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Duroy PO, Seguin J, Ravel S, Rajendran R, Laboureau N, Salmon F, Delos JM, Pooggin M, Iskra-Caruana ML, Chabannes M. Endogenous viral elements are targeted by RNA silencing pathways in banana. THE NEW PHYTOLOGIST 2024; 244:1519-1536. [PMID: 39294885 DOI: 10.1111/nph.20112] [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: 03/25/2024] [Accepted: 08/05/2024] [Indexed: 09/21/2024]
Abstract
Endogenous banana streak virus (eBSV) integrants derived from three distinct species, present in Musa balbisiana (B) but not Musa acuminata (A) banana genomes are able to reconstitute functional episomal viruses causing banana streak disease in interspecific triploid AAB banana hybrids but not in the diploid (BB) parent line, which harbours identical eBSV loci. Here, we investigated the regulation of these eBSV. In-depth characterization of siRNAs, transcripts and methylation derived from eBSV using Illumina and bisulfite sequencing were carried out on eBSV-free Musa acuminata AAA plants and BB or AAB banana plants with eBSV. eBSV loci produce low-abundance transcripts covering most of the viral sequence and generate predominantly 24-nt siRNAs. siRNA accumulation is restricted to duplicated and inverted viral sequences present in eBSV. Both siRNA-accumulating and nonaccumulating sequences of eBSV in BB plants are heavily methylated in all three CG, CHG and CHH contexts. Our data suggest that eBSVs are controlled at the epigenetic level in BB diploids. This regulation not only prevents their awakening and systemic infection of the plant but is also probably involved in the inherent resistance of the BB plants to mealybug-transmitted viral infection. These findings are thus of relevance to other plant resources hosting integrated viruses.
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Affiliation(s)
- Pierre-Olivier Duroy
- CIRAD, UMR PHIM, Montpellier, F-34398, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jonathan Seguin
- Department of Plant Physiology, Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, Basel, Switzerland
| | - Sébastien Ravel
- CIRAD, UMR PHIM, Montpellier, F-34398, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Rajeswaran Rajendran
- Department of Plant Physiology, Botanical Institute, Zürich-Basel Plant Science Center, University of Basel, Basel, Switzerland
| | - Nathalie Laboureau
- CIRAD, UMR PHIM, Montpellier, F-34398, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Frédéric Salmon
- CIRAD, UMR AGAP Institut, Capesterre-Belle-Eau, Guadeloupe, F-97130, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, Guadeloupe, France
| | - Jean-Marie Delos
- CIRAD, UMR AGAP Institut, Capesterre-Belle-Eau, Guadeloupe, F-97130, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Capesterre-Belle-Eau, Guadeloupe, France
| | - Mikhail Pooggin
- CIRAD, UMR PHIM, Montpellier, F-34398, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - Matthieu Chabannes
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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Lu G, Ye ZX, Qi YH, Lu JB, Mao QZ, Zhuo JC, Huang HJ, He YJ, Li YY, Xu ZT, Chen JP, Zhang CX, Li JM. Endogenous nege-like viral elements in arthropod genomes reveal virus-host coevolution and ancient history of two plant virus families. J Virol 2024; 98:e0099724. [PMID: 39212930 PMCID: PMC11494950 DOI: 10.1128/jvi.00997-24] [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: 06/06/2024] [Accepted: 08/03/2024] [Indexed: 09/04/2024] Open
Abstract
Negevirus is a recently proposed taxon of arthropod-infecting virus, which is associated with plant viruses of two families (Virgaviridae and Kitaviridae). Nevertheless, the evolutionary history of negevirus-host and its relationship with plant viruses remain poorly understood. Endogenous nege-like viral elements (ENVEs) are ancient nege-like viral sequences integrated into the arthropod genomes, which can serve as the molecular fossil records of previous viral infection. In this study, 292 ENVEs were identified in 150 published arthropod genomes, revealing the evolutionary history of nege-like viruses and two related plant virus families. We discovered three novel and eight strains of nege-like viruses in 11 aphid species. Further analysis indicated that 10 ENVEs were detected in six aphid genomes, and they were divided into four types (ENVE1-ENVE4). Orthologous integration and phylogenetic analyses revealed that nege-like viruses had a history of infection of over 60 My and coexisted with aphid ancestors throughout the Cenozoic Era. Moreover, two nege-like viral proteins (CP and SP24) were highly homologous to those of plant viruses in the families Virgaviridae and Kitaviridae. CP- and SP24-derived ENVEs were widely integrated into numerous arthropod genomes. These results demonstrate that nege-like viruses have a long-term coexistence with arthropod hosts and plant viruses of the two families, Virgaviridae and Kitaviridae, which may have evolved from the nege-like virus ancestor through horizontal virus transfer events. These findings broaden our perspective on the history of viral infection in arthropods and the origins of plant viruses. IMPORTANCE Although negevirus is phylogenetically related to plant virus, the evolutionary history of negevirus-host and its relationship with plant virus remain largely unknown. In this study, we used endogenous nege-like viral elements (ENVEs) as the molecular fossil records to investigate the history of nege-like viral infection in arthropod hosts and the evolution of two related plant virus families (Virgaviridae and Kitaviridae). Our results showed the infection of nege-like viruses for over 60 My during the arthropod evolution. ENVEs highly homologous to viral sequences in Virgaviridae and Kitaviridae were present in a wide range of arthropod genomes but were absent in plant genomes, indicating that plant viruses in these two families possibly evolved from the nege-like virus ancestor through cross-species horizontal virus transmission. Our findings provide a new perspective on the virus-host coevolution and the origins of plant viruses.
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Affiliation(s)
- Gang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Zhuang-Xin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Yu-Hua Qi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jia-Bao Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Qian-Zhuo Mao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Ji-Chong Zhuo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Hai-Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Yu-Juan He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Yi-Yuan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Zhong-Tian Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian-Ping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Chuan-Xi Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jun-Min Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
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Erazo-Garcia MP, Sheyn U, Barth ZK, Craig RJ, Wessman P, Jivaji AM, Ray WK, Svensson-Coelho M, Cornwallis CK, Rengefors K, Brussaard CPD, Moniruzzaman M, Aylward FO. Latent infection of an active giant endogenous virus in a unicellular green alga. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.03.611062. [PMID: 39282281 PMCID: PMC11398304 DOI: 10.1101/2024.09.03.611062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/21/2024]
Abstract
Latency is a common strategy in a wide range of viral lineages, but its prevalence in giant viruses remains unknown. Here we describe the activity and viral production from a 617 kbp integrated giant viral element in the model green alga Chlamydomonas reinhardtii. We resolve the integrated viral region using long-read sequencing and show that viral particles are produced and released in otherwise healthy cultures. A diverse array of viral-encoded selfish genetic elements are expressed during GEVE reactivation and produce proteins that are packaged in virions. In addition, we show that field isolates of Chlamydomonas sp. harbor latent giant viruses related to the C. reinhardtii GEVE that exhibit similar infection dynamics, demonstrating that giant virus latency is prevalent in natural host communities. Our work reports the largest temperate virus documented to date and the first active GEVE identified in a unicellular eukaryote, substantially expanding the known limits of viral latency.
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Affiliation(s)
| | - Uri Sheyn
- Department of Biological Sciences, Virginia Tech; Blacksburg, 24061, USA
| | - Zachary K. Barth
- Department of Biological Sciences, Virginia Tech; Blacksburg, 24061, USA
| | - Rory J. Craig
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen; Tübingen, 72076, Germany
| | | | - Abdeali M. Jivaji
- Department of Biological Sciences, Virginia Tech; Blacksburg, 24061, USA
| | - W. Keith Ray
- Mass Spectrometry Incubator, Fralin Life Sciences Institute, Virginia Tech; Blacksburg, 24061, USA
| | - Maria Svensson-Coelho
- Department of Biology, Lund University; Lund, 223 62, Sweden
- Division of Molecular Biology, Department of Laboratory Medicine, Ryhov County Hospital; Jönköping, 55185, Sweden
| | | | - Karin Rengefors
- Department of Biology, Lund University; Lund, 223 62, Sweden
| | - Corina P. D. Brussaard
- Department of Biology, Lund University; Lund, 223 62, Sweden
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ); Texel, 1790 AB, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam; Amsterdam, 1090 GE, The Netherlands
| | - Mohammad Moniruzzaman
- Department of Marine Biology and Ecology, University of Miami; Coral Gables, 33149, USA
| | - Frank O. Aylward
- Department of Biological Sciences, Virginia Tech; Blacksburg, 24061, USA
- Center for Emerging, Zoonotic, and Arthropod-Borne Infectious Disease, Virginia Tech; Blacksburg, 24061, USA
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Sa'diyah W, Zhao YJ, Chiba Y, Kondo H, Suzuki N, Ban S, Yaguchi T, Urayama SI, Hagiwara D. New lineages of RNA viruses from clinical isolates of Rhizopus microsporus revealed by fragmented and primer-ligated dsRNA sequencing (FLDS) analysis. mSphere 2024; 9:e0034524. [PMID: 39072615 PMCID: PMC11351042 DOI: 10.1128/msphere.00345-24] [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: 04/25/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024] Open
Abstract
Rhizopus microsporus is a species in the order Mucorales that is known to cause mucormycosis, but it is poorly understood as a host of viruses. Here, we examined 25 clinical strains of R. microsporus for viral infection with a conventional double-stranded RNA (dsRNA) assay using agarose gel electrophoresis (AGE) and the recently established fragmented and primer-ligated dsRNA sequencing (FLDS) protocol. By AGE, five virus-infected strains were detected. Then, full-length genomic sequences of 12 novel RNA viruses were revealed by FLDS, which were related to the families Mitoviridae, Narnaviridae, and Endornaviridae, ill-defined groups of single-stranded RNA (ssRNA) viruses with similarity to the established families Virgaviridae and Phasmaviridae, and the proposed family "Ambiguiviridae." All the characterized viruses, except a potential phasmavirid with a negative-sense RNA genome, had positive-sense RNA genomes. One virus belonged to a previously established species within the family Mitoviridae, whereas the other 11 viruses represented new species or even new genera. These results show that the fungal pathogen R. microsporus harbors diverse RNA viruses and extend our understanding of the diversity of RNA viruses in the fungal order Mucorales, division Mucoromycota. Identifying RNA viruses from clinical isolates of R. microsporus may expand the repertoire of natural therapeutic agents for mucormycosis in the future.IMPORTANCEThe diversity of mycoviruses in fungal hosts in the division Mucoromycota has been underestimated, mainly within the species Rhizopus microsporus. Only five positive-sense RNA genomes had previously been discovered in this species. Because current sequencing methods poorly complete the termini of genomes, we used fragmented and primer-ligated double-stranded RNA sequencing to acquire the full-length genomes. Eleven novel mycoviruses were detected in this study, including the first negative-sense RNA genome reported in R. microsporus. Our findings extend the understanding of the viral diversity in clinical strains of Mucoromycota, may provide insights into the pathogenesis and ecology of this fungus, and may offer therapeutic options.
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Grants
- Institute for Fermentation, Osaka (IFO)
- 22KJ0440 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 22H04879 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 21K18217 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
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Affiliation(s)
- Wasiatus Sa'diyah
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba, Ibaraki, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Yan-Jie Zhao
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba, Ibaraki, Japan
| | - Yuto Chiba
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba, Ibaraki, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Sayaka Ban
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Takashi Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Syun-ichi Urayama
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
| | - Daisuke Hagiwara
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (Donated by IFO), University of Tsukuba, Ibaraki, Japan
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, Tsukuba, Japan
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Wang Z, Liu J, Qi X, Su D, Yang J, Cui X. Study of Endogenous Viruses in the Strawberry Plants. Viruses 2024; 16:1306. [PMID: 39205280 PMCID: PMC11359110 DOI: 10.3390/v16081306] [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: 07/24/2024] [Revised: 08/12/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Endogenous viral elements (EVEs) have been reported to exist widely in the genomes of eukaryotic organisms, and they are closely associated with the growth, development, genetics, adaptation, and evolution of their hosts. In this study, two methods-homologous sequence search and genome alignment-were used to explore the endogenous viral sequences in the genomes of Fragaria species. Results revealed abundant endogenous pararetroviruses (EPRVs) in the genomes of Fragaria species, including 786 sequences belonging to five known taxa such as Caulimovirus and other unclassified taxa. Differences were observed in the detected EPRVs between the two methods, with the homologous sequence search having a greater number of EPRVs. On the contrary, genome alignment identified various types and sources of virus-like sequences. Furthermore, through genome alignment, a 267-bp sequence with 95% similarity to the gene encoding the aphid-transmitted protein of Strawberry vein banding virus (Caulimovirus venafragariae) was discovered in the F. chiloensis genome, which was likely a recent insertion. In addition, the statistical analysis of the genome alignment results indicated a remarkably higher abundance of virus-like sequences in the genomes of polyploid strawberries compared with diploid ones. Moreover, the differences in virus-like sequences were observed between the genomes of Fragaria species and those of their close relatives. This study enriched the diversity of viruses that infect strawberries, and laid a theoretical foundation for further research on the origin of endogenous viruses in the strawberry genome, host-virus interactions, adaptation, evolution, and their functions.
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Affiliation(s)
- Zongneng Wang
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
| | - Jian Liu
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
| | - Xingyang Qi
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
| | - Daifa Su
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
| | - Junyu Yang
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
- Yunnan International Joint Laboratory of Virology and Immunology, Kunming 650500, China
| | - Xiaolong Cui
- School of Life Sciences, Yunnan University, Kunming 650500, China; (Z.W.); (J.L.); (X.Q.); (D.S.)
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6
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Telengech P, Hyodo K, Ichikawa H, Kuwata R, Kondo H, Suzuki N. Replication of single viruses across the kingdoms, Fungi, Plantae, and Animalia. Proc Natl Acad Sci U S A 2024; 121:e2318150121. [PMID: 38865269 PMCID: PMC11194502 DOI: 10.1073/pnas.2318150121] [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: 10/24/2023] [Accepted: 05/10/2024] [Indexed: 06/14/2024] Open
Abstract
It is extremely rare that a single virus crosses host barriers across multiple kingdoms. Based on phylogenetic and paleovirological analyses, it has previously been hypothesized that single members of the family Partitiviridae could cross multiple kingdoms. Partitiviridae accommodates members characterized by their simple bisegmented double-stranded RNA genome; asymptomatic infections of host organisms; the absence of an extracellular route for entry in nature; and collectively broad host range. Herein, we show the replicability of single fungal partitiviruses in three kingdoms of host organisms: Fungi, Plantae, and Animalia. Betapartitiviruses of the phytopathogenic fungusRosellinia necatrix could replicate in protoplasts of the carrot (Daucus carota), Nicotiana benthamiana and Nicotiana tabacum, in some cases reaching a level detectable by agarose gel electrophoresis. Moreover, betapartitiviruses showed more robust replication than the tested alphapartitiviruses. One of the fungal betapartitiviruses, RnPV18, could persistently and stably infect carrot plants regenerated from virion-transfected protoplasts. Both alpha- and betapartitiviruses, although with different host preference, could replicate in two insect cell lines derived from the fall armyworm Spodoptera frugiperda and the fruit fly Drosophila melanogaster. Our results indicate the replicability of single partitiviruses in members of three kingdoms and provide insights into virus adaptation, host jumping, and evolution.
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Affiliation(s)
- Paul Telengech
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
| | - Kiwamu Hyodo
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
| | - Hiroaki Ichikawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki305-8634, Japan
| | - Ryusei Kuwata
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime794-8555, Japan
| | - Hideki Kondo
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
| | - Nobuhiro Suzuki
- Agrivirology Laboratory, Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama710-0046, Japan
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Blanco-Melo D, Campbell MA, Zhu H, Dennis TPW, Modha S, Lytras S, Hughes J, Gatseva A, Gifford RJ. A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record. Genome Biol 2024; 25:120. [PMID: 38741126 PMCID: PMC11089739 DOI: 10.1186/s13059-024-03258-y] [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: 11/03/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Genomic regions that remain poorly understood, often referred to as the dark genome, contain a variety of functionally relevant and biologically informative features. These include endogenous viral elements (EVEs)-virus-derived sequences that can dramatically impact host biology and serve as a virus fossil record. In this study, we introduce a database-integrated genome screening (DIGS) approach to investigate the dark genome in silico, focusing on EVEs found within vertebrate genomes. RESULTS Using DIGS on 874 vertebrate genomes, we uncover approximately 1.1 million EVE sequences, with over 99% originating from endogenous retroviruses or transposable elements that contain EVE DNA. We show that the remaining 6038 sequences represent over a thousand distinct horizontal gene transfer events across 10 virus families, including some that have not previously been reported as EVEs. We explore the genomic and phylogenetic characteristics of non-retroviral EVEs and determine their rates of acquisition during vertebrate evolution. Our study uncovers novel virus diversity, broadens knowledge of virus distribution among vertebrate hosts, and provides new insights into the ecology and evolution of vertebrate viruses. CONCLUSIONS We comprehensively catalog and analyze EVEs within 874 vertebrate genomes, shedding light on the distribution, diversity, and long-term evolution of viruses and reveal their extensive impact on vertebrate genome evolution. Our results demonstrate the power of linking a relational database management system to a similarity search-based screening pipeline for in silico exploration of the dark genome.
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Affiliation(s)
- Daniel Blanco-Melo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | | | - Henan Zhu
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Tristan P W Dennis
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Sejal Modha
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Spyros Lytras
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Anna Gatseva
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow, G61 1QH, UK.
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa.
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8
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Tempone AJ, Zezza-Ramalho MDS, Borely D, Pitaluga AN, Brazil RP, Brandão-Filho SP, Pessoa FAC, Bruno RV, Carvalho-Costa FA, Salomón OD, Volf P, Burleigh BA, Aguiar ERGR, Traub-Cseko YM. Rhabdoviral Endogenous Sequences Identified in the Leishmaniasis Vector Lutzomyia longipalpis Are Widespread in Sandflies from South America. Viruses 2024; 16:395. [PMID: 38543761 PMCID: PMC10974309 DOI: 10.3390/v16030395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024] Open
Abstract
Sandflies are known vectors of leishmaniasis. In the Old World, sandflies are also vectors of viruses while little is known about the capacity of New World insects to transmit viruses to humans. Here, we relate the identification of RNA sequences with homology to rhabdovirus nucleocapsids (NcPs) genes, initially in the Lutzomyia longipalpis LL5 cell lineage, named NcP1.1 and NcP2. The Rhabdoviridae family never retrotranscribes its RNA genome to DNA. The sequences here described were identified in cDNA and DNA from LL-5 cells and in adult insects indicating that they are transcribed endogenous viral elements (EVEs). The presence of NcP1.1 and NcP2 in the L. longipalpis genome was confirmed in silico. In addition to showing the genomic location of NcP1.1 and NcP2, we identified another rhabdoviral insertion named NcP1.2. Analysis of small RNA molecules derived from these sequences showed that NcP1.1 and NcP1.2 present a profile consistent with elements targeted by primary piRNAs, while NcP2 was restricted to the degradation profile. The presence of NcP1.1 and NcP2 was investigated in sandfly populations from South America and the Old World. These EVEs are shared by different sandfly populations in South America while none of the Old World species studied presented the insertions.
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Affiliation(s)
- Antonio J. Tempone
- Laboratório de Biologia Molecular de Parasitas e Vetores, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (M.d.S.Z.-R.); (D.B.); (A.N.P.)
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular/CNPq, Rio de Janeiro 21040-360, RJ, Brazil;
| | - Monique de Souza Zezza-Ramalho
- Laboratório de Biologia Molecular de Parasitas e Vetores, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (M.d.S.Z.-R.); (D.B.); (A.N.P.)
| | - Daniel Borely
- Laboratório de Biologia Molecular de Parasitas e Vetores, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (M.d.S.Z.-R.); (D.B.); (A.N.P.)
| | - André N. Pitaluga
- Laboratório de Biologia Molecular de Parasitas e Vetores, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (M.d.S.Z.-R.); (D.B.); (A.N.P.)
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular/CNPq, Rio de Janeiro 21040-360, RJ, Brazil;
| | - Reginaldo Peçanha Brazil
- Laboratório de Doenças Parasitárias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil;
| | - Sinval P. Brandão-Filho
- Departamento de Imunologia, Instituto Aggeu Magalhães, Fiocruz, Recife 50740-465, PE, Brazil;
| | - Felipe A. C. Pessoa
- Laboratório de Ecologia de Doenças Transmissíveis na Amazônia, Instituto Leônidas e Maria Deane, Fiocruz Amazônia, Manaus 69027-070, AM, Brazil;
| | - Rafaela V. Bruno
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular/CNPq, Rio de Janeiro 21040-360, RJ, Brazil;
- Laboratório de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil
| | - Filipe A. Carvalho-Costa
- Laboratório de Epidemiologia e Sistemática Molecular, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil;
| | - Oscar D. Salomón
- Instituto Nacional de Medicina Tropical, Ministerio de Salud de la Nación, ANLIS, Puerto Iguazu 3370, Misiones, Argentina;
| | - Petr Volf
- Department of Parasitology, Charles University, 12800 Prague, Czech Republic;
| | - Barbara A. Burleigh
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Cambridge, MA 02115, USA;
| | - Eric R. G. R. Aguiar
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Yara M. Traub-Cseko
- Laboratório de Biologia Molecular de Parasitas e Vetores, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil; (M.d.S.Z.-R.); (D.B.); (A.N.P.)
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular/CNPq, Rio de Janeiro 21040-360, RJ, Brazil;
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9
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Ghafari M, Sõmera M, Sarmiento C, Niehl A, Hébrard E, Tsoleridis T, Ball J, Moury B, Lemey P, Katzourakis A, Fargette D. Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses. PLoS Pathog 2024; 20:e1011911. [PMID: 38206964 PMCID: PMC10807823 DOI: 10.1371/journal.ppat.1011911] [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: 10/02/2023] [Revised: 01/24/2024] [Accepted: 12/18/2023] [Indexed: 01/13/2024] Open
Abstract
The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. A mechanistic evolutionary model, the Prisoner of War (PoW) model, has been proposed to address TDRP in viruses. Although TDRP has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. Here, we investigated the consequences of TDRP in plant viruses by applying the PoW model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. Our analysis showed that the Sobemovirus genus dates back over four million years, indicating an ancient origin. We found evidence that supports deep host jumps to Poaceae, Fabaceae, and Solanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. Remarkably, the TDRP-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence nearly 9,000 years ago, a time coinciding with the Neolithic period in the Near East. By incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species. We identified major radiation events beginning between 4,600 to 2,000 years ago, which aligns with the Neolithic period in various regions, suggesting a period of rapid diversification from then to the present. Our findings make a case for the possibility of deep evolutionary origins of plant viruses.
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Affiliation(s)
- Mahan Ghafari
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Annette Niehl
- Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Eugénie Hébrard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Theocharis Tsoleridis
- The Wolfson Centre for Global Virus Research and School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Jonathan Ball
- The Wolfson Centre for Global Virus Research and School of Life Sciences, The University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Denis Fargette
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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10
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Aboughanem-Sabanadzovic N, Allen TW, Frelichowski J, Scheffler J, Sabanadzovic S. Discovery and Analyses of Caulimovirid-like Sequences in Upland Cotton ( Gossypium hirsutum). Viruses 2023; 15:1643. [PMID: 37631986 PMCID: PMC10458927 DOI: 10.3390/v15081643] [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: 06/15/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Analyses of Illumina-based high-throughput sequencing data generated during characterization of the cotton leafroll dwarf virus population in Mississippi (2020-2022) consistently yielded contigs varying in size (most frequently from 4 to 7 kb) with identical nucleotide content and sharing similarities with reverse transcriptases (RTases) encoded by extant plant pararetroviruses (family Caulimoviridiae). Initial data prompted an in-depth study involving molecular and bioinformatic approaches to characterize the nature and origins of these caulimovirid-like sequences. As a result, here, we report on endogenous viral elements (EVEs) related to extant members of the family Caulimoviridae, integrated into a genome of upland cotton (Gossypium hirsutum), for which we propose the provisional name "endogenous cotton pararetroviral elements" (eCPRVE). Our investigations pinpointed a ~15 kbp-long locus on the A04 chromosome consisting of head-to-head orientated tandem copies located on positive- and negative-sense DNA strands (eCPRVE+ and eCPRVE-). Sequences of the eCPRVE+ comprised nearly complete and slightly decayed genome information, including ORFs coding for the viral movement protein (MP), coat protein (CP), RTase, and transactivator/viroplasm protein (TA). Phylogenetic analyses of major viral proteins suggest that the eCPRVE+ may have been initially derived from a genome of a cognate virus belonging to a putative new genus within the family. Unexpectedly, an identical 15 kb-long locus composed of two eCPRVE copies was also detected in a newly recognized species G. ekmanianum, shedding some light on the relatively recent evolution within the cotton family.
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Affiliation(s)
- Nina Aboughanem-Sabanadzovic
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, 2 Research Park, Mailstop 9627, Mississippi, MS 39762, USA;
| | - Thomas W. Allen
- Delta Research and Extension Center, Mississippi State University, 82 Stoneville Road, P.O. Box 197, Stoneville, MS 38776, USA;
| | | | - Jodi Scheffler
- USDA-ARS Mid-South Area, 141 Experiment Station Road, Stoneville, MS 38776, USA;
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Twelve Lane, Mail Stop 9775, Mississippi, MS 39762, USA
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11
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Veglia AJ, Bistolas KSI, Voolstra CR, Hume BCC, Ruscheweyh HJ, Planes S, Allemand D, Boissin E, Wincker P, Poulain J, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Zoccola D, Correa AMS, Vega Thurber RL. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Commun Biol 2023; 6:566. [PMID: 37264063 DOI: 10.1038/s42003-023-04917-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
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Affiliation(s)
- Alex J Veglia
- BioSciences Department, Rice University, Houston, TX, USA
| | | | | | | | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
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12
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Olendraite I, Brown K, Firth AE. Identification of RNA Virus-Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets. Mol Biol Evol 2023; 40:msad060. [PMID: 37014783 PMCID: PMC10101049 DOI: 10.1093/molbev/msad060] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/15/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023] Open
Abstract
RNA viruses are abundant and highly diverse and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost-effectively expand the diversity of known RNA virus sequences, we mined publicly available transcriptomic data sets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA-dependent RNA polymerase (RdRp)-the only universal "hallmark" gene of RNA viruses. By using these to search the National Center for Biotechnology Information Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analyzed their diversity, taxonomic classification, phylogeny, and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp Profile Hidden Markov Models provide a useful resource for the virus discovery community.
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Affiliation(s)
- Ingrida Olendraite
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Brown
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Andrew E Firth
- Division of Virology, Department of Pathology, Addenbrookes Hospital, University of Cambridge, Cambridge, United Kingdom
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13
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Ayllón MA, Vainio EJ. Mycoviruses as a part of the global virome: Diversity, evolutionary links and lifestyle. Adv Virus Res 2023; 115:1-86. [PMID: 37173063 DOI: 10.1016/bs.aivir.2023.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Knowledge of mycovirus diversity, evolution, horizontal gene transfer and shared ancestry with viruses infecting distantly related hosts, such as plants and arthropods, has increased vastly during the last few years due to advances in the high throughput sequencing methodologies. This also has enabled the discovery of novel mycoviruses with previously unknown genome types, mainly new positive and negative single-stranded RNA mycoviruses ((+) ssRNA and (-) ssRNA) and single-stranded DNA mycoviruses (ssDNA), and has increased our knowledge of double-stranded RNA mycoviruses (dsRNA), which in the past were thought to be the most common viruses infecting fungi. Fungi and oomycetes (Stramenopila) share similar lifestyles and also have similar viromes. Hypothesis about the origin and cross-kingdom transmission events of viruses have been raised and are supported by phylogenetic analysis and by the discovery of natural exchange of viruses between different hosts during virus-fungus coinfection in planta. In this review we make a compilation of the current information on the genome organization, diversity and taxonomy of mycoviruses, discussing their possible origins. Our focus is in recent findings suggesting the expansion of the host range of many viral taxa previously considered to be exclusively fungal, but we also address factors affecting virus transmissibility and coexistence in single fungal or oomycete isolates, as well as the development of synthetic mycoviruses and their use in investigating mycovirus replication cycles and pathogenicity.
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Affiliation(s)
- María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain; Departamento Biotecnología-Biología Vegetal, E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain.
| | - Eeva J Vainio
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Helsinki, Finland
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14
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de Tomás C, Vicient CM. Genome-wide identification of Reverse Transcriptase domains of recently inserted endogenous plant pararetrovirus ( Caulimoviridae). FRONTIERS IN PLANT SCIENCE 2022; 13:1011565. [PMID: 36589050 PMCID: PMC9794742 DOI: 10.3389/fpls.2022.1011565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/15/2022] [Indexed: 06/17/2023]
Abstract
Endogenous viral elements (EVEs) are viral sequences that have been integrated into the nuclear chromosomes. Endogenous pararetrovirus (EPRV) are a class of EVEs derived from DNA viruses of the family Caulimoviridae. Previous works based on a limited number of genome assemblies demonstrated that EPRVs are abundant in plants and are present in several species. The availability of genome sequences has been immensely increased in the recent years and we took advantage of these resources to have a more extensive view of the presence of EPRVs in plant genomes. We analyzed 278 genome assemblies corresponding to 267 species (254 from Viridiplantae) using tBLASTn against a collection of conserved domains of the Reverse Transcriptases (RT) of Caulimoviridae. We concentrated our search on complete and well-conserved RT domains with an uninterrupted ORF comprising the genetic information for at least 300 amino acids. We obtained 11.527 sequences from the genomes of 202 species spanning the whole Tracheophyta clade. These elements were grouped in 57 clusters and classified in 13 genera, including a newly proposed genus we called Wendovirus. Wendoviruses are characterized by the presence of four open reading frames and two of them encode for aspartic proteinases. Comparing plant genomes, we observed important differences between the plant families and genera in the number and type of EPRVs found. In general, florendoviruses are the most abundant and widely distributed EPRVs. The presence of multiple identical RT domain sequences in some of the genomes suggests their recent amplification.
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15
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Heisserer C, Selosse MA, Drezen JM. [Plants and animals biological functions obtained from viruses]. Med Sci (Paris) 2022; 38:1016-1027. [PMID: 36692281 DOI: 10.1051/medsci/2022171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Viruses can provide new biological functions to plants and animals. Some viruses persisting at low levels in plants might confer resistance to stress and parasites. In animals, more numerous examples of genes originating from viruses and used by different organisms have been described. For examples these genes might contribute to protect from new infections, or to ensure communication between neurons or to enable placenta development. In parasitic wasps, a complex viral machinery has been conserved as an endogenous virus dispersed in the wasp genome, which produces virions. These virions infect the parasitized host resulting in the production of virulence factors that inhibit defense mechanisms against the parasite. Different organisms have used the same viral functions repeatedly during animal evolution.
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Affiliation(s)
- Camille Heisserer
- Institut de recherche sur la biologie de l'insecte, UMR 7261 CNRS-Université de Tours, Parc de Grandmont 37200 Tours, France
| | - Marc-André Selosse
- Institut de systématique, évolution, biodiversité, UMR 7205 MNHN-CNRS-SU-EPHE-UA, 12 rue Buffon 75005 Paris, France
| | - Jean-Michel Drezen
- Institut de recherche sur la biologie de l'insecte, UMR 7261 CNRS-Université de Tours, Parc de Grandmont 37200 Tours, France
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16
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Sammarco I, Pieters J, Salony S, Toman I, Zolotarov G, Lafon Placette C. Epigenetic targeting of transposon relics: beating the dead horses of the genome? Epigenetics 2022; 17:1331-1344. [PMID: 36255200 PMCID: PMC9586680 DOI: 10.1080/15592294.2021.2022066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Transposable elements (TEs) have been seen as selfish genetic elements that can propagate in a host genome. Their propagation success is however hindered by a combination of mechanisms such as mutations, selection, and their epigenetic silencing by the host genome. As a result, most copies of TEs in a given genome are dead relics: their sequence is too degenerated to allow any transposition. Nevertheless, these TE relics often, but not always, remain epigenetically silenced, and if not to prevent transposition anymore, one can wonder the reason for this phenomenon. The mere self-perpetuating loop inherent to epigenetic silencing could alone explain that even when inactive, TE copies remain silenced. Beyond this process, nevertheless, antagonistic selective forces are likely to act on TE relic silencing. Especially, without the benefit of preventing transposition, TE relic silencing may prove deleterious to the host fitness, suggesting that the maintenance of TE relic silencing is the result of a fine, and perhaps case-by-case, evolutionary trade-off between beneficial and deleterious effects. Ultimately, the release of TE relics silencing may provide a 'safe' ground for adaptive epimutations to arise. In this review, we provide an overview of these questions in both plants and animals.
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Affiliation(s)
- Iris Sammarco
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic,Institute of Botany, Czech Academy of Sciences, Pruhonice, Czech Republic
| | - Janto Pieters
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Prague, Czech Republic,Department of Plant Experimental Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Susnata Salony
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Izabela Toman
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Grygoriy Zolotarov
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Clément Lafon Placette
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic,CONTACT Clément Lafon Placette Department of Botany, Faculty of Science, Charles University, PragueCZ-128 01, Czech Republic
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17
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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: 77] [Impact Index Per Article: 38.5] [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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Schulz F, Abergel C, Woyke T. Giant virus biology and diversity in the era of genome-resolved metagenomics. Nat Rev Microbiol 2022; 20:721-736. [PMID: 35902763 DOI: 10.1038/s41579-022-00754-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2022] [Indexed: 11/09/2022]
Abstract
The discovery of giant viruses, with capsids as large as some bacteria, megabase-range genomes and a variety of traits typically found only in cellular organisms, was one of the most remarkable breakthroughs in biology. Until recently, most of our knowledge of giant viruses came from ~100 species-level isolates for which genome sequences were available. However, these isolates were primarily derived from laboratory-based co-cultivation with few cultured protists and algae and, thus, did not reflect the true diversity of giant viruses. Although virus co-cultures enabled valuable insights into giant virus biology, many questions regarding their origin, evolution and ecological importance remain unanswered. With advances in sequencing technologies and bioinformatics, our understanding of giant viruses has drastically expanded. In this Review, we summarize our understanding of giant virus diversity and biology based on viral isolates as laboratory cultivation has enabled extensive insights into viral morphology and infection strategies. We then explore how cultivation-independent approaches have heightened our understanding of the coding potential and diversity of the Nucleocytoviricota. We discuss how metagenomics has revolutionized our perspective of giant viruses by revealing their distribution across our planet's biomes, where they impact the biology and ecology of a wide range of eukaryotic hosts and ultimately affect global nutrient cycles.
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Affiliation(s)
- Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Chantal Abergel
- Aix Marseille University, CNRS, IGS UMR7256, IMM FR3479, IM2B, IO, Marseille, France
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,University of California Merced, Merced, CA, USA.
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19
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Jiang Y, Yang B, Liu X, Tian X, Wang Q, Wang B, Zhang Q, Yu W, Qi X, Jiang Y, Hsiang T. A Satellite dsRNA Attenuates the Induction of Helper Virus-Mediated Symptoms in Aspergillus flavus. Front Microbiol 2022; 13:895844. [PMID: 35711767 PMCID: PMC9195127 DOI: 10.3389/fmicb.2022.895844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Aspergillus flavus is an important fungal pathogen of animals and plants. Previously, we reported a novel partitivirus, Aspergillus flavus partitivirus 1 (AfPV1), infecting A. flavus. In this study, we obtained a small double-stranded (ds) RNA segment (734 bp), which is a satellite RNA of the helper virus, AfPV1. The presence of AfPV1 altered the colony morphology, decreased the number of conidiophores, created significantly larger vacuoles, and caused more sensitivity to osmotic, oxidative, and UV stresses in A. flavus, but the small RNA segment could attenuate the above symptoms caused by the helper virus AfPV1 in A. flavus. Moreover, AfPV1 infection reduced the pathogenicity of A. flavus in corn (Zea mays), honeycomb moth (Galleria mellonella), mice (Mus musculus), and the adhesion of conidia to host epithelial cells, and increased conidial death by macrophages. However, the small RNA segment could also attenuate the above symptoms caused by the helper virus AfPV1 in A. flavus, perhaps by reducing the genomic accumulation of the helper virus AfPV1 in A. flavus. We used this model to investigate transcriptional genes regulated by AfPV1 and the small RNA segment in A. flavus, and their role in generating different phenotypes. We found that the pathways of the genes regulated by AfPV1 in its host were similar to those of retroviral viruses. Therefore, some pathways may be of benefit to non-retroviral viral integration or endogenization into the genomes of its host. Moreover, some potential antiviral substances were also found in A. flavus using this system.
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Affiliation(s)
- Yinhui Jiang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Bi Yang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Xiang Liu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Xun Tian
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Qinrong Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Bi Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Qifang Zhang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Wenfeng Yu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, China
- Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, China
| | - Yanping Jiang
- Department of Dermatology, The Affiliated Hospital, Guizhou Medical University, Guiyang, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
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20
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Shimura H, Kim H, Matsuzawa A, Akino S, Masuta C. Coat protein of partitiviruses isolated from mycorrhizal fungi functions as an RNA silencing suppressor in plants and fungi. Sci Rep 2022; 12:7855. [PMID: 35551196 PMCID: PMC9098641 DOI: 10.1038/s41598-022-11403-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/19/2022] [Indexed: 12/11/2022] Open
Abstract
Orchid seeds depend on colonization by orchid mycorrhizal (OM) fungi for their germination; therefore, the orchids and OM fungi have long maintained a close relationship (e.g., formation of the hyphal mass structure, peloton) during their evolution. In the present study, we isolated new partitiviruses from OM fungi; partitivirus were separately found in different subcultures from the same fungi. Partitiviruses have been believed to lack an RNA silencing suppressor (RSS), which is generally associated with viral pathogenicity, because most partitiviruses isolated so far are latent in both plants and fungi. However, we found that the coat protein (CP) of our partitiviruses indeed had RSS activity, which differed among the virus isolates from OM fungi; one CP showed RSS activity in both plants and fungi, while another CP showed no activity. The family Partitiviridae include viruses isolated from plants and fungi, and it has been suggested that these viruses may occasionally be transmitted between plant and fungal hosts. Given that there are several reports showing that viruses can adapt to nonhost using strong RSS, we here discussed the idea that partitiviruses may be better able to migrate between the orchid and fungus probably through the pelotons formed in the orchid cells, if host RNA silencing is suppressed by partitivirus RSS.
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Affiliation(s)
- Hanako Shimura
- Research Faculty of Agriculture, Hokkaido University, Kita-ku, Kita 9, Nishi 9, Sapporo, 060-8589, Japan.
| | - Hangil Kim
- Research Faculty of Agriculture, Hokkaido University, Kita-ku, Kita 9, Nishi 9, Sapporo, 060-8589, Japan
| | - Akihiko Matsuzawa
- Research Faculty of Agriculture, Hokkaido University, Kita-ku, Kita 9, Nishi 9, Sapporo, 060-8589, Japan
| | - Seishi Akino
- Research Faculty of Agriculture, Hokkaido University, Kita-ku, Kita 9, Nishi 9, Sapporo, 060-8589, Japan
| | - Chikara Masuta
- Research Faculty of Agriculture, Hokkaido University, Kita-ku, Kita 9, Nishi 9, Sapporo, 060-8589, Japan.
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21
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Khan HA, Shamsi W, Jamal A, Javaied M, Sadiq M, Fatma T, Ahmed A, Arshad M, Waseem M, Babar S, Dogar MM, Virk N, Janjua HA, Kondo H, Suzuki N, Bhatti MF. Assessment of mycoviral diversity in Pakistani fungal isolates revealed infection by 11 novel viruses of a single strain of Fusarium mangiferae isolate SP1. J Gen Virol 2021; 102. [PMID: 34850675 DOI: 10.1099/jgv.0.001690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An extensive screening survey was conducted on Pakistani filamentous fungal isolates for the identification of viral infections. A total of 396 fungal samples were screened, of which 36 isolates were found double-stranded (ds) RNA positive with an overall frequency of 9% when analysed by a classical dsRNA isolation method. One of 36 dsRNA-positive strains, strain SP1 of a plant pathogenic fungus Fusarium mangiferae, was subjected to virome analysis. Next-generation sequencing and subsequent completion of the entire genome sequencing by a classical Sanger sequencing method showed the SP1 strain to be co-infected by 11 distinct viruses, at least seven of which should be described as new taxa at the species level according to the ICTV (International Committee on Taxonomy of Viruses) species demarcation criteria. The newly identified F. mangiferae viruses (FmVs) include two partitivirids, one betapartitivirus (FmPV1) and one gammapartitivirus (FmPV2); six mitovirids, three unuamitovirus (FmMV2, FmMV4, FmMV6), one duamitovirus (FmMV5), and two unclassified mitovirids (FmMV1, FmMV3); and three botourmiavirids, two magoulivirus (FmBOV1, FmBOV3) and one scleroulivirus (FmBOV2). The number of coinfecting viruses is among the largest ones of fungal coinfections. Their molecular features are thoroughly described here. This represents the first large virus survey in the Indian sub-continent.
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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, 44000, Islamabad, Pakistan.,Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Wajeeha Shamsi
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan.,Present address: Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - Atif Jamal
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Memoona Javaied
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Mashal Sadiq
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Tehsin Fatma
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Aqeel Ahmed
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Maleeha Arshad
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Mubashra Waseem
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Samra Babar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Midhat Mustafa Dogar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Nasar Virk
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan.,Present address: EBS Universität für Wirtschaft und Recht, EBS Business School, Rheingaustrasse 1, 65375, Oestrich-Winkel, Germany
| | - Hussnain Ahmed Janjua
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - 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
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
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22
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Niraula PM, Fondong VN. Development and Adoption of Genetically Engineered Plants for Virus Resistance: Advances, Opportunities and Challenges. PLANTS 2021; 10:plants10112339. [PMID: 34834702 PMCID: PMC8623320 DOI: 10.3390/plants10112339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/24/2021] [Accepted: 10/27/2021] [Indexed: 11/20/2022]
Abstract
Plant viruses cause yield losses to crops of agronomic and economic significance and are a challenge to the achievement of global food security. Although conventional plant breeding has played an important role in managing plant viral diseases, it will unlikely meet the challenges posed by the frequent emergence of novel and more virulent viral species or viral strains. Hence there is an urgent need to seek alternative strategies of virus control that can be more readily deployed to contain viral diseases. The discovery in the late 1980s that viral genes can be introduced into plants to engineer resistance to the cognate virus provided a new avenue for virus disease control. Subsequent advances in genomics and biotechnology have led to the refinement and expansion of genetic engineering (GE) strategies in crop improvement. Importantly, many of the drawbacks of conventional breeding, such as long lead times, inability or difficulty to cross fertilize, loss of desirable plant traits, are overcome by GE. Unfortunately, public skepticism towards genetically modified (GM) crops and other factors have dampened the early promise of GE efforts. These concerns are principally about the possible negative effects of transgenes to humans and animals, as well as to the environment. However, with regards to engineering for virus resistance, these risks are overstated given that most virus resistance engineering strategies involve transfer of viral genes or genomic segments to plants. These viral genomes are found in infected plant cells and have not been associated with any adverse effects in humans or animals. Thus, integrating antiviral genes of virus origin into plant genomes is hardly unnatural as suggested by GM crop skeptics. Moreover, advances in deep sequencing have resulted in the sequencing of large numbers of plant genomes and the revelation of widespread endogenization of viral genomes into plant genomes. This has raised the possibility that viral genome endogenization is part of an antiviral defense mechanism deployed by the plant during its evolutionary past. Thus, GM crops engineered for viral resistance would likely be acceptable to the public if regulatory policies were product-based (the North America regulatory model), as opposed to process-based. This review discusses some of the benefits to be gained from adopting GE for virus resistance, as well as the challenges that must be overcome to leverage this technology. Furthermore, regulatory policies impacting virus-resistant GM crops and some success cases of virus-resistant GM crops approved so far for cultivation are discussed.
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23
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Abstract
The RNA-dependent RNA polymerase (RdRp) of all known double-stranded RNA viruses is located within the viral particle and is responsible for the transcription and replication of the viral genome. Through an RT-PCR assay, we determined that purified virions, in vitro translated RdRp proteins, and purified recombinant RdRp proteins of partitiviruses also have reverse transcriptase (RT) function. We show that partitivirus RdRps 1) synthesized DNA from homologous and heterologous dsRNA templates; 2) are active using both ssRNA and dsRNA templates; and 3) are active at lower temperatures compared to an optimal reaction temperature of commercial RT enzymes. This finding poses an intriguing question: why do partitiviruses, with dsRNA genomes, have a polymerase with RT functions? In comparison, 3Dpol, the RdRp of poliovirus, did not show any RT activity. Our findings lead us to propose a new evolutionary model for RNA viruses where the RdRp of dsRNA viruses could be the ancestor of RdRps.
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Affiliation(s)
- Mahtab Peyambari
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, PA, USA
| | | | - Marilyn J Roossinck
- Center for Infectious Disease Dynamics, Millennium Science Complex, Pennsylvania State University, University Park, PA, USA
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24
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Boutanaev AM, Nemchinov LG. Genome-wide identification of endogenous viral sequences in alfalfa (Medicago sativa L.). Virol J 2021; 18:185. [PMID: 34503524 PMCID: PMC8428138 DOI: 10.1186/s12985-021-01650-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/26/2021] [Indexed: 11/10/2022] Open
Abstract
Endogenous viral elements (EVEs) have been for the most part described in animals and to a less extent in plants. The endogenization was proposed to contribute toward evolution of living organisms via horizontal gene transfer of novel genetic material and resultant genetic diversity. During the last two decades, several full-length and fragmented EVEs of pararetroviral and non-retroviral nature have been identified in different plant genomes, both monocots and eudicots. Prior to this work, no EVEs have been reported in alfalfa (Medicago sativa L.), the most cultivated forage legume in the world. In this study, taking advantage of the most recent developments in the field of alfalfa research, we have assessed alfalfa genome on the presence of viral-related sequences. Our analysis revealed segmented EVEs resembling two dsDNA reverse-transcribing virus species: Soybean chlorotic mottle virus (family Caulimoviridae, genus Soymovirus) and Figwort mosaic virus (family Caulimoviridae, genus Caulimovirus). The EVEs appear to be stable constituents of the host genome and in that capacity could potentially acquire functional roles in alfalfa’s development and response to environmental stresses.
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Affiliation(s)
- Alexander M Boutanaev
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Lev G Nemchinov
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD, 20705, USA.
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25
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Citiulo F, Crosatti C, Cattivelli L, Biselli C. Frontiers in the Standardization of the Plant Platform for High Scale Production of Vaccines. PLANTS (BASEL, SWITZERLAND) 2021; 10:1828. [PMID: 34579360 PMCID: PMC8467261 DOI: 10.3390/plants10091828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/13/2022]
Abstract
The recent COVID-19 pandemic has highlighted the value of technologies that allow a fast setup and production of biopharmaceuticals in emergency situations. The plant factory system can provide a fast response to epidemics/pandemics. Thanks to their scalability and genome plasticity, plants represent advantageous platforms to produce vaccines. Plant systems imply less complicated production processes and quality controls with respect to mammalian and bacterial cells. The expression of vaccines in plants is based on transient or stable transformation systems and the recent progresses in genome editing techniques, based on the CRISPR/Cas method, allow the manipulation of DNA in an efficient, fast, and easy way by introducing specific modifications in specific sites of a genome. Nonetheless, CRISPR/Cas is far away from being fully exploited for vaccine expression in plants. In this review, an overview of the potential conjugation of the renewed vaccine technologies (i.e., virus-like particles-VLPs, and industrialization of the production process) with genome editing to produce vaccines in plants is reported, illustrating the potential advantages in the standardization of the plant platforms, with the overtaking of constancy of large-scale production challenges, facilitating regulatory requirements and expediting the release and commercialization of the vaccine products of genome edited plants.
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Affiliation(s)
- Francesco Citiulo
- GSK Vaccines Institute for Global Health, Via Fiorentina 1, 53100 Siena, Italy;
| | - Cristina Crosatti
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (C.C.); (L.C.)
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (C.C.); (L.C.)
| | - Chiara Biselli
- Council for Agricultural Research and Economics, Research Centre for Viticulture and Enology, Viale Santa Margherita 80, 52100 Arezzo, Italy
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26
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Cheng RL, Li XF, Zhang CX. Novel Dicistroviruses in an Unexpected Wide Range of Invertebrates. FOOD AND ENVIRONMENTAL VIROLOGY 2021; 13:423-431. [PMID: 33837925 DOI: 10.1007/s12560-021-09472-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Dicistroviruses are members of a rapidly growing family of small RNA viruses. Related sequences have been discovered in many environmental samples, indicating that our knowledge about dicistrovirus diversity and host range is still limited. In this study, we performed a systematic search against the publicly available transcriptome database, and identified large numbers of dicistrovirus-like sequences in a wide variety of eukaryotic species. The origins of these sequences were 108 invertebrates (including 77 insect species belonging to 18 orders) and 11 plants, revealing new associations between dicistroviruses and hosts. Finally, 83 transcripts corresponding to nearly-complete viral genomes were retrieved from the RNA-seq data, of which most sequences showed limited similarity to known dicistroviruses and might present previously unreported virus species. Phylogenetic analysis suggested that horizontal virus transfer has occurred between diverse hosts and has important implications for dicistrovirus evolution. The results will provide new insight into the hidden diversity of the Dicistroviridae, and help us to better understand the viral evolution, host range and the possible way of transmission.
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Affiliation(s)
- Ruo-Lin Cheng
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Xiao-Feng Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen, China
| | - Chuan-Xi Zhang
- Institute of Plant Virology, Ningbo University, Ningbo, China.
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27
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Bradamante G, Mittelsten Scheid O, Incarbone M. Under siege: virus control in plant meristems and progeny. THE PLANT CELL 2021; 33:2523-2537. [PMID: 34015140 PMCID: PMC8408453 DOI: 10.1093/plcell/koab140] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/14/2021] [Indexed: 05/29/2023]
Abstract
In the arms race between plants and viruses, two frontiers have been utilized for decades to combat viral infections in agriculture. First, many pathogenic viruses are excluded from plant meristems, which allows the regeneration of virus-free plant material by tissue culture. Second, vertical transmission of viruses to the host progeny is often inefficient, thereby reducing the danger of viral transmission through seeds. Numerous reports point to the existence of tightly linked meristematic and transgenerational antiviral barriers that remain poorly understood. In this review, we summarize the current understanding of the molecular mechanisms that exclude viruses from plant stem cells and progeny. We also discuss the evidence connecting viral invasion of meristematic cells and the ability of plants to recover from acute infections. Research spanning decades performed on a variety of virus/host combinations has made clear that, beside morphological barriers, RNA interference (RNAi) plays a crucial role in preventing-or allowing-meristem invasion and vertical transmission. How a virus interacts with plant RNAi pathways in the meristem has profound effects on its symptomatology, persistence, replication rates, and, ultimately, entry into the host progeny.
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Affiliation(s)
- Gabriele Bradamante
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Marco Incarbone
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
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28
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Yang M, Xu W, Zhou X, Yang Z, Wang Y, Xiao F, Guo Y, Hong N, Wang G. Discovery and Characterization of a Novel Bipartite Botrexvirus From the Phytopathogenic Fungus Botryosphaeria dothidea. Front Microbiol 2021; 12:696125. [PMID: 34276630 PMCID: PMC8280476 DOI: 10.3389/fmicb.2021.696125] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 05/31/2021] [Indexed: 11/15/2022] Open
Abstract
In this study, we describe a novel positive, single-stranded (+ss) RNA mycovirus, named Botryosphaeria dothidea botrexvirus 1 (BdBV1), from a phytopathogenic fungus Botryosphaeria dothidea showing abnormal morphology and attenuated virulence. BdBV1 is phylogenetically related to Botrytis virus X (BotVX) and is the second potential member of the proposed genus Botrexvirus in the family Alphaflexiviridae. However, it differs from the monopartite BotVX in that BdBV1 possesses a bipartite genome comprised of two ssRNA segments (RNA1 and RNA2 with lengths of 5,035 and 1,063 nt, respectively). BdBV1 RNA1 and RNA2 encode putative RNA-dependent RNA polymerase (RdRp) and coat protein (CP) genes, which share significant identity with corresponding genes in both fungal and plant viruses. Moreover, open reading frames (ORFs) 2-4 of BdBV1 RNA1 shared no detectable identity with any known viral proteins. Immunosorbent electron microscopy (ISEM) analysis using an antibody against the virus CP generated in vitro revealed that BdBV1 is encapsidated in filamentous particles. A comparison of the biological effects of BdBV1 infection on symptoms and growth in isogenic lines of virus-free and virus-infected B. dothidea revealed that BdBV1 is probably involved in reduced growth and virulence of the host fungus. This study describes and characterizes a novel bipartite botrexvirus, which is closely related to uni- and multi-partite fungal and plant viruses and contributes useful information to a better understanding of virus evolution.
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Affiliation(s)
- Mengmeng Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Wenxing Xu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Xiaoqi Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zuokun Yang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanxiang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Feng Xiao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yashuang Guo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
- Key Lab of Plant Pathology of Hubei Province, Wuhan, China
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Honda S, Eusebio-Cope A, Miyashita S, Yokoyama A, Aulia A, Shahi S, Kondo H, Suzuki N. Establishment of Neurospora crassa as a model organism for fungal virology. Nat Commun 2020; 11:5627. [PMID: 33159072 PMCID: PMC7648066 DOI: 10.1038/s41467-020-19355-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/08/2020] [Indexed: 01/07/2023] Open
Abstract
The filamentous fungus Neurospora crassa is used as a model organism for genetics, developmental biology and molecular biology. Remarkably, it is not known to host or to be susceptible to infection with any viruses. Here, we identify diverse RNA viruses in N. crassa and other Neurospora species, and show that N. crassa supports the replication of these viruses as well as some viruses from other fungi. Several encapsidated double-stranded RNA viruses and capsid-less positive-sense single-stranded RNA viruses can be experimentally introduced into N. crassa protoplasts or spheroplasts. This allowed us to examine viral replication and RNAi-mediated antiviral responses in this organism. We show that viral infection upregulates the transcription of RNAi components, and that Dicer proteins (DCL-1, DCL-2) and an Argonaute (QDE-2) participate in suppression of viral replication. Our study thus establishes N. crassa as a model system for the study of host-virus interactions. The fungus Neurospora crassa is a model organism for the study of various biological processes, but it is not known to be infected by any viruses. Here, Honda et al. identify RNA viruses that infect N. crassa and examine viral replication and RNAi-mediated antiviral responses, thus establishing this fungus as a model for the study of host-virus interactions.
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Affiliation(s)
- Shinji Honda
- Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan
| | - Ana Eusebio-Cope
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Shuhei Miyashita
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza- Aoba, Sendai, 980-0845, Japan
| | - Ayumi Yokoyama
- Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan
| | - Annisa Aulia
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Sabitree Shahi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan.
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30
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Piñar G, Tafer H, Schreiner M, Miklas H, Sterflinger K. Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value. Environ Microbiol 2020; 22:3218-3233. [PMID: 32400083 PMCID: PMC7687136 DOI: 10.1111/1462-2920.15064] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 02/06/2023]
Abstract
This study provides an example in the emerging field of biocodicology showing how metagenomics can help answer relevant questions that may contribute to a better understanding of the history of ancient manuscripts. To this end, two Slavonic codices dating from the 11th century were investigated through shotgun metagenomics. Endogenous DNA enabled to infer the animal origin of the skins used in the manufacture of the two codices, while nucleic sequences recovered from viruses were investigated for the first time in this material, opening up new possibilities in the field of biocodicology. In addition, the microbiomes colonizing the surface of the parchments served to determine their conservation status and their latent risk of deterioration. The saline environment provided by the parchments selected halophilic and halotolerant microorganisms, which are known to be responsible for the biodegradation of parchment. Species of Nocardiopsis, Gracilibacillus and Saccharopolyspora, but also members of the Aspergillaceae family were detected in this study, all possessing enzymatic capabilities for the biodeterioration of this material. Finally, a relative abundance of microorganisms originating from the human skin microbiome were identified, most probably related to the intensive manipulation of the manuscripts throughout the centuries, which should be taken with caution as they can be potential pathogens.
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Affiliation(s)
- Guadalupe Piñar
- Institute of Microbiology and Microbial Biotechnology, Department of BiotechnologyUniversity of Natural Resources and Life Sciences, Muthgasse 11, A‐1190ViennaAustria
| | - Hakim Tafer
- Institute of Microbiology and Microbial Biotechnology, Department of BiotechnologyUniversity of Natural Resources and Life Sciences, Muthgasse 11, A‐1190ViennaAustria
| | - Manfred Schreiner
- Institute of Science and Technology in Art (ISTA)Academy of Fine Arts ViennaSchillerplatz 3, A‐1010 ViennaAustria
| | - Heinz Miklas
- Department of Slavonic StudiesUniversity of ViennaSpitalgasse 2‐4, Hof 3, A‐1090 ViennaAustria
| | - Katja Sterflinger
- Institute of Microbiology and Microbial Biotechnology, Department of BiotechnologyUniversity of Natural Resources and Life Sciences, Muthgasse 11, A‐1190ViennaAustria
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31
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Di Paola N, Sanchez-Lockhart M, Zeng X, Kuhn JH, Palacios G. Viral genomics in Ebola virus research. Nat Rev Microbiol 2020; 18:365-378. [PMID: 32367066 PMCID: PMC7223634 DOI: 10.1038/s41579-020-0354-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 12/20/2022]
Abstract
Filoviruses such as Ebola virus continue to pose a substantial health risk to humans. Advances in the sequencing and functional characterization of both pathogen and host genomes have provided a wealth of knowledge to clinicians, epidemiologists and public health responders during outbreaks of high-consequence viral disease. Here, we describe how genomics has been historically used to investigate Ebola virus disease outbreaks and how new technologies allow for rapid, large-scale data generation at the point of care. We highlight how genomics extends beyond consensus-level sequencing of the virus to include intra-host viral transcriptomics and the characterization of host responses in acute and persistently infected patients. Similar genomics techniques can also be applied to the characterization of non-human primate animal models and to known natural reservoirs of filoviruses, and metagenomic sequencing can be the key to the discovery of novel filoviruses. Finally, we outline the importance of reverse genetics systems that can swiftly characterize filoviruses as soon as their genome sequences are available.
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Affiliation(s)
- Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Mariano Sanchez-Lockhart
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Xiankun Zeng
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA.
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Telengech P, Hisano S, Mugambi C, Hyodo K, Arjona-López JM, López-Herrera CJ, Kanematsu S, Kondo H, Suzuki N. Diverse Partitiviruses From the Phytopathogenic Fungus, Rosellinia necatrix. Front Microbiol 2020; 11:1064. [PMID: 32670213 PMCID: PMC7332551 DOI: 10.3389/fmicb.2020.01064] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/29/2020] [Indexed: 01/18/2023] Open
Abstract
Partitiviruses (dsRNA viruses, family Partitiviridae) are ubiquitously detected in plants and fungi. Although previous surveys suggested their omnipresence in the white root rot fungus, Rosellinia necatrix, only a few of them have been molecularly and biologically characterized thus far. We report the characterization of a total of 20 partitiviruses from 16 R. necatrix strains belonging to 15 new species, for which “Rosellinia necatrix partitivirus 11–Rosellinia necatrix partitivirus 25” were proposed, and 5 previously reported species. The newly identified partitiviruses have been taxonomically placed in two genera, Alphapartitivirus, and Betapartitivirus. Some partitiviruses were transfected into reference strains of the natural host, R. necatrix, and an experimental host, Cryphonectria parasitica, using purified virions. A comparative analysis of resultant transfectants revealed interesting differences and similarities between the RNA accumulation and symptom induction patterns of R. necatrix and C. parasitica. Other interesting findings include the identification of a probable reassortment event and a quintuple partitivirus infection of a single fungal strain. These combined results provide a foundation for further studies aimed at elucidating mechanisms that underly the differences observed.
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Affiliation(s)
- Paul Telengech
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Sakae Hisano
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Cyrus Mugambi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kiwamu Hyodo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Juan Manuel Arjona-López
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan.,Institute for Sustainable Agriculture, Spanish Research Council, Córdoba, Spain
| | | | - Satoko Kanematsu
- Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Morioka, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
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33
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Takahashi H, Fukuhara T, Kitazawa H, Kormelink R. Virus Latency and the Impact on Plants. Front Microbiol 2019; 10:2764. [PMID: 31866963 PMCID: PMC6908805 DOI: 10.3389/fmicb.2019.02764] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/12/2019] [Indexed: 11/15/2022] Open
Abstract
Plant viruses are thought to be essentially harmful to the lives of their cultivated crop hosts. In most cases studied, the interaction between viruses and cultivated crop plants negatively affects host morphology and physiology, thereby resulting in disease. Native wild/non-cultivated plants are often latently infected with viruses without any clear symptoms. Although seemingly non-harmful, these viruses pose a threat to cultivated crops because they can be transmitted by vectors and cause disease. Reports are accumulating on infections with latent plant viruses that do not cause disease but rather seem to be beneficial to the lives of wild host plants. In a few cases, viral latency involves the integration of full-length genome copies into the host genome that, in response to environmental stress or during certain developmental stages of host plants, can become activated to generate and replicate episomal copies, a transition from latency to reactivation and causation of disease development. The interaction between viruses and host plants may also lead to the integration of partial-length segments of viral DNA genomes or copy DNA of viral RNA genome sequences into the host genome. Transcripts derived from such integrated viral elements (EVEs) may be beneficial to host plants, for example, by conferring levels of virus resistance and/or causing persistence/latency of viral infections. Studies on viral latency in wild host plants might help us to understand and elucidate the underlying mechanisms of latency and provide insights into the raison d’être for viruses in the lives of plants.
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Affiliation(s)
- Hideki Takahashi
- Laboratory of Plant Pathology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Plant Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences and Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University, Wageningen, Netherlands
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34
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Discovery and characterization of a novel alphavirus-like RNA virus from the red firebug Pyrrhocoris apterus L. (Heteroptera). J Invertebr Pathol 2019; 166:107213. [DOI: 10.1016/j.jip.2019.107213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/25/2019] [Accepted: 06/27/2019] [Indexed: 11/22/2022]
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35
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Zhao JH, Guo HS. Trans-kingdom RNA interactions drive the evolutionary arms race between hosts and pathogens. Curr Opin Genet Dev 2019; 58-59:62-69. [PMID: 31472442 DOI: 10.1016/j.gde.2019.07.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/23/2019] [Accepted: 07/30/2019] [Indexed: 12/12/2022]
Abstract
Trans-kingdom RNA plays a key role in host-parasite interactions. Hosts export specific endogenous microRNAs (miRNAs) into pathogens to target pathogen virulence genes and inhibit their invasion. In addition, trans-kingdom sRNAs produced by parasites may function as RNA effectors to suppress host immunity. Here, we summarize recent, important findings regarding trans-kingdom RNA and focus on the roles of trans-kingdom RNA in driving an evolutionary arms race between host and pathogen. We suggest that trans-kingdom RNA is a new platform for such arms races. Furthermore, we conjecture that trans-kingdom RNA contributes to horizontal gene transfer (HGT) involved in host-pathogen interactions. In addition, we propose that trans-kingdom RNA exchange and RNA driven HGT can have a great impact on the evolutionary ecology of interacting species.
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Affiliation(s)
- Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China; CAS Center for Excellence in Biotic Interactions, University of the Chinese Academy of Sciences, 100049 Beijing, China.
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36
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Vainio EJ. Mitoviruses in the conifer root rot pathogens Heterobasidion annosum and H. parviporum. Virus Res 2019; 271:197681. [PMID: 31394105 DOI: 10.1016/j.virusres.2019.197681] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 10/26/2022]
Abstract
Mitoviral infections are highly common among fungi, but so far only one mitovirus has been described in Heterobasidion spp. conifer pathogens. Here, the occurrence of further mitoviruses was investigated using a previously published RNA-Seq dataset for de novo contig assembly. This allowed the identification of two additional mitovirus strains designated as Heterobasidion mitovirus 2 (HetMV2) and HetMV3 with genome lengths of ca. 2.9 and 5.0 kb. Furthermore, the occurrence of similar viruses was screened among a collection of Heterobasidion isolates using RT-PCR. Mitoviruses were detected in six more fungal isolates and two different host species, H. annosum and H. parviporum.
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Affiliation(s)
- Eeva J Vainio
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790 Helsinki, Finland.
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37
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Petrzik K. Evolutionary forces at work in partitiviruses. Virus Genes 2019; 55:563-573. [PMID: 31230256 DOI: 10.1007/s11262-019-01680-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023]
Abstract
The family Partitiviridae consists of dsRNA viruses with genome separated into two segments and encoding replicase and capsid protein only. We examined the nucleotide diversity expressed as the ratio dN/dS of nonsynonymous and synonymous substitutions, which has been calculated for 12 representative viruses of all five genera of partitiviruses. We can state that strong purifying selection works on both the RdRp and CP genes and propose that putative positive selection occurs also on the RdRp genes in two viruses. Among the 95 evaluated viruses, wherein both segments had been sequenced, 8 viruses in betapartitiviruses and 9 in alphapartitiviruses were identified as reassortment candidates because they differ extremely in their CP identity even as they are related in terms of RdRp. Furthermore, there are indications that reassortants are present among isolates of different viruses.
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Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic.
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Li CX, Zhu JZ, Gao BD, Zhu HJ, Zhou Q, Zhong J. Characterization of a Novel Ourmia-Like Mycovirus Infecting Magnaporthe oryzae and Implications for Viral Diversity and Evolution. Viruses 2019; 11:v11030223. [PMID: 30841545 PMCID: PMC6465991 DOI: 10.3390/v11030223] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 01/06/2023] Open
Abstract
Here, the molecular characterization of a novel mycovirus that was isolated from a phytopathogenic fungus Magnaporthe oryzae and designed as Magnaporthe oryzae ourmia-like virus 4 (MOLV4) is reported. MOLV4 has a genome that is 2497 bp long and possesses a single open reading frame (ORF), which encodes the product RNA-dependent RNA polymerase (RdRp). Sequence similarities were found between the MOLV4 encoded RdRp and the counterparts of a few previously reported ourmia-like mycoviruses. Virus-curing and biological comparison indicate that the virus has no or mild effects on the morphology and mycelium growth rate of the host fungus. Phylogenetic analysis using the RdRp aa sequences was performed. The results show that MOLV4 is clustered with the ourmia-like mycoviruses, forming a clade closely related to ourmiaviruses but distinct from narnaviruses. In addition, database searches revealed that several MOLV4-related sequences are present in the transcriptome shotgun assembly (TSA) library, expressed sequence tag database (ESTdb), whole-genome shotgun (WGS) library, and genomic survey sequences (GSS) libraries of a few other species of eukaryote organisms. Our results show that MOLV4, together with other similar ourmia-like mycoviruses, might represent a virus clade that links the plant ourmiaviruses and fungal narnaviruses and has a wide range of hosts.
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Affiliation(s)
- Chang Xin Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha 410128, China.
| | - Jun Zi Zhu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha 410128, China.
| | - Bi Da Gao
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha 410128, China.
| | - Hong Jian Zhu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha 410128, China.
| | - Qian Zhou
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha 410128, China.
| | - Jie Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha 410128, China.
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Investigation of Host Range of and Host Defense against a Mitochondrially Replicating Mitovirus. J Virol 2019; 93:JVI.01503-18. [PMID: 30626664 DOI: 10.1128/jvi.01503-18] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/18/2018] [Indexed: 01/19/2023] Open
Abstract
Mitoviruses (genus Mitovirus, family Narnaviridae) are mitochondrially replicating viruses that have the simplest positive-sense RNA genomes of 2.2 to 4.4 kb with a single open reading frame (ORF) encoding an RNA-dependent RNA polymerase. Cryphonectria parasitica mitovirus 1 (CpMV1) from U.S. strain NB631 of the chestnut blight fungus, Cryphonectria parasitica, was the first virus identified as a mitochondrially replicating virus. Despite subsequent discovery of many other mitoviruses from diverse fungi, no great advances in understanding mitovirus biology have emerged, partly because of the lack of inoculation methods. Here we developed a protoplast fusion-based protocol for horizontal transmission of CpMV1 that entailed fusion of recipient and donor protoplasts, hyphal anastomosis, and single-conidium isolation. This method allowed expansion of the host range to many other C. parasitica strains. Species within and outside the family Cryphonectriaceae, Cryphonectria radicalis and Valsa ceratosperma, also supported the replication of CpMV1 at a level comparable to that in the natural host. No stable maintenance of CpMV1 was observed in Helminthosporium victoriae PCR-based haplotyping of virus-infected fungal strains confirmed the recipient mitochondrial genetic background. Phenotypic comparison between CpMV1-free and -infected isogenic strains revealed no overt effects of the virus. Taking advantage of the infectivity to the standard strain C. parasitica EP155, accumulation levels were compared among antiviral RNA silencing-proficient and -deficient strains in the EP155 background. Comparable accumulation levels were observed among these strains, suggesting the avoidance of antiviral RNA silencing by CpMV1, which is consistent with its mitochondrial replication. Collectively, the results of study provide a foundation to further explore the biology of mitoviruses.IMPORTANCE Capsidless mitoviruses, which are ubiquitously detected in filamentous fungi, have the simplest RNA genomes of 2.2 to 4.4 kb, encoding only RNA-dependent RNA polymerase. Despite their simple genomes, detailed biological characterization of mitoviruses has been hampered by their mitochondrial location within the cell, posing challenges to their experimental introduction and study. Here we developed a protoplast fusion-based protocol for horizontal transfer of the prototype mitovirus, Cryphonectria parasitica mitovirus 1 (CpMV1), which was isolated from strain NB631 of the chestnut blight fungus (Cryphonectria parasitica), a model filamentous fungus for studying virus-host interactions. The host range of CpMV1 has been expanded to many different strains of C. parasitica and different fungal species within and outside the Cryphonectriaceae. Comparison of CpMV1 accumulation among various RNA silencing-deficient and -competent strains showed clearly that the virus was unaffected by RNA silencing. This study provides a solid foundation for further exploration of mitovirus-host interactions.
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Horizontal Transfer of a Retrotransposon from the Rice Planthopper to the Genome of an Insect DNA Virus. J Virol 2019; 93:JVI.01516-18. [PMID: 30626674 PMCID: PMC6401454 DOI: 10.1128/jvi.01516-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/28/2018] [Indexed: 12/15/2022] Open
Abstract
This study provides an example of the horizontal transfer event from a rice planthopper genome to an IIV-6 genome. A small region of the IIV-6 genome (∼300 nt) is highly homologous to the sequences presented in high copy numbers of three rice planthopper genomes that are related to the SINEs, a class of retroposons. The expression of these planthopper SINE-like sequences was confirmed, and corresponding Piwi-interacting RNA-like small RNAs were identified and comprehensively characterized. Phylogenetic analysis suggests that the giant invertebrate iridovirus IIV-6 obtains this SINE-related sequence from Sogatella furcifera through a horizontal transfer event in the past. To the best of our knowledge, this is the first report of a horizontal transfer event between a planthopper and a giant DNA virus and also is the first evidence for the eukaryotic origin of genetic material in iridoviruses. Horizontal transfer of genetic materials between virus and host has been frequently identified. Three rice planthoppers, Laodelphax striatellus, Nilaparvata lugens, and Sogatella furcifera, are agriculturally important insects because they are destructive rice pests and also the vector of a number of phytopathogenic viruses. In this study, we discovered that a small region (∼300 nucleotides [nt]) of the genome of invertebrate iridescent virus 6 (IIV-6; genus Iridovirus, family Iridoviridae), a giant DNA virus that infects invertebrates but is not known to infect planthoppers, is highly homologous to the sequences present in high copy numbers in these three planthopper genomes. These sequences are related to the short interspersed nuclear elements (SINEs), a class of non-long terminal repeat (LTR) retrotransposons (retroposons), suggesting a horizontal transfer event of a transposable element from the rice planthopper genome to the IIV-6 genome. In addition, a number of planthopper transcripts mapped to these rice planthopper SINE-like sequences (RPSlSs) were identified and appear to be transcriptionally regulated along the different developmental stages of planthoppers. Small RNAs derived from these RPSlSs are predominantly 26 to 28 nt long, which is a typical characteristic of PIWI-interacting RNAs. Phylogenetic analysis suggests that IIV-6 acquires a SINE-like retrotransposon from S. furcifera after the evolutionary divergence of the three rice planthoppers. This study provides further examples of the horizontal transfer of an insect transposon to virus and suggests the association of rice planthoppers with iridoviruses in the past or present. IMPORTANCE This study provides an example of the horizontal transfer event from a rice planthopper genome to an IIV-6 genome. A small region of the IIV-6 genome (∼300 nt) is highly homologous to the sequences presented in high copy numbers of three rice planthopper genomes that are related to the SINEs, a class of retroposons. The expression of these planthopper SINE-like sequences was confirmed, and corresponding Piwi-interacting RNA-like small RNAs were identified and comprehensively characterized. Phylogenetic analysis suggests that the giant invertebrate iridovirus IIV-6 obtains this SINE-related sequence from Sogatella furcifera through a horizontal transfer event in the past. To the best of our knowledge, this is the first report of a horizontal transfer event between a planthopper and a giant DNA virus and also is the first evidence for the eukaryotic origin of genetic material in iridoviruses.
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41
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Roossinck MJ. Evolutionary and ecological links between plant and fungal viruses. THE NEW PHYTOLOGIST 2019; 221:86-92. [PMID: 30084143 DOI: 10.1111/nph.15364] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
Contents Summary 86 I. Introduction 86 II. Lineages shared by plant and fungal viruses 87 III. Virus transmission between plants and fungi 90 IV. Additional plant virus families identified in fungi by metagenomics 91 Acknowledgements 91 References 91 SUMMARY: Plants and microorganisms have been interacting in both positive and negative ways for millions of years. They are also frequently infected with viruses that can have positive or negative impacts. A majority of virus families with members that infect fungi have counterparts that infect plants, and in some cases the phylogenetic analyses of these virus families indicate transmission between the plant and fungal kingdoms. These similarities reflect the host relationships; fungi are evolutionarily more closely related to animals than to plants but share very few viral signatures with animal viruses. The details of several of these interactions are described, and the evolutionary implications of viral cross-kingdom interactions and horizontal gene transfer are proposed.
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Affiliation(s)
- Marilyn J Roossinck
- Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
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42
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Kyrychenko AN, Tsyganenko KS, Olishevska SV. Hypovirulence of Mycoviruses as a Tool for Biotechnological Control of Phytopathogenic Fungi. CYTOL GENET+ 2018. [DOI: 10.3103/s0095452718050043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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43
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Warner BE, Ballinger MJ, Yerramsetty P, Reed J, Taylor DJ, Smith TJ, Bruenn JA. Cellular production of a counterfeit viral protein confers immunity to infection by a related virus. PeerJ 2018; 6:e5679. [PMID: 30280045 PMCID: PMC6166632 DOI: 10.7717/peerj.5679] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/29/2018] [Indexed: 11/20/2022] Open
Abstract
DNA copies of many non-retroviral RNA virus genes or portions thereof (NIRVs) are present in the nuclear genomes of many eukaryotes. These have often been preserved for millions of years of evolution, suggesting that they play an important cellular function. One possible function is resistance to infection by related viruses. In some cases, this appears to occur through the piRNA system, but in others by way of counterfeit viral proteins encoded by NIRVs. In the fungi, NIRVs may be as long as 1,400 uninterrupted codons. In one such case in the yeast Debaryomyces hansenii, one of these genes provides immunity to a related virus by virtue of expression of a counterfeit viral capsid protein, which interferes with assembly of viral capsids by negative complementation. The widespread occurrence of non-retroviral RNA virus genes in eukaryotes may reflect an underappreciated method of host resistance to infection. This work demonstrates for the first time that an endogenous host protein encoded by a gene that has been naturally acquired from a virus and fixed in a eukaryote can interfere with the replication of a related virus and do so by negative complementation.
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Affiliation(s)
- Benjamin E Warner
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Matthew J Ballinger
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Pradeep Yerramsetty
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Jennifer Reed
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Derek J Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
| | - Thomas J Smith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch Galveston, Galveston, TX, United States of America
| | - Jeremy A Bruenn
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, USA
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Chu H, Jo Y, Choi H, Lee BC, Cho WK. Identification of viral domains integrated into Arabidopsis proteome. Mol Phylogenet Evol 2018; 128:246-257. [PMID: 30125655 DOI: 10.1016/j.ympev.2018.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 08/05/2018] [Accepted: 08/15/2018] [Indexed: 10/28/2022]
Abstract
Horizontal gene transfer (HGT) contributes to the genome evolution of living organisms. In particular, several recent studies provide convincing data on the integration of viral sequences into diverse organisms. Here, we identified 101 viral domains integrated into the model plant Arabidopsis proteome. Functional analysis based on gene ontology (GO) terms indicates that viral domains in the Arabidopsis proteome were involved in various stress responses with binding functions. Protein interaction networks support the strong protein interactions of viral domains with other Arabidopsis proteins. A proteome-wide analysis gave a comprehensive evolutionary view of viral domains integrated into 41 plant proteomes, revealing the specific and conserved integration of viral domains into plant proteomes. Phylogenetic analyses revealed the possible HGT between viral domains and plant proteomes. Our results provide an overview of the integration of viral domains into plant proteomes and their possible functional roles associated with plant defense mechanisms.
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Affiliation(s)
- Hyosub Chu
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeonhwa Jo
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hoseong Choi
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Bong Choon Lee
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju 55365, Republic of Korea
| | - Won Kyong Cho
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; The Taejin Genome Institute, Gadam-gil 61, Hoeongseong 25239, Republic of Korea.
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Nibert ML, Vong M, Fugate KK, Debat HJ. Evidence for contemporary plant mitoviruses. Virology 2018; 518:14-24. [PMID: 29438872 PMCID: PMC6668999 DOI: 10.1016/j.virol.2018.02.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/02/2018] [Accepted: 02/03/2018] [Indexed: 10/18/2022]
Abstract
Mitoviruses have small RNA(+) genomes, replicate in mitochondria, and have been shown to infect only fungi to date. For this report, sequences that appear to represent nearly complete plant mitovirus genomes were recovered from publicly available transcriptome data. Twenty of the refined sequences, 2684-2898 nt long and derived from 10 different species of land plants, appear to encompass the complete coding regions of contemporary plant mitoviruses, which furthermore constitute a monophyletic cluster within genus Mitovirus. Complete coding sequences of several of these viruses were recovered from multiple transcriptome (but not genome) studies of the same plant species and also from multiple plant tissues. Crop plants among implicated hosts include beet and hemp. Other new results suggest that such genuine plant mitoviruses were immediate ancestors to endogenized mitovirus elements now widespread in land plant genomes. Whether these mitoviruses are wholly cryptic with regard to plant health remains to be investigated.
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Affiliation(s)
- Max L Nibert
- Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Minh Vong
- Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Karen K Fugate
- Sugarbeet and Potato Research, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Red River Valley Agricultural Research Center, Fargo, ND 58102, USA
| | - Humberto J Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), X5020ICA, Córdoba, Argentina
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46
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Arjona-Lopez JM, Telengech P, Jamal A, Hisano S, Kondo H, Yelin MD, Arjona-Girona I, Kanematsu S, Lopez-Herrera CJ, Suzuki N. Novel, diverse RNA viruses from Mediterranean isolates of the phytopathogenic fungus, Rosellinia necatrix: insights into evolutionary biology of fungal viruses. Environ Microbiol 2018; 20:1464-1483. [PMID: 29411500 DOI: 10.1111/1462-2920.14065] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/02/2018] [Indexed: 11/30/2022]
Abstract
To reveal mycovirus diversity, we conducted a search of as-yet-unexplored Mediterranean isolates of the phytopathogenic ascomycete Rosellinia necatrix for virus infections. Of seventy-nine, eleven fungal isolates tested RNA virus-positive, with many showing coinfections, indicating a virus incidence of 14%, which is slightly lower than that (approximately 20%) previously reported for extensive surveys of over 1000 Japanese R. necatrix isolates. All viral sequences were fully or partially characterized by Sanger and next-generation sequencing. These sequences appear to represent isolates of various new species spanning at least 6 established or previously proposed families such as Partiti-, Hypo-, Megabirna-, Yado-kari-, Fusagra- and Fusarividae, as well as a newly proposed family, Megatotiviridae. This observation greatly expands the diversity of R. necatrix viruses, because no hypo-, fusagra- or megatotiviruses were previously reported from R. necatrix. The sequence analyses showed a rare horizontal gene transfer event of the 2A-like protease domain between a dsRNA (phlegivirus) and a positive-sense, single-stranded RNA virus (hypovirus). Moreover, many of the newly detected viruses showed the closest relation to viruses reported from fungi other than R. necatrix, such as Fusarium spp., which are sympatric to R. necatrix. These combined results imply horizontal virus transfer between these soil-inhabitant fungi.
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Affiliation(s)
- Juan Manuel Arjona-Lopez
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046, Japan.,Instituto de Agricultura Sostenible C.S.I.C., Alameda del Obispo, s/n. CP: 14004, Cordoba, Spain
| | - Paul Telengech
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046, Japan
| | - Atif Jamal
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046, Japan.,Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad 45500, Pakistan
| | - Sakae Hisano
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046, Japan
| | - Mery Dafny Yelin
- Northern Agriculture Research & Development, Migal Galilee Technology Center, P.O.B. 831, Kiryat Shemona 11016, Israel
| | - Isabel Arjona-Girona
- Instituto de Agricultura Sostenible C.S.I.C., Alameda del Obispo, s/n. CP: 14004, Cordoba, Spain
| | - Satoko Kanematsu
- NARO Headquarter, National Agriculture and Food Research Organization (NARO), 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517, Japan.,Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Morioka, Iwate 020-0123, Japan
| | | | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, 710-0046, Japan
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Fisher CR, Streicker DG, Schnell MJ. The spread and evolution of rabies virus: conquering new frontiers. Nat Rev Microbiol 2018; 16:241-255. [PMID: 29479072 PMCID: PMC6899062 DOI: 10.1038/nrmicro.2018.11] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Rabies is a lethal zoonotic disease that is caused by lyssaviruses, most often rabies virus. Despite control efforts, sporadic outbreaks in wildlife populations are largely unpredictable, underscoring our incomplete knowledge of what governs viral transmission and spread in reservoir hosts. Furthermore, the evolutionary history of rabies virus and related lyssaviruses remains largely unclear. Robust surveillance efforts combined with diagnostics and disease modelling are now providing insights into the epidemiology and evolution of rabies virus. The immune status of the host, the nature of exposure and strain differences all clearly influence infection and transmission dynamics. In this Review, we focus on rabies virus infections in the wildlife and synthesize current knowledge in the rapidly advancing fields of rabies virus epidemiology and evolution, and advocate for multidisciplinary approaches to advance our understanding of this disease.
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Affiliation(s)
- Christine R. Fisher
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Daniel G. Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, Scotland, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Matthias J. Schnell
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Vaccine Center at Thomas Jefferson University, Philadelphia, PA, USA
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Abstract
In contrast to well-established internal ribosomal entry site (IRES)-mediated translational initiation in animals and plants, no IRESs were established in fungal viral or cellular RNAs. To identify IRES elements in mycoviruses, we developed a luciferase-based dual-reporter detection system in Cryphonectria parasitica, a model filamentous fungus for virus-host interactions. A bicistronic construct entails a codon-optimized Renilla and firefly luciferase (ORluc and OFluc, respectively) gene, between which potential IRES sequences can be inserted. In this system, ORluc serves as an internal control, while OFluc represents IRES activity. Virus sequences in the 5′ untranslated regions (UTRs) of the genomes of diverse positive-sense single-stranded RNA and double-stranded RNA (dsRNA) viruses were analyzed. The results show relatively high IRES activities for Cryphonectria hypovirus 1 (CHV1) and CHV2 and faint but measurable activity for CHV3. The weak IRES signal of CHV3 may be explained by its monocistronic nature, differing from the bicistronic nature of CHV1 and CHV2. This would allow these three hypoviruses to have similar rates of translation of replication-associated protein per viral mRNA molecule. The importance of 24 5′-proximal codons of CHV1 as well as the 5′ UTR for IRES function was confirmed. Furthermore, victoriviruses and chrysoviruses tested IRES positive, whereas mycoreoviruses, partitiviruses, and quadriviruses showed similar Fluc activities as the negative controls. Overall, this study represents the first development of an IRES identification system in filamentous fungi based on the codon-optimized dual-luciferase assay and provides evidence for IRESs in filamentous fungi. Cap-independent, internal ribosomal entry site (IRES)-mediated translational initiation is often used by virus mRNAs and infrequently by cellular mRNAs in animals and plants. However, no IRESs have been established in fungal virus RNAs or cellular RNAs in filamentous fungi. Here, we report the development of a dual-luciferase assay system and measurement of the IRES activities of fungal RNA viruses in a model filamentous fungal host, Cryphonectria parasitica. Viruses identified as IRES positive include hypoviruses (positive-sense RNA viruses, members of the expanded Picornavirus supergroup), totiviruses (nonsegmented dsRNA viruses), and chrysoviruses (tetrasegmented dsRNA viruses). No IRES activities were observed in the 5′ untranslated regions of mycoreoviruses (11-segmented dsRNA viruses), quadriviruses (tetrasegmented dsRNA viruses), or partitiviruses (bisegmented dsRNA viruses). This study provides the first evidence for IRES activities in diverse RNA viruses in filamentous fungi and is a first step toward identifying trans-acting host factors and cis-regulatory viral RNA elements.
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49
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Carrasco JL, Sánchez-Navarro JA, Elena SF. Exploring the role of cellular homologous of the 30K-superfamily of plant virus movement proteins. Virus Res 2018; 262:54-61. [PMID: 29475053 DOI: 10.1016/j.virusres.2018.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 12/22/2022]
Abstract
Genes orthologous to the 30K-superfamily of movement proteins (MP) from plant viruses have been recently discovered by bioinformatics analyses as integrated elements in the genome of most vascular plants. However, their functional relevance for plants is still unclear. Here, we undertake some preliminary steps into the functional characterization of one of these putative MP genes found in Arabidopsis thaliana. We found that the AtMP gene is expressed at different stages of the plant development, with accumulation being highest in flowers but lowest in mature siliques. We also found down-regulation of the gene may result in a small delay in plant development and in an exacerbation of the negative effect of salinity in germination efficiency. We have also explored whether changes in expression of the endogenous AtMP have any effect on susceptibility to infection with several viruses, and found that the infectivity of tobacco rattle tobravirus was strongly dependent on the expression of the endogenous AtMP. Finally, we have cloned the endogenous MP from four different plant species into an expression vector that allows for specifically assessing their activity as cell-to-cell movement proteins and have shown that though some may still retain the ancestral activity, they do so in a quite inefficient manner, thus suggesting they have acquired a novel function during adaptation to the host genome.
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Affiliation(s)
- José L Carrasco
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain
| | - Jesús A Sánchez-Navarro
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain; Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-UV, Parc Científic UV, Catedrático Agustín Escardino 9, 46980, Paterna, València, Spain; The Santa Fe Institute,1399 Hyde Park Road, Santa Fe, NM, 87501, USA.
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50
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Elena SF. Evolutionary transitions during RNA virus experimental evolution. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0441. [PMID: 27431519 DOI: 10.1098/rstb.2015.0441] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2016] [Indexed: 12/27/2022] Open
Abstract
In their search to understand the evolution of biological complexity, John Maynard Smith and Eörs Szathmáry put forward the notion of major evolutionary transitions as those in which elementary units get together to generate something new, larger and more complex. The origins of chromosomes, eukaryotic cells, multicellular organisms, colonies and, more recently, language and technological societies are examples that clearly illustrate this notion. However, a transition may be considered as anecdotal or as major depending on the specific level of biological organization under study. In this contribution, I will argue that transitions may also be occurring at a much smaller scale of biological organization: the viral world. Not only that, but also that we can observe in real time how these major transitions take place during experimental evolution. I will review the outcome of recent evolution experiments with viruses that illustrate four major evolutionary transitions: (i) the origin of a new virus that infects an otherwise inaccessible host and completely changes the way it interacts with the host regulatory and metabolic networks, (ii) the incorporation and loss of genes, (iii) the origin of segmented genomes from a non-segmented one, and (iv) the evolution of cooperative behaviour and cheating between different viruses or strains during co-infection of the same host.This article is part of the themed issue 'The major synthetic evolutionary transitions'.
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Affiliation(s)
- Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain Instituto de Biología Integrativa y de Sistemas, Consejo Superior de Investigaciones Científicas-Universitat de València, Parc Científic de la Universitat de València, Catedrático Agustín Escardino 9, 46980 Paterna, Valencia, Spain Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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