In vitro transcription of the inverted terminal repetition of the vaccinia virus genome: correspondence of initiation and cap sites

Ternary complex formation by vaccinia virus RNA polymerase at an early viral promoter: analysis by native gel electrophoresis

We have resolved, by native gel electrophoresis, two intermediates in the transcription of a vaccinia virus early gene by the virus-encoded RNA polymerase. Polymerase holoenzyme containing the vaccinia virus early transcription factor (VETF) forms a complex of VETF bound to the promoter as the first step in a pathway leading to establishment of a committed ternary elongation complex. Formation of the VETF-DNA complex is stimulated by magnesium but is uninfluenced by nucleoside triphosphates. A stable binary complex of RNA polymerase bound to DNA is not detected. Assembly of a gel-stable polymerase-DNA complex depends on conditions permissive for RNA synthesis. Nucleotide omission experiments suggest that at least a tetrameric RNA must be made before a ternary complex is stabilized. RNA analysis indicates that complexes containing nascent transcripts 20 nucleotides long are stable and active. Ternary complex formation requires hydrolyzable ATP. This is consistent with an essential role for the ATPase activity of VETF at a step subsequent to DNA binding, as proposed by Broyles (S. S. Broyles, J. Biol. Chem. 266:15545-15548, 1991). The ternary complex, once formed, is resistant to dissociation by competitor DNA, as well as by salt, Sarkosyl, and heparin. The effects of these inhibitory agents on transcription complex formation suggest that they target different steps in the assembly pathway.

Transcription of orthopoxvirus telomeres at late times during infection

The telomeres of orthopoxvirus DNAs consists largely of short repeated sequences organized into at least two separate sets. Although the sequence composition of the orthopoxvirus telomeres is highly conserved, these regions do not appear to encode any proteins. At late times during infection, the telomeres of vaccinia virus are transcribed. A promoter in the region between the two sets of repeats directs transcription towards the hairpin-loop end of the viral DNA. This promoter resembles the promoters of other poxvirus late genes, and directs the synthesis of RNAs whose structure is consistent with the presence of 5' poly(A) sequences typical of late RNAs. The lengths of these late transcripts suggest that some transcription extends through the hairpin-loop region. This might occur either when the genome is in a monomeric form or when the genome is in the concatemeric form of the DNA replication intermediate. The function of late transcription of the telomeres is unclear, but similar transcription of the telomeres of vaccinia virus, cowpox virus, and raccoonpox virus suggests that such transcription may have a role in viral replication.

Vaccinia virus directs the synthesis of early mRNAs containing 5' poly(A) sequences

mRNAs transcribed from late promoters of several poxvirus genes contain 5' poly(A) sequences that are not complementary to the viral DNA. In contrast, early mRNAs containing 5' poly(A) sequences have not previously been identified. Modifications to the sequence of the promoter of an early gene of cowpox virus enable this promoter to direct the synthesis of RNAs containing 5' poly(A) sequences. When the sequence 3'-ATTTA-5', which is present at the RNA start-sites of several late promoters, is positioned such that the RNA start-site of the early promoter is at the first thymidylate in this sequence, this early promoter directs the synthesis of early RNAs containing 4-11 adenylates at their 5' ends. When two of the thymidylates in the sequence 3'-ATTTA-5' are removed, the promoter directs the synthesis of early RNAs lacking 5' poly(A) sequences. These results are consistent with the proposal that 5' polyadenylylation of poxvirus RNAs occurs by repetitive transcription of thymidylates in the sequence 3'-ATTTA-5' often present at the sites of transcriptional initiation. In addition, these results demonstrate that 5' polyadenylylation of viral RNAs is not exclusively a late function. The promoter regions of a few early genes of vaccinia virus contain the sequence 3'-ATTTA-5'. Analyses of the transcripts of one of these genes, the D5 gene, indicated that these mRNAs contain 5' poly(A) sequences, suggesting that early mRNAs of a subset of viral genes contain 5' poly(A) sequences.

Structure of vaccinia virus early promoters

Functional elements of a vaccinia virus early promoter were characterized by making a complete set of single nucleotide substitutions, as well as more complex mutations, and assaying their effects on gene expression. Synthetic oligonucleotides, based primarily on the sequence of the 7.5-kD early promoter, were inserted into a plasmid vector containing the lacZ gene of Escherichia coli flanked by sequences from the thymidine kinase (TK) gene of vaccinia virus. The lacZ gene, under control of the synthetic promoter, was introduced into the vaccinia virus genome at the TK locus by homologous recombination, and each of the 331 different recombinant viruses thus obtained was assayed for beta-galactosidase expression. The relative amounts and precise 5' ends of lacZ mRNAs specified by a subset of the recombinants were determined by primer extension. Many promoters were tested for their ability to direct specific transcription in vitro. A generally good correlation was noted between measurements of promoter strength estimated by beta-galactosidase expression, primer extension of in vivo mRNA and transcription in vitro. A relatively simple picture emerged from the analysis. The early promoter consists of a 16 base-pair critical region, in which most single nucleotide substitutions have a major effect on expression, separated by 11 base-pairs of a less critical T-rich sequence from a seven base-pair region within which initiation with a purine usually occurs. For the critical region of the 7.5-kD promoter, AAAAgTaGAAAataTA, any substitution of an upper-case nucleotide reduced expression, usually drastically, whereas certain substitutions of lower-case nucleotides maintained or significantly enhanced expression. On the basis of this analysis, the wide range of activities of natural promoters could be attributed to the presence of one or more non-optimal nucleotides in the critical region. Moreover, single nucleotide substitutions in such promoters had the predicted enhancing effects. Most mutations in the critical region of the 7.5-kD promoter behaved independently, but some nucleotide substitutions compensated for potentially detrimental nucleotides at other positions. Promoters substantially stronger than any natural ones examined were constructed by combining several up-mutations within the critical region of the 7.5-kD promoter and by repeating the critical region sequence. Like the TATA box of eukaryotic RNA polymerase II promoters, the critical region specifies the site of transcriptional initiation.

Identification of factors specific for transcription of the late class of vaccinia virus genes

Cytoplasmic extracts made from HeLa cells that have been harvested late after infection with vaccinia virus are capable of specifically transcribing templates containing vaccinia virus late-gene promoters. We applied such an extract to a phosphocellulose column and eluted the proteins with a series of buffers containing successively higher concentrations of NaCl. None of three column fractions alone was capable of specific transcription of a late-gene template. However, specific transcriptase activity could be reconstituted by mixing column fractions, with maximal activity seen when all three fractions were present. The activities present in all fractions were heat labile, resistant to micrococcal nuclease, and present only in extracts from vaccinia virus-infected cells. A quantitative complementation assay was used to further purify one factor, named VLTF-1, over subsequent columns of DEAE-cellulose and hydroxylapatite. VLTF-1 was separated from endogenous RNA polymerase, was a late-promoter-specific transcription factor, and had a sedimentation rate consistent with an apparent Mr of 45,000. The RNA polymerase-containing fraction was not only necessary for transcription with a late-promoter template but alone was capable of specifically transcribing a vaccinia virus early-gene promoter. A further difference between early and late gene transcription in this system was in the ability of the ATP analog beta-8-imidoadenosine-5'-triphosphate (AMP-PNP) to substitute for ATP in supporting specific transcription of only the late-promoter template. The system reconstituted from the various fractions retained the ability to produce the novel poly(A) sequence found on the 5' end of vaccinia virus late messages.

Cyclic-AMP-dependent switch in initiation of transcription from the two promoters of the Escherichia coli gal operon: identification and assay of 5'-triphosphate ends of mRNA by GTP:RNA guanyltransferase

We have studied the initiation of transcription of the gal operon in Escherichia coli (i) by analyzing the 5'-triphosphate ends and (ii) by measuring the level of promoter-proximal gal mRNA made in vivo. The 5' termini were identified and quantified by capping with GTP:mRNA guanyltransferase, and the mRNA levels were determined by hybridization of pulse-labeled [32P]RNA with a specific DNA probe. Our results conclusively demonstrate the in vivo activities of two promoters, P1 and P2, with separate initiation sites (S1 and S2) as suggested before from in vitro and in vivo experiments (S. Adhya and W. Miller, Nature [London] 279:492-494, 1979; R. E. Musso, R. DiLauro, S. Adhya, and B. de Crombrugghe, Cell 12:847-854, 1977). We have also studied the effect of cyclic AMP (cAMP) on in vivo gal transcription and found that whereas total gal transcription remains largely unchanged, the relative proportions of the S1 and S2 mRNAs are influenced by the level of cAMP in the cell. In strains devoid of cAMP (cya), transcription initiates equally at S1 and S2; in cAMP-proficient cells (cya+), the S1 initiation increases twofold with a concomitant decrease in S2 initiation. Addition of a saturating amount of exogenous cAMP to cya mutant cells results in a relatively larger switch from S2 to S1. Our results clearly show that while cAMP is an inhibitor of S2, it is not an absolute requirement for transcription initiation at S1, but only acts to increase low-level transcription from the P1 promoter. Using these approaches, we have also studied gal promoter mutants (P211, P18, and P35) which show altered behavior in transcription initiations and in response to cAMP. On the basis of these results, we have discussed models by which transcription initiates at the two overlapping gal promoters (P1 and P2) and discussed how cAMP level modulates the switch between them.

Capped poly(A) leaders of variable lengths at the 5' ends of vaccinia virus late mRNAs

Evidence for capped poly(A) leaders of variable lengths located immediately upstream of the translation initiation codon was obtained by direct analyses of a major late mRNA species. A decapping-recapping method was used to specifically substitute a radioactively labeled phosphate for an unlabeled one within the cap structure. RNase H-susceptible sites were made by hybridizing synthetic oligodeoxyribonucleotides to the mRNA encoding a late major structural protein of 11 kilodaltons. Sequences of the type m7G(5')pppAmp (Ap)nUpG. . ., where n varies from a few to more than 40 nucleotides, were deduced by analysis of the length and sequence of RNase H, RNase T1, and RNase U2 digestion products.

Viral RNA polymerases

Recent progress in molecular biological techniques revealed that genomes of animal viruses are complex in structure, for example, with respect to the chemical nature (DNA or RNA), strandedness (double or single), genetic sense (positive or negative), circularity (circle or linear), and so on. In agreement with this complexity in the genome structure, the modes of transcription and replication are various among virus families. The purpose of this article is to review and bring up to date the literature on viral RNA polymerases involved in transcription of animal DNA viruses and in both transcription and replication of RNA viruses. This review shows that the viral RNA polymerases are complex in both structure and function, being composed of multiple subunits and carrying multiple functions. The functions exposed seem to be controlled through structural interconversion.

In vitro synthesis of vaccinia virus late mRNA containing a 5' poly(A) leader sequence

We have shown that an extract made from HeLa cells harvested 6 hr after infection with vaccinia virus can transcribe a duplex DNA template containing a late viral gene. S1 nuclease analyses using genomic and synthetic probes indicated that the 5' ends of RNA synthesized in vitro are similar to those of RNA made in vivo and contain 5' poly(A) sequences contiguous with the translation initiation codon. Kinetic analysis of RNA synthesized in vitro demonstrated that a correctly initiated and 5' polyadenylylated product appeared within 5 min after transcription reactions were started. A cis-splicing mechanism of poly(A) addition can be ruled out because the DNA template used in vitro had no poly(dT) sequence and could contain as few as 37 base pairs upstream of the start of the RNA. In addition, we found that a point mutation in the first of two consecutively encoded adenylate residues preceding the ATG initiation codon abolished transcription in vitro. These data are consistent with at least three models: (i) RNA polymerase initiates RNA synthesis with a run of adenylate residues; (ii) a poly(A) primer is used for initiation; or (iii) the poly(A) leader is rapidly and efficiently attached to the RNA by ligation.

Vaccinia virus produces late mRNAs by discontinuous synthesis

We describe the unusual structure of a vaccinia virus late mRNA. In these molecules, the protein-coding sequences of a major late structural polypeptide are preceded by long leader RNAs, which in some cases are thousands of nucleotides long. These sequences map to different regions of the viral genome and in one instance are separated from the late gene by more than 100 kb of DNA. Moreover, the leader sequences map either upstream or downstream of the late gene, are transcribed from either DNA strand, and are fused to the late gene coding sequence via a poly(A) stretch. This demonstrates that vaccinia virus produces late mRNAs by tagging the protein-coding sequences onto the 3' end of other RNAs.

Transient expression system to measure the efficiency of vaccinia promoter regions

A transient expression system has been developed to compare the relative efficiency of expression of various vaccinia virus DNA sequences containing transcriptional regulatory elements. A plasmid vector was constructed containing both the Escherichia coli galactokinase gene (galK) and the guanine phosphoribosyltransferase gene (gpt). To direct the expression of gpt within this vector, a vaccinia virus promoter region was isolated from the HindIII-F fragment of the genome and inserted 5' to gpt coding sequence. Four unique cloning sites in front of galK allow simple and precise fusion of various vaccinia virus DNA fragments that contain the regulatory site of interest to galK. Sequences containing promoter regions were ligated to the coding segment of the galK to create four recombinant plasmids, which were introduced into vaccinia virus-infected cells by transfection. Both galK and gpt were thus expressed under the control of vaccinia virus transcriptional units, and the enzymatic activities were measured in the same cell extract with a filter-binding assay. The major advantage of this transient expression system is that the variations in galK expression are always measured relative to the internal gpt standard. Changes in the galK/gpt ratio resulting from different vaccinia promoters of galK are thus a quantitative measurement of promoter strength.

Tumorigenic poxviruses: transcriptional mapping of the terminal inverted repeats of Shope fibroma virus

A composite transcriptional map for the entire 12.4-kb terminal inverted repeat (TIR) region of the Shope fibroma virus (SFV) genome has been determined. Northern blotting and S1-nuclease mapping were used to determine the regions which are transcribed, their temporal relationships, as well as the transcriptional initiation sites. Sequences representing the entire TIR are transcribed into poly(A)+ mRNA at both early and late times in the infection. Fifteen transcriptional initiation sites were mapped, 12 within the TIRs and 3 within the unique sequences close to the junction between the right TIR and the unique internal sequences. Ten of the 12 transcriptional initiation sites within the TIR and 2 of the 3 sites outside the right TIR correspond to the 5'-ends of the major open reading frames (ORFs) T1 to T9 plus the SFV growth factor gene. The 3 other initiation sites map within ORFs but near potential start codons for shorter polypeptides. All the expressed ORFs are tandemly arranged and transcribed toward the hairpin terminus. At early times during SFV infection of cultured rabbit cells, transcription of each ORF gives rise to a transcript of distinct size, while at late times termination of transcription is imprecise and substantial read-through into downstream sequences occurs. These results are discussed in light of recent observations on the related recombinant leporipoxvirus, malignant rabbit fibroma virus, which suggest that one or more gene products from this region of the SFV genome are implicated in viral tumorigenicity.

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.

Nucleotide sequence of the vaccinia virus hemagglutinin gene

Vaccinia virus hemagglutinin (HA) is expressed at late time of infection cycle, and it is nonessential for virus growth. Location of the HA structural gene was determined by hybrid-arrested and hybrid-selected translation methods at the right terminus of the HindIII A fragment. The position of the HA gene was confirmed by the production of the complete HA protein in the cells transfected with the plasmid containing that region. Examination of this nucleotide sequence revealed the positions of cleavage sites for a number of restriction endonucleases. The deduced amino acid sequence revealed that the HA protein is a member of typical surface membrane glycoproteins. Comparison of the nucleotide sequence upstream of the HA coding region with corresponding region of other late genes suggested the existence of the consensus decanucleotides TTCATTTa/tGT between 34 to 18 bp upstream to the initiation codon followed by a cluster of A or T, a unique feature of the late genes of vaccinia virus. These results in conjunction with the ease of isolating HA- mutants provide a basis for a new site suitable for inserting foreign genes.

Transcription signals for stable RNA genes in Methanococcus

A previous survey of upstream sequences of tRNA genes from the archaebacterium Methanococcus vannielii has revealed that there are two boxes of sequence homology: A box "A" of about 20 conserved nucleotides at a distance of 30 to 49 basepairs upstream from the gene and a box "B" 18 to 19 nucleotides downstream from box "A" (Wich, G., Sibold, L., and Böck, A. (1985) System. Appl. Microbiol. (in press). Nuclease S1 mapping experiments were carried out with two of these tRNA transcriptional units and with a ribosomal RNA operon, to determine whether these consensus sequences have a function in the initiation of transcription. Use was made of the fact that cells from Methanococcus accumulate primary transcript and processing intermediates of ribosomal RNA under conditions of protein synthesis inhibition. The following results were obtained: (i) Transcription in all three systems starts at the G within the conserved trinucleotide TGC of box "B". Since the box "B" motif, 5'TGCaagT3', also occurs at the site of transcription initiation of protein encoding genes, both in methanogenic and halophilic organisms, it appears to constitute a frequently used transcription start signal within these archaebacterial groups. (ii) The box "A" motif occurs with constant spacing, relative to box "B", in all 10 tRNA and ribosomal RNA transcriptional units investigated from Methanococcus. Since it is not present in the leader region of genes coding for proteins, it seems to function as a specific element which is required for the expression of genes for stable RNA. (iii) Termination of transcription of the ribosomal RNA operon from Methanococcus occurs at a distinct T within an oligo-T stretch immediately downstream from the 3'-terminal 5S RNA gene. This signal occurs in all 3'-flanking regions of transcriptional units for stable RNA from the Methanococcus strains studied. Termination signals for stable RNA genes in Methanococcus appear to be similar with those of stable RNA genes in eukaryotes. (iv) By nuclease S1 mapping a recognition site was identified for a processing enzyme involved in the maturation of preribosomal RNA.

Transcription of vaccinia virus early genes by a template-dependent soluble extract of purified virions

An extract capable of selectively transcribing early vaccinia virus genes was prepared by disrupting purified vaccinia virions and passing the soluble material through a DEAE-cellulose column to remove endogenous DNA. Runoff transcripts of predicted size were synthesized by using double-stranded DNA templates that contained truncated early vaccinia virus genes, whereas several late vaccinia virus genes were not transcribed under these conditions. Proper dilution of the enzyme extract was critical, and a threshold concentration of DNA was required. At 30 degrees C, runoff transcripts were detected after 5 min and synthesis slowed appreciably after 30 min. Mg2+ was the preferred divalent cation, and KCl concentrations above 20 mM were inhibitory. Correct initiation of transcription was demonstrated by high-resolution analysis of S1 nuclease-digested hybrids formed by annealing in vitro-synthesized RNA with 5'-end-labeled DNA. A requirement for a 31-base-pair transcriptional regulatory sequence was found by using templates with deletions in an early promoter region. This in vitro system may be useful for mapping early transcriptional initiation sites, measuring the effects of additional promoter mutations, and isolating transcription factors.

Expression of Sindbis virus structural proteins via recombinant vaccinia virus: synthesis, processing, and incorporation into mature Sindbis virions

We have obtained a vaccinia virus recombinant which contains a complete cDNA copy of the 26S RNA of Sindbis virus within the thymidine kinase gene of the vaccinia virus genome. This recombinant constitutively transcribed the Sindbis sequences throughout the infectious cycle, reflecting the dual early-late vaccinia promoter used in this construction. The Sindbis-derived transcripts were translationally active, giving rise to both precursor and mature structural proteins of Sindbis virus, including the capsid protein (C), the precursor of glycoprotein E2 (PE2), and the two mature envelope glycoproteins (E1 and E2). These are the same products translated from the 26S mRNA during Sindbis infection, and thus these proteins were apparently cleaved, glycosylated, and transported in a manner analogous to that seen during authentic Sindbis infections. By using epitope-specific antibodies, it was possible to demonstrate that recombinant-derived proteins were incorporated into Sindbis virions during coinfections with monoclonal antibody-resistant Sindbis variants. These results suggest that all the information necessary to specify the proper biogenesis of Sindbis virus structural proteins resides within the 26S sequences and that vaccinia may provide an appropriate system for using DNA molecular genetic manipulations to unravel a variety of questions pertinent to RNA virus replication.

In vitro mutagenesis of the promoter region for a vaccinia virus gene: evidence for tandem early and late regulatory signals

A vaccinia virus gene that is expressed throughout the reproductive cycle was found to have two sets of RNA start sites approximately 55 nucleotides apart. The site nearest to the coding segment is used early in infection and the one further upstream is used after DNA replication. A series of 5' to 3' deletions were made in the promoter region, and the truncated DNA segments were then ligated to the coding portion of the procaryotic chloramphenicol acetyltransferase gene to measure expression. The effects of these mutations on chloramphenicol acetyltransferase synthesis were determined in a vaccinia virus helper-dependent transient expression system and by forming infectious vaccinia virus recombinants that contain the chimeric genes. Deletions extending up to 31 nucleotides before the late RNA start site had no effect on either early or late expression. Removal of an additional 15 nucleotides produced a dramatic decrease in late expression but had no effect on early expression. The latter was not diminished until the deletion was extended from 31 to 24 nucleotides before the early RNA start site. These results were confirmed by transcriptional analyses. We concluded that this vaccinia virus gene has two promoters and that the regulatory signals for each are located within 31 nucleotides of their sites of transcription.

In vitro transcription of a cloned vaccinia virus gene by a soluble extract prepared from vaccinia virus-infected HeLa cells

Faithful transcription of a vaccinia virus gene was accomplished in vitro by using a soluble extract prepared from vaccinia virus-infected HeLa cells. Specific transcription of the cloned vaccinia virus gene was detected by using template DNA restricted within the transcribed region. The vaccinia virus gene was not transcribed by extracts prepared from uninfected HeLa cells even with supplementation by purified vaccinia virus RNA polymerase, nor was a clone of adenovirus 2 DNA bearing the major late promoter transcribed by the extract from vaccinia virus-infected HeLa cells. Thus, infection by vaccinia virus altered cellular transcriptional specificity to favor expression of vaccinia virus genes. RNA synthesis by the infected cell extract was resistant to alpha-amanitin but strongly inhibited by beta, gamma-imido ATP and novobiocin.

A soluble transcription system derived from purified vaccinia virions

A soluble extract from purified vaccinia virus particles has been developed which displays site-specific initiation of transcription on exogenous DNA templates that carry cloned vaccinia virus early gene sequences. Bacterial plasmid vectors with segments of a strongly expressed early region of the vaccinia virus genome were active templates, whether in supercoiled or linear, truncated forms. Correct initiation, corresponding to that found in vivo, was observed for all early genes tested. The involvement of other factors besides the viral RNA polymerase was demonstrated by the loss of specific initiation upon partial purification of the enzyme. Initiation activity was restored by reconstitution of the system with factors lacking polymerase activity. The soluble system retained properties of transcription characteristic of intact viral cores, including (i) similar relative rates of initiation of various genes, (ii) multiple requirement for ATP, (iii) methylation and polyadenylation of transcripts, and (iv) inhibition by a topoisomerase antagonist.

Identification of the DNA sequences encoding the large subunit of the mRNA-capping enzyme of vaccinia virus

The DNA sequences encoding the large subunit of the mRNA-capping enzyme of vaccinia virus were located on the viral genome. The formation of an enzyme-guanylate covalent intermediate labeled with [alpha-32P]GTP allowed the identification of the large subunit of the capping enzyme and was used to monitor the appearance of the enzyme during the infectious cycle. This assay confirmed that after vaccinia infection, a novel 84,000-molecular-weight polypeptide corresponding to the large subunit was rapidly synthesized before viral DNA replication. Hybrid-selected cell-free translation of early viral mRNA established that vaccinia virus encoded a polypeptide identical in molecular weight with the 32P-labeled 84,000-molecular-weight polypeptide found in vaccinia virions. Like the authentic capping enzyme, this virus-encoded cell-free translation product bound specifically to DNA-cellulose. A comparison of the partial proteolytic digestion fragments generated by V8 protease, chymotrypsin, and trypsin demonstrated that the 32P-labeled large subunit and the [35S]methionine-labeled cell-free translation product were identical. The mRNA encoding the large subunit of the capping enzyme was located 3.1 kilobase pairs to the left of the HindIII D restriction fragment of the vaccinia genome. Furthermore, the mRNA was determined to be 3.0 kilobases in size, and its 5' and 3' termini were precisely located by S1 nuclease analysis.

Regulation of expression and nucleotide sequence of a late vaccinia virus gene

A subset of vaccinia virus genes are expressed only after DNA replication. To investigate the regulation of such transcriptional units, a representative gene encoding a major late polypeptide (Mr, 28,000) was mapped and sequenced. Translatable mRNAs were heterogeneous in length and overlapped several early genes downstream. The 5' end of the message was located, and the DNA segment upstream was excised and ligated to the coding sequence of the easily assayable procaryotic chloramphenicol acetyltransferase gene. The resulting chimeric gene was recombined into the thymidine kinase locus of the vaccinia virus genome, and infectious recombinant virus was isolated. Both the time of chloramphenicol acetyltransferase synthesis in infected cells and the requirement for DNA replication indicate that the sequence upstream of the late gene contains cis-acting transcriptional regulatory signals.

Organization of RNA transcripts from a vaccinia virus early gene cluster

The detailed organization of the RNAs transcribed from an early gene cluster encoded by vaccinia virus has been determined from the information derived from several complementary techniques. These include hybrid selection coupled with cell-free translation to locate DNA sequences complementary to mRNAs encoding specific polypeptides; RNA filter hybridization to size and locate on the DNA mature RNAs as well as higher-molecular-weight RNAs; S1 nuclease mapping to precisely locate the 5' and 3' ends of the RNAs; S1 nuclease mapping to precisely locate the 5' and 3' ends of the RNAs; and fractionation of hybrid-selected mRNAs in an agarose gel containing methyl mercury hydroxide followed by the cell-free translation of these mRNAs to definitively ascertain the size of the mRNA encoding each polypeptide. The early gene cluster is located between 21 and 26 kilobases from the left end of the vaccinia virus genome and is encoded by a 5.0-kilobase EcoRI fragment which spans the HindIII-N, -M, and -K fragments. Transcribed towards the left terminus are four mature mRNAs, 1,450, 950, 780, and 400 nucleotides in size, encoding polypeptides of 55, 30, 20, and 10 kilodaltons, respectively. These mRNAs are colinear with the DNA template and are closely spaced such that the 5' terminus of one mRNA is within 50 base pairs of the 3' terminus of the adjacent RNA. In addition to the mature size mRNAs, there are higher-molecular-weight RNAs, 5,000, 3,300, 2,350, 2,300, 1,800, 1,700, and 1,350 nucleotides in size. The 5' and 3' termini of the high-molecular-weight RNAs are coterminal with the 5' and 3' termini of the mature size mRNA. The implications of this arrangement and the biogenesis of these early mRNAs are discussed.

General method for production and selection of infectious vaccinia virus recombinants expressing foreign genes

The production and selection of infectious vaccinia virus recombinants expressing foreign genes was facilitated by the construction of plasmid vectors. These vectors contain all or part of the vaccinia virus thymidine kinase (TK) gene interrupted by multiple unique restriction endonuclease sites placed adjacent to the TK promoter or another promoter translocated within the TK gene. The insertion of a continuous coding sequence for a foreign protein at one of the unique restriction endonuclease sites juxtaposes the transcriptional start site of a vaccinia promoter and the translational start site of a foreign gene. After transfection of vaccinia virus-infected cells with such plasmids, homologous recombination occurs between the vaccinia virus sequences flanking the chimeric gene and the same sequences within the virus genome. Recombinants formed in this manner have the chimeric gene inserted within the body of the vaccinia virus TK gene under control of a vaccinia virus promoter. Since recombinants have an interrupted TK gene, they are selected on the basis of their TK- phenotype and then checked for the presence and expression of the foreign gene. Infectious recombinant viruses expressing the procaryotic enzyme chloramphenicol acetyltransferase were constructed to optimize the system. The absence of chloramphenicol acetyltransferase activity in uninfected cells or in cells infected with wild-type vaccinia virus and the availability of a sensitive and quantitative enzyme assay allowed an estimation of the relative strengths of various promoter constructs. The expression of chloramphenicol acetyltransferase was detected within 1 h after infection of cells with recombinant virus, reflecting the early nature of the promoters used.

Transcriptional and translational analysis of a strongly expressed early region of the vaccinia virus genome

A transcriptional and translational map was obtained for a 7-kilobase pair EcoRI fragment of vaccinia virus DNA containing 4% of the viral genome. This particular region contains a cluster of early genes which are transcribed in viral cores in vitro and in infected cells before uncoating of the viral DNA. Expression of this region was characterized by using vaccinia virus DNA sequences cloned in phage and plasmid vectors. Polypeptides encoded on the 7-kilobase pair fragment were identified by cell-free translation of viral mRNA selected by hybridization to immobilized DNA fragments. Early RNA programmed the synthesis of six proteins having apparent molecular weights of 63,000, 38,000, 37,000, 25,000, 15,000, and 13,000. The same result was obtained with RNA synthesized in vitro. A new species of 40 kilodaltons was synthesized in response to late RNA. Of the six "early" polypeptides, only the 13-kilodalton component was synthesized from late mRNA. RNA derived from the 7-kilobase pair region was analyzed by a variety of methods including hybridization blot, in vitro recapping, and S1 nuclease techniques. A surprisingly complex pattern of early transcription was found, indicating the existence of families of overlapping RNA species which share common 5'-proximal sequences. In addition, larger RNAs were identified spanning two or more adjacent genes. These RNAs appear to possess a common 5' terminus with transcripts derived from the first gene and are coterminal at the 3' end with RNAs from the downstream gene. Late RNA encoding the 40-kilodalton protein was shown to be heterogeneous in size. A single 5' terminus but no unique 3' terminus was identified for this class of transcripts. RNA species synthesized by cores in vitro were of similar size to authentic transcripts isolated from infected cells at early times.

Selective transcription of vaccinia virus genes in template dependent soluble extracts of infected cells

A soluble system that specifically and accurately initiates transcription on defined vaccinia virus templates has been obtained from lysates of infected cells. The required regulatory signals are contained within a DNA segment extending about 230 bp upstream and 30 bp downstream of the RNA start site. Transcription is resistant to alpha-amanitin and inhibited by antibodies to the viral RNA polymerase. Whole cell extracts from uninfected cells cannot accurately transcribe vaccinia DNA. Conversely, extracts prepared at 2 hr or later after vaccinia infection no longer transcribe RNA polymerase II templates but retain the ability to transcribe RNA polymerase III templates as well as vaccinia virus DNA. These profound changes in transcriptional specificity may contribute to the selective expression of viral genes following vaccinia infection.

Electron microscopic studies of transcriptional complexes released from vaccinia cores during RNA-synthesis in vitro: methods for fractionation of transcriptional complexes

Electron microscopic (EM) and biochemical methods were employed to study the transcriptional complexes present in detergent lysates of vaccinia virus cores actively synthesizing RNA in vitro. When processed and examined in the EM, 14 'transcriptional sites' could be observed on full-length DNA templates. Fractionation of lysates by equilibrium density centrifugation in CsSO4, chromatography on hydroxyapatite columns or by sedimentation in sucrose gradients, allowed isolation of DNA templates associated with transcripts but these manipulations often resulted in fragmentation of the DNA template or promoted the release of transcripts from the template. It is suggested that RNA transcripts remain associated with the template in regions of supercoiling. These regions, in turn, may be maintained by DNA-protein interactions which are compromised as the transcriptional complexes are fractionated and purified.

Discriminatory inhibition of protein synthesis in cell-free systems by vaccinia virus transcripts

The effect of vaccinia virus early transcripts on cellular (globin, HeLa, Chinese hamster ovary) and viral (vaccinia, encephalomyocarditis) mRNA function was studied in reticulocyte and wheat germ cell-free protein-synthesizing systems. Vaccinia virus transcripts of two size classes (8-10 S and 4-7 S), generated in vitro by viral cores, inhibited function of cellular and encephalomyocarditis virus mRNA but not that of vaccinia virus in reticulocyte lysate systems. Mild alkaline hydrolysis or micrococcal nuclease treatment of vaccinia virus in vitro transcripts resulted in a loss of their ability to inhibit protein synthesis directed by HeLa cell RNA. Vaccinia virus in vitro transcripts also selectively inhibited HeLa cell protein synthesis in wheat germ systems, suggesting that double-stranded RNA is not involved in this inhibition of protein synthesis. The addition, to the reticulocyte translating system, of cytoplasmic RNA obtained from infected cells in conjunction with cellular mRNA (globin, HeLa) resulted in the inhibition of synthesis of the globin or HeLa polypeptides with little or no effect on the translation of the vaccinia virus proteins. RNA extracted from vaccinia virions inhibited cellular but not vaccinia virus mRNA function when added to the reticulocyte lysate systems with uninfected or infected HeLa cell cytoplasmic RNA.

Complete nucleotide sequences of two adjacent early vaccinia virus genes located within the inverted terminal repetition

The proximal part of the 10,000-base pair (bp) inverted terminal repetition of vaccinia virus DNA encodes at least three early mRNAs. A 2,236-bp segment of the repetition was sequenced to characterize two of the genes. This task was facilitated by constructing a series of recombinants containing overlapping deletions; oligonucleotide linkers with synthetic restriction sites provided points for radioactive labeling before sequencing by the chemical degradation method of Maxam and Gilbert (Methods Enzymol. 65:499-560, 1980). The ends of the transcripts were mapped by hybridizing labeled DNA fragments to early viral RNA and resolving nuclease S1-protected fragments in sequencing gels, by sequencing cDNA clones, and from the lengths of the RNAs. The nucleotide sequences for at least 60 bp upstream of both transcriptional initiation sites are more than 80% adenine . thymine rich and contain long runs of adenines and thymines with some homology to procaryotic and eucaryotic consensus sequences. The gene transcribed in the rightward direction encodes an RNA of approximately 530 nucleotides with a single open reading frame of 420 nucleotides. Preceding the first AUG, there is a heptanucleotide that can hybridize to the 3' end of 18S rRNA with only one mismatch. The derived amino acid sequence of the protein indicated a molecular weight of 15,500. The gene transcribed in the leftward direction encodes an RNA 1,000 to 1,100 nucleotides long with an open reading frame of 996 nucleotides and a leader sequence of only 5 to 6 nucleotides. The derived amino acid sequence of this protein indicated a molecular weight of 38,500. The 3' ends of the two transcripts were located within 100 bp of each other. Although there are adenine . thymine-rich clusters near the putative transcriptional termination sites, specific AATAAA polyadenylic acid signal sequences are absent.

Restriction enzyme mapping of vaccinia virus DNA

The cleavage sites for the restriction enzymes Bg/I, HindIII, KpnI, SalI, SmaI, and XhoI were located, from primary data, on the DNA isolated from the WR strain of vaccinia virus. Bg/I and SmaI divide the DNA into five segments which can be isolated by sucrose gradient centrifugation. These large segments provide a convenient means to group segments produced by other enzymes. The construction of physical maps was initiated by identifying the segments at each end of the DNA and then finding segments which were adjacent to these terminal sections. This was accomplished by isolating large shear fragments which contained the covalently linked termini of the DNA. Most of the data needed to derive the maps were obtained by isolating segments produce by one enzyme and then cleaving these individual segments with a second enzyme.

Colinearity of RNAs with the vaccinia virus genome: anomalies with two complementary early and late RNAs result from a small deletion or rearrangement within the inverted terminal repetition

The colinearity of RNA transcripts with the vaccinia virus genome was investigated. Cytoplasmic RNA from infected cells was annealed to a cloned DNA segment that extended from 9 to 15.6 kilobase pairs from the left end of the genome and contained approximately 800 base pairs of the inverted terminal repetition (ITR). Remaining unhybridized single strands of DNA were digested with nuclease S1, and the lengths of the protected DNA fragments were determined by agarose gel electrophoresis under neutral and alkaline conditions. Uniformly 32P-labeled cloned DNA insert, separated recombinant DNA strands, and smaller restriction fragments, as well as 3' and 5' end-labeled DNA, were employed to map five early RNAs and one late RNA. One of the early RNAs hybridized to sequences within the ITR, and the other four hybridized to sequences proximal to the ITR. The late RNA was initiated proximal to the ITR but extended into it. Interestingly, the 3' portion of this late RNA was complementary to the early RNA transcribed from the opposite strand of the ITR. From a comparison of the lengths of the protected DNA fragments on neutral and alkaline gels, all except the complementary early and late RNAs appeared to be colinear with the genome. Although the anomalous nuclease S1 data obtained with the latter RNAs mimicked splicing, they were shown by DNA-DNA hybridization to result from a small deletion or rearrangement within the ITR. Thus far, no true examples of spliced vaccinia virus RNAs have been found.

Organization and expression of the poxvirus genome

Poxviruses comprise a large group of very complex animal DNA viruses which replicate in the cytoplasm of infected cells. Vaccinia virus, the most studied poxvirus, has a linear, double stranded DNA genome with an approximate molecular weight of 120 x 10(6) (180 kilobase pairs). The two strands of the DNA molecule are naturally cross-linked at both termini. In addition, the vaccinia virus genome contains very long inverted terminal repetitions of approximately 10 kilobase pairs which are further characterized by the presence of direct tandem repeats of a 70-base-pair sequence arranged in two blocks of 13 and 17 copies, respectively. A central region of the genome is highly conserved between different orthopoxviruses. In contrast, the ends are hypervariable and may contain extensive deletions and complex, symmetrical sequences rearrangements. Vaccinia virus gene expression is divided into two stages. Early in infection, RNA complementary to one half of one strand-equivalent of the genome is transcribed within subviral particles by the virion-associated RNA polymerase. Later in infection, after DNA replication, RNA complementary to one entire strand-equivalent is transcribed. RNA made late in infection is very heterogeneous in length and a large fraction of it contains self-complementary sequences. Late genes are clustered near the central region of the genome. Vaccinia virus mRNAs do not appear to be synthesized by a splicing mechanism.

Mapping of the vaccinia virus thymidine kinase gene by marker rescue and by cell-free translation of selected mRNA

A selective plaque assay that uses thymidine kinase (TK)-deficient human 143 cells was developed to titer mixtures of TK(+) and TK(-) vaccinia virus. With this assay it could be shown that methotrexate-resistant TK(+) virus was formed in cells coinfected with TK(-) virus and wild-type virus DNA. By substituting vaccinia DNA fragments cloned in plasmids for virion DNA, this marker rescue system provided the basis for mapping the TK gene. Of the 15 HindIII fragments, only J could rescue five independently derived TK(-) mutants. This 5000-base-pair (bp) fragment maps approximately 80,000 bp from the left-end of the 180,000-bp vaccinia genome. Marker rescue could be detected with 18 ng or less of plasmid and was proportionate to DNA concentration. The resistance to methotrexate of the TK(+) recombinants was shown to be due to TK synthesis. Evidence that the HindIII J fragment contains the structural TK gene and not a regulatory element was demonstrated by the synthesis of active TK in a cell-free system programmed with mRNA selected by hybridization to the plasmid. Previous studies [Belle-Isle, H., Venkatesan, S. & Moss, B. (1981) Virology 112, 306-317] indicated that mRNAs coding for three immediate early polypeptides with molecular weights of 41,000, 21,000, and 17,000 map within HindIII J. The mapping of the easily selectable vaccinia virus TK gene now opens the way to genetic manipulations that should increase our understanding of vaccinia virus gene expression and facilitate the use of vaccinia virus as an efficient cloning vector for foreign genes.

Incompletely base-paired flip-flop terminal loops link the two DNA strands of the vaccinia virus genome into one uninterrupted polynucleotide chain

The nature of the ends of the vaccinia virus genome was determined by nucleotide sequencing. Our finding of terminal hairpins indicated that the linear double-stranded DNA molecule consists of a single continuous polynucleotide chain. The 104 nucleotide apex of the hairpin contains predominantly A and T residues and is incompletely based-paired. These loops exist in two forms, which when inverted with respect to each other are complementary in sequence. Both forms of the 104 nucleotide loop are present in nearly equimolar amounts of each end of the genome. A set of 13 tandem 70 bp repeats begins 87 bp from the proximal segment of the terminal loop, followed by a unique sequence of 325 bp, and then by a second set of 18 tandem 70 bp repeats. The sequence of the 70 bp repeats reveals a 13 bp internal redundancy. Self-priming and de novo start replication models, which involve a site-specific nick in one DNA strand proximal to the 104 nucleotide loop, account for the observed sequence inversions and incomplete base-pairing. Similar mechanisms may be involved in replication of the ends of the eucaryotic chromosome.

Extension of the transcriptional and translational map of the left end of the vaccinia virus genome to 21 kilobase pairs

Physical, transcriptional, and translational maps of an EcoRI fragment located between 15,800 and 20,600 base pairs from the left end of the vaccinia virus genome were prepared. Major polypeptides with molecular weights of 14,000 (14K polypeptide), 32,000 and 38,000 were synthesized in a reticulocyte cell-free system programmed with immediate early RNA made in the presence of cycloheximide and selected by hybridization to lambda recombinant DNA containing the EcoRI fragment. With early RNA made in the presence of cytosine arabinoside, an inhibitor of DNA replication, the polypeptide pattern was similar except for quantitative differences in which less 38K polypeptide was detected as a translation product. With late RNA, isolated 6 h after infection without inhibitors, only traces of the early translation products were found and a new 40K polypeptide was detected. The size of the mRNA's for the 14K, 32K, and 38K polypeptides were determined to be approximately 760,880, and 1,150 nucleotides, respectively, by several independent procedures. Several large early RNAs not shown to code for any additional translation products were also detected. The size of the late message for the 40K polypeptide varied from 920 to 3,100 nucleotides. This heterogeneity appeared to be a general property of vaccinia virus late mRNA's. No evidence of RNA splicing was obtained by analysis of RNA-DNA hybrids after nuclease S1 treatment. Further analyses using separated recombinant DNA strands and restriction fragments indicated that all mRNA's were encoded by the leftward-reading DNA strand and at least two were overlapping. Since early and late mRNA's were encoded by the same DNA strand, the possibility of temporal regulation by transcriptional strand switching was eliminated. In conjunction with previous studies, a transcriptional map of the left 20,600 base pairs of the vaccinia virus genome was derived.

Transcriptional and translational mapping of a 6.6-kilobase-pair DNA fragment containing the junction of the terminal repetition and unique sequence at the left end of the vaccinia virus genome

The penultimate EcoRI fragments from the left and right ends of the vaccinia virus genomes were cloned in phage lambda. Heteroduplex analysis and comparison of restriction fragments indicated that the inverted terminal repetition extended 780 base pairs (bp) beyond the EcoRI site or about 9,800 bp from each end of the genome. Detailed physical, transcriptional, and translational maps of the 6,600-bp left penultimate EcoRI fragment were prepared so as to extend previous maps of the 9,000-bp terminal EcoRI fragment. Polypeptides with molecular weights of 6,000 (6K polypeptide), 13,000, 19,000, 21,000, and 60,000 were synthesized in a reticulocyte cell-free system programmed with immediate early RNA (made in the presence of cycloheximide) or early RNA (made in the presence of cytosine arabinoside) and selected by hybridization to immobilized recombinant DNA. A 22K polypeptide was detected as a translation product of late RNA that hybridized to this DNA fragment. A variety of biochemical procedures were used to size and map the mRNA's. Of the five messages that hybridized to this 6,600-bp EcoRI fragment, only the one for the 21K polypeptide was encoded within the inverted terminal repetition and hybridized to the rightward-reading DNA strand. (Three additional early polypeptides were encoded within the first 9,000 bp of the inverted terminal repetition.) The remaining early polypeptides were encoded within the unique portion of the penultimate EcoRI fragment and were transcribed from the leftward-reading strand. Additional high-molecular-weight early RNAs of unknown function were also detected; however, there was no evidence indicating that mature mRNA's were spliced.

Distinctive nucleotide sequences adjacent to multiple initiation and termination sites of an early vaccinia virus gene

Poxviruses, unlike other DNA viruses, replicate in the cytoplasm of infected cells and use their own system of transcription. Examination on one early mRNA synthesized in vivo and in vitro indicated that it has multiple closely spaced 5' and 3' ends. A remarkable 88% AT-rich 60 bp DNA sequence was found immediately upstream of the initiation of transcription sites. Although DNA sequences that bear some homology to Pribnow and Hogness boxes are present, additional recognition sequences located further upstream of procaryotic and eucaryotic initiation sites are absent. A possible initiation of translation codon occurs about 50 nucleotides from the 5' end of the message. The transcript terminates near or within a hexanucleotide CTATTC that is tandemly repeated four times. Sequences similar to those regulating termination of transcription in procaryotes or poly (A) addition in eucaryotes were not found, suggesting that poxviruses have evolved unique recognition signals.