Transcription and sequence studies of a 4.3-kbp fragment from a ds-DNA eukaryotic algal virus

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.

Deep RNA sequencing reveals hidden features and dynamics of early gene transcription in Paramecium bursaria chlorella virus 1

Paramecium bursaria chlorella virus 1 (PBCV-1) is the prototype of the genus Chlorovirus (family Phycodnaviridae) that infects the unicellular, eukaryotic green alga Chlorella variabilis NC64A. The 331-kb PBCV-1 genome contains 416 major open reading frames. A mRNA-seq approach was used to analyze PBCV-1 transcriptomes at 6 progressive times during the first hour of infection. The alignment of 17 million reads to the PBCV-1 genome allowed the construction of single-base transcriptome maps. Significant transcription was detected for a subset of 50 viral genes as soon as 7 min after infection. By 20 min post infection (p.i.), transcripts were detected for most PBCV-1 genes and transcript levels continued to increase globally up to 60 min p.i., at which time 41% or the poly (A+)-containing RNAs in the infected cells mapped to the PBCV-1 genome. For some viral genes, the number of transcripts in the latter time points (20 to 60 min p.i.) was much higher than that of the most highly expressed host genes. RNA-seq data revealed putative polyadenylation signal sequences in PBCV-1 genes that were identical to the polyadenylation signal AAUAAA of green algae. Several transcripts have an RNA fragment excised. However, the frequency of excision and the resulting putative shortened protein products suggest that most of these excision events have no functional role but are probably the result of the activity of misled splicesomes.

The A312L 5'-UTR of Chlorella virus PBCV-1 is a translational enhancer in Arabidopsis thaliana

PBCV-1 (Paramecium bursaria Chlorella virus) is a large double stranded DNA virus that replicates in certain eukaryotic chlorella like green algae. The PBCV-1 A312L gene encodes a 33-kDa protein whose function currently is unknown. The 5'-UTR of the A312L mRNA is 153 nucleotides, longer than the 5'-UTR in any other PBCV-1 gene. The sequence 5'-AAAC was repeated 17 times within 156bp 5' to the A312L gene start codon and this sequence was repeated 13 times continuously in the 5'-UTR of the mRNA. Recombinant genes were constructed in vector pBI121 that contained the A312L 5'-UTR, in both the forward and inverse-complement orientations, fused to the GUS gene under the control of the CaMV 35S promoter. These constructs were introduced into Arabidopsis thaliana and the results indicated that the A312L 5'-UTR functions as a translational enhancer only in the forward orientation. Overall, the ratio of GUS enzyme activity to GUS mRNA was 15-fold higher in constructs derived from the A312L 5'-UTR in the forward orientation as compared to constructs containing the 5'-UTR in the inverse-complement orientation or those lacking the A312L 5'-UTR.

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.

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).

Chlorovirus: a genus of Phycodnaviridae that infects certain chlorella-like green algae

SUMMARY Taxonomy: Chlorella viruses are assigned to the family Phycodnaviridae, genus Chlorovirus, and are divided into three species: Chlorella NC64A viruses, Chlorella Pbi viruses and Hydra viridis Chlorella viruses. Chlorella viruses are large, icosahedral, plaque-forming, dsDNA viruses that infect certain unicellular, chlorella-like green algae. The type member is Paramecium bursaria chlorella virus 1 (PBCV-1). Physical properties: Chlorella virus particles are large (molecular weight approximately 1 x 10(9) Da) and complex. The virion of PBCV-1 contains more than 100 different proteins; the major capsid protein, Vp54, comprises approximately 40% of the virus protein. Cryoelectron microscopy and three-dimensional image reconstruction of PBCV-1 virions indicate that the outer glycoprotein-containing capsid shell is icosahedral and surrounds a lipid bilayered membrane. The diameter of the viral capsid ranges from 1650 A along the two- and three-fold axes to 1900 A along the five-fold axis. The virus contains 5040 copies of Vp54, and the triangulation number is 169. The PBCV-1 genome is a linear, 330 744-bp, non-permuted dsDNA with covalently closed hairpin ends. The PBCV-1 genome contains approximately 375 protein-encoding genes and 11 tRNA genes. About 50% of the protein-encoding genes match proteins in the databases. Hosts: Chlorella NC64A and Chlorella Pbi, the hosts for NC64A viruses and Pbi viruses, respectively, are endosymbionts of the protozoan Paramecium bursaria. However, they can be grown in the laboratory free of both the paramecium and the virus. These two chlorella species are hosts to viruses that have been isolated from fresh water collected around the world. The host for hydra chlorella virus, a symbiotic chlorella from Hydra viridis, has not been grown independently of its host; thus the virus can only be obtained from chlorella cells freshly released from hydra.

Genetic diversity in chlorella viruses flanking kcv, a gene that encodes a potassium ion channel protein

The chlorella virus PBCV-1 encodes a 94-amino acid protein named Kcv that produces a K+-selective and slightly voltage-sensitive conductance when expressed in heterologous systems. As reported herein, (i) Northern analysis of kcv expression in PBCV-1-infected cells revealed a complicated pattern suggesting that the gene might be transcribed as a di- or tri-cistronic mRNA both at early and late times after virus infection. (ii) The protein kinase inhibitors H-89, A3, and staurosporine inhibited PBCV-1 Kcv activity in Xenopus oocytes, suggesting that Kcv activity might be controlled by phosphorylation or dephosphorylation. (iii) The PBCV-1 genomic sequence revealed a gene encoding a putative protein kinase (pkx) adjacent to kcv. These findings prompted us to examine the kcv flanking regions in 16 additional chlorella viruses and transcription in two of these viruses, as well as the effect of the three protein kinase inhibitors on two Kcv homologs in Xenopus oocytes. The results indicate (i) pkx is always located 5' to kcv, but the spacing between the two genes varies from 31 to 1588 nucleotides. More variation occurs in the kcv 3' flanking region of the 16 viruses. (ii) The kcv gene is expressed as a late mono-cistronic mRNA. (iii) Unlike the affect on PBCV-1 Kcv, the three protein kinase inhibitors have little or no effect on the activity of the two Kcv homologs in oocytes. (iv) A comparison of the kcv 5' upstream sequences from the 16 viruses identified a highly conserved 10-nucleotide sequence that is present in the promoter region of all of the viruses.

Immediate early genes expressed in chlorovirus infections

Twenty-three chlorovirus genes expressed in host cells as early as 5-10 min postinfection (p.i.), or immediate early, were isolated and characterized. Some showed significant homology with those for transcriptional factors and mRNA-processing proteins including TFIIB, helicases, mRNA capping enzyme, nucleolin, and bean transcription factor. Others code for (i) factors influencing translation such as aminoacyl tRNA synthetases and ribosomal protein, and (ii) unknown proteins. Enzymes involved in polysaccharide synthesis were also found. All transcripts of these genes had a poly(A) tail, which decreased in size after 20 min p.i., possibly caused by the shortening by an exonuclease. Often, due to readthrough either from an upstream ORF or into a downstream ORF, a few extra transcripts for each gene appeared after 40 min p.i., suggesting a change in promoter selection and termination accuracy at this point. A typical TATA-box and a common element 5'-ATGACAA were in the promoter region of almost all of the immediate early genes, which may be recognized by host RNA polymerase and transcription factors.

Unusual life style of giant chlorella viruses

Paramecium bursaria chlorella virus (PBCV-1) is the prototype of a family of large, icosahedral, plaque-forming, dsDNA viruses that replicate in certain unicellular, eukaryotic chlorella-like green algae. Its 330-kb genome contains approximately 373 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 unexpected for a virus, e.g., ornithine decarboxylase, hyaluronan synthase, GDP-D-mannose 4,6 dehydratase, and a potassium ion channel protein. In addition to their large genome size, the chlorella viruses have other features that distinguish them from most viruses. These features include: (a) The viruses encode multiple DNA methyltransferases and DNA site-specific endonucleases. (b) The viruses encode at least some, if not all, of the enzymes required to glycosylate their proteins. (c) PBCV-1 has at least three types of introns, a self-splicing intron in a transcription factor-like gene, a spliceosomal processed intron in its DNA polymerase gene, and a small intron in one of its tRNA genes. (d) Many chlorella virus-encoded proteins are either the smallest or among the smallest proteins of their class. (e) Accumulating evidence indicates that the chlorella viruses have a very long evolutionary history.

Comparisons of two large phaeoviral genomes and evolutionary implications

The evolution of viral genomes has recently attracted considerable attention. We compare the sequences of two large viral genomes, EsV-1 and FirrV-1, belonging to the family of phaeoviruses which infect different species of marine brown algae. Although their genomes differ substantially in size, these viruses share similar morphologies and similar latent infection cycles. In fact, sequence comparisons show that the viruses have more than 60% of their genes in common. However, the order of genes is completely different in the two genomes, suggesting that extensive recombinational events in addition to several large deletions had occurred during the separate evolutionary routes from a common ancestor. We investigated genes encoding components of signal transduction pathways and genes encoding replicative functions in more detail. We found that the two genomes possess different, although overlapping, sets of genes in both classes, suggesting that different genes from each class were lost, perhaps randomly, after the separate evolution from an ancestral genome. Random loss would also account for the fact that more than one-third of the genes in one viral genome has no counterparts in the other genome. We speculate that the ancestral genome belonged to a cellular organism that had once invaded a primordial brown algal host.

Chitin synthesis in chlorovirus CVK2-infected chlorella cells

Hyaluronan synthesis in chlorovirus PBCV-1-infected Chlorella cells was previously reported (DeAngelis et al., 1997). In contrast, we report here on the detection, characterization, and expression of a gene for chitin synthase (chs) encoded by chlorovirus CVK2 isolated in Kyoto, Japan. The CVK2 chs gene encoding an open reading frame of 516 aa was expressed as early as 10 min postinfection (p.i.), peaked at 20-40 min p.i., and disappeared at 120-180 min p.i. The chitin polysaccharide began to accumulate as chitinase-sensitive, hair-like fibers on the outside of the virus-infected Chlorella cell wall by 30 min p.i. All chloroviruses without the gene for hyaluronan synthase (has) alternatively contained the chs gene, suggesting the importance of polysaccharide production in the course of virus infection. A few chloroviruses possessed both the chs and has genes and produced chitin and hyaluronan simultaneously. Polysaccharide accumulation on the algal surface may protect virus-infected algae from uptake by other organisms, such as protozoa. Since CVK2 was reported to encode two chitinases and one chitosanase, CVK2 is a very peculiar virus that encodes enzymes required for both the synthesis and the degradation of chitin materials.

A variable region on the chlorovirus CVK2 genome contains five copies of the gene for Vp260, a viral-surface glycoprotein

A 22.2-kb variable region near the left end of the chlorovirus CVK2 genome that was previously supposed to be expanded compared to the PBCV-1 genome was characterized. This region contains a tandem array of five gene copies for the Vp260-like protein, a viral-surface glycoprotein. The authentic 104-kDa Vp260 was found to be encoded at another site on the genome and to contain 13 internal tandem repeats of 61-65 amino acids, similar to the prominent Rickettsia surface antigen. The extra copies were also found to retain 10 of the internal repeats, despite the C-terminal deletions or extensions. These extra copies are conserved among chloroviruses isolated in various areas of Japan. By Northern blot analysis, these genes were demonstrated to be expressed late in infection. The proteins are incorporated into virions, as revealed by comparing viral structural proteins between wild-type and deletion mutants. These results indicate that extra copies of Vp260-like proteins encoded in a variable region on the genome may give variations in the surface nature of the chloroviral particles.

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.

Aminoacylation of tRNAs encoded by Chlorella virus CVK2

Viruses that infect certain strains of the unicellular green alga, Chlorella, have a large, linear dsDNA genome that is 330-380 kb in size; this genomic size is the largest known among viruses and is equivalent to approximately 60% of the smallest prokaryotic genome of Mycoplasma genitalium (580 kb). Besides many putative protein-coding genes, a cluster of 10-15 tRNA genes is present in these viral genomes. Some of these tRNA genes contain peculiar insertions. In infected host cells, the viral tRNAs of CVK2, a Chlorella virus isolate, have been demonstrated to be cotranscribed as a large precursor, approximately 1.0 kb in size, that is precisely processed into individual mature tRNA species. Acidic Northern blot analysis of eight of these tRNAs has revealed that they are actually aminoacylated in vivo, indicating their involvement in viral protein synthesis. They may help the virus reach maximal replication potential by overcoming codon usage barriers that exist between the virus and its host. These results provide evidence that some components of the host protein synthesis machinery can be replaced by viral gene products. This is the first report of tRNA aminoacylation encoded by viruses of eukaryotes.

Giant viruses infecting algae

Paramecium bursaria chlorella virus (PBCV-1) is the prototype of a family of large, icosahedral, plaque-forming, double-stranded-DNA-containing viruses that replicate in certain unicellular, eukaryotic chlorella-like green algae. DNA sequence analysis of its 330, 742-bp genome leads to the prediction that this phycodnavirus has 376 protein-encoding genes and 10 transfer RNA genes. The predicted gene products of approximately 40% of these genes resemble proteins of known function. The chlorella viruses have other features that distinguish them from most viruses, in addition to their large genome size. These features include the following: (a) The viruses encode multiple DNA methyltransferases and DNA site-specific endonucleases; (b) PBCV-1 encodes at least part, if not the entire machinery to glycosylate its proteins; (c) PBCV-1 has at least two types of introns--a self-splicing intron in a transcription factor-like gene and a splicesomal processed type of intron in its DNA polymerase gene. Unlike the chlorella viruses, large double-stranded-DNA-containing viruses that infect marine, filamentous brown algae have a circular genome and a lysogenic phase in their life cycle.

Chlorella virus PBCV-1 encodes functional glutamine: fructose-6-phosphate amidotransferase and UDP-glucose dehydrogenase enzymes

DNA sequence analysis of the 330-kb Chlorella virus PBCV-1 genome unexpectedly revealed several open reading frames which encode proteins that are homologous to sugar-manipulating enzymes including glutamine:fructose-6-phosphate amidotransferase (GFAT), UDP-glucose dehydrogenase (UDP-GlcDH), and hyaluronan synthase (HAS). PBCV-1 genes encoding the putative GFAT and UDP-GlcDH enzymes were expressed in Escherichia coli, and both recombinant proteins have the predicted enzyme activity in cell free extracts. These same two genes are transcribed early in PBCV-1 infection, and both genes are widespread among the Chlorella viruses. The products of the reactions catalyzed by these two enzymes are precursors in the biosynthesis of hyaluronan polysaccharide. Previous experiments established that, like the GFAT and UDP-GlcDH genes, the HAS gene is transcribed early and encodes a functional enzyme (DeAngelis, P. L., Jing. W., Graves, M. V., Burbank, D. E., and Van Etten, J. L. (1997) Science 278, 1800-1803). Interestingly, the predicted amino-acid sequences of the PBCV-1 GFAT and UDP-GlcDH enzymes are more similar to bacterial GFAT and UDP-GlcDH enzymes than to their eukaryotic counterparts. In contrast, the amino-acid sequence of the PBCV-1 HAS enzyme more closely resembles eukaryotic enzymes.

Alternative expression of a chitosanase gene produces two different proteins in cells infected with Chlorella virus CVK2

Several Chlorella virus CVK2 proteins had chitosanase and/or chitinase activities. A gene coding for an ORF of 328 amino acids (aa) with a predicted molecular mass of 36,769 Da was cloned from the viral genome. The predicted amino acid sequence of an N'-portion (174 aa) of this gene product (vChta-1) showed 22 to 25% identity with various bacterial chitosanases. A glutathione S-transferase (GST)-vChta-1 fusion protein had strong chitosanase activity. Western blot analysis with antisera raised against the vChta-1 protein identified two proteins of 37 and 65 kDa in virus-infected Chlorella cells beginning at 240 min postinfection and continuing until cell lysis. The larger protein was packaged in the virion, while the smaller one remained in the cell lysate. Both chitosanase proteins were produced from the single gene, vChta-1, by a mechanism of alternative gene expression.

Cloning and applications of the two/three-base restriction endonuclease R.CviJI from IL-3A virus-infected Chlorella

The gene (cviJIR) encoding the two/three-base R.CviJI eukaryotic restriction endonuclease (ENase) from IL-3A virus-infected Chlorella was cloned into Escherichia coli. A high frequency of DNA cleavage by R.CviJI required overexpression of the gene encoding the M.CviJI methyltransferase prior to cloning the gene for the ENase. Both genes were sequenced and their organization was determined to be in head-to-tail order. The open reading frame coding for R.CviJI can potentially translate a 41.4-kDa protein; however, in the E. coli host, a truncated version of the enzyme is produced (32.5 kDa). The recombinant ENase does not exhibit ATP-induced 'star' activity (R.CviJI cleaves at RGCY, while R.CviJI* also cleaves at RGCR and YGCY, but not at YGCR), as is characteristic for native R.CviJI. The very high frequency of DNA cleavage by R.CviJI* was exploited in the development of a quasi-random shotgun library method. R.CviJI*-generated oligodeoxyribonucleotides were applied to improve certain molecular biology applications, i.e., DNA labeling, detection, high-resolution restriction mapping, amplification and epitope mapping.

Characterization of a protein kinase gene from two Chlorella viruses

An open reading frame (ORF) with strong homology to eukaryotic serine/threonine protein kinases was found in the two Chlorella viruses SC-1A and PBCV-1. The deduced molecular weights of each putative protein kinase were 35 kDa and the predicted amino acid sequences of the two proteins were 95% identical. The ORF encoding the SC-1A protein kinase was over-expressed as a fusion protein in Escherichia coli. The recombinant fusion protein had autophosphorylation activity and could phosphorylate certain exogenous proteins. Antiserum against the recombinant fusion protein reacted with a 35 kDa protein plus three larger proteins from virus infected cells. The 35 kDa protein was a late protein; however, the 35 kDa protein was not packaged in the virion, even though virions contain protein kinase activity.

Analysis of 45 kb of DNA located at the left end of the chlorella virus PBCV-1 genome

Forty-five kilobases of DNA, including the previously sequenced 2.2-kb inverted repeat region, located at the left termini of the 330-kb Chlorella virus PBCV-1 genome were sequenced and analyzed. Eighty-five complete open reading frames (ORFs) larger than 195 nucleotides were identified. Thirty-seven of the 85 ORFs, which are densely packed on both strands of the DNA, were considered major ORFs. Fifteen of the major ORFs have similarity to genes in the databases, including bacterial glycerophosphoryl diester phosphodiesterase, bacteriophage T4 endonuclease V, D-isomer specific 2-hydroxyacid dehydrogenases, and beta-alanine synthetase and bacterial nitrilases. Two major ORFs resemble the virus major capsid protein. Three major ORFs contain three or more ankyrin-like repeat elements and four ORFs encode proline-rich proteins.

Coat protein of the Ectocarpus siliculosus virus

Ectocarpus siliculosus virus, EsV, multiplies in sporangia and gametangia of the marine brown alga Ectocarpus siliculosus. We describe an improved method for the isolation of morphologically intact and infectious virus from diseased plants. We show that treatment of virus particles with high concentrations of CsCl results in a substantial loss of structural proteins. One of the proteins which resists CsCl treatment is glycoprotein-1, the largest of the three viral glycoproteins. We have isolated an EsV genomic fragment with an open reading frame encoding glycoprotein-1. The predicted amino acid sequence is rich in hydrophilic amino acids, but contains hydrophobic regions close to the amino and carboxy termini. A discrepancy between the molecular weight predicted from the coding region and the molecular weight determined by gel electrophoresis suggests that proteolytic processing is required for the maturation of the protein.

Characterization of Chlorella virus PBCV-1 CviAII restriction and modification system

A second DNA site-specific (restriction) endonuclease (R.CviAII) and its cognate adenine DNA methyltransferase (M.CviAII) were isolated from virus PBCV-1 infected Chlorella strain NC64A cells. R.CviAII, a heteroschizomer of the bacterial restriction endonuclease NlaIII, recognizes the sequence CATG, and does not cleave CmATG sequences. However, unlike NlaIII, which cleaves after the G and does not cleave either CmATG or mCATG sequences, CviAII cleaves between the C and A and is unaffected by mCATG methylation. The M.CviAII and R.CviAII genes were cloned and their DNA sequences were determined. These genes are tandemly arranged head-to-tail such that the TAA termination codon of the M.CviAII methyltransferase gene overlaps the ATG translational start site of R.CviAII endonuclease. R.CviAII is the first chlorella virus site-specific endonuclease gene to be cloned and sequenced.

The DNA polymerase gene from chlorella viruses PBCV-1 and NY-2A contains an intron with nuclear splicing sequences

The deduced amino acid sequences of two eukaryotic chlorella virus (PBCV-1 and NY-2A) DNA polymerases are 90% identical and contain amino acid motifs typical of alpha-like (Family B) DNA polymerases. The open reading frames of both PBCV-1 and NY-2A DNA polymerases are interrupted by an identically located, small (101 or 86 nucleotides, respectively) intron that resembles eukaryotic nuclear-spliced messenger RNA introns. This discovery suggests that chlorella virus replication has a nuclear phase.

Characterization of the major capsid protein and cloning of its gene from algal virus PBCV-1

The major capsid protein (Vp54) from Chlorella virus PBCV-1 is a glycoprotein and the most abundant viral structural protein. The gene encoding Vp54 has been cloned and sequenced. Initially, a region of the gene was amplified using the polymerase chain reaction (PCR) primed with oligonucleotides derived from the N-terminal amino acid sequences of purified protein and cyanogen bromide cleavage fragments. The PCR product was used as a probe to map the location of the gene to PBCV-1 genomic Pstl restriction fragment P8. A 1314-bp open reading frame (ORF) was identified which contained the predicted coding regions from the derived amino acid sequences. The peptide encoded by this ORF had a predicted molecular weight of 48.2 kDa and contained six putative N-linked and 63 putative O-linked glycosylation sites. Primer extension analysis indicated that transcription started 14 bp 5' to the ATG. The gene for Vp54 was transcribed late in infection and this transcript was the most abundant viral RNA present in infected cells.

Characterization of the gene encoding the most abundant in vitro translation product from virus-infected Chlorella-like algae

The gene (33kDa) encoding a 33-kDa peptide from Chlorella virus, PBCV-1, was cloned and sequenced. This gene encodes the most abundant in vitro translation product synthesized from viral mRNAs isolated beginning at 20 min post-infection. The message persisted throughout the remainder of the viral life cycle. An open reading frame (ORF) of 717 bp, which encodes a polypeptide of 238 amino acids with a predicted M(r) or 26,613, was found on a 2752-bp cloned fragment from PBCV-1 HindIII restriction fragment 9. Transcriptional analysis of this ORF indicated that it was expressed both early and late, and as the viral life cycle progressed, the mRNA increased in size and abundance. Three other ORFs were also found; the largest of which (741 bp) hybridized to a low-abundance transcript which would encode a polypeptide with a predicted M(r) of 27,854.

Viruses and viruslike particles of eukaryotic algae

Until recently there was little interest or information on viruses and viruslike particles of eukaryotic algae. However, this situation is changing. In the past decade many large double-stranded DNA-containing viruses that infect two culturable, unicellular, eukaryotic green algae have been discovered. These viruses can be produced in large quantities, assayed by plaque formation, and analyzed by standard bacteriophage techniques. The viruses are structurally similar to animal iridoviruses, their genomes are similar to but larger (greater than 300 kbp) than that of poxviruses, and their infection process resembles that of bacteriophages. Some of the viruses have DNAs with low levels of methylated bases, whereas others have DNAs with high concentrations of 5-methylcytosine and N6-methyladenine. Virus-encoded DNA methyltransferases are associated with the methylation and are accompanied by virus-encoded DNA site-specific (restriction) endonucleases. Some of these enzymes have sequence specificities identical to those of known bacterial enzymes, and others have previously unrecognized specificities. A separate rod-shaped RNA-containing algal virus has structural and nucleotide sequence affinities to higher plant viruses. Quite recently, viruses have been associated with rapid changes in marine algal populations. In the next decade we envision the discovery of new algal viruses, clarification of their role in various ecosystems, discovery of commercially useful genes in these viruses, and exploitation of algal virus genetic elements in plant and algal biotechnology.

The termini of the chlorella virus PBCV-1 genome are identical 2.2-kbp inverted repeats

The Chlorella virus PBCV-1 genome is a linear nonpermuted 333-kbp dsDNA molecule with covalently closed hairpin termini. The termini (minus the hairpin) are identical inverted repeats of at least 2185 bases after which the sequence diverges. The inverted repeats contain two small potential open reading frames and several direct repeats. However, neither the open reading frames nor the remainder of the inverted repeats are transcribed during PBCV-1 replication. Twenty-nine other Chlorella virus DNAs, of 36 tested, hybridized to the PBCV-1 terminal fragments.

Molecular cloning and characterization of the gene encoding the adenine methyltransferase M.CviRI from Chlorella virus XZ-6E

The gene encoding the DNA methyltransferase M.CviRI from Chlorella virus XZ-6E was cloned and expressed in Escherichia coli. M.CviRI methylates adenine in TGCA sequences. DNA containing the M.CviRI gene was sequenced and a single open reading frame of 1137 bp was identified which could code for a polypeptide of 379 amino acids with a predicted molecular weight of 42,814. Comparison of the M.CviRI predicted amino acid sequence with another Chlorella virus and 14 bacterial adenine methyltransferases revealed extensive similarity to the other Chlorella virus enzyme.