Structural differentiation of the three eukaryotic RNA polymerases

All eukaryotes have three different RNA polymerases (RNAPs) which transcribe different types of genes. RNA polymerase I transcribes rRNA genes, RNA polymerase II transcribes mRNA, miRNA, snRNA, and snoRNA genes, and RNA polymerase III transcribes tRNA and 5S rRNA genes. Here, we use an in silico approach to identify putative functional differences between these three RNAPs. Our results show that cleft loops are the most conserved regions of RNAPs, but that these regions have several significant length differences between the three RNAPs. There were also significant shifts in the rates of evolution of some amino acid sites in all three enzymes prior to the diversification of eukaryotes and these amino acids are preferentially located near the catalytic center of the three enzymes. These results suggest that functional differences exist between the three RNAPs and that these differences are all clustered near the active sites.