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Grant D. Stentiford - One of the best experts on this subject based on the ideXlab platform.
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Identification and Full Characterisation of Two Novel Crustacean Infecting Members of the Family Nudiviridae Provides Support for Two Subfamilies
'MDPI AG', 2021Co-Authors: Kelly S. Bateman, Benigna Van Eynde, Olivier Christiaens, Daan Delbare, Grant D. Stentiford, Chantelle Hooper, Rose Kerr, Tim P. Bean, Jamie Bojko, Clauvis N. T. TaningAbstract:Multiple enveloped viruses with rod-shaped nucleocapsids have been described, infecting the epithelial cell nuclei within the hepatopancreas tubules of crustaceans. These bacilliform viruses share the ultrastructural characteristics of nudiviruses, a specific clade of viruses infecting arthropods. Using histology, electron microscopy and high throughput sequencing, we characterise two further bacilliform viruses from aquatic hosts, the brown shrimp (Crangon crangon) and the European shore crab (Carcinus maenas). We assembled the full double stranded, circular DNA genome sequences of these viruses (~113 and 132 kbp, respectively). Comparative genomics and phylogenetic analyses confirm that both belong within the family Nudiviridae but in separate clades representing nudiviruses found in freshwater and marine environments. We show that the three thymidine kinase (tk) genes present in all sequenced nudivirus genomes, thus far, were absent in the Crangon crangon nudivirus, suggesting there are twenty-eight core genes shared by all nudiviruses. Furthermore, the phylogenetic data no longer support the subdivision of the family Nudiviridae into four genera (Alphanudivirus to Deltanudivirus), as recently adopted by the International Committee on Taxonomy of Viruses (ICTV), but rather shows two main branches of the family that are further subdivided. Our data support a recent proposal to create two subfamilies within the family Nudiviridae, each subdivided into several genera
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The first clawed lobster virus Homarus gammarus nudivirus (HgNV n. sp.) expands the diversity of the Nudiviridae
Scientific Reports, 2019Co-Authors: Corey C. Holt, Carly L. Daniels, David Bass, Kelly S. Bateman, Michelle Stone, Ronny Van Aerle, Mark Van Der Giezen, Stuart H. Ross, Chantelle Hooper, Grant D. StentifordAbstract:Viral diseases of crustaceans are increasingly recognised as challenges to shellfish farms and fisheries. Here we describe the first naturally-occurring virus reported in any clawed lobster species. Hypertrophied nuclei with emarginated chromatin, characteristic histopathological lesions of DNA virus infection, were observed within the hepatopancreatic epithelial cells of juvenile European lobsters ( Homarus gammarus ). Transmission electron microscopy revealed infection with a bacilliform virus containing a rod shaped nucleocapsid enveloped in an elliptical membrane. Assembly of PCR-free shotgun metagenomic sequencing produced a circular genome of 107,063 bp containing 97 open reading frames, the majority of which share sequence similarity with a virus infecting the black tiger shrimp: Penaeus monodon nudivirus (PmNV). Multiple phylogenetic analyses confirm the new virus to be a novel member of the Nudiviridae: Homarus gammarus nudivirus (HgNV). Evidence of occlusion body formation, characteristic of PmNV and its closest relatives, was not observed, questioning the horizontal transmission strategy of HgNV outside of the host. We discuss the potential impacts of HgNV on juvenile lobster growth and mortality and present HgNV-specific primers to serve as a diagnostic tool for monitoring the virus in wild and farmed lobster stocks.
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The first clawed lobster virus Homarus gammarus nudivirus (HgNV n. sp.) expands the diversity of the Nudiviridae
'Springer Science and Business Media LLC', 2019Co-Authors: Cc Holt, Stone M, Bass D, Ks Bateman, Van Aerle R, Cl Daniels, Van Der Giezen M, Sh Ross, Hooper C, Grant D. StentifordAbstract:This is the final version. Available from Nature Research via the DOI in this record. Viral diseases of crustaceans are increasingly recognised as challenges to shellfish farms and fisheries. Here we describe the first naturally-occurring virus reported in any clawed lobster species. Hypertrophied nuclei with emarginated chromatin, characteristic histopathological lesions of DNA virus infection, were observed within the hepatopancreatic epithelial cells of juvenile European lobsters (Homarus gammarus). Transmission electron microscopy revealed infection with a bacilliform virus containing a rod shaped nucleocapsid enveloped in an elliptical membrane. Assembly of PCR-free shotgun metagenomic sequencing produced a circular genome of 107,063 bp containing 97 open reading frames, the majority of which share sequence similarity with a virus infecting the black tiger shrimp: Penaeus monodon nudivirus (PmNV). Multiple phylogenetic analyses confirm the new virus to be a novel member of the Nudiviridae: Homarus gammarus nudivirus (HgNV). Evidence of occlusion body formation, characteristic of PmNV and its closest relatives, was not observed, questioning the horizontal transmission strategy of HgNV outside of the host. We discuss the potential impacts of HgNV on juvenile lobster growth and mortality and present HgNV-specific primers to serve as a diagnostic tool for monitoring the virus in wild and farmed lobster stocks.Centre for Environment, Fisheries and Aquaculture Science (CEFAS)Innovate UKBBSR
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Development and application of a duplex PCR assay for detection of Crangon crangon bacilliform virus in populations of European brown shrimp (Crangon crangon).
Journal of invertebrate pathology, 2018Co-Authors: Benigna Van Eynde, Olivier Christiaens, Daan Delbare, K. Cooreman, Kelly S. Bateman, Grant D. Stentiford, Annette M. Dullemans, Monique M. Van Oers, Guy SmaggheAbstract:Abstract Crangon crangon bacilliform virus (CcBV) was first discovered in 2004 in European brown shrimp (Crangon crangon) caught along the English coast. This study describes a duplex PCR assay developed for the detection of CcBV, based on amplification of the lef-8 gene (211 bp) of CcBV and the E75 gene (105 bp) of C. crangon as an internal amplification control. The lef-8 and E75 primer pairs were designed based on preliminary genome sequencing information of the virus and transcriptomic data available for C. crangon, respectively. Sequencing of the resulting amplicons confirmed the specificity of this PCR assay and sequence analysis of the lef-8 fragment revealed amino acid identity percentages ranging between 31 and 42% with members of the Nudiviridae, proposing that CcBV may reside within this family. Finally, the duplex PCR assay was applied to samples of C. crangon hepatopancreas tissue collected along the Belgian coast to screen for the presence of CcBV. The prevalence of CcBV averaged 87%, which is comparable to previous reports of high prevalence, based upon histological analysis, in shrimp collected along the English coast. Development of a specific and sensitive PCR assay to detect CcBV will provide a useful tool for future aquaculture and research programs involving C. crangon.
Valérie Campanacci - One of the best experts on this subject based on the ideXlab platform.
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ORF157 from the Archaeal Virus Acidianus Filamentous Virus 1 Defines a New Class of Nuclease
Journal of virology, 2010Co-Authors: Adeline Goulet, Nicolas Leulliot, H. Van Tilbeurgh, Peter Redder, Mery Pina, Laura Vera, Julie Lichière, Miguel Ortiz-lombardía, Valérie CampanacciAbstract:The properties of double-stranded DNA (dsDNA) viruses that infect Crenarchaea living in acidic hot springs (pH 1.5 to 3 and 75 to 95°C) are radically different from those of the viruses that infect Bacteria and Eukarya. Not only are the shapes of these viruses distinct from those of all other known viruses, but ∼80% of their open reading frames (ORFs) do not share any sequence similarity with ORFs of other viruses or of cellular life forms apart from other archaeal viruses (44). Seven novel viral families have been created to categorize their unique characteristics: the spindle-shaped Fuselloviridae, the filamentous Rudiviridae and Lipothrixviridae, the bottle-shaped Ampullaviridae, the droplet-shaped Guttaviridae, the spherical Globuloviridae, the two-tailed Bicaudaviridae, and the unclassified Sulfolobus turreted icosahedral virus (STIV) (43). The study of archaeal viruses is still in its infancy compared to that of eukaryal and bacterial viruses, and little is known regarding crenarchaeal virus life cycles, virus-host relationships, genetics, or biochemistry. Further studies of these viruses are expected to provide genetic, biochemical, and evolutionary insight into their crenarchaeal hosts and the requirements for life in the harsh environments. Transcription cycles of the fusellovirus Sulfolobus spindle-shaped virus 1 (SSV1) (16) and the rudiviruses Sulfolobus islandicus rod-shaped virus 1 and 2 (SIRV1 and SIRV2) (24) have been analyzed. Also, recent results concerning the lytic viruses STIV and SIRV2 shed new light on their replication cycle and interaction with their hosts (7, 9, 38). Because structures generally are much better conserved than sequences, structural studies have aimed at uncovering functional and evolutionary relationships that are not apparent from the primary sequence. To date, 11 protein structures from crenarchaeal viruses have been reported (18, 19, 22, 23, 25-30, 33). Most of these proteins share structural similarity with proteins of known function: three winged-helix proteins are likely involved in transcriptional regulation (two from the fusellovirus SSV1 [27, 33] and one from STIV [28]); one glycosyltransferase from STIV displays the GT-A fold (30); one adaptor protein from SSV1 is similar to the repressor of primer (ROP) of Escherichia coli (26); and the major coat protein of STIV has revealed the first evolutionary relationship spanning the three domains of life (25). The structures of the highly conserved ORFs among these viruses, ORF109 of lipothrixvirus AFV3 (22) and ORFB116 from STIV (29), suggest that they are DNA-binding proteins that function in transcriptional regulation. Filamentous viruses, the most abundant morphotype in these extreme environments, form the new viral order Ligamenvirales, which is divided into the Rudiviridae and Lipothrixviridae families (43). Lipothrixviruses (Acidianus filamentous virus 1 to 9, Thermoproteus tenax virus 1 to 3, and Sulfolobus islandicus filamentous virus) (8, 43), which were the first enveloped filamentous viruses with linear dsDNA genomes discovered, infect acidophilic and hyperthermophilic Crenarchaea. They are classified into α, β, γ, and δ genera based on their genomic properties and on the diversity of their terminal appendages, which are involved in host cell recognition. AFV1 is a γ-lipothrixvirus isolated from an acidic hot spring in Yellowstone National Park, where the temperature is above 85°C and the pH below 3 (6). The linear, double-stranded 20.8-kb DNA genome of AFV1 encodes 40 putative ORFs, 32% of which are homologous to viral ORFs from the lipothrixvirus SIFV and the rudiviruses SIRV1 and SIRV2. The predicted products generally are too dissimilar to the sequences in the public databases to allow functional assignment; only two glycosyltransferases, two CopG-like proteins, and one transcription regulator have been detected (6). It is highly unlikely that all of the encoded proteins consist entirely of unique protein folds serving novel functions. Therefore, to get insight into the biology of the Lipothrixviridae, we performed crystallographic studies of the AFV1 proteome. Although the solved structures of AFV1-102 (23) and the homologs AFV1-99 (19) and SIFV-014 (18) have not revealed any structural homologs, they have suggested that the proteins are involved in protein-protein interaction and are minor structural components, respectively. Here, we report the crystal structure of AFV1-157 and its biochemical characterization. AFV1-157 is a 157-residue protein with one homolog in the fusellovirus Sulfolobus spindle-shaped virus Ragged Hills (SSVRH). It has a novel α+β fold that remotely resembles the nucleotidyltransferase topology. We demonstrated that (i) AFV1-157 exhibits in vitro nuclease activity that degrades linear dsDNA, and (ii) the E86 residue is essential for the nuclease activity.
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Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage.
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Adeline Goulet, Stéphanie Blangy, Valérie Campanacci, Peter Redder, Catarina Felisberto-rodrigues, Patrick Forterre, Christian CambillauAbstract:Acidianus filamentous virus 1 (AFV1), a member of the Lipothrixviridae family, infects the hyperthermophilic, acidophilic crenarchaeaon Acidianus hospitalis. The virion, covered with a lipidic outer shell, is 9,100-A long and contains a 20.8-kb linear dsDNA genome. We have identified the two major coat proteins of the virion (MCPs; 132 and 140 amino acids). They bind DNA and form filaments when incubated with linear dsDNA. A C-terminal domain is identified in their crystal structure with a four-helix-bundle fold. In the topological model of the virion filament core, the genomic dsDNA superhelix wraps around the AFV1-132 basic protein, and the AFV1-140 basic N terminus binds genomic DNA, while its lipophilic C-terminal domain is imbedded in the lipidic outer shell. The four-helix bundle fold of the MCPs from AFV1 is identical to that of the coat protein (CP) of Sulfolobus islandicus rod-shaped virus (SIRV), a member of the Rudiviridae family. Despite low sequence identity between these proteins, their high degree of structural similarity suggests that they could have derived from a common ancestor and could thus define an yet undescribed viral lineage.
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Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses
Virology Journal, 2007Co-Authors: Jenny Keller, Christian Cambillau, Valérie Campanacci, Patrick Forterre, Stéphanie Porciero, Diego Cortez, Sophie Quevillon-cheruelAbstract:The extraordinary morphologies of viruses infecting hyperthermophilic archaea clearly distinguish them from bacterial and eukaryotic viruses. Moreover, their genomes code for proteins that to a large extend have no related sequences in the extent databases. However, a small pool of genes is shared by overlapping subsets of these viruses, and the most conserved gene, exemplified by the ORF109 of the Acidianus Filamentous Virus 3, AFV3, is present on genomes of members of three viral familes, the Lipothrixviridae, Rudiviridae , and "Bicaudaviridae" , as well as of the unclassified Sulfolobus Turreted Icosahedral Virus, STIV. We present here the crystal structure of the protein (Mr = 13.1 kD, 109 residues) encoded by the AFV3 ORF 109 in two different crystal forms at 1.5 and 1.3 Å resolution. The structure of AFV3-109 is a five stranded β-sheet with loops on one side and three helices on the other. It forms a dimer adopting the shape of a cradle that encompasses the best conserved regions of the sequence. No protein with a related fold could be identified except for the ortholog from STIV1, whose structure was deposited at the Protein Data Bank. We could clearly identify a well bound glycerol inside the cradle, contacting exclusively totally conserved residues. This interaction was confirmed in solution by fluorescence titration. Although the function of AFV3-109 cannot be deduced directly from its structure, structural homology with the STIV1 protein, and the size and charge distribution of the cavity suggested it could interact with nucleic acids. Fluorescence quenching titrations also showed that AFV3-109 interacts with dsDNA. Genomic sequence analysis revealed bacterial homologs of AFV3-109 as a part of a putative previously unidentified prophage sequences in some Firmicutes.
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Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses.
Virology, 2007Co-Authors: Jenny Keller, Christian Cambillau, Valérie Campanacci, Patrick Forterre, Stéphanie Porciero, Diego Cortez, Sophie Quevillon-cheruelAbstract:The extraordinary morphologies of viruses infecting hyperthermophilic archaea clearly distinguish them from bacterial and eukaryotic viruses. Moreover, their genomes code for proteins that to a large extend have no related sequences in the extent databases. However, a small pool of genes is shared by overlapping subsets of these viruses, and the most conserved gene, exemplified by the ORF109 of the Acidianus Filamentous Virus 3, AFV3, is present on genomes of members of three viral familes, the Lipothrixviridae, Rudiviridae, and "Bicaudaviridae", as well as of the unclassified Sulfolobus Turreted Icosahedral Virus, STIV. We present here the crystal structure of the protein (Mr = 13.1 kD, 109 residues) encoded by the AFV3 ORF 109 in two different crystal forms at 1.5 and 1.3 A resolution. The structure of AFV3-109 is a five stranded beta-sheet with loops on one side and three helices on the other. It forms a dimer adopting the shape of a cradle that encompasses the best conserved regions of the sequence. No protein with a related fold could be identified except for the ortholog from STIV1, whose structure was deposited at the Protein Data Bank. We could clearly identify a well bound glycerol inside the cradle, contacting exclusively totally conserved residues. This interaction was confirmed in solution by fluorescence titration. Although the function of AFV3-109 cannot be deduced directly from its structure, structural homology with the STIV1 protein, and the size and charge distribution of the cavity suggested it could interact with nucleic acids. Fluorescence quenching titrations also showed that AFV3-109 interacts with dsDNA. Genomic sequence analysis revealed bacterial homologs of AFV3-109 as a part of a putative previously unidentified prophage sequences in some Firmicutes.
Christian Cambillau - One of the best experts on this subject based on the ideXlab platform.
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Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage.
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Adeline Goulet, Stéphanie Blangy, Valérie Campanacci, Peter Redder, Catarina Felisberto-rodrigues, Patrick Forterre, Christian CambillauAbstract:Acidianus filamentous virus 1 (AFV1), a member of the Lipothrixviridae family, infects the hyperthermophilic, acidophilic crenarchaeaon Acidianus hospitalis. The virion, covered with a lipidic outer shell, is 9,100-A long and contains a 20.8-kb linear dsDNA genome. We have identified the two major coat proteins of the virion (MCPs; 132 and 140 amino acids). They bind DNA and form filaments when incubated with linear dsDNA. A C-terminal domain is identified in their crystal structure with a four-helix-bundle fold. In the topological model of the virion filament core, the genomic dsDNA superhelix wraps around the AFV1-132 basic protein, and the AFV1-140 basic N terminus binds genomic DNA, while its lipophilic C-terminal domain is imbedded in the lipidic outer shell. The four-helix bundle fold of the MCPs from AFV1 is identical to that of the coat protein (CP) of Sulfolobus islandicus rod-shaped virus (SIRV), a member of the Rudiviridae family. Despite low sequence identity between these proteins, their high degree of structural similarity suggests that they could have derived from a common ancestor and could thus define an yet undescribed viral lineage.
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Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses
Virology Journal, 2007Co-Authors: Jenny Keller, Christian Cambillau, Valérie Campanacci, Patrick Forterre, Stéphanie Porciero, Diego Cortez, Sophie Quevillon-cheruelAbstract:The extraordinary morphologies of viruses infecting hyperthermophilic archaea clearly distinguish them from bacterial and eukaryotic viruses. Moreover, their genomes code for proteins that to a large extend have no related sequences in the extent databases. However, a small pool of genes is shared by overlapping subsets of these viruses, and the most conserved gene, exemplified by the ORF109 of the Acidianus Filamentous Virus 3, AFV3, is present on genomes of members of three viral familes, the Lipothrixviridae, Rudiviridae , and "Bicaudaviridae" , as well as of the unclassified Sulfolobus Turreted Icosahedral Virus, STIV. We present here the crystal structure of the protein (Mr = 13.1 kD, 109 residues) encoded by the AFV3 ORF 109 in two different crystal forms at 1.5 and 1.3 Å resolution. The structure of AFV3-109 is a five stranded β-sheet with loops on one side and three helices on the other. It forms a dimer adopting the shape of a cradle that encompasses the best conserved regions of the sequence. No protein with a related fold could be identified except for the ortholog from STIV1, whose structure was deposited at the Protein Data Bank. We could clearly identify a well bound glycerol inside the cradle, contacting exclusively totally conserved residues. This interaction was confirmed in solution by fluorescence titration. Although the function of AFV3-109 cannot be deduced directly from its structure, structural homology with the STIV1 protein, and the size and charge distribution of the cavity suggested it could interact with nucleic acids. Fluorescence quenching titrations also showed that AFV3-109 interacts with dsDNA. Genomic sequence analysis revealed bacterial homologs of AFV3-109 as a part of a putative previously unidentified prophage sequences in some Firmicutes.
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Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses.
Virology, 2007Co-Authors: Jenny Keller, Christian Cambillau, Valérie Campanacci, Patrick Forterre, Stéphanie Porciero, Diego Cortez, Sophie Quevillon-cheruelAbstract:The extraordinary morphologies of viruses infecting hyperthermophilic archaea clearly distinguish them from bacterial and eukaryotic viruses. Moreover, their genomes code for proteins that to a large extend have no related sequences in the extent databases. However, a small pool of genes is shared by overlapping subsets of these viruses, and the most conserved gene, exemplified by the ORF109 of the Acidianus Filamentous Virus 3, AFV3, is present on genomes of members of three viral familes, the Lipothrixviridae, Rudiviridae, and "Bicaudaviridae", as well as of the unclassified Sulfolobus Turreted Icosahedral Virus, STIV. We present here the crystal structure of the protein (Mr = 13.1 kD, 109 residues) encoded by the AFV3 ORF 109 in two different crystal forms at 1.5 and 1.3 A resolution. The structure of AFV3-109 is a five stranded beta-sheet with loops on one side and three helices on the other. It forms a dimer adopting the shape of a cradle that encompasses the best conserved regions of the sequence. No protein with a related fold could be identified except for the ortholog from STIV1, whose structure was deposited at the Protein Data Bank. We could clearly identify a well bound glycerol inside the cradle, contacting exclusively totally conserved residues. This interaction was confirmed in solution by fluorescence titration. Although the function of AFV3-109 cannot be deduced directly from its structure, structural homology with the STIV1 protein, and the size and charge distribution of the cavity suggested it could interact with nucleic acids. Fluorescence quenching titrations also showed that AFV3-109 interacts with dsDNA. Genomic sequence analysis revealed bacterial homologs of AFV3-109 as a part of a putative previously unidentified prophage sequences in some Firmicutes.
Adeline Goulet - One of the best experts on this subject based on the ideXlab platform.
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ORF157 from the Archaeal Virus Acidianus Filamentous Virus 1 Defines a New Class of Nuclease
Journal of virology, 2010Co-Authors: Adeline Goulet, Nicolas Leulliot, H. Van Tilbeurgh, Peter Redder, Mery Pina, Laura Vera, Julie Lichière, Miguel Ortiz-lombardía, Valérie CampanacciAbstract:The properties of double-stranded DNA (dsDNA) viruses that infect Crenarchaea living in acidic hot springs (pH 1.5 to 3 and 75 to 95°C) are radically different from those of the viruses that infect Bacteria and Eukarya. Not only are the shapes of these viruses distinct from those of all other known viruses, but ∼80% of their open reading frames (ORFs) do not share any sequence similarity with ORFs of other viruses or of cellular life forms apart from other archaeal viruses (44). Seven novel viral families have been created to categorize their unique characteristics: the spindle-shaped Fuselloviridae, the filamentous Rudiviridae and Lipothrixviridae, the bottle-shaped Ampullaviridae, the droplet-shaped Guttaviridae, the spherical Globuloviridae, the two-tailed Bicaudaviridae, and the unclassified Sulfolobus turreted icosahedral virus (STIV) (43). The study of archaeal viruses is still in its infancy compared to that of eukaryal and bacterial viruses, and little is known regarding crenarchaeal virus life cycles, virus-host relationships, genetics, or biochemistry. Further studies of these viruses are expected to provide genetic, biochemical, and evolutionary insight into their crenarchaeal hosts and the requirements for life in the harsh environments. Transcription cycles of the fusellovirus Sulfolobus spindle-shaped virus 1 (SSV1) (16) and the rudiviruses Sulfolobus islandicus rod-shaped virus 1 and 2 (SIRV1 and SIRV2) (24) have been analyzed. Also, recent results concerning the lytic viruses STIV and SIRV2 shed new light on their replication cycle and interaction with their hosts (7, 9, 38). Because structures generally are much better conserved than sequences, structural studies have aimed at uncovering functional and evolutionary relationships that are not apparent from the primary sequence. To date, 11 protein structures from crenarchaeal viruses have been reported (18, 19, 22, 23, 25-30, 33). Most of these proteins share structural similarity with proteins of known function: three winged-helix proteins are likely involved in transcriptional regulation (two from the fusellovirus SSV1 [27, 33] and one from STIV [28]); one glycosyltransferase from STIV displays the GT-A fold (30); one adaptor protein from SSV1 is similar to the repressor of primer (ROP) of Escherichia coli (26); and the major coat protein of STIV has revealed the first evolutionary relationship spanning the three domains of life (25). The structures of the highly conserved ORFs among these viruses, ORF109 of lipothrixvirus AFV3 (22) and ORFB116 from STIV (29), suggest that they are DNA-binding proteins that function in transcriptional regulation. Filamentous viruses, the most abundant morphotype in these extreme environments, form the new viral order Ligamenvirales, which is divided into the Rudiviridae and Lipothrixviridae families (43). Lipothrixviruses (Acidianus filamentous virus 1 to 9, Thermoproteus tenax virus 1 to 3, and Sulfolobus islandicus filamentous virus) (8, 43), which were the first enveloped filamentous viruses with linear dsDNA genomes discovered, infect acidophilic and hyperthermophilic Crenarchaea. They are classified into α, β, γ, and δ genera based on their genomic properties and on the diversity of their terminal appendages, which are involved in host cell recognition. AFV1 is a γ-lipothrixvirus isolated from an acidic hot spring in Yellowstone National Park, where the temperature is above 85°C and the pH below 3 (6). The linear, double-stranded 20.8-kb DNA genome of AFV1 encodes 40 putative ORFs, 32% of which are homologous to viral ORFs from the lipothrixvirus SIFV and the rudiviruses SIRV1 and SIRV2. The predicted products generally are too dissimilar to the sequences in the public databases to allow functional assignment; only two glycosyltransferases, two CopG-like proteins, and one transcription regulator have been detected (6). It is highly unlikely that all of the encoded proteins consist entirely of unique protein folds serving novel functions. Therefore, to get insight into the biology of the Lipothrixviridae, we performed crystallographic studies of the AFV1 proteome. Although the solved structures of AFV1-102 (23) and the homologs AFV1-99 (19) and SIFV-014 (18) have not revealed any structural homologs, they have suggested that the proteins are involved in protein-protein interaction and are minor structural components, respectively. Here, we report the crystal structure of AFV1-157 and its biochemical characterization. AFV1-157 is a 157-residue protein with one homolog in the fusellovirus Sulfolobus spindle-shaped virus Ragged Hills (SSVRH). It has a novel α+β fold that remotely resembles the nucleotidyltransferase topology. We demonstrated that (i) AFV1-157 exhibits in vitro nuclease activity that degrades linear dsDNA, and (ii) the E86 residue is essential for the nuclease activity.
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Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage.
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Adeline Goulet, Stéphanie Blangy, Valérie Campanacci, Peter Redder, Catarina Felisberto-rodrigues, Patrick Forterre, Christian CambillauAbstract:Acidianus filamentous virus 1 (AFV1), a member of the Lipothrixviridae family, infects the hyperthermophilic, acidophilic crenarchaeaon Acidianus hospitalis. The virion, covered with a lipidic outer shell, is 9,100-A long and contains a 20.8-kb linear dsDNA genome. We have identified the two major coat proteins of the virion (MCPs; 132 and 140 amino acids). They bind DNA and form filaments when incubated with linear dsDNA. A C-terminal domain is identified in their crystal structure with a four-helix-bundle fold. In the topological model of the virion filament core, the genomic dsDNA superhelix wraps around the AFV1-132 basic protein, and the AFV1-140 basic N terminus binds genomic DNA, while its lipophilic C-terminal domain is imbedded in the lipidic outer shell. The four-helix bundle fold of the MCPs from AFV1 is identical to that of the coat protein (CP) of Sulfolobus islandicus rod-shaped virus (SIRV), a member of the Rudiviridae family. Despite low sequence identity between these proteins, their high degree of structural similarity suggests that they could have derived from a common ancestor and could thus define an yet undescribed viral lineage.
Kelly S. Bateman - One of the best experts on this subject based on the ideXlab platform.
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Identification and Full Characterisation of Two Novel Crustacean Infecting Members of the Family Nudiviridae Provides Support for Two Subfamilies
'MDPI AG', 2021Co-Authors: Kelly S. Bateman, Benigna Van Eynde, Olivier Christiaens, Daan Delbare, Grant D. Stentiford, Chantelle Hooper, Rose Kerr, Tim P. Bean, Jamie Bojko, Clauvis N. T. TaningAbstract:Multiple enveloped viruses with rod-shaped nucleocapsids have been described, infecting the epithelial cell nuclei within the hepatopancreas tubules of crustaceans. These bacilliform viruses share the ultrastructural characteristics of nudiviruses, a specific clade of viruses infecting arthropods. Using histology, electron microscopy and high throughput sequencing, we characterise two further bacilliform viruses from aquatic hosts, the brown shrimp (Crangon crangon) and the European shore crab (Carcinus maenas). We assembled the full double stranded, circular DNA genome sequences of these viruses (~113 and 132 kbp, respectively). Comparative genomics and phylogenetic analyses confirm that both belong within the family Nudiviridae but in separate clades representing nudiviruses found in freshwater and marine environments. We show that the three thymidine kinase (tk) genes present in all sequenced nudivirus genomes, thus far, were absent in the Crangon crangon nudivirus, suggesting there are twenty-eight core genes shared by all nudiviruses. Furthermore, the phylogenetic data no longer support the subdivision of the family Nudiviridae into four genera (Alphanudivirus to Deltanudivirus), as recently adopted by the International Committee on Taxonomy of Viruses (ICTV), but rather shows two main branches of the family that are further subdivided. Our data support a recent proposal to create two subfamilies within the family Nudiviridae, each subdivided into several genera
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The first clawed lobster virus Homarus gammarus nudivirus (HgNV n. sp.) expands the diversity of the Nudiviridae
Scientific Reports, 2019Co-Authors: Corey C. Holt, Carly L. Daniels, David Bass, Kelly S. Bateman, Michelle Stone, Ronny Van Aerle, Mark Van Der Giezen, Stuart H. Ross, Chantelle Hooper, Grant D. StentifordAbstract:Viral diseases of crustaceans are increasingly recognised as challenges to shellfish farms and fisheries. Here we describe the first naturally-occurring virus reported in any clawed lobster species. Hypertrophied nuclei with emarginated chromatin, characteristic histopathological lesions of DNA virus infection, were observed within the hepatopancreatic epithelial cells of juvenile European lobsters ( Homarus gammarus ). Transmission electron microscopy revealed infection with a bacilliform virus containing a rod shaped nucleocapsid enveloped in an elliptical membrane. Assembly of PCR-free shotgun metagenomic sequencing produced a circular genome of 107,063 bp containing 97 open reading frames, the majority of which share sequence similarity with a virus infecting the black tiger shrimp: Penaeus monodon nudivirus (PmNV). Multiple phylogenetic analyses confirm the new virus to be a novel member of the Nudiviridae: Homarus gammarus nudivirus (HgNV). Evidence of occlusion body formation, characteristic of PmNV and its closest relatives, was not observed, questioning the horizontal transmission strategy of HgNV outside of the host. We discuss the potential impacts of HgNV on juvenile lobster growth and mortality and present HgNV-specific primers to serve as a diagnostic tool for monitoring the virus in wild and farmed lobster stocks.
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Development and application of a duplex PCR assay for detection of Crangon crangon bacilliform virus in populations of European brown shrimp (Crangon crangon).
Journal of invertebrate pathology, 2018Co-Authors: Benigna Van Eynde, Olivier Christiaens, Daan Delbare, K. Cooreman, Kelly S. Bateman, Grant D. Stentiford, Annette M. Dullemans, Monique M. Van Oers, Guy SmaggheAbstract:Abstract Crangon crangon bacilliform virus (CcBV) was first discovered in 2004 in European brown shrimp (Crangon crangon) caught along the English coast. This study describes a duplex PCR assay developed for the detection of CcBV, based on amplification of the lef-8 gene (211 bp) of CcBV and the E75 gene (105 bp) of C. crangon as an internal amplification control. The lef-8 and E75 primer pairs were designed based on preliminary genome sequencing information of the virus and transcriptomic data available for C. crangon, respectively. Sequencing of the resulting amplicons confirmed the specificity of this PCR assay and sequence analysis of the lef-8 fragment revealed amino acid identity percentages ranging between 31 and 42% with members of the Nudiviridae, proposing that CcBV may reside within this family. Finally, the duplex PCR assay was applied to samples of C. crangon hepatopancreas tissue collected along the Belgian coast to screen for the presence of CcBV. The prevalence of CcBV averaged 87%, which is comparable to previous reports of high prevalence, based upon histological analysis, in shrimp collected along the English coast. Development of a specific and sensitive PCR assay to detect CcBV will provide a useful tool for future aquaculture and research programs involving C. crangon.
