Replication-associated purine asymmetry may contribute to strand-biased gene distribution

Among prokaryotic genomes, the distribution of genes on the leading and tagging strands of the replication fork is known to be biased. Several hypotheses explaining this strand-biased gene distribution (SGD) have been proposed, but none have been tested or supported by sufficient data analyses. In this work we have analyzed 211 prokaryotic genomes in terms of compositional strand asymmetries and the presence or absence of po1C and have found that SGD correlates not only with po1C, but also with purine asymmetry (PAS). Furthermore, SGD, PAS, and po1C are all features associated with a group of low-GC, gram-positive bacteria (Firmicutes). We conclude that PAS is a characteristic of organisms with a heterodimeric DNA polymerase III alpha-subunit constituted by po1C and dnaE, which may play a direct role in the maintenance of SGD. (c) 2007 Elsevier Inc. All rights reserved.