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Open Access Research article

Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC

Stefan Engelen12, David Vallenet2, Claudine Médigue2 and Antoine Danchin13*

Author Affiliations

1 AMAbiotics SAS, Bâtiment G1, 2 rue Gaston Crémieux, 91000 Evry, France

2 CEA, DSV, IG, Genoscope & CNRS-UMR8030, Laboratoire d'Analyse Bioinformatiques en Génomique et Métabolisme (LABGeM), 2 rue Gaston Crémieux, 91057 Evry, France

3 Department of Biochemistry, Faculty of Medicine, Hong Kong University, 21 Sassoon Road, Pokfulam, Hong Kong

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BMC Genomics 2012, 13:69  doi:10.1186/1471-2164-13-69

Published: 14 February 2012

Abstract

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.

Keywords:
replication; degradosome; LUCA; phylogenetic profiling; nanoRNase