Similarity relations of DNA and RNA polymerases investigated by the principal component analysis of amino acid sequences

The principal component analysis based on the physicochemical properties of amino acid residues is applied to DNA and RNA polymerases to assign the se quence motifs for the polymerization activities of these proteins. After th e reconfirmation of the sequence motifs of families A and B of DNA polymera ses indicated previously, it elucidates the sequence motifs for the polymer ization activity of DNA polymerase III (family C) by the similarity to the polymerization center of multimeric DNA dependent RNA polymerases. This ide ntification proceeds to clarify the sequence motifs for polymerization acti vities of primases; eukaryotic and archaebacterial primases carry motifs si milar to those of family C, while the motifs of eubacterial primase fall in to the category of the motifs in family B DNA polymerases such as alpha, de lta, epsilon and II. This finding means that DNA dependent RNA polymerases are also divided into groups corresponding to three families, A, B and C, b ecause the monomeric DNA dependent RNA polymerases in phages are reconfirme d to carry sequence motifs similar to those of family A DNA polymerases. Fu rthermore, the three families of polymerization motifs are found to fall wi thin the variation range of polymerization motifs displayed by many RNA dep endent RNA polymerases, suggesting a close evolutionary relation between th em. The sequence motifs for polymerization activities of reverse transcript ase and telomerase seem to be the intermediate between family A DNA polymer ase and some RNA dependent RNA polymerases, e.g., from Leviviridae. On the contrary, the sequence fragments similar to the nucleotidyltransferase supe rfamily including DNA polymerase beta are not found in any RNA dependent RN A polymerase, suggesting their other lineage of polymerization motifs. (C) 1999 Elsevier Science B.V. All rights reserved.