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Kron NS, Neuman BW, Kumar S, Blackwelder PL, Vidal D, Walker-Phelan DZ, Gibbs PDI, Fieber LA, Schmale MC. Expression dynamics of the aplysia abyssovirus. Virology 2024; 589:109890. [PMID: 37951086 PMCID: PMC10842508 DOI: 10.1016/j.virol.2023.109890] [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: 07/11/2023] [Revised: 09/12/2023] [Accepted: 09/25/2023] [Indexed: 11/13/2023]
Abstract
Two recent studies documented the genome of a novel, extremely large (35.9 kb), nidovirus in RNA sequence databases from the marine neural model Aplysia californica. The goal of the present study was to document the distribution and transcriptional dynamics of this virus, Aplysia abyssovirus 1 (AAbV), in maricultured and wild animals. We confirmed previous findings that AAbV RNA is widespread and reaches extraordinary levels in apparently healthy animals. Transmission electron microscopy identified viral replication factories in ciliated gill epithelial cells but not in neurons where viral RNA is most highly expressed. Viral transcripts do not exhibit evidence of discontinuous RNA synthesis as in coronaviruses but are consistent with production of a single leaderless subgenomic RNA, as in the Gill-associated virus of Penaeus monodon. Splicing patterns in chronically infected adults suggested high levels of defective genomes, possibly explaining the lack of obvious disease signs in high viral load animals.
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Affiliation(s)
- Nicholas S Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149.
| | - Benjamin W Neuman
- Department of Biology, Department of Molecular Pathogenesis and Immunology and Division of Research, Texas A&M University, 400 Bizzell St., College Station, TX, USA, 77843
| | - Sathish Kumar
- Department of Biology, Department of Molecular Pathogenesis and Immunology and Division of Research, Texas A&M University, 400 Bizzell St., College Station, TX, USA, 77843
| | - Patricia L Blackwelder
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149; University of Miami Center for Advanced Microscopy, University of Miami, 142B Physics, Coral Gables, FL, USA, 33146
| | - Dayana Vidal
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149
| | - Delphina Z Walker-Phelan
- Department of Immunology, University of Washington, South Lake Union E-411 750 Republican St. UW Box 358059, Seattle, WA, 98109, USA
| | - Patrick D I Gibbs
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149
| | - Lynne A Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149
| | - Michael C Schmale
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, USA, 33149
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Ujike M, Taguchi F. Recent Progress in Torovirus Molecular Biology. Viruses 2021; 13:435. [PMID: 33800523 PMCID: PMC7998386 DOI: 10.3390/v13030435] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 11/16/2022] Open
Abstract
Torovirus (ToV) has recently been classified into the new family Tobaniviridae, although it belonged to the Coronavirus (CoV) family historically. ToVs are associated with enteric diseases in animals and humans. In contrast to CoVs, which are recognised as pathogens of veterinary and medical importance, little attention has been paid to ToVs because their infections are usually asymptomatic or not severe; for a long time, only one equine ToV could be propagated in cultured cells. However, bovine ToVs, which predominantly cause diarrhoea in calves, have been detected worldwide, leading to economic losses. Porcine ToVs have also spread globally; although they have not caused serious economic losses, coinfections with other pathogens can exacerbate their symptoms. In addition, frequent inter- or intra-recombination among ToVs can increase pathogenesis or unpredicted host adaptation. These findings have highlighted the importance of ToVs as pathogens and the need for basic ToV research. Here, we review recent progress in the study of ToV molecular biology including reverse genetics, focusing on the similarities and differences between ToVs and CoVs.
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Affiliation(s)
- Makoto Ujike
- Laboratory of Veterinary Infectious Diseases, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan;
- Research Center for Animal Life Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan
| | - Fumihiro Taguchi
- Laboratory of Veterinary Infectious Diseases, Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-8602, Japan;
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3
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Gulyaeva AA, Gorbalenya AE. A nidovirus perspective on SARS-CoV-2. Biochem Biophys Res Commun 2020; 538:24-34. [PMID: 33413979 PMCID: PMC7664520 DOI: 10.1016/j.bbrc.2020.11.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023]
Abstract
Two pandemics of respiratory distress diseases associated with zoonotic introductions of the species Severe acute respiratory syndrome-related coronavirus in the human population during 21st century raised unprecedented interest in coronavirus research and assigned it unseen urgency. The two viruses responsible for the outbreaks, SARS-CoV and SARS-CoV-2, respectively, are in the spotlight, and SARS-CoV-2 is the focus of the current fast-paced research. Its foundation was laid down by studies of many corona- and related viruses that collectively form the vast order Nidovirales. Comparative genomics of nidoviruses played a key role in this advancement over more than 30 years. It facilitated the transfer of knowledge from characterized to newly identified viruses, including SARS-CoV and SARS-CoV-2, as well as contributed to the dissection of the nidovirus proteome and identification of patterns of variations between different taxonomic groups, from species to families. This review revisits selected cases of protein conservation and variation that define nidoviruses, illustrates the remarkable plasticity of the proteome during nidovirus adaptation, and asks questions at the interface of the proteome and processes that are vital for nidovirus reproduction and could inform the ongoing research of SARS-CoV-2.
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Affiliation(s)
- Anastasia A Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, the Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, 2300 RC, Leiden, the Netherlands; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119899, Moscow, Russia.
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4
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Cowley JA. The genomes of Mourilyan virus and Wēnzhōu shrimp virus 1 of prawns comprise 4 RNA segments. Virus Res 2020; 292:198225. [PMID: 33181202 DOI: 10.1016/j.virusres.2020.198225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/16/2022]
Abstract
Reported here is the complete genome sequence of Mourilyan virus (MoV) that infects giant tiger (Penaeus monodon) and kuruma prawns (P. japonicas) in Australia. Its genome was determined using various PCR strategies based on the sequences of 3 randomly-amplified cDNA clones to its L and M RNA segments discovered in a library generated to determine the genome sequence of gill-associated ronivirus. The sequences of PCR products and clones obtained showed the MoV genome to comprise 4 ssRNA segments (L, M, S1 and S2), as confirmed by Northern blotting using RNA from naïve and MoV-infected prawns, and by Illumina sequence analysis of semi-purified MoV. BLASTn searches identified the MoV L, M and S1 RNA segments to be homologous to Wēnzhōu shrimp virus 1 (WzSV1) segments discovered recently in a P. monodon RNA-Seq library (SRR1745808). Mapping this read library to the MoV S2 RNA segment identified WzSV1 to also possess an equivalent segment. BLASTp searches identified the putative non-structural protein (NSs2; 393-394 aa) encoded in their S2 RNA segments to have no homologs in GenBank. Possibly due to NSs2 being encoded in a discrete RNA segment rather than in ambisense relative to the N protein as in the S RNA segments of other phenuiviruses, each of 6 MoV S1 RNA segment clones sequenced possessed a variable-length (≤ 645 nt) imperfect GA-repeat extending from the N protein stop codon to the more variable ∼90 nt segment terminal sequence. Read mapping of RNA-Seq library SRR1745808 showed the WzSV1 S1 RNA segment to possess a similar GA-repeat. However, paired-read variations hindered definitive assembly of a consensus sequence. All 4 MoV and WzSV1 RNA segments terminated with a 10 nt inverted repeat sequence (5'-ACACAAAGAC.) identical to the RNA segment termini of uukuviruses. Phylogenetic analyses of MoV/WzSV1 RNA-dependant RNA polymerase (L RNA), G1G2 precursor glycoprotein (M RNA) and nucleocapsid (N) protein (S1 RNA) sequences generally clustered them with as yet unassigned crustacean/diptera bunya-like viruses on branches positioned closely to others containing tick-transmitted phenuiviruses. As genome sequences of most phenuiviruses discovered recently have originated from meta-transcriptomics studies, the data presented here showing the MoV and WzSV1 genomes to comprise more than 3 RNA segments, like the plant tenuiviruses, suggests a need to investigate the genomes of these unassigned viruses more closely.
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Affiliation(s)
- Jeff A Cowley
- Livestock & Aquaculture, CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD, 4067, Australia.
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TaqMan real-time and conventional nested PCR tests specific to yellow head virus genotype 7 (YHV7) identified in giant tiger shrimp in Australia. J Virol Methods 2019; 273:113689. [PMID: 31276700 DOI: 10.1016/j.jviromet.2019.113689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/01/2019] [Accepted: 07/01/2019] [Indexed: 12/11/2022]
Abstract
In 2013, a unique seventh yellow head virus genotype (YHV7) was detected in Black Tiger shrimp (Penaeus monodon) broodstock that suffered high mortality following their capture from Joseph Bonaparte Gulf (JBG) in northern Australia. To assist with its diagnosis and assessment of its distribution, prevalence and pathogenicity, YHV7-specific TaqMan real-time qPCR and conventional nested PCR primer sets were designed to ORF1b gene sequences divergent from the other YHV genotypes. Using high (≥108) copies of plasmid (p)DNA controls containing ORF1b gene inserts of representative strains of YHV genotypes 1-7, both PCR tests displayed specificity for YHV7. Amplifications of serial 10-fold dilutions of quantified YHV7 pDNA and synthetic ssRNA showed that both tests could reliably detect 10 genome copies. Pleopods/gills from wild P. monodon sourced from locations in geographically disparate regions across northern Australia as well as 96 juveniles (48 either appearing normal or displaying signs of morbidity) from a commercial pond experiencing mortalities were screened to partially validate the diagnostic capacity of the qPCR test. Based on these data and PCR primer/probe sequence mismatches with other newly identified YHV genotypes, both YHV7-specific PCR tests should prove useful in the sensitive detection and discrimination of this genotype from YHV 2 (gill-associated virus) and YHV6 that can occur in Australian P. monodon, as well as from YHV genotypes currently listed as exotic to Australia.
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6
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Stewart H, Brown K, Dinan AM, Irigoyen N, Snijder EJ, Firth AE. Transcriptional and Translational Landscape of Equine Torovirus. J Virol 2018; 92:e00589-18. [PMID: 29950409 PMCID: PMC6096809 DOI: 10.1128/jvi.00589-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/13/2018] [Indexed: 12/15/2022] Open
Abstract
The genus Torovirus (subfamily Torovirinae, family Coronaviridae, order Nidovirales) encompasses a range of species that infect domestic ungulates, including cattle, sheep, goats, pigs, and horses, causing an acute self-limiting gastroenteritis. Using the prototype species equine torovirus (EToV), we performed parallel RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) to analyze the relative expression levels of the known torovirus proteins and transcripts, chimeric sequences produced via discontinuous RNA synthesis (a characteristic of the nidovirus replication cycle), and changes in host transcription and translation as a result of EToV infection. RNA sequencing confirmed that EToV utilizes a unique combination of discontinuous and nondiscontinuous RNA synthesis to produce its subgenomic RNAs (sgRNAs); indeed, we identified transcripts arising from both mechanisms that would result in sgRNAs encoding the nucleocapsid. Our ribosome profiling analysis revealed that ribosomes efficiently translate two novel CUG-initiated open reading frames (ORFs), located within the so-called 5' untranslated region. We have termed the resulting proteins U1 and U2. Comparative genomic analysis confirmed that these ORFs are conserved across all available torovirus sequences, and the inferred amino acid sequences are subject to purifying selection, indicating that U1 and U2 are functionally relevant. This study provides the first high-resolution analysis of transcription and translation in this neglected group of livestock pathogens.IMPORTANCE Toroviruses infect cattle, goats, pigs, and horses worldwide and can cause gastrointestinal disease. There is no treatment or vaccine, and their ability to spill over into humans has not been assessed. These viruses are related to important human pathogens, including severe acute respiratory syndrome (SARS) coronavirus, and they share some common features; however, the mechanism that they use to produce sgRNA molecules differs. Here, we performed deep sequencing to determine how equine torovirus produces sgRNAs. In doing so, we also identified two previously unknown open reading frames "hidden" within the genome. Together these results highlight the similarities and differences between this domestic animal virus and related pathogens of humans and livestock.
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Affiliation(s)
- Hazel Stewart
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Brown
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Adam M Dinan
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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Di H, McIntyre AA, Brinton MA. New insights about the regulation of Nidovirus subgenomic mRNA synthesis. Virology 2018; 517:38-43. [PMID: 29475599 PMCID: PMC5987246 DOI: 10.1016/j.virol.2018.01.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 01/23/2018] [Accepted: 01/29/2018] [Indexed: 01/19/2023]
Abstract
The members of the Order Nidovirales share a similar genome organization with two overlapping nonstructural polyproteins encoded in the 5' two-thirds and the structural proteins encoded in the 3' third. They also express their 3' region proteins from a nested set of 3' co-terminal subgenomic messenger RNAs (sg mRNAs). Some but not all of the Nidovirus sg mRNAs also have a common 5' leader sequence that is acquired by a discontinuous RNA synthesis mechanism regulated by multiple 3' body transcription regulating sequences (TRSs) and the 5' leader TRS. Initial studies detected a single major body TRS for each 3' sg mRNA with a few alternative functional TRSs reported. The recent application of advanced techniques, such as next generation sequencing and ribosomal profiling, in studies of arteriviruses and coronaviruses has revealed an expanded sg mRNA transcriptome and coding capacity.
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Affiliation(s)
- Han Di
- Department of Biology, Georgia State University, P.O. Box 4010, Atlanta, GA 30303, USA
| | - Ayisha A McIntyre
- Department of Biology, Georgia State University, P.O. Box 4010, Atlanta, GA 30303, USA
| | - Margo A Brinton
- Department of Biology, Georgia State University, P.O. Box 4010, Atlanta, GA 30303, USA.
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8
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Rappe JCF, de Wilde A, Di H, Müller C, Stalder H, V'kovski P, Snijder E, Brinton MA, Ziebuhr J, Ruggli N, Thiel V. Antiviral activity of K22 against members of the order Nidovirales. Virus Res 2018; 246:28-34. [PMID: 29337162 PMCID: PMC7114538 DOI: 10.1016/j.virusres.2018.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/10/2018] [Accepted: 01/10/2018] [Indexed: 01/31/2023]
Abstract
Recently, a novel antiviral compound (K22) that inhibits replication of a broad range of animal and human coronaviruses was reported to interfere with viral RNA synthesis by impairing double-membrane vesicle (DMV) formation (Lundin et al., 2014). Here we assessed potential antiviral activities of K22 against a range of viruses representing two (sub)families of the order Nidovirales, the Arteriviridae (porcine reproductive and respiratory syndrome virus [PRRSV], equine arteritis virus [EAV] and simian hemorrhagic fever virus [SHFV]), and the Torovirinae (equine torovirus [EToV] and White Bream virus [WBV]). Possible effects of K22 on nidovirus replication were studied in suitable cell lines. K22 concentrations significantly decreasing infectious titres of the viruses included in this study ranged from 25 to 50 μM. Reduction of double-stranded RNA intermediates of viral replication in nidovirus-infected cells treated with K22 confirmed the anti-viral potential of K22. Collectively, the data show that K22 has antiviral activity against diverse lineages of nidoviruses, suggesting that the inhibitor targets a critical and conserved step during nidovirus replication.
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Affiliation(s)
- Julie Christiane Françoise Rappe
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
| | - Adriaan de Wilde
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Han Di
- Department of Biology, 623 Petit Science Center, Georgia State University, 161 Jesse Hill Jr Drive, Atlanta, GA 30303, United States.
| | - Christin Müller
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany.
| | - Hanspeter Stalder
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
| | - Philip V'kovski
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
| | - Eric Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Margo A Brinton
- Department of Biology, 623 Petit Science Center, Georgia State University, 161 Jesse Hill Jr Drive, Atlanta, GA 30303, United States.
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany.
| | - Nicolas Ruggli
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
| | - Volker Thiel
- Institute for Virology and Immunology IVI, Mittelhäusern and Bern, Switzerland; Department of Infectious Diseases and Pathobiology, University of Bern, Switzerland.
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Ryabov EV. Invertebrate RNA virus diversity from a taxonomic point of view. J Invertebr Pathol 2017; 147:37-50. [PMID: 27793741 PMCID: PMC7094257 DOI: 10.1016/j.jip.2016.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 10/03/2016] [Accepted: 10/14/2016] [Indexed: 02/04/2023]
Abstract
Invertebrates are hosts to diverse RNA viruses that have all possible types of encapsidated genomes (positive, negative and ambisense single stranded RNA genomes, or a double stranded RNA genome). These viruses also differ markedly in virion morphology and genome structure. Invertebrate RNA viruses are present in three out of four currently recognized orders of RNA viruses: Mononegavirales, Nidovirales, and Picornavirales, and 10 out of 37 RNA virus families that have yet to be assigned to an order. This mini-review describes general properties of the taxonomic groups, which include invertebrate RNA viruses on the basis of their current classification by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Eugene V Ryabov
- ER Healthcare Consulting Ltd., Poundgate Lane, Coventry CV4 8HJ, United Kingdom.
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10
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Posthuma CC, Te Velthuis AJW, Snijder EJ. Nidovirus RNA polymerases: Complex enzymes handling exceptional RNA genomes. Virus Res 2017; 234:58-73. [PMID: 28174054 PMCID: PMC7114556 DOI: 10.1016/j.virusres.2017.01.023] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/24/2017] [Accepted: 01/26/2017] [Indexed: 12/22/2022]
Abstract
Coronaviruses and arteriviruses are distantly related human and animal pathogens that belong to the order Nidovirales. Nidoviruses are characterized by their polycistronic plus-stranded RNA genome, the production of subgenomic mRNAs and the conservation of a specific array of replicase domains, including key RNA-synthesizing enzymes. Coronaviruses (26-34 kilobases) have the largest known RNA genomes and their replication presumably requires a processive RNA-dependent RNA polymerase (RdRp) and enzymatic functions that suppress the consequences of the typically high error rate of viral RdRps. The arteriviruses have significantly smaller genomes and form an intriguing package with the coronaviruses to analyse viral RdRp evolution and function. The RdRp domain of nidoviruses resides in a cleavage product of the replicase polyprotein named non-structural protein (nsp) 12 in coronaviruses and nsp9 in arteriviruses. In all nidoviruses, the C-terminal RdRp domain is linked to a conserved N-terminal domain, which has been coined NiRAN (nidovirus RdRp-associated nucleotidyl transferase). Although no structural information is available, the functional characterization of the nidovirus RdRp and the larger enzyme complex of which it is part, has progressed significantly over the past decade. In coronaviruses several smaller, non-enzymatic nsps were characterized that direct RdRp function, while a 3'-to-5' exoribonuclease activity in nsp14 was implicated in fidelity. In arteriviruses, the nsp1 subunit was found to maintain the balance between genome replication and subgenomic mRNA production. Understanding RdRp behaviour and interactions during RNA synthesis and subsequent processing will be key to rationalising the evolutionary success of nidoviruses and the development of antiviral strategies.
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Affiliation(s)
- Clara C Posthuma
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Aartjan J W Te Velthuis
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
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11
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van der Hoeven B, Oudshoorn D, Koster AJ, Snijder EJ, Kikkert M, Bárcena M. Biogenesis and architecture of arterivirus replication organelles. Virus Res 2016; 220:70-90. [PMID: 27071852 PMCID: PMC7111217 DOI: 10.1016/j.virusres.2016.04.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 02/06/2023]
Abstract
Arterivirus RNA synthesis presumably is associated with double-membrane vesicles (DMVs). Putative intermediates in DMV formation were detected in infected cells. Arterivirus-induced DMVs form a highly interconnected reticulovesicular network (RVN). Expression of the nsp2-3 replicase polyprotein fragment induces a comparable RVN. Nsp2-7 expression results in smaller DMVs, closer in size to DMVs found in infection.
All eukaryotic positive-stranded RNA (+RNA) viruses appropriate host cell membranes and transform them into replication organelles, specialized micro-environments that are thought to support viral RNA synthesis. Arteriviruses (order Nidovirales) belong to the subset of +RNA viruses that induce double-membrane vesicles (DMVs), similar to the structures induced by e.g. coronaviruses, picornaviruses and hepatitis C virus. In the last years, electron tomography has revealed substantial differences between the structures induced by these different virus groups. Arterivirus-induced DMVs appear to be closed compartments that are continuous with endoplasmic reticulum membranes, thus forming an extensive reticulovesicular network (RVN) of intriguing complexity. This RVN is remarkably similar to that described for the distantly related coronaviruses (also order Nidovirales) and sets them apart from other DMV-inducing viruses analysed to date. We review here the current knowledge and open questions on arterivirus replication organelles and discuss them in the light of the latest studies on other DMV-inducing viruses, particularly coronaviruses. Using the equine arteritis virus (EAV) model system and electron tomography, we present new data regarding the biogenesis of arterivirus-induced DMVs and uncover numerous putative intermediates in DMV formation. We generated cell lines that can be induced to express specific EAV replicase proteins and showed that DMVs induced by the transmembrane proteins nsp2 and nsp3 form an RVN and are comparable in topology and architecture to those formed during viral infection. Co-expression of the third EAV transmembrane protein (nsp5), expressed as part of a self-cleaving polypeptide that mimics viral polyprotein processing in infected cells, led to the formation of DMVs whose size was more homogenous and closer to what is observed upon EAV infection, suggesting a regulatory role for nsp5 in modulating membrane curvature and DMV formation.
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Affiliation(s)
- Barbara van der Hoeven
- Electron Microscopy Section, Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Diede Oudshoorn
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Abraham J Koster
- Electron Microscopy Section, Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Kikkert
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Montserrat Bárcena
- Electron Microscopy Section, Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands.
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12
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Cowley J. Nidoviruses of Fish and Crustaceans. AQUACULTURE VIROLOGY 2016. [PMCID: PMC7150020 DOI: 10.1016/b978-0-12-801573-5.00032-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Viruses with diverse virion architectures demarcated into four families in the order Nidovirales have been discovered in vertebrate mammalian and fish species, as well as in invertebrate crustacean and mosquito species. The order is unified by nidoviruses sharing intermediate (12.7 kb) to very long (31.7 kb) (+) ssRNA genomes, each possessing a long 5′-terminal gene encoding overlapping ORF1a and ORF1b reading frames that contain a diversity of functionally related enzymes and that are translated in toto using a −1 ribosomal frameshift mechanism, as well as by semiconserved strategies for transcribing a nested set of 3′-coterminal subgenomic mRNAs that translate the viral proteins. The nidovirus that is most important to an aquaculture species is yellow head virus (YHV), which causes disease in shrimp farmed throughout the Eastern Hemisphere and is classified in the genus Okavirus, family Roniviridae. Fathead minnow nidovirus, genus Bafinivirus, subfamily Torovirinae, family Coronaviridae, also causes disease in minnows grown for the baitfish industry in the United States. Virions similar in morphology to okaviruses and bafiniviruses have also been detected in several crab species. Of these, however, only Eriocheir sinensis ronivirus, which causes disease in the Chinese mitten crab, an important freshwater aquaculture species in China, has been shown to possess a ~22 kb ssRNA genome that supports its being a nidovirus, but its taxonomic classification awaits genome sequence analysis. This chapter provides an overview of the structure, replication and biology of these viruses with a particular focus on YHV disease characteristics, diagnostic methods and disease prevention strategies.
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Lehmann KC, Snijder EJ, Posthuma CC, Gorbalenya AE. What we know but do not understand about nidovirus helicases. Virus Res 2014; 202:12-32. [PMID: 25497126 PMCID: PMC7114383 DOI: 10.1016/j.virusres.2014.12.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/28/2014] [Accepted: 12/01/2014] [Indexed: 01/24/2023]
Abstract
The ubiquitous nidovirus helicase is a multi-functional enzyme of superfamily 1. Its unique N-terminal domain is most similar to the Upf1 multinuclear zinc-binding domain. It has been implicated in replication, transcription, virion biogenesis, translation and post-transcriptional viral RNA processing. Four different classes of antiviral compounds targeting the helicase have been identified.
Helicases are versatile NTP-dependent motor proteins of monophyletic origin that are found in all kingdoms of life. Their functions range from nucleic acid duplex unwinding to protein displacement and double-strand translocation. This explains their participation in virtually every metabolic process that involves nucleic acids, including DNA replication, recombination and repair, transcription, translation, as well as RNA processing. Helicases are encoded by all plant and animal viruses with a positive-sense RNA genome that is larger than 7 kb, indicating a link to genome size evolution in this virus class. Viral helicases belong to three out of the six currently recognized superfamilies, SF1, SF2, and SF3. Despite being omnipresent, highly conserved and essential, only a few viral helicases, mostly from SF2, have been studied extensively. In general, their specific roles in the viral replication cycle remain poorly understood at present. The SF1 helicase protein of viruses classified in the order Nidovirales is encoded in replicase open reading frame 1b (ORF1b), which is translated to give rise to a large polyprotein following a ribosomal frameshift from the upstream ORF1a. Proteolytic processing of the replicase polyprotein yields a dozen or so mature proteins, one of which includes a helicase. Its hallmark is the presence of an N-terminal multi-nuclear zinc-binding domain, the nidoviral genetic marker and one of the most conserved domains across members of the order. This review summarizes biochemical, structural, and genetic data, including drug development studies, obtained using helicases originating from several mammalian nidoviruses, along with the results of the genomics characterization of a much larger number of (putative) helicases of vertebrate and invertebrate nidoviruses. In the context of our knowledge of related helicases of cellular and viral origin, it discusses the implications of these results for the protein's emerging critical function(s) in nidovirus evolution, genome replication and expression, virion biogenesis, and possibly also post-transcriptional processing of viral RNAs. Using our accumulated knowledge and highlighting gaps in our data, concepts and approaches, it concludes with a perspective on future research aimed at elucidating the role of helicases in the nidovirus replication cycle.
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Affiliation(s)
- Kathleen C Lehmann
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Clara C Posthuma
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia.
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Uccellini L, Ossiboff RJ, de Matos REC, Morrisey JK, Petrosov A, Navarrete-Macias I, Jain K, Hicks AL, Buckles EL, Tokarz R, McAloose D, Lipkin WI. Identification of a novel nidovirus in an outbreak of fatal respiratory disease in ball pythons (Python regius). Virol J 2014; 11:144. [PMID: 25106433 PMCID: PMC4254391 DOI: 10.1186/1743-422x-11-144] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 08/08/2014] [Indexed: 11/23/2022] Open
Abstract
Background Respiratory infections are important causes of morbidity and mortality in reptiles; however, the causative agents are only infrequently identified. Findings Pneumonia, tracheitis and esophagitis were reported in a collection of ball pythons (Python regius). Eight of 12 snakes had evidence of bacterial pneumonia. High-throughput sequencing of total extracted nucleic acids from lung, esophagus and spleen revealed a novel nidovirus. PCR indicated the presence of viral RNA in lung, trachea, esophagus, liver, and spleen. In situ hybridization confirmed the presence of intracellular, intracytoplasmic viral nucleic acids in the lungs of infected snakes. Phylogenetic analysis based on a 1,136 amino acid segment of the polyprotein suggests that this virus may represent a new species in the subfamily Torovirinae. Conclusions This report of a novel nidovirus in ball pythons may provide insight into the pathogenesis of respiratory disease in this species and enhances our knowledge of the diversity of nidoviruses.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Walter Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, USA.
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Ke TY, Liao WY, Wu HY. A leaderless genome identified during persistent bovine coronavirus infection is associated with attenuation of gene expression. PLoS One 2013; 8:e82176. [PMID: 24349214 PMCID: PMC3861326 DOI: 10.1371/journal.pone.0082176] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/21/2013] [Indexed: 01/22/2023] Open
Abstract
The establishment of persistent viral infection is often associated with the selection of one or more mutant viruses. For example, it has been found that an intraleader open reading frame (ORF) in genomic and subgenomic mRNA (sgmRNA) molecules is selected during bovine coronavirus (BCoV) persistence which leads to translation attenuation of the downstream ORF. Here, we report the unexpected identification of leaderless genomes, in addition to leader-containing genomes, in a cell culture persistently infected with BCoV. The discovery was made by using a head-to-tail ligation method that examines genomic 5′-terminal sequences at different times postinfection. Functional analyses of the leaderless genomic RNA in a BCoV defective interfering (DI) RNA revealed that (1) the leaderless genome was able to serve as a template for the synthesis of negative-strand genome, although it cannot perform replicative positive-strand genomic RNA synthesis, and (2) the leaderless genome retained its function in translation and transcription, although the efficiency of these processes was impaired. Therefore, this previously unidentified leaderless genome is associated with the attenuation of genome expression. Whether the leaderless genome contributes to the establishment of persistent infection remains to be determined.
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Affiliation(s)
- Ting-Yung Ke
- Institute of Pathobiology, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan ROC
| | - Wei-Yu Liao
- Institute of Pathobiology, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan ROC
| | - Hung-Yi Wu
- Institute of Pathobiology, College of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan ROC
- * E-mail:
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Zirkel F, Roth H, Kurth A, Drosten C, Ziebuhr J, Junglen S. Identification and characterization of genetically divergent members of the newly established family Mesoniviridae. J Virol 2013; 87:6346-58. [PMID: 23536661 PMCID: PMC3648093 DOI: 10.1128/jvi.00416-13] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 03/18/2013] [Indexed: 12/16/2022] Open
Abstract
The recently established family Mesoniviridae (order Nidovirales) contains a single species represented by two closely related viruses, Cavally virus (CavV) and Nam Dinh virus (NDiV), which were isolated from mosquitoes collected in Côte d'Ivoire and Vietnam, respectively. They represent the first nidoviruses to be discovered in insects. Here, we report the molecular characterization of four novel mesoniviruses, Hana virus, Méno virus, Nsé virus, and Moumo virus, all of which were identified in a geographical region in Côte d'Ivoire with high CavV prevalence. The viruses were found with prevalences between 0.5 and 2.8%, and genome sequence analyses and phylogenetic studies suggest that they represent at least three novel species. Electron microscopy revealed prominent club-shaped surface projections protruding from spherical, enveloped virions of about 120 nm. Northern blot data show that the four mesoniviruses analyzed in this study produce two major 3'-coterminal subgenomic mRNAs containing two types of 5' leader sequences resulting from the use of different pairs of leader and body transcription-regulating sequences that are conserved among mesoniviruses. Protein sequencing, mass spectroscopy, and Western blot data show that mesonivirus particles contain eight major structural protein species, including the putative nucleocapsid protein (25 kDa), differentially glycosylated forms of the putative membrane protein (20, 19, 18, and 17 kDa), and the putative spike (S) protein (77 kDa), which is proteolytically cleaved at a conserved site to produce S protein subunits of 23 and 57 kDa. The data provide fundamental new insight into common and distinguishing biological properties of members of this newly identified virus family.
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Affiliation(s)
- Florian Zirkel
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany
| | - Hanna Roth
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany
| | - Andreas Kurth
- Center for Biological Safety, Robert Koch Institute, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Sandra Junglen
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany
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17
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Multiplex real-time PCR and high-resolution melting analysis for detection of white spot syndrome virus, yellow-head virus, and Penaeus monodon densovirus in penaeid shrimp. J Virol Methods 2011; 178:16-21. [PMID: 21906627 DOI: 10.1016/j.jviromet.2011.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 07/11/2011] [Accepted: 07/20/2011] [Indexed: 12/11/2022]
Abstract
A multiplex real-time PCR and high-resolution melting (HRM) analysis was developed to detect simultaneously three of the major viruses of penaeid shrimp including white spot syndrome virus (WSSV), yellow-head virus (YHV), and Penaeus monodon densovirus (PmDNV). Plasmids containing DNA/cDNA fragments of WSSV and YHV, and genomic DNAs of PmDNV and normal shrimp were used to test sensitivity of the procedure. Without the need of any probe, the products were identified by HRM analysis after real-time PCR amplification using three sets of viral specific primers. The results showed DNA melting curves that were specific for individual virus. No positive result was detected with nucleic acids from shrimp, Penaeus monodon nucleopolyhedrovirus (PemoNPV), Penaeus stylirostris densovirus (PstDNV), or Taura syndrome virus (TSV). The detection limit for PmDNV, YHV and WSSV DNAs were 40fg, 50fg, and 500fg, respectively, which was 10 times more sensitive than multiplex real-time PCR analyzed by agarose gel electrophoresis. In viral nucleic acid mixtures, HRM analysis clearly identified each virus in dual and triple infection. To test the capability to use this method in field, forty-one of field samples were examined by HRM analysis in comparison with agarose gel electrophoresis. For HRM analysis, 11 (26.83%), 9 (21.95%), and 4 (9.76%) were infected with WSSV, PmDNV, and YHV, respectively. Agarose gel electrophoresis detected lesser number of PmDNV infection which may due to the limit of sensitivity. No multiple infection was found in these samples. This method provides a rapid, sensitive, specific, and simultaneous detection of three major viruses making it as a useful tool for diagnosis and epidemiological studies of these viruses in shrimp and carriers.
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Abstract
Tropical rainforests show the highest level of terrestrial biodiversity and may be an important contributor to microbial diversity. Exploitation of these ecosystems may foster the emergence of novel pathogens. We report the discovery of the first insect-associated nidovirus, tentatively named Cavally virus (CAVV). CAVV was found with a prevalence of 9.3% during a survey of mosquito-associated viruses along an anthropogenic disturbance gradient in Côte d’Ivoire. Analysis of habitat-specific virus diversity and ancestral state reconstruction demonstrated an origin of CAVV in a pristine rainforest with subsequent spread into agriculture and human settlements. Virus extension from the forest was associated with a decrease in virus diversity (P < 0.01) and an increase in virus prevalence (P < 0.00001). CAVV is an enveloped virus with large surface projections. The RNA genome comprises 20,108 nucleotides with seven major open reading frames (ORFs). ORF1a and -1b encode two large proteins that share essential features with phylogenetically higher representatives of the order Nidovirales, including the families Coronavirinae and Torovirinae, but also with families in a basal phylogenetic relationship, including the families Roniviridae and Arteriviridae. Genetic markers uniquely conserved in nidoviruses, such as an endoribonuclease- and helicase-associated zinc-binding domain, are conserved in CAVV. ORF2a and -2b are predicted to code for structural proteins S and N, respectively, while ORF3a and -3b encode proteins with membrane-spanning regions. CAVV produces three subgenomic mRNAs with 5′ leader sequences (of different lengths) derived from the 5′ end of the genome. This novel cluster of mosquito-associated nidoviruses is likely to represent a novel family within the order Nidovirales. Knowledge of microbial diversity in tropical rainforests is sparse, and factors driving the emergence of novel pathogens are poorly understood. We discovered and mapped the spread and genetic evolution of a novel mosquito nidovirus from a pristine rainforest to human settlements. Notably, virus diversity decreased and prevalence increased during the process of spreading into disturbed habitats. The novel virus, tentatively termed Cavally virus, contains genetic features common to members of the order Nidovirales (families Coronaviridae, Arteriviridae, and Roniviridae), including conservation of the replicase machinery and expression of subgenomic RNA messages, has a basal phylogenetic relationship to the family Coronaviridae, and clearly differs from the established nidovirus families. Inclusion of this putative novel family in the nidovirus phylogeny suggests that nidoviruses may have evolved from arthropods.
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Sellars MJ, Rao M, Arnold SJ, Wade NM, Cowley JA. Penaeus monodon is protected against gill-associated virus by muscle injection but not oral delivery of bacterially expressed dsRNAs. DISEASES OF AQUATIC ORGANISMS 2011; 95:19-30. [PMID: 21797032 DOI: 10.3354/dao02343] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Gill-associated virus (GAV) is a nidovirus that commonly infects Penaeus monodon (black tiger shrimp) in eastern Australia, causing morbidity and mortalities in the acute stage of disease. Here we explored the possibility of inhibiting GAV replication and disease using double-stranded (ds)RNAs expressed in bacteria and delivered either orally or by muscle injection. To enhance potential RNA interference (RNAi) responses, 5 long dsRNAs were used that targeted open reading frame 1a/1b (ORF1a/b) gene regions and thus only the genomic length RNA. To examine oral delivery, P. monodon were fed pellets incorporating a pool of formalin-fixed bacteria containing the 5 GAV-specific dsRNAs before being injected with a minimal lethal GAV dose. Feeding with the pellets continued post-challenge but did not reduce mortality accumulation and elevation in GAV loads. In contrast, muscle injection of the dsRNAs purified from bacteria was highly effective at slowing GAV replication and protecting shrimp against acute disease and mortalities. In synergy with these data, dsRNA targeted to P. monodon beta-actin mRNA caused 100% mortality following injection, whilst its oral delivery caused no mortality. Findings confirm that injected dsRNA can mount effective RNAi responses in P. monodon to endogenous shrimp mRNA and exogenous viral RNAs, but when delivered orally in bacteria as a feed component, the same dsRNAs are ineffective. The efficacy of the RNAi response against GAV provided by injection of dsRNAs targeted to multiple genome sites suggests that this strategy might have general applicability in enhancing protection against other shrimp single-stranded (ss)RNA viruses, particularly in hatcheries or breeding programs where injection-based delivery systems are practical.
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Affiliation(s)
- Melony J Sellars
- CSIRO Food Futures National Research Flagship, CSIRO Marine and Atmospheric Research, Cleveland, Queensland 4163, Australia.
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20
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Sztuba-Solińska J, Stollar V, Bujarski JJ. Subgenomic messenger RNAs: mastering regulation of (+)-strand RNA virus life cycle. Virology 2011; 412:245-55. [PMID: 21377709 PMCID: PMC7111999 DOI: 10.1016/j.virol.2011.02.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 12/14/2010] [Accepted: 02/04/2011] [Indexed: 12/12/2022]
Abstract
Many (+)-strand RNA viruses use subgenomic (SG) RNAs as messengers for protein expression, or to regulate their viral life cycle. Three different mechanisms have been described for the synthesis of SG RNAs. The first mechanism involves internal initiation on a (−)-strand RNA template and requires an internal SGP promoter. The second mechanism makes a prematurely terminated (−)-strand RNA which is used as template to make the SG RNA. The third mechanism uses discontinuous RNA synthesis while making the (−)-strand RNA templates. Most SG RNAs are translated into structural proteins or proteins related to pathogenesis: however other SG RNAs regulate the transition between translation and replication, function as riboregulators of replication or translation, or support RNA–RNA recombination. In this review we discuss these functions of SG RNAs and how they influence viral replication, translation and recombination.
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Affiliation(s)
- Joanna Sztuba-Solińska
- Plant Molecular Biology Center and the Department of Biological Sciences, Northern Illinois University, De Kalb, IL 60115, USA
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21
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Cedano-Thomas Y, De La Rosa-Vélez J, Bonami JR, Vargas-Albores F. Gene expression kinetics of the yellow head virus in experimentally infected Litopenaeus vannamei. AQUACULTURE RESEARCH 2010; 41:1432-1443. [PMID: 32313428 PMCID: PMC7159739 DOI: 10.1111/j.1365-2109.2009.02434.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The yellow head virus (YHV) has been reported to be one of most pathogenic viruses for cultivated shrimp; however, serious problems have only been reported in farms in south and southeastern Asian. Recently, a YHV strain was detected in Litopenaeus vannamei cultivated in Mexican farms that lacked virus-associated mortalities or epizooties, and the animals were apparently healthy. The identity of the virus was confirmed by sequencing replicative and structural protein-encoding regions and comparing with homologous virus sequences. Phylogenic relationships and genetic distances were also determined and, although some differences were observed, an influence on virulence was uncertain. In addition, the expression levels of several transcripts (3CLPRO, POL, GP64 and GP116) were evaluated by quantitative real-time polymerase chain reaction during an experimental infection. Although the transcript showed varying kinetics, viral genes were expressed in infected L. vannamei, demonstrating the replicative capability of this YHV strain.
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Affiliation(s)
| | | | - Jean Robert Bonami
- Pathogens and Environment, UMR 5119, ECOLAG, CNRS/UM2, cc 093, Université Montpellier 2, Montpellier Cedex, France
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Wijegoonawardane PKM, Cowley JA, Walker PJ. A consensus real-time RT-PCR for detection of all genotypic variants of yellow head virus of penaeid shrimp. J Virol Methods 2010; 167:5-9. [PMID: 20219544 DOI: 10.1016/j.jviromet.2010.02.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 02/18/2010] [Accepted: 02/18/2010] [Indexed: 11/24/2022]
Abstract
A real-time quantitative (q)RT-PCR employing consensus degenerate PCR primers was developed to detect all six genotypes known currently to comprise the yellow head virus (YHV) complex and found commonly in Penaeus monodon shrimp. The test primers possess only limited (eight-fold) degeneracy and target ORF1b gene sequences identified to be highly conserved amongst 57 strains of the six genotypes detected in P. monodon sourced from various regions of the Indo-Pacific. The qRT-PCR amplifies a 147bp sequence and analysis of dilutions of synthetic genotype 2 RNA showed it to be 99.8% efficient and capable of detecting as few as 2.5 RNA copies reliably. As the test detects all six YH-complex genotypes, is extremely sensitive, capable of quantifying infection loads, and amenable to high-throughput application, it should prove useful for managing infections in P. monodon broodstock and seedstock used for aquaculture.
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23
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Firth AE, Atkins JF. Evidence for a novel coding sequence overlapping the 5'-terminal approximately 90 codons of the gill-associated and yellow head okavirus envelope glycoprotein gene. Virol J 2009; 6:222. [PMID: 20017924 PMCID: PMC2805633 DOI: 10.1186/1743-422x-6-222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 12/17/2009] [Indexed: 11/23/2022] Open
Abstract
The genus Okavirus (order Nidovirales) includes a number of viruses that infect crustaceans, causing major losses in the shrimp industry. These viruses have a linear positive-sense ssRNA genome of ~26-27 kb, encoding a large replicase polyprotein that is expressed from the genomic RNA, and several additional proteins that are expressed from a nested set of 3'-coterminal subgenomic RNAs. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF that overlaps the 5' end of the envelope glycoprotein encoding sequence, ORF3, in the +2 reading frame. The new ORF has a strong coding signature and, in fact, is more conserved at the amino acid level than the overlapping region of ORF3. We propose that translation of the new ORF initiates at a conserved AUG codon separated by just 2 nt from the ORF3 AUG initiation codon, resulting in a novel 86 amino acid protein.
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Affiliation(s)
- Andrew E Firth
- BioSciences Institute, University College Cork, Cork, Ireland.
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Wijegoonawardane PK, Sittidilokratna N, Petchampai N, Cowley JA, Gudkovs N, Walker PJ. Homologous genetic recombination in the yellow head complex of nidoviruses infecting Penaeus monodon shrimp. Virology 2009; 390:79-88. [PMID: 19487006 PMCID: PMC7127526 DOI: 10.1016/j.virol.2009.04.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2009] [Revised: 04/15/2009] [Accepted: 04/20/2009] [Indexed: 11/28/2022]
Abstract
Yellow head virus (YHV) is a highly virulent pathogen of Penaeus monodon shrimp. It is one of six known genotypes in the yellow head complex of nidoviruses which also includes mildly pathogenic gill-associated virus (GAV, genotype 2) and four other genotypes (genotypes 3-6) that have been detected only in healthy shrimp. In this study, comparative phylogenetic analyses conducted on replicase- (ORF1b) and glycoprotein- (ORF3) gene amplicons identified 10 putative natural recombinants amongst 28 viruses representing all six genotypes from across the Indo-Pacific region. The approximately 4.6 kb genomic region spanning the two amplicons was sequenced for three putative recombinant viruses from Vietnam (genotype 3/5), the Philippines (genotype 5/2) and Indonesia (genotype 3/2). SimPlot analysis using these and representative parental virus sequences confirmed that each was a recombinant genotype and identified a recombination hotspot in a region just upstream of the ORF1b C-terminus. Maximum-likelihood breakpoint analysis predicted identical crossover positions in the Vietnamese and Indonesian recombinants, and a crossover position 12 nt upstream in the Philippine recombinant. Homologous genetic recombination in the same genome region was also demonstrated in recombinants generated experimentally in shrimp co-infected with YHV and GAV. The high frequency with which natural recombinants were identified indicates that genetic exchange amongst genotypes is occurring commonly in Asia and playing a significant role in expanding the genetic diversity in the yellow head complex. This is the first evidence of genetic recombination in viruses infecting crustaceans and has significant implications for the pathogenesis of infection and diagnosis of these newly emerging invertebrate pathogens.
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Affiliation(s)
| | - Nusra Sittidilokratna
- CSIRO Livestock Industries, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, Victoria 3220, Australia
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Phathumthani 12120, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Phyathai, Bangkok 10400, Thailand
| | - Natthida Petchampai
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Rama VI Road, Phyathai, Bangkok 10400, Thailand
| | - Jeff A. Cowley
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
| | - Nicholas Gudkovs
- CSIRO Livestock Industries, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, Victoria 3220, Australia
| | - Peter J. Walker
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Queensland 4067, Australia
- CSIRO Livestock Industries, Australian Animal Health Laboratory, 5 Portarlington Road, Geelong, Victoria 3220, Australia
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Wijegoonawardane PKM, Cowley JA, Phan T, Hodgson RAJ, Nielsen L, Kiatpathomchai W, Walker PJ. Genetic diversity in the yellow head nidovirus complex. Virology 2008; 380:213-25. [PMID: 18768192 PMCID: PMC7103379 DOI: 10.1016/j.virol.2008.07.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 05/23/2008] [Accepted: 07/08/2008] [Indexed: 12/14/2022]
Abstract
Penaeus monodon shrimp collected from across the Indo-Pacific region during 1997-2004 were screened for the presence of yellow head-related viruses. Phylogenetic analyses of amplified ORF1b gene segments identified at least six distinct genetic lineages (genotypes). Genotype 1 (YHV) was detected only in shrimp with yellow head disease. Genotype 2 (GAV) was detected in diseased shrimp with the less severe condition described as mid-crop mortality syndrome and in healthy shrimp from Australia, Thailand and Vietnam. Other genotypes occurred commonly in healthy shrimp. Sequence comparisons of structural protein genes (ORF2 and ORF3), intergenic regions (IGRs) and the long 3'-UTR supported the delineation of genotypes and identified both conserved and variant structural features. In putative transcription regulating sequences (TRSs) encompassing the sub-genomic mRNA 5'-termini, a core motif (5'-GUCAAUUACAAC-3') is absolutely conserved. A small (83 nt) open reading frame (ORF4) in the 3'-UTR of GAV is variously truncated in all other genotypes and a TRS-like element preceding ORF4 is invariably corrupted by a A>G/U substitution in the central core motif (5'-UU(G/U)CAAC-3'). The data support previous evidence that ORF4 is a non-functional gene under construction or deconstruction. The 3'-UTRs also contain predicted 3'-terminal hairpin-loop structures that are preserved in all genotypes by compensatory nucleotide substitutions, suggesting a role in polymerase recognition for minus-strand RNA synthesis.
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Sittidilokratna N, Dangtip S, Cowley JA, Walker PJ. RNA transcription analysis and completion of the genome sequence of yellow head nidovirus. Virus Res 2008; 136:157-65. [PMID: 18582978 PMCID: PMC7114370 DOI: 10.1016/j.virusres.2008.05.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 04/30/2008] [Accepted: 05/03/2008] [Indexed: 11/25/2022]
Abstract
Yellow head virus (YHV) is a pathogen of the black tiger shrimp (Penaeus monodon) and, with gill-associated virus (GAV), is one of two known invertebrate nidoviruses. We describe sequences of the large replicase gene (ORF1a) and 5′- and 3′-terminal UTRs, completing the 26,662 nt sequence of the YHV genome. ORF1a (12,219 nt) encodes a ∼462,662 Da polypeptide containing a putative 3C-like protease and a putative papain-like protease with the canonical C/H catalytic dyad and α + β fold. The read-through pp1ab polyprotein contains putative uridylate-specific endoribonuclease and ribose-2′-O-methyl transferase domains, and an exonuclease domain incorporating unusual dual Zn2+-binding fingers. Upstream of ORF1a, the 71 nt 5′-UTR shares 82.4% identity with the 68 nt 5′-UTR of GAV. The 677 nt 3′-terminal region contains a single 60 nt ORF, commencing 298 nt downstream of ORF3, that is identical to N-terminal coding region of the 249 nt GAV ORF4. Northern blots using RNA from YHV-infected shrimp and probes directed at ORF1a, ORF1b, ORF2 and ORF3 identified a nested set of 3′-coterminal RNAs comprising the full-length genomic RNA and two sub-genomic (sg) mRNAs. Intergenic sequences upstream of ORF2 and ORF3 share high identity with GAV, particularly in the conserved domains predicted to mediate sgmRNA transcription.
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Affiliation(s)
- Nusra Sittidilokratna
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Phathumthani 12120, Thailand
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Walker P, Sittidilokratna N. Yellow Head Virus. ENCYCLOPEDIA OF VIROLOGY 2008. [PMCID: PMC7173420 DOI: 10.1016/b978-012374410-4.00779-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Yellow head virus (YHV) infects the black tiger shrimp (Penaeus monodon) – one of the world's major aquaculture species. It is a highly virulent pathogen that can cause 100% mortality within a few days of the first signs of disease in a pond. YHV is a rod-shaped, enveloped (+) single-stranded RNA (ssRNA) virus with a helical nucleocaspsid. In genome organization and transcription strategy, it resembles coronaviruses, toroviruses, and arteriviruses with which it has been classified within the order Nidovirales (genus Okavirus, family Roniviridae). The 26 662 nt genome comprises four long open reading frames (ORFs). ORF1a and ORF1b encode nonstructural proteins that are expressed as polyproteins (pp1a and pp1ab) and processed to generate elements of a replicase complex. ORF1b is expressed only as an extension of ORF1a via a ribosomal frameshift. ORF2 encodes the nucleocapsid protein (p20). ORF3 encodes envelope glycoproteins (gp64 and gp116) and a small, nonstructural, triple-membrane-spanning protein (p22). YHV is one genotype in a complex of closely related viruses that are endemic in black tiger shrimp in the Indo-Pacific region. These include gill-associated virus which has been associated with less severe forms of disease in Australia and at least four other genotypes that cause low-level chronic infections in healthy shrimp.
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Uncoupling RNA virus replication from transcription via the polymerase: functional and evolutionary insights. EMBO J 2007; 26:5120-30. [PMID: 18034156 DOI: 10.1038/sj.emboj.7601931] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Accepted: 10/29/2007] [Indexed: 01/11/2023] Open
Abstract
Many eukaryotic positive-strand RNA viruses transcribe subgenomic (sg) mRNAs that are virus-derived messages that template the translation of a subset of viral proteins. Currently, the premature termination (PT) mechanism of sg mRNA transcription, a process thought to operate in a variety of viruses, is best understood in tombusviruses. The viral RNA elements involved in regulating this mechanism have been well characterized in several systems; however, no corresponding protein factors have been identified yet. Here we show that tombusvirus genome replication can be effectively uncoupled from sg mRNA transcription in vivo by C-terminal modifications in its RNA-dependent RNA polymerase (RdRp). Systematic analysis of the PT transcriptional pathway using viral genomes harboring mutant RdRps revealed that the C-terminus functions primarily at an early step in this mechanism by mediating both efficient and accurate production of minus-strand templates for sg mRNA transcription. Our results also suggest a simple evolutionary scheme by which the virus could gain or enhance its transcriptional activity, and define global folding of the viral RNA genome as a previously unappreciated determinant of RdRp evolution.
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Wu HY, Brian DA. 5'-proximal hot spot for an inducible positive-to-negative-strand template switch by coronavirus RNA-dependent RNA polymerase. J Virol 2007; 81:3206-15. [PMID: 17229702 PMCID: PMC1866079 DOI: 10.1128/jvi.01817-06] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 01/07/2007] [Indexed: 01/27/2023] Open
Abstract
Coronaviruses have a positive-strand RNA genome and replicate through the use of a 3' nested set of subgenomic mRNAs each possessing a leader (65 to 90 nucleotides [nt] in length, depending on the viral species) identical to and derived from the genomic leader. One widely supported model for leader acquisition states that a template switch takes place during the generation of negative-strand antileader-containing templates used subsequently for subgenomic mRNA synthesis. In this process, the switch is largely driven by canonical heptameric donor sequences at intergenic sites on the genome that match an acceptor sequence at the 3' end of the genomic leader. With experimentally placed 22-nt-long donor sequences within a bovine coronavirus defective interfering (DI) RNA we have shown that matching sites occurring anywhere within a 65-nt-wide 5'-proximal genomic acceptor hot spot (nt 33 through 97) can be used for production of templates for subgenomic mRNA synthesis from the DI RNA. Here we report that with the same experimental approach, template switches can be induced in trans from an internal site in the DI RNA to the negative-strand antigenome of the helper virus. For these, a 3'-proximal 89-nt acceptor hot spot on the viral antigenome (nt 35 through 123), largely complementary to that described above, was found. Molecules resulting from these switches were not templates for subgenomic mRNA synthesis but, rather, ambisense chimeras potentially exceeding the viral genome in length. The results suggest the existence of a coronavirus 5'-proximal partially double-stranded template switch-facilitating structure of discrete width that contains both the viral genome and antigenome.
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Affiliation(s)
- Hung-Yi Wu
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996-0845, USA
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30
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Schütze H, Ulferts R, Schelle B, Bayer S, Granzow H, Hoffmann B, Mettenleiter TC, Ziebuhr J. Characterization of White bream virus reveals a novel genetic cluster of nidoviruses. J Virol 2006; 80:11598-609. [PMID: 16987966 PMCID: PMC1642614 DOI: 10.1128/jvi.01758-06] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The order Nidovirales comprises viruses from the families Coronaviridae (genera Coronavirus and Torovirus), Roniviridae (genus Okavirus), and Arteriviridae (genus Arterivirus). In this study, we characterized White bream virus (WBV), a bacilliform plus-strand RNA virus isolated from fish. Analysis of the nucleotide sequence, organization, and expression of the 26.6-kb genome provided conclusive evidence for a phylogenetic relationship between WBV and nidoviruses. The polycistronic genome of WBV contains five open reading frames (ORFs), called ORF1a, -1b, -2, -3, and -4. In WBV-infected cells, three subgenomic RNAs expressing the structural proteins S, M, and N were identified. The subgenomic RNAs were revealed to share a 42-nucleotide, 5' leader sequence that is identical to the 5'-terminal genome sequence. The data suggest that a conserved nonanucleotide sequence, CA(G/A)CACUAC, located downstream of the leader and upstream of the structural protein genes acts as the core transcription-regulating sequence element in WBV. Like other nidoviruses with large genomes (>26 kb), WBV encodes in its ORF1b an extensive set of enzymes, including putative polymerase, helicase, ribose methyltransferase, exoribonuclease, and endoribonuclease activities. ORF1a encodes several membrane domains, a putative ADP-ribose 1"-phosphatase, and a chymotrypsin-like serine protease whose activity was established in this study. Comparative sequence analysis revealed that WBV represents a separate cluster of nidoviruses that significantly diverged from toroviruses and, even more, from coronaviruses, roniviruses, and arteriviruses. The study adds to the amazing diversity of nidoviruses and appeals for a more extensive characterization of nonmammalian nidoviruses to better understand the evolution of these largest known RNA viruses.
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Affiliation(s)
- Heike Schütze
- The Queen's University of Belfast, School of Biomedical Sciences, 97 Lisburn Road, Belfast BT9 7BL, United Kingdom
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31
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Pasternak AO, Spaan WJM, Snijder EJ. Nidovirus transcription: how to make sense...? J Gen Virol 2006; 87:1403-1421. [PMID: 16690906 DOI: 10.1099/vir.0.81611-0] [Citation(s) in RCA: 255] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many positive-stranded RNA viruses use subgenomic mRNAs to express part of their genetic information. To produce structural and accessory proteins, members of the order Nidovirales (corona-, toro-, arteri- and roniviruses) generate a 3' co-terminal nested set of at least three and often seven to nine mRNAs. Coronavirus and arterivirus subgenomic transcripts are not only 3' co-terminal but also contain a common 5' leader sequence, which is derived from the genomic 5' end. Their synthesis involves a process of discontinuous RNA synthesis that resembles similarity-assisted RNA recombination. Most models proposed over the past 25 years assume co-transcriptional fusion of subgenomic RNA leader and body sequences, but there has been controversy over the question of whether this occurs during plus- or minus-strand synthesis. In the latter model, which has now gained considerable support, subgenomic mRNA synthesis takes place from a complementary set of subgenome-size minus-strand RNAs, produced by discontinuous minus-strand synthesis. Sense-antisense base-pairing interactions between short conserved sequences play a key regulatory role in this process. In view of the presumed common ancestry of nidoviruses, the recent finding that ronivirus and torovirus mRNAs do not contain a common 5' leader sequence is surprising. Apparently, major mechanistic differences must exist between nidoviruses, which raises questions about the functions of the common leader sequence and nidovirus transcriptase proteins and the evolution of nidovirus transcription. In this review, nidovirus transcription mechanisms are compared, the experimental systems used are critically assessed and, in particular, the impact of recently developed reverse genetic systems is discussed.
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Affiliation(s)
- Alexander O Pasternak
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, LUMC P4-26, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Willy J M Spaan
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, LUMC P4-26, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, LUMC P4-26, PO Box 9600, 2300 RC Leiden, The Netherlands
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32
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Wu HY, Ozdarendeli A, Brian DA. Bovine coronavirus 5'-proximal genomic acceptor hotspot for discontinuous transcription is 65 nucleotides wide. J Virol 2006; 80:2183-93. [PMID: 16474126 PMCID: PMC1395388 DOI: 10.1128/jvi.80.5.2183-2193.2006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 12/08/2005] [Indexed: 01/17/2023] Open
Abstract
Coronaviruses are positive-strand, RNA-dependent RNA polymerase-utilizing viruses that require a polymerase template switch, characterized as discontinuous transcription, to place a 5'-terminal genomic leader onto subgenomic mRNAs (sgmRNAs). The usually precise switch is thought to occur during the synthesis of negative-strand templates for sgmRNA production and to be directed by heptameric core donor sequences within the genome that match an acceptor core (UCUAAAC in the case of bovine coronavirus) near the 3' end of the 5'-terminal genomic leader. Here it is shown that a 22-nucleotide (nt) donor sequence engineered into a packageable bovine coronavirus defective interfering (DI) RNA and made to match a sequence within the 65-nt virus genomic leader caused a template switch yielding an sgmRNA with only a 33-nt minileader. By changing the donor sequence, acceptor sites between genomic nt 33 and 97 (identical between the DI RNA and the viral genome) could be used to generate sgmRNAs detectable by Northern analysis (approximately 2 to 32 molecules per cell) by 24 h postinfection. Whether the switch was intramolecular only was not determined since a potentially distinguishing acceptor region in the DI RNA rapidly conformed to that in the helper virus genome through a previously described template switch known as leader switching. These results show that crossover acceptor sites for discontinuous transcription (i) need not include the UCUAAAC core and (ii) rest within a surprisingly wide 5'-proximal "hotspot." Overlap of this hotspot with that for leader switching and with elements required for RNA replication suggests that it is part of a larger 5'-proximal multifunctional structure.
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Affiliation(s)
- Hung-Yi Wu
- Department of Microbiology, University of Tennessee, College of Veterinary Medicine, Knoxville, 37996-0845, USA
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33
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Gorbalenya AE, Enjuanes L, Ziebuhr J, Snijder EJ. Nidovirales: evolving the largest RNA virus genome. Virus Res 2006; 117:17-37. [PMID: 16503362 PMCID: PMC7114179 DOI: 10.1016/j.virusres.2006.01.017] [Citation(s) in RCA: 640] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Revised: 01/13/2006] [Accepted: 01/18/2006] [Indexed: 11/19/2022]
Abstract
This review focuses on the monophyletic group of animal RNA viruses united in the order Nidovirales. The order includes the distantly related coronaviruses, toroviruses, and roniviruses, which possess the largest known RNA genomes (from 26 to 32 kb) and will therefore be called ‘large’ nidoviruses in this review. They are compared with their arterivirus cousins, which also belong to the Nidovirales despite having a much smaller genome (13–16 kb). Common and unique features that have been identified for either large or all nidoviruses are outlined. These include the nidovirus genetic plan and genome diversity, the composition of the replicase machinery and virus particles, virus-specific accessory genes, the mechanisms of RNA and protein synthesis, and the origin and evolution of nidoviruses with small and large genomes. Nidoviruses employ single-stranded, polycistronic RNA genomes of positive polarity that direct the synthesis of the subunits of the replicative complex, including the RNA-dependent RNA polymerase and helicase. Replicase gene expression is under the principal control of a ribosomal frameshifting signal and a chymotrypsin-like protease, which is assisted by one or more papain-like proteases. A nested set of subgenomic RNAs is synthesized to express the 3′-proximal ORFs that encode most conserved structural proteins and, in some large nidoviruses, also diverse accessory proteins that may promote virus adaptation to specific hosts. The replicase machinery includes a set of RNA-processing enzymes some of which are unique for either all or large nidoviruses. The acquisition of these enzymes may have improved the low fidelity of RNA replication to allow genome expansion and give rise to the ancestors of small and, subsequently, large nidoviruses.
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Affiliation(s)
- Alexander E Gorbalenya
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, LUMC E4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
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34
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Posthuma CC, Nedialkova DD, Zevenhoven-Dobbe JC, Blokhuis JH, Gorbalenya AE, Snijder EJ. Site-directed mutagenesis of the Nidovirus replicative endoribonuclease NendoU exerts pleiotropic effects on the arterivirus life cycle. J Virol 2006; 80:1653-61. [PMID: 16439522 PMCID: PMC1367138 DOI: 10.1128/jvi.80.4.1653-1661.2006] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2005] [Accepted: 12/02/2005] [Indexed: 11/20/2022] Open
Abstract
The highly conserved NendoU replicative domain of nidoviruses (arteriviruses, coronaviruses, and roniviruses) belongs to a small protein family whose cellular branch is prototyped by XendoU, a Xenopus laevis endoribonuclease involved in nucleolar RNA processing. Recently, sequence-specific in vitro endoribonuclease activity was demonstrated for the NendoU-containing nonstructural protein (nsp) 15 of several coronaviruses. To investigate the biological role of this novel enzymatic activity, we have characterized a comprehensive set of arterivirus NendoU mutants. Deleting parts of the NendoU domain from nsp11 of equine arteritis virus was lethal. Site-directed mutagenesis of conserved residues exerted pleiotropic effects. In a first-cycle analysis, replacement of two conserved Asp residues in the C-terminal part of NendoU rendered viral RNA synthesis and virus production undetectable. In contrast, mutagenesis of other conserved residues, including two putative catalytic His residues that are absolutely conserved in NendoU and cellular homologs, produced viable mutants displaying reduced plaque sizes (20 to 80% reduction) and reduced yields of infectious progeny of up to 5 log units. A more detailed analysis of these mutants revealed a moderate reduction in RNA synthesis, with subgenomic RNA synthesis consistently being more strongly affected than genome replication. Our data suggest that the arterivirus nsp11 is a multifunctional protein with a key role in viral RNA synthesis and additional functions in the viral life cycle that are as yet poorly defined.
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Affiliation(s)
- Clara C Posthuma
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, LUMC P4-26, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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35
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Sittidilokratna N, Phetchampai N, Boonsaeng V, Walker PJ. Structural and antigenic analysis of the yellow head virus nucleocapsid protein p20. Virus Res 2005; 116:21-9. [PMID: 16213055 PMCID: PMC7172242 DOI: 10.1016/j.virusres.2005.08.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Revised: 05/27/2005] [Accepted: 08/18/2005] [Indexed: 12/25/2022]
Abstract
Yellow head virus (YHV) is an invertebrate nidovirus that is highly pathogenic for marine shrimp. Nucleotide sequence analysis indicated that the YHV ORF2 gene encodes a basic protein (pI = 9.9) of 146 amino acids with a predicted molecular weight of 16,325.5 Da. The deduced amino acid sequence indicated a predominance of basic (15.1%), acidic (9.6%) and hydrophilic polar (34.3%) residues and a high proportion proline and glycine residues (16.4%). The ORF2 gene was cloned and expressed in Escherichia coli as a Mr = 21 kDa His6-protein that reacted with YHV nucleoprotein (p20) monoclonal antibody. Segments representing the four linear quadrants of the nucleoprotein were also expressed in E. coli as GST-fusion proteins. Immunoblot analysis using YHV polyclonal rabbit antiserum indicated the presence of linear epitopes in all except the V37–Q74 quadrant. Immunoblot analysis of the GST-fusion proteins and C-terminally truncated segments of the nucleoprotein allowed mapping of YHV monoclonal antibodies Y19, Y20 and YII4 to linear epitopes in the acidic domain between amino acids I116 and E137. The full-length nucleoprotein was expressed at high level in E. coli and was easily purified in quantity from the soluble cell fraction by Ni+-NTA affinity chromatography.
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Affiliation(s)
- Nusra Sittidilokratna
- National Center for Genetic Engineering and Biotechnology, BIOTEC, National Science and Technology Development Agency, NSTDA, Phathumthani 12120, Thailand.
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36
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Wu WH, Fang Y, Rowland RR, Lawson SR, Christopher-Hennings J, Yoon KJ, Nelson EA. The 2b protein as a minor structural component of PRRSV. Virus Res 2005; 114:177-81. [PMID: 16095746 PMCID: PMC7127422 DOI: 10.1016/j.virusres.2005.06.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Revised: 06/27/2005] [Accepted: 06/27/2005] [Indexed: 12/03/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) ORF2 contains an internal ORF that codes for a small non-glycosylated protein known as 2b. Previous work had identified the presence of a 10 kDa 2b protein in virus-infected cells and the induction of an anti-2b response in PRRSV-infected pigs, as well as a possible association of 2b with the virion (Wu et al., 2001, Virology 287:183–191). In this study, we utilized two experimental approaches, including the use of a 2b peptide-specific monoclonal antibody, to demonstrate that the PRRSV 2b protein is an integral component of the PRRSV virion. This study suggests that 2b in PRRSV is similar to the E protein in EAV and forms a minor structural component of the virion.
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Affiliation(s)
- Wai-Hong Wu
- Department of Veterinary Science, South Dakota State University, Box 2175, Brookings, SD 57007, USA
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Ying Fang
- Department of Veterinary Science, South Dakota State University, Box 2175, Brookings, SD 57007, USA
| | - Raymond R.R. Rowland
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
| | - Steven R. Lawson
- Department of Veterinary Science, South Dakota State University, Box 2175, Brookings, SD 57007, USA
| | | | - Kyoung-Jin Yoon
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Eric A. Nelson
- Department of Veterinary Science, South Dakota State University, Box 2175, Brookings, SD 57007, USA
- Corresponding author. Tel.: +1 605 688 5653; fax: +1 605 688 6003.
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Smits SL, van Vliet ALW, Segeren K, el Azzouzi H, van Essen M, de Groot RJ. Torovirus non-discontinuous transcription: mutational analysis of a subgenomic mRNA promoter. J Virol 2005; 79:8275-81. [PMID: 15956573 PMCID: PMC1143767 DOI: 10.1128/jvi.79.13.8275-8281.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Accepted: 03/08/2005] [Indexed: 11/20/2022] Open
Abstract
Toroviruses (order Nidovirales) are enveloped positive-strand RNA viruses of mammals. The prototype torovirus, equine torovirus strain Berne (Berne virus [BEV]), uses two different transcription strategies to produce a 3'-coterminal nested set of subgenomic (sg) mRNAs. Its mRNA 2 carries a leader sequence derived from the 5' end of the genome and is produced via discontinuous transcription. The remaining three sg mRNAs, 3 to 5, are colinear with the 3' end of the genome and are made via non-discontinuous RNA synthesis. Their synthesis is supposedly regulated by short conserved sequence motifs, 5'-ACN3-4CUUUAGA-3', within the noncoding intergenic regions that precede the M, HE, and N genes (A. L. van Vliet, S. L. Smits, P. J. Rottier, and R. J. de Groot, EMBO J. 21:6571-6580, 2002). We have now studied the--for nidoviruses unusual--non-discontinuous transcription mechanism in further detail by probing the role of the postulated transcription-regulating sequences (TRSs). To this end, we constructed a synthetic defective interfering (DI) RNA, carrying a 24-nucleotide segment of the intergenic region between the HE and N genes. We demonstrate that this DI RNA, when introduced into BEV-infected cells, directs the synthesis of a sg DI RNA species; in fact, a 16-nucleotide cassette containing the TRS already proved sufficient. Synthesis of this sg DI RNA, like that of mRNAs 3 to 5 of the standard virus, initiated at the 5'-most adenylate of the TRS. An extensive mutational analysis of the TRS is presented. Our results provide first and formal experimental evidence that the conserved motifs within the BEV intergenic sequences indeed drive sg RNA synthesis.
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Affiliation(s)
- Saskia L Smits
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
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38
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van den Born E, Posthuma CC, Gultyaev AP, Snijder EJ. Discontinuous subgenomic RNA synthesis in arteriviruses is guided by an RNA hairpin structure located in the genomic leader region. J Virol 2005; 79:6312-24. [PMID: 15858015 PMCID: PMC1091703 DOI: 10.1128/jvi.79.10.6312-6324.2005] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Accepted: 12/28/2004] [Indexed: 11/20/2022] Open
Abstract
Nidoviruses produce an extensive 3'-coterminal nested set of subgenomic (sg) mRNAs, which are used to express structural proteins and sometimes accessory proteins. In arteriviruses and coronaviruses, these mRNAs contain a common 5' leader sequence, derived from the genomic 5' end. The joining of the leader sequence to different segments derived from the 3'-proximal part of the genome (mRNA bodies) presumably involves a unique mechanism of discontinuous minus-strand RNA synthesis in which base pairing between sense and antisense transcription-regulating sequences (TRSs) plays an essential role. The leader TRS is present in the loop of a hairpin structure that functions in sg mRNA synthesis. In this study, the minimal sequences in the 5'-proximal region of the Equine arteritis virus genome that are required for sg RNA synthesis were delimited through mutagenesis. A full-length cDNA clone was engineered in which this domain was duplicated, allowing us to make mutations and monitor their effects on sg RNA synthesis without seriously affecting genome replication and translation. The leader TRS present in the duplicated sequence was used and yielded novel sg mRNAs with significantly extended leaders. Our combined findings suggest that the leader TRS hairpin (LTH) and its immediate flanking sequences are essential for efficient sg RNA synthesis and form an independent functional entity that could be moved 300 nucleotides downstream of its original position in the genome. We hypothesize that a conformational switch in the LTH region regulates the role of the 5'-proximal region of the arterivirus genome in subgenomic RNA synthesis.
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Affiliation(s)
- Erwin van den Born
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, LUMC P4-26, PO Box 9600, 2300 RC Leiden, The Netherlands
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39
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Cowley JA, Cadogan LC, Spann KM, Sittidilokratna N, Walker PJ. The gene encoding the nucleocapsid protein of Gill-associated nidovirus of Penaeus monodon prawns is located upstream of the glycoprotein gene. J Virol 2004; 78:8935-41. [PMID: 15280504 PMCID: PMC479087 DOI: 10.1128/jvi.78.16.8935-8941.2004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The ORF2 gene of Gill-associated virus (GAV) of Penaeus monodon prawns resides 93 nucleotides downstream of the ORF1a-ORF1b gene and encodes a 144-amino-acid hydrophilic polypeptide (15,998 Da; pI, 9.75) containing 20 basic (14%) and 13 acidic (9%) residues and 19 prolines (13%). Antiserum to a synthetic ORF2 peptide or an Escherichia coli-expressed glutathione S-transferase-ORF2 fusion protein detected a 20-kDa protein in infected lymphoid organ and gill tissues in Western blots. The GAV ORF2 fusion protein antiserum also cross-reacted with the p20 nucleoprotein in virions of the closely related Yellow head virus. By immuno-gold electron microscopy, it was observed that the ORF2 peptide antibody localized to tubular GAV nucleocapsids, often at the ends or at lateral cross sections. As GAV appears to contain only two structural protein genes (ORF2 and ORF3), these data indicate that GAV differs from vertebrate nidoviruses in that the gene encoding the nucleocapsid protein is located upstream of the gene encoding the virion glycoproteins.
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Affiliation(s)
- Jeff A Cowley
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia 4067, Australia.
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Pasternak AO, Spaan WJM, Snijder EJ. Regulation of relative abundance of arterivirus subgenomic mRNAs. J Virol 2004; 78:8102-13. [PMID: 15254182 PMCID: PMC446141 DOI: 10.1128/jvi.78.15.8102-8113.2004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Accepted: 03/22/2004] [Indexed: 11/20/2022] Open
Abstract
The subgenomic (sg) mRNAs of arteriviruses (order Nidovirales) form a 5'- and 3'-coterminal nested set with the viral genome. Their 5' common leader sequence is derived from the genomic 5'-proximal region. Fusion of sg RNA leader and "body" segments involves a discontinuous transcription step. Presumably during minus-strand synthesis, the nascent RNA strand is transferred from one site in the genomic template to another, a process guided by conserved transcription-regulating sequences (TRSs) at these template sites. Subgenomic RNA species are produced in different but constant molar ratios, with the smallest RNAs usually being most abundant. Factors thought to influence sg RNA synthesis are size differences between sg RNA species, differences in sequence context between body TRSs, and the mutual influence (or competition) between strand transfer reactions occurring at different body TRSs. Using an Equine arteritis virus infectious cDNA clone, we investigated how body TRS activity affected sg RNA synthesis from neighboring body TRSs. Flanking sequences were standardized by head-to-tail insertion of several copies of an RNA7 body TRS cassette. A perfect gradient of sg RNA abundance, progressively favoring smaller RNA species, was observed. Disruption of body TRS function by mutagenesis did not have a significant effect on the activity of other TRSs. However, deletion of body TRS-containing regions enhanced synthesis of sg RNAs from upstream TRSs but not of those produced from downstream TRSs. The results of this study provide considerable support for the proposed discontinuous extension of minus-strand RNA synthesis as a crucial step in sg RNA synthesis.
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Affiliation(s)
- Alexander O Pasternak
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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Van Den Born E, Gultyaev AP, Snijder EJ. Secondary structure and function of the 5'-proximal region of the equine arteritis virus RNA genome. RNA (NEW YORK, N.Y.) 2004; 10:424-37. [PMID: 14970388 PMCID: PMC1370938 DOI: 10.1261/rna.5174804] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2003] [Accepted: 11/20/2003] [Indexed: 05/21/2023]
Abstract
Nidoviruses produce an extensive 3'-coterminal nested set of subgenomic mRNAs, which are used to express their structural proteins. In addition, arterivirus and coronavirus mRNAs contain a common 5' leader sequence, derived from the genomic 5' end. The joining of this leader sequence to different segments (mRNA bodies) from the genomic 3'-proximal region presumably involves a unique mechanism of discontinuous minus-strand RNA synthesis. Key elements in this process are the so-called transcription-regulating sequences (TRSs), which determine a base-pairing interaction between sense and antisense viral RNA that is essential for leader-to-body joining. To identify RNA structures in the 5'-proximal region of the equine arteritis virus genome that may be involved in subgenomic mRNA synthesis, a detailed secondary RNA structure model was established using bioinformatics, phylogenetic analysis, and RNA structure probing. According to this structure model, the leader TRS is located in the loop of a prominent hairpin (leader TRS hairpin; LTH). The importance of the LTH was supported by the results of a mutagenesis study using an EAV molecular clone. Besides evidence for a direct role of the LTH in subgenomic RNA synthesis, indications for a role of the LTH region in genome replication and/or translation were obtained. Similar LTH structures could be predicted for the 5'-proximal region of all arterivirus genomes and, interestingly, also for most coronaviruses. Thus, we postulate that the LTH is a key structural element in the discontinuous subgenomic RNA synthesis and is likely critical for leader TRS function.
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Affiliation(s)
- Erwin Van Den Born
- Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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Wieringa R, De Vries AAF, Post SM, Rottier PJM. Intra- and intermolecular disulfide bonds of the GP2b glycoprotein of equine arteritis virus: relevance for virus assembly and infectivity. J Virol 2004; 77:12996-3004. [PMID: 14645556 PMCID: PMC296049 DOI: 10.1128/jvi.77.24.12996-13004.2003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Equine arteritis virus (EAV) is an enveloped, positive-strand RNA virus belonging to the family Arteriviridae of the order NIDOVIRALES: EAV virions contain six different envelope proteins. The glycoprotein GP(5) (previously named G(L)) and the unglycosylated membrane protein M are the major envelope proteins, while the glycoproteins GP(2b) (previously named G(S)), GP(3), and GP(4) are minor structural proteins. The unglycosylated small hydrophobic envelope protein E is present in virus particles in intermediate molar amounts compared to the other transmembrane proteins. The GP(5) and M proteins are both essential for particle assembly. They occur as covalently linked heterodimers that constitute the basic protein matrix of the envelope. The GP(2b), GP(3), and GP(4) proteins occur as a heterotrimeric complex in which disulfide bonds play an important role. The function of this complex has not been established yet, but the available data suggest it to be involved in the viral entry process. Here we investigated the role of the four cysteine residues of the mature GP(2b) protein in the assembly of the GP(2b)/GP(3)/GP(4) complex. Open reading frames encoding cysteine-to-serine mutants of the GP(2b) protein were expressed independently or from a full-length infectious EAV cDNA clone. The results of these experiments support a model in which the cysteine residue at position 102 of GP(2b) forms an intermolecular cystine bridge with one of the cysteines of the GP(4) protein, while the cysteine residues at positions 48 and 137 of GP(2b) are linked by an intrachain disulfide bond. In this model, another cysteine residue in the GP(4) protein is responsible for the covalent association of GP(3) with the disulfide-linked GP(2b)/GP(4) heterodimer. In addition, our data highlight the importance of the correct association of the minor EAV envelope glycoproteins for their efficient incorporation into viral particles and for virus infectivity.
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Affiliation(s)
- Roeland Wieringa
- Department of Infectious Diseases and Immunology, Virology Division, Faculty of Veterinary Medicine, and Institute of Biomembranes, Utrecht University, 3584 CL Utrecht, The Netherlands
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Dhar AK, Cowley JA, Hasson KW, Walker PJ. Genomic organization, biology, and diagnosis of Taura syndrome virus and yellowhead virus of penaeid shrimp. Adv Virus Res 2004; 63:353-421. [PMID: 15530565 PMCID: PMC7127055 DOI: 10.1016/s0065-3527(04)63006-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Arun K Dhar
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
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Ayllón MA, Gowda S, Satyanarayana T, Karasev AV, Adkins S, Mawassi M, Guerri J, Moreno P, Dawson WO. Effects of modification of the transcription initiation site context on citrus tristeza virus subgenomic RNA synthesis. J Virol 2003; 77:9232-43. [PMID: 12915539 PMCID: PMC187412 DOI: 10.1128/jvi.77.17.9232-9243.2003] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Citrus tristeza virus (CTV), a member of the Closteroviridae, has a positive-sense RNA genome of about 20 kb organized into 12 open reading frames (ORFs). The last 10 ORFs are expressed through 3'-coterminal subgenomic RNAs (sgRNAs) regulated in both amounts and timing. Additionally, relatively large amounts of complementary sgRNAs are produced. We have been unable to determine whether these sgRNAs are produced by internal promotion from the full-length template minus strand or by transcription from the minus-stranded sgRNAs. Understanding the regulation of 10 sgRNAs is a conceptual challenge. In analyzing commonalities of a replicase complex in producing so many sgRNAs, we examined initiating nucleotides of the sgRNAs. We mapped the 5' termini of intermediate- (CP and p13) and low- (p18) produced sgRNAs that, like the two highly abundant sgRNAs (p20 and p23) previously mapped, all initiate with an adenylate. We then examined modifications of the initiation site, which has been shown to be useful in defining mechanisms of sgRNA synthesis. Surprisingly, mutation of the initiating nucleotide of the CTV sgRNAs did not prevent sgRNA accumulation. Based on our results, the CTV replication complex appears to initiate sgRNA synthesis with purines, preferably with adenylates, and is able to initiate synthesis using a nucleotide a few positions 5' or 3' of the native initiation nucleotide. Furthermore, the context of the initiation site appears to be a regulatory mechanism for levels of sgRNA production. These data do not support either of the established mechanisms for synthesis of sgRNAs, suggesting that CTV sgRNA production utilizes a different mechanism.
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Affiliation(s)
- María A Ayllón
- Department of Plant Pathology, University of Florida, Citrus Research and Education Center, Lake Alfred, Florida 33850, USA
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Ziebuhr J, Bayer S, Cowley JA, Gorbalenya AE. The 3C-like proteinase of an invertebrate nidovirus links coronavirus and potyvirus homologs. J Virol 2003; 77:1415-26. [PMID: 12502857 PMCID: PMC140795 DOI: 10.1128/jvi.77.2.1415-1426.2003] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2002] [Accepted: 10/15/2002] [Indexed: 11/20/2022] Open
Abstract
Gill-associated virus (GAV), a positive-stranded RNA virus of prawns, is the prototype of newly recognized taxa (genus Okavirus, family Roniviridae) within the order NIDOVIRALES: In this study, a putative GAV cysteine proteinase (3C-like proteinase [3CL(pro)]), which is predicted to be the key enzyme involved in processing of the GAV replicase polyprotein precursors, pp1a and pp1ab, was characterized. Comparative sequence analysis indicated that, like its coronavirus homologs, 3CL(pro) has a three-domain organization and is flanked by hydrophobic domains. The putative 3CL(pro) domain including flanking regions (pp1a residues 2793 to 3143) was fused to the Escherichia coli maltose-binding protein (MBP) and, when expressed in E. coli, was found to possess N-terminal autoprocessing activity that was not dependent on the presence of the 3CL(pro) C-terminal domain. N-terminal sequence analysis of the processed protein revealed that cleavage occurred at the location (2827)LVTHE downward arrow VRTGN(2836). The trans-processing activity of the purified recombinant 3CL(pro) (pp1a residues 2832 to 3126) was used to identify another cleavage site, (6441)KVNHE downward arrow LYHVA(6450), in the C-terminal pp1ab region. Taken together, the data tentatively identify VxHE downward arrow (L,V) as the substrate consensus sequence for the GAV 3CL(pro). The study revealed that the GAV and potyvirus 3CL(pro)s possess similar substrate specificities which correlate with structural similarities in their respective substrate-binding sites, identified in sequence comparisons. Analysis of the proteolytic activities of MBP-3CL(pro) fusion proteins carrying replacements of putative active-site residues provided evidence that, in contrast to most other 3C/3CL(pro)s but in common with coronavirus 3CL(pro)s, the GAV 3CL(pro) employs a Cys(2968)-His(2879) catalytic dyad. The properties of the GAV 3CL(pro) define a novel RNA virus proteinase variant that bridges the gap between the distantly related chymotrypsin-like cysteine proteinases of coronaviruses and potyviruses.
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Affiliation(s)
- John Ziebuhr
- Institute of Virology and Immunology, University of Würzburg, Germany.
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van Vliet A, Smits S, Rottier P, de Groot R. Discontinuous and non-discontinuous subgenomic RNA transcription in a nidovirus. EMBO J 2002; 21:6571-80. [PMID: 12456663 PMCID: PMC136939 DOI: 10.1093/emboj/cdf635] [Citation(s) in RCA: 87] [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: 06/26/2002] [Revised: 09/16/2002] [Accepted: 10/09/2002] [Indexed: 12/14/2022] Open
Abstract
Arteri-, corona-, toro- and roniviruses are evolutionarily related positive-strand RNA viruses, united in the order Nidovirales. The best studied nidoviruses, the corona- and arteriviruses, employ a unique transcription mechanism, which involves discontinuous RNA synthesis, a process resembling similarity-assisted copy-choice RNA recombination. During infection, multiple subgenomic (sg) mRNAs are transcribed from a mirror set of sg negative-strand RNA templates. The sg mRNAs all possess a short 5' common leader sequence, derived from the 5' end of the genomic RNA. The joining of the non-contiguous 'leader' and 'body' sequences presumably occurs during minus-strand synthesis. To study whether toroviruses use a similar transcription mechanism, we characterized the 5' termini of the genome and the four sg mRNAs of Berne virus (BEV). We show that BEV mRNAs 3-5 lack a leader sequence. Surprisingly, however, RNA 2 does contain a leader, identical to the 5'-terminal 18 residues of the genome. Apparently, BEV combines discontinuous and non-discontinuous RNA synthesis to produce its sg mRNAs. Our findings have important implications for the understanding of the mechanism and evolution of nidovirus transcription.
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Affiliation(s)
| | | | | | - R.J. de Groot
- Institute of Virology, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
Corresponding author e-mail:
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