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Jeong DE, Sundrani S, Hall RN, Krupovic M, Koonin EV, Fire AZ. DNA Polymerase Diversity Reveals Multiple Incursions of Polintons During Nematode Evolution. Mol Biol Evol 2023; 40:msad274. [PMID: 38069639 DOI: 10.1093/molbev/msad274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/01/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023] Open
Abstract
Polintons are double-stranded DNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family but encode a distinct protein-primed DNA polymerase B (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda. Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting interphylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of an HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.
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Affiliation(s)
- Dae-Eun Jeong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sameer Sundrani
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Present address: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, Paris, France
| | - Eugene V Koonin
- National National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
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Jeong DE, Sundrani S, Hall RN, Krupovic M, Koonin EV, Fire AZ. DNA polymerase diversity reveals multiple incursions of Polintons during nematode evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554363. [PMID: 37662302 PMCID: PMC10473752 DOI: 10.1101/2023.08.22.554363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Polintons are dsDNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family, but encode a distinct protein-primed B family DNA polymerase (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda . Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting inter-phylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of a HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.
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A Novel Rhabdovirus Associated with the Idaho Population of Potato Cyst Nematode Globodera pallida. Viruses 2022; 14:v14122718. [PMID: 36560722 PMCID: PMC9783950 DOI: 10.3390/v14122718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Globodera pallida, a potato cyst nematode (PCN), is a quarantine endoparasitic pest of potato (Solanum tuberosum) in the US due to its effects on yield and quality of potato tubers. A new rhabdovirus, named potato cyst nematode rhabdovirus (PcRV), was revealed and characterized in the G. pallida populations collected in Idaho through use of high-throughput sequencing (HTS) and RT-PCR and found to be most closely related to soybean cyst nematode rhabdovirus (ScRV). PcRV has a 13,604 bp long, single-stranded RNA genome encoding five open reading frames, including four rhabdovirus-specific genes, N, P, G, and L, and one unknown gene. PcRV was found present in eggs, invasive second-stage juveniles, and parasitic females of G. pallida, implying a vertical transmission mode. RT-PCR and partial sequencing of PcRV in laboratory-reared G. pallida populations maintained over five years suggested that the virus is highly persistent and genetically stable. Two other Globodera spp. reproducing on potato and reported in the US, G. rostochiensis and G. ellingtonae, tested negative for PcRV presence. To the best of our knowledge, PcRV is the first virus experimentally found infecting G. pallida. Based on their similar genome organizations, the phylogeny of their RNA-dependent RNA polymerase domains (L gene), and relatively high identity levels in their protein products, PcRV and ScRV are proposed to form a new genus, provisionally named "Gammanemrhavirus", within the family Rhabdoviridae.
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Vieira P, Subbotin SA, Alkharouf N, Eisenback J, Nemchinov LG. Expanding the RNA virome of nematodes and other soil-inhabiting organisms. Virus Evol 2022; 8:veac019. [PMID: 35371560 PMCID: PMC8967085 DOI: 10.1093/ve/veac019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/02/2022] [Accepted: 03/10/2022] [Indexed: 07/25/2023] Open
Abstract
In recent years, several newly discovered viruses infecting free-living nematodes, sedentary plant-parasitic nematodes, and migratory root lesion nematodes have been described. However, to the best of our knowledge, no comprehensive research focusing exclusively on metagenomic analysis of the soil nematode community virome has thus far been carried out. In this work, we have attempted to bridge this gap by investigating viral communities that are associated with soil-inhabiting organisms, particularly nematodes. This study demonstrates a remarkable diversity of RNA viruses in the natural soil environment. Over 150 viruses were identified in different soil-inhabiting hosts, of which more than 139 are potentially new virus species. Many of these viruses belong to the nematode virome, thereby enriching our understanding of the diversity and evolution of this complex part of the natural ecosystem.
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Affiliation(s)
- Paulo Vieira
- USDA-ARS Mycology & Nematology Genetic Diversity & Biology Laboratory, Beltsville, MD 20705, USA
| | - Sergei A Subbotin
- Plant Pest Diagnostics Branch, California Department of Food & Agriculture, Sacramento, CA 95832, USA
- Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, Moscow 117071, Russia
| | - Nadim Alkharouf
- Department of Computer & Information Sciences Faculty, Towson University, Towson, MD 21204, USA
| | - Jonathan Eisenback
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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Ruark-Seward CL, Davis EL, Sit TL. Localization of viral and host RNA within soybean cyst nematode via fluorescence in situ hybridization. Exp Parasitol 2020; 211:107866. [PMID: 32113861 DOI: 10.1016/j.exppara.2020.107866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/19/2019] [Accepted: 02/23/2020] [Indexed: 10/24/2022]
Abstract
Nematode-infecting RNA viruses have recently been discovered via transcriptome sequencing. In soybean cyst nematode (SCN; Heterodera glycines), seven single-stranded RNA viruses have been identified from transcriptome data and experimentally confirmed with qRT-PCR and Sanger sequencing. Presently, there is still much unknown about the relationship between these viruses and the nematode host. In this study, we localize three viruses within the soybean cyst nematode: SCN socyvirus-1 (SbCNV-1), SCN nyami-like virus (NLV), and SCN bunya-like virus (BLV). To visually locate the viruses, whole-mount fluorescence in situ hybridization (FISH) methodology was developed for SCN pre-parasitic second-stage juveniles (ppJ2s). Two SCN populations with differing viral titers (LY1 and MM21) were used as a comparison for viral probe fluorescence intensity. Viral RNAs for all three viruses were abundant in cells throughout the SCN ppJ2 body of the high titer (LY1) population but absent within the majority of the intestinal tract. A significant reduction in viral fluorescence intensity was observed in a similar body pattern in ppJ2 of the low-titer (MM21) SCN, highlighting the specificity of the FISH method. As controls, viral RNAs were colocalized with host mRNA glyceraldehyde 3-phosphate dehydrogenase (GAPDH) for full body localization and a secretory ubiquitin protein (4G06) expressed specifically within the subventral esophageal glands. In addition, viral replication was confirmed in SCN eggs and ppJ2s via qRT-PCR detection of the anti-genomic RNA strands.
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Affiliation(s)
- Casey L Ruark-Seward
- Department of Entomology and Plant Pathology, North Carolina State University, 1575 Varsity Drive, Raleigh, NC, 27606, USA.
| | - Eric L Davis
- Department of Entomology and Plant Pathology, North Carolina State University, 1575 Varsity Drive, Raleigh, NC, 27606, USA
| | - Tim L Sit
- Department of Entomology and Plant Pathology, North Carolina State University, 1575 Varsity Drive, Raleigh, NC, 27606, USA
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Vieira P, Peetz A, Mimee B, Saikai K, Mollov D, MacGuidwin A, Zasada I, Nemchinov LG. Prevalence of the root lesion nematode virus (RLNV1) in populations of Pratylenchus penetrans from North America. J Nematol 2020; 52:1-10. [PMID: 32421266 PMCID: PMC7266026 DOI: 10.21307/jofnem-2020-045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Indexed: 11/11/2022] Open
Abstract
Root lesion nematode virus 1 (RLNV1) was discovered in the migratory endoparasitic nematode species Pratylenchus penetrans. It was found in a P. penetrans population collected from soil samples in Beltsville, Maryland, USA. In this study, the distribution of the RLNV1 in 31 geographically distinct P. penetrans populations obtained from different crops was examined. The results demonstrate that RLNV1 is widespread in North American populations of P. penetrans and exhibits low genetic variability in the helicase and RNA-dependent RNA polymerase regions of the genome.
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Affiliation(s)
- Paulo Vieira
- Molecular Plant Pathology Laboratory , USDA-ARS , Beltsville, MD 20705 ; School of Plant Environmental Science , Virginia Tech , Blacksburg, VA 24061
| | - Amy Peetz
- Horticultural Crops Research Laboratory , USDA-ARS , Corvallis, OR 97330
| | - Benjamin Mimee
- St-Jean-sur-Richelieu Research and Development Center , Agriculture and Agri-Food Canada , St-Jean-sur-Richelieu , Canada
| | - Kanan Saikai
- Department of Plant Pathology, University of Wisconsin-Madison , Madison, WI 53706
| | - Dimitre Mollov
- National Germplasm Resources Laboratory , USDA-ARS , Beltsville, MD 20705
| | - Ann MacGuidwin
- Department of Plant Pathology, University of Wisconsin-Madison , Madison, WI 53706
| | - Inga Zasada
- Horticultural Crops Research Laboratory , USDA-ARS , Corvallis, OR 97330
| | - Lev G Nemchinov
- Molecular Plant Pathology Laboratory , USDA-ARS , Beltsville, MD 20705
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Abstract
Caenorhabditis elegans has long been a laboratory model organism with no known natural pathogens. In the past ten years, however, natural viruses have been isolated from wild-caught C. elegans (Orsay virus) and its relative Caenorhabditis briggsae (Santeuil virus, Le Blanc virus, and Melnik virus). All are RNA positive-sense viruses related to Nodaviridae; they infect intestinal cells and are horizontally transmitted. The Orsay virus capsid structure has been determined and the virus can be reconstituted by transgenesis of the host. Recent use of the Orsay virus has enabled researchers to identify evolutionarily conserved proviral and antiviral genes that function in nematodes and mammals. These pathways include endocytosis through SID-3 and WASP; a uridylyltransferase that destabilizes viral RNAs by uridylation of their 3′ end; ubiquitin protein modifications and turnover; and the RNA interference pathway, which recognizes and degrades viral RNA.
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Affiliation(s)
- Marie-Anne Félix
- Institute of Biology of the École Normale Supérieure, CNRS UMR8197, INSERM U1024, 75230 Paris CEDEX 05, France
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri 63110, USA
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Vieira P, Nemchinov LG. A novel species of RNA virus associated with root lesion nematode Pratylenchus penetrans. J Gen Virol 2019; 100:704-708. [DOI: 10.1099/jgv.0.001246] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Paulo Vieira
- 1Molecular Plant Pathology Laboratory, Agricultural Research Service, USA Department of Agriculture, Beltsville, USA
- 2School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, USA
| | - Lev G. Nemchinov
- 1Molecular Plant Pathology Laboratory, Agricultural Research Service, USA Department of Agriculture, Beltsville, USA
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