Compilation and alignment of DNA polymerase sequences.

More than 40 different DNA polymerases, including some putative DNA polymerase sequences deduced from nucleotide sequence data, have recently been reported (1-39). The amino acid sequences of these DNA polymerases have been aligned and partial homologous regions identified by many investigators (2-4,9,10,12-25,27-36,42-51). Based on the segmental amino acid sequence similarities, DNA polymerases have been classified into two major groups; E. coli DNA polymerase I-Type and eukaryotic DNA polymerase ca-Type (14,44,47,48,51), or family A DNA polymerases and family B DNA polymerases (4,9,50). As the number of DNA polymerase sequences increases, the classification of DNA polymerases becomes increasingly ambiguous. For example, DNA polymerase delta of yeast was shown to have amino acid sequence similarity to the a-Type DNA polymerases (17). It has become necessary to establish a unified classification of DNA polymerases. Here we propose to classify DNA polymerases into families A, B, and C (Figure 1: A, B, and C), according to the amino acid sequence homologies with E. coli DNA polymerases I, II, and III, respectively. As new and different prokaryotic and eukaryotic DNA polymerases are identified, the number of families can easily be expanded by using additional letters of the alphabet (i.e., D, E, etc.). The bacterium E. coli (strain K12) contains three distinct DNA polymerases I, II, and HI (52). E. coli DNA polymerase I, the first DNA polymerase discovered, is specified by the polA gene (52). E. coli DNA polymerase II, encoded by the polB gene, was recently sequenced and found to be identical to the dinA gene, a DNA damage inducible gene whose expression is regulated by the SOS system in E. coli (8,53). Amino acid sequence alignment shows that E. coli DNA polymerase II has significant homology with family B (a-Type) DNA polymerases (8,53,54). E. coli DNA polymerase IH is a multisubunit enzyme encoded by various dna genes (55); the DNA polymerizing a-subunit encoded by the polC (dnaE) gene (56) and the 3'5' exonuclease performing e-subunit encoded by the dnaQ gene (57). The asubunit of E. coli DNA polymerase III exhibits an extensive homology with the corresponding a-subunit of Salmonella typhimurium DNA polymerase m (35); and both show significant homology to Bacillus subtilis DNA polymerase HI, a singlepolypeptide encoded by the polC gene (36). In summary, family A DNA polymerases are named for their homology to the product of the polA gene encoding E. coli DNA polymerase I; family B DNA polymerases are named for their homology to the product of the polB gene encoding E. coli DNA polymerase 11; and family C DNA polymerases are named for their homology to the product of the polC gene encoding E. coli DNA polymerase HI. The eukaryotic DNA polymerase (3, the smallest known DNA polymerase, does not have homology with those of any of the DNA polymerase families described above. Instead, DNA polymerase (3 has homology with terminal transferases (37). This ,B group we will call family X (Figure ID). The classification and original reference(s) for the amino acid sequences of each DNA polymerase are shown in Table 1. All of the family A DNA polymerases, except for yeast mitochondrial DNA polymerase I, are prokaryotic and are very sensitive to dideoxynucleotide inhibitors, and therefore are useful enzymes for DNA sequencing by the chain-termination method (58). The family A DNA polymerases are resistant to aphidicolin. The family B DNA polymerases are quite extensive in number and variety. Most of the family B DNA polymerases, if not all, are sensitive to aphidicolin and relatively resistant to dideoxynucleotide inhibitors. Most of the family B DNA polymerases, except for pAI2 (33) and yeast DNA polymerase II (16), contain the highly conserved amino acid sequence motif YGDTD, which has been suggested to form part of the dNTP binding site. Amino acid substitutions in this conserved sequence resulted in defects in the DNA polymerase activity without affecting the 3'5' exonuclease activity (59,60,61). The family C DNA polymerases are major bacterial replicative DNA polymerases which do not have appreciable homology with those of family A and B DNA polymerases. B. subtilis DNA polymerase Im is a single polypeptide that is highly sensitive to hydroxyphenylazouracil (62). It is anticipated that the number of sequenced family C DNA polymerases will increase rapidly, since all of the aerobic bacteria may contain a member of this family of DNA polymerases.