Nucleotide sequence of 42 kbp of vaccinia virus strain WR from near the right inverted terminal repeat

Abstract

The nucleotide sequence of 42 090 bp of vaccinia virus strain WR is presented. The sequence includes the SalI L, F, G and I fragments and starts near the centre of the HindIII A fragment and extends rightwards towards the genomic terminus, finishing approximately 0-5 kb internal of the inverted terminal repeat (ITR). Translation of this region has identified 65 open reading frames (ORFs) of greater than 65 amino acids in length. Fifty-one of these which do not extensively overlap other larger ORFs have been subjected to further analysis; the other 14 are termed minor ORFs. In the rightmost 28.7 kb, the genes are, with one exception, transcribed towards the genomic terminus, similar to the arrangement of genes at the left end of the virus genome. Internal of this region the genes are expressed off either DNA strand but still predominately rightwards. ORFs are tightly packed with few intergenic non-coding regions of greater than 250 bp. Protein sequence comparisons have established a remarkably high number of homologies with entries in existing protein databases. Of these, DNA ligase, thymidylate kinase, two serine-threonine protein kinases, two serine proteinase inhibitors (serpins), two interleukin-1 receptor homologues and a discontinuous ORF related to tumour necrosis factor receptor have been reported. Other homologies include lectins, profilin, 3fl-hydroxy steroid dehydrogenase, superoxide dismutase, guanylate kinase, ankyrin and complement factor H. In addition, there are a number of polypeptides with predicted properties of membraneassociated, secretory or glyco-proteins. Twelve gene families are described here and elsewhere. There is considerable similarity between genes from the right and left end of the virus genome that may have arisen by terminal transposition events. Several differences from the corresponding region of vaccinia virus strain Copenhagen sequence are noted. Near the right terminus the sequences diverge completely, and internal of this there are multiple examples of deletion of short sequences (eight to 10 nucleotides) that lie within penta-or hexanucleotide direct repeats.

Nucleotide sequence analysis of a unique near-terminal region of the tumorigenic poxvirus, Shope fibroma virus

“…The partial ORFs located at either end of the BamHI H fragment, designated H0R and H4R, also potentially encode proteins similar in sequence to various poxvirus and cellular proteins. The H4R ORF product displayed 29-2~0 amino acid identity with the erythrocyte ankyrin protein• The H0R ORF, which overlaps the amino terminus of the H IR ORF, encodes a protein with similarity to the carboxy-terminal portion of the vaccinia virus B5R ORF product Smith et al, 1991), also referred to as the plaque size/host range gene product for the Lister strain of vaccinia virus (Takahashi-Nishimaki et al, 1991). The similarity to the Lister protein (shown in Table 1) is higher due to several amino acid differences compared to the vaccinia virus WR strain protein, which are also conserved in the SFV ORF product.…”

Detection of RNA-protein complex in vaccinia virus core in vitro transcription system

“…This procedure revealed the presence of five proteins with apparent Mrs of 60K, 43K, 28K, 18K and 14-5K with affinity for viral core mRNA. A ribonucleoprotein (RNP) with a typical RNA-binding motif and an Mr of 14-2K was predicted within the genome of vaccinia virus Copenhagen strain (A31R) (Goebel et al, 1990) and an equivalent protein was found in the WR strain (SalL1 R) with an apparent Mr of 14"9K (Smith et al, 1991). The possibility of this protein being one of the proteins identified in this work, and the formation of RNAprotein complexes during in vitro mRNA synthesis, are discussed.…”

Vaccinia virus glycoproteins and immune evasion: The Sixteenth Fleming Lecture

“…There are two cellular TNFRs which each have an external domain consisting of four repeats of a cysteine-rich motif followed by a transmembrane anchor sequence and different cytoplasmic domains for signal transduction. The sequence of vaccinia virus strain WR shows that ORF SalF19R (A53R in Copenhagen) is related to the external domain of TNFR but the repeated domains are fragmented by frameshift and nonsense mutations (Howard et al, 1991). Similarly, the complete sequence of vaccinia virus strain Copenhagen (Goebel et al, 1990) shows an ORF identical to WR SalF19R and another ORF related to TNFR within each ITR (C22L and B28R) .…”

“…Vaccinia virus nucleotide sequence data predict that several other genes encode secretory proteins that may be glycosylated (Goebel et al, 1990;Howard et al, 1991;.…”