title: The unusual nucleotide content of the HIV RNA genome results in a biased amino acid composition of HIV proteins.
abstract: Extremely high frequencies of the A nucleotide are found in the RNA genomes of the lentivirus group of retroviruses. It is presently unknown what molecular force is responsible for this A-pressure. In this manuscript, we demonstrate a correlation between this 'A-pressure' and the amino acid-usage of the lentivirus family. We compared the amino acid composition of the Gag and Pol proteins of the human immunodeficiency viruses type 1 and 2 (HIV-1 and HIV-2) with that of the second group of human retroviruses; the human T-cell leukemia viruses type I and II (HTLV-I and HTLV-II). Differences in total amino acid content correlate with the preference for A-rich codons in the HIV genome. A pair-wise comparison of homologous amino acid positions in the Pol proteins indicates that both conservative and non-conservative changes can be accounted for by this A-bias. The putative molecular mechanism underlying this A-pressure and the evolutionary consequences are discussed.
authors.affiliation: Department of Virology, University of Amsterdam, The Netherlands.
authors.forename: B
authors.initials: B
authors.lastname: Berkhout
authors.forename: F J
authors.initials: FJ
authors.lastname: van Hemert
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000235:genetics*; D001482:Base Composition; D003062:Codon; D015683:Gene Products, gag / Q000737:chemistry / Q000235:genetics*; D015684:Gene Products, pol / Q000737:chemistry / Q000235:genetics*; D016679:Genome, Viral; D006678:HIV / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics; D015498:HIV-2 / Q000235:genetics; D015368:Human T-lymphotropic virus 1 / Q000235:genetics; D015367:Human T-lymphotropic virus 2 / Q000235:genetics; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000737:chemistry / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*; D017386:Sequence Homology, Amino Acid
chemical_list: D000596:Amino Acids; D003062:Codon; D015683:Gene Products, gag; D015684:Gene Products, pol; D009711:Nucleotides; D012367:RNA, Viral