title: Structural differentiation of the three eukaryotic RNA polymerases.
abstract: 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.
authors.affiliation: Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, Ontario, Canada K1N 6N5.
authors.forename: Robert
authors.initials: R
authors.lastname: Carter
authors.forename: Guy
authors.initials: G
authors.lastname: Drouin
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D029681:Arabidopsis Proteins / Q000737:chemistry; D001665:Binding Sites; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry; D020134:Catalytic Domain; D003062:Codon / Q000235:genetics; D056890:Eukaryota / Q000201:enzymology*; D005656:Fungal Proteins / Q000737:chemistry; D006801:Humans; D019476:Insect Proteins / Q000737:chemistry; D051379:Mice; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D015800:Protozoan Proteins / Q000737:chemistry; D012318:RNA Polymerase I / Q000737:chemistry*; D012319:RNA Polymerase II / Q000737:chemistry*; D012320:RNA Polymerase III / Q000737:chemistry*; D016415:Sequence Alignment; D017385:Sequence Homology
chemical_list: D029681:Arabidopsis Proteins; D029742:Caenorhabditis elegans Proteins; D003062:Codon; D005656:Fungal Proteins; D019476:Insect Proteins; D015800:Protozoan Proteins; D012319:RNA Polymerase II; D012318:RNA Polymerase I; D012320:RNA Polymerase III