Comparative Analysis Of Internal Repeating Segments In Proteins Of Species From The Three Kingdoms Of Life

In 1970's, Ohno proposed that primordial proteins might evolve from periodic amplification of oligo-peptides[1,2,3]. Internal repeating segments in proteins may play important roles in functional evolution of proteins. In this study, a new method was designed to extract internal repeating segments from proteomes of 8 modern species belong to eukaryota, bacteria and archaea, respectively. The repeating patterns and the frequencies they occur within proteomes of each kingdom were analyzed by matrix plot. Simple repeat segments were found to exist in eukaryotic proteins with high frequencies, but were much lower in bacteria and none in archaea. Further analysis showed that, the biased usage of amino acids in the internal repeating segments was positively related to the frequencies of individual amino acids in the proteome of a given species. The correlation coefficient was up to 0.95 in prokaryota, with the eukaryota to be lower. The high frequency of simple repeat sequences in eukaryotic proteomes, as well as the disparate relationships of amino acid compositions between the internal repeating segments and their haboring eukaryotic proteomes imply that the fast evolution of simple repeat sequences could be one force that generates the high complexity of eukarytic proteomes.