Comparative Analysis of Eubacterial DNA Polymerase III Alpha Subunits

DNA polymerase III is one of the five eubacterial DNA polymerases that is re-sponsible for the replication of DNA duplex. Among the ten subunits of the DNApolymerase III core enzyme, the alpha subunit catalyzes the reaction for polymer-izing both DNA strands. In this study, we extracted genomic sequences of thealpha subunit from 159 sequenced eubacterial genomes, and carried out sequence-based phylogenetic and structural analyses. We found that all eubacterial genomeshave one or more alpha subunits, which form either homodimers or heterodimers.Phylogenetic and domain structural analyses as well as copy number variations ofthe alpha subunit in each bacterium indicate the classification of alpha subunit intofour basic groups: polC, dnaE1, dnaE2, and dnaE3. This classification is of essencein genome composition analysis. We also consolidated the naming convention toavoid further confusion in gene annotations.