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Khan HA, Mukhtar M, Bhatti MF. Mycovirus-induced hypovirulence in notorious fungi Sclerotinia: a comprehensive review. Braz J Microbiol 2023; 54:1459-1478. [PMID: 37523037 PMCID: PMC10485235 DOI: 10.1007/s42770-023-01073-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023] Open
Abstract
Members of the genus Sclerotinia are notorious plant pathogens with a diverse host range that includes many important crops. A huge number of mycoviruses have been identified in this genus; some of these viruses are reported to have a hypovirulent effect on the fitness of their fungal hosts. These mycoviruses are important to researchers from a biocontrol perspective which was first implemented against fungal diseases in 1990. In this review, we have presented the data of all hypovirulent mycoviruses infecting Sclerotinia sclerotiorum isolates. The data of hypovirulent mycoviruses ranges from 1992 to 2023. Currently, mycoviruses belonging to 17 different families, including (+) ssRNA, (-ssRNA), dsRNA, and ssDNA viruses, have been reported from this genus. Advances in studies had shown a changed expression of certain host genes (responsible for cell cycle regulation, DNA replication, repair pathways, ubiquitin proteolysis, gene silencing, methylation, pathogenesis-related, sclerotial development, carbohydrate metabolism, and oxalic acid biosynthesis) during the course of mycoviral infection, which were termed differentially expressed genes (DEGs). Together, research on fungal viruses and hypovirulence in Sclerotinia species can deepen our understanding of the cellular processes that affect how virulence manifests in these phytopathogenic fungi and increase the potential of mycoviruses as a distinct mode of biological control. Furthermore, the gathered data can also be used for in-silico analysis, which includes finding the signature sites [e.g., hypovirus papain-like protease (HPP) domain, "CCHH" motif, specific stem-loop structures, p29 motif as in CHV1, A-rich sequence, CA-rich sequences as in MoV1, GCU motif as in RnMBV1, Core motifs in hypovirus-associated RNA elements (HAREs) as in CHV1] that are possibly responsible for hypovirulence in mycoviruses.
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Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan.
- Department of Biotechnology, University of Mianwali, Mianwali, Punjab, 42200, Pakistan.
| | - Mamuna Mukhtar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, Islamabad, 44000, Pakistan
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Abstract
RNA viruses usually have linear genomes and are encapsidated by their own capsids. Here, we newly identified four mycoviruses and two previously reported mycoviruses (a fungal reovirus and a botybirnavirus) in the hypovirulent strain SCH941 of Sclerotinia sclerotiorum. One of the newly discovered mycoviruses, Sclerotinia sclerotiorum yadokarivirus 1 (SsYkV1), with a nonsegmented positive-sense single-stranded RNA (+ssRNA) genome, was molecularly characterized. SsYkV1 is 5,256 nucleotides (nt) in length, excluding the poly(A) structure, and has a large open reading frame that putatively encodes a polyprotein with the RNA-dependent RNA polymerase (RdRp) domain and a 2A-like motif. SsYkV1 was phylogenetically positioned into the family Yadokariviridae and was most closely related to Rosellinia necatrix yadokarivirus 2 (RnYkV2), with 40.55% identity (78% coverage). Although SsYkV1 does not encode its own capsid protein, the RNA and RdRp of SsYkV1 are trans-encapsidated in virions of Sclerotinia sclerotiorum botybirnavirus 3 (SsBV3), a bisegmented double-stranded RNA (dsRNA) mycovirus within the genus Botybirnavirus. In this way, SsYkV1 likely replicates inside the heterocapsid comprised of the SsBV3 capsid protein, like a dsRNA virus. SsYkV1 has a limited impact on the biological features of S. sclerotiorum. This study represents an example of a yadokarivirus trans-encapsidated by an unrelated dsRNA virus, which greatly deepens our knowledge and understanding of the unique life cycles of RNA viruses. IMPORTANCE RNA viruses typically encase their linear genomes in their own capsids. However, a capsidless +ssRNA virus (RnYkV1) highjacks the capsid of a nonsegmented dsRNA virus for the trans-encapsidation of its own RNA and RdRp. RnYkV1 belongs to the family Yadokariviridae, which already contains more than a dozen mycoviruses. However, it is unknown whether other yadokariviruses except RnYkV1 are also hosted by a heterocapsid, although dsRNA viruses with capsid proteins were detected in fungi harboring yadokarivirus. It is noteworthy that almost all presumed partner dsRNA viruses of yadokariviruses belong to the order Ghabrivirales (most probably a totivirus or toti-like virus). Here, we found a capsidless +ssRNA mycovirus, SsYkV1, from hypovirulent strain SCH941 of S. sclerotiorum, and the RNA and RdRp of this mycovirus are trans-encapsidated in virions of a bisegmented dsRNA virus within the free-floating genus Botybirnavirus. Our results greatly expand our knowledge of the unique life cycles of RNA viruses.
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Urayama SI, Takaki Y, Chiba Y, Zhao Y, Kuroki M, Hagiwara D, Nunoura T. Eukaryotic Microbial RNA Viruses-Acute or Persistent? Insights into Their Function in the Aquatic Ecosystem. Microbes Environ 2022; 37:ME22034. [PMID: 35922920 PMCID: PMC9763035 DOI: 10.1264/jsme2.me22034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Isolated RNA viruses mainly parasitize eukaryotes. RNA viruses either expand horizontally by infecting hosts (acute type) or coexist with the host and are vertically inherited (persistent type). The significance of persistent-type RNA viruses in environmental viromes (the main hosts are expected to be microbes) was only recently reported because they had previously been overlooked in virology. In this review, we summarize the host-virus relationships of eukaryotic microbial RNA viruses. Picornavirales and Reoviridae are recognized as representative acute-type virus families, and most of the microbial viruses in Narnaviridae, Totiviridae, and Partitiviridae are categorized as representative persistent-type viruses. Acute-type viruses have only been found in aquatic environments, while persistent-type viruses are present in various environments, including aquatic environments. Moreover, persistent-type viruses are potentially widely spread in the RNA viral sequence space. This emerging evidence provides novel insights into RNA viral diversity, host-virus relationships, and their history of co-evolution.
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Affiliation(s)
- Syun-ichi Urayama
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan, Corresponding author. E-mail: ; Tel: +81–29–853–6636; Fax: +81–29–853–4605
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Yuto Chiba
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan
| | - Yanjie Zhao
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan
| | - Misa Kuroki
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan
| | - Daisuke Hagiwara
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), JAMSTEC, 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
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Hirai J, Urayama SI, Takaki Y, Hirai M, Nagasaki K, Nunoura T. RNA Virosphere in a Marine Zooplankton Community in the Subtropical Western North Pacific. Microbes Environ 2022; 37:ME21066. [PMID: 34980753 PMCID: PMC9763039 DOI: 10.1264/jsme2.me21066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Zooplankton and viruses play a key role in marine ecosystems; however, their interactions have not been examined in detail. In the present study, the diversity of viruses associated with zooplankton collected using a plankton net (mesh size: 100 μm) in the subtropical western North Pacific was investigated by fragmented and primer ligated dsRNA sequencing. We obtained 21 and 168 operational taxonomic units (OTUs) of ssRNA and dsRNA viruses, respectively, containing RNA-dependent RNA polymerase (RdRp). These OTUs presented average amino acid similarities of 43.5 and 44.0% to the RdRp genes of known viruses in ssRNA viruses and dsRNA viruses, respectively. Dominant OTUs mainly belonged to narna-like and picorna-like ssRNA viruses and chryso-like, partiti-like, picobirna-like, reo-like, and toti-like dsRNA viruses. Phylogenetic ana-lyses of the RdRp gene revealed that OTUs were phylogenetically diverse and clustered into distinct clades from known viral groups. The community structure of the same zooplankton sample was investigated using small subunit (SSU) rRNA sequences assembled from the metatranscriptome of single-stranded RNA. More than 90% of the sequence reads were derived from metazoan zooplankton; copepods comprised approximately 70% of the sequence reads. Although this ana-lysis provided no direct evidence of the host species of RNA viruses, these dominant zooplankton are expected to be associated with the RNA viruses detected in the present study. The present results indicate that zooplankton function as a reservoir of diverse RNA viruses and suggest that investigations of zooplankton viruses will provide a more detailed understanding of the role of viruses in marine ecosystems.
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Affiliation(s)
- Junya Hirai
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5–1–5 Kashiwanoha, Kashiwa, Chiba 277–8564, Japan, Corresponding author. E-mail: ; Tel: +81–4–7136–6163; Fax: +81–4–7136–6172
| | - Syun-ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan,Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Yoshiro Takaki
- Super-cuttingedge Grand and Advanced Research (SUGAR) Program, JAMSTEC, 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Miho Hirai
- Super-cuttingedge Grand and Advanced Research (SUGAR) Program, JAMSTEC, 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Keizo Nagasaki
- Faculty of Science and Technology, Kochi University, 200 Monobe Otsu, Nankoku, Kochi 783–8502, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
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Degola F, Spadola G, Forgia M, Turina M, Dramis L, Chitarra W, Nerva L. Aspergillus Goes Viral: Ecological Insights from the Geographical Distribution of the Mycovirome within an Aspergillus flavus Population and Its Possible Correlation with Aflatoxin Biosynthesis. J Fungi (Basel) 2021; 7:833. [PMID: 34682254 PMCID: PMC8538035 DOI: 10.3390/jof7100833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/14/2021] [Accepted: 10/03/2021] [Indexed: 12/13/2022] Open
Abstract
Microbial multi-level interactions are essential to control the success of spreading and survival of most microbes in natural environments. Phytopathogenic mycotoxigenic fungal species, such as Aspergillus flavus, represent an important issue in food safety. Usually, non-toxigenic strains are exploited for biocontrol strategies to mitigate infections by toxigenic strains. To comprehend all the biological variables involved in the aflatoxin biosynthesis, and to possibly evaluate the interplay between A. flavus toxigenic and non-toxigenic strains during intraspecific biocompetition, the "virological" perspective should be considered. For these reasons, investigations on mycoviruses associated to A. flavus populations inhabiting specific agroecosystems are highly desirable. Here, we provide the first accurate characterization of the novel mycovirome identified within an A. flavus wild population colonizing the maize fields of northern Italy: a selection of A. flavus strains was biologically characterized and subjected to RNAseq analysis, revealing new mycoviruses and a peculiar geographic pattern distribution in addition to a 20% rate of infection. More interestingly, a negative correlation between viral infection and aflatoxin production was found. Results significantly expanded the limited existent data about mycoviruses in wild A. flavus, opening new and intriguing hypotheses about the ecological significance of mycoviruses.
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Affiliation(s)
- Francesca Degola
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy; (G.S.); (L.D.)
| | - Giorgio Spadola
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy; (G.S.); (L.D.)
| | - Marco Forgia
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy; (M.F.); (M.T.); (W.C.)
| | - Massimo Turina
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy; (M.F.); (M.T.); (W.C.)
| | - Lucia Dramis
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy; (G.S.); (L.D.)
| | - Walter Chitarra
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy; (M.F.); (M.T.); (W.C.)
- Council for Agricultural Research and Economics—Research Centre for Viticulture and Enology CREA-VE, Via XXVIII Aprile 26, 31015 Conegliano, Italy
| | - Luca Nerva
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, 10135 Torino, Italy; (M.F.); (M.T.); (W.C.)
- Council for Agricultural Research and Economics—Research Centre for Viticulture and Enology CREA-VE, Via XXVIII Aprile 26, 31015 Conegliano, Italy
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Grimm M, Grube M, Schiefelbein U, Zühlke D, Bernhardt J, Riedel K. The Lichens' Microbiota, Still a Mystery? Front Microbiol 2021; 12:623839. [PMID: 33859626 PMCID: PMC8042158 DOI: 10.3389/fmicb.2021.623839] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/10/2021] [Indexed: 01/03/2023] Open
Abstract
Lichens represent self-supporting symbioses, which occur in a wide range of terrestrial habitats and which contribute significantly to mineral cycling and energy flow at a global scale. Lichens usually grow much slower than higher plants. Nevertheless, lichens can contribute substantially to biomass production. This review focuses on the lichen symbiosis in general and especially on the model species Lobaria pulmonaria L. Hoffm., which is a large foliose lichen that occurs worldwide on tree trunks in undisturbed forests with long ecological continuity. In comparison to many other lichens, L. pulmonaria is less tolerant to desiccation and highly sensitive to air pollution. The name-giving mycobiont (belonging to the Ascomycota), provides a protective layer covering a layer of the green-algal photobiont (Dictyochloropsis reticulata) and interspersed cyanobacterial cell clusters (Nostoc spec.). Recently performed metaproteome analyses confirm the partition of functions in lichen partnerships. The ample functional diversity of the mycobiont contrasts the predominant function of the photobiont in production (and secretion) of energy-rich carbohydrates, and the cyanobiont's contribution by nitrogen fixation. In addition, high throughput and state-of-the-art metagenomics and community fingerprinting, metatranscriptomics, and MS-based metaproteomics identify the bacterial community present on L. pulmonaria as a surprisingly abundant and structurally integrated element of the lichen symbiosis. Comparative metaproteome analyses of lichens from different sampling sites suggest the presence of a relatively stable core microbiome and a sampling site-specific portion of the microbiome. Moreover, these studies indicate how the microbiota may contribute to the symbiotic system, to improve its health, growth and fitness.
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Affiliation(s)
- Maria Grimm
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Martin Grube
- Institute of Plant Sciences, Karl-Franzens-University Graz, Graz, Austria
| | | | - Daniela Zühlke
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, University Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University Greifswald, Greifswald, Germany
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Mahillon M, Decroës A, Caulier S, Tiendrebeogo A, Legrève A, Bragard C. Genomic and biological characterization of a novel partitivirus infecting Fusarium equiseti. Virus Res 2021; 297:198386. [PMID: 33716183 DOI: 10.1016/j.virusres.2021.198386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 12/18/2022]
Abstract
This study describes a new mycovirus infecting a strain from the Fusarium incarnatum-equiseti species complex. Based on phylogenetic and genomic analyses, this virus belongs to the recently proposed genus "Zetapartitivirus" in the family Partitiviridae. The name "Fusarium equiseti partitivirus 1″ (FePV1) is therefore suggested for this novel viral species. Similar to other partitiviruses, FePV1 genome is composed by two dsRNA segments that exhibit each one large ORF encoding for an RdRp and a CP, respectively. A smaller dsRNA was also detected in infected mycelium and could be a satellite RNA of FePV1. In addition to characterized zetapartitiviruses, other FePV1-related sequences were retrieved from online databases and their significance is discussed. Following conidial isolation, an FePV1-free isogenic line of the fungal host was obtained. In comparison with the original infected strain, this line showed higher growth, biomass production and pathogenicity on tomato, advocating that FePV1 induces hypovirulence on its host.
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Affiliation(s)
- Mathieu Mahillon
- Earth and Life Institute, Applied Microbiology-Phytopathology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Alain Decroës
- Earth and Life Institute, Applied Microbiology-Phytopathology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Simon Caulier
- Earth and Life Institute, Applied Microbiology-Phytopathology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Assiata Tiendrebeogo
- Earth and Life Institute, Applied Microbiology-Phytopathology, UCLouvain, Louvain-la-Neuve, Belgium; Natural System, Agrosystem and Environmental Engineering, Phytopathology, Nazi Boni University, Bobo-Dioulasso, Burkina-Faso
| | - Anne Legrève
- Earth and Life Institute, Applied Microbiology-Phytopathology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Claude Bragard
- Earth and Life Institute, Applied Microbiology-Phytopathology, UCLouvain, Louvain-la-Neuve, Belgium.
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