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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| Format: | Article |
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BMC
2012-02-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/13/69 |
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| author | Engelen Stefan Vallenet David Médigue Claudine Danchin Antoine |
| author_facet | Engelen Stefan Vallenet David Médigue Claudine Danchin Antoine |
| author_sort | Engelen Stefan |
| collection | DOAJ |
| 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> |
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| format | Article |
| id | doaj.art-0f033841d03d4e45bcbf602d1a5f2cb1 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T01:56:47Z |
| publishDate | 2012-02-01 |
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| series | BMC Genomics |
| spelling | doaj.art-0f033841d03d4e45bcbf602d1a5f2cb12022-12-21T23:21:09ZengBMCBMC 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 |
| 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 |
| title | 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_short | 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 |
| topic | replication degradosome LUCA phylogenetic profiling nanoRNase |
| url | http://www.biomedcentral.com/1471-2164/13/69 |
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