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Jia J, Nan L, Song Z, Chen X, Xia J, Cheng L, Zhang B, Mu F. Cross-species transmission of a novel bisegmented orfanplasmovirus in the phytopathogenic fungus Exserohilum rostratum. Front Microbiol 2024; 15:1409677. [PMID: 38846572 PMCID: PMC11153860 DOI: 10.3389/fmicb.2024.1409677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
Mycoviruses have been found in various fungal species across different taxonomic groups, while no viruses have been reported yet in the fungus Exserohilum rostratum. In this study, a novel orfanplasmovirus, namely Exserohilum rostratum orfanplasmovirus 1 (ErOrfV1), was identified in the Exserohilum rostratum strain JZ1 from maize leaf. The complete genome of ErOrfV1 consists of two positive single-stranded RNA segments, encoding an RNA-dependent RNA polymerase and a hypothetical protein with unknown function, respectively. Phylogenetic analysis revealed that ErOrfV1 clusters with other orfanplasmoviruses, forming a distinct phyletic clade. A new family, Orfanplasmoviridae, is proposed to encompass this newly discovered ErOrfV1 and its associated orfanplasmoviruses. ErOrfV1 exhibits effective vertical transmission through conidia, as evidenced by its 100% presence in over 200 single conidium isolates. Moreover, it can be horizontally transmitted to Exserohilum turcicum. Additionally, the infection of ErOrfV1 is cryptic in E. turcicum because there were no significant differences in mycelial growth rate and colony morphology between ErOrfV1-infected and ErOrfV1-free strains. This study represents the inaugural report of a mycovirus in E. rostratum, as well as the first documentation of the biological and transmission characteristics of orfanplasmovirus. These discoveries significantly contribute to our understanding of orfanplasmovirus.
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Affiliation(s)
- Jichun Jia
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Linjie Nan
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Zehao Song
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Xu Chen
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Jinsheng Xia
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Lihong Cheng
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Baojun Zhang
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
| | - Fan Mu
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, Taiyuan, Shanxi, China
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Prasad A, Sharma S, Prasad M. Deeper look into viruses: replication intermediates do code! PLANT CELL REPORTS 2024; 43:52. [PMID: 38308009 DOI: 10.1007/s00299-023-03135-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 02/04/2024]
Affiliation(s)
- Ashish Prasad
- Department of Botany, Kurukshetra University, Kurukshetra, India
| | | | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India.
- Department of Genetics, University of Delhi South Campus, New Delhi, India.
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3
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Li F, Jia M, Wang A. Hidden viral proteins: How powerful are they? PLoS Pathog 2024; 20:e1011905. [PMID: 38236814 PMCID: PMC10795976 DOI: 10.1371/journal.ppat.1011905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2024] Open
Affiliation(s)
- Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingxuan Jia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
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4
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Cheng X, Wu X, Fang R. The minus strand of positive-sense RNA viruses encodes small proteins. Trends Microbiol 2024; 32:6-7. [PMID: 37951770 DOI: 10.1016/j.tim.2023.10.012] [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: 10/19/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
It is widely accepted that the minus strands of positive single-strand RNA (+ssRNA) viruses function as replication templates only. Gong et al. revealed that the minus strand of two unrelated +ssRNA viruses encodes proteins. This textbook-changing discovery calls for the reconsideration of the molecular mechanisms underlying the infection cycle of +ssRNA viruses.
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Affiliation(s)
- Xiaofei Cheng
- College of Plant Protection/Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, Northeast Agricultural University, 150030 Harbin, Heilongjiang, China.
| | - Xiaoyun Wu
- College of Plant Protection/Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, Northeast Agricultural University, 150030 Harbin, Heilongjiang, China
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
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5
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Litov AG, Belova OA, Kholodilov IS, Kalyanova AS, Gadzhikurbanov MN, Rogova AA, Gmyl LV, Karganova GG. Viromes of Tabanids from Russia. Viruses 2023; 15:2368. [PMID: 38140608 PMCID: PMC10748123 DOI: 10.3390/v15122368] [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: 10/30/2023] [Revised: 11/21/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Advances in sequencing technologies and bioinformatics have greatly enhanced our knowledge of virus biodiversity. Currently, the viromes of hematophagous invertebrates, such as mosquitoes and ixodid ticks, are being actively studied. Tabanidae (Diptera) are a widespread family, with members mostly known for their persistent hematophagous behavior. They transmit viral, bacterial, and other pathogens, both biologically and mechanically. However, tabanid viromes remain severely understudied. In this study, we used high-throughput sequencing to describe the viromes of several species in the Hybomitra, Tabanus, Chrysops, and Haematopota genera, which were collected in two distant parts of Russia: the Primorye Territory and Ryazan Region. We assembled fourteen full coding genomes of novel viruses, four partial coding genomes, as well as several fragmented viral sequences, which presumably belong to another twelve new viruses. All the discovered viruses were tested for their ability to replicate in mammalian porcine embryo kidney (PEK), tick HAE/CTVM8, and mosquito C6/36 cell lines. In total, 16 viruses were detected in at least one cell culture after three passages (for PEK and C6/36) or 3 weeks of persistence in HAE/CTVM8. However, in the majority of cases, qPCR showed a decline in virus load over time.
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Affiliation(s)
- Alexander G. Litov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Oxana A. Belova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Ivan S. Kholodilov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Anna S. Kalyanova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Magomed N. Gadzhikurbanov
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
- Department of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Anastasia A. Rogova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Larissa V. Gmyl
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
| | - Galina G. Karganova
- Laboratory of Biology of Arboviruses, FSASI Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS, 108819 Moscow, Russia; (A.G.L.); (O.A.B.); (I.S.K.); (M.N.G.); (A.A.R.); (L.V.G.)
- Institute for Translational Medicine and Biotechnology, Sechenov University, 119991 Moscow, Russia
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6
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Gong P, Shen Q, Zhang M, Qiao R, Jiang J, Su L, Zhao S, Fu S, Ma Y, Ge L, Wang Y, Lozano-Durán R, Wang A, Li F, Zhou X. Plant and animal positive-sense single-stranded RNA viruses encode small proteins important for viral infection in their negative-sense strand. MOLECULAR PLANT 2023; 16:1794-1810. [PMID: 37777826 DOI: 10.1016/j.molp.2023.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/03/2023] [Accepted: 09/26/2023] [Indexed: 10/02/2023]
Abstract
Positive-sense single-stranded RNA (+ssRNA) viruses, the most abundant viruses of eukaryotes in nature, require the synthesis of negative-sense RNA (-RNA) using their genomic (positive-sense) RNA (+RNA) as a template for replication. Based on current evidence, viral proteins are translated via viral +RNAs, whereas -RNA is considered to be a viral replication intermediate without coding capacity. Here, we report that plant and animal +ssRNA viruses contain small open reading frames (ORFs) in their -RNA (reverse ORFs [rORFs]). Using turnip mosaic virus (TuMV) as a model for plant +ssRNA viruses, we demonstrate that small proteins encoded by rORFs display specific subcellular localizations, and confirm the presence of rORF2 in infected cells through mass spectrometry analysis. The protein encoded by TuMV rORF2 forms punctuate granules that are localized in the perinuclear region and co-localized with viral replication complexes. The rORF2 protein can directly interact with the viral RNA-dependent RNA polymerase, and mutation of rORF2 completely abolishes virus infection, whereas ectopic expression of rORF2 rescues the mutant virus. Furthermore, we show that several rORFs in the -RNA of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have the ability to suppress type I interferon production and facilitate the infection of vesicular stomatitis virus. In addition, we provide evidence that TuMV might utilize internal ribosome entry sites to translate these small rORFs. Taken together, these findings indicate that the -RNA of +ssRNA viruses can also have the coding capacity and that small proteins encoded therein play critical roles in viral infection, revealing a viral proteome larger than previously thought.
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Affiliation(s)
- Pan Gong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingtang Shen
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Mingzhen Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Qiao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Jiang
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Lili Su
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Siwen Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuai Fu
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yu Ma
- University of the Chinese Academy of Sciences, Beijing, China
| | - Linhao Ge
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Rosa Lozano-Durán
- Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, 72076 Tübingen, Germany
| | - Aiming Wang
- London Research and Development Center, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; State Key Laboratory of Rice Biology and Breeding, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China.
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7
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Andika IB, Cao X, Kondo H, Sun L. The intriguing phenomenon of cross-kingdom infections of plant and insect viruses to fungi: Can other animal viruses also cross-infect fungi? PLoS Pathog 2023; 19:e1011726. [PMID: 37883353 PMCID: PMC10602238 DOI: 10.1371/journal.ppat.1011726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
Fungi are highly widespread and commonly colonize multicellular organisms that live in natural environments. Notably, studies on viruses infecting plant-associated fungi have revealed the interesting phenomenon of the cross-kingdom transmission of viruses and viroids from plants to fungi. This implies that fungi, in addition to absorbing water, nutrients, and other molecules from the host, can acquire intracellular parasites that reside in the host. These findings further suggest that fungi can serve as suitable alternative hosts for certain plant viruses and viroids. Given the frequent coinfection of fungi and viruses in humans/animals, the question of whether fungi can also acquire animal viruses and serve as their hosts is very intriguing. In fact, the transmission of viruses from insects to fungi has been observed. Furthermore, the common release of animal viruses into the extracellular space (viral shedding) could potentially facilitate their acquisition by fungi. Investigations of the cross-infection of animal viruses in fungi may provide new insights into the epidemiology of viral diseases in humans and animals.
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Affiliation(s)
- Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xinran Cao
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Shandong Agricultural University, Tai’an, China
- Shouguang International Vegetable Sci-tech Fair Management Service Center, Shouguang, China
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Xianyang, China
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8
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Abbo SR, de Almeida JPP, Olmo RP, Balvers C, Griep JS, Linthout C, Koenraadt CJM, Silva BM, Fros JJ, Aguiar ERGR, Marois E, Pijlman GP, Marques JT. The virome of the invasive Asian bush mosquito Aedes japonicus in Europe. Virus Evol 2023; 9:vead041. [PMID: 37636319 PMCID: PMC10460169 DOI: 10.1093/ve/vead041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/05/2023] [Accepted: 06/30/2023] [Indexed: 08/29/2023] Open
Abstract
The Asian bush mosquito Aedes japonicus is rapidly invading North America and Europe. Due to its potential to transmit multiple pathogenic arthropod-borne (arbo)viruses including Zika virus, West Nile virus, and chikungunya virus, it is important to understand the biology of this vector mosquito in more detail. In addition to arboviruses, mosquitoes can also carry insect-specific viruses that are receiving increasing attention due to their potential effects on host physiology and arbovirus transmission. In this study, we characterized the collection of viruses, referred to as the virome, circulating in Ae. japonicus populations in the Netherlands and France. Applying a small RNA-based metagenomic approach to Ae. japonicus, we uncovered a distinct group of viruses present in samples from both the Netherlands and France. These included one known virus, Ae. japonicus narnavirus 1 (AejapNV1), and three new virus species that we named Ae. japonicus totivirus 1 (AejapTV1), Ae. japonicus anphevirus 1 (AejapAV1) and Ae. japonicus bunyavirus 1 (AejapBV1). We also discovered sequences that were presumably derived from two additional novel viruses: Ae. japonicus bunyavirus 2 (AejapBV2) and Ae. japonicus rhabdovirus 1 (AejapRV1). All six viruses induced strong RNA interference responses, including the production of twenty-one nucleotide-sized small interfering RNAs, a signature of active replication in the host. Notably, AejapBV1 and AejapBV2 belong to different viral families; however, no RNA-dependent RNA polymerase sequence has been found for AejapBV2. Intriguingly, our small RNA-based approach identified an ∼1-kb long ambigrammatic RNA that is associated with AejapNV1 as a secondary segment but showed no similarity to any sequence in public databases. We confirmed the presence of AejapNV1 primary and secondary segments, AejapTV1, AejapAV1, and AejapBV1 by reverse transcriptase polymerase chain reaction (PCR) in wild-caught Ae. japonicus mosquitoes. AejapNV1 and AejapTV1 were found at high prevalence (87-100 per cent) in adult females, adult males, and larvae. Using a small RNA-based, sequence-independent metagenomic strategy, we uncovered a conserved and prevalent virome among Ae. japonicus mosquito populations. The high prevalence of AejapNV1 and AejapTV1 across all tested mosquito life stages suggests that these viruses are intimately associated with Ae. japonicus.
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Affiliation(s)
- Sandra R Abbo
- Laboratory of Virology, Wageningen University & Research, Droevendaalsesteeg 4, Wageningen 6708 PB, The Netherlands
| | - João P P de Almeida
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, Belo Horizonte 31270-901, Brazil
| | - Roenick P Olmo
- Insect Models of Innate Immunity, Université de Strasbourg, CNRS UPR9022, INSERM U1257, 2 Allee Konrad Roentgen, Strasbourg 67000, France
| | - Carlijn Balvers
- Laboratory of Virology, Wageningen University & Research, Droevendaalsesteeg 4, Wageningen 6708 PB, The Netherlands
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 4, Wageningen 6708 PB, The Netherlands
| | - Jet S Griep
- Laboratory of Virology, Wageningen University & Research, Droevendaalsesteeg 4, Wageningen 6708 PB, The Netherlands
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 4, Wageningen 6708 PB, The Netherlands
| | - Charlotte Linthout
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 4, Wageningen 6708 PB, The Netherlands
| | - Constantianus J M Koenraadt
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 4, Wageningen 6708 PB, The Netherlands
| | - Bruno M Silva
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, Belo Horizonte 31270-901, Brazil
| | - Jelke J Fros
- Laboratory of Virology, Wageningen University & Research, Droevendaalsesteeg 4, Wageningen 6708 PB, The Netherlands
| | - Eric R G R Aguiar
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, Belo Horizonte 31270-901, Brazil
- Department of Biological Science, Center of Biotechnology and Genetics, State University of Santa Cruz, Rod. Jorge Amado Km 16, Ilhéus 45662-900, Brazil
| | - Eric Marois
- Insect Models of Innate Immunity, Université de Strasbourg, CNRS UPR9022, INSERM U1257, 2 Allee Konrad Roentgen, Strasbourg 67000, France
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University & Research, Droevendaalsesteeg 4, Wageningen 6708 PB, The Netherlands
| | - João T Marques
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antonio Carlos 6627, Belo Horizonte 31270-901, Brazil
- Insect Models of Innate Immunity, Université de Strasbourg, CNRS UPR9022, INSERM U1257, 2 Allee Konrad Roentgen, Strasbourg 67000, France
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Zhang Y, Liang X, Zhao M, Qi T, Guo H, Zhao J, Zhao J, Zhan G, Kang Z, Zheng L. A novel ambigrammatic mycovirus, PsV5, works hand in glove with wheat stripe rust fungus to facilitate infection. PLANT COMMUNICATIONS 2023; 4:100505. [PMID: 36527233 DOI: 10.1016/j.xplc.2022.100505] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/16/2022] [Accepted: 12/14/2022] [Indexed: 05/11/2023]
Abstract
Here we describe a novel narnavirus, Puccinia striiformis virus 5 (PsV5), from the devastating wheat stripe rust fungus P. striiformis f. sp. tritici (Pst). The genome of PsV5 contains two predicted open reading frames (ORFs) that largely overlap on reverse strands: an RNA-dependent RNA polymerase (RdRp) and a reverse-frame ORF (rORF) with unknown function. Protein translations of both ORFs were demonstrated by immune technology. Transgenic wheat lines overexpressing PsV5 (RdRp-rORF), RdRp ORF, or rORF were more susceptible to Pst infection, whereas PsV5-RNA interference (RNAi) lines were more resistant. Overexpression of PsV5 (RdRp-rORF), RdRp ORF, or rORF in Fusarium graminearum also boosted fungal virulence. We thus report a novel ambigrammatic mycovirus that promotes the virulence of its fungal host. The results are a significant addition to our understanding of virosphere diversity and offer insights for sustainable wheat rust disease control.
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Affiliation(s)
- Yanhui Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaofei Liang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengxin Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tuo Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, State Key Laboratory of Hybrid Rice, Key Laboratory of Major Crop Diseases & Collaborative Innovation Center for Hybrid Rice in Yangtze River Basin, Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Hualong Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gangming Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Li Zheng
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education and School of Plant Protection, Hainan University, Haikou, Hainan 570228, China.
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10
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Identification of Three Viruses Infecting Mulberry Varieties. Viruses 2022; 14:v14112564. [PMID: 36423172 PMCID: PMC9696721 DOI: 10.3390/v14112564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Viruses-mediated genome editing in plants is a powerful strategy to develop plant cultivars with important and novel agricultural traits. Mulberry alba is an important economic tree species that has been cultivated in China for more than 5000 years. So far, only a few viruses have been identified from mulberry trees, and their application potential is largely unknown. Therefore, mining more virus resources from the mulberry tree can pave the way for the establishment of useful engineering tools. In this study, eight old mulberry plants were gathered in seven geographic areas for virome analysis. Based on transcriptome analysis, we discovered three viruses associated with mulberries: Citrus leaf blotch virus isolate mulberry alba 2 (CLBV-ML2), Mulberry-associated virga-like virus (MaVLV), and Mulberry-associated narna-like virus (MaNLV). The genome of CLBV-ML2 was completely sequenced and exhibited high homology with Citriviruses, considered to be members of the genus Citrivirus, while the genomes of MaVLV and MaNLV were nearly completed lacking the 5' and 3' termini sequences. We tentatively consider MaVLV to be members of the family Virgaviridae and MaNLV to be members of the genus Narnavirus based on the results of phylogenetic trees. The infection experiments showed that CLBV-ML2 could be detected in the inoculated seedlings of both N. benthamiana and Morus alba, while MaVLV could only be detected in N. benthamiana. All of the infected seedlings did not show obvious symptoms.
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11
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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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12
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Kondo H, Botella L, Suzuki N. Mycovirus Diversity and Evolution Revealed/Inferred from Recent Studies. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:307-336. [PMID: 35609970 DOI: 10.1146/annurev-phyto-021621-122122] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
High-throughput virome analyses with various fungi, from cultured or uncultured sources, have led to the discovery of diverse viruses with unique genome structures and even neo-lifestyles. Examples in the former category include splipalmiviruses and ambiviruses. Splipalmiviruses, related to yeast narnaviruses, have multiple positive-sense (+) single-stranded (ss) RNA genomic segments that separately encode the RNA-dependent RNA polymerase motifs, the hallmark of RNA viruses (members of the kingdom Orthornavirae). Ambiviruses appear to have an undivided ssRNA genome of 3∼5 kb with two large open reading frames (ORFs) separated by intergenic regions. Another narna-like virus group has two fully overlapping ORFs on both strands of a genomic segment that span more than 90% of the genome size. New virus lifestyles exhibited by mycoviruses include the yado-kari/yado-nushi nature characterized by the partnership between the (+)ssRNA yadokarivirus and an unrelated dsRNA virus (donor of the capsid for the former) and the hadaka nature of capsidless 10-11 segmented (+)ssRNA accessible by RNase in infected mycelial homogenates. Furthermore, dsRNA polymycoviruses with phylogenetic affinity to (+)ssRNA animal caliciviruses have been shown to be infectious as dsRNA-protein complexes or deproteinized naked dsRNA. Many previous phylogenetic gaps have been filled by recently discovered fungal and other viruses, which haveprovided interesting evolutionary insights. Phylogenetic analyses and the discovery of natural and experimental cross-kingdom infections suggest that horizontal virus transfer may have occurred and continue to occur between fungi and other kingdoms.
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Affiliation(s)
- Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
| | - Leticia Botella
- Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University, Brno, Czech Republic
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
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Galán-Cubero R, Córdoba L, Rodríguez-Romero J, Chiapello M, Turina M, Ayllón MA. Molecular Data of a Novel Penoulivirus Associated with the Plant-Pathogenic Fungus Erysiphe necator. PHYTOPATHOLOGY 2022; 112:1587-1591. [PMID: 35509205 DOI: 10.1094/phyto-12-21-0536-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Rocío Galán-Cubero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain
| | - Laura Córdoba
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain
| | - Julio Rodríguez-Romero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28040, Spain
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28040, Spain
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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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15
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Wilkinson M, Yllanes D, Huber G. Polysomally protected viruses. Phys Biol 2021; 18. [PMID: 33827061 DOI: 10.1088/1478-3975/abf5b5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/07/2021] [Indexed: 11/12/2022]
Abstract
It is conceivable that an RNA virus could use a polysome, that is, a string of ribosomes covering the RNA strand, to protect the genetic material from degradation inside a host cell. This paper discusses how such a virus might operate, and how its presence might be detected by ribosome profiling. There are two possible forms for such apolysomally protected virus, depending upon whether just the forward strand or both the forward and complementary strands can be encased by ribosomes (these will be termed type 1 and type 2, respectively). It is argued that in the type 2 case the viral RNA would evolve anambigrammaticproperty, whereby the viral genes are free of stop codons in a reverse reading frame (with forward and reverse codons aligned). Recent observations of ribosome profiles of ambigrammatic narnavirus sequences are consistent with our predictions for the type 2 case.
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Affiliation(s)
- Michael Wilkinson
- Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, United States of America.,School of Mathematics and Statistics, The Open University, Walton Hall, Milton Keynes, MK7 6AA, United Kingdom
| | - David Yllanes
- Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, United States of America
| | - Greg Huber
- Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, United States of America
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Abstract
Double synonyms in the genetic code can be used as a tool to test competing hypotheses regarding ambigrammatic narnavirus genomes. Applying the analysis to recent observations of Culex narnavirus 1 and Zhejiang mosquito virus 3 ambigrammatic viruses indicates that the open reading frame on the complementary strand of the segment coding for RNA-dependent RNA polymerase does not code for a functional protein. Culex narnavirus 1 has been shown to possess a second segment, also ambigrammatic, termed 'Robin'. We find a comparable segment for Zhejiang mosquito virus 3, a moderately diverged relative of Culex narnavirus 1. Our analysis of Robin polymorphisms suggests that its reverse open reading frame also does not code for a functional protein. We make a hypothesis about its role.
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Affiliation(s)
- Gytis Dudas
- Gothenburg Global Biodiversity Centre, Carl Skottsbergs Gata 22B, 413 19 Gothenburg, Sweden
| | - Greg Huber
- Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, USA
| | - Michael Wilkinson
- Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, USA
- School of Mathematics and Statistics, The Open University, Walton Hall, Milton Keynes MK7 6AA, UK
| | - David Yllanes
- Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, USA
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