Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC
<p>Abstract</p> <p>Background</p> <p>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...
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doaj-0f033841d03d4e45bcbf602d1a5f2cb12020-11-24T22:30:23ZengBMCBMC Genomics1471-21642012-02-011316910.1186/1471-2164-13-69Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolCEngelen StefanVallenet DavidMédigue ClaudineDanchin Antoine<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>Extending previous in silico heuristics for the analysis of gene co-evolution, we analyzed the function of genes clustering with <it>dnaE </it>and <it>polC</it>. 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.</p> <p>Conclusion</p> <p>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.</p> http://www.biomedcentral.com/1471-2164/13/69replicationdegradosomeLUCAphylogenetic profilingnanoRNase |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Engelen Stefan Vallenet David Médigue Claudine Danchin Antoine |
spellingShingle |
Engelen Stefan Vallenet David Médigue Claudine Danchin Antoine Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC BMC Genomics replication degradosome LUCA phylogenetic profiling nanoRNase |
author_facet |
Engelen Stefan Vallenet David Médigue Claudine Danchin Antoine |
author_sort |
Engelen Stefan |
title |
Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC |
title_short |
Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC |
title_full |
Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC |
title_fullStr |
Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC |
title_full_unstemmed |
Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC |
title_sort |
distinct co-evolution patterns of genes associated to dna polymerase iii dnae and polc |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2012-02-01 |
description |
<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>Extending previous in silico heuristics for the analysis of gene co-evolution, we analyzed the function of genes clustering with <it>dnaE </it>and <it>polC</it>. 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.</p> <p>Conclusion</p> <p>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.</p> |
topic |
replication degradosome LUCA phylogenetic profiling nanoRNase |
url |
http://www.biomedcentral.com/1471-2164/13/69 |
work_keys_str_mv |
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