Characterization of vaccinia virus early promoters and evaluation of their informational content

Construction and characterization of recombinant vaccinia viruses co-expressing a respiratory syncytial virus protein and a cytokine

Recombinant vaccinia viruses are well-characterized tools that can be used to define novel approaches to vaccine formulation and delivery. While vector co-expression of immune mediators has enormous potential for optimizing the composition of vaccine-induced immune responses, the impact on antigen expression and vector antigenicity must also be considered. Co-expression of IL-4 increased vaccinia virus vector titres, while IFN-gamma co-expression reduced vaccinia virus replication in BALB/c mice and in C57BL/6 mice infected with some recombinant viruses. Protection against respiratory syncytial virus (RSV) challenge was similar in mice immunized with vaccinia virus expressing RSV G glycoprotein and IFN-gamma, even though the replication efficiency of the vector was diminished. These data demonstrate the ability of vector-expressed cytokine to influence the virulence of the vector and to direct the development of selected immune responses. This suggests that the co-expression of cytokines and other immunomodulators has the potential to improve the safety of vaccine vectors while improving the immunogenicity of vaccine antigens.

The vaccinia virus J5L open reading frame encodes a polypeptide expressed late during infection and required for viral multiplication

A number of open reading frames (ORFs) are found in the vaccinia virus (VV) genome whose activities in the viral life cycle have not yet been determined. This report examines one such ORF, designated J5L, which was demonstrated to be essential for viral multiplication. Stable inactivation of the J5L ORF by insertion of a lacZ ORF was impossible unless another copy of the J5L ORF was present in the VV genome. Fusion genes between the J5L ORF and either the lacZ gene or the VV K1L gene were employed to study its temporal expression as well as its protein product. These experiments showed that J5L is transcribed late in infection and gives rise to a protein product which migrates by SDS-PAGE with the expected molecular weight (16 kDa). Numerous unsuccessful attempts to establish a stable cell line expressing J5L suggest that the J5L gene product could be cytotoxic.

Sequence and transcriptional analysis of a near-terminal region of the orf virus genome

A 3605 bp region located approximately 6.6 kb from the left end of the orf virus genome (strain NZ2) was sequenced. The sequence revealed two open reading frames, which we have designated G2L and B1L. The predicted amino acid sequences of G2L and B1L were found to be homologous to the vaccinia virus (VAC) F11L and F12L gene products, respectively, and were found to be arranged on the genome in the same orientation and relative position as their VAC counterparts. Transcriptional analysis of both G2L and B1L showed they were transcribed toward the genome terminus during the early phase of infection. S1 nuclease and primer-extension analyses showed that the transcriptional start sites of both genes were located a short distance downstream from A+T-rich sequences, similar to vac virus early promoters.

Sequence and transcriptional analysis of an orf virus gene encoding ankyrin-like repeat sequences

A 1608 bp region located approximately 5.0 kb from the left end of the orf virus (OV) genome (strain NZ2) was sequenced. The sequence revealed a single open reading frame designated G1L. The predicted amino acid sequence of G1L contained eight ankyrinlike repeat sequences. Transcriptional analysis of G1L showed it was transcribed towards the genome terminus during the early phase of infection. S1 nuclease and primer extension analyses showed that the transcriptional start site of the gene was located a short distance downstream from an A + T-rich sequence similar to a vaccinia virus early promoter.

Analysis of the imperfect octamer-containing human immunoglobulin VH6 gene promoter

The octamer sequence ATGCAAAT is highly conserved in the promoter of immunoglobulin heavy and light chain genes and is one of the sequence motifs involved in the control of transcription of these genes. The promoter region of an human immunoglobulin heavy chain variable gene, the sole member of the VH6 gene family, was found to differ from other VH gene promoters: it contains neither the conserved octamer motif nor a heptamer sequence, and generally bears little resemblance to other VH gene transcriptional control regions. An imperfect octamer sequence with a single nucleotide substitution (AgGCAAAT) is located 108 bp upstream of the ATG translation start site, and 81 bp upstream of the transcription initiation site. We sought to determine which sequence elements within the VH6 promoter were responsible for transcription initiation by creating progressive deletions of a 1 kb fragment from this region and testing their ability to function as promoter elements in B and non-B cells (HeLa). The minimum fragment required for full promoter function was 110 bp, but a fragment with only 65 bp retained 30-50% activity in B cells. Similar levels of transcription were seen when the -146 bp promoter containing two point mutations in the imperfect octamer was tested. Mutation of a possible pyrimidine box sequence located downstream of the TATA box was shown to have only a minor effect (10-30%) on transcription when three nucleotides were changed. Surprisingly, CAT activity was not B cell-specific, as all constructs had virtually the same activity in several B cell lines and in HeLa cells. Removal of the TATA box led to a 50% reduction in CAT activity, and the region upstream of the TATA box functioned as a promoter in both orientations. The transcriptional activity of the VH6 promoter was virtually enhancer independent: only a minor increase was observed when the immunoglobulin or SV40 enhancer was added to the promoter construct. Electrophoretic mobility shift assays of transcription factor binding to the region around the imperfect octamer indicated that binding was weak when nuclear extracts from either B cells or HeLa cells were used. The amount of complex shifted was increased by mutating the imperfect octamer to a perfect one. Chimeras produced between the VH6 promoter and a B cell-specific promoter from a member of the human VH2 gene family demonstrated that the lack of tissue specificity was due to the absence of a repressor of non-B cell transcription in the VH6 promoter. These results indicate that the VH6 promoter is relatively simple, requiring little more than the TATA element and the imperfect octamer, and transcription from this promoter lacks B cell specificity and is not dependent on the enhancer element.

Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites

An information analysis of the 5' (donor) and 3' (acceptor) sequences spanning the ends of nearly 1800 human introns has provided evidence for structural features of splice sites that bear upon spliceosome evolution and function: (1) 82% of the sequence information (i.e. sequence conservation) at donor junctions and 97% of the sequence information at acceptor junctions is confined to the introns, allowing codon choices throughout exons to be largely unrestricted. The distribution of information at intron-exon junctions is also described in detail and compared with footprints. (2) Acceptor sites are found to possess enough information to be located in the transcribed portion of the human genome, whereas donor sites possess about one bit less than the information needed to locate them independently. This difference suggests that acceptor sites are located first in humans and, having been located, reduce by a factor of two the number of alternative sites available as donors. Direct experimental evidence exists to support this conclusion. (3) The sequences of donor and acceptor splice sites exhibit a striking similarity. This suggests that the two junctions derive from a common ancestor and that during evolution the information of both sites shifted onto the intron. If so, the protein and RNA components that are found in contemporary spliceosomes, and which are responsible for recognizing donor and acceptor sequences, should also be related. This conclusion is supported by the common structures found in different parts of the spliceosome.

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.

In vitro recognition of an orf virus early promoter in a vaccinia virus extract

DNA fragments containing varying lengths of the 5' end of an orf virus early gene (ORF3) and its associated promoter were introduced into sodium deoxycholate-solubilized vaccinia virus extracts capable of initiating transcription in vitro from vaccinia virus early promoters. After separation of the radiolabelled products of the reactions on a 5% polyacrylamide/7 M urea gel, discrete transcripts were detected the sizes of which were consistent with initiation of transcription from the orf virus early promoter. This is the first demonstration in a functional assay of the conservation of early transcriptional promoters between an orthopoxvirus and a parapoxvirus.

Vaccinia virus-like early transcriptional control sequences flank an early gene in orf virus

The purpose of this study was to map the initiation (tsp) and termination points of transcripts arising from an open reading frame (ORF3) found in the inverted terminal repeat of the orf virus genome and also, to identify probable transcriptional control sequences. Early transcripts of approx. 0.76 kb were mapped to ORF3 and found to be transcribed toward the ends of the genome. Using the S1 nuclease and primer-extension methods, the bulk of the tsp were mapped to a position 12-13 nucleotides (nt) downstream from a sequence which resembles A + T-rich vaccinia virus early promoters. The 5' ends were 81-82 nt upstream from the first ATG in ORF3. Most of 3' ends of the transcripts mapped to a region 24-32 nt downstream from a T5NT sequence found near the ORF3 stop codon. A second transcription termination point was found 25 nt downstream from another T5NT sequence located downstream and separated by 85 nt from the first. These results infer that the A + T-rich, early transcriptional control sequences found in other poxvirus genomes have been conserved in the G + C-rich genome of orf virus.

Nucleotide sequence comparison of homologous genomic regions from variola, monkeypox, and vaccinia viruses

The nucleotide sequences of homologous regions from the genomes of variola major strain Harvey, variola minor strains Butler and Garcia, and monkeypox strain Denmark were determined. The nucleotide sequences were compared to the homologous region in vaccinia virus which contains part of one of the genes involved in determining host range. Two major differences were detected; these corresponded to a deletion in the promoter region and the presence of a premature stop codon. It was concluded that this region of the genome may not be actively expressed in either variola- or monkeypox-virus-infected cells. It was also concluded that diagnostic nucleic acid hybridisation probes for differentiating between these members of the Orthopoxviridae may be difficult to identify.

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.

Transcription of a poxvirus early gene is regulated both by a short promoter element and by a transcriptional termination signal controlling transcriptional interference

The promoter region of an early gene (38K gene) of cowpox virus has been characterized by deletion and linker scanning mutational analyses. Modified versions of this promoter region were placed into the genome of vaccinia virus, and their transcriptional efficiencies were assessed by quantifying RNAs transcribed from these sequences. These analyses showed that the sequences in the region between 33 and 4 base pairs upstream of the transcriptional start site affect the efficiency of transcription from this promoter. Linker scanning mutations in the -27 to -10 region inhibited transcription. This region contains the sequence 5'-GAAAATATATT-3', which is present in at least two other early genes in the same positions (-21 to -11) relative to the transcriptional start sites of these genes. Elements of this sequence are similarly positioned in the promoter regions of several other poxvirus genes, suggesting that this sequence represents a transcriptional control element of at least a subset of poxvirus genes. The -8 to -2 sequence (5'-TTTTTAT-3') contains a transcriptional termination signal. Mutation of this sequence had two separate effects: (i) it reduced the efficiency of transcription from the promoter by approximately 30%, and (ii) it prevented this sequence from terminating the transcription from upstream genes. When overlapping transcription from upstream genes was not prevented by a termination signal present either within the 38K promoter or upstream of the promoter, transcription from this promoter was reduced by about 30%. This indicates that transcriptional termination has a role in the regulation of viral gene expression by controlling transcriptional interference.

Tumorigenic poxviruses: characterization of an early promoter from Shope fibroma virus

A strong early promoter from the T1 open reading frame (ORF) within the terminal inverted repeat (TIR) of Shope fibroma virus (SFV) has been isolated and characterized. Promoter activity was determined by a transient gene expression assay in poxvirus-infected cells using the bacterial chloramphenicol acetyltransferase as a reporter gene. The sequences which constitute the boundaries of the promoter element were determined by 5' and 3' deletion analysis. The functional SFV T1 promoter domain comprises about 28 bp and includes, in addition to the transcriptional initiation site, a stretch of eight continuous A residues from position -18 to -11 which is critical for promoter function. Both the SFV T1 promoter and the vaccinia 7.5-kDa early/late promoter are active in the transient expression assay when the cells are infected with either the leporipoxvirus SFV or the orthopoxvirus vaccinia. To look more closely at the conservation of promoter function between poxvirus genera, a recombinant vaccinia virus containing the CAT gene driven by the SFV T1 promoter and a recombinant SFV containing the CAT gene driven by the vaccinia 7.5-kDa early/late promoters was constructed. The SFV T1 promoter behaves as an early promoter in the vaccinia genome, and both the T1 and the 7.5-kDa early/late promoters use transcriptional initiation sites in their heterologous genomic environment that are identical to the ones used in the native viral genome. The results from this work indicate that despite the relative lack of absolute sequence conservation, the transcriptional machinery, at least with respect to temporal regulation of early promoters and the position of transcript initiation, is conserved between these two poxvirus genera.

Expression of herpes simplex virus thymidine kinase, mediated by vaccinia virus early promoters

We measured herpes virus thymidine kinase (HSV-TK) activity in extracts from cells infected with eight vaccinia virus recombinants (VpT), each expressing HSV-TK under the control of an early promoter previously isolated by a shotgun procedure. The HSV-TK activities induced by the VpT recombinants were compared to that produced under the control of the vaccinia virus thymidine kinase (VV-TK) promoter in VMM5-TK recombinant virus. The insert from VpT38 was approximately 10 times more efficient than the VV-TK promoter for HSV-TK expression, reflecting a similar relative strength of the promoters. HSV-TK activities induced by the other VpT recombinants varied between one and ten times that expressed by the VV-TK promoter, but the nucleotide sequence of the 5'-end region of their mRNA suggested that these values did not necessarily reflect the strength of corresponding promoters. No significant reduction in HSV-TK activity was noted for two VpT and the VMM5-TK recombinants when viral DNA replication was prevented, but a significant reduction (30 to 75%) was observed for the other six recombinants studied. These results suggested that some early genes of vaccinia virus are expressed only during the early stage of infection, whereas others continue to be expressed at the late stage. The strength of two vaccinia early promoters (VpT38, PF) relative to that of the VV-TK promoter was deduced from HSV-TK activities induced by comparable vaccinia virus recombinants.