| Bovine leukemia virus (BLV) is an important agricultural problem with high costs to the dairy industry. In chapter 1, we examine the variation in the BLV tax and rex genes, which share 420 bases and have overlapping reading frames. The tax gene encodes a protein that functions as a transactivator of the BLV promoter, is required for viral replication, acts on cellular promoters, and is responsible for oncogenesis. Rex facilitates the export of viral mRNAs from the nucleus and regulates transcription. We have sequenced 5 new isolates of the tax/rex gene. We examined the 5 new and 3 previously published tax/rex DNA and predicted amino acid sequences of bovine leukemia virus isolates from cattle in representative regions worldwide. The highest variation among nucleic acid sequences for tax and rex was 7% and 5%, respectively; among predicted amino acid sequences for Tax and Rex, 9% and 11%, respectively. Significantly more nucleotide changes resulted in predicted amino acid changes in the rex gene than in the tax gene (p≤0.0006). This variability is higher than previously reported for any region of the BLV genome. This research may also have practical implications for the design of Tax-based vaccines for cattle.; In chapter 2 we go on to further examine the tax and rex genes of BLV along with HTLV-1 and II, other members of the Deltaretrovirus group that cause disease in humans. We analyzed the number of synonymous and nonsynonymous mutations in each gene of all three viruses and found that in all viruses the highest ratio of nonsynonymous to synonymous changes was found in the rex gene: Regarding the percentage of each nucleotide that makes up each gene of each virus, we confirmed that the members of the Deltaretrovirus group have a nucleotide C bias and that this bias is most pronounced in the rex gene. More specifically we found that the C bias is strongest at the second codon position of Rex, which is the third codon position of Tax in the area where tax and rex overlap. The highest number of nucleotide differences from the consensus sequence also occurs at this position. Nucleotide substitutions in the second codon position of Rex always resulted in amino acid change whereas substitutions in the third codon position of Tax resulted in amino acid changes less than a third of the time. Analysis of the amino acid frequencies in both proteins shows that there is a disproportionately large percentage of the amino acids alanine, proline, serine and threonine (the four amino acids whose second codon position is C) in Rex. These findings, in light of the fact that tax is more functionally complex, led us to hypothesize that the Rex protein can withstand more amino acid changes than can the Tax protein, suggesting that the Tax protein experiences higher evolutionary constraints. We also hypothesize that rex is a gene that evolved more recently than tax, and resulted in a selective advantage to the virus. |
