title: Tax & rex: overlapping genes of the Deltaretrovirus group.
abstract: Bovine leukemia virus and human T-cell leukemia viruses I and II, members of the Deltaretrovirus group, have two regulatory genes, tax and rex, that are coded in overlapping reading frames. We found that sequence variations in the rex gene of each virus result in amino acid differences significantly more often than variations in the tax gene. For all three viruses the highest ratio of non-synonymous to synonymous changes was found in the rex gene. In the overlapping regions of tax and rex, the second codon position of Rex corresponds to the third codon position of Tax. Nucleotide C was present in all genes of the three viruses at the highest frequency and this bias was most pronounced in the rex gene. More specifically we found that the C bias and nucleotide variation is greatest at the second codon position of Rex and the third codon position of Tax in the area of tax/rex overlap. Changes in the second codon position of Rex always resulted in amino acid change whereas changes 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 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 and is the more conserved of the two proteins.
authors.affiliation: School of Public Health, Division of Infectious Diseases, University of California, Berkeley, CA 94720, USA. katy@uclink4.berkeley.edu
authors.forename: Kathleen Margaret
authors.initials: KM
authors.lastname: McGirr
authors.forename: Gertrude Case
authors.initials: GC
authors.lastname: Buehuring
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002417:Cattle; D003062:Codon; D019295:Computational Biology; D016384:Consensus Sequence; D017977:Deltaretrovirus / Q000235:genetics*; D005807:Genes, Overlapping; D016355:Genes, pX; D015368:Human T-lymphotropic virus 1 / Q000235:genetics; D015367:Human T-lymphotropic virus 2 / Q000235:genetics; D006801:Humans; D001909:Leukemia Virus, Bovine / Q000235:genetics; D016415:Sequence Alignment; D012984:Software
chemical_list: D003062:Codon