SEARCH · PubMed Health

Results for “Phycodnaviridae”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

PubMed2002

Phycodnaviridae--large DNA algal viruses.

Members and prospective members of the family Phycodnaviridae are large icosahedral, dsDNA (180 to 560 kb) viruses that infect eukaryotic algae. The genomes of two phycodnaviruses have been sequenced: the 331 kb genome of Paramecium bursaria chlorella virus (PBCV-1) and more recently, the 336 kb genome of the Ectocarpus siliculosus virus (EsV-1). EsV-1 has approximately 231 protein-encoding genes whereas, the slightly smaller PBCV-1 genome has 11 tRNA genes and approximately 375 protein-encoding genes. Surprisingly, the two viruses only have 33 genes in common, of which 17 have no counterparts in the databases. The low number of homologous genes between the two viruses can probably be attributed to their different life styles. PBCV-1 is a lytic virus that infects a unicellular, endosymbiotic freshwater green alga whereas, EsV-1 is a lysogenic virus that infects a free-living filamentous marine brown alga. Furthermore, accumulating evidence indicates that the phycodnaviruses and their genes are ancient, thus allowing significant differences to have evolved. This review briefly describes some of the biological properties of the phycodnaviruses, focusing on PBCV-1 and EsV-1, and then compares their genomes.

Chlorella↗

PubMed2002

Coccolithovirus (Phycodnaviridae): characterisation of a new large dsDNA algal virus that infects Emiliana huxleyi.

Emiliania huxleyi-specific viruses ( EhV) were isolated from E. huxleyi blooms off the coast of Plymouth, UK, in July 1999 and July/August 2001, and from an E. huxleyi bloom induced during a mesocosm experiment in a fjord off Bergen, Norway, during June 2000. Transmission electron microscopy revealed that all 10 virus isolates are 170-200 nm in diameter with an icosahedral symmetry. Their density is approximately 1.2 in CsCl gradients and they have large double stranded DNA genomes approximately 410 kb in size. Phylogenetic analysis of the DNA polymerase genes of these viruses suggests that EhV belongs to a new genus within the family of algal viruses, Phycodnaviridae. We propose to name this new virus genus Coccolithovirus. Differences within members of the Coccolithovirus were elucidated by host range analysis of the virus isolates and sequence analysis of a gene fragment encoding part of their putative major capsid protein. All 10 virus isolates within this new genus only infected E. huxleyi strains that have previously been shown to exhibit low dimethylsulphoniopropionate lyase (DMSP-lyase) activity (CCMP1516, CCMP374 and L), while E. huxleyi strains with high DMSP-lyase activity (CCMP373 and CCMP379) were resistant to infection.

Base Sequence↗

PubMed2003

Structural analyses of Phycodnaviridae and Iridoviridae.

The Phycodnaviridae, Iridoviridae and related viruses, with diameters of 1500-2000 A, are formed from large trigonal arrays of hexagonally close-packed capsomers forming the faces of icosahedra [Yan et al. (2000), Nature Struct. Biol. 7, 101-103; Nandhagopal et al. (2002), Proc. Natl Acad. Sci. USA, 99, 14758-14763]. Caspar and Klug predicted that such structures could be assembled from hexameric capsomers [Caspar & Klug (1962), Cold Spring Harbor. Symp. Quant. Biol. 27, 1-24], as was subsequently found in numerous icosahedral viruses. During the course of evolution, some viruses, including the virus families mentioned above, replaced hexameric capsomers with pseudo-hexameric trimers by gene duplication. In large dsDNA icosahedral viruses, the capsomers are organized into 'pentasymmetrons' and 'trisymmetrons'. The interactions between the trimeric capsomers can be divided into three groups, one between similarly oriented trimers and two between oppositely oriented trimers (trimers related by an approximately sixfold rotation). The interactions within a trisymmetron belong to the first class, whereas those between trisymmetrons and within the pentasymmetron are of the other two types. Knowledge of these distances permits a more accurate fitting of the atomic structure of the capsomer into the cryo-electron microscopy (cryoEM) reconstruction of the whole virus. The adoption of pseudo-hexagonal capsomers places these viruses into a subset of the Caspar and Klug surface lattices.

Capsid Proteins↗

PubMed2005

Evolutionary history of the Coccolithoviridae.

We recently determined the genome sequence of the Coccolithoviridae strain Emiliania huxleyi virus 86 (EhV-86), a giant double-stranded DNA (dsDNA) algal virus from the family Phycodnaviridae that infects the marine coccolithophorid E. huxleyi. Here, we determine the phylogenetic relationship between EhV-86 and other large dsDNA viruses. Twenty-five core genes common to nuclear-cytoplasmic large dsDNA virus genomes were identified in the EhV-86 genome; sequence from eight of these genes were used to create a phylogenetic tree in which EhV-86 was placed firmly with the two other members of the Phycodnaviridae. We have also identified a 100-kb region of the EhV-86 genome which appears to have transferred into this genome from an unknown source. Furthermore, the presence of six RNA polymerase subunits (unique among the Phycodnaviridae) suggests both a unique evolutionary history and a unique lifestyle for this intriguing virus.

Cluster Analysis↗

PubMed1999

Several genes in Chlorella virus strain CVG-1 encode putative virion components.

We have started to characterize the capsid components of European Chlorella virus isolate CVG-1, a member of the Pbi subgroup of the Phycodnaviridae. The major coat protein, Vp49, was biochemically characterized and the amino acid sequence of the N terminus was determined. Subsequently, the corresponding gene was isolated from CVG-1 genomic DNA. Sequence data were compared to those available from PBCV-1 and other Chlorella virus isolates representing the NC64A subgroup of the Phycodnaviridae. The major coat proteins of all strains are homologous and similar in size, but apparently differ in their degree of glycosylation. Like PBCV-1, the major coat protein of CVG-1 is part of a gene family, as two open reading frames with high similarity to Vp49 were also isolated and characterized in this study. The predicted amino acid sequences of the CVG-1 and PBCV-1 virus genes examined show, with one exception, a divergence of about 25%. Taking into account that corresponding genes of NC64A viruses are almost identical, this divergence supports the original placement of the NC64A and Pbi viruses into separate subgroups of the Phycodnaviridae.

Amino Acid Sequence↗

PubMed1996

Evolutionary relationships among large double-stranded DNA viruses that infect microalgae and other organisms as inferred from DNA polymerase genes.

In order to examine genetic relatedness among viruses that infect microalgae, DNA polymerase gene (DNA pol) fragments were amplified and sequenced from 13 virus clones that infect three genera of distantly related microalgae (Chlorella strains NC64A and Pbi, Micromonas pusilla and Chrysochromulina spp.). Phylogenetic trees based on DNA pol sequences and hybridization of total genomic DNA showed similar branching patterns. Genetic relatedness calculated from the hybridization and sequence data showed good concordance (r=0.90), indicating that DNA pol sequences can be used to determine genetic relatedness and infer phylogenetic relationships among these viruses. The phylogenetic tree inferred from the deduced amino acid sequences of DNA pol from 24 dsDNA viruses, including phycodnaviruses, herpesviruses, poxviruses, baculoviruses, and African swine fever virus corresponded well with groupings based on the International Committee on Taxonomy of Viruses. Microalgal viruses are more closely related to each other than to the other dsDNA viruses and form a distinct phyletic group, suggesting that they share a common ancestor and belong to the Phycodnaviridae. Moreover, the Phycodnaviridae are more closely related to the Herpesviridae than to other virus families for which DNA pol sequences are available.

Amino Acid Sequence↗

PubMed2006

Phycodnaviruses: a peek at genetic diversity.

The family Phycodnaviridae encompasses a diverse collection of large icosahedral, dsDNA viruses infecting algae. These viruses have genomes ranging from 160 to 560kb. 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 with several other families of large DNA viruses, referred to as the nucleocytoplasmic large DNA viruses (NCLDV). The genomes of members in three genera in the Phycodnaviridae have recently been sequenced and the purpose of this manuscript is to summarize these data. The viruses have diverse genome structures, some with large regions of non-coding sequence and others with regions of single-stranded DNA. Typically, phycodnaviruses have the coding capacity for hundreds of genes. The genome analyses have revealed in excess of 1000 unique genes, with only 14 homologous genes held in common among the three genera of the phycodnavirses sequenced to date. Thus, the gene diversity far exceeds the number of so-called "core" genes. Little is known about the replication of these viruses, but the consequences of these infections of the phytoplankton have global affects, including altered geochemical cycling and weather patterns.

DNA Viruses↗

PubMed1999

Chlorella viruses as a source of novel enzymes.

A special advantage has been conferred upon Chlorella cells as tools in biotechnology when viruses (Phycodnaviridae) infecting Chlorella cells were discovered and isolated. The viruses are large icosahedral particles (150-200 nm in diameter), containing a giant, 330-380 kbp long, linear dsDNA genome. Recently, the nucleotide sequence of the 330,740-bp genome of PBCV-1, the prototype virus of Phycodnaviridae, was determined, and up to 702 open reading frames (ORFs) were identified along the genome. The possible genes present include those encoding a variety of enzymes involved in the modification of DNA, RNA, protein and polysaccharides as well as those involved in the metabolism of sugars, amino acids, lipids, nucleotides and nucleosides. Many of these genes are actually expressed during viral infection, with functional enzymes detected in the host cytoplasm or incorporated into the virion. The successful utilization of these viral enzymes as various DNA restriction and modification enzymes (Cvi enzymes) that are now commercially available is well documented. Also noteworthy are virion-associated chitinase and chitosanase activities that have potentially important applications in the recycling of natural resources. The virions of Chlorella viruses contain more than 50 different structural proteins, ranging in size from 10 to 200 kDa. Some of these proteins may be replaced with useful foreign proteins using recombinant DNA technology. The proteins of interest can be recovered easily from the viral particles, and collected by centrifugation after complete lysis of the host Chlorella cells.

Journal Article↗

PubMed1998

Is the major capsid protein of iridoviruses a suitable target for the study of viral evolution?

Iridoviruses are large cytoplasmic DNA viruses that are specific for different insect or vertebrate hosts. The major structural component of the non-enveloped icosahedral virus particles is the major capsid protein (MCP) which appears to be highly conserved among members of the family Iridoviridae, Phycodnaviridae, and African swine fever virus. The amino acid sequences of the known MCPs were used in comparative analyses to elucidate the phylogenic relationships between different cytoplasmic DNA viruses including three insect iridoviruses (Tipula iridescent virus, Simulium iridescent virus, Chilo iridescent virus), seven vertebrate iridoviruses isolated either from fish (lymphocystis disease virus, rainbow trout virus, European catfish virus, doctor fish virus), amphibians (frog virus 3), or reptiles (turtle virus 3, turtle virus 5), one member of the family Phycodnaviridae (Paramecium bursaria Chlorella virus type 1), and African swine fever virus. These analyses revealed that the amino acid sequence of the MCP is a suitable target for the study of viral evolution since it contains highly conserved domains, but is sufficiently diverse to distinguish closely related iridovirus isolates. Furthermore the results suggest that a substantial revision of the taxonomy of iridoviruses based on molecular phylogeny is required.

Amino Acid Sequence↗

PubMed1996

Genetic diversity in marine algal virus communities as revealed by sequence analysis of DNA polymerase genes.

Algal-virus-specific PCR primers were used to amplify DNA polymerase gene (pol) fragments (683 to 689 bp) from the virus-sized fraction (0.02 to 0.2 microns) concentrated from inshore and offshore water samples collected from the Gulf of Mexico. Algal-virus-like DNA pol genes were detected in five samples collected from the surface and deep chlorophyll maximum. PCR products from an offshore station were cloned, and the genetic diversity of 33 fragments was examined by restriction fragment length polymorphism and sequence analysis. The five different genotypes or operational taxonomic units (OTUs) that were identified on the basis of restriction fragment length polymorphism banding patterns were present in different relative abundances (9 to 34%). One clone from each OTU was sequenced, and phylogenetic analysis showed that all of the OTUs fell within the family Phycodnaviridae. Four of the OTUs fell within a group of viruses (MpV) which infect the photosynthetic picoplankter Micromonas pusilla. The genetic diversity among these genotypes was as large as that previously found for MpV isolates from different oceans. The remaining genotype formed its own clade between viruses which infect M. pusilla and Chrysochromulina brevifilum. These results imply that marine virus communities contain a diverse assemblage of MpV-like viruses, as well as other unknown members of the Phycodnaviridae.

Base Sequence↗

PubMed1997

Proteolytic processing of Chlorella virus CVK2 capsid proteins.

Chlorella virus CVK2 particles contain several capsid proteins that are selectively released by treatment with 4 M urea. Seven of them (Vp52, Vp45, Vp41, Vp25, Vp20.5, Vp20, and Vp16.2) have been identified based on amino acid sequences at the N-terminus. Comparison of the amino acid sequences with the corresponding ORFs deduced from the nucleotide sequence of PBCV-1, the prototype member of Phycodnaviridae, revealed that the CVK2 proteins were processed at the N-terminal region by two different proteolytic activities.

Amino Acid Sequence↗

PubMed1999

Genetic variation of chlorella viruses: variable regions localized on the CVK2 genomic DNA.

A physical map of the Chlorella virus CVK2 genomic DNA has been constructed based on a cosmid contig covering the entire genomic region. By using Southern blot analysis with 22 gene probes, the gene arrangement along the genome was compared between CVK2 and PBCV-1, the prototypic member of Phycodnaviridae, whose genomic sequence is now available. The major rearrangements were (1) an insertion of a 20-kbp region around the left end of CVK2 DNA, (2) a duplication of the gene for major capsid protein in CVK2 DNA, (3) deletions/insertions of some open reading frames, and (4) divergence in the terminal inverted repeat sequences. Despite these changes, extensive colinearity was revealed between most of the genes along the CVK2 and PBCV-1 genomes. These data imply that the Chlorella virus genome has an overall high degree of genomic stability, encompassing specific islands of rearrangements.

Amino Acid Sequence↗

PubMed2001

The complete DNA sequence of the Ectocarpus siliculosus Virus EsV-1 genome.

The Ectocarpus siliculosus Virus-1, EsV-1, is the type-species of a genus of Phycodnaviridae, the phaeoviruses, infecting marine filamentous brown algae. The EsV-1 genome of 335,593 bp contains tandem and dispersed repetitive elements in addition to a large number of open reading frames of which 231 are currently counted as genes. Many genes can be assigned to functional groups involved in DNA synthesis, DNA integration, transposition, and polysaccharide metabolism. Furthermore, EsV-1 contains components of a surprisingly complex signal transduction system with six different hybrid histidine protein kinases and four putative serine/threonine protein kinases. Several other genes encode polypeptides with protein-protein interaction domains. However, 50% of the predicted genes have no counterparts in data banks. Only 28 of the 231 identified genes have significant sequence similarities to genes of the Chlorella virus PBCV-1, another phycodnavirus. To our knowledge, the EsV-1 genome is the largest viral DNA sequenced to date.

Amino Acid Sequence↗

PubMed2001

Isolation and characterization of two viruses with large genome size infecting Chrysochromulina ericina (Prymnesiophyceae) and Pyramimonas orientalis (Prasinophyceae).

Two lytic viruses specific for Chrysochromulina ericina (Prymnesiophyceae) and for Pyramimonas orientalis (Prasinophyceae) were isolated from Norwegian coastal waters in June 1998. The lytic cycle was 14-19 h for both viruses; the burst size was estimated at 1800-4100 viruses per host cell for the Chrysochromulina virus and 800-1000 for the Pyramimonas virus. Thin sections of infected cells show that both viruses replicate in the cytoplasm and that they have a hexagonal cross section, indicating icosahedral symmetry. The Chrysochromulina virus had a particle size of 160 nm and a genome size of 510 kbp; the size of the major polypeptide was 73 kDa. The Pyramimonas virus had a particle size of 220 x 180 nm and a genome size of 560 kbp; the size of the major polypeptide was 44 kDa. The genome sizes of these viruses are among the largest ever reported for viruses and they are larger than the minimum required for cellular life. The Chrysochromulina virus clone CeV-01B and the Pyramimonas virus clone PoV-01B described in this study have several properties in common with other viruses infecting microalgae, suggesting that they belong to the Phycodnaviridae.

Chlorophyta↗

PubMed2005

Preliminary characterisation of repeat families in the genome of EhV-86, a giant algal virus that infects the marine microalga Emiliania huxleyi.

EhV-86 is a large double stranded DNA virus with a 407,339 base pair circular genome that infects the globally important microalga Emiliania huxleyi. It belongs to a new genus of viruses termed the Coccolithoviridae within the algal virus family Phycodnaviridae. By plotting the EhV-86 genome against itself in a dot-plot analysis we revealed three families of distinctly different repeat sequences throughout its genome, designated Family A, B and C. Family A repeats are non-coding, found immediately upstream of 86 predicted coding sequences (CDSs) and are likely to play a crucial role in controlling the expression of the associated CDSs. Family B repeats are GC rich, coding and correspond to possible calcium binding sites in 22 proline-rich domains found in the protein products of eight predicted EhV-86 CDSs. Family C repeats are AT-rich, non-coding and are likely to form part of the origin of replication. We suggest that these repeat regions are of fundamental importance during virus propagation being involved with transcriptional control (Family A), virus adsorption/release (Family B) and DNA replication (Family C).

Base Composition↗

PubMed2004

The use of degenerate-primed random amplification of polymorphic DNA (DP-RAPD) for strain-typing and inferring the genetic similarity among closely related viruses.

Often it is necessary to distinguish among strains of closely related viruses, as well as infer the genetic relatedness within large groups of viruses. Current methods for strain-typing viruses are time-consuming, require significant quantities of extracted DNA, and/or may require a priori genetic information. In this study we modified random amplification of polymorphic DNA (RAPD) by using a degenerate primer to produce unique and reproducible banding patterns from viral genomes. In the degenerate-primed RAPD analysis (DP-RAPD), a selection of algal virus and bacteriophage strains were profiled that encompassed an array of genome sizes and virus families. Closely related viruses (e.g. strains infecting Micromonas pusilla) generated similar, yet unique DP-RAPD patterns that could be readily distinguished from viruses within the same family (Phycodnaviridae) infecting a Chlorella-like alga. As well, marine vibriophage from the families Myoviridae, Siphoviridae, and Podoviridae showed high diversity and were distinct from coliphage and cyanophage. Contamination of host DNA, even at levels above those that would normally be encountered, did not interfere with the viral patterns. These findings describe a rapid, PCR-based tool for strain-typing viral isolates that allows inferences to be made on genetic relatedness within groups of closely related viruses.

Caudovirales↗

PubMed2005

Characterization of different viruses infecting the marine harmful algal bloom species Phaeocystis globosa.

Twelve lytic viruses (PgV) infecting the marine unicellular eukaryotic harmful algal bloom species Phaeocystis globosa were isolated from the southern North Sea in 2000-2001 and partially characterized. All PgV isolates shared common phenotypic features with other algal viruses belonging to the family Phycodnaviridae and could be categorized in four different groups. Two main groups (PgV Group I and II) were discriminated based on particle size (150 and 100 nm respectively), genome size (466 and 177 kb) and structural protein composition. The lytic cycle showed a latent period of 10 h for PgV Group I and latent periods of 12 h and 16 h for PgV Group IIA and IIB. Host specificity and temperature sensitivity finally defined a fourth group (PgV Group IIC). Our results imply that viral infection plays an important role not only in P. globosa dynamics but also in the diversity of both host and virus community.

Eukaryota↗

PubMed2006

Sequence and annotation of the 369-kb NY-2A and the 345-kb AR158 viruses that infect Chlorella NC64A.

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.

Amino Acid Sequence↗