GC content variability of eubacteria is governed by the pol III α subunit
Section snippets
Materials and methods
We collected 381 complete genome sequences from eubacterial data available in GenBank (November 26, 2006) [19] and extracted the sequences of all α subunits from the genome annotations and subsequent manual identification by using blast-based tools. With a length cut-off of 625 amino acids, we had 380 eubacterial genomes containing 596 α subunits (Figure S2). Only one bacterium, Saccharophagus degradans 2–40, was excluded from further analyses since its two α subunits are too short (471 and 571
DNA polymerase III α subunit governs the gGC variability
According to the dimeric combination of α subunits [17], we plotted 380 eubacterial genomes in our dataset into three groups, namely dnaE1 (homodimer), dnaE2/dnaE1 (heterodimer), and polC/dnaE3 (heterodimer) (Fig. 1). Unlike eukaryotic genomes whose average gGC contents are rather constant around 0.40 [3], [4], the GC content of eubacterial genomes varies widely from 0.17 to 0.75 (Fig. 2), and the extremities are represented by Candidatus Carsonella ruddii for the minimum [20] and
Acknowledgments
We thank our colleague Mr. Chen Chen for valuable discussions. This work was supported by a grant from the Chinese Academy of Sciences awarded to J.Y. (KSCX2-SW-331).
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These authors contributed equally to this work.