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.

Fig. 1

Phylogeny of the alpha subunit gene groups. Genomes are labeled in abbreviated characters for the phylum names (Table S1). The Arabian number after the becterium number denotes whether it is classified based on the first alpha subunit gene or other co-existed isoforms. For instance, FI Bact181 1 stands for the Firmicute bacterium No. 181 in the collection, which is classified based on its first alpha subunit gene. AC, Actinobacteria; AQ, Aquificae; BA, Bacteroidetes/Chlorobi group; CH, Chlamydiae/Verrucomicrobia group; CI, Chloroflexi; CY, Cyanobacteria; DE, Deinococcus-Thermus; FI, Firmicutes; FU, Fusobacteria; PL, Planctomycetes; PR, Proteobacteria; TH, Thermotogae; SP, Spirochaetes.

Fig. 2

The length distribution of all alpha subunit genes in the collection. Among the 248 genes, there are 129 dnaE1 genes (average length of 1,174 a.a.), 44 dnaE2 genes (average length of 1,078 a.a.), 34 dnaE3 genes (average length of 1,033 a.a.), and 41 polC genes (average length of 1,455 a.a.). The shortest sequence is a dnaE3 gene found in Onion yellows phytoplasma (Bact134; 625 a.a.). The longest one is a single dnaE1 gene from Thermus thermophilus HB27 (Bact204; 2,067 a.a.).

Fig. 3

Phylogeny of four alpha subunit groups from a partial and random selection. Five alpha subunits are randomly selected from each group. The same nomenclature is used as in Figure 1. The trees are constructed with the program MEGA (V3.1) by neighbor-joining with Kimura 2-parameter distance (scale bar). The reliability of the branching orders is estimated by bootstrapping (500 replicates), and bootstrap values (percentage after 500 iterations) for major branches are shown.

Fig. 4

Alpha subunits in different bacterial phyla. One solid circle represents one alpha subunit. We mark the bacterial genome numbers together with phylum names; for example, “17 Actinobacteria” represents 17 bacterial genomes included in Actinobacteria.

Fig. 5

Domain alignments of the four groups of alpha subunit genes. InterProScan has been used to identify the domains. Scale bar marks the length measured by amino acids.

Fig. 6

Protein motifs among the three groups of dnaE genes. The MEME tool has been employed for this analysis. Each motif describes a pattern of a fixed width, and no gaps are allowed in MEME motifs. MEME numbers the motifs consecutively starting from 1 as it found them, and the most statistically significant (low E-value) motifs are usually found first. Relative to dnaE1 and dnaE3, dnaE2 appears to miss motif 5. Scale bar indicates amino acid positions.