Chloroviruses

Chloroviruses are large dsDNA, plaque-forming viruses that infect certain chlorella-like green algae; the algae are normally mutualistic endosymbionts of protists and metazoans and are often referred to as zoochlorellae. The viruses are ubiquitous in inland aqueous environments throughout the world and occasionally single types reach titers of thousands of plaque-forming units per ml of native water. The viruses are icosahedral in shape with a spike structure located at one of the vertices. They contain an internal membrane that is required for infectivity. The viral genomes are 290 to 370 kb in size, which encode up to 16 tRNAs and 330 to ~415 proteins, including many not previously seen in viruses. Examples include genes encoding DNA restriction and modification enzymes, hyaluronan and chitin biosynthetic enzymes, polyamine biosynthetic enzymes, ion channel and transport proteins, and enzymes involved in the glycan synthesis of the virus major capsid glycoproteins. The proteins encoded by many of these viruses are often the smallest or among the smallest proteins of their class. Consequently, some of the viral proteins are the subject of intensive biochemical and structural investigation.

Algal Viruses: The (Atomic) Shape of Things to Come

Visualization of algal viruses has been paramount to their study and understanding. The direct observation of the morphological dynamics of infection is a highly desired capability and the focus of instrument development across a variety of microscopy technologies. However, the high temporal (ms) and spatial resolution (nm) required, combined with the need to operate in physiologically relevant conditions presents a significant challenge. Here we present a short history of virus structure study and its relation to algal viruses and highlight current work, concentrating on electron microscopy and atomic force microscopy, towards the direct observation of individual algae⁻virus interactions. Finally, we make predictions towards future algal virus study direction with particular focus on the exciting opportunities offered by modern high-speed atomic force microscopy methods and instrumentation.

Structural studies demonstrating a bacteriophage-like replication cycle of the eukaryote-infecting Paramecium bursaria chlorella virus-1

A fundamental stage in viral infection is the internalization of viral genomes in host cells. Although extensively studied, the mechanisms and factors responsible for the genome internalization process remain poorly understood. Here we report our observations, derived from diverse imaging methods on genome internalization of the large dsDNA Paramecium bursaria chlorella virus-1 (PBCV-1). Our studies reveal that early infection stages of this eukaryotic-infecting virus occurs by a bacteriophage-like pathway, whereby PBCV-1 generates a hole in the host cell wall and ejects its dsDNA genome in a linear, base-pair-by-base-pair process, through a membrane tunnel generated by the fusion of the virus internal membrane with the host membrane. Furthermore, our results imply that PBCV-1 DNA condensation that occurs shortly after infection probably plays a role in genome internalization, as hypothesized for the infection of some bacteriophages. The subsequent perforation of the host photosynthetic membranes presumably enables trafficking of viral genomes towards host nuclei. Previous studies established that at late infection stages PBCV-1 generates cytoplasmic organelles, termed viral factories, where viral assembly takes place, a feature characteristic of many large dsDNA viruses that infect eukaryotic organisms. PBCV-1 thus appears to combine a bacteriophage-like mechanism during early infection stages with a eukaryotic-like infection pathway in its late replication cycle.

Although extensively studied, the mechanisms responsible for internalization of viral genomes into their host cells remain unclear. A particularly interesting case of genome release and internalization is provided by the large Paramecium bursaria chlorella virus-1 (PBCV-1), which infects unicellular eukaryotic photosynthetic chlorella cells. In order to release its long dsDNA genome and to enable its translocation to the host nucleus, PBCV-1 must overcome multiple hurdles, including a thick host cell wall and multilayered chloroplast membranes that surround the host cytoplasm. Our observations indicate that these obstacles are dealt with perforations of the host wall, the host cellular membrane, and the host photosynthetic membranes by viral-encoded proteins. Furthermore, our results highlight a bacteriophage-like nature of early PBCV-1 infection stages, thus implying that this virus uniquely combines bacteriophage-like and eukaryotic-like pathways to accomplish its replication cycle.

Chloroviruses: not your everyday plant virus

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.

An icosahedral algal virus has a complex unique vertex decorated by a spike

Paramecium bursaria Chlorella virus-1 is an icosahedrally shaped, 1,900-A-diameter virus that infects unicellular eukaryotic green algae. A 5-fold symmetric, 3D reconstruction using cryoelectron microscopy images has now shown that the quasiicosahedral virus has a unique vertex, with a pocket on the inside and a spike structure on the outside of the capsid. The pocket might contain enzymes for use in the initial stages of infection. The unique vertex consists of virally coded proteins, some of which have been identified. Comparison of shape, size, and location of the spike with similar features in bacteriophages T4 and P22 suggests that the spike might be a cell-puncturing device. Similar asymmetric features may have been missed in previous analyses of many other viruses that had been assumed to be perfectly icosahedral.

The Phycodnaviridae: the story of how tiny giants rule the world

The family Phycodnaviridae encompasses a diverse and rapidly expanding 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). The phycodnaviruses have diverse genome structures, some with large regions of noncoding sequence and others with regions of ssDNA. The genomes of members in three genera in the Phycodnaviridae have been sequenced. The genome analyses have revealed more than 1000 unique genes, with only 14 homologous genes in common among the three genera of phycodnaviruses sequenced to date. Thus, their gene diversity far exceeds the number of so-called core genes. Not much is known about the replication of these viruses, but the consequences of these infections on phytoplankton have global affects, including influencing geochemical cycling and weather patterns.

Chlorella viruses

Chlorella viruses or chloroviruses are large, icosahedral, plaque-forming, double-stranded-DNA-containing viruses that replicate in certain strains of the unicellular green alga Chlorella. DNA sequence analysis of the 330-kbp genome of Paramecium bursaria chlorella virus 1 (PBCV-1), the prototype of this virus family (Phycodnaviridae), predict approximately 366 protein-encoding genes and 11 tRNA genes. The predicted gene products of approximately 50% of these genes resemble proteins of known function, including many that are completely unexpected for a virus. In addition, the chlorella viruses have several features and encode many gene products that distinguish them from most viruses. These products include: (1) multiple DNA methyltransferases and DNA site-specific endonucleases, (2) the enzymes required to glycosylate their proteins and synthesize polysaccharides such as hyaluronan and chitin, (3) a virus-encoded K(+) channel (called Kcv) located in the internal membrane of the virions, (4) a SET domain containing protein (referred to as vSET) that dimethylates Lys27 in histone 3, and (5) PBCV-1 has three types of introns; a self-splicing intron, a spliceosomal processed intron, and a small tRNA intron. Accumulating evidence indicates that the chlorella viruses have a very long evolutionary history. This review mainly deals with research on the virion structure, genome rearrangements, gene expression, cell wall degradation, polysaccharide synthesis, and evolution of PBCV-1 as well as other related viruses.

A model-based parallel origin and orientation refinement algorithm for cryoTEM and its application to the study of virus structures

We present a model-based parallel algorithm for origin and orientation refinement for 3D reconstruction in cryoTEM. The algorithm is based upon the Projection Theorem of the Fourier Transform. Rather than projecting the current 3D model and searching for the best match between an experimental view and the calculated projections, the algorithm computes the Discrete Fourier Transform (DFT) of each projection and searches for the central section ("cut") of the 3D DFT that best matches the DFT of the projection. Factors that affect the efficiency of a parallel program are first reviewed and then the performance and limitations of the proposed algorithm are discussed. The parallel program that implements this algorithm, called PO(2)R, has been used for the refinement of several virus structures, including those of the 500 Angstroms diameter dengue virus (to 9.5 Angstroms resolution), the 850 Angstroms mammalian reovirus (to better than 7A), and the 1800 Angstroms paramecium bursaria chlorella virus (to 15 Angstroms).

Isolation and characterization of a new type of chlorovirus that infects an endosymbiotic Chlorella strain of the heliozoon Acanthocystis turfacea

A novel virus, named Acanthocystis turfacea Chlorella virus (ATCV), that infects endosymbiotic Chlorella algae of the heliozoon Acanthocystis turfacea was isolated from freshwater samples. Electron microscopic analysis of ATCV revealed that the viral capsid has a distinct icosahedral shape with a diameter of 140-190 nm. Filamentous structures extending from some of the virus vertices, which may aid attachment of the virus to host cells, were also observed. The capsid is made up of one major coat protein of about 50 kDa and contains a large dsDNA genome. ATCV is a member of the genus Chlorovirus, which belongs to the family Phycodnaviridae, a group of large, icosahedral, dsDNA-containing viruses that infect algae and are ubiquitous in natural environments. However, ATCV is clearly distinct from the prototype Chlorovirus, Paramecium bursaria Chlorella virus (PBCV-1), in some aspects of its genome structure and gene content and therefore must be regarded as a member of a new group of Chlorella viruses.

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.

Structural analyses ofPhycodnaviridaeandIridoviridae

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.

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.

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.

The brown algal virus EsV-1 particle contains a putative hybrid histidine kinase

The Ectocarpus siliculosus virus, EsV-1, occurs worldwide in all populations of the filamentous marine brown alga E. siliculosus. We have screened an expression library of EsV-1 restriction fragments and identified a DNA clone with the potential to code for a 52-kDa histidine protein kinase. The derived amino acid sequence includes all homology boxes diagnostic for histidine protein kinases and, in addition, amino acid motifs that are commonly found in response regulators of bacterial two-component signal transduction proteins. Thus, the novel viral protein can be classified as a hybrid histidine protein kinase of a type that has previously been detected in fungi, slime molds, and plants. By using purified antibodies, we found that the protein with its potential kinase activity is located on the outer shell of viral particles. This is the first report on a two-component regulator-like protein in viruses and could provide the basis for speculations with regard to the evolution of EsV-1 and related viruses.

Characterization and immunolocalization of major structural proteins in the brown algal virus EsV-1

The Ectocarpus siliculosus virus (EsV-1) is endemic in all populations of the cosmopolitan filamentous brown alga Ectocarpus siliculosus. EsV-1 has a large circular double-stranded DNA genome of about 320 kilobase pairs, and a complex virion structure with a central nucleoprotein core surrounded by several proteinaceous layers. To investigate the protein composition of the virion, we screened an expression library of EsV-1 with antibodies raised against purified detergent-disrupted viral particles. We isolated several clones encoding novel structural proteins and investigated two of them in detail. These clones encode viral proteins vp55 and vp74. Electron microscopy reveals that vp55 is most likely a component of the surface of the viral core, whereas vp74 may be part of an inner core structure. To initiate a genetic analysis, we sequenced regions of the EsV-1 genome encoding vp55 and vp74 and found several adjacent open reading frames with the potential to code for several interesting viral proteins including a putative calcium-binding protein, a collagen-like protein, and a RING finger protein.

Comparison of two DNA viruses infecting the marine brown algae Ectocarpus siliculosus and E. fasciculatus

The marine brown algal genus Ectocarpus contains two species, E. siliculosus and E. fasciculatus. Field populations of both species include plants with infection symptoms caused by DNA viruses. We have established clonal cultures from infected and normal host plants and investigated the properties of the endogenous viruses. Both host species contain virus particles with a hexagonal cross-section and a diameter of ca. 150 nm. The genomes of both virus types consist of double-stranded DNA, approximately 320 kb in size. Restriction digestion with Sfil revealed differences between the two virus genomes. However, PCR experiments suggest that at least one gene, which encodes a major capsid protein, is quite similar in both virus species. In cross-infection experiments the E. siliculosus virus did not initiate an infection cycle in E. fasciculatus. In contrast, the E. fasciculatus virus infected E. siliculosus zoospores. The resulting plants showed aberrant symptoms and produced virus particles which were not infectious. We conclude that the two Ectocarpus species are hosts for different, but closely related viruses.

Hairpin loop structure at the termini of the chlorella virus PBCV-1 genome

The termini of the chlorella virus PBCV-1 330-kb dsDNA genome consist of 35-nucleotide-long, incompletely base-paired, covalently closed hairpin loops that exist in one of two forms. The two forms are complementary when the 35 nucleotide sequences are inverted with respect to one another (flip and flop). Each hairpin loop structure is followed by an identical 2221-bp inverted repeat sequence after which the DNA sequence diverges. The strategy for cloning the PBCV-1 DNA hairpin ends may be useful for cloning other hairpin termini.