BACKGROUND: Bacterial genomes displaying a strong bias between the leading and 
the lagging strand of DNA replication encode two DNA polymerases III, DnaE and 
PolC, rather than a single one. Replication is a highly unsymmetrical process, 
and the presence of two polymerases is therefore not unexpected. Using 
comparative genomics, we explored whether other processes have evolved in 
parallel with each polymerase.
RESULTS: Extending previous in silico heuristics for the analysis of gene 
co-evolution, we analyzed the function of genes clustering with dnaE and polC. 
Clusters were highly informative. DnaE co-evolves with the ribosome, the 
transcription machinery, the core of intermediary metabolism enzymes. It is also 
connected to the energy-saving enzyme necessary for RNA degradation, 
polynucleotide phosphorylase. Most of the proteins of this co-evolving set 
belong to the persistent set in bacterial proteomes, that is fairly ubiquitously 
distributed. In contrast, PolC co-evolves with RNA degradation enzymes that are 
present only in the A+T-rich Firmicutes clade, suggesting at least two origins 
for the degradosome.
CONCLUSION: DNA replication involves two machineries, DnaE and PolC. DnaE 
co-evolves with the core functions of bacterial life. In contrast PolC 
co-evolves with a set of RNA degradation enzymes that does not derive from the 
degradosome identified in gamma-Proteobacteria. This suggests that at least two 
independent RNA degradation pathways existed in the progenote community at the 
end of the RNA genome world.