The unusual nucleotide content of the HIV RNA genome results in a biased amino acid composition of HIV proteins

Nucleic Acids Res. 1994 May 11;22(9):1705-11. doi: 10.1093/nar/22.9.1705.

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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / genetics*
  • Base Composition
  • Codon
  • Gene Products, gag / chemistry
  • Gene Products, gag / genetics*
  • Gene Products, pol / chemistry
  • Gene Products, pol / genetics*
  • Genome, Viral
  • HIV / genetics*
  • HIV-1 / genetics
  • HIV-2 / genetics
  • Human T-lymphotropic virus 1 / genetics
  • Human T-lymphotropic virus 2 / genetics
  • Molecular Sequence Data
  • Nucleotides / chemistry
  • Nucleotides / genetics
  • RNA, Viral / chemistry
  • RNA, Viral / genetics*
  • Sequence Homology, Amino Acid

Substances

  • Amino Acids
  • Codon
  • Gene Products, gag
  • Gene Products, pol
  • Nucleotides
  • RNA, Viral