1
|
Hays M. Genetic conflicts in budding yeast: The 2μ plasmid as a model selfish element. Semin Cell Dev Biol 2024; 161-162:31-41. [PMID: 38598944 DOI: 10.1016/j.semcdb.2024.04.002] [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: 09/26/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
Antagonistic coevolution, arising from genetic conflict, can drive rapid evolution and biological innovation. Conflict can arise both between organisms and within genomes. This review focuses on budding yeasts as a model system for exploring intra- and inter-genomic genetic conflict, highlighting in particular the 2-micron (2μ) plasmid as a model selfish element. The 2μ is found widely in laboratory strains and industrial isolates of Saccharomyces cerevisiae and has long been known to cause host fitness defects. Nevertheless, the plasmid is frequently ignored in the context of genetic, fitness, and evolution studies. Here, I make a case for further exploring the evolutionary impact of the 2μ plasmid as well as other selfish elements of budding yeasts, discuss recent advances, and, finally, future directions for the field.
Collapse
Affiliation(s)
- Michelle Hays
- Department of Genetics, Stanford University, Stanford, CA, United States.
| |
Collapse
|
2
|
Nobre SVA, de Andrade GAK, Metz GF, Lucini F, de Albuquerque MP, Victória FDC. Antarctica's hidden mycoviral treasures in fungi isolated from mosses: A first genomic approach. J Basic Microbiol 2024:e202300671. [PMID: 38736205 DOI: 10.1002/jobm.202300671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/15/2024] [Accepted: 04/27/2024] [Indexed: 05/14/2024]
Abstract
This study investigates the presence of mycoviruses in Antarctic fungi and elucidates their evolutionary relationships. To achieve this, we aligned mycoviral gene sequences with genomes of previously sequenced Antarctic endophytic fungi, made available by our research group and accessible via Joint Genome Institute. Our findings reveal that the most prevalent genetic regions in all endophytic fungi are homologous to Partitiviruses, Baculoviridae, and Phycodnaviridae. These regions display evidence of positive selection pressure, suggesting genetic diversity and the accumulation of nonsynonymous mutations. This phenomenon implies a crucial role for these regions in the adaptation and survival of these fungi in the challenging Antarctic ecosystems. The presence of mycoviruses in Antarctic endophytic fungi may indicate shared survival strategies between the virus and its host, shedding light on their evolutionary dynamics. This study underscores the significance of exploring mycoviruses within endophytic fungi and their contributions to genetic diversity. Future research avenues could delve into the functional implications of these conserved mycoviral genetic regions in Antarctic endophytic fungi, providing a comprehensive understanding of this intriguing association and genomic retention of viral region in fungi.
Collapse
Affiliation(s)
- Steffany V A Nobre
- Curso de Biotecnologia, Universidade Federal do Pampa, São Gabriel, Brazil
- Núcleo de Estudos da Vegetação Antártica, São Gabriel, Brazil
| | - Guilherme A K de Andrade
- Núcleo de Estudos da Vegetação Antártica, São Gabriel, Brazil
- PPGCB-UNIPAMPA, Programa de Pós-Graduação em Ciências Biológicas, São Gabriel, Brazil
| | - Geferson F Metz
- Núcleo de Estudos da Vegetação Antártica, São Gabriel, Brazil
- PPGCB-UNIPAMPA, Programa de Pós-Graduação em Ciências Biológicas, São Gabriel, Brazil
| | - Fabíola Lucini
- Programa Antártico Brasileiro, Brasilia-DF, Brazil
- Faculdade de Ciências da Saúde-FCS, Federal University of Grande Dourados (UFGD), Dourados, Brazil
| | - Margéli P de Albuquerque
- Núcleo de Estudos da Vegetação Antártica, São Gabriel, Brazil
- Programa Antártico Brasileiro, Brasilia-DF, Brazil
| | - Filipe de C Victória
- Núcleo de Estudos da Vegetação Antártica, São Gabriel, Brazil
- PPGCB-UNIPAMPA, Programa de Pós-Graduação em Ciências Biológicas, São Gabriel, Brazil
- Faculdade de Ciências da Saúde-FCS, Federal University of Grande Dourados (UFGD), Dourados, Brazil
| |
Collapse
|
3
|
Grybchuk D, Galan A, Klocek D, Macedo DH, Wolf YI, Votýpka J, Butenko A, Lukeš J, Neri U, Záhonová K, Kostygov AY, Koonin EV, Yurchenko V. Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae). Virus Evol 2024; 10:veae037. [PMID: 38774311 PMCID: PMC11108086 DOI: 10.1093/ve/veae037] [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: 10/26/2023] [Revised: 04/03/2024] [Accepted: 04/29/2024] [Indexed: 05/24/2024] Open
Abstract
Trypanosomatids (Euglenozoa) are a diverse group of unicellular flagellates predominately infecting insects (monoxenous species) or circulating between insects and vertebrates or plants (dixenous species). Monoxenous trypanosomatids harbor a wide range of RNA viruses belonging to the families Narnaviridae, Totiviridae, Qinviridae, Leishbuviridae, and a putative group of tombus-like viruses. Here, we focus on the subfamily Blastocrithidiinae, a previously unexplored divergent group of monoxenous trypanosomatids comprising two related genera: Obscuromonas and Blastocrithidia. Members of the genus Blastocrithidia employ a unique genetic code, in which all three stop codons are repurposed to encode amino acids, with TAA also used to terminate translation. Obscuromonas isolates studied here bear viruses of three families: Narnaviridae, Qinviridae, and Mitoviridae. The latter viral group is documented in trypanosomatid flagellates for the first time. While other known mitoviruses replicate in the mitochondria, those of trypanosomatids appear to reside in the cytoplasm. Although no RNA viruses were detected in Blastocrithidia spp., we identified an endogenous viral element in the genome of B. triatomae indicating its past encounter(s) with tombus-like viruses.
Collapse
Affiliation(s)
- Danyil Grybchuk
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czechia
| | - Arnau Galan
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| | - Donnamae Klocek
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| | - Diego H Macedo
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| | - Yuri I Wolf
- National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda 20894, USA
| | - Jan Votýpka
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Department of Parasitology, Faculty of Science, Charles University, Prague 128 00, Czechia
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czechia
| | - Uri Neri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 39040, Israel
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec 252 50, Czechia
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Alexei Yu Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Zoological Institute of the Ruian Academy of Sciences, St. Petersburg 199034, Russia
| | - Eugene V Koonin
- National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda 20894, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| |
Collapse
|
4
|
Sahin E, Edis G, Keskin E, Akata I. Molecular characterization of the complete genome of a novel ormycovirus infecting the ectomycorrhizal fungus Hortiboletus rubellus. Arch Virol 2024; 169:110. [PMID: 38664287 DOI: 10.1007/s00705-024-06027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/11/2024] [Indexed: 05/24/2024]
Abstract
Advancements in high-throughput sequencing and the development of new bioinformatics tools for large-scale data analysis play a crucial role in uncovering virus diversity and enhancing our understanding of virus evolution. The discovery of the ormycovirus clades, a group of RNA viruses that are phylogenetically distinct from all known Riboviria members and are found in fungi, highlights the value of these tools for the discovery of novel viruses. The aim of this study was to examine viral populations in fungal hosts to gain insights into the diversity, evolution, and classification of these viruses. Here, we report the molecular characterization of a newly discovered ormycovirus, which we have named "Hortiboletus rubellus ormycovirus 1" (HrOMV1), that was found in the ectomycorrhizal fungus Hortiboletus rubellus. The bipartite genome of HrOMV1, whose nucleotide sequence was determined by HTS and RLM-RACE, consists of two RNA segments (RNA1 and RNA2) that exhibit similarity to those of previously studied ormycoviruses in their organization and the proteins they encode. The presence of upstream, in-frame AUG triplets in the 5' termini of both RNA segments suggests that HrOMV1, like certain other ormycoviruses, employs a non-canonical translation initiation strategy. Phylogenetic analysis showed that HrOMV1 is positioned within the gammaormycovirus clade. Its putative RNA-dependent RNA polymerase (RdRp) exhibits sequence similarity to those of other gammaormycovirus members, the most similarity to that of Termitomyces ormycovirus 1, with 33.05% sequence identity. This protein was found to contain conserved motifs that are crucial for RNA replication, including the distinctive GDQ catalytic triad observed in gammaormycovirus RdRps. The results of this study underscore the significance of investigating the ecological role of mycoviruses in mycorrhizal fungi. This is the first report of an ormycovirus infecting a member of the ectomycorrhizal genus Hortiboletus.
Collapse
Affiliation(s)
- Ergin Sahin
- Faculty of Science, Department of Biology, Dokuz Eylul University, Buca, Izmir, 35390, Turkey.
- Fauna and Flora Research and Application Center, Dokuz Eylul University, Buca, Izmir, 35390, Turkey.
| | - Gulce Edis
- Graduate School of Natural and Applied Sciences, Ankara University, Dışkapı, Ankara, 06110, Turkey
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Faculty of Agriculture Department of Fisheries and Aquaculture, Ankara University, Dışkapı, Ankara, 06110, Turkey
| | - Ilgaz Akata
- Faculty of Science Department of Biology, Ankara University, Tandogan, Ankara, 06100, Turkey
| |
Collapse
|
5
|
Hough B, Steenkamp E, Wingfield B, Read D. Correction: Hough et al. Fungal Viruses Unveiled: A Comprehensive Review of Mycoviruses. Viruses 2023, 15, 1202. Viruses 2024; 16:632. [PMID: 38675997 PMCID: PMC11053809 DOI: 10.3390/v16040632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
In the original publication [...].
Collapse
Affiliation(s)
| | | | - Brenda Wingfield
- Forestry & Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria 0002, South Africa; (B.H.); (E.S.); (D.R.)
| | | |
Collapse
|
6
|
Moubset O, Filloux D, Fontes H, Julian C, Fernandez E, Galzi S, Blondin L, Chehida SB, Lett JM, Mesléard F, Kraberger S, Custer JM, Salywon A, Makings E, Marais A, Chiroleu F, Lefeuvre P, Martin DP, Candresse T, Varsani A, Ravigné V, Roumagnac P. Virome release of an invasive exotic plant species in southern France. Virus Evol 2024; 10:veae025. [PMID: 38566975 PMCID: PMC10986800 DOI: 10.1093/ve/veae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/27/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.
Collapse
Affiliation(s)
- Oumaima Moubset
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Denis Filloux
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Hugo Fontes
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles 13200, France
- Institut Méditerranéen de Biodiversité et Ecologie, UMR CNRS-IRD, Avignon Université, Aix-Marseille Université, IUT d’Avignon, Avignon 84911, France
| | - Charlotte Julian
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Emmanuel Fernandez
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Serge Galzi
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Laurence Blondin
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | | | | | - François Mesléard
- Tour du Valat, Institut de recherche pour la conservation des zones humides méditerranéennes, Le Sambuc, Arles 13200, France
- Institut Méditerranéen de Biodiversité et Ecologie, UMR CNRS-IRD, Avignon Université, Aix-Marseille Université, IUT d’Avignon, Avignon 84911, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew Salywon
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ 85008, USA
| | - Elizabeth Makings
- Vascular Plant Herbarium, School of Life Sciences, Arizona State University, 734 West Alameda Drive, Tempe Tempe, AZ 85282, USA
| | - Armelle Marais
- UMR BFP, University Bordeaux, INRAE, Villenave d’Ornon 33140, France
| | | | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of infectious Diseases and Molecular Medicine, University of Cape Town, Anzio Rd, Cape Town 7925, South Africa
| | - Thierry Candresse
- UMR BFP, University Bordeaux, INRAE, Villenave d’Ornon 33140, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7700, South Africa
| | - Virginie Ravigné
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| | - Philippe Roumagnac
- UMR PHIM, CIRAD, Baillarguet TA A-54/K, Montpellier 34090, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Baillarguet TA A-54/K, Montpellier 34090, France
| |
Collapse
|
7
|
Comont G, Faure C, Candresse T, Laurens M, Valière S, Lluch J, Lefebvre M, Gambier S, Jolivet J, Corio-Costet MF, Marais A. Characterization of the RNA Mycovirome Associated with Grapevine Fungal Pathogens: Analysis of Mycovirus Distribution and Their Genetic Variability within a Collection of Botryosphaeriaceae Isolates. Viruses 2024; 16:392. [PMID: 38543758 PMCID: PMC10975779 DOI: 10.3390/v16030392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 05/23/2024] Open
Abstract
Botryosphaeriaceae are fungi involved in the decay of various woody species, including the grapevine, leading to significant production losses. This fungal family is largely ubiquitous, and seven species of Botryosphaeriaceae have been identified in French vineyards, with variable levels of aggressiveness, both in vitro and in planta. Mycoviruses can impact the life traits of their fungal hosts, including aggressiveness, and are one of the factors influencing fungal pathogenicity. In this study, the RNA mycovirome of fifteen Botryosphaeriaceae isolates was characterized through the high-throughput sequencing of double-stranded RNA preparations from the respective samples. Eight mycoviruses were detected, including three potential novel species in the Narnaviridae family, as well as in the proposed Mycobunyaviridae and Fusagraviridae families. A large collection of Botryosphaeriaceae isolates was screened using RT-PCR assays specific for 20 Botryosphaeriaceae-infecting mycoviruses. Among the mycoviruses detected, some appeared to be specialists within a single host species, while others infected isolates belonging to multiple Botryosphaeriaceae species. This screening allowed us to conclude that one-third of the Botryosphaeriaceae isolates were infected by at least one mycovirus, and a significant proportion of isolates (43.5%) were found to be coinfected by several viruses, with very complex RNA mycoviromes for some N. parvum isolates.
Collapse
Affiliation(s)
- Gwenaëlle Comont
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Chantal Faure
- UMR BFP, INRAE, University of Bordeaux, 33140 Villenave d’Ornon, France; (C.F.); (T.C.); (M.L.)
| | - Thierry Candresse
- UMR BFP, INRAE, University of Bordeaux, 33140 Villenave d’Ornon, France; (C.F.); (T.C.); (M.L.)
| | - Marie Laurens
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Sophie Valière
- INRAE, US 1426, GeT-PlaGe, GenoToul, 31320 Castanet-Tolosan, France; (S.V.); (J.L.)
| | - Jérôme Lluch
- INRAE, US 1426, GeT-PlaGe, GenoToul, 31320 Castanet-Tolosan, France; (S.V.); (J.L.)
| | - Marie Lefebvre
- UMR BFP, INRAE, University of Bordeaux, 33140 Villenave d’Ornon, France; (C.F.); (T.C.); (M.L.)
| | - Sébastien Gambier
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Jérôme Jolivet
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Marie-France Corio-Costet
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Armelle Marais
- UMR BFP, INRAE, University of Bordeaux, 33140 Villenave d’Ornon, France; (C.F.); (T.C.); (M.L.)
| |
Collapse
|
8
|
Domènech-Eres R, Jaeckel M, Hadeler B, Lienemann T, Lutz T, Heinze C. A GFP-expressing minigenome of a chrysovirus replicating in fungi. Virology 2024; 591:109987. [PMID: 38219372 DOI: 10.1016/j.virol.2024.109987] [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: 10/30/2023] [Revised: 12/11/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024]
Abstract
The Fusarium graminearum virus China 9 (FgV-ch9) is a member of the genus Betachrysovirus in the Chrysoviridae family and causes hypovirulence in its host, Fusarium graminearum, the causal agent of Fusarium head blight. Although insights into viral biology of FgV-ch9 have expanded in recent years, questions regarding the function of virus-encoded proteins, cis-acting elements, and virus transmission are yet to be answered. Therefore, we developed a tool for the establishment of an artificial 6th segment of FgV-ch9, which encodes a GFP gene flanked by the non-translated regions of FgV-ch9 segment 1. Subsequently, we have proved successful encapsidation of this artificial segment into virus particles as well as its horizontal transmission. Expression of GFP was further verified via immunoassay and life cell imaging. Thus far, we were able to establish for the first time a mini-replicon system for segmented dsRNA viruses replicating in fungi.
Collapse
Affiliation(s)
- Robert Domènech-Eres
- University of Hamburg, Institute of Plant Science and Microbiology, Molecular Phytopathology, Ohnhorststr. 18, 22609, Hamburg, Germany.
| | - Mareike Jaeckel
- University of Hamburg, Institute of Plant Science and Microbiology, Molecular Phytopathology, Ohnhorststr. 18, 22609, Hamburg, Germany.
| | - Birgit Hadeler
- University of Hamburg, Institute of Plant Science and Microbiology, Molecular Phytopathology, Ohnhorststr. 18, 22609, Hamburg, Germany.
| | - Tim Lienemann
- University of Hamburg, Institute of Plant Science and Microbiology, Molecular Phytopathology, Ohnhorststr. 18, 22609, Hamburg, Germany.
| | - Tobias Lutz
- University of Hamburg, Institute of Plant Science and Microbiology, Molecular Phytopathology, Ohnhorststr. 18, 22609, Hamburg, Germany.
| | - Cornelia Heinze
- University of Hamburg, Institute of Plant Science and Microbiology, Molecular Phytopathology, Ohnhorststr. 18, 22609, Hamburg, Germany.
| |
Collapse
|
9
|
Erkmen S, Sahin E, Akata I. Full-length genome characterization of a novel mitovirus isolated from the root rot fungus Armillaria mellea. Virus Genes 2024; 60:65-70. [PMID: 38103104 DOI: 10.1007/s11262-023-02041-8] [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: 08/24/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Members of the genus Armillaria belong to the group of pathogenic and facultative saprotrophic fungi that are generally known as one of the causative agents of white root rot in infected plants including deciduous and evergreen trees and shrubs. Although several single-stranded RNA mycoviruses were previously described in different Armillaria species, there is no report on mitoviruses (one of the simplest RNA viruses of fungal hosts) known to infect Armillaria taxa. In this study, a new mitovirus denominated "Armillaria mellea mitovirus 1" (AmMV1) was identified in the sporophore samples of Armillaria mellea, commonly known as honey mushroom. AmMV1 has a genome length of 4440 nucleotides and a G + C content of 48%. It encompasses a single open reading frame (ORF) that encodes an RNA-dependent RNA polymerase (RdRp). Comparison through BLASTp analysis revealed that the RdRp domain of AmMV1 shares a sequence identity ranging from 33.43% to 43.27% with RdRp domains of Duamitovirus genus members, having the highest similarity (43.27%) to Rhizoctonia solani mitovirus 94. According to phylogenetic analysis, AmMV1 is classified as a member of the genus Duamitovirus belonging to the Mitoviridae family. This marks the initial instance of a mitovirus identified in Armillaria spp..
Collapse
Affiliation(s)
- Sıla Erkmen
- Faculty of Science, Department of Biology, Dokuz Eylul University, 35390, Buca, Izmir, Turkey
| | - Ergin Sahin
- Faculty of Science, Department of Biology, Dokuz Eylul University, 35390, Buca, Izmir, Turkey.
- Fauna and Flora Research and Application Center, Dokuz Eylul University, 35390, Buca, Izmir, Turkey.
| | - Ilgaz Akata
- Faculty of Science, Department of Biology, Ankara University, 06100, Tandogan, Ankara, Turkey
| |
Collapse
|
10
|
De Jesús Andino F, Davydenko A, Webb RJ, Robert J. The Binding, Infection, and Promoted Growth of Batrachochytrium dendrobatidis by the Ranavirus FV3. Viruses 2024; 16:154. [PMID: 38275964 PMCID: PMC10818972 DOI: 10.3390/v16010154] [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: 12/21/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Increasing reports suggest the occurrence of co-infection between Ranaviruses such as Frog Virus 3 (FV3) and the chytrid fungus Batrachochytrium dendrobatidis (Bd) in various amphibian species. However, the potential direct interaction of these two pathogens has not been examined to date. In this study, we investigated whether FV3 can interact with Bd in vitro using qPCR, conventional microscopy, and immunofluorescent microscopy. Our results reveal the unexpected ability of FV3 to bind, promote aggregation, productively infect, and significantly increase Bd growth in vitro. To extend these results in vivo, we assessed the impact of FV3 on Xenopus tropicalis frogs previously infected with Bd. Consistent with in vitro results, FV3 exposure to previously Bd-infected X. tropicalis significantly increased Bd loads and decreased the host's survival.
Collapse
Affiliation(s)
- Francisco De Jesús Andino
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (F.D.J.A.); (A.D.)
| | - Anton Davydenko
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (F.D.J.A.); (A.D.)
| | - Rebecca J. Webb
- Veterinary Biosciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA; (F.D.J.A.); (A.D.)
| |
Collapse
|
11
|
Koonin EV, Kuhn JH, Dolja VV, Krupovic M. Megataxonomy and global ecology of the virosphere. THE ISME JOURNAL 2024; 18:wrad042. [PMID: 38365236 PMCID: PMC10848233 DOI: 10.1093/ismejo/wrad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 02/18/2024]
Abstract
Nearly all organisms are hosts to multiple viruses that collectively appear to be the most abundant biological entities in the biosphere. With recent advances in metagenomics and metatranscriptomics, the known diversity of viruses substantially expanded. Comparative analysis of these viruses using advanced computational methods culminated in the reconstruction of the evolution of major groups of viruses and enabled the construction of a virus megataxonomy, which has been formally adopted by the International Committee on Taxonomy of Viruses. This comprehensive taxonomy consists of six virus realms, which are aspired to be monophyletic and assembled based on the conservation of hallmark proteins involved in capsid structure formation or genome replication. The viruses in different major taxa substantially differ in host range and accordingly in ecological niches. In this review article, we outline the latest developments in virus megataxonomy and the recent discoveries that will likely lead to reassessment of some major taxa, in particular, split of three of the current six realms into two or more independent realms. We then discuss the correspondence between virus taxonomy and the distribution of viruses among hosts and ecological niches, as well as the abundance of viruses versus cells in different habitats. The distribution of viruses across environments appears to be primarily determined by the host ranges, i.e. the virome is shaped by the composition of the biome in a given habitat, which itself is affected by abiotic factors.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, United States
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, 75015 Paris, France
| |
Collapse
|
12
|
Contreras-Soto MB, Tovar-Pedraza JM. Viruses of plant-pathogenic fungi: a promising biocontrol strategy for Sclerotinia sclerotiorum. Arch Microbiol 2023; 206:38. [PMID: 38142438 DOI: 10.1007/s00203-023-03774-8] [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: 10/20/2023] [Revised: 11/17/2023] [Accepted: 11/26/2023] [Indexed: 12/26/2023]
Abstract
Plant pathogenic fungi pose a significant and ongoing threat to agriculture and food security, causing economic losses and significantly reducing crop yields. Effectively managing these fungal diseases is crucial for sustaining agricultural productivity, and in this context, mycoviruses have emerged as a promising biocontrol option. These viruses alter the physiology of their fungal hosts and their interactions with the host plants. This review encompasses the extensive diversity of reported mycoviruses, including their taxonomic classification and range of fungal hosts. We highlight representative examples of mycoviruses that affect economically significant plant-pathogenic fungi and their distinctive characteristics, with a particular emphasis on mycoviruses impacting Sclerotinia sclerotiorum. These mycoviruses exhibit significant potential for biocontrol, supported by their specificity, efficacy, and environmental safety. This positions mycoviruses as valuable tools in crop protection against diseases caused by this pathogen, maintaining their study and application as promising research areas in agricultural biotechnology. The remarkable diversity of mycoviruses, coupled with their ability to infect a broad range of plant-pathogenic fungi, inspires optimism, and suggests that these viruses have the potential to serve as an effective management strategy against major fungi-causing plant diseases worldwide.
Collapse
Affiliation(s)
- María Belia Contreras-Soto
- Laboratorio de Fitopatología, Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, 80110, Culiacán, Sinaloa, Mexico
| | - Juan Manuel Tovar-Pedraza
- Laboratorio de Fitopatología, Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, 80110, Culiacán, Sinaloa, Mexico.
| |
Collapse
|
13
|
Wang H, Luo J, Dai R, Shah KU, Andika IB, Sun L. Complete genome sequence of a novel double-stranded RNA virus infecting the phytopathogenic fungus Rhizopus stolonifer. Arch Virol 2023; 168:239. [PMID: 37661219 DOI: 10.1007/s00705-023-05869-5] [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: 06/14/2023] [Accepted: 07/26/2023] [Indexed: 09/05/2023]
Abstract
In this study, we report the complete genome sequence of a novel toti-like virus, tentatively named "Rhizopus stolonifer double-stranded RNA virus 1" (RsDSV1), identified from a phytopathogenic fungal agent of apple fruit rot disease, Rhizopus stolonifer strain A2-1. RsDSV1 has a double-stranded RNA genome. The complete RsDSV1 genome is 5178 nucleotides (nt) in length and contains two open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis based on RdRp and CP amino acid sequences revealed that RsDSV1 is closely related to unclassified members of the family Totiviridae. In stress-inducing Vogel's minimal and sodium dodecyl sulfate-containing media, hyphal growth of A2-1 was suppressed, but the accumulation of RsDSV1 RNA increased, indicating that stresses promote RsDSV1 replication. To our knowledge, this is the first report of a mycovirus found in R. stolonifer.
Collapse
Affiliation(s)
- Hao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jingxian Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Ruoyin Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Kaleem Ullah Shah
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China.
| |
Collapse
|
14
|
Kelliher JM, Robinson AJ, Longley R, Johnson LYD, Hanson BT, Morales DP, Cailleau G, Junier P, Bonito G, Chain PSG. The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research. MICROBIOME 2023; 11:192. [PMID: 37626434 PMCID: PMC10463477 DOI: 10.1186/s40168-023-01634-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023]
Abstract
As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.
Collapse
Affiliation(s)
| | | | - Reid Longley
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Seitz JM, Voegele RT, Link TI. Mycoviruses in the Rust Fungus Uromyces fabae. Viruses 2023; 15:1692. [PMID: 37632034 PMCID: PMC10459897 DOI: 10.3390/v15081692] [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: 07/06/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Uromyces fabae, the causal agent of broad bean rust, is a major cause of yield losses in North and East Africa, China, and Australia. It has also served as an important model species for research on rust fungi. Early EST sequencing in U. fabae showed that viruses might be present in this species; however, no follow-up investigations were conducted. In order to identify these viruses, we performed purification of dsRNA followed by Illumina sequencing. We also used ultracentrifugation followed by negative staining electron microscopy to visualize virus particles. We identified 20 viral sequences, which we termed Ufvss. A phylogenetic analysis was performed that grouped Ufvss into totiviruses, polymycoviruses, and virgaviruse; three sequences could not be included in the phylogeny. We also found isometric particles. Our findings contribute to the knowledge of mycoviral diversity in rust fungi and point to the importance of further investigation of these viruses.
Collapse
Affiliation(s)
| | | | - Tobias I. Link
- Department of Phytopathology, Institute of Phytomedicine, Faculty of Agricultural Sciences, University of Hohenheim, Otto-Sander-Straße 5, 70599 Stuttgart, Germany; (J.M.S.); (R.T.V.)
| |
Collapse
|