Restriction endonuclease activity induced by PBCV-1 virus infection of a Chlorella-like green alga

Structure-Based Deep Mining Reveals First-Time Annotations for 46 Percent of the Dark Annotation Space of the 9,671-Member Superproteome of the Nucleocytoplasmic Large DNA Viruses

We conducted an exhaustive search for three-dimensional structural homologs to the proteins of 20 key phylogenetically distinct nucleocytoplasmic DNA viruses (NCLDV). Structural matches covered 429 known protein domain superfamilies, with the most highly represented being ankyrin repeat, P-loop NTPase, F-box, protein kinase, and membrane occupation and recognition nexus (MORN) repeat. Domain superfamily diversity correlated with genome size, but a diversity of around 200 superfamilies appeared to correlate with an abrupt switch to paralogization. Extensive structural homology was found across the range of eukaryotic RNA polymerase II subunits and their associated basal transcription factors, with the coordinated gain and loss of clusters of subunits on a virus-by-virus basis. The total number of predicted endonucleases across the 20 NCLDV was nearly quadrupled from 36 to 132, covering much of the structural and functional diversity of endonucleases throughout the biosphere in DNA restriction, repair, and homing. Unexpected findings included capsid protein-transcription factor chimeras; endonuclease chimeras; enzymes for detoxification; antimicrobial peptides and toxin-antitoxin systems associated with symbiosis, immunity, and addiction; and novel proteins for membrane abscission and protein turnover.IMPORTANCE We extended the known annotation space for the NCLDV by 46%, revealing high-probability structural matches for fully 45% of the 9,671 query proteins and confirming up to 98% of existing annotations per virus. The most prevalent protein families included ankyrin repeat- and MORN repeat-containing proteins, many of which included an F-box, suggesting extensive host cell modulation among the NCLDV. Regression suggested a minimum requirement for around 36 protein structural superfamilies for a viable NCLDV, and beyond around 200 superfamilies, genome expansion by the acquisition of new functions was abruptly replaced by paralogization. We found homologs to herpesvirus surface glycoprotein gB in cytoplasmic viruses. This study provided the first prediction of an endonuclease in 10 of the 20 viruses examined; the first report in a virus of a phenolic acid decarboxylase, proteasomal subunit, or cysteine knot (defensin) protein; and the first report of a prokaryotic-type ribosomal protein in a eukaryotic virus.

SMRT Sequencing of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability in Adenines Targeted by Restriction Modification Systems

Chloroviruses (family Phycodnaviridae) infect eukaryotic, freshwater, unicellular green algae. A unique feature of these viruses is an abundance of DNA methyltransferases, with isolates dedicating up to 4.5% of their protein coding potential to these genes. This diversity highlights just one of the long-standing values of the chlorovirus model system; where group-wide epigenomic characterization might begin to elucidate the function(s) of DNA methylation in large dsDNA viruses. We characterized DNA modifications in the prototype chlorovirus, PBCV-1, using single-molecule real time (SMRT) sequencing (aka PacBio). Results were compared to total available sites predicted in silico based on DNA sequence alone. SMRT-software detected N6-methyl-adenine (m6A) at GATC and CATG recognition sites, motifs previously shown to be targeted by PBCV-1 DNA methyltransferases M.CviAI and M. CviAII, respectively. At the same time, PacBio analyses indicated that 10.9% of the PBCV-1 genome had large interpulse duration ratio (ipdRatio) values, the primary metric for DNA modification identification. These events represent 20.6x more sites than can be accounted for by all available adenines in GATC and CATG motifs, suggesting base or backbone modifications other than methylation might be present. To define methylation stability, we cross-compared methylation status of each GATC and CATG sequence in three biological replicates and found ∼81% of sites were stably methylated, while ∼2% consistently lack methylation. The remaining 17% of sites were stochastically methylated. When methylation status was analyzed for both strands of each target, we show that palindromes existed in completely non-methylated states, fully-methylated states, or hemi-methylated states, though GATC sites more often lack methylation than CATG sequences. Given that both sequences are targeted by not just methyltransferases, but by restriction endonucleases that are together encoded by PBCV-1 as virus-originating restriction modification (RM) systems, there is strong selective pressure to modify all target sites. The finding that most instances of non-methylation are associated with hemi-methylation is congruent with observations that hemi-methylated palindromes are resistant to cleavage by restriction endonucleases. However, sites where hemi-methylation is conserved might represent a unique regulatory function for PBCV-1. This study serves as a baseline for future investigation into the epigenomics of chloroviruses and their giant virus relatives.

Schrödinger's Cheshire Cat: Are Haploid Emiliania huxleyi Cells Resistant to Viral Infection or Not?

Emiliania huxleyi is the main calcite producer on Earth and is routinely infected by a virus (EhV); a double stranded DNA (dsDNA) virus belonging to the family Phycodnaviridae. E. huxleyi exhibits a haplodiploid life cycle; the calcified diploid stage is non-motile and forms extensive blooms. The haploid phase is a non-calcified biflagellated cell bearing organic scales. Haploid cells are thought to resist infection, through a process deemed the “Cheshire Cat” escape strategy; however, a recent study detected the presence of viral lipids in the same haploid strain. Here we report on the application of an E. huxleyi CCMP1516 EhV-86 combined tiling array (TA) that further confirms an EhV infection in the RCC1217 haploid strain, which grew without any signs of cell lysis. Reverse transcription polymerase chain reaction (RT-PCR) and PCR verified the presence of viral RNA in the haploid cells, yet indicated an absence of viral DNA, respectively. These infected cells are an alternative stage of the virus life cycle deemed the haplococcolithovirocell. In this instance, the host is both resistant to and infected by EhV, i.e., the viral transcriptome is present in haploid cells whilst there is no evidence of viral lysis. This superimposed state is reminiscent of Schrödinger’s cat; of being simultaneously both dead and alive.

The salivary secretome of the tsetse fly Glossina pallidipes (Diptera: Glossinidae) infected by salivary gland hypertrophy virus

BACKGROUND

The competence of the tsetse fly Glossina pallidipes (Diptera; Glossinidae) to acquire salivary gland hypertrophy virus (SGHV), to support virus replication and successfully transmit the virus depends on complex interactions between Glossina and SGHV macromolecules. Critical requisites to SGHV transmission are its replication and secretion of mature virions into the fly's salivary gland (SG) lumen. However, secretion of host proteins is of equal importance for successful transmission and requires cataloging of G. pallidipes secretome proteins from hypertrophied and non-hypertrophied SGs.

METHODOLOGY/PRINCIPAL FINDINGS

After electrophoretic profiling and in-gel trypsin digestion, saliva proteins were analyzed by nano-LC-MS/MS. MaxQuant/Andromeda search of the MS data against the non-redundant (nr) GenBank database and a G. morsitans morsitans SG EST database, yielded a total of 521 hits, 31 of which were SGHV-encoded. On a false discovery rate limit of 1% and detection threshold of least 2 unique peptides per protein, the analysis resulted in 292 Glossina and 25 SGHV MS-supported proteins. When annotated by the Blast2GO suite, at least one gene ontology (GO) term could be assigned to 89.9% (285/317) of the detected proteins. Five (∼1.8%) Glossina and three (∼12%) SGHV proteins remained without a predicted function after blast searches against the nr database. Sixty-five of the 292 detected Glossina proteins contained an N-terminal signal/secretion peptide sequence. Eight of the SGHV proteins were predicted to be non-structural (NS), and fourteen are known structural (VP) proteins.

CONCLUSIONS/SIGNIFICANCE

SGHV alters the protein expression pattern in Glossina. The G. pallidipes SG secretome encompasses a spectrum of proteins that may be required during the SGHV infection cycle. These detected proteins have putative interactions with at least 21 of the 25 SGHV-encoded proteins. Our findings opens venues for developing novel SGHV mitigation strategies to block SGHV infections in tsetse production facilities such as using SGHV-specific antibodies and phage display-selected gut epithelia-binding peptides.

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.

Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga Ostreococcus tauri

Large DNA viruses are ubiquitous, infecting diverse organisms ranging from algae to man, and have probably evolved from an ancient common ancestor. In aquatic environments, such algal viruses control blooms and shape the evolution of biodiversity in phytoplankton, but little is known about their biological functions. We show that Ostreococcus tauri, the smallest known marine photosynthetic eukaryote, whose genome is completely characterized, is a host for large DNA viruses, and present an analysis of the life-cycle and 186,234 bp long linear genome of OtV5. OtV5 is a lytic phycodnavirus which unexpectedly does not degrade its host chromosomes before the host cell bursts. Analysis of its complete genome sequence confirmed that it lacks expected site-specific endonucleases, and revealed the presence of 16 genes whose predicted functions are novel to this group of viruses. OtV5 carries at least one predicted gene whose protein closely resembles its host counterpart and several other host-like sequences, suggesting that horizontal gene transfers between host and viral genomes may occur frequently on an evolutionary scale. Fifty seven percent of the 268 predicted proteins present no similarities with any known protein in Genbank, underlining the wealth of undiscovered biological diversity present in oceanic viruses, which are estimated to harbour 200Mt of carbon.

Molecular cloning and characterization of the DNA adenine methyltransferase gene in Feldmannia sp. virus

The genome of Feldmannia sp. virus (FsV), a marine brown alga virus, contains a putative DNA adenine methyltransferase (dam) gene of 1,245 bp that encodes a polypeptide of 45.8 kDa. A BLAST search with the FsV dam gene showed high amino acid identity to two putative methyltransferase genes, ORF B29 of Feldmannia irregularis virus (FirrV, 54%) and ORF129 of Ectocarpus siliculosus virus (EsV, 36%); and a PSI BLAST search revealed similarity to the N(6)-adenine methyltransferases (MTases) of other species. Most conserved motifs of beta-class MTases were observed in the FsV dam gene. However, neither of the highly conserved sequences in motifs I (FxGxG) or IV [(S/N/D)PP(Y/F/W)] perfectly matched those in the FsV dam gene. The highly conserved DPPY consensus sequence in motif IV was NTPW in the FsV dam gene, perfectly matching the sequences in ORF B29 of FirrV and ORF129 of EsV. Therefore, the dam genes in brown algae viruses may belong to a yet undiscovered group. The FsV Dam protein expressed from the cloned FsV dam gene methylated E. coli chromosomal DNA. This is the first report showing that a virus infecting marine filamentous brown algae encodes a functional Dam protein.

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.

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.

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.

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.

Chlorella viruses encode multiple DNA methyltransferases

The >320 kb dsDNA genomes of 16 viruses which infect Chlorella strain NC64A and 5 viruses infecting Chlorella strain Pbi were tested for their sensitivity/resistance to more than 80 DNA restriction endonucleases. From the known methylation sensitivities of these enzymes to site-specific 5-methylcytosine and N6-methyladenine DNA modifications, we deduce that the 16 NC64A viruses encode at least 13 different sequence-specific DNA methyltransferases and the 5 Pbi viruses encode at least 7 sequence-specific DNA methyltransferases. Each DNA methyltransferase has a 2 to 4 base pair DNA recognition sequence. Some individual viruses encode as many as ten different DNA methyltransferases, making these chlorella virus genomes among the most concentrated sources of DNA methyltransferase genes known.

Chlorella virus NY-2A encodes at least 12 DNA endonuclease/methyltransferase genes

The 380-kb chlorella virus NY-2A genome is highly methylated; 45% of the cytosines are 5-methylcytosine (5mC) and 37% of the adenines are N6-methyladenine (6mA). Based on the sensitivity/resistance of NY-2A DNA to 80 methylation-sensitive DNA restriction endonucleases, the virus is predicted to encode at least 10 DNA methyltransferases: 7 6mA-specific methyltransferases, M.CviQI (GTmAC), M.CvQII (RmAR), M.CviQIII (TCGmA), M.CviQIV (GmATC), M.CviQV (TGCmA), M.CviQVI (GmANTC), and M.CviQVII (CmATG): and 3 5mC-specific methyltransferases, M.CviQVIII [RGmC(T/C/G)], M.CviQIX (mCC), and M.CviQX (mCGR). Five of the 6mA methyltransferase genes, M.CviQI, M.CviQIII, M.CviQV, M.CviQVI, and M.CviQVII, were cloned and sequenced. In addition, 2 site-specific endonuclease activities, R.CviQI (G/TAC) and NY2A-nickase (R/AG), were detected in cell-free extracts from NY-2A virus-infected chlorella. Therefore, the NY-2A genome contains at least 12 DNA methyltransferase and endonuclease genes which, altogether, compose about 3-4% of the virus genome.

Analysis of 74 kb of DNA located at the right end of the 330-kb chlorella virus PBCV-1 genome

This report completes a preliminary analysis of the sequence of the 330,740-bp chlorella virus PBCV-1 genome, the largest virus genome to be sequenced to date. The PBCV-1 genome is 57% the size of the genome from the smallest self-replicating organism, Mycoplasma genitalium. Analysis of 74 kb of newly sequenced DNA, from the right terminus of the PBCV-1 genome, revealed 153 open reading frames (ORFs) of 65 codons or longer. Eighty-five of these ORFs, which are evenly distributed on both strands of the DNA, were considered major ORFs. Fifty-nine of the major ORFs were separated by less than 100 bp. The largest intergenic distance was 729 bp, which occurred between two ORFs located in the 2.2-kb inverted terminal repeat region of the PBCV-1 genome. Twenty-seven of the 85 major ORFs resemble proteins in databases, including the large subunit of ribonucleotide diphosphate reductase, ATP-dependent DNA ligase, type II DNA topoisomerase, a helicase, histidine decarboxylase, dCMP deaminase, dUTP pyrophosphatase, proliferating cell nuclear antigen, a transposase, fungal translation elongation factor 3 (EF-3), UDP glucose dehydrogenase, a protein kinase, and an adenine DNA methyltransferase and its corresponding DNA site-specific endonuclease. Seventeen of the 153 ORFs resembled other PBCV-1 ORFs, suggesting that they represent either gene duplications or gene families.

Chlorella virus SC-1A encodes at least five functional and one nonfunctional DNA methyltransferases

Chlorella virus SC-1A encodes at least six DNA methyltransferases (MTases): four N6-methyldeoxyadenine (m6A) MTases, M x CviSI (TGCmA), M x CviSII (CmATG), M x CviSIII (TCGmA) and M x CviSIV (GmATC), one 5-methyldeoxycytosine (m5C) MTase, M x CviSV (approximately RCmCG), and one nonfunctional m5C MTase, M x CviSVI, which is homologous to the MTase M x CviJI [RGmC(T/C/G)] produced by another chlorella virus IL-3A. Genes encoding three of the SC-1A m6A MTases (M x CviSI, M x CviSII, and M x CviSIII) and the nonfunctional m5C MTase were cloned and sequenced. Neither M x CviSI nor M x CviSIII genes hybridized to genes for their respective isomethylomers, M x CviRI and M x CviBIII, from other chlorella viruses. However, the M x CviSII gene hybridized strongly to its M x CviAII isomethylomer gene from virus PBCV-1. Like the prototype chlorella virus PBCV-1, the SC-1A genome contains inverted terminal repeats, one of which is adjacent to the nonfunctional m5C MTase. The three cloned m6A MTase genes are distributed throughout the approx. 345 kb SC-1A genome.

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.

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

A 4.3-kbp portion of the genome from the Chlorella virus, PBCV-1, has been cloned and sequenced. Minimally, five open reading frames (ORFs) were identified on this fragment. Transcriptional analysis indicates that each ORF encodes complex patterns of RNA. The total length of transcribed RNA exceeds that of the ORF indicating either post-transcriptional modification or multiple transcriptional start/stop sites. The sequence TTTTTNT, previously described as the transcriptional stop site for the early genes of vaccinia virus, is also found downstream of each of our ORFs. The regions 5' to each ORF were very A + T-rich (approx 80%) but distinct promoter sequences were not unambiguously identified.

Cloning and sequencing the cytosine methyltransferase gene M. CviJI from Chlorella virus IL-3A

The Chlorella virus IL-3A gene encoding the DNA methyltransferase M.CviJI, which methylates the internal cytosine in (G/A)GC(T/C/G) sequences, was cloned and expressed in Escherichia coli. The region containing the M.CviJI gene was sequenced and a single open reading frame of 1101 bp was identified that could code for a polypeptide of 367 amino acids with a predicted molecular weight of 41,864. M.CviJI contained regions of amino acids which were similar to bacterial cytosine methyltransferases. Eighteen other Chlorella viruses, of 36 tested, contained DNA sequences which hybridized to the M.CviJI gene; DNA from some, but not all, of these 18 viruses also contained 5-methylcytosine in (G/A)GC(T/C/G) sequences.

5-Azacytidine-resistant mutants of Chlorella virus IL-3A

Many dsDNA-containing viruses which infect the unicellular, eukaryotic Chlorella-like green alga strain NC64A encode for DNA methyltransferases and DNA site-specific (restriction) endonucleases. We have hypothesized that these endonucleases help degrade host DNA permitting deoxynucleotides to recycle into virus DNA. This hypothesis was tested by isolating deletion mutants of Chlorella virus IL-3A lacking functional genes for the cytosine methyltransferase M.CviJI and the cognate site-specific endonuclease CviJI. The growth and burst sizes of the mutants and parent virus were identical. Also host nuclear and chloroplast DNAs disappeared from infected cells at the same rates. Thus M.CviJI and CviJI activities are not required for IL-3A replication and CviJI activity is not essential for host DNA degradation.

A comparison of viruses infecting two different Chlorella-like green algae

Five plaque-forming viruses (Pbi viruses) of the unicellular, eukaryotic, exsymbiotic Chlorella-like green alga strain Pbi were isolated from fresh water collected in Germany. The viruses were compared to two previously characterized plaque-forming viruses (NC64A viruses) of Chlorella strain NC64A. The Pbi viruses do not infect Chlorella NC64A and vice versa. Like the NC64A viruses the Pbi viruses are large polyhedron with a diameter of 140 to 150 nm, are chloroform sensitive, have many structural proteins, and have large dsDNA genomes of at least 300 kb. However, the Pbi viruses are serologically distinct from the NC64A viruses. The five Pbi virus genomes contain 5-methylcytosine, which varied from 14.2 to 43.1% of the cytosine, and two of them also contained N6-methyladenine. DNAs from the Pbi viruses hybridized poorly with the two NC64A virus DNAs and they have a higher guanine plus cytosine content (ca. 46%) than the NC64A virus DNAs (ca. 40%).

Method for rapid isolation and analysis of algal virus DNA

A quick method has been developed for isolating viral DNA from small cultures of eukaryotic algae infected with PBCV-1 or similar viruses. The DNA preparations are virtually free of contaminating host DNA and are suitable substrates for restriction enzymes. 5 ml cultures yield 8-25 micrograms of viral DNA. Many plaque-purified isolates from environmental water samples can be analyzed in a day.

Restriction site map of the Chlorella virus PBCV-1 genome

The virus PBCV-1, which replicates in a Chlorella-like green alga, has a dsDNA genome. The DNA was mapped for BamHI, HindIII, and PstI restriction sites. The resulting map has a size of 333 kbp and is circular-indicating either covalently closed circular DNA or circularly permuted linear DNA. Several regions of repetitive DNA were also identified and located on the restriction map.

Properties and uses of restriction endonucleases

It is clear that we have still not exhausted all the restriction endonuclease specificities to be found in nature. Recently discovered BsmI is the first endonuclease recognizing a nonpalindromic sequence that cleaves within the site. Certainly other endonucleases belonging to this class will soon be discovered. More endonucleases are now being sought that recognize longer recognition sequences, because large fragments can now be readily separated by pulse-field electrophoresis. New sources of endonucleases are also being found; for example, a group of viruses that grow on Chlorella algae produce type II-like site-specific endonucleases. As the number and variety of known restriction endonucleases increase, the number and variety of applications keep pace. There is still no end in sight.

Specificity of restriction endonucleases and methylases--a review

The properties and sources of all known restriction endonucleases and methylases are listed. The enzymes are cross-indexed (Table I), classified according to their recognition sequence homologies (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the double-stranded DNA of the bacteriophages lambda, phi X174 and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328, and the microorganisms from which they originate. Other tabulated properties of the restriction endonucleases include relaxed specificities (integrated into Table II), the structure of the generated fragment ends (Table III), and the sensitivity to different kinds of DNA methylation (Table V). In Table IV the conversion of two- and four-base 5'-protruding ends into new recognition sequences is compiled which is obtained by the fill-in reaction with Klenow fragment of the Escherichia coli DNA polymerase I or additional nuclease S1 treatment followed by ligation of the modified fragment termini [P3]. Interconversion of restriction sites generates novel cloning sites without the need of linkers. This should improve the flexibility of genetic engineering experiments. Table VI classifies the restriction methylases according to the nature of the methylated base(s) within their recognition sequences. This table also comprises restriction endonucleases which are known to be inhibited or activated by the modified nucleotides. The detailed sequences of those overlapping restriction sites are also included which become resistant to cleavage after the sequential action of corresponding restriction methylases and endonucleases [N11, M21]. By this approach large DNA fragments can be generated which is helpful in the construction of genomic libraries. The data given in both Tables IV and VI allow the design of novel sequence specificities. These procedures complement the creation of universal cleavage specificities applying class IIS enzymes and bivalent DNA adapter molecules [P17, S82].