Structure of frog virus 3 genome: size and arrangement of nucleotide sequences as determined by electron microscopy

[Red sea bream iridoviral disease]

The first outbreak of red sea bream iridoviral disease caused by red sea bream iridovirus (RSIV) was recorded in cultured red sea bream Pagrus major in Shikoku Island, Japan in 1990. Since 1991, the disease has caused mass mortalities of cultured marine fishes not only red sea bream but also many other species. The affected fish were lethargic and exhibited severe anemia, petechiae of the gills, and enlargement of the spleen. The causative agent was a large, icosahedral, cytoplasmic DNA virus classified as a member of the family Iridoviridae and was designated as red sea bream iridovirus (RSIV). The genome of RSIV is liner dsDNA and considered to be circularly permitted and terminally redundant like other iridoviruses. The length of physical map of RSIV genome is 112,415bp. An indirect immunofluorescence test with a monoclonal antibody and PCR are commonly used for the rapid diagnosis of RSIV infected fish in the field. For the control of this disease, a formalin-killed vaccine against red sea bream iridoviral disease was developed and now commercially available.

A fully 5'-CG-3' but not a 5'-CCGG-3' methylated late frog virus 3 promoter retains activity

Several lines of evidence demonstrate that the DNA of the iridovirus frog virus 3 (FV3) is methylated in all 5'-CG-3' sequences both in virion DNA and in the intracellular viral DNA at late times after infection. The 5-methyldeoxycytidine residues in this viral DNA occur exclusively in 5'-CG-3' dinucleotide positions. We have cloned and determined the nucleotide sequence of the L1140 gene and its promoter from FV3 DNA. The gene encodes a 40-kDa protein. The results of transcriptional pattern analyses for this gene in fathead minnow fish cells document that this gene is transcribed exclusively late after FV3 infection. The L1140 gene and its promoter are fully methylated at late times after infection. We have been interested in resolving the apparent paradox that the methylated L1140 promoter is methylated and active late in FV3-infected cells. Of course, the possibility cannot be excluded that one or a few 5'-CG-3' sequences outside restriction endonuclease sites escaped de novo methylation after FV3 DNA replication. We have devised a construct that places the chloramphenicol acetyltransferase gene under the control of the L1140 promoter. Upon transfection, this construct exhibits activity only in FV3-infected BHK-21 hamster cells, not in uninfected BHK-21 cells. The fully 5'-CG-3' or 5'-GCGC-3' (HhaI) methylated, HpaII-mock-methylated, or unmethylated L1140 promoter-chloramphenicol acetyltransferase gene construct is active in FV3-infected BHK-21 cells, whereas the same construct 5'-CCGG-3' (HpaII) methylated has lost activity. Apparently, complete methylation of the late L1140 promoter in FV3 DNA is compatible with activity. However, a very specific 5'-CCGG-3' methylation pattern that does not naturally occur in authentic FV3 DNA in infected cells abrogates promoter function. These results further support the notion that very specific patterns of methylation are required to inhibit or inactivate viral promoters.

A preliminary translational map of the frog virus 3 genome

A preliminary map of the frog virus 3 (FV 3) genome was constructed by hybridization-selection of mRNAs to cloned DNA fragments and translation in reticulocyte lysates. FV 3 mRNAs were hybridized to KpnI, HindIII, and SalI restriction fragments representing the entire FV 3 genome. Two different hybridization conditions were employed in order to discriminate between the hybridization of early and late mRNAs. A total of 43 major and 18 minor early genes and nine major and three minor late genes were mapped. A 24 kb region comprised of the KpnI D, H, and E fragments encodes 8 of the 12 late genes that were mapped.

Role of the host cell nucleus in the replication of African swine fever virus DNA

An examination by autoradiography of African swine fever virus-infected alveolar macrophages pulse labeled with [3H]thymidine showed that, at early times of viral DNA replication, the grains were localized exclusively in the nucleus in 20% of the cells, while in 45% the label was found in the cytoplasm. In the remaining 35%, newly synthesized DNA was detected in both the nucleus and the cytoplasm. At later times, the percentage of cells with grains in the nucleus decreased considerably. Pulse-chase experiments indicated that the DNA synthesized in the nucleus is then transported to the cytoplasm. The presence of virus-specific DNA sequences in the nucleus was confirmed by in situ hybridization of infected macrophages. Similar hybridization experiments with African swine fever virus-infected VERO cells followed by confocal microscopy also indicated the existence of a nuclear stage in the localization of the viral DNA. These results suggest a mechanism for African swine fever virus DNA replication with an initial stage in the nucleus followed by a cytoplasmic phase. Specific nuclear forms associated with the hybridization signal have been observed in African swine fever virus-infected macrophages and VERO cells. The nuclear forms seen in macrophages are consistent with a mechanism for the egress of the viral DNA from the nucleus that involves initial budding at the nuclear membrane.

Bacteriophage P22 portal protein is part of the gauge that regulates packing density of intravirion DNA

The complex double-stranded DNA bacteriophages assemble DNA-free protein shells (procapsids) that subsequently package DNA. In the case of several double-stranded DNA bacteriophages, including P22, packaging is associated with cutting of DNA from the concatemeric molecule that results from replication. The mature intravirion P22 DNA has both non-unique (circularly permuted) ends and a length that is determined by the procapsid. In all known cases, procapsids consist of an outer coat protein, an interior scaffolding protein that assists in the assembly of the coat protein shell, and a ring of 12 identical portal protein subunits through which the DNA is presumed to enter the procapsid. To investigate the role of the portal protein in cutting permuted DNA from concatemers, we have characterized P22 portal protein mutants. The effects of several single amino acid changes in the P22 portal protein on the length of the DNA packaged, the density to which DNA is condensed within the virion, and the outer radius of the capsid have been determined. The results obtained with one mutant (NT5/1a) indicate no change (+/- 0.5%) in the radius of the capsid, but mature DNA that is 4.7% longer and a packing density that is commensurately higher than those of wild-type P22. Thus, the portal protein is part of the gauge that regulates the length and packaging density of DNA in bacteriophage P22. We argue that these findings make models for DNA packaging less likely in which the packing density is a property solely of the coat protein shell or of the DNA itself.

A frog virus 3 gene codes for a protein containing the motif characteristic of the INT family of integrases

The integrase (INT) family of bacteriophage coded integrase-recombinase proteins are responsible for catalyzing strand exchange between DNA molecules and play an important role in the DNA replication of many bacteriophages. Within the frog virus 3 (FV3) genome we have identified an open reading frame (ORF) of which the deduced amino acid sequence contains a motif characteristic of the INT family of integrases-recombinases. The ORF consists of 825 bp which codes for a protein of 275 amino acids with a predicted Mr of 29,945. RNA transcribed from this ORF during virus infection was detected by Northern blot analysis and it is a delayed early message of approximately 1100 bases. The 5' and 3' ends of the putative FV3 integrase-recombinase transcript were mapped. The transcriptional start site is preceded by a presumptive TATA box, and a region of hyphenated dyad symmetry is present at the 3' end of the message. A protein with an Mr of approximately 30,500 was synthesized by a rabbit reticulocyte lysate programmed with capped runoff transcripts from the cloned gene, indicating that the ORF can be transcribed into a message coding for a viral protein. In the FV3 life cycle, DNA replication occurs in a large complex formed through the recombination of small viral DNA molecules. Thus, at this stage, DNA replication and recombination are interlinked. Resolution of concatameric DNA is required for the packaging of genomes into virus particles. The putative FV3 INT gene may be involved in one or more of these functions.

Nucleotide sequence of the bacteriophage P22 genes required for DNA packaging

The mechanism of DNA packaging by dsDNA viruses is not well understood in any system. In bacteriophage P22 only five genes are required for successful condensation of DNA within the capsid. The products of three of these genes, the portal, scaffolding, and coat proteins, are structural components of the precursor particle, and two, the products of genes 2 and 3, are not. The scaffolding protein is lost from the structure during packaging, and only the portal and coat proteins are present in the mature virus particle. These five genes map in a contiguous cluster at the left end of the P22 genetic map. Three additional genes, 4, 10, and 26, are required for stabilizing of the condensed DNA within the capsid. In this report we present the nucleotide sequence of 7461 bp of P22 DNA that contains the five genes required for DNA condensation, as well as a nonessential open reading frame (ORF109), gene 4, and a portion of gene 10. N-terminal amino acid sequencing of the encoded proteins accurately located the translation starts of six genes in the sequence. Despite the fact that most of these proteins have striking analogs in the other dsDNA bacteriophage groups, which perform highly analogous functions, no amino acid sequence similarity between these analogous proteins has been found, indicating either that they diverged a very long time ago or that they are the products of spectacular convergent evolution.

Organization of RNA transcripts from a 7.8-kb region of the frog virus 3 genome

The detailed organization of the RNAs transcribed from a region of the FV 3 genome (Sa/I-F fragment and adjacent sequences) has been determined. The information was derived from the cell-free translation of hybrid-selected RNA to locate the genes encoding specific polypeptides, RNA filter hybridization to size the transcripts, and S1 nuclease mapping to locate the 5'- and 3'-ends of the RNAs on the genome. Three genes are contiguous and are transcribed from the same strand: two immediate early genes encoding transcripts of about 1.3 kb that directed the in vitro synthesis of 42K and 46K polypeptides, separated by the late gene encoding the major capsid protein (48K). At an advanced stage in infection, transcripts derived from the immediate early genes are also present. A set of RNAs with different 5'-ends ranging from 1.7 to 0.58 kb is produced from the p46 gene region whereas RNAs, 0.98 and 0.6 kb in size, complementary to the 5'-end of the p42 message, are synthesized. This gene cluster is located between two genes transcribed in the opposite direction from the rightward-reading strand: a late gene whose message is 0.5 kb in size and encodes a 15K polypeptide and a gene transcribed at immediate early and late times of infection which encodes a protein of 70 kDa. The 5'-end of the late RNA maps downstream of the 5'-end of the early one, their sizes being 1.85 and 2 kb, respectively, but both of them can be translated in vitro into a 70K polypeptide. These observations suggest that transcription is not regulated by the organization of the genes; they suggest rather that specific DNA sequences are responsible for the promotion of immediate early and late transcriptions.

Molecular cloning and physical and translational mapping of the frog virus 3 genome

A library of cloned fragments representing nearly the entire frog virus 3 (FV 3) genome (99.65%) has been constituted. Individual plasmid recombinants, labeled by nick-translation, were hybridized to Southern blots of genomic FV 3 DNA fragments obtained with XbaI, HindIII, SmaI, and SalI. From these results physical maps were generated and the distribution of restriction sites in the genome was established by double digestion of the fragments. A preliminary translational map was likewise developed. The viral messages were selected by hybridization to the recombinant DNAs immobilized on nitrocellulose filters and were translated in the reticulocyte cell-free system. About 30 polypeptides were detected among the translation products of RNA synthesized in the presence of cycloheximide. It appears that these genes are not clustered but in several cases more than one polypeptide is encoded by a given fragment. The 15 new polypeptide obtained by translation of late mRNAs derive from genes located on one-half of the genome.

Mutation in a DNA-binding protein reveals an association between DNA-methyltransferase activity and a 26,000-Da polypeptide in frog virus 3-infected cells

The DNA of frog virus 3 (FV3), an iridovirus, is highly methylated; more than 20% of the cytosine bases are methylated at the 5-carbon position by an FV3-induced DNA methyltransferase (DNA-mt). To determine the role of this enzyme in virus replication and regulation of gene expression, we have analyzed an FV3 mutant that lacks DNA-mt activity and is resistant to 5-azacytidine (an inhibitor of DNA-mt). Comparative polypeptide analysis, using cytoplasmic extracts from the wild-type FV3 and mutant-infected cells, revealed that a single protein of 26,000 (26K) molecular weight was altered in the mutant-infected cells. The altered polypeptide migrated faster in SDS-polyacrylamide gel as compared to the wild-type FV3 26K protein. Five spontaneous revertants derived from the mutant regained the migrational characteristic of the wild-type 26K protein, DNA-mt activity, and methylation of their DNA. We further show that the 26K polypeptide is a DNA-binding protein and that 80% of the enzyme activity can be eluted from an ssDNA affinity column. Taken together, these data support the conclusion that the 26K polypeptide is associated with DNA-mt activity.

Biochemical and structural studies of fish lymphocystis disease virions isolated from skin tumours of Pleuronectes

Fish lymphocystis disease viruses (FLDV) were isolated directly from lymphocystis disease lesions of various flatfish species and further purified. Subunits could be identified only after the purified virus was disrupted. In combination with different types of treatment, Nonidet-P40, dithiothreitol, proteases digestion and after ultrasonication and ultracentrifugation, the inner region of FLDV was studied. The purified virus was used for isolation of the virus nucleoid and for further study of the viral genome. Contour length measurements of 20 DNA molecules gave an average length of 40.44 +/- 3.2 micron. Lines of precipitation between isolated nucleoid material and FLDV-antibodies were shown by immunoelectrophoresis.

Temperature-sensitive mutants of frog virus 3: biochemical and genetic characterization

Nineteen frog virus 3 temperature-sensitive mutants were isolated after mutagenesis with nitrosoguanidine and assayed for viral DNA, RNA, and protein synthesis, as well as assembly site formation at permissive (25 degrees C) and nonpermissive (30 degrees C) temperatures. In addition, mutants were characterized for complementation by both quantitative and qualitative assays. Based on the genetic and biochemical data, the 19 mutants, along with 9 mutants isolated earlier, were ordered into four phenotypic classes which define defects in virion morphogenesis (class I), late mRNA synthesis (class II), viral assembly site formation (class III), and viral DNA synthesis (class IV). In addition, we used two-factor crosses to order 11 mutants, comprising 7 complementation groups, onto a linkage map spanning 77 recombination units.

Isolation and characterization of a frog virus 3 variant resistant to phosphonoacetate: genetic evidence for a virus-specific DNA polymerase

A variant of frog virus 3 (FV3) resistant to 200 micrograms/ml phosphonoacetate was isolated, and used to establish that the DNA polymerase induced in FV3-infected cells was virus coded. In addition, inhibitor studies showed that the FV3 polymerase is similar to eukaryotic polymerase alpha in its sensitivity to aphidicolin, and that resistance to phosphonoacetate does not confer cross-resistance to thymidine arabinoside or acycloguanosine.

The organization of frog virus 3 as revealed by freeze-etching

A variety of freeze-fracture techniques has been employed in this study with the aim of dissecting the frog virus 3 virion and obtaining further information about its architecture. The icosahedral capsid has a skew symmetry with a triangulation number of 133 or 147. The capsomers are closely packed with a center-to-center spacing of 72 A. The inner membrane contains transmembrane proteins which appear as intra-membranous particles on both fracture faces. Rod-like structures (about 100 A in diameter) are present in the virus interior suggesting that the DNA-protein complex is highly organized.

The role of DNA methylation in virus replication: inhibition of frog virus 3 replication by 5-azacytidine

Frog virus 3 (FV3) DNA is the most highly methylated DNA of any known DNA virus; about 20% of the cytosine residues in FV3 DNA are methylated (D. Willis and A. Granoff, 1980, Virology 107, 250-257). To understand the role of DNA methylation in virus replication, we have examined the effect of 5-azacytidine, a drug that inhibits DNA methylation. 5-Azacytidine (10 microM) reduced the production of infectious FV3 by 100-fold or more and inhibited methylation of viral DNA by about 80%. Inhibition of DNA methylation did not affect viral gene expression since there was no detectable inhibition of virus-specific RNA or protein synthesis in 5-azacytidine-treated cells. In contrast, the size of the replicating DNA measured under completely denaturing conditions, was much smaller than that found during infection in the absence of drug. These results suggest that the undermethylated DNA was susceptible to endodeoxyribonuclease(s). Additionally, electron microscopic examination of FV3-infected, 5-azacytidine-treated cells revealed that preformed capsids remained empty or were only partially filled with viral DNA. Based on these data, it is suggested that methylation of DNA protects it from endonucleolytic cleavage and that the integrity of genomic DNA is required for its proper packaging into virions.

A temperature-sensitive (TS) mutant of frog virus 3 (FV3) is defective in second-stage DNA replication

It has been suggested that FV3 DNA replication occurs in two stages [R. Goorha (1982) J. Virol. 43, 519-528]. First-stage DNA synthesis is restricted to the nucleus, where the replicating DNA ranges from genome to twice genome size; second-stage DNA replication occurs exclusively in the cytoplasm, and the replicating DNA is concatameric. A temperature-sensitive mutant (ts 12488) of FV3, at a nonpermissive temperature (30 degrees), synthesized DNA in the nucleus only, and the size of the replicative complex (as determined by neutral sucrose gradient analysis) was between genome and twice genome length. These characteristics establish that at nonpermissive temperature, ts 12488 is arrested in the first stage of DNA replication. Temperature shift-down (30 degrees----25 degrees) of ts 12488-infected cells at 4 hr postinfection showed that, within 30 min of the shift, the replicative complex became very large (more than 10 times genome size). Furthermore, newly synthesized DNA was now found in the cytoplasmic fraction also. These results suggest that ts 12488, upon shift-down, enters into the second stage of DNA replication where progeny DNA is synthesized as a large concatamer. In shift-down experiments, de novo protein synthesis was not required to initiate second-stage DNA replication, strongly suggesting that the thermosensitive protein is directly involved in second-stage DNA replication. This genetic evidence establishes the previous biochemical findings of a two-stage replication scheme for FV3 DNA.

Interaction of frog virus-3 with the cytoskeleton. I. Altered organization of microtubules, intermediate filaments, and microfilaments

The progressive cytoskeletal alterations of frog virus 3-infected baby hamster kidney (BHK) and fathead minnow (FHM) cells were studied by immunofluorescence and electron microscopy. The virus assembly sites, which contain viral genomes and viral proteins, were detected in the cytoplasm at 4 h (FHM) or 6 h (BHK) and mature virions appeared 2 h later. When infected cells were treated with Triton X-100, the assembly sites were found in association with the cytoskeleton. In infected cells, the number of microtubules progressively decreased but a few microtubules traversing in the vicinity of the assembly sites remained intact. Early in infection, the intermediate filaments retracted from the cell periphery, delimited the forming assembly sites, and remained there throughout infection. We suggest that intermediate filaments are involved in the formation of assembly sites. In addition, the filaments either by themselves or in conjunction with microtubules may anchor the assembly sites near the nucleus. The microfilament bundles (stress fibers) disappeared with the formation of assembly sites, and late in infection many projections containing microfilaments and virus particles appeared at the cell surface. The observation suggests a role for microfilaments in virus release. Taken together, these results provide the first example of a virus-infected cell in which all three cytoskeletal filaments show profound organizational changes and suggest an active participation of the host cytoskeleton in viral functions.

Analysis of the genome of fish lymphocystis disease virus isolated directly from epidermal tumours of pleuronectes

Virions of fish lymphocystis disease virus (FLDV), a member of the iridovirus family, were isolated directly from lymphocystis disease lesions of individual flatfishes and purified by sucrose and subsequent cesium chloride gradient centrifugation to homogeneity as judged by electron microscopy. The isolated FLDV DNAs appear to be heterogeneous in size. Contour length measurements of 43 DNA molecules gave an average length of 49 +/- 23 microns, corresponding to 93 +/- 44 X 10(6) D. Molecular weight estimations of FLDV DNA by restriction enzyme analysis resulted in only 64.8 X 10(6) D indicating an excess length of the DNA of about 50%. FLDV DNA was sensitive to lambda 5'-exonuclease and to E. coli 3'-exonuclease III without preference of any one terminal DNA restriction fragment. Denaturation and reannealing experiments of FLDV DNA resulted in the formation of circular DNA molecules of 34.25 microns contour length (= 65.22 X 10(6) D). This result suggests that FLDV DNA contains directly repeated sequences at both ends and that it is terminally redundant. FLDV DNA is methylated in cytosine. FLDV DNA did not hybridize with frog virus DNA indicating that the two iridoviruses are not closely related to each other. Restriction enzyme analysis and Southern blot hybridizations revealed that FLDV isolates can be classified into two different strains: FLDV strain 1 occurs in flounders and plaice, whereas strain 2 is usually found in lesions of dabs.

Restriction endonuclease mapping of the frog virus 3 genome

A physical map for the frog virus 3 (FV 3) genome was constructed after digestion with the following restriction endonucleases: EcoRI, HindIII, KpnI, and XbaI. Mapping of the DNA was accomplished by partial digestion and recutting, double-digestion, and Southern blot hybridization with deduction of overlaps. Although the virion DNA is physically linear, the restriction map was circular, supporting the data that the FV 3 genome is circularly permuted (Goorha and Murti, Proc. Nat. Acad. Sci USA 79, 248-252, 1982), a unique feature among eukaryotic viruses.

Restriction mapping and molecular cloning of adenovirus type 4 (subgroup E) DNA

The locations of thirty restriction endonuclease cleavage sites were determined on the genome of adenovirus type 4 (Ad4), the sole member of the subgroup E adenovirions. The restriction endonucleases Bg/II, EcoRI, HindIII, HpaI, KpnI, SalI, and XbaI cut Ad4 DNA 10, 3, 2, 3, 5, 5 and 3 times, respectively. Orientation of the linear Ad4 map with respect to left and right molecular ends was accomplished by taking advantage of the limited sequence homology between Ad2 and Ad4. Ten non-overlapping fragments of Ad4 DNA representing 98% of the genome, map units 1.6 to 99.6, have been cloned into the plasmid vector pKC7.