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Chiba Y, Yabuki A, Takaki Y, Nunoura T, Urayama SI, Hagiwara D. The First Identification of a Narnavirus in Bigyra, a Marine Protist. Microbes Environ 2023; 38. [PMID: 36858534 PMCID: PMC10037099 DOI: 10.1264/jsme2.me22077] [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] [Indexed: 03/03/2023] Open
Abstract
Current information on the diversity and evolution of eukaryotic RNA viruses is biased towards host lineages, such as animals, plants, and fungi. Although protists represent the majority of eukaryotic diversity, our understanding of the protist RNA virosphere is still limited. To reveal untapped RNA viral diversity, we screened RNA viruses from 30 marine protist isolates and identified a novel RNA virus named Haloplacidia narnavirus 1 (HpNV1). A phylogenetic ana-lysis revealed that HpNV1 is a new member of the family Narnaviridae. The present study filled a gap in the distribution of narnaviruses and implies their wide distribution in Stramenopiles.
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Affiliation(s)
- Yuto Chiba
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba
| | - Akinori Yabuki
- Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, JAMSTEC
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), JAMSTEC
| | - Syun-Ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba
| | - Daisuke Hagiwara
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba
- Microbiology Research Center for Sustainability (MiCS), University of Tsukuba
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Urayama SI, Takaki Y, Chiba Y, Zhao Y, Kuroki M, Hagiwara D, Nunoura T. Eukaryotic Microbial RNA Viruses-Acute or Persistent? Insights into Their Function in the Aquatic Ecosystem. Microbes Environ 2022; 37:ME22034. [PMID: 35922920 PMCID: PMC9763035 DOI: 10.1264/jsme2.me22034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Isolated RNA viruses mainly parasitize eukaryotes. RNA viruses either expand horizontally by infecting hosts (acute type) or coexist with the host and are vertically inherited (persistent type). The significance of persistent-type RNA viruses in environmental viromes (the main hosts are expected to be microbes) was only recently reported because they had previously been overlooked in virology. In this review, we summarize the host-virus relationships of eukaryotic microbial RNA viruses. Picornavirales and Reoviridae are recognized as representative acute-type virus families, and most of the microbial viruses in Narnaviridae, Totiviridae, and Partitiviridae are categorized as representative persistent-type viruses. Acute-type viruses have only been found in aquatic environments, while persistent-type viruses are present in various environments, including aquatic environments. Moreover, persistent-type viruses are potentially widely spread in the RNA viral sequence space. This emerging evidence provides novel insights into RNA viral diversity, host-virus relationships, and their history of co-evolution.
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Affiliation(s)
- Syun-ichi Urayama
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan, Corresponding author. E-mail: ; Tel: +81–29–853–6636; Fax: +81–29–853–4605
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
| | - Yuto Chiba
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan
| | - Yanjie Zhao
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan
| | - Misa Kuroki
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan
| | - Daisuke Hagiwara
- Department of Life and Environmental Sciences, Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki 305–8577, Japan
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), JAMSTEC, 2–15 Natsushima-cho, Yokosuka, Kanagawa 237–0061, Japan
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Lang AS, Vlok M, Culley AI, Suttle CA, Takao Y, Tomaru Y, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Marnaviridae 2021. J Gen Virol 2021; 102. [PMID: 34356002 PMCID: PMC8513639 DOI: 10.1099/jgv.0.001633] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The family Marnaviridae comprises small non-enveloped viruses with positive-sense RNA genomes of 8.6-9.6 kb. Isolates infect marine single-celled eukaryotes (protists) that come from diverse lineages. Some members are known from metagenomic studies of ocean virioplankton, with additional unclassified viruses described from metagenomic datasets derived from marine and freshwater environments. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Marnaviridae, which is available at ictv.global/report/marnaviridae.
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Affiliation(s)
- Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Marli Vlok
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Alexander I Culley
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Curtis A Suttle
- Departments of Botany, Earth, Ocean and Atmospheric Sciences and Microbiology and Immunology, Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC, Canada
| | - Yoshitake Takao
- Department of Marine Bioscience, Fukui Prefectural University, Fukui, Japan
| | - Yuji Tomaru
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Hatsukaichi, Hiroshima, Japan
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Sadeghi M, Tomaru Y, Ahola T. RNA Viruses in Aquatic Unicellular Eukaryotes. Viruses 2021; 13:v13030362. [PMID: 33668994 PMCID: PMC7996518 DOI: 10.3390/v13030362] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 12/24/2022] Open
Abstract
Increasing sequence information indicates that RNA viruses constitute a major fraction of marine virus assemblages. However, only 12 RNA virus species have been described, infecting known host species of marine single-celled eukaryotes. Eight of these use diatoms as hosts, while four are resident in dinoflagellate, raphidophyte, thraustochytrid, or prasinophyte species. Most of these belong to the order Picornavirales, while two are divergent and fall into the families Alvernaviridae and Reoviridae. However, a very recent study has suggested that there is extraordinary diversity in aquatic RNA viromes, describing thousands of viruses, many of which likely use protist hosts. Thus, RNA viruses are expected to play a major ecological role for marine unicellular eukaryotic hosts. In this review, we describe in detail what has to date been discovered concerning viruses with RNA genomes that infect aquatic unicellular eukaryotes.
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Affiliation(s)
- Mohammadreza Sadeghi
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
| | - Yuji Tomaru
- Environment and Fisheries Applied Techniques Research Department, Fisheries Technology Institute, Fisheries Research and Education Agency, Hatsukaichi, Hiroshima 739-0452, Japan;
| | - Tero Ahola
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, 00014 Helsinki, Finland
- Correspondence: (M.S.); (T.A.)
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Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean. iScience 2020; 24:102002. [PMID: 33490910 PMCID: PMC7811142 DOI: 10.1016/j.isci.2020.102002] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/13/2020] [Accepted: 12/23/2020] [Indexed: 11/24/2022] Open
Abstract
The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earth's carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral “shunt” and “shuttle”). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics. Eukaryotic virus community composition is shown to predict carbon export efficiency Tens of viruses are highly important in the prediction of the efficiency These viruses are inferred to infect ecologically important hosts
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López-Bueno A, Rastrojo A, Peiró R, Arenas M, Alcamí A. Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake. Mol Ecol 2015. [DOI: 10.1111/mec.13321] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- A. López-Bueno
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - A. Rastrojo
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - R. Peiró
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - M. Arenas
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
| | - A. Alcamí
- Department of Virology and Microbiology; Centro de Biología Molecular ‘Severo Ochoa’ (Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid); Nicolás Cabrera 1 Cantoblanco 28049 Madrid Spain
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Takao Y, Tomaru Y, Nagasaki K, Honda D. Ecological Dynamics of Two Distinct Viruses Infecting Marine Eukaryotic Decomposer Thraustochytrids (Labyrinthulomycetes, Stramenopiles). PLoS One 2015. [PMID: 26203654 PMCID: PMC4512727 DOI: 10.1371/journal.pone.0133395] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thraustochytrids are cosmopolitan osmotrophic or heterotrophic microorganisms that are considered as important decomposers in coastal ecosystems. However, because of a lack of estimation method for each genus or systematic group of them, relatively little is known about their ecology in situ. Previously, we reported two distinct types of virus infecting thraustochytrids (AuRNAV: reported as SssRNAV, and SmDNAV) suggesting they have wide distributions in the host-virus systems of coastal environments. Here we conducted a field survey from 2004 through 2005 to show the fluctuation pattern of thraustochytrids and their viruses in Hiroshima Bay, Japan. During the field survey, we monitored the dynamics of the two types of thraustochytrid-infecting virus: small viruses causing lysis of Aurantiochytrium sp. NIBH N1-27 (identified as AuRNAV) and the large viruses of Sicyoidochytrium minutum NBRC 102975 (similar to SmDNAV in physiology and morphology). Fluctuation patterns of the two distinct types of virus were different from each other. This may reflect the difference in the preference of organic substrates; i.e., it may be likely the host of AuRNAV (Aurantiochytrium sp.) increases utilizing algal dead bodies or feeble cells as the virus shows a large increase in abundance following raphidophyte blooms; whereas, the trophic nutrient supply for S. minutum may primarily depend on other constantly-supplied organic compounds because it did not show any significant change in abundance throughout the survey. Further study concerning the population composition of thraustochytrids and their viruses may demonstrate the microbial ecology (especially concerning the detrital food web) of marine environments.
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Affiliation(s)
- Yoshitake Takao
- Department of Marine Bioscience, Fukui Prefectural University, 1–1 Gakuencho, Obama, Fukui, 917–0003, Japan
- * E-mail:
| | - Yuji Tomaru
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, 739–0452, Japan
| | - Keizo Nagasaki
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, 739–0452, Japan
| | - Daiske Honda
- Department of Biology, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada, Kobe, 658–8501, Japan
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Neuman BW, Angelini MM, Buchmeier MJ. Does form meet function in the coronavirus replicative organelle? Trends Microbiol 2014; 22:642-7. [PMID: 25037114 PMCID: PMC7127430 DOI: 10.1016/j.tim.2014.06.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/10/2014] [Accepted: 06/13/2014] [Indexed: 12/14/2022]
Abstract
If we use the analogy of a virus as a living entity, then the replicative organelle is the part of the body where its metabolic and reproductive activities are concentrated. Recent studies have illuminated the intricately complex replicative organelles of coronaviruses, a group that includes the largest known RNA virus genomes. This review takes a virus-centric look at the coronavirus replication transcription complex organelle in the context of the wider world of positive sense RNA viruses, examining how the mechanisms of protein expression and function act to produce the factories that power the viral replication cycle.
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Affiliation(s)
- Benjamin W Neuman
- School of Biological Sciences, University of Reading, Reading, Berkshire, UK.
| | - Megan M Angelini
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA; Department of Medicine, Division of Infectious Disease, University of California Irvine, Irvine, CA, USA
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Abstract
UNLABELLED Viruses have a profound influence on the ecology and evolution of plankton, but our understanding of the composition of the aquatic viral communities is still rudimentary. This is especially true of those viruses having RNA genomes. The limited data that have been published suggest that the RNA virioplankton is dominated by viruses with positive-sense, single-stranded (+ss) genomes that have features in common with those of eukaryote-infecting viruses in the order Picornavirales (picornavirads). In this study, we investigated the diversity of the RNA virus assemblages in tropical coastal seawater samples using targeted PCR and metagenomics. Amplification of RNA-dependent RNA polymerase (RdRp) genes from fractions of a buoyant density gradient suggested that the distribution of two major subclades of the marine picornavirads was largely congruent with the distribution of total virus-like RNA, a finding consistent with their proposed dominance. Analyses of the RdRp sequences in the library revealed the presence of many diverse phylotypes, most of which were related only distantly to those of cultivated viruses. Phylogenetic analysis suggests that there were hundreds of unique picornavirad-like phylotypes in one 35-liter sample that differed from one another by at least as much as the differences among currently recognized species. Assembly of the sequences in the metagenome resulted in the reconstruction of six essentially complete viral genomes that had features similar to viruses in the families Bacillarna-, Dicistro-, and Marnaviridae. Comparison of the tropical seawater metagenomes with those from other habitats suggests that +ssRNA viruses are generally the most common types of RNA viruses in aquatic environments, but biases in library preparation remain a possible explanation for this observation. IMPORTANCE Marine plankton account for much of the photosynthesis and respiration on our planet, and they influence the cycling of carbon and the distribution of nutrients on a global scale. Despite the fundamental importance of viruses to plankton ecology and evolution, most of the viruses in the sea, and the identities of their hosts, are unknown. This report is one of very few that delves into the genetic diversity within RNA-containing viruses in the ocean. The data expand the known range of viral diversity and shed new light on the physical properties and genetic composition of RNA viruses in the ocean.
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Global morphological analysis of marine viruses shows minimal regional variation and dominance of non-tailed viruses. ISME JOURNAL 2013; 7:1738-51. [PMID: 23635867 DOI: 10.1038/ismej.2013.67] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/16/2013] [Accepted: 03/19/2013] [Indexed: 11/08/2022]
Abstract
Viruses influence oceanic ecosystems by causing mortality of microorganisms, altering nutrient and organic matter flux via lysis and auxiliary metabolic gene expression and changing the trajectory of microbial evolution through horizontal gene transfer. Limited host range and differing genetic potential of individual virus types mean that investigations into the types of viruses that exist in the ocean and their spatial distribution throughout the world's oceans are critical to understanding the global impacts of marine viruses. Here we evaluate viral morphological characteristics (morphotype, capsid diameter and tail length) using a quantitative transmission electron microscopy (qTEM) method across six of the world's oceans and seas sampled through the Tara Oceans Expedition. Extensive experimental validation of the qTEM method shows that neither sample preservation nor preparation significantly alters natural viral morphological characteristics. The global sampling analysis demonstrated that morphological characteristics did not vary consistently with depth (surface versus deep chlorophyll maximum waters) or oceanic region. Instead, temperature, salinity and oxygen concentration, but not chlorophyll a concentration, were more explanatory in evaluating differences in viral assemblage morphological characteristics. Surprisingly, given that the majority of cultivated bacterial viruses are tailed, non-tailed viruses appear to numerically dominate the upper oceans as they comprised 51-92% of the viral particles observed. Together, these results document global marine viral morphological characteristics, show that their minimal variability is more explained by environmental conditions than geography and suggest that non-tailed viruses might represent the most ecologically important targets for future research.
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Abstract
Viruses are abundant in the ocean and a major driving force in plankton ecology and evolution. It has been assumed that most of the viruses in seawater contain DNA and infect bacteria, but RNA-containing viruses in the ocean, which almost exclusively infect eukaryotes, have never been quantified. We compared the total mass of RNA and DNA in the viral fraction harvested from seawater and using data on the mass of nucleic acid per RNA- or DNA-containing virion, estimated the abundances of each. Our data suggest that the abundance of RNA viruses rivaled or exceeded that of DNA viruses in samples of coastal seawater. The dominant RNA viruses in the samples were marine picorna-like viruses, which have small genomes and are at or below the detection limit of common fluorescence-based counting methods. If our results are typical, this means that counts of viruses and the rate measurements that depend on them, such as viral production, are significantly underestimated by current practices. As these RNA viruses infect eukaryotes, our data imply that protists contribute more to marine viral dynamics than one might expect based on their relatively low abundance. This conclusion is a departure from the prevailing view of viruses in the ocean, but is consistent with earlier theoretical predictions.
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Wada K, Kimura K, Hasegawa A, Fukuyama K, Nagasaki K. Establishment of a bacterial expression system and immunoassay platform for the major capsid protein of HcRNAV, a dinoflagellate-infecting RNA virus. Microbes Environ 2012; 27:483-9. [PMID: 23047150 PMCID: PMC4103558 DOI: 10.1264/jsme2.me12046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HcRNAV is a small icosahedral virus that infects the shellfish-killing marine dinoflagellate Heterocapsa circularisquama, which harbors a dicistronic linear single-stranded RNA (ssRNA) genome ca. 4.4 kb in length. Its major capsid protein (MCP) gene sequence is not expressed by various strains of Escherichia coli, possibly because of a codon usage problem. To solve this problem, a chemically modified (i.e., de novo synthesized) gene was designed and cloned into the pCold-GST expression vector, and transformed into E. coli strain C41 (DE3), in which codon usage was universally optimized to efficiently express the polypeptide having the viral MCP amino acid sequence. The bacterially expressed protein, which was purified after a procedure involving denaturation and refolding, successfully formed virus-like particles that significantly resembled native HcRNAV particles. The purified, denatured protein was used as an antigen to immunize rabbits, and the resulting antiserum was shown to be strongly reactive to not only the bacterially expressed recombinant protein, but also to native HcRNAV MCP by Western blotting and dot immunoassays, respectively. These results indicate that an antiserum recognizing native HcRNAV MCP was successfully obtained using bacterially expressed HcRNAV MCP as the antigen.
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Affiliation(s)
- Kei Wada
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560–0043, Japan
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Hyman P, Abedon ST. Smaller fleas: viruses of microorganisms. SCIENTIFICA 2012; 2012:734023. [PMID: 24278736 PMCID: PMC3820453 DOI: 10.6064/2012/734023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 06/20/2012] [Indexed: 05/31/2023]
Abstract
Life forms can be roughly differentiated into those that are microscopic versus those that are not as well as those that are multicellular and those that, instead, are unicellular. Cellular organisms seem generally able to host viruses, and this propensity carries over to those that are both microscopic and less than truly multicellular. These viruses of microorganisms, or VoMs, in fact exist as the world's most abundant somewhat autonomous genetic entities and include the viruses of domain Bacteria (bacteriophages), the viruses of domain Archaea (archaeal viruses), the viruses of protists, the viruses of microscopic fungi such as yeasts (mycoviruses), and even the viruses of other viruses (satellite viruses). In this paper we provide an introduction to the concept of viruses of microorganisms, a.k.a., viruses of microbes. We provide broad discussion particularly of VoM diversity. VoM diversity currently spans, in total, at least three-dozen virus families. This is roughly ten families per category-bacterial, archaeal, fungal, and protist-with some virus families infecting more than one of these microorganism major taxa. Such estimations, however, will vary with further discovery and taxon assignment and also are dependent upon what forms of life one includes among microorganisms.
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Affiliation(s)
- Paul Hyman
- Department of Biology, Ashland University, 401 College Avenue, Ashland, OH 44805, USA
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, OH 44906, USA
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Boros Á, Pankovics P, Simmonds P, Reuter G. Novel positive-sense, single-stranded RNA (+ssRNA) virus with di-cistronic genome from intestinal content of freshwater carp (Cyprinus carpio). PLoS One 2011; 6:e29145. [PMID: 22195010 PMCID: PMC3241695 DOI: 10.1371/journal.pone.0029145] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 11/21/2011] [Indexed: 11/18/2022] Open
Abstract
A novel positive-sense, single-stranded RNA (+ssRNA) virus (Halastavi árva RNA virus, HalV; JN000306) with di-cistronic genome organization was serendipitously identified in intestinal contents of freshwater carps (Cyprinus carpio) fished by line-fishing from fishpond "Lőrinte halastó" located in Veszprém County, Hungary. The complete nucleotide (nt) sequence of the genomic RNA is 9565 nt in length and contains two long--non-in-frame--open reading frames (ORFs), which are separated by an intergenic region. The ORF1 (replicase) is preceded by an untranslated sequence of 827 nt, while an untranslated region of 139 nt follows the ORF2 (capsid proteins). The deduced amino acid (aa) sequences of the ORFs showed only low (less than 32%) and partial similarity to the non-structural (2C-like helicase, 3C-like cystein protease and 3D-like RNA dependent RNA polymerase) and structural proteins (VP2/VP4/VP3) of virus families in Picornavirales especially to members of the viruses with dicistronic genome. Halastavi árva RNA virus is present in intestinal contents of omnivorous freshwater carps but the origin and the host species of this virus remains unknown. The unique viral sequence and the actual position indicate that Halastavi árva RNA virus seems to be the first member of a new di-cistronic ssRNA virus. Further studies are required to investigate the specific host species (and spectrum), ecology and role of Halastavi árva RNA virus in the nature.
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Affiliation(s)
- Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Péter Pankovics
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Peter Simmonds
- University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
- * E-mail:
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Yang HL, Lu CK, Chen SF, Chen YM, Chen YM. Isolation and characterization of Taiwanese heterotrophic microalgae: screening of strains for docosahexaenoic acid (DHA) production. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2010; 12:173-185. [PMID: 19609613 DOI: 10.1007/s10126-009-9207-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Accepted: 06/01/2009] [Indexed: 05/28/2023]
Abstract
Marine heterotrophic microalgal species which are potentially rich in docosahexaenoic acid (DHA, C22:6n-3) have been found in Taiwan; however, there was a lack of detailed analysis and characterization of these indigenous algae which is needed for the development of commercial applications. Hence, the objective of this study was to screen DHA-rich heterotrophic microalgae species indigenous to Taiwan for commercial purposes. Heterotrophic microalgae from a variety of marine habitats were isolated, cultivated, and then identified according to their 18S rRNA gene sequences and morphological characteristics. A comparison was made of their fatty acid profiles, fatty acid content, and amount of biomass. For the strain with highest DHA yield, the optimal growth conditions were determined in order to establish the best fermentation conditions for scale-up. In this study, 25 heterotrophic microalgal strains were successfully isolated from marine habitats around Taiwan. All of the isolated strains showed a close phylogenic relationship with the Thraustochytriaceae family according to their 18S rRNA gene sequences. GC/MS analysis discerned seven distinctive fatty acid profiles of these strains, with the production of eicosapentaenoic acid (C20:5n-3) ranging from 0.02 to 2.61 mg L(-1), and DHA ranging from 0.8 to 18.0 mg L(-1). An Aurantiochytrium strain BL10 with high DHA production was subsequently chosen for further manipulation. Under optimal growth conditions it could produce up to 59.0 g of dry biomass per liter of culture, with dry biomass containing 73% total fatty acid and 29% DHA, revealing BL10 as an excellent source of microbial DHA.
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Affiliation(s)
- Huey-Lang Yang
- Institute of Biotechnology, National Cheng Kung University, Tainan, Taiwan
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17
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Abstract
Dicistroviruses are members of a recently defined and rapidly growing family of picornavirus-like RNA viruses called the Dicistroviridae. Dicistroviruses are pathogenic to beneficial arthropods such as honey bees and shrimp and to insect pests of medical and agricultural importance. Our understanding of these viruses is uneven. We present highly advanced studies of the virus particle structure, remarkable mechanisms of internal ribosome entry in translation of viral RNA, and the use of dicistroviruses to study the insect immune system. However, little is known about dicistrovirus RNA replication mechanisms or gene function, except by comparison with picornaviruses. The recent construction of infectious clones of dicistrovirus genomes may fill these gaps in knowledge. We discuss economically important diseases caused by dicistroviruses. Future research may lead to protection of beneficial arthropods from dicistroviruses and to application of dicistroviruses as biopesticides targeting pestiferous insects.
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Affiliation(s)
- Bryony C Bonning
- Department of Entomology, Iowa State University, Ames, IA 50011, USA.
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18
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Abstract
Viruses are ubiquitous in the sea and appear to outnumber all other forms of marine life by at least an order of magnitude. Through selective infection, viruses influence nutrient cycling, community structure, and evolution in the ocean. Over the past 20 years we have learned a great deal about the diversity and ecology of the viruses that constitute the marine virioplankton, but until recently the emphasis has been on DNA viruses. Along with expanding knowledge about RNA viruses that infect important marine animals, recent isolations of RNA viruses that infect single-celled eukaryotes and molecular analyses of the RNA virioplankton have revealed that marine RNA viruses are novel, widespread, and genetically diverse. Discoveries in marine RNA virology are broadening our understanding of the biology, ecology, and evolution of viruses, and the epidemiology of viral diseases, but there is still much that we need to learn about the ecology and diversity of RNA viruses before we can fully appreciate their contributions to the dynamics of marine ecosystems. As a step toward making sense of how RNA viruses contribute to the extraordinary viral diversity in the sea, we summarize in this review what is currently known about RNA viruses that infect marine organisms.
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Affiliation(s)
- Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada.
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19
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Isolation and characterization of a single-stranded RNA virus infecting the bloom-forming diatom Chaetoceros socialis. Appl Environ Microbiol 2009; 75:2375-81. [PMID: 19233955 DOI: 10.1128/aem.02580-08] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diatoms are very significant primary producers in the world's oceans. Various environmental factors affect the depletion of diatom populations. The importance of viruses as a potential mortality source has recently been recognized. We isolated and characterized a new diatom virus (Chaetoceros socialis f. radians RNA virus [CsfrRNAV]) causing the lysis of the bloom-forming species Chaetoceros socialis Lauder f. radians (Schütt) Proschkina-Lavrenko. The virus infectious to C. socialis f. radians was isolated from water samples collected in Hiroshima Bay. Here we show the physiology, morphology, and genome characteristics of the virus clone. Virions were 22 nm in diameter and accumulated in the cytoplasm of the host cells. The latent period and the burst size were estimated to be <48 h and 66 infectious units per host cell, respectively. CsfrRNAV harbors a single-stranded RNA (ssRNA) genome and encodes at least three polypeptides of 32.0, 28.5, and 25.0 kDa. Sequencing analysis shows the length of the genome is 9,467 bases, excluding a poly(A) tail. The monophyly of CsfrRNAV and other diatom-infecting RNA viruses, Rhizosolenia setigera RNA virus and Chaetoceros tenuissimus RNA virus, was strongly supported by phylogenetic analysis based on the amino acid sequence of the RNA-dependent RNA polymerase domains. This suggested a new ssRNA virus family, Bacillariornaviridae. This discovery of CsfrRNAV may aid in further understanding the ecological dynamics of the C. socialis f. radians population in nature and the relationships between ssRNA diatom viruses and their hosts.
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20
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Aquatic virus diversity accessed through omic techniques: a route map to function. Curr Opin Microbiol 2008; 11:226-32. [PMID: 18554975 DOI: 10.1016/j.mib.2008.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 05/07/2008] [Accepted: 05/08/2008] [Indexed: 11/22/2022]
Abstract
Viruses are arguably the simplest form of life yet they play a crucial role in regulating planetary processes. From shuttling genes to 'lubricating' microbial loop dynamics, viruses are integral in shaping microbial ecology. In every environment on Earth the role of viruses goes far beyond the simple infect-replicate-kill cycle. Their enormous abundance and seemingly infinite diversity provide the vital clues to the true function of viruses. New 'omic' approaches are now allowing researchers to gain extraordinary insights into virus diversity and inferred function, particularly within aquatic environments. The development of molecular markers and application of techniques including microarrays, metagenomic sequencing and proteomic analysis are now being applied to virus communities. Despite this shift towards culture-independent approaches it has proved difficult to derive useful information about infection strategies since so much of the sequence information has no database matches. Future advances will involve tools such as microarrays to help determine the functionality of unknown genes. Sequence information should be considered as a starting point for asking questions and developing hypotheses about the role of viruses. It is an exciting new era for virus ecology and when used in combination with more traditional approaches, virus genomics will give us access to their ecological function on an unprecedented scale.
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21
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Sandaa RA. Burden or benefit? Virus-host interactions in the marine environment. Res Microbiol 2008; 159:374-81. [PMID: 18571902 DOI: 10.1016/j.resmic.2008.04.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Revised: 04/23/2008] [Accepted: 04/23/2008] [Indexed: 10/22/2022]
Abstract
Viruses are the most numerous and diverse biological entities in the oceans. We are now beginning to understand the ecological role of viruses in the marine environment. As a result, we believe that viruses have important roles in both biochemical cycling and structuring of marine communities.
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Affiliation(s)
- Ruth-Anne Sandaa
- Department of Biology, University of Bergen, Post Box 7800, N-5020 Bergen, Norway.
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22
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Isolation and characterization of a single-stranded RNA virus infecting the marine planktonic diatom Chaetoceros tenuissimus Meunier. Appl Environ Microbiol 2008; 74:4022-7. [PMID: 18469125 DOI: 10.1128/aem.00509-08] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diatoms are important components of the biological community and food web in the aquatic environment. Here, we report the characteristics of a single-stranded RNA (ssRNA) virus (CtenRNAV01) that infects the marine diatom Chaetoceros tenuissimus Meunier (Bacillariophyceae). The ca. 31-nm virus particle is icosahedral and lacks a tail. CtenRNAV01 forms crystalline arrays occupying most of the infected host's cytoplasm. By growth experiments, the lytic cycle and the burst size were estimated to be <24 h and approximately 1 x 10(4) infectious units per host cell, respectively. Stationary-phase C. tenuissimus cultures were shown to be more sensitive to CtenRNAV01 than logarithmic-phase cultures. The most noticeable feature of this virus is its exceptionally high yields of approximately 10(10) infectious units ml(-1); this is much higher than those of any other algal viruses previously characterized. CtenRNAV01 has two molecules of ssRNA of approximately 8.9 and 4.3 kb and three major proteins (33.5, 31.5, and 30.0 kDa). Sequencing of the total viral genome has produced only one large contig [9,431 bases excluding the poly(A) tail], suggesting considerable overlapping between the two RNA molecules. The monophyly of CtenRNAV01 compared to another diatom-infecting virus, Rhizosolenia setigera RNA virus, was strongly supported in a maximum likelihood phylogenetic tree constructed based on the concatenated amino acid sequences of the RNA-dependent RNA polymerase domains. Although further analysis is required to determine the detailed classification and nomenclature of this virus, these data strongly suggest the existence of a diatom-infecting ssRNA virus group in natural waters.
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23
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Taoka Y, Nagano N, Okita Y, Izumida H, Sugimoto S, Hayashi M. Effect of addition of Tween 80 and potassium dihydrogenphosphate to basal medium on the isolation of marine eukaryotes, thraustochytrids. J Biosci Bioeng 2008; 105:562-5. [DOI: 10.1263/jbb.105.562] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 02/21/2008] [Indexed: 11/17/2022]
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24
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Massana R, del Campo J, Dinter C, Sommaruga R. Crash of a population of the marine heterotrophic flagellate Cafeteria roenbergensis by viral infection. Environ Microbiol 2008; 9:2660-9. [PMID: 17922751 DOI: 10.1111/j.1462-2920.2007.01378.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Viruses are known as important mortality agents of marine microorganisms. Most studies focus on bacterial and algal viruses, and few reports exist on viruses infecting marine heterotrophic protists. Here we show results from several incubations initiated with a microbial assemblage from the central Indian Ocean and amended with different amounts of organic matter. Heterotrophic flagellates developed up to 30,000 cells ml(-1) in the most enriched incubation. A 18S rDNA clone library and fluorescent in situ hybridization counts with newly designed probes indicated that the peak was formed by Cafeteria roenbergensis and Caecitellus paraparvulus (90% and 10% of the cells respectively). Both taxa were below detection in the original sample, indicating a strong positive selective bias during the enrichment. During the peak, C. roenbergensis cells were observed with virus-like particles in the cytoplasm, and 4 days later this taxa could not be detected. Transmission electron microscopy confirmed the viral nature of these particles, which were large (280 nm), had double-stranded DNA, and were produced with a burst size of approximately 70. This virus was specific of C. roenbergensis as neither C. paraparvulus that was never seen infected, nor other flagellate taxa that developed in later stages of the incubation, appeared attacked. This is one of the few reports on a heterotrophic flagellate virus and the implications of this finding in the Indian Ocean are discussed.
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Affiliation(s)
- Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC. Passeig Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalonia, Spain.
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25
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Jakobsen AN, Aasen IM, Strøm AR. Endogenously synthesized (-)-proto-quercitol and glycine betaine are principal compatible solutes of Schizochytrium sp. strain S8 (ATCC 20889) and three new isolates of phylogenetically related thraustochytrids. Appl Environ Microbiol 2007; 73:5848-56. [PMID: 17660311 PMCID: PMC2074927 DOI: 10.1128/aem.00610-07] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report that endogenously synthesized (-)-proto-quercitol (1D-1,3,4/2,5-cyclohexanepentol) and glycine betaine were the principal compatible solutes of Schizochytrium sp. strain S8 (ATCC 20889) and three new osmotolerant isolates of thraustochytrids (strains T65, T66, and T67). The compatible solutes were identified and quantified by use of nuclear magnetic resonance spectroscopy, and their identity was confirmed by mass spectroscopy and measurement of the specific optical rotation. The cellular content of compatible solutes increased with increasing NaCl concentration of a defined medium. (-)-proto-Quercitol was the dominating solute at all NaCl concentrations tested (0.25 to 1.0 M), e.g., cells of S8 and T66 stressed with 1.0 M NaCl accumulated about 500 micromol (-)-proto-quercitol and 100 micromol glycine betaine per g dry weight. To our knowledge, (-)-proto-quercitol has previously been found only in eucalyptus. The 18S rRNA gene sequences of the four (-)-proto-quercitol-producing strains showed 99% identity, and they displayed the same fatty acid profile. The only polyunsaturated fatty acids accumulated were docosahexaenoic acid (78%) and docosapentaenoic acid (22%). A less osmotolerant isolate (strain T29), which was closely phylogenetically related to Thraustochytrium aureum (ATCC 34304), did not contain (-)-proto-quercitol or glycine betaine. Thus, the level of osmotolerance and the osmolyte systems vary among thraustochytrids.
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Affiliation(s)
- Anita N Jakobsen
- Department of Biotechnology, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
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26
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Culley AI, Steward GF. New genera of RNA viruses in subtropical seawater, inferred from polymerase gene sequences. Appl Environ Microbiol 2007; 73:5937-44. [PMID: 17644642 PMCID: PMC2074930 DOI: 10.1128/aem.01065-07] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Viruses are an integral component of the marine food web, contributing to the disease and mortality of essentially every type of marine life, yet the diversity of viruses in the sea, especially those with RNA genomes, remains very poorly characterized. Isolates of RNA-containing viruses that infect marine plankton are still rare, and the only cultivation-independent surveys of RNA viral diversity reported so far were conducted for temperate coastal waters of British Columbia. Here, we report on our improvements to a previously used protocol to investigate the diversity of marine picorna-like viruses and our results from applying this protocol in subtropical waters. The original protocol was simplified by using direct filtration, rather than tangential flow filtration, to harvest viruses from seawater, and new degenerate primers were designed to amplify a fragment of the RNA-dependent RNA polymerase gene by reverse transcription-PCR from RNA extracted from the filters. Whereas the original protocol was unsuccessful in a preliminary test, the new protocol resulted in amplification of picorna-like virus sequences in every sample of subtropical and temperate coastal seawater assayed. These polymerase sequences formed a diverse, but monophyletic cluster along with other sequences amplified previously from seawater and sequences from isolates infecting marine protists. Phylogenetic analysis suggested that our sequences represent at least five new genera and 24 new species of RNA viruses. These results contribute to our understanding of RNA virus diversity and suggest that picorna-like viruses are a source of mortality for a wide variety of marine protists.
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Affiliation(s)
- Alexander I Culley
- Department of Oceanography, University of Hawaii at Mānoa, 1000 Pope Road, Marine Sciences Building, Honolulu, HI 96822, USA.
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27
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Culley AI, Lang AS, Suttle CA. The complete genomes of three viruses assembled from shotgun libraries of marine RNA virus communities. Virol J 2007; 4:69. [PMID: 17617913 PMCID: PMC1948888 DOI: 10.1186/1743-422x-4-69] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 07/06/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNA viruses have been isolated that infect marine organisms ranging from bacteria to whales, but little is known about the composition and population structure of the in situ marine RNA virus community. In a recent study, the majority of three genomes of previously unknown positive-sense single-stranded (ss) RNA viruses were assembled from reverse-transcribed whole-genome shotgun libraries. The present contribution comparatively analyzes these genomes with respect to representative viruses from established viral taxa. RESULTS Two of the genomes (JP-A and JP-B), appear to be polycistronic viruses in the proposed order Picornavirales that fall into a well-supported clade of marine picorna-like viruses, the characterized members of which all infect marine protists. A temporal and geographic survey indicates that the JP genomes are persistent and widespread in British Columbia waters. The third genome, SOG, encodes a putative RNA-dependent RNA polymerase (RdRp) that is related to the RdRp of viruses in the family Tombusviridae, but the remaining SOG sequence has no significant similarity to any sequences in the NCBI database. CONCLUSION The complete genomes of these viruses permitted analyses that resulted in a more comprehensive comparison of these pathogens with established taxa. For example, in concordance with phylogenies based on the RdRp, our results support a close homology between JP-A and JP-B and RsRNAV. In contrast, although classification of the SOG genome based on the RdRp places SOG within the Tombusviridae, SOG lacks a capsid and movement protein conserved within this family and SOG is thus likely more distantly related to the Tombusivridae than the RdRp phylogeney indicates.
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Affiliation(s)
- Alexander I Culley
- University of British Columbia, Department of Botany, 3529-6270 University Blvd, Vancouver, B.C. V6T 1Z4, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada
| | - Curtis A Suttle
- University of British Columbia, Department of Botany, 3529-6270 University Blvd, Vancouver, B.C. V6T 1Z4, Canada
- University of British Columbia, Department of Earth and Ocean Sciences, Department of Microbiology and Immunology, 1461-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
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28
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Takao Y, Mise K, Nagasaki K, Okuno T, Honda D. Complete nucleotide sequence and genome organization of a single-stranded RNA virus infecting the marine fungoid protist Schizochytrium sp. J Gen Virol 2006; 87:723-733. [PMID: 16476996 DOI: 10.1099/vir.0.81204-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The complete nucleotide sequence of the genomic RNA of a marine fungoid protist-infecting virus (Schizochytrium single-stranded RNA virus; SssRNAV) has been determined. The viral RNA is single-stranded with a positive sense and is 9018 nt in length [excluding the 3′ poly(A) tail]. It contains two long open reading frames (ORFs), which are separated by an intergenic region of 92 nt. The 5′ ORF (ORF1) is preceded by an untranslated leader sequence of 554 nt. The 3′ large ORF (ORF2) and an additional ORF (ORF3) overlap ORF2 by 431 nt and are followed by an untranslated region of 70 nt [excluding the 3′ poly(A) tail]. The deduced amino acid sequences of ORF1 and ORF2 products show similarity to non-structural and structural proteins of dicistroviruses, respectively. However, Northern blot analysis suggests that SssRNAV synthesizes subgenomic RNAs to translate ORF2 and ORF3, showing that the translation mechanism of downstream ORFs is distinct from that of dicistroviruses. Furthermore, although considerable similarities were detected by using a blast genome database search, phylogenetic analysis based on both the nucleotide and amino acid sequences of the putative RNA-dependent RNA polymerase (RdRp) and the RNA helicase suggests that SssRNAV is phylogenetically distinct from other virus families. Therefore, it is concluded that SssRNAV is not a member of any currently defined virus family and belongs to a novel, unrecognized virus group.
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Affiliation(s)
- Yoshitake Takao
- Department of Biology, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada, Kobe 658-8501, Japan
| | - Kazuyuki Mise
- Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Keizo Nagasaki
- Harmful Algal Bloom Division, National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, Hiroshima, Japan
| | - Tetsuro Okuno
- Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Daiske Honda
- Department of Biology, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada, Kobe 658-8501, Japan
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Nagasaki K, Shirai Y, Takao Y, Mizumoto H, Nishida K, Tomaru Y. Comparison of genome sequences of single-stranded RNA viruses infecting the bivalve-killing dinoflagellate Heterocapsa circularisquama. Appl Environ Microbiol 2006; 71:8888-94. [PMID: 16332886 PMCID: PMC1317472 DOI: 10.1128/aem.71.12.8888-8894.2005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heterocapsa circularisquama RNA virus (HcRNAV) has at least two ecotypes (types UA and CY) that have intraspecies host specificities which are complementary to each other. We determined the complete genomic RNA sequence of two typical HcRNAV strains, HcRNAV34 and HcRNAV109, one of each ecotype. The nucleotide sequences of the viruses were 97.0% similar, and each had two open reading frames (ORFs), ORF-1 coding for a putative polyprotein having protease and RNA-dependent RNA polymerase (RdRp) domains and ORF-2 encoding a single major capsid protein. Phylogenetic analysis of the RdRp amino acid sequence suggested that HcRNAV belongs to a new previously unrecognized virus group. Four regions in ORF-2 had amino acid substitutions when HcRNAV34 was compared to HcRNAV109. We used a reverse transcription-nested PCR system to amplify the corresponding regions and also examined RNAs purified from six other HcRNAV strains with known host ranges. We also looked at natural marine sediment samples. Phylogenetic dendrograms for the amplicons correlated with the intraspecies host specificities of the test virus strains. The cloned sequences found in sediment also exhibited considerable similarities to either the UA-type or CY-type sequence. The tertiary structure of the capsid proteins predicted using computer modeling indicated that many of the amino acid substitutions were located in regions on the outside of the viral capsid proteins. This strongly suggests that the intraspecies host specificity of HcRNAV is determined by nanostructures on the virus surface that may affect binding to suitable host cells. Our study shows that capsid alterations can change the phytoplankton-virus (host-parasite) interactions in marine systems.
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Affiliation(s)
- Keizo Nagasaki
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan.
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30
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Abstract
Viruses exist wherever life is found. They are a major cause of mortality, a driver of global geochemical cycles and a reservoir of the greatest genetic diversity on Earth. In the oceans, viruses probably infect all living things, from bacteria to whales. They affect the form of available nutrients and the termination of algal blooms. Viruses can move between marine and terrestrial reservoirs, raising the spectre of emerging pathogens. Our understanding of the effect of viruses on global systems and processes continues to unfold, overthrowing the idea that viruses and virus-mediated processes are sidebars to global processes.
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Affiliation(s)
- Curtis A Suttle
- Department of Chemistry, University of California, Berkeley and the Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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