Compositional transitions between Oryza sativa and Arabidopsis thaliana genes are linked to the functional change of encoded proteins

Compositional transition was previously reported between homologous pairs of Oryza sativa and Arabidopsis thaliana. We analysed 2041 homologous gene pairs of O. sativa and A. thaliana and found that the genes that underwent compositional transition have significantly high frequency of amino acids encoded by GC rich codons. Amino acid substitution matrix calculated among hydrophobic, hydrophilic and amphipathic amino acid groups' shows that amphipathic and hydrophilic amino acids are strongly substituted by hydrophobic amino acids, whereas the substitution from hydrophobic to hydrophilic and amphipathic acids are not so frequent. Moreover, O. sativa genes that experienced compositional transition are more hydrophobic than their A. thaliana counterpart. This indicates that nucleotide bias induces a directional changes in proteome composition in such a way that underwent strong changes in hydropathy values. Further analysis of amino acid composition and hydrophobicity on the three different protein secondary structures confirm that natural selection is the main driving force for compositional transition in O. sativa genome. (c) 2005 Elsevier Ireland Ltd. All rights reserved.