Transcriptional and translational analysis of the vaccinia virus late gene L65

Protein composition of the vaccinia virus mature virion

The protein content of vaccinia virus mature virions, purified by rate zonal and isopycnic centrifugations and solubilized by SDS or a solution of urea and thiourea, was determined by the accurate mass and time tag technology which uses both tandem mass spectrometry and Fourier transform-ion cyclotron resonance mass spectrometry to detect tryptic peptides separated by high-resolution liquid chromatography. Eighty vaccinia virus-encoded proteins representing 37% of the 218 genes annotated in the complete genome sequence were detected in at least three analyses. Ten proteins accounted for approximately 80% of the virion mass. Thirteen identified proteins were not previously reported as components of virions. On the other hand, 8 previously described virion proteins were not detected here, presumably due to technical reasons including small size and hydrophobicity. In addition to vaccinia virus-encoded proteins, 24 host proteins omitting isoforms were detected. The most abundant of these were cytoskeletal proteins, heat shock proteins and proteins involved in translation.

External scaffold of spherical immature poxvirus particles is made of protein trimers, forming a honeycomb lattice

During morphogenesis, poxviruses undergo a remarkable transition from spherical immature forms to brick-shaped infectious particles lacking helical or icosahedral symmetry. In this study, we show that the transitory honeycomb lattice coating the lipoprotein membrane of immature vaccinia virus particles is formed from trimers of a 62-kD protein encoded by the viral D13L gene. Deep-etch electron microscopy demonstrated that anti-D13 antibodies bound to the external protein coat and that lattice fragments were in affinity-purified D13 preparations. Soluble D13 appeared mostly trimeric by gel electrophoresis and ultracentrifugation, which is consistent with structural requirements for a honeycomb. In the presence or absence of other virion proteins, a mutated D13 with one amino acid substitution formed stacks of membrane-unassociated flat sheets that closely resembled the curved honeycombs of immature virions except for the absence of pentagonal facets. A homologous domain that is present in D13 and capsid proteins of certain other lipid-containing viruses support the idea that the developmental stages of poxviruses reflect their evolution from an icosahedral ancestor.

Complementation analysis of the dales collection of vaccinia virus temperature-sensitive mutants

A collection of randomly generated temperature-sensitive (ts) vaccinia virus (strain IHD-W) mutants were reported by S. Dales et al., (1978, Virology, 84, 403-428) in 1978 and characterized by electron microscopy. We have performed further genetic analysis on the Dales collection of mutants to make the mutants more useful to the scientific community. We obtained the entire Dales collection, 97 mutants, from the American Type Culture Center (ATCC). All 97 mutants were grown and reassessed for temperature sensitivity. Of these, 16 mutants were either very leaky or showed unacceptably high reversion indices even after plaque purification and therefore were not used for further analysis. The remaining 81 ts mutants were used to perform a complete complementation analysis with each other and the existing Condit collection of ts vaccinia virus (strain WR) mutants. Twenty-two of these 81 Dales mutants were dropped during complementation analysis due to erratic or weak behavior in the complementation test. Of the 59 mutants that were fit for further investigation, 30 fall into 13 of Condit's existing complementation groups, 5 comprise 3 previously identified complementation groups independent of the Condit collection, and 24 comprise 18 new complementation groups. The 59 mutants which were successfully characterized by complementation will be accessioned by and made available to the scientific community through the ATCC.

A 43-nucleotide RNA cis-acting element governs the site-specific formation of the 3' end of a poxvirus late mRNA

The 3' ends of late mRNAs of the ati gene, encoding the major component of the A-type inclusions, are generated by endoribonucleolytic cleavage at a specific site in the primary transcript [Antczak et al., (1992), Proc. Natl. Acad. Sci. USA 89, 12033-12037]. In this study, sequence analysis of cDNAs of the 3' ends of ati mRNAs showed these mRNAs are 3' polyadenylated at the RNA cleavage site. This suggests that ati mRNA 3' end formation involves cleavage of a late transcript, with subsequent 3' polyadenylation of the 5' cleavage product. The RNA cis-acting element, the AX element, directing orientation-dependent formation of these mRNA 3' ends, was mapped to a 345-bp AluI-XbaI fragment. Deletion analyses of this fragment showed that the boundaries of the AX element are within -5 and +38 of the RNA cleavage site. Scanning mutagenesis showed that the AX element contains at least two subelements: subelement I, 5'-UUUAU downward arrowCCGAUAAUUC-3', containing the cleavage site ( downward arrow), separated from the downstream subelement II, 5'-AAUUUCGGAUUUGAAUGC-3', by a 10-nucleotide region, whose composition may be altered without effect on RNA 3' end formation. These features, which differ from those of other elements controlling RNA processing, suggest that the AX element is a component of a novel mechanism of RNA 3' end formation.

Cyclosporin A inhibits vaccinia virus replication in vitro

The effect of the immune modulator, Cyclosporin A (CsA) on vaccinia virus replication has been examined in cell cultures. In the present study we report that CsA is anti-viral towards vaccinia virus. Viral yield was inhibited by more than 97% after 24 h postinfection in the presence of 16 microM to 40 microM CsA. An analysis of the infectious cycle in greater detail revealed that CsA did not effect the total level of [35S] methionine incorporation into vaccinia infected cells. However, both early and late viral gene expression were inhibited by CsA. Late viral protein synthesis appeared to be more sensitive to the drug. At least one late viral polypeptide of approximately Mr 38,000 was virtually undetected up to 8 h postinfection in the presence of 40 microM CsA. Host protein synthesis which is normally inhibited by the virus was not turned off until very late in infection. Viral DNA replication was also inhibited by the addition of CsA at levels comparable to those observed for late protein synthesis.

Assembly of vaccinia virus: effects of rifampin on the intracellular distribution of viral protein p65

The cytoplasmic assembly of vaccinia virus is reversibly blocked by the antibiotic rifampin, leading to the accumulation of partially membrane-delineated rifampin bodies in infected cells. Rifampin-resistant vaccinia virus mutants have point mutations in the D13L gene, which is controlled by a late promoter and expresses a 65-kDa protein, designated p65. To further characterize the mechanism of rifampin inhibition and the function of p65 in virus assembly, we raised antibodies to this protein. Immunoreactive p65 was expressed at late times of infection, and neither its expression nor its turnover was affected by rifampin. Virus-associated p65 could be extracted only with denaturing detergents from purified virions, suggesting that it is an integral viral component. Immunofluorescence studies showed that p65 is localized to the sites of virus assembly. Also, immunoelectron microscopy showed p65 to be associated with viral crescents as well as spherical, immature virions, in both cases predominantly on the inner or concave surface. In the presence of rifampin, p65 was found in large, cytoplasmic inclusion bodies that were distinct from rifampin bodies. The rifampin bodies themselves were labeled with p65 antibodies only after reversal of the rifampin block, predominantly on the viral crescents which rapidly formed following removal of the drug. We propose that p65 functions as an internal scaffold in the formation of viral crescents and immature virions, analogously to the matrix proteins of other viruses.

A temperature-sensitive lesion in the small subunit of the vaccinia virus-encoded mRNA capping enzyme causes a defect in viral telomere resolution

Using pulsed-field gel electrophoresis, we demonstrated that the temperature-sensitive (ts) conditional lethal mutant ts9383 is, at the nonpermissive temperature, defective in the resolution of concatemeric replicative intermediate DNA to linear 185-kb monomeric DNA genomes. The resolution defect was shown to be the result of a partial failure of the mutant virus to convert the replicated form of the viral telomere to hairpin termini. In contrast to other mutants of this phenotype, pulse-labeling of viral proteins at various times postinfection revealed no obvious difference in the quantity or temporal appearance of members of the late class of polypeptides. Using the marker rescue technique, we localized the ts lesion in ts9383 to an approximately 1-kb region within the HindIII D fragment. Both the ts phenotype and the resolution defect were shown to be caused by a single-base C----T point mutation resulting in the conversion of the amino acid proline to serine in codon 23 of open reading frame D12. This gene encodes a 33-kDa polypeptide which is known to be the small subunit of the virus-encoded mRNA capping enzyme (E. G. Niles, G. J. Lee-Chen, S. Shuman, B. Moss, and S. S. Broyles, Virology 172:513-522, 1989). The data are consistent with a role for this capping enzyme subunit during poxviral telomere resolution.

The vaccinia virus HindIII F fragment: nucleotide sequence of the left 6.2 kb

The nucleotide sequence of the left 6.2 kb of the 13.2-kb HindIII F fragment of vaccinia virus was determined. Translation of the sequence revealed nine closely spaced, tandemly oriented open reading frames (ORFs), all reading leftward. The transcriptional organization of this region was determined by Northern blot and S1 nuclease mapping. The analysis suggested that ORFs 1, 2, 4, 5, 6, 7, and 8 are transcribed early in infection, whereas ORFs 3 and 9 are probably late genes. Two of these ORFs have been reported previously. ORF F4L encodes the small subunit of ribonucleotide reductase and ORF F2L is homologous to a retroviral protease-like gene.

Multiple tandem promoters of the major outer membrane protein gene (omp1) of Chlamydia psittaci

The transcription of omp1, the gene encoding the major outer membrane protein, was studied for two strains of Chlamydia psittaci, guinea pig inclusion conjunctivitis (GPIC) and mouse pneumonitis (Mn). The transcriptional initiation sites for the omp1 of each strain were mapped by S1 nuclease and primer extension analyses. Three different sizes of omp1 transcripts were observed for GPIC and four were observed for Mn. The production of these transcripts appeared to be the consequence of multiple tandem promoters. The order in which the omp1 RNA transcripts appeared during the growth cycle of the C. psittaci strains was found to differ from that of C. trachomatis.

Orthopoxvirus genetics

Genetic analysis of orthopoxviruses has contributed substantially to our understanding of the functional organization of the poxvirus genome, and individual mutants provide invaluable tools for future studies of poxvirus biology. Deletion and transposition mutants, localized primarily in the termini of the genome, may be particularly useful for studying virus host range and pathogenicity. Numerous drug resistant and dependent mutants provide keys to understanding a wide variety of virus genes. A large number of well-characterized ts mutants, clustered in the center of the virus genome, are taking on an increasingly important role in research on the function of essential poxvirus genes. Genetic characterization of orthopoxviruses has progressed rapidly during the past decade, and one can reasonably anticipate a time when mutants will be available for the study of any poxvirus gene. Considerable progress toward this goal can be achieved through organized attempts to integrate and further characterize existing mutant collections and through the continued isolation and characterization of deletion, drug resistant, and ts mutants using established techniques. The most exciting possibility is that soon techniques will be available for directed mutagenesis to conditional lethality of any essential poxvirus gene.

DNA sequences that regulate expression of a vaccinia virus late gene (L65) and interact with a DNA-binding protein from infected cells

To be efficiently expressed in vivo, the vaccinia virus late gene, L65, requires 5'-proximal cis-acting elements which bind a factor from infected cells. Deletion mutagenesis and vaccinia virus helper-dependent transient expression procedures were used to demonstrate that two distinct late promoter elements direct transcription from two different start sites (proximal [+1] and distal [-92]). The -128 to -112 region was essential for L65 distal promoter function, while sequences between -59 and +50 were sufficient for L65 proximal promoter function. The proximal DNA sequences interact with a protein, binding factor I (BF-I), which was isolated and partially purified from vaccinia virus-infected cells at late times postinfection. This activity is not detectable in uninfected cells or in purified virions. This factor binds specifically to two different sites within the proximal promoter, one 5' and one 3' to the transcription start site, but does not bind to the distal promoter element.

Retroviral protease-like gene in the vaccinia virus genome

The retroviral protease-encoding region, PR, situated between the gag and pol genes, underwent gene duplication in the lineage now represented by simian retrovirus type 1; the sequence of the duplicated segment has diverged considerably from the present PR sequence [Power, M.D., Marx, P.A., Bryant, M.L., Gardner, M.B., Barr, P.J. & Luciw, P.A. (1986) Science 231, 1567-1572]. The PR-like duplicated gene segment was at some point translocated to a new site within the pol gene of a lentivirus (subsequent to the divergence of human immunodeficiency virus type 1), where it has been maintained. We have identified in the vaccinia virus genome a sequence that is homologous to the PR-like duplicated gene segment of both types of retrovirus in an open reading frame whose product is predicted to be a 16.2-kDa protein. The vaccinia PR-like gene is located in the HindIII F fragment, and its product displays 31-34% amino acid identity to the two types of retroviral duplicated protease sequences over a region encompassing 125 amino acid residues. Sequences flanking the vaccinia gene showed no significant homology at either the DNA or amino acid level to the retroviruses. Nuclease S1 and primer extension analyses determined that the vaccinia gene is transcribed early in infection.

Rifampicin prevents virosome localization of L65, an essential vaccinia virus polypeptide

In contrast to its irreversible effect on the Escherichia coliRNA polymerase beta-subunit, the antibiotic rifampicin reversibly inhibits vaccinia virus morphogenesis at a step during the formation of immature viral particles. The protein affected by the presence of rifampicin is L65, a major late vaccinia polypeptide to which mutations that confer rifampicin resistance have been mapped. We now provide evidence using a monospecific anti-L65 serum in concert with immunofluorescence and sucrose gradient analysis that the mechanism of action of rifampicin on vaccinia virus replication involves the inhibition of localization of L65 to the viral factories (virosomes) thereby blocking further development. Studies on the expression and distribution of L65 during the infection cycle reveal that L65 is a stable, nonglycosylated late protein associated with virions. These results are discussed in relationship to the possible in vivo functions of the L65 protein.

Nucleotide sequence and molecular genetic analysis of the large subunit of ribonucleotide reductase encoded by vaccinia virus

We have mapped the vaccinia virus (VV) gene encoding the large subunit of ribonucleotide reductase (VV M1) within the HindIII I restriction fragment by using an oligonucleotide probe. Nucleotide sequencing revealed a 2340-bp open reading frame (orf), 1-3, whose amino acid sequence is highly homologous to the mouse M1 protein. The 1-3 gene was expressed as an immediate-early gene product, being transcribed in a leftward direction into a 2.7-kb polyadenylated transcript. Hybrid-selected translation of cycloheximide-amplified immediate-early viral RNA demonstrated that this mRNA encoded an 86-kd protein, which agrees with the expected size of the reductase large subunit. The 5'- and 3'-boundaries of the 1-3 transcriptional unit were determined by primer extension and S1-nuclease analysis, respectively, and shown to contain sequence elements typical of other VV early genes. Surprisingly, the predicted amino acid sequence of the VV enzyme subunit shares 72.5% homology with the mouse large subunit, M1.

Transcription and translation mapping of the 13 genes in the vaccinia virus HindIII D fragment

The vaccinia virus HindIII D fragment is 160,060 bp in length and encodes 13 complete open reading frames [Niles et al. (1986) Virology 153, 96-112; S. L. Weinrich and D. E. Hruby (1986). Nucleic Acids Res. 14, 3003-3016]. We have employed a two-step Northern hybridization protocol using single-stranded DNA probes from M13 recombinants in order to identify the mRNA products from the 13 genes. Six of these genes are expressed only at early times after infection; six are transcribed only at late times; one gene is expressed at both early and late times after virus infection. The D11 gene is transcribed into two late mRNA species, one full-length and the other derived from the 3' one-third of the coding sequence. Translation of hybrid-selected mRNA was carried out in an attempt to identify the protein products encoded by each mRNA. Protein products were found for each early gene but translation was successful for only two of the eight late mRNAs. With the completion of the physical map it is apparent that the early and late genes in the HindIII D fragment are arranged in order to minimize potential interference caused by the expression of closely packed viral genes.

Vaccinia virus-encoded ribonucleotide reductase: sequence conservation of the gene for the small subunit and its amplification in hydroxyurea-resistant mutants

The vaccinia virus gene that encodes the small subunit of ribonucleotide reductase was localized to the HindIII F fragment by using degenerate oligonucleotide probes. DNA sequencing revealed a leftward-reading open reading frame that predicted a protein of 37 kilodaltons whose amino acid sequence was much more homologous to the mouse and clam M2 sequences (approximately 80%) than to the corresponding herpesvirus (approximately 27%) or procaryotic (approximately 19%) gene products. Vaccinia virus mutants selected for the ability to grow in high concentrations of a specific inhibitor of ribonucleotide reductase, hydroxyurea, amplified the M2 gene and harbored tandem arrays (2 to 15 copies) of the gene within the HindIII F region. RNA isolated at early times after infection with wild-type virus and probed with an internal fragment of the M2 gene indicated one major (1.2 kilobases) and two minor (4.0 and 2.1 kilobases) transcripts. S1 nuclease analysis and primer extension experiments identified an RNA start site 12 nucleotides upstream of the putative initiation ATG codon.

Inhibition of vaccinia virus replication by nicotinamide: evidence for ADP-ribosylation of viral proteins

Replication of vaccinia virus (VV) in monolayers of BSC40 cells was inhibited 99.9% in the presence of 60 mM nicotinamide (NIC), a competitive inhibitor of ADP-ribosylation reactions. Dot-blot hybridization analysis of infected cell extracts utilizing a VV DNA-specific probe indicated that the drug had only minimal effects on viral DNA synthesis. SDS-polyacrylamide gel electrophoresis of newly synthesized VV proteins pulse-labeled at early (2 h) or late (8 h) times post-infection revealed that although the full spectrum of expected viral polypeptides was evident, quantitative differences in the levels of expression of a distinct subset of viral proteins were observed in the presence of the drug. Velocity sedimentation of virus-infected cell lysates established that no mature particles were assembled in drug treated cells. Additional evidence suggesting that VV morphogenesis was abortive in the presence of NIC was obtained by pulse-chase labeling experiments that demonstrated that the two VV major late core polypeptide precursors P94 and P65, whose proteolytic processing to VP62 and VP60 is intimately associated with viral assembly, were not cleaved in the presence of NIC. Interestingly, growth of VV in the presence of [3H]adenosine resulted in the metabolic labeling of eight proteins that were associated with purified virions. These proteins co-migrated with proteins labeled with [3H]adenosine that were present in extracts of VV-infected, but not uninfected, cells. These analyses also revealed that the [3H]adenosine-labeling of a subset of cellular proteins (MW 18-20 kDa, possibly histones) was increased 4-fold by VV infection. The observed induction of either increased synthesis or hyper-modification of these 18-20 kDa proteins was inhibited by NIC. These results are discussed with respect to whether one or more VV polypeptides are subject to obligatory ADP-ribosylation modification reactions in order to attain their active configuration, and if so, whether the enzymes catalyzing these reactions are specified by the virus or host cell.

Molecular dissection of cis-acting regulatory elements from 5'-proximal regions of a vaccinia virus late gene cluster

Promoter elements responsible for directing the transcription of six tightly clustered vaccinia virus (VV) late genes (open reading frames [ORFs] D11, D12, D13, A1, A2, and A3) from the HindIII D/A region of the viral genome were identified within the upstream sequences proximal to each individual locus. These regions were identified as promoters by excising them from the VV genome, abutting them to the bacterial chloramphenicol acetyl transferase gene, and demonstrating their ability to drive expression of the reporter gene in transient-expression assays in an orientation-specific manner. To delineate the 5' boundary of the upstream elements, two of the VV late gene (A1 and D13) promoter: CAT constructs were subjected to deletion mutagenesis procedures. A series of 5' deletions of the ORF A1 promoter from -114 to -24 showed no reduction in promoter activity, whereas additional deletion of the sequences from -24 to +2 resulted in the complete loss of activity. Deletion of the ORF A1 fragment from -114 to -104 resulted in a 24% increase in activity, suggesting the presence of a negative regulatory region. In marked contrast to previous 5' deletion analyses which have identified VV late promoters as 20- to 30-base-pair cap-proximal sequences, 5' deletions to define the upstream boundary of the ORF D13 promoter identified two positive regulatory regions, the first between -235 and -170 and the second between -123 and -106. Background levels of chloramphenicol acetyltransferase expression were obtained with deletions past -88. Significantly, this places the ORF D13 regulatory regions within the upstream coding sequences of the ORF A1. A high-stringency computer search for homologies between VV late promoters that have been thus far characterized was carried out. Several potential consensus sequences were found just upstream from RNA start sites of temporally related promoter elements. Three major conclusions are drawn from these experiments. (i) The presence of promoters preceding each late ORF supports the hypothesis that each is expressed as an individual transcriptional unit. (ii) Promoter elements can be located within the coding portion of the upstream gene. (iii) Sequence homologies between temporally related promoter elements support the notion of kinetic subclasses of late genes.

Tandemly repeated sequences are present at the ends of the DNA of raccoonpox virus

The DNA of raccoonpox virus (RCN) has been characterized by restriction enzyme analysis. DNA hybridization studies showed that all HindIII fragments of the 215-kbp RCN DNA share some nucleotide sequence similarity with fragments of the DNA of cowpox virus (CPV). This information was used to construct a HindIII restriction map of the RCN DNA. The nucleotide sequence of the 2.2-kbp Sal 1 end fragment of the RCN DNA has been determined from a cloned copy of the HindIII O fragment. Of this 2.2-kb region 75% consists of short, tandemly repeated sequences. It does not contain any open reading frames capable of encoding polypeptide chains of more than 62 amino acids. There are six related types of repeated sequence, and these are arranged into two separate sets, each flanked by nonrepeated sequences. The nucleotide sequences of both repeated and nonrepeated sequences within this Sal 1 fragment are extremely similar to those of the Sal 1-generated end fragments of the DNas of CPV and vaccinia virus. The arrangements of the repeated and nonrepeated sequences are also similar in the DNAs of these three viruses. In contrast, the remainder of the RCN DNA is markedly different from the DNAs of other orthopoxviruses. The high degree of similarity between the ends of the RCN DNA and the ends of the other orthopoxvirus DNAs suggest that the complex arrays of repeated and nonrepeated sequences have been conserved because they have a role in virus multiplication.

Genetic map of the vaccinia virus HindIII D Fragment

Seventeen ts mutants of vaccinia virus known to map to the viral HindIII D fragment (R. C. Condit and A. Motyczka, 1981, Virology 113, 224-241; R. C. Condit, A. Motyczka, and G. Spizz, 1983, Virology 128, 429-443; M. J. Ensinger and M. Rovinsky, 1983, J. Virol. 48, 419-428) have been sorted into seven complementation groups. The precise location of each mutant on the HindIII D DNA fragment has been identified by either one-step or two-step marker rescue. By a comparison of this genetic map and the known sequence of this DNA fragment (E. G. Niles et al., 1986, Virology 153, 96-112; S. L. Weinrich and D. E. Hruby, 1986, Nucleic Acids Res. 14, 3003-3016), each mutant has been assigned to a single gene in the HindIII D fragment. In several cases, the map position of a mutant has been localized to a region of fewer than 300 bp in length. The complementation groups are evenly distributed along the DNA. However, within a single gene, the mutants are often clustered.

Nucleotide sequence and transcript organization of a region of the vaccinia virus genome which encodes a constitutively expressed gene required for DNA replication

A vaccinia virus (VV) gene required for DNA replication has been mapped to the left side of the 16-kilobase (kb) VV HindIII D DNA fragment by marker rescue of a DNA- temperature-sensitive mutant, ts17, using cloned fragments of the viral genome. The region of VV DNA containing the ts17 locus (3.6 kb) was sequenced. This nucleotide sequence contains one complete open reading frame (ORF) and two incomplete ORFs reading from left to right. Analysis of this region at early times revealed that transcription from the incomplete upstream ORF terminates coincidentally with the complete ORF encoding the ts17 gene product, which is directly downstream. The predicted proteins encoded by this region correlate well with polypeptides mapped by in vitro translation of hybrid-selected early mRNA. The nucleotide sequences of a 1.3-kb BglII fragment derived from ts17 and from two ts17 revertants were also determined, and the nature of the ts17 mutation was identified. S1 nuclease protection studies were carried out to determine the 5' and 3' ends of the transcripts and to examine the kinetics of expression of the ts17 gene during viral infection. The ts17 transcript is present at both early and late times postinfection, indicating that this gene is constitutively expressed. Surprisingly, the transcriptional start throughout infection occurs at the proposed late regulatory element TAA, which immediately precedes the putative initiation codon ATG. Although the biological activity of the ts17-encoded polypeptide was not identified, it was noted that in ts17-infected cells, expression of a nonlinked VV immediate-early gene (thymidine kinase) was deregulated at the nonpermissive temperature. This result may indicate that the ts17 gene product is functionally required at an early step of the VV replicative cycle.

Noncoordinate regulation of a vaccinia virus late gene cluster

Identification of a tightly spaced and tandemly oriented late gene cluster within the central conserved region of the vaccinia virus genome suggested the possibility of coordinate regulation of the genes within this domain (S.L. Weinrich and D.E. Hruby, Nucleic Acids Res. 14:3003-3016, 1986). To test this hypothesis, the steady-state levels of transcripts derived from the individual late genes were examined. Cytoplasmic RNA was isolated from infected cells at hourly intervals throughout infection and was used in concert with 5' S1 nuclease mapping procedures to detect transcripts from specific late genes. Among the set of six closely linked late genes, marked differences were observed in both the levels of transcription and the kinetic patterns of expression, providing direct evidence for the existence of differentially regulated gene subsets within the late gene class. Furthermore, these experiments identified one of the genes (encoding a 33,000-molecular-weight polypeptide) as being expressed both early and late postinfection. Interestingly, although transcripts from the constitutively expressed gene were initiated at the same start sites throughout infection, a discrete terminus for these transcripts was detected only at early times. These data suggest that the lack of cis-acting termination signals is not the reason for the late gene transcript heterogeneity observed in vaccinia virus-infected cells.

Resistance of vaccinia virus to rifampicin conferred by a single nucleotide substitution near the predicted NH2 terminus of a gene encoding an Mr 62,000 polypeptide

Marker transfer procedures were used to locate the site of mutation in the genome of a previously characterized (B. Moss, E. N. Rosenblum, and P. Grimley, 1971), Virology 45, 135-148) rifampicin-resistant (RifR) vaccinia virus isolate. Starting with a cosmid library prepared from the mutant genome, recombination with successively smaller DNA fragments was shown to transfer drug resistance to wild-type vaccinia virus. In this manner, the mutation was mapped within a 485-bp DNA segment in the central region of the genome at the extreme right end of the HindIII D fragment. Nucleotide sequencing indicated that this DNA segment differed from the homologous region of wild-type DNA by a single C/G----A/T substitution. Sequencing of the flanking 2195 bp revealed two tandem nonoverlapping open reading frames (ORFs) encoding putative polypeptides of Mr 16,908 and 61,840. The RifR mutation resulted in a predicted glutamine----lysine change only 27 amino acids from the NH2 terminus of the longer ORF. A predicted asparagine to aspartic acid substitution, found in another RifR vaccinia virus mutant by J. Tartaglia and E. Paoletti (Virology 147, 394-404, 1985), mapped near the carboxyl terminus of the same ORF. These data suggest a model in which head-to-tail interaction between Mr 61,840 polypeptides occurs and in which rifampicin blocks virus assembly by preventing this association.

Molecular cloning, encoding sequence, and expression of vaccinia virus nucleic acid-dependent nucleoside triphosphatase gene

A rabbit poxvirus genomic library contained within the expression vector lambda gt11 was screened with polyclonal antiserum prepared against vaccinia virus nucleic acid-dependent nucleoside triphosphatase (NTPase)-I enzyme. Five positive phage clones containing from 0.72- to 2.5-kilobase-pair (kbp) inserts expressed a beta-galactosidase fusion protein that was reactive by immunoblotting with the NTPase-I antibody. Hybridization analysis allowed the location of this gene within the vaccinia HindIIID restriction fragment. From the known nucleotide sequence of the 16-kbp vaccinia HindIIID fragment, we identified a region that contains a 1896-base open reading frame coding for a 631-amino acid protein. Analysis of the complete sequence revealed a highly basic protein, with hydrophilic COOH and NH2 termini, various hydrophobic domains, and no significant homology to other known proteins. Translational studies demonstrate that NTPase-I belongs to a late class of viral genes. This protein is highly conserved among Orthopoxviruses.

Nucleotide sequence and genetic map of the 16-kb vaccinia virus HindIII D fragment

We have determined the nucleotide sequence of the 16,059-bp HindIII D fragment from vaccinia virus strain WR. Translation in all 6 reading frames reveals a set of 22 open reading frames (ORFs), which are capable of encoding proteins ranging from 61 to 844 amino acids in length. With one exception, ORF 12, we have divided them into two primary sets according to their size. The minor group contains eight members ranging in length from 61 to 84 amino acids. The major group has thirteen members varying from 146 to 844 amino acids in length, and, in addition, due to its location on the DNA, one small ORF, 61 amino acids long. The neighboring major ORFs are closely packed along the DNA, being separated by 42 or fewer base pairs. In several instances the ends of adjoining ORFs overlap for up to 11 triplet codons. In three cases, 1 or 2 bases are shared between translation start and stop signals in adjacent ORFs. Regions of both strands of the DNA are transcribed. Two sets of temperature-sensitive mutations, totaling 17, which map to the HindIII D fragment, have been combined into eight complementation groups. The results of marker rescue analysis map one or more member of each group to a site in the HindIII D fragment within a defined open reading frame.

Vaccinia virus rifampicin-resistance locus specifies a late 63,000 Da gene product

The genetic locus specifying rifampicin-resistance (RifR) in a vaccinia virus mutant has been localized by marker rescue analysis (J. Tartaglia and E. Paoletti (1985) Virology 147, 394-404). The mutation was defined by DNA sequence analysis as an AT to GC transition occurring 56 bp to the left of the unique XhoI site within HindIII D. The point mutation resulted in an asparagine to aspartic acid substitution 60 amino acids from the predicted C-terminus. Specific DNA probes were used to characterize the RifR designated gene at the transcriptional and translational levels. This region is transcriptionally active only after vaccinia virus DNA synthesis, but not in the presence of cytosine arabinoside suggesting that the RifR function is a late gene product. Translation of hybrid selected RNA to DNA surrounding the mutant marker directed the synthesis of a polypeptide with an apparent mol wt of 63 kDa. Transcriptional and translational mapping studies showed that the mRNA encoding this 63-kDa polypeptide was initiated approximately 460 bp to the right of the HindIII D-A junction and was transcribed in a leftward direction into the HindIII D region.

A tandemly-oriented late gene cluster within the vaccinia virus genome

The nucleotide sequence of a 5.1 kilobase-pair fragment from the central portion of the vaccinia virus genome has been determined. Within this region, five complete and two incomplete open reading frames (orfs) are tightly-clustered, tandemly-oriented, and read in the leftward direction. Late mRNA start sites for the five complete orfs and one incomplete orf were determined by S1 nuclease mapping. The two leftmost complete orfs correlated with late polypeptides of 65,000 and 32,000 molecular weight previously mapped to this region. When compared with each other and with sequences present in protein data banks, the five complete orfs showed no significant homology matches amongst themselves or any previously reported sequence. The six putative promoters were aligned with three previously sequenced late gene promoters. While all of the nine are A-T rich, the only apparent consensus sequence is TAA immediately preceeding the initiator ATG. Identification of this tandemly-oriented late gene cluster suggests local organization of the viral genome.