title: Comparative analysis of eubacterial DNA polymerase III alpha subunits.
abstract: DNA polymerase III is one of the five eubacterial DNA polymerases that is responsible for the replication of DNA duplex. Among the ten subunits of the DNA polymerase III core enzyme, the alpha subunit catalyzes the reaction for polymerizing both DNA strands. In this study, we extracted genomic sequences of the alpha subunit from 159 sequenced eubacterial genomes, and carried out sequence-based phylogenetic and structural analyses. We found that all eubacterial genomes have one or more alpha subunits, which form either homodimers or heterodimers. Phylogenetic and domain structural analyses as well as copy number variations of the alpha subunit in each bacterium indicate the classification of alpha subunit into four basic groups: polC, dnaE1, dnaE2, and dnaE3. This classification is of essence in genome composition analysis. We also consolidated the naming convention to avoid further confusion in gene annotations.
authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China.
authors.forename: Xiao-Qian
authors.initials: XQ
authors.lastname: Zhao
authors.forename: Jian-Fei
authors.initials: JF
authors.lastname: Hu
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D004258:DNA Polymerase III / Q000737:chemistry* / Q000235:genetics; D019281:Dimerization; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000737:chemistry / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D021122:Protein Subunits; C074904:DNA polymerase III, alpha subunit; D004258:DNA Polymerase III