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

Engelen S, Vallenet D, Médigue C, Danchin A - BMC Genomics (2012)

Bottom Line: 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.

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Affiliation: AMAbiotics SAS, Bâtiment G1, 2 rue Gaston Crémieux, 91000 Evry, France.

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.

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Distribution d(s) of orthologs s values (equation 1) for gene hisI of B. subtilis. Orthologs of hisI which have their s values indicated in grey correspond to orthologs selected applying equation 4.
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Figure 3: Distribution d(s) of orthologs s values (equation 1) for gene hisI of B. subtilis. Orthologs of hisI which have their s values indicated in grey correspond to orthologs selected applying equation 4.

Mentions: Figure 3 shows an example of this selection (selected orthologs genes have their s values indicated in grey) for hisI orthologs.


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

Engelen S, Vallenet D, Médigue C, Danchin A - BMC Genomics (2012)

Distribution d(s) of orthologs s values (equation 1) for gene hisI of B. subtilis. Orthologs of hisI which have their s values indicated in grey correspond to orthologs selected applying equation 4.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814617&req=5

Figure 3: Distribution d(s) of orthologs s values (equation 1) for gene hisI of B. subtilis. Orthologs of hisI which have their s values indicated in grey correspond to orthologs selected applying equation 4.
Mentions: Figure 3 shows an example of this selection (selected orthologs genes have their s values indicated in grey) for hisI orthologs.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: AMAbiotics SAS, Bâtiment G1, 2 rue Gaston Crémieux, 91000 Evry, France.

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.

Show MeSH