus was nominated Leptosphaeria biglobosa quadrivirus-1 (LbQV-1). Sequence and phylogenetic analysis using the P3 sequence, which encodes an RdRP, revealed that LbQV-1 was most closely related to known and suspected quadriviruses and monopartite totiviruses rather than other quadripartite mycoviruses including chrysoviruses and alternaviruses. Of the remaining encoded proteins, LbQV-1 P2 and P4 are structural proteins but the function of P1 is unknown. We propose that LbQV-1 is a novel member of the family Quadriviridae.
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Affiliation(s)
- Unnati A Shah
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.
| | - Ioly Kotta-Loizou
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
| | - Bruce D L Fitt
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.
| | - Robert H A Coutts
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK.
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23
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Affiliation(s)
| | - Stéphane Blanc
- BGPI, INRA, CIRAD, Montpellier SupAgro, Univ Montpellier, Montpellier, France.
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24
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Capsid Structure of dsRNA Fungal Viruses. Viruses 2018; 10:v10090481. [PMID: 30205532 PMCID: PMC6164181 DOI: 10.3390/v10090481] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/05/2018] [Accepted: 09/05/2018] [Indexed: 01/27/2023] Open
Abstract
Most fungal, double-stranded (ds) RNA viruses lack an extracellular life cycle stage and are transmitted by cytoplasmic interchange. dsRNA mycovirus capsids are based on a 120-subunit T = 1 capsid, with a dimer as the asymmetric unit. These capsids, which remain structurally undisturbed throughout the viral cycle, nevertheless, are dynamic particles involved in the organization of the viral genome and the viral polymerase necessary for RNA synthesis. The atomic structure of the T = 1 capsids of four mycoviruses was resolved: the L-A virus of Saccharomyces cerevisiae (ScV-L-A), Penicillium chrysogenum virus (PcV), Penicillium stoloniferum virus F (PsV-F), and Rosellinia necatrix quadrivirus 1 (RnQV1). These capsids show structural variations of the same framework, with 60 asymmetric or symmetric homodimers for ScV-L-A and PsV-F, respectively, monomers with a duplicated similar domain for PcV, and heterodimers of two different proteins for RnQV1. Mycovirus capsid proteins (CP) share a conserved α-helical domain, although the latter may carry different peptides inserted at preferential hotspots. Insertions in the CP outer surface are likely associated with enzymatic activities. Within the capsid, fungal dsRNA viruses show a low degree of genome compaction compared to reoviruses, and contain one to two copies of the RNA-polymerase complex per virion.
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25
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Lucía-Sanz A, Aguirre J, Manrubia S. Theoretical approaches to disclosing the emergence and adaptive advantages of multipartite viruses. Curr Opin Virol 2018; 33:89-95. [PMID: 30121469 DOI: 10.1016/j.coviro.2018.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/19/2018] [Accepted: 07/31/2018] [Indexed: 01/02/2023]
Abstract
Multipartite viruses have a segmented genome encapsidated in different viral particles that, in principle, propagate independently. Current empirical knowledge on the molecular, ecological and evolutionary features underlying the very existence of multipartitism is fragmented and puzzling. Although it is generally assumed that multipartitism is viable only when propagation occurs at high multiplicity of infection, evidence indicates that severe population bottlenecks are common. Mathematical models aimed at describing the dynamics of multipartite viruses typically assign an advantage to the multipartite form to compensate for the cost of high multiplicity of infection. Since progress in the theoretical understanding of the evolutionary ecology of multipartitism is strongly conditioned by empirical advances, both aspects are jointly revised in this contribution.
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Affiliation(s)
- Adriana Lucía-Sanz
- Spanish National Centre for Biotechnology (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| | - Jacobo Aguirre
- Spanish National Centre for Biotechnology (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
| | - Susanna Manrubia
- Spanish National Centre for Biotechnology (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
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