Charged amino acids (AAs) are targets for selective
forces in protein evolution. To fully explore the trend of charged AA
frequencies evolution in macroevolutionary process from prokaryotes to
eukaryotes, we extend the analysis of five charged AAs separately and total
basic and acidic AAs in protein sequences of 158 prokaryotic and 63 eukaryotic
predicted proteomes and 456 clusters of orthologous groups (COGs). Also, we
eliminate the biases that may caused by extreme organisms in both predicted
proteomes and COGs analyses. More basic AAs, His,Lysand Glu were found in eukaryotic proteins compared with prokaryotic proteins by
predicted proteomes analysis. By COGs analysis, we found that basic AAs andLysfrequencies are higher in eukaryotic orthologous
proteins than their prokaryotic companions, while the trend of Arg frequency is
the opposite. We discussed the agreements and disagreements of two analyses and
gained a more credible trend of charged AAs evolution in macroevolutionary time
scale.
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