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Nucleotide sequence of the 26 S mRNA of the virulent Trinidad donkey strain of Venezuelan equine encephalitis virus and deduced sequence of the encoded structural proteins.
Abstract: A cDNA clone containing all of the 26 S mRNA coding region of the RNA genome of Venezuelan equine encephalitis (VEE) virus, virulent strain Trinidad donkey (TRD), has been constructed and sequenced. The nucleotide and deduced amino acid sequences of the 26 S RNA of VEE virus conform to the general organization of the alphavirus subgenomic mRNA. Excluding the poly(A) tail, the VEE 26 S RNA is 3913 nucleotides long with a protein coding region of 3762 nucleotides. Codon usage in the translated region is nonrandom and correlates well with that reported for Sindbis (SIN), Semliki Forest (SF), and Ross River (RR) alphaviruses. Highly conserved sequences of 19 to 22 nucleotides representing putative replicase recognition sites occur at the 26 S RNA junction region of the 42 S genomic RNA and at the 3' terminus immediately preceding the poly(A) tail. The conserved sequence at the 26 S/42 S junction region of VEE virus differs from that of other alphaviruses in that an ochre termination codon (UAA) is substituted for a GGU (Gly) codon present in the other viruses. The 5' and 3' noncoding regions (30 and 121 nucleotides, respectively) of the VEE 26 S RNA are shorter than has been reported for several other alphaviruses. The approximate transmembrane domains of the VEE E1 and E2 envelope glycoproteins have been identified. VEE E1 contains a single asparagine-linked glycosylation site, whereas E2 has three such sites, all of which are apparently glycosylated. The deduced amino acid sequence of the VEE polyprotein shows an overall homology of 44 to 46% with the precursor polyproteins of SIN, SF, and RR viruses. VEE virus capsid, E1, and E2 structural proteins show 43 to 46%, 50 to 53%, and 36 to 41% homology, respectively, with the cognate proteins of SIN, SF, and RR viruses.
Publication Date: 1986-07-30 PubMed ID: 3088830DOI: 10.1016/0042-6822(86)90142-xGoogle Scholar: Lookup The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
- Journal Article
Summary
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This research paper focuses on the nucleotide sequencing of the 26 S mRNA coding region of the Venezuelan equine encephalitis (VEE) virus, specifically from the Trinidad donkey strain. The results reveal key characteristics about the virus’s protein coding region, its nonrandom codon usage, conserved sequences, 5′ and 3′ noncoding regions, and structural proteins.
Sequence Analysis and RNA Structure
- The researchers have successfully constructed and sequenced a cDNA clone, containing the full 26 S mRNA coding region of the VEE virus from the Trinidad donkey strain. The VEE 26 S RNA fits perfectly into the general arrangement of alphavirus subgenomic mRNA.
- Not including the poly(A) tail, the VEE 26 S RNA has a length of 3913 nucleotides, along with a protein coding region that spans 3762 nucleotides.
Codon Usage and Conserved Sequences
- There is nonrandom usage of codons in the translated region, which aligns well with those reported for Sindbis (SIN), Semliki Forest (SF), and Ross River (RR) alphaviruses.
- The researchers also identified 19 to 22 nucleotide long sequences that are highly conserved, suggested to be replicase recognition sites either at the 26 S RNA junction region of the 42 S genomic RNA or at the 3′ terminus just before the poly(A) tail.
Differences from Other Alphaviruses
- The VEE virus differs from other alphaviruses at the conserved sequence of the 26 S/42 S junction region, with an ochre termination codon (UAA) instead of a GGU (Gly) codon.
- The 5′ and 3′ noncoding regions of the VEE 26 S RNA, measuring 30 and 121 nucleotides respectively, are shorter than those of several other alphaviruses.
Analysis of Structural Proteins
- The transmembrane domains of the VEE E1 and E2 envelope glycoproteins have been pinpointed. The E1 contains one asparagine-linked glycosylation site, while the E2 has three, suggesting all are glycosylated.
- The researchers found the VEE polyprotein’s deduced amino acid sequence to have about 44 to 46% homology with the precursor polyproteins of SIN, SF, and RR viruses. Similar homologies were seen in the VEE capsid, E1, and E2 structural proteins compared to those from SIN, SF, and RR viruses.
Cite This Article
APA
Kinney RM, Johnson BJ, Brown VL, Trent DW.
(1986).
Nucleotide sequence of the 26 S mRNA of the virulent Trinidad donkey strain of Venezuelan equine encephalitis virus and deduced sequence of the encoded structural proteins.
Virology, 152(2), 400-413.
https://doi.org/10.1016/0042-6822(86)90142-x Publication
Researcher Affiliations
MeSH Terms
- Amino Acid Sequence
- Amino Acids / analysis
- Animals
- Base Sequence
- Capsid
- Cell Line
- Cloning, Molecular
- DNA / analysis
- Encephalitis Virus, Venezuelan Equine / genetics
- Genes
- Haplorhini
- Protein Biosynthesis
- RNA, Messenger / analysis
- Viral Proteins / analysis
- Viral Structural Proteins
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