Dinucleotide Sequences at the 5' Ends of Vaccinia Virus mRNA's Synthesized In Vitro

Identification and nucleotide sequence of the gene encoding a surface antigen induced by vaccinia virus

The gene encoding the specific antigen (S antigen) induced on the surface of vaccinia virus-infected cells was mapped on the viral genome by the construction of recombinant viruses. The S gene is located in the 1.5-kbp XbaI-AccII fragment between 11.1 and 12.6 kbp from the right end of the viral genome. Nucleotide sequencing of the fragment revealed an open reading frame (ORF) of 351 codons capable of producing a polypeptide with a molecular weight (MW) of 40,701 Da. Mapping of the S mRNA by primer extension indicates the presence of the transcription initiation site that precedes the translation initiation codon by 14 nucleotides. The region preceding the S mRNA start site is extremely A/T-rich and has sequence similarity with other early genes. The signal for termination of transcription of the early genes, TTTTTAT, is included near the end of the ORF. The deduced amino acid sequence contains a typical membrane signal characterized by a hydrophobic region in the N-terminus. An early polypeptide with a MW of 40 kDa, in agreement with the size predicted from the ORF, was synthesized by cell-free translation of the mRNA selected by hybridization to a plasmid containing the region of the ORF.

Multiple 3' ends of mRNA encoding vaccinia virus growth factor occur within a series of repeated sequences downstream of T clusters

Analysis of the 5' ends of six apparently full-length cloned cDNA copies of the vaccinia virus growth factor gene suggested precise transcriptional initiation at the first purine following a run of five pyrimidines in the noncoding strand. By contrast, the 3' ends exhibited heterogeneity and were distributed over a 46-base-pair region. In each of the six cDNAs, the nucleotide immediately preceding the retained copy of the poly(A) tail corresponded to the first or second T of a TATGT repeat. Clusters of Ts occurred upstream of the 3' ends, but the AATAAA polyadenylation consensus sequence of higher eucaryotes was absent. Determination of the complete sequence of one cDNA revealed exact correspondence with the vaccinia virus growth factor gene, indicating the absence of internal RNA processing.

Homology between DNA polymerases of poxviruses, herpesviruses, and adenoviruses: nucleotide sequence of the vaccinia virus DNA polymerase gene

A 5400-base-pair segment of the vaccinia virus genome was sequenced and an open reading frame of 938 codons was found precisely where the DNA polymerase had been mapped by transfer of a phosphonoacetate-resistance marker. A single nucleotide substitution changing glycine at position 347 to aspartic acid accounts for the drug resistance of the mutant vaccinia virus. The 5' end of the DNA polymerase mRNA was located 80 base pairs before the methionine codon initiating the open reading frame. Correspondence between the predicted Mr 108,577 polypeptide and the 110,000 purified enzyme indicates that little or no proteolytic processing occurs. Extensive homology, extending over 435 amino acids, was found upon comparing the DNA polymerase of vaccinia virus and DNA polymerase of Epstein-Barr virus. A highly conserved sequence of 14 amino acids in the carboxyl-terminal regions of the above DNA polymerases is also present at a similar location in adenovirus DNA polymerase. This structure, which is predicted to form a turn flanked by beta-pleated sheets, may form part of an essential binding or catalytic site that accounts for its presence in DNA polymerases of poxviruses, herpesviruses, and adenoviruses.

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

Specific RNAs synthesized in vitro by vaccinia virus cores were analyzed with the aid of DNA from the terminal 9,000 base pairs of the genome that was cloned in phage lambda, pBR322, and the single-stranded phage fl. Three mRNA's coding for polypeptides with molecular weights of 7,500 (7.5K), 19K, and 42K were shown to have sizes and map positions similar to those described for mRNA's made early in infection. A previously undescribed transcript made in vivo and in vitro, with a 5' end at about 8.7 kilobase pairs from the end of the genome, was also detected. After chemical removal of the terminal 7-methylguanosine residue, the 5' ends of the RNAs were specifically labeled by enzymatic capping and the mapped by gel electrophoresis of nuclease-resistant RNA.DNA hybrids, as well as by hybridization of the end-labeled RNA to immobilized DNA restriction fragments. Analysis of the purified cap structures demonstrated that three of the mRNA's have both m7G(5')pppAm and, m7G(5')pppGm ends, indicating some degree of terminal heterogeneity. The fourth transcript has exclusively m7G(5')pppAm ends. By synthesizing RNA in the presence of [beta-32P]GTP, it could be shown that cap sites correspond to sites of initiation of RNA synthesis.