The Experts below are selected from a list of 579 Experts worldwide ranked by ideXlab platform
James L. Van Etten - One of the best experts on this subject based on the ideXlab platform.
-
Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes
Viruses, 2018Co-Authors: Phillip Seitzer, James L. Van Etten, Adrien Jeanniard, Fangrui Ma, Marc T. Facciotti, David D. DuniganAbstract:Chloroviruses (family Phycodnaviridae) are dsDNA viruses found throughout the world's inland waters. The open reading frames in the genomes of 41 sequenced chloroviruses (330 ± 40 kbp each) representing three virus types were analyzed for evidence of evolutionarily conserved local genomic "contexts", the organization of biological information into units of a scale larger than a gene. Despite a general loss of synteny between virus types, we informatically detected a highly conserved genomic context defined by groups of three or more genes that we have termed "gene gangs". Unlike previously described local genomic contexts, the definition of gene gangs requires only that member genes be consistently co-localized and are not constrained by strand, regulatory sites, or intervening sequences (and therefore represent a new type of conserved structural genomic element). An analysis of functional annotations and transcriptomic data suggests that some of the gene gangs may organize genes involved in specific biochemical processes, but that this organization does not involve their coordinated expression.
-
Chloroviruses: Not Your Everyday Plant Virus
Trends in Plant Science, 2011Co-Authors: James L. Van Etten, David D. DuniganAbstract:Viruses infecting higher plants are among the smallest viruses known and typically have four to ten protein-encoding genes. By contrast, many viruses that infect algae (classified in the virus family Phycodnaviridae ) are among the largest viruses found to date and have up to 600 protein-encoding genes. This brief review focuses on one group of plaque-forming phycodnaviruses that infect unicellular chlorella-like green algae. The prototype chlorovirus PBCV-1 has more than 400 protein-encoding genes and 11 tRNA genes. About 40% of the PBCV-1 encoded proteins resemble proteins of known function including many that are completely unexpected for a virus. In many respects, chlorovirus infection resembles bacterial infection by tailed bacteriophages.
-
Crystal Structure of a Virus-Encoded Putative Glycosyltransferase
Journal of Virology, 2010Co-Authors: Ye Xiang, James L. Van Etten, Ulrich Baxa, Ying Zhang, Alasdair C. Steven, Gentry L. Lewis, Michael G RossmannAbstract:The chloroviruses (family Phycodnaviridae), unlike most viruses, encode some, if not most, of the enzymes involved in the glycosylation of their structural proteins. Annotation of the gene product B736L from chlorovirus NY-2A suggests that it is a glycosyltransferase. The structure of the recombinantly expressed B736L protein was determined by X-ray crystallography to 2.3-A resolution, and the protein was shown to have two nucleotide-binding folds like other glycosyltransferase type B enzymes. This is the second structure of a chlorovirus-encoded glycosyltransferase and the first structure of a chlorovirus type B enzyme to be determined. B736L is a retaining enzyme and belongs to glycosyltransferase family 4. The donor substrate was identified as GDP-mannose by isothermal titration calorimetry and was shown to bind into the cleft between the two domains in the protein. The active form of the enzyme is probably a dimer in which the active centers are separated by about 40 A.
-
Isolation of the phycodnavirus PBCV-1 by biological laser printing
Journal of Virological Methods, 2010Co-Authors: Lisa A. Fitzgerald, Peter K. Wu, James R. Gurnon, Justin C. Biffinger, Bradley R. Ringeisen, James L. Van EttenAbstract:The Phycodnaviridae family of viruses is diverse genetically but similar morphologically. These viruses infect eukaryotic algal hosts from both fresh and marine waters, and are an important component of aqueous environments. They play important roles in the dynamics of algal blooms, nutrient cycling, algal community structure, and possibly gene transfer between organisms. As such, it is important to identify new viruses within the Phycodnaviridae family. Biological laser printing (BioLP) was used to isolate single virus particles from solution. BioLP prints droplets containing a single virus particle directly onto a host medium, thereby enabling viruses to be isolated from unmodified samples. This manuscript demonstrates how BioLP can be used as a single-step method to separate and possibly identify viruses from complex environmental specimens. Published by Elsevier B.V.
-
Initial Events Associated with Virus PBCV-1 Infection of Chlorella NC64A
Progress in botany. Fortschritte der Botanik, 2010Co-Authors: Gerhard Thiel, David D. Dunigan, Anna Moroni, James L. Van EttenAbstract:Chlorella viruses (or chloroviruses) are very large, plaque-forming viruses. The viruses are multilayered structures containing a large double-stranded DNA genome, a lipid bilayered membrane, and an outer icosahedral capsid shell. The viruses replicate in certain isolates of the coccal green alga, Chlorella. Sequence analysis of the 330-kbp genome of Paramecium bursaria Chlorella virus 1 (PBCV-1), the prototype of the virus family Phycodnaviridae, reveals
William H. Wilson - One of the best experts on this subject based on the ideXlab platform.
-
Genome of brown tide virus (AaV), the little giant of the Megaviridae, elucidates NCLDV genome expansion and host-virus coevolution.
Virology, 2014Co-Authors: Mohammad Moniruzzaman, William H. Wilson, Gary R. Lecleir, Christopher M. Brown, Christopher J. Gobler, Kay D. Bidle, Steven W. WilhelmAbstract:Aureococcus anophagefferens causes economically and ecologically destructive “brown tides” in the United States, China and South Africa. Here we report the 370,920 bp genomic sequence of AaV, a virus capable of infecting and lysing A. anophagefferens. AaV is a member of the nucleocytoplasmic large DNA virus (NCLDV) group, harboring 377 putative coding sequences and 8 tRNAs. Despite being an algal virus, AaV shows no phylogenetic affinity to the Phycodnaviridae family, to which most algae-infecting viruses belong. Core gene phylogenies, shared gene content and genome-wide similarities suggest AaV is the smallest member of the emerging clade “Megaviridae”. The genomic architecture of AaV demonstrates that the ancestral virus had an even smaller genome, which expanded through gene duplication and assimilation of genes from diverse sources including the host itself – some of which probably modulate important host processes. AaV also harbors a number of genes exclusive to phycodnaviruses – reinforcing the hypothesis that Phycodna- and Mimiviridae share a common ancestor.
-
Marine viruses, a genetic reservoir revealed by targeted viromics
The ISME Journal, 2014Co-Authors: Joaquín Martínez Martínez, Brandon K Swan, William H. WilsonAbstract:Metagenomics has opened new windows on investigating viral diversity and functions. Viromic studies typically require large sample volumes and filtration through 0.2 μm pore-size filters, consequently excluding or under-sampling tailed and very large viruses. We have optimized a targeted viromic approach that employs fluorescence-activated sorting and whole genome amplification to produce dsDNA-enriched libraries from discrete viral populations from a 1-ml water sample. Using this approach on an environmental sample from the Patagonian Shelf, we produced three distinct libraries. One of the virus libraries was dominated (79.65% of sequences with known viral homology) by giant viruses from the Mimiviridae and Phycodnaviridae families, while the two other viromes were dominated by smaller phycodnaviruses, cyanophages and other bacteriophages. The estimated genotypic richness and diversity in our sorted viromes, with 52–163 estimated genotypes, was much lower than in previous virome reports. Fragment recruitment of metagenome reads to selected reference viral genomes yields high genome coverage, suggesting little amplification and sequencing bias against some genomic regions. These results underscore the value of our approach as an effective way to target and investigate specific virus groups. In particular, it will help reveal the diversity and abundance of giant viruses in marine ecosystems.
-
Application of the major capsid protein as a marker of the phylogenetic diversity of Emiliania huxleyi viruses
FEMS Microbiology Ecology, 2011Co-Authors: Janet M. Rowe, William H. Wilson, Marie-françoise Fabre, Daniel Gobena, Steven W. WilhelmAbstract:Studies of the Phycodnaviridae have traditionally relied on the DNA polymerase (pol) gene as a biomarker. However, recent investigations have suggested that the major capsid protein (MCP) gene may be a reliable phylogenetic biomarker. We used MCP gene amplicons gathered across the North Atlantic to assess the diversity of Emiliania huxleyi-infecting Phycodnaviridae. Nucleotide sequences were examined across >6000 km of open ocean, with comparisons between concentrates of the virus-size fraction of seawater and of lysates generated by exposing host strains to these same virus concentrates. Analyses revealed that many sequences were only sampled once, while several were over-represented. Analyses also revealed nucleotide sequences distinct from previous coastal isolates. Examination of lysed cultures revealed a new richness in phylogeny, as MCP sequences previously unrepresented within the existing collection of E. huxleyi viruses (EhV) were associated with viruses lysing cultures. Sequences were compared with previously described EhV MCP sequences from the North Sea and a Norwegian Fjord, as well as from the Gulf of Maine. Principal component analysis indicates that location-specific distinctions exist despite the presence of sequences common across these environments. Overall, this investigation provides new sequence data and an assessment on the use of the MCP gene.
-
From small hosts come big viruses: the complete genome of a second Ostreococcus tauri virus, OtV-1.
Environmental Microbiology, 2009Co-Authors: Karen D. Weynberg, Michael J. Allen, Kevin E. Ashelford, David J. Scanlan, William H. WilsonAbstract:Ostreococcus tauri virus (OtV-1) is a large double-stranded DNA virus and a prospective member of the family Phycodnaviridae, genus Prasinovirus. OtV-1 infects the unicellular marine green alga O. tauri, the smallest known free-living eukaryote. Here we present the 191 761 base pair genome sequence of OtV-1, which has 232 putative protein-encoding and 4 tRNA-encoding genes. Approximately 31% of the viral gene products exhibit a similarity to proteins of known functions in public databases. These include a variety of unexpected genes, for example, a PhoH-like protein, a N-myristoyltransferase, a 3-dehydroquinate synthase, a number of glycosyltransferases and methyltransferases, a prolyl 4-hydroxylase, 6-phosphofructokinase and a total of 8 capsid proteins. A total of 11 predicted genes share homology with genes found in the Ostreococcus host genome. In addition, an intein was identified in the DNA polymerase gene of OtV-1. This is the first report of an intein in the genome of a virus that infects O. tauri. Fifteen core genes common to nuclear-cytoplasmic large dsDNA virus (NCLDV) genomes were identified in the OtV-1 genome. This new sequence data may help to redefine the classification of the core genes of these viruses and shed new light on their evolutionary history.
-
A unicellular algal virus, Emiliania huxleyi virus 86, exploits an animal-like infection strategy
Journal of General Virology, 2009Co-Authors: Luke C. M. Mackinder, William H. Wilson, Charlotte A. Worthy, Gaia F. Biggi, Matthew Hall, Keith P. Ryan, Arvind Varsani, Glenn M. Harper, Colin Brownlee, Declan C. SchroederAbstract:Emiliania huxleyi virus 86 (EhV-86) belongs to the family Phycodnaviridae, a group of viruses that infect a wide range of freshwater and marine eukaryotic algae. Phycodnaviridae is one of the five families that belong to a large and phylogenetically diverse group of viruses known as nucleocytoplasmic large dsDNA viruses (NCLDVs). To date, our understanding of algal NCLDV entry is based on the entry mechanisms of members of the genera Chlorovirus and Phaeovirus, both of which consist of non-enveloped viruses that ‘inject’ their genome into their host via a viral inner-membrane host plasma membrane fusion mechanism, leaving an extracellular viral capsid. Using a combination of confocal and electron microscopy, this study demonstrated for the first time that EhV-86 differs from its algal virus counterparts in two fundamental areas. Firstly, its capsid is enveloped by a lipid membrane, and secondly, EhV-86 enters its host via either an endocytotic or an envelope fusion mechanism in which an intact nucleoprotein core still encapsulated by its capsid is seen in the host cytoplasm. Real-time fluorescence microscopy showed that viral internalization and virion breakdown took place within the host on a timescale of seconds. At around 4.5 h post-infection, virus progeny were released via a budding mechanism during which EhV-86 virions became enveloped with host plasma membrane. EhV-86 therefore appears to have an infection mechanism different from that employed by other algal NCLDVs, with entry and exit strategies showing a greater analogy to animal-like NCLDVs.
David D. Dunigan - One of the best experts on this subject based on the ideXlab platform.
-
Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes
Viruses, 2018Co-Authors: Phillip Seitzer, James L. Van Etten, Adrien Jeanniard, Fangrui Ma, Marc T. Facciotti, David D. DuniganAbstract:Chloroviruses (family Phycodnaviridae) are dsDNA viruses found throughout the world's inland waters. The open reading frames in the genomes of 41 sequenced chloroviruses (330 ± 40 kbp each) representing three virus types were analyzed for evidence of evolutionarily conserved local genomic "contexts", the organization of biological information into units of a scale larger than a gene. Despite a general loss of synteny between virus types, we informatically detected a highly conserved genomic context defined by groups of three or more genes that we have termed "gene gangs". Unlike previously described local genomic contexts, the definition of gene gangs requires only that member genes be consistently co-localized and are not constrained by strand, regulatory sites, or intervening sequences (and therefore represent a new type of conserved structural genomic element). An analysis of functional annotations and transcriptomic data suggests that some of the gene gangs may organize genes involved in specific biochemical processes, but that this organization does not involve their coordinated expression.
-
Coccolithoviruses: A Review of Cross-Kingdom Genomic Thievery and Metabolic Thuggery
Viruses, 2017Co-Authors: Jozef I. Nissimov, David D. Dunigan, António Pagarete, Fangrui Ma, Sean Cody, Susan A. Kimmance, Michael J. AllenAbstract:Coccolithoviruses (Phycodnaviridae) infect and lyse the most ubiquitous and successful coccolithophorid in modern oceans, Emiliania huxleyi. So far, the genomes of 13 of these giant lytic viruses (i.e., Emiliania huxleyi viruses—EhVs) have been sequenced, assembled, and annotated. Here, we performed an in-depth comparison of their genomes to try and contextualize the ecological and evolutionary traits of these viruses. The genomes of these EhVs have from 444 to 548 coding sequences (CDSs). Presence/absence analysis of CDSs identified putative genes with particular ecological significance, namely sialidase, phosphate permease, and sphingolipid biosynthesis. The viruses clustered into distinct clades, based on their DNA polymerase gene as well as full genome comparisons. We discuss the use of such clustering and suggest that a gene-by-gene investigation approach may be more useful when the goal is to reveal differences related to functionally important genes. A multi domain “Best BLAST hit” analysis revealed that 84% of the EhV genes have closer similarities to the domain Eukarya. However, 16% of the EhV CDSs were very similar to bacterial genes, contributing to the idea that a significant portion of the gene flow in the planktonic world inter-crosses the domains of life.
-
Chlorovirus ATCV-1 is part of the human oropharyngeal virome and is associated with changes in cognitive functions in humans and mice.
Proceedings of the National Academy of Sciences of the United States of America, 2014Co-Authors: Robert H. Yolken, David D. Dunigan, Lorraine Jones-brando, Geetha Kannan, Faith Dickerson, Emily G. Severance, Sarven Sabunciyan, C. Conover Talbot, Emese Prandovszky, James R. GurnonAbstract:Chloroviruses (family Phycodnaviridae) are large DNA viruses known to infect certain eukaryotic green algae and have not been previously shown to infect humans or to be part of the human virome. We unexpectedly found sequences homologous to the chlorovirus Acanthocystis turfacea chlorella virus 1 (ATCV-1) in a metagenomic analysis of DNA extracted from human oropharyngeal samples. These samples were obtained by throat swabs of adults without a psychiatric disorder or serious physical illness who were participating in a study that included measures of cognitive functioning. The presence of ATCV-1 DNA was confirmed by quantitative PCR with ATCV-1 DNA being documented in oropharyngeal samples obtained from 40 (43.5%) of 92 individuals. The presence of ATCV-1 DNA was not associated with demographic variables but was associated with a modest but statistically significant decrease in the performance on cognitive assessments of visual processing and visual motor speed. We further explored the effects of ATCV-1 in a mouse model. The inoculation of ATCV-1 into the intestinal tract of 9–11-wk-old mice resulted in a subsequent decrease in performance in several cognitive domains, including ones involving recognition memory and sensory-motor gating. ATCV-1 exposure in mice also resulted in the altered expression of genes within the hippocampus. These genes comprised pathways related to synaptic plasticity, learning, memory formation, and the immune response to viral exposure.
-
Chloroviruses: Not Your Everyday Plant Virus
Trends in Plant Science, 2011Co-Authors: James L. Van Etten, David D. DuniganAbstract:Viruses infecting higher plants are among the smallest viruses known and typically have four to ten protein-encoding genes. By contrast, many viruses that infect algae (classified in the virus family Phycodnaviridae ) are among the largest viruses found to date and have up to 600 protein-encoding genes. This brief review focuses on one group of plaque-forming phycodnaviruses that infect unicellular chlorella-like green algae. The prototype chlorovirus PBCV-1 has more than 400 protein-encoding genes and 11 tRNA genes. About 40% of the PBCV-1 encoded proteins resemble proteins of known function including many that are completely unexpected for a virus. In many respects, chlorovirus infection resembles bacterial infection by tailed bacteriophages.
-
Initial Events Associated with Virus PBCV-1 Infection of Chlorella NC64A
Progress in botany. Fortschritte der Botanik, 2010Co-Authors: Gerhard Thiel, David D. Dunigan, Anna Moroni, James L. Van EttenAbstract:Chlorella viruses (or chloroviruses) are very large, plaque-forming viruses. The viruses are multilayered structures containing a large double-stranded DNA genome, a lipid bilayered membrane, and an outer icosahedral capsid shell. The viruses replicate in certain isolates of the coccal green alga, Chlorella. Sequence analysis of the 330-kbp genome of Paramecium bursaria Chlorella virus 1 (PBCV-1), the prototype of the virus family Phycodnaviridae, reveals
Lisa A. Fitzgerald - One of the best experts on this subject based on the ideXlab platform.
-
Isolation of the phycodnavirus PBCV-1 by biological laser printing
Journal of Virological Methods, 2010Co-Authors: Lisa A. Fitzgerald, Peter K. Wu, James R. Gurnon, Justin C. Biffinger, Bradley R. Ringeisen, James L. Van EttenAbstract:The Phycodnaviridae family of viruses is diverse genetically but similar morphologically. These viruses infect eukaryotic algal hosts from both fresh and marine waters, and are an important component of aqueous environments. They play important roles in the dynamics of algal blooms, nutrient cycling, algal community structure, and possibly gene transfer between organisms. As such, it is important to identify new viruses within the Phycodnaviridae family. Biological laser printing (BioLP) was used to isolate single virus particles from solution. BioLP prints droplets containing a single virus particle directly onto a host medium, thereby enabling viruses to be isolated from unmodified samples. This manuscript demonstrates how BioLP can be used as a single-step method to separate and possibly identify viruses from complex environmental specimens. Published by Elsevier B.V.
-
Putative gene promoter sequences in the chlorella viruses
Virology, 2008Co-Authors: Lisa A. Fitzgerald, Philip T. Boucher, Giane M. Yanai-balser, Karsten Suhre, Michael C. Graves, James L. Van EttenAbstract:Three short (7 to 9 nucleotides) highly conserved nucleotide sequences were identified in the putative promoter regions (150 bp upstream and 50 bp downstream of the ATG translation start site) of three members of the genus Chlorovirus, family Phycodnaviridae. Most of these sequences occurred in similar locations within the defined promoter regions. The sequence and location of the motifs were often conserved among homologous ORFs within the Chlorovirus family. One of these conserved sequences (AATGACA) is predominately associated with genes expressed early in virus replication.
-
Sequence and annotation of the 288-kb ATCV-1 virus that infects an endosymbiotic chlorella strain of the heliozoon Acanthocystis turfacea
Virology, 2007Co-Authors: Lisa A. Fitzgerald, Michael C. Graves, Xiao Li, James Hartigan, Artur J. P. Pfitzner, Ella Hoffart, James L. Van EttenAbstract:Abstract Acanthocystis turfacea chlorella virus (ATCV-1), a prospective member of the family Phycodnaviridae , genus Chlorovirus , infects a unicellular, eukaryotic, chlorella-like green alga, Chlorella SAG 3.83, that is a symbiont in the heliozoon A. turfacea . The 288,047-bp ATCV-1 genome is the first virus to be sequenced that infects Chlorella SAG 3.83. ATCV-1 contains 329 putative protein-encoding and 11 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands and intergenic space is minimal. Thirty-four percent of the viral gene products resemble entries in the public databases, including some that are unexpected for a virus. For example, these unique gene products include ribonucleoside-triphosphate reductase, dTDP- d -glucose 4,6 dehydratase, potassium ion transporter, aquaglyceroporin, and mucin-desulfating sulfatase. Comparison of ATCV-1 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that about 80% of the ATCV-1 genes are present in PBCV-1.
-
Supplementary Data for “Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64A”: Appendix A: Gene Names b002R – b797R
2007Co-Authors: Lisa A. Fitzgerald, Michael C. Graves, Xiao Li, Tamara V. Feldblyum, William C. Nierman, James L. Van EttenAbstract:Viruses NY-2A and AR158, members of the family Phycodnaviridae, genus Chlorovirus, infect the fresh water, unicellular, eukaryotic, chlorella-like green alga, Chlorella NC64A. The 368,683-bp genome of NY-2A and the 344,690-bp genome of AR158 are the two largest chlorella virus genomes sequenced to date; NY-2A contains 404 putative protein-encoding and 7 tRNA-encoding genes and AR158 contains 360 putative protein-encoding and 6 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands, and intergenic space is minimal. Two of the NY-2A genes encode inteins, the large subunit of ribonucleotide reductase and a superfamily II helicase. These are the first inteins to be detected in the chlorella viruses. Approximately 40% of the viral gene products resemble entries in the public databases, including some that are unexpected for a virus. These include GDP-d-mannose dehydratase, fucose synthase, aspartate transcarbamylase, Ca transporting ATPase and ubiquitin. Comparison of NY-2A and AR158 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that 85% of the genes are present in all three viruses.
-
Sequence and annotation of the 314-kb MT325 and the 321-kb FR483 viruses that infect Chlorella Pbi
Virology, 2006Co-Authors: Lisa A. Fitzgerald, Michael C. Graves, Xiao Li, James Hartigan, Tamara V. Feldblyum, James L. Van EttenAbstract:Viruses MT325 and FR483, members of the family Phycodnaviridae, genus Chlorovirus, infect the fresh water, unicellular, eukaryotic, chlorella-like green alga, Chlorella Pbi. The 314,335-bp genome of MT325 and the 321,240-bp genome of FR483 are the first viruses that infect Chlorella Pbi to have their genomes sequenced and annotated. Furthermore, these genomes are the two smallest chlorella virus genomes sequenced to date, MT325 has 331 putative protein-encoding and 10 tRNA-encoding genes and FR483 has 335 putative protein-encoding and 9 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands, and intergenic space is minimal. Approximately 40% of the viral gene products resemble entries in public databases, including some that are the first of their kind to be detected in a virus. For example, these unique gene products include an aquaglyceroporin in MT325, a potassium ion transporter protein and an alkyl sulfatase in FR483, and a dTDP-glucose pyrophosphorylase in both viruses. Comparison of MT325 and FR483 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that approximately 82% of the genes are present in all three viruses.
Michael J. Allen - One of the best experts on this subject based on the ideXlab platform.
-
Coccolithoviruses: A Review of Cross-Kingdom Genomic Thievery and Metabolic Thuggery
Viruses, 2017Co-Authors: Jozef I. Nissimov, David D. Dunigan, António Pagarete, Fangrui Ma, Sean Cody, Susan A. Kimmance, Michael J. AllenAbstract:Coccolithoviruses (Phycodnaviridae) infect and lyse the most ubiquitous and successful coccolithophorid in modern oceans, Emiliania huxleyi. So far, the genomes of 13 of these giant lytic viruses (i.e., Emiliania huxleyi viruses—EhVs) have been sequenced, assembled, and annotated. Here, we performed an in-depth comparison of their genomes to try and contextualize the ecological and evolutionary traits of these viruses. The genomes of these EhVs have from 444 to 548 coding sequences (CDSs). Presence/absence analysis of CDSs identified putative genes with particular ecological significance, namely sialidase, phosphate permease, and sphingolipid biosynthesis. The viruses clustered into distinct clades, based on their DNA polymerase gene as well as full genome comparisons. We discuss the use of such clustering and suggest that a gene-by-gene investigation approach may be more useful when the goal is to reveal differences related to functionally important genes. A multi domain “Best BLAST hit” analysis revealed that 84% of the EhV genes have closer similarities to the domain Eukarya. However, 16% of the EhV CDSs were very similar to bacterial genes, contributing to the idea that a significant portion of the gene flow in the planktonic world inter-crosses the domains of life.
-
From small hosts come big viruses: the complete genome of a second Ostreococcus tauri virus, OtV-1.
Environmental Microbiology, 2009Co-Authors: Karen D. Weynberg, Michael J. Allen, Kevin E. Ashelford, David J. Scanlan, William H. WilsonAbstract:Ostreococcus tauri virus (OtV-1) is a large double-stranded DNA virus and a prospective member of the family Phycodnaviridae, genus Prasinovirus. OtV-1 infects the unicellular marine green alga O. tauri, the smallest known free-living eukaryote. Here we present the 191 761 base pair genome sequence of OtV-1, which has 232 putative protein-encoding and 4 tRNA-encoding genes. Approximately 31% of the viral gene products exhibit a similarity to proteins of known functions in public databases. These include a variety of unexpected genes, for example, a PhoH-like protein, a N-myristoyltransferase, a 3-dehydroquinate synthase, a number of glycosyltransferases and methyltransferases, a prolyl 4-hydroxylase, 6-phosphofructokinase and a total of 8 capsid proteins. A total of 11 predicted genes share homology with genes found in the Ostreococcus host genome. In addition, an intein was identified in the DNA polymerase gene of OtV-1. This is the first report of an intein in the genome of a virus that infects O. tauri. Fifteen core genes common to nuclear-cytoplasmic large dsDNA virus (NCLDV) genomes were identified in the OtV-1 genome. This new sequence data may help to redefine the classification of the core genes of these viruses and shed new light on their evolutionary history.
-
the Phycodnaviridae the story of how tiny giants rule the world
Current Topics in Microbiology and Immunology, 2009Co-Authors: William H. Wilson, J. L. Van Etten, Michael J. AllenAbstract:The family Phycodnaviridae encompasses a diverse and rapidly expand- ing collection of large icosahedral, dsDNA viruses that infect algae. These lytic and lysogenic viruses have genomes ranging from 160 to 560 kb. The family consists of six genera based initially on host range and supported by sequence comparisons. The family is monophyletic with branches for each genus, but the phycodnaviruses have evolutionary roots that connect them with several other families of large DNA viruses, referred to as the nucleocytoplasmic large DNA viruses (NCLDV).
-
Proteomic analysis of the EhV-86 virion
Proteome Science, 2008Co-Authors: Michael J. Allen, Julie Howard, Kathryn S. Lilley, William H. WilsonAbstract:Background Emiliania huxleyi virus 86 (EhV-86) is the type species of the genus Coccolithovirus within the family Phycodnaviridae. The fully sequenced 407,339 bp genome is predicted to encode 473 protein coding sequences (CDSs) and is the largest Phycodnaviridae sequenced to date. The majority of EhV-86 CDSs exhibit no similarity to proteins in the public databases.
-
Proteomic analysis of the EhV-86 virion
Proteome Science, 2008Co-Authors: Michael J. Allen, Kathryn S. Lilley, Julie A Howard, William H. WilsonAbstract:Background Emiliania huxleyi virus 86 (EhV-86) is the type species of the genus Coccolithovirus within the family Phycodnaviridae . The fully sequenced 407,339 bp genome is predicted to encode 473 protein coding sequences (CDSs) and is the largest Phycodnaviridae sequenced to date. The majority of EhV-86 CDSs exhibit no similarity to proteins in the public databases. Results Proteomic analysis by 1-DE and then LC-MS/MS determined that the virion of EhV-86 is composed of at least 28 proteins, 23 of which are predicted to be membrane proteins. Besides the major capsid protein, putative function can be assigned to 4 other components of the virion: two lectin proteins, a thioredoxin and a serine/threonine protein kinase. Conclusion This study represents the first steps toward the identification of the protein components that make up the EhV-86 virion. Aside from the major capsid protein, whose function in the virion is well known and defined, the nature of the other proteins suggest roles involved with viral budding, caspase activation, signalling, anti-oxidation, virus adsorption and host range determination.