Fowlpox virus thymidine kinase: nucleotide sequence and relationships to other thymidine kinases

Viral taxonomy needs a spring clean; its exploration era is over

The International Committee on Taxonomy of Viruses has recently changed its approved definition of a viral species, and also discontinued work on its database of virus descriptions. These events indicate that the exploration era of viral taxonomy has ended; over the past century the principles of viral taxonomy have been established, the tools for phylogenetic inference invented, and the ultimate discriminatory data required for taxonomy, namely gene sequences, are now readily available. Further changes would make viral taxonomy more informative. First, the status of a ‘taxonomic species’ with an italicized name should only be given to viruses that are specifically linked with a single ‘type genomic sequence’ like those in the NCBI Reference Sequence Database. Secondly all approved taxa should be predominately monophyletic, and uninformative higher taxa disendorsed. These are ‘quality assurance’ measures and would improve the value of viral nomenclature to its users. The ICTV should also promote the use of a public database, such as Wikipedia, to replace the ICTV database as a store of the primary metadata of individual viruses, and should publish abstracts of the ICTV Reports in that database, so that they are ‘Open Access’.

Risks from GMOs due to horizontal gene transfer

Horizontal gene transfer (HGT) is the stable transfer of genetic material from one organism to another without reproduction or human intervention. Transfer occurs by the passage of donor genetic material across cellular boundaries, followed by heritable incorporation to the genome of the recipient organism. In addition to conjugation, transformation and transduction, other diverse mechanisms of DNA and RNA uptake occur in nature. The genome of almost every organism reveals the footprint of many ancient HGT events. Most commonly, HGT involves the transmission of genes on viruses or mobile genetic elements. HGT first became an issue of public concern in the 1970s through the natural spread of antibiotic resistance genes amongst pathogenic bacteria, and more recently with commercial production of genetically modified (GM) crops. However, the frequency of HGT from plants to other eukaryotes or prokaryotes is extremely low. The frequency of HGT to viruses is potentially greater, but is restricted by stringent selection pressures. In most cases the occurrence of HGT from GM crops to other organisms is expected to be lower than background rates. Therefore, HGT from GM plants poses negligible risks to human health or the environment.

Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach

Background

Poxviruses are important pathogens of humans, livestock and wild animals. These large dsDNA viruses have a set of core orthologs whose gene order is extremely well conserved throughout poxvirus genera. They also contain many genes with sequence and functional similarity to host genes which were probably acquired by horizontal gene transfer.

Although phylogenetic trees can indicate the occurrence of horizontal gene transfer and even uncover multiple events, their use may be hampered by uncertainties in both the topology and the rooting of the tree. We propose to use synteny conservation around the horizontally transferred gene (HTgene) to distinguish between single and multiple events.

Results

Here we devise a method that incorporates comparative genomic information into the investigation of horizontal gene transfer, and we apply this method to poxvirus genomes. We examined the synteny conservation around twenty four pox genes that we identified, or which were reported in the literature, as candidate HTgenes. We found support for multiple independent transfers into poxviruses for five HTgenes. Three of these genes are known to be important for the survival of the virus in or out of the host cell and one of them increases susceptibility to some antiviral drugs.

Conclusion

In related genomes conserved synteny information can provide convincing evidence for multiple independent horizontal gene transfer events even in the absence of a robust phylogenetic tree for the HTgene.

Recombinant fowlpox virus forin vitrogene delivery to pancreatic islet tissue

The feasibility of using avipox virus as a vector for gene delivery to islet tissue (adult islets and fetal proislets) was examined using a recombinant fowlpox virus (FPV) engineered to express the reporter gene LacZ (FPV-LacZ). The efficiency of in vitro transduction was dose-dependent and influenced by the donor species and maturation status of the islet tissue. Reporter gene expression in FPV-LacZ-transduced islet grafts was transient (3-7 days) in immunoincompetent nude mice and was not prolonged by in vivo treatment with anti-IFN-gamma mAb. In contrast, FPV-LacZ-transduced NIT-1 cells (a mouse islet beta cell line) expressed the LacZ gene beyond 18 days in vitro. Silencing of transgene expression therefore appeared to occur in vivo and was T cell- and IFN-gamma-independent. Isografts of FPV-LacZ-transduced islets in immunocompetent mice underwent immunological destruction by 7 days, suggesting that either FPV proteins or the reporter protein beta-galactosidase induced an adaptive immune response. Co-delivery of the rat bioactive immunoregulatory cytokine gene TGF-beta to islets using FPV-TGF-beta led to enhanced expression of TGF-beta mRNA in isografts but no long-term protection. Nevertheless, compared to control islet isografts at 5 days, FPV-transduced islets remained embedded in the clotted blood used to facilitate implantation. This phenomenon was TGF-beta transgene-independent, correlated with lack of cellular infiltration, and suggested that the FPV vector transformed the blood clot into a temporary immunological barrier.

Experimental vaccines against measles in a world of changing epidemiology

Vaccination with the current live attenuated measles vaccine is one of the most successful and cost-effective medical interventions. However, as a result of persisting maternal antibodies and immaturity of the infant immune system, this vaccine is poorly immunogenic in children <9 months old. Immunity against the live vaccine is less robust than natural immunity and protection less durable. There may also be some concern about (vaccine) virus spread during the final stage of an eventual measles eradication program. Opinions may differ with respect to the potential threat that some of these concerns may be to the World Health Organisation goal of measles elimination, but there is a consensus that the development of new measles vaccines cannot wait. Candidate vaccines are based on viral or bacterial vectors expressing recombinant viral proteins, naked DNA, immune stimulating complexes or synthetic peptides mimicking neutralising epitopes. While some of these candidate vaccines have proven their efficacy in monkey studies, aerosol formulated live attenuated measles vaccine are evaluated in clinical trials.

Fowlpox virus encodes a novel DNA repair enzyme, CPD-photolyase, that restores infectivity of UV light-damaged virus

Fowlpox virus (FPV), a pathogen of poultry, can persist in desiccated scabs shed from infected hosts. Although the mechanisms which ensure virus survival are unknown, it is likely that some type of remedial action against environmentally induced damage is required. In this regard, we have identified an open reading frame (ORF) coding for a putative class II cyclobutane pyrimidine dimer (CPD)-photolyase in the genome of FPV. This enzyme repairs the UV light-induced formation of CPDs in DNA by using blue light as an energy source and thus could enhance the viability of FPV during its exposure to sunlight. Based on transcriptional analyses, the photolyase gene was found to be expressed late during the FPV replicative cycle. That the resultant protein retained DNA repair activity was demonstrated by the ability of the corresponding FPV ORF to complement functionally a photolyase-deficient Escherichia coli strain. Interestingly, insertional inactivation of the FPV photolyase gene did not impair the replication of such a genetically altered virus in cultured cells. However, greater sensitivity of this mutant than of the parental virus to UV light irradiation was evident when both were subsequently photoreactivated in the absence of host participation. Therefore, FPV appears to incorporate its photolyase into mature virions where the enzyme can promote their survival in the environment. Although expression of a homologous protein has been predicted for some chordopoxviruses, this report is the first to demonstrate that a poxvirus can utilize light to repair damage to its genome.

Identification and characterization of a shrimp white spot syndrome virus (WSSV) gene that encodes a novel chimeric polypeptide of cellular-type thymidine kinase and thymidylate kinase

From previously constructed genomic libraries of a Taiwan WSSV isolate, a putative WSSV tk-tmk gene was identified. Uniquely, the open reading frame (ORF) of this gene was predicted to encode a novel chimeric protein of 388 amino acids with significant homology to two proteins: thymidine kinase (TK) and thymidylate kinase (TMK). Northern blot analysis with a WSSV tk-tmk-specific riboprobe detected a major transcript of 1.6 kb. When healthy adult Penaeus monodon shrimp were inoculated with WSSV, the tk-tmk gene transcript was first detected by RT-PCR analysis at 4 h postinfection and transcription levels continued to increase over the first 18 h. The gene's major in vitro transcription and translation product, equivalent to the predicted size (43 kDa), is a single chimeric protein that includes both the TK and TMK functional motifs. Evidence for phylogenetic analysis and sequence alignment suggested that the gene may have resulted from the fusion of a cellular-type TK gene and a cellular-type TMK gene. Its unique arrangement may also provide a valuable gene marker for WSSV.

Identification of the canarypox virus thymidine kinase gene and insertion of foreign genes

We mapped the canarypox virus (CaPV) thymidine kinase (TK) gene within a 5.8-kbp XbaI fragment of the genome by Southern blotting using the fowlpox virus (FPV) TK gene as a probe. Nucleotide sequence analysis of the fragment revealed seven open reading frames (ORFs) showing gene organization similar to that of FPV. The TK gene contained in this region had an ORF of 179 amino acids encoding a polypeptide with a putative molecular mass of 20.0 kDa. An A/T-rich region and a transcription termination signal, TTTTTAT, were found upstream and at the end of the ORF, which is consistent with poxvirus early gene regulation. The consensus sequence of the late promoter TAAAT also overlapped with the initiation codon of the ORF. The amino acid sequence similarity between the TK genes of CaPV and FPV, avipoxviruses, was 64.2%, which was lower than the similarities between vaccinia and variola orthopoxviruses (97.2%) and between Shope fibroma and myxoma leporipoxviruses (82.6%). However, the monophyly of avian clades of CaPV and FPV was supported by phylogenetic analysis. We then inserted the genes encoding lacZ, luciferase (luci), and envelope of human T-lymphotropic virus type 1 (HTLV-1 env) into the TK gene of CaPV to evaluate its suitability as an expression vector. The recombinant viruses obtained were unstable, although the foreign genes were expressed efficiently in the mammalian cells infected with the viruses.

Induction of humoral and cellular immune responses in mice by a recombinant fowlpox virus expressing the E2 protein of bovine viral diarrhea virus

A recombinant fowlpox virus (rFPV/E2) expressing the E2 protein of bovine viral diarrhea virus (BVDV) was constructed and characterized. Mice were immunized with recombinant virus and both humoral and cellular immune responses were studied. rFPV/E2 induced BVDV-specific antibodies which were detected by ELISA. In addition, mouse sera were shown to neutralize BVDV. A cytokine ELISA assay revealed that mice vaccinated with rFPV/E2 induced 7-fold more interferon-gamma than parental fowlpox virus.

Nucleotide sequence of the 4.3 kbp BamHI-N fragment of fowlpox virus FP9

Nucleotide sequence analysis of the 4.3 kbp BamHI-N fragment of the fowlpox virus (FPV) genome revealed that it encodes 7 proteins with homology to vaccinia virus (VV) E11L, E10R, O1L, O3L, I1L, I2L and I3L encoded proteins. No evidence of FPV homolog of VV O2L could be found.

Human thymidine kinase can functionally replace herpes simplex virus type 1 thymidine kinase for viral replication in mouse sensory ganglia and reactivation from latency upon explant

Herpes simplex virus type 1 thymidine kinase exhibits a strikingly broad substrate specificity. It is capable of phosphorylating deoxythymidine and deoxyuridine as does human thymidine kinase, deoxycytidine as does human deoxycytidine kinase, the cytosolic kinase whose amino acid sequence it most closely resembles, and thymidylate as does human thymidylate kinase. Following peripheral inoculation of mice, viral thymidine kinase is ordinarily required for viral replication in ganglia and for reactivation from latency following ganglionic explant. To determine which activity of the viral kinase is important for replication and reactivation in mouse ganglia, recombinant viruses lacking viral thymidine kinase but expressing individual human kinases were constructed. Each recombinant virus expressed the appropriate kinase activity with early kinetics following infection of cultured cells. The virus expressing human thymidine kinase exhibited thymidine phosphorylation activity equivalent to approximately 5% of that of wild-type virus in a quantitative plaque autoradiography assay. Nevertheless, it was competent for ganglionic replication and reactivation following corneal inoculation of mice. The virus expressing human thymidylate kinase was partially competent for these activities despite failing to express detectable thymidine kinase activity. The virus expressing human deoxycytidine kinase failed to replicate acutely in neurons or to reactivate from latency. Therefore, it appears that low levels of thymidine phosphorylation suffice to fulfill the role of the viral enzyme in ganglia and that this role can be partially fulfilled by thymidylate kinase activity alone.

Recombinant fowlpox virus vaccines against Australian virulent Marek's disease virus: gene sequence analysis and comparison of vaccine efficacy in specific pathogen free and production chickens

We have cloned and sequenced the glycoprotein genes gB, gC and gD of the Australian virulent Marek's disease virus (MDV) isolate Woodlands No. 1. The glycoprotein gB and gC sequences were identical to the homologs of other virulent MDV type 1 strains, and the glycoprotein gD sequence contained only one unique amino acid substitution. Recombinant fowlpox viruses (rFPVs) expressing the MDV glycoprotein genes were constructed and their efficacy as vaccines was evaluated in specific pathogen free (SPF) and production chickens. Vaccination with the FPV-gB recombinant protected SPF chickens from Marek's disease mortality and tumour formation following challenge with virulent MDV Woodlands No. 1. The degree of protection from Marek's disease was dependent on the vaccine dose and route of inoculation. The rFPVs expressing gC or gD did not provide protection from Marek's disease. A rFPV expressing both gB and gC did not provide enhanced protection in comparison with the rFPV-gB alone. The rFPV-gB vaccine failed to protect commercial chickens from MD mortality and provided little protection from tumour formation in comparison with the commercial herpesvirus of turkey (HVT) vaccine. The failure to provide protection against MD may be related to the impact of maternally derived immunity to MDV and FPV and possibly the genotype of the chickens.

Evaluation of the thymidine kinase (tk) locus as an insertion site in the highly attenuated vaccinia MVA strain

The highly attenuated 'modified vaccinia Ankara' (MVA) strain is a potential live vaccine vector. Insertional inactivation of the tk-gene resulted in viruses difficult to purify. Co-integration of a functional fowlpox virus tk-gene allowed easy generation of recombinants, indicating that the genetically stable tk-gene region is a suitable insertion site, if tk-gene activity is substituted.

Selective induction of immune responses by cytokines coexpressed in recombinant fowlpox virus

Avipoxviruses have recently been studied as potential vectors for the delivery of heterologous vaccine antigen. Because these viruses abortively infect mammalian cells yet still effectively present encoded foreign genes to the host immune system, they offer a safer but effective alternative to other live virus vectors. We have examined the effect of coexpressing the cytokine interleukin-6 or gamma interferon on immune responses to a recombinant fowlpox virus expressing influenza virus hemagglutinin. The encoded cytokine was expressed for prolonged periods in infected cell culture with little cytopathic effect due to the abortive nature of the infection. In mice, vector-expressed cytokine dramatically altered immune responses induced by the coexpressed hemagglutinin antigen. Expression of interleukin-6 augmented both primary systemic and mucosal antibody responses and primed for enhanced recall responses. In contrast, expression of gamma interferon markedly inhibited antibody responses without affecting the generation of cell-mediated immunity. The safety of these constructs was demonstrated in mice with severe combined immunodeficiency, and no side effects due to cytokine expression were observed. In summary, fowlpox virus vectors encoding cytokines represent a safe and effective vaccine strategy which may be used to selectively manipulate the immune response.

Studies of fowlpox virus recombination in the generation of recombinant vaccines

A p7.5/beta-galactosidase (7.5 lacZ) gene construct, cloned adjacent to the fowlpox virus (FPV) thymidine kinase (tk) gene was used as a marker to identify the products of recombination as 'blue' FPV plaques. The rFPVs were detected as early as 4 h after the introduction of plasmid DNAs and by 72 h post-infection (p.i.) for one transfer vector comprised 0.48% of the viral population. The proportion of rFPV increased linearly from 0.073% to 0.62% as the cumulative length of homologous sequences in the transfer vector increased from 0.73 to 4.5 kb. Two approaches using a second reporter gene, the Newcastle disease virus haemagglutinin-neuraminidase (NDV HN) gene were tested to differentiate between single and double cross-over events. In one, the HN gene was cloned into the FPV tk gene and the 7.5 lacZ cloned outside of the homologous region. Progeny of a single cross-over with FPV DNA generated an unstable plaque containing the HN gene and subsequent intramolecular recombination resulted in excision of the 7.5 lacZ and the generation of a stable 'white' plaque. For virus grown in CEF cells (tk+) in the presence of 5-bromo-deoxyuridine, only those viruses which contained a tk gene disrupted by the HN gene formed plaques. This approach allowed us to easily identify rFPV containing the HN gene but lacking 7.5 lacZ or other bacterial sequences. In a second approach, a double cross-over between rFPV DNA containing a stably expressed beta-galactosidase gene cloned into the tk gene (blue plaque) and plasmid DNA containing the HN gene flanked by tk sequences would allow transplacement of the 7.5 lacZ gene with the HN gene, and generating a white plaque. We were unable to generate recombinant viruses with the HN gene and which generated a white plaque, indicating that double cross-over events do not occur at a sufficiently high frequency in FPV.

Modification of infectious bursal disease virus antigen VP2 for cell surface location fails to enhance immunogenicity

The host protective antigen gene VP2 of infectious bursal disease virus (IBDV) was genetically modified and expressed by recombinant fowlpox viruses (rFPV). To achieve cell surface localization, VP2 was expressed as a hybrid protein with signal sequence and membrane anchors of influenza virus hemagglutinin or neuraminidase. Native VP2 was expressed as VP2 alone or as self-processing VP2-VP4-VP3 polyprotein for coexpression of IBDV structural proteins. VP2 hybrid protein containing the carboxy-terminal membrane anchor sequence of influenza virus hemagglutinin was located on the cell surface and was N-glycosylated. The expression of VP2 fused to the N-terminal signal/anchor sequence of influenza virus neuraminidase led to cell lysis and the VP2 protein remained mainly unglycosylated. Cell surface localization of VP2 reduced immunogenicity (antibody induction) and abolished protection in poultry in comparison with the native VP2 expressed by FPV as VP2 alone or as the self-processing VP2-VP4-VP3. Vaccination of poultry with rFPV expressing native VP2 protein alone provided better protection from IBDV infection than VP2 derived from the VP2-VP4-VP3 polyprotein.

Infectious bursal disease virus structural protein VP2 expressed by a fowlpox virus recombinant confers protection against disease in chickens

Two fowlpox virus recombinants were constructed which expressed the host-protective antigen, VP2, of infectious bursal disease virus (IBDV). Recombinant FPV-VP 2.4.3 contained the gene for the VP 2-VP4-VP3 polyprotein under the control of the vaccinia virus late promoter P.L 11 inserted within the thymidine kinase (TK) gene of FPV. In infected chicken embryo skin (CES) cells VP2 and VP3 proteins were correctly processed from the polyprotein precursor molecule. Recombinant FPV-VP2 contained only the VP2 encoding region under the control of the fowlpox early/late promoter P.E/L inserted immediately downstream of the TK gene. The expression level of VP2 from FPV-VP2 was approximately 5 times higher than from FPV-VP2.4.3. Wing web inoculation of birds resulted in the development of typical fowlpox lesions and the development of antibodies to FPV with either of the recombinants, but only birds vaccinated with FPV-VP2 developed antibodies to IBDV. When challenged with IBDV (strain 002-73), a significant level of protection was provided by FPV-VP2 vaccination, although the level was lower than the protection provided by an oil adjuvanted inactivated whole IBDV vaccine. Birds vaccinated with FPV-VP2.4.3 were not protected from infection as assessed by ELISA for the presence of IBD virus in bursae.

Role of the TK+ phenotype in the stability of pigeonpox virus recombinant

Insertion of foreign DNA containing the E. coli gpt marker by homologous recombination in the pigeonpox virus (PPV) thymidine kinase (TK) gene and selection for the presence of this DNA in the viral genome produced unstable recombinants after 3 plaque purifications. We highlight the persistence of duplicated TK DNA sequences arising from single crossing over, due to the growth advantage of TK+ virus. Restoration of the TK function by coinsertion of the vaccinia virus TK gene led to stable TK+ recombinants arising from double crossing over.

Gene translocations in poxviruses: the fowlpox virus thymidine kinase gene is flanked by 15 bp direct repeats and occupies the locus which in vaccinia virus is occupied by the ribonucleotide reductase large subunit gene

By sequencing a fragment of 7351 bp the fowlpox virus thymidine kinase gene has been found to map to a position within the equivalent of the vaccinia HindIII I fragment. The deduced gene arrangement in fowlpox virus is I3, X, TK, I5, I6, I7, I8, G1, indicating that the homologue of the vaccinia I4 gene has been replaced by two genes X and TK. The non-essential TK gene has therefore replaced another non-essential gene, I4 (the ribonucleotide reductase large subunit) in this region. The X/TK insertion in fowlpox virus is precisely flanked by direct repeats of 15 bp suggesting that the translocation event may have involved transposition. The % identities between the fowlpox virus and vaccinia virus proteins ranged between 58.5% and 31.3%.

In vivo recognition of orf virus early transcriptional promoters in a vaccinia virus recombinant

The 4.4-kb BamHI-E fragment of the orf virus (OV) genome contains three discrete open reading frames designated ORF-pp, ORF-1, and ORF-3, all of which are flanked by vaccinia virus-like early transcriptional control sequences. To determine whether the vaccinia transcriptional machinery would recognize these promoters and faithfully transcribe OV genes in vivo the BamHI-E fragment was inserted into the thymidine kinase (TK) locus of vaccinia virus and the recombinant used in transcription studies. Northern blotting analysis of early RNA isolated from 143B-TK- cells infected with the recombinant virus showed that OV genes were transcribed and that the three transcripts of 0.70-(ORF-pp), 0.48- (ORF1), and 0.75-kb (ORF-3) were the same size as their counterparts in OV-infected cells. Analysis of the 5' end of transcripts by S1 nuclease and primer extension showed that the transcriptional start points (tsp) of ORF-pp, ORF-1, and ORF-3 in the recombinant were identical or within four nucleotides of the tsps of the same ORFs in OV. However, there were quantitative differences. ORF-1 was transcribed more efficiently in recombinant virus-infected cells than in those infected with OV and analysis of the putative promoter, 5'-AAAATTGTAAATGTA, showed that it was similar to the 7.5-kDa early promoter of vaccinia virus. This demonstrates that the transcriptional control sequences of OV genes are recognized by vaccinia virus transcriptional factors but that quantitative differences exist suggesting that the generically different transcriptional factors have different promoter sequence requirements for maximal transcription.

Evolution of thymidine and thymidylate kinases: the possibility of independent capture of TK genes by different groups of viruses

Phylogenetic analysis of viral and cellular thymidine and thymidylate kinases was performed using computer-assisted methods. Multiple alignments and tentative phylogenetic trees were generated for the two families of these enzymes, which include a) thymidine kinases (TK) of mammals, poxviruses, African swine fever virus, E. coli, and bacteriophage T4; and b) thymidylate kinases (ThyK) of yeast and poxviruses and distantly related herpesvirus proteins with both enzymatic activities. Analysis of the alignment of the TKs of the first family highlighted three strongly conserved segments. Two of these corresponded to the A and B motifs of the purine NTP-binding pattern. The third, C-terminal segment, showing the highest conservation, encompassed a modified Zn finger motif. It is speculated that this motif might be involved in TK oligomerization. Phylogenetic trees constructed by three different methods suggested that cellular TK genes could be captured independently by T4 bacteriophage, African swine fever virus, fowlpox virus, and the other poxviruses. The observed tree topologies appear to contradict the popular virus-host coevolution schemes and to imply that different subdivisions of poxviruses diverged at earlier stages of evolution than their hosts did. It was shown that deoxynucleoside monophosphate kinase of bacteriophage T4 is related to the ThyK family. Phylogenetic analysis suggested that ThyK genes probably have been acquired independently by phage T4, poxviruses, and herpes-viruses.

Mapping and molecular characterization of a functional thymidine kinase from Amsacta moorei entomopoxvirus

A thymidine kinase (TK) gene from the entomopoxvirus of Amsacta moorei (AmEPV) has been identified, mapped, cloned, and sequenced. The AmEPV TK was shown to be biologically functional as cloning of the gene into a TK-derivative of the orthopoxvirus vaccinia creates a TK+ virus. The gene has been localized to a 1.5-kb EcoRI-Q DNA fragment which maps to the far left end of the viral genome. Sequence analysis reveals an open reading frame (ORF) of 182 amino acids potentially encoding a polypeptide of 21.2 kDa. Amino acid homology comparisons indicate that the gene is most closely related to the TKs of a variety of poxviruses (approximately 45%) and less so to the TKs of vertebrates (approximately 40%). The TK from African swine fever virus (ASF) showed the least homology (31.4%) to the AmEPV TK gene, suggesting that these two viruses are not closely related although ASF shares some biological features of poxviruses, and both ASF and AmEPV can replicate within arthropod hosts.

Viral thymidine kinases and their relatives

Thymidine kinases were described for cellular life long before it was shown that they could also be encoded by viruses, but the viral thymidine kinase genes were the first to be sequenced. These enzymes have been extraordinarily useful to the researcher, serving first to help label DNA, then to get thymidine analogs incorporated into DNA for therapeutic and other purposes and more recently to move genes from one genome to another. Knowledge of the nucleotide and amino acid sequences of these enzymes has allowed some deductions about their possible three-dimensional structure, as well as the location on the polypeptide of various functions; it has also allowed their classification into two main groups: the herpesviral thymidine/eukaryotic deoxycytidine kinases and the poxviral and cellular thymidine kinases; the relationships of the mitochondrial enzyme are still not clear.

Computer-aided active-site-directed modeling of the herpes simplex virus 1 and human thymidine kinase

Thymidine kinase (TK), which is induced by Herpes Simplex Virus 1 (HSV1), plays a key role in the antiviral activity of guanine derivatives such as aciclovir (ACV). In contrast, ACV shows only low affinity to the corresponding host cell enzyme. In order to define the differences in substrate binding of the two enzymes on molecular level, models for the three-dimensional (3-D) structures of the active sites of HSV1-TK and human TK were developed. The reconstruction of the active sites of HSV1-TK and human TK were developed. The reconstruction of the active sites started from primary and secondary structure analysis of various kinases. The results were validated to homologous enzymes with known 3-D structures. The models predict that both enzymes consist of a central core beta-sheet structure, connected by loops and alpha-helices very similar to the overall structure of other nucleotide binding enzymes. The phosphate binding site is made up of a highly conserved glycine-rich loop at the N-terminus of the proteins and a conserved region at the C-terminus. The thymidine recognition site was found about 100 amino acids downstream from the phosphate binding loop. The differing substrate specificity of human and HSV1-TK can be explained by amino-acid substitutions in the homologous regions. To achieve a better understanding of the structure of the active site and how the thymidine kinase proteins interact with their substrates, the corresponding complexes of thymidine and dihydroxypropoxyguanine (DHPG) with HSV1 and human TK were built. For the docking of the guanine derivative, the X-ray structure of Elongation Factor Tu (EF-Tu), co-crystallized with guanosine diphosphate, was taken as reference. Fitting of thymidine into the active sites was done with respect to similar interactions found in thymidylate kinase. To complement the analysis of the 3-D structures of the two kinases and the substrate enzyme interactions, site-directed mutagenesis of the thymidine recognition site of HSV1-TK has been undertaken, changing Asp162 in the thymidine recognition site into Asn. First investigations reveal that the enzymatic activity of the mutant protein is destroyed.

Isolation and molecular characterization of the swinepox virus thymidine kinase gene

Swinepox virus (SPV), the only member of the Suipoxvirus genus, shows little antigenic relatedness or DNA homology to members of the other poxvirus genera. A SPV thymidine kinase (TK) gene was detected and mapped to the left end of the HindIII G fragment using degenerate oligonucleotide probes. Cloning and sequencing of a 1.8-kb HindIII-BamHI fragment containing the SPV TK gene revealed an open reading frame (ORF) of 181 amino acids yielding a predicted polypeptide of Mr 20.6 kDa with significant homology to both poxvirus and vertebrate thymidine kinases. Comparison with other TK protein sequences showed that the SPV thymidine kinase was closely related to the TK genes of avipoxviruses (52.0%) and vertebrates (57.1-59.7%). The TK gene from African swine fever virus (ASF) showed little homology (30.5%) to the SPV TK gene suggesting that these two viruses are not closely related though they share many biochemical features and infect a single, common mammalian host (swine). The SPV TK gene, like that of other poxviruses, is transcribed early, and when cloned into a TK- strain of vaccinia converted the virus to a TK+ phenotype. BUdRR mutants of SPV contained frameshift, deletion, and missense mutations in the TK ORF.

The primary structure of the thymidine kinase gene of fish lymphocystis disease virus

The DNA nucleotide sequence of the thymidine kinase (TK) gene of fish lymphocystis disease virus (FLDV) which has been localized between the coordinates 0.678 to 0.688 of the viral genome was determined. The analysis of the DNA nucleotide sequence located between the recognition sites of HindIII (0.669 map unit; nucleotide position 1) and AccI (nucleotide position 2032) revealed the presence of an open reading frame of 954 bp on the lower strand of this region between nucleotide positions 1868 (ATG) and 915 (TAA). It encodes for a protein of 318 amino acid residues. The evolutionary relationships of the TK gene of FLDV to the other known TK genes was investigated using the method of progressive sequence alignment. These analyses revealed a high degree of diversity between the protein sequence of FLDV TK gene and the amino acid composition of other TKs tested. However, significant conservations were detected at several regions of amino acid residues of the FLDV TK protein when compared to the amino acid sequence of TKs of African swine fever virus, fowlpox virus, shope fibroma virus, and vaccinia virus and to the amino acid sequences of the cellular cytoplasmic TK of chicken, mouse, and man.

Escherichia coli thymidine kinase: nucleotide sequence of the gene and relationships to other thymidine kinases

The thymidine kinase (TK)-encoding gene (tdk) of Escherichia coli is located at min 27 of the E. coli genetic map. Sequence analysis of this region revealed an open reading frame of 205 codons. Identification of this region as the E. coli tdk gene was confirmed by its similarity to other TK-encoding genes. The E. coli amino acid (aa) sequence showed significant similarity to the corresponding TK polypeptides of vertebrates and large DNA viruses, but showed no similarity to known herpes virus TK enzymes. Mapping of highly conserved positions among all sequences indicates the importance of these residues for catalytic activity and may facilitate further functional studies. Using a distance matrix method, the evolutionary relationships among the TK aa sequence of poxviruses, eukaryotes and prokaryotes were analyzed and a potential phylogenetic tree was established.

Identification and nucleotide sequence of the thymidine kinase gene of swinepox virus

Using degenerative oligonucleotide probes, representing two different conserved regions of poxvirus and mammalian thymidine kinase (TK) genes, the swinepox virus (SPV) TK gene was mapped to a 1.7-kb BamHI-HindIII fragment of the viral genome. Nucleotide sequencing of this DNA piece revealed that the SPV TK gene was encoded by an open reading frame (ORF) of 177 codons. Immediately downstream of the TK gene was a second ORF with homologues at the same location in both capripoxvirus and leporipoxvirus genomes. A similar gene had translocated to near the left hand terminus of the vaccinia virus (orthopoxvirus) genome. Flanking the two SPV genes were ORFs whose counterparts in other poxvirus genera are located at the same relative positions. SPV appeared to be most closely related to capripoxvirus, based on the organization of the four genes and on the percentage of identical amino acid residues of the respective encoded proteins.

Construction of a pigeonpox virus recombinant: expression of the Newcastle disease virus (NDV) fusion glycoprotein and protection of chickens against NDV challenge

A pigeonpox transfer plasmid was constructed by cloning a 2.5 kb DNA fragment containing the viral thymidine kinase (TK) gene in the psp65 plasmid. The vaccinia virus P11K promoter followed by the NDV fusion (F) gene was inserted in the TK gene. The F gene was transferred to the viral genome by homologous recombination in pigeonpox virus infected CEF cells, transfected with the recombinant plasmid. Recombinant viruses were selected with BUdR and screened for their ability to induce fusion between adjacent cells. Because of the unexpected growth advantage of the TK+ WT over the TK- recombinants, viral purification was needed to obtain stable recombinants expressing a glycosylated and cleaved F protein. Vaccination of chickens by the follicular method induced high anti-F antibody titers and good protection against challenge with the virulent Italian NDV strain. Half of the oculonasal vaccinated chickens showed anti F antibodies and also half of them were protected. Although protection seems to be correlated with antibody titers, no neutralizing antibodies were found.

Nucleotide sequence of the Escherichia coli thymidine kinase gene provides evidence for conservation of functional domains and quaternary structure

Using lambda bacteriophage clones from the Kohara Escherichia coli library spanning minutes 25.5 to 28.5 on the E. coli chromosome (strain W3110), two overlapping DNA fragments were identified which were able to confer thymidine kinase (TK) enzyme activity to a TK- strain of E. coli (KY895). This genetic complementation assay was used in concert with subcloning procedures to identify the minimal region (a 900 bp EcoRI-SalI fragment) which contained the E. coli thymidine kinase gene (tdk). The nucleotide sequence of the EcoRI-SalI fragment and a small portion of the adjoining downstream fragment was determined. Computer analysis of the derived sequence indicated the presence of a rightward-reading open reading frame of 615 bp which was capable of encoding a 205-amino-acid polypeptide with a predicted Mr of 23458 daltons. The in vivo transcriptional activity of this locus was confirmed by Northern blot hybridization analysis of RNA isolated from E. coli JM101 or KY895 which detected a 650-nucleotide RNA transcribed from this region. This places the tdk gene at approximately minute 27.35 on the E. coli W3110 chromosome, about 15 kb downstream from the narG locus and approximately 25 kb upstream of the trp operon. Although the predicted Mr of the E. coli TK protein was 23.5 kDa, gel-filtration analyses suggested that, like eukaryotic thymidine kinases, the active form of this enzyme is a multimeric complex.(ABSTRACT TRUNCATED AT 250 WORDS)

Expression and characterization of the thymidine kinase gene of African swine fever virus

The thymidine kinase (TK) gene of African swine fever virus (ASFV) was located within the viral genome by using two degenerate oligonucleotide probes derived from sequences of the vaccinia virus and cellular TK genes. The TK gene was mapped within a 0.72-kbp BglII-XhoI fragment (0.242 to 0.246 map units) derived from a 23.9-kbp SalI-B fragment of the ASFV genome. Identification of this region as the ASFV TK gene was confirmed by expression of TK in Escherichia coli and by the synthesis of active TK in a cell-free system programmed with RNA synthesized in vitro. The sequenced gene for TK includes an open reading frame of 588 nucleotides encoding a protein of 196 amino acids. The deduced amino acid sequence shows 32.4% identity with the TK of vaccinia virus.

An improved dot-blot method for virus detection in chicken embryo fibroblast cultures

A simplified dot-blot procedure is described for the detection of fowlpox virus (FPV) in infected monolayers of chicken embryo fibroblasts (CEF) cultured in 96-well microtiter plates. The relative resistance of DNA to hot NaOH, which hydrolyzes other macromolecules including RNA and protein, was exploited to solubilize virus infected cells and denature intracellular DNA in a simple, quick manner. Moreover, there was no need to purify virus or isolate viral DNA from cellular DNA prior to dot blotting. After incubation of CEF with FPV, the extracellular fluid from infected cells was collected for storage in 96-well microtiter plates. The remaining cell monolayers in each well were then solubilized with hot NaOH. The solubilized and denatured DNA was transferred to a nylon membrane using a dot-blot vacuum filtration manifold. Hybridization was carried out with a 32P-labeled FPV DNA probe. With this methodology it was possible to detect specific viral DNA sequences following the infection of cell monolayers with as little as 1 infectious unit per well. The ability to detect specific viral DNA sequences in infected cells, without the need to isolate pure viral DNA, made it possible to analyze large numbers of samples in a single experiment. Moreover, sufficient fowlpox virus was present in the extracellular media from each well for further amplification and analysis of selected samples.

Restriction endonuclease mapping of the fowlpox virus genome

The genome of fowlpox virus (Webster's mild vaccine strain) is composed of a single, double-stranded DNA molecule with covalently linked terminal hairpins and approximately 300 kb in length. Sites for cleavage by restriction endonucleases Pstl, Sal/l, Smal, and Notl have been identified with partial maps for EcoRI and BamHI. Differences in Pstl restriction fragment profiles for two separately prepared viruses (FPV-M and FPV-M3), both derived from the vaccine strain, indicate the presence of a nonessential region and potential insertion site for foreign DNA, toward one end of the viral genome. The size of the fowlpox virus genome, which is more than 100 kb larger than the orthopoxvirus vaccinia, indicates that the avipox viruses have the potential to code for more proteins than other groups of poxviruses.

Distribution of mutations around rearranged heavy-chain antibody variable-region genes

The mechanism of somatic hypermutation in the variable region of immunoglobulin genes expressed in mammalian B cells is a major unexplained phenomenon in the generation of diversity in the immune system. To evaluate possible mechanisms, the distribution of somatic mutations was examined for a group of five cloned, rearranged, somatically mutated VH genes generated in C57BL/6j mice. These mutated VH genes were sequenced and compared with their germ line counterparts from a point approximately 550 base pairs upstream of the transcription start site to an EcoRI site some 1,200 base pairs downstream of JH-4. The location of the transcription start (cap) sites was also precisely determined. Most (greater than or equal to 94%) of the 118 mutations scored occurred between the transcription start site and the distal end of JH-4. However, seven mutations occurred upstream of the transcribed region, and at least four were found downstream of JH-4. The target region for the mutator mechanism therefore clearly extends into the 3' nontranslated and 5' nontranscribed regions. Thus, models which propose the transcribed region of the DNA as the sole substrate for the mutation process are not ruled out but are inadequate to explain the upstream distribution of somatic mutations.

Distribution of mutations around rearranged heavy-chain antibody variable-region genes

The mechanism of somatic hypermutation in the variable region of immunoglobulin genes expressed in mammalian B cells is a major unexplained phenomenon in the generation of diversity in the immune system. To evaluate possible mechanisms, the distribution of somatic mutations was examined for a group of five cloned, rearranged, somatically mutated VH genes generated in C57BL/6j mice. These mutated VH genes were sequenced and compared with their germ line counterparts from a point approximately 550 base pairs upstream of the transcription start site to an EcoRI site some 1,200 base pairs downstream of JH-4. The location of the transcription start (cap) sites was also precisely determined. Most (greater than or equal to 94%) of the 118 mutations scored occurred between the transcription start site and the distal end of JH-4. However, seven mutations occurred upstream of the transcribed region, and at least four were found downstream of JH-4. The target region for the mutator mechanism therefore clearly extends into the 3' nontranslated and 5' nontranscribed regions. Thus, models which propose the transcribed region of the DNA as the sole substrate for the mutation process are not ruled out but are inadequate to explain the upstream distribution of somatic mutations.

Sequence and evolutionary relationships of African swine fever virus thymidine kinase

The thymidine kinase gene of African swine fever virus was mapped in a 1.4-kb EcoRI-PstI fragment located in the left half of the Eco RI K fragment of African swine fever virus DNA by using degenerate oligonucleotide probes derived from regions of the thymidine kinase sequence conserved in several poxviruses, man, mouse, and chicken. The nucleotide sequence of this region revealed an open reading frame of 196 codons, whose translated amino acid sequence showed significant similarity to the thymidine kinases of vaccinia virus, variola virus, monkeypox virus, shope fibroma virus, fowlpox virus, capripox virus, man, mouse, and chicken. The similarity scores obtained after comparison of known thymidine kinase sequences indicated that the African swine fever virus thymidine kinase is more distantly related than the poxvirus thymidine kinases to their cellular homologs. The evolutionary implications of these findings are discussed.

Activity of a fowlpox virus late gene promoter in vaccinia and fowlpox virus recombinants

Characterization of a late promoter of fowlpox virus (FPV) and a study of its activity in FPV and vaccinia virus (VV) was carried out. The 5'-mRNA start site of the FPV late gene mapped to a TAAAT sequence near the translation start site (ATG). A cloned DNA fragment of FPV genome (PFL1) comprising of the 5'-end of the late gene was used to express the LacZ gene of E. coli in FPV and VV recombinants. A comparative analysis of beta-galactosidase (BG) expression from the LacZ gene under the control of the FPV promoter and a VV late promoter (PL11) was performed. Like FPV-PL11-LacZ and VV-PL11-LacZ constructs, FPV-PFL1-LacZ and VV-PFL1-LacZ virus recombinants expressed BG indicating that essential features of transcription were conserved in the two viruses. Furthermore, the LacZ transcripts originating from PFL1 in FPV and VV recombinants mapped to the expected TAAAT sequence. Time course analysis of BG expressed by VV and FPV recombinants suggested that although the transcription machinery in the two viruses was essentially conserved, subtle differences in the efficiency of transcription or translation may exist.

Quaternary structure of vaccinia virus thymidine kinase

Thymidine kinase enzymes isolated from a variety of sources are generally considered to have a native molecular weight of 80-90 kDa composed of two 40-45 kDa subunits. Although these parameters may accurately describe the atypical deoxypyrimidine kinases expressed by members of the Herpesviridae, the nucleotide sequences of thymidine kinase genes isolated from human, mouse, chicken and variety of poxviruses (vaccinia virus, monkeypox virus, variola virus, fowlpox virus and capripoxvirus) predict molecular weights on the order of 20-25 kDa for the derived primary translation products. To resolve this apparent dilemma, velocity sedimentation centrifugation, gel filtration chromatography and protein cross-linking procedures were employed to provide experimental evidence that enzymatically-active vaccinia virus thymidine kinase is a homotetrameric complex of 20 kDa monomers with a native Mr of 80 kDa.

Comparative analysis of vaccinia virus promoter activity in fowlpox and vaccinia virus recombinants

A quantitative and qualitative comparison of vaccinia virus (VV) promoter activity in fowlpox virus (FPV) and VV recombinants was performed. The VV PL11 late promoter was used to express beta-galactosidase from the E. coli LacZ gene in FPV (FPV-LacZ) and VV (VV-LacZ) recombinants. Time courses of FPV-LacZ beta-galactosidase expression in chicken embryo skin (CES) cells demonstrated temporal regulation of the PL11 promoter with maximum enzyme activity nine- and four-fold lower than those obtained in VV-LacZ infected 143B and CES cells, respectively. The level of beta-galactosidase activity per LacZ DNA gene copy was determined for each recombinant and found to be greater for VV-LacZ than FPV-LacZ. The VV P7.5 early/late promoter was used to express the E. coli xanthine-guanine phosphoribosyl transferase (Ecogpt) gene in FPV and VV recombinants. Northern blot analysis showed early Ecogpt RNA transcripts to be of defined lengths. Transcript size estimations mapped the termination sites to regions containing sequences associated with VV early transcript termination, providing supportive evidence for a common poxvirus early transcript termination signal. Late LacZ and Ecogpt transcripts were heterogeneous in length. S1 nuclease mapping of the 5'-ends of early and late Ecogpt RNA transcripts produced by FPV and VV recombinants showed transcription initiation occurred at the same sites in both poxviruses and corresponded to the regions previously identified as the early and late start sites of the P7.5 promoter. These results would indicate a high level of conservation in the expression and regulation of genes by poxviruses.

Temperature-sensitive vaccinia virus mutants identify a gene with an essential role in viral replication

Vaccinia virus mutants ts2 and ts25, members of the same complementation group, exhibit a temperature-dependent arrest at the stage of viral DNA replication. The lesions responsible for the mutant phenotypes have been localized to the far left region of the HindIII B genomic fragment by marker rescue studies. Hybrid selection analyses established that the DNA fragments positive for rescue represented the first open reading frame of the HindIII B fragment and encoded a 30-kilodalton protein. The gene is expressed early after infection as a rightwardly transcribed 1-kilobase-pair mRNA whose coordinates were determined by S1 nuclease mapping. To further the phenotypic analysis of the mutants, the accumulation of viral DNA sequences during permissive and nonpermissive infections was quantitated. The extent of the DNA- phenotype was shown to vary in different cell types. In mouse L cells at either high or low multiplicity of infection, nonpermissive DNA synthesis was less than 5% of that seen in permissive infections. This severe defect was mirrored by correspondingly low viral yields. In infections of BSC40 monkey cells, however, the deficiencies in both DNA synthesis and virus production were far less severe. For one mutant (ts2), the temperature sensitivity in BSC40 cells varied inversely with the multiplicity of infection.

Mapping of a major early/late gene of fowlpox virus

Identification, cloning and mapping of a major gene expressed during the early and late stages of infection with fowlpox virus is described. The gene is located within a 17.3 kb PstI fragment of the fowlpox virus genome and has an open reading frame of 501 bp. Analysis of the 5'-ends of mRNA transcribed from this gene showed that the start sites of both early and late transcripts map to the sequence TAAAT near the translation start site (ATG). This is the first poxvirus early/late gene described in which both early and late transcription start sites map to same DNA sequence. From northern hybridization analysis it was shown that the early function of this gene gives rise to the most abundant early mRNA coded by 17% of the fowlpox virus genome. The strong early function of this gene promoter will be useful in the construction of recombinant fowlpox viruses.