title: Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: AMAbiotics SAS, Bâtiment G1, 2 rue Gaston Crémieux, 91000 Evry, France.
authors.forename: Stefan
authors.initials: S
authors.lastname: Engelen
authors.forename: David
authors.initials: D
authors.lastname: Vallenet
authors.forename: Claudine
authors.initials: C
authors.lastname: Médigue
authors.forename: Antoine
authors.initials: A
authors.lastname: Danchin
mesh_terms: D001419:Bacteria / Q000201:enzymology* / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics*; D004258:DNA Polymerase III / Q000235:genetics*; D004259:DNA-Directed DNA Polymerase / Q000235:genetics*; D004722:Endoribonucleases / Q000235:genetics; D019143:Evolution, Molecular; D005798:Genes, Bacterial / Q000235:genetics*; D023281:Genomics; D009097:Multienzyme Complexes / Q000235:genetics; D010802:Phylogeny; D011117:Polyribonucleotide Nucleotidyltransferase / Q000235:genetics; D020365:RNA Helicases / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D009097:Multienzyme Complexes; C111244:degradosome; C074904:DNA polymerase III, alpha subunit; C446929:PolC protein, bacteria; D004258:DNA Polymerase III; D004259:DNA-Directed DNA Polymerase; D011117:Polyribonucleotide Nucleotidyltransferase; D004722:Endoribonucleases; D020365:RNA Helicases