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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.

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.

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Hierarchical clustering of occurrence proportion vectors of B. subtilis essential genes in clades of the domain Bacteria. Squares show the proportion of a phylum (ascending from white to black) having an occurrence of a gene. The dendogram depicts distances between the proportion vectors. This dendogram separates B. subtilis essential genes into three clusters. The first one (red) contains dnaE and corresponds to genes occurring in the majority of bacterial clades. The second one (blue) contains dnaA and spans the whole domain of bacteria. The last one (green) contains polC and is composed of genes essentially specific to Firmicutes. The computing and visualization of the clusters was performed using the JMP® software (SAS Institute, Cary, NC).
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Figure 4: Hierarchical clustering of occurrence proportion vectors of B. subtilis essential genes in clades of the domain Bacteria. Squares show the proportion of a phylum (ascending from white to black) having an occurrence of a gene. The dendogram depicts distances between the proportion vectors. This dendogram separates B. subtilis essential genes into three clusters. The first one (red) contains dnaE and corresponds to genes occurring in the majority of bacterial clades. The second one (blue) contains dnaA and spans the whole domain of bacteria. The last one (green) contains polC and is composed of genes essentially specific to Firmicutes. The computing and visualization of the clusters was performed using the JMP® software (SAS Institute, Cary, NC).

Mentions: To get a first crude view of the processes underlying this replication-associated bias we used the JMP® software (SAS Institute, Cary, NC) to compute a hierarchical clustering of the B. subtilis essential genes [34] according to their occurrence proportion in different Bacteria clades (Figure 4). Three main clusters were obtained. Unexpectedly, they were all related to DNA replication. This substantiated the conjecture that the way replication is organized was indeed at the core of some important functional variation specific to bacteria forming a given clade.


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)

Hierarchical clustering of occurrence proportion vectors of B. subtilis essential genes in clades of the domain Bacteria. Squares show the proportion of a phylum (ascending from white to black) having an occurrence of a gene. The dendogram depicts distances between the proportion vectors. This dendogram separates B. subtilis essential genes into three clusters. The first one (red) contains dnaE and corresponds to genes occurring in the majority of bacterial clades. The second one (blue) contains dnaA and spans the whole domain of bacteria. The last one (green) contains polC and is composed of genes essentially specific to Firmicutes. The computing and visualization of the clusters was performed using the JMP® software (SAS Institute, Cary, NC).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Hierarchical clustering of occurrence proportion vectors of B. subtilis essential genes in clades of the domain Bacteria. Squares show the proportion of a phylum (ascending from white to black) having an occurrence of a gene. The dendogram depicts distances between the proportion vectors. This dendogram separates B. subtilis essential genes into three clusters. The first one (red) contains dnaE and corresponds to genes occurring in the majority of bacterial clades. The second one (blue) contains dnaA and spans the whole domain of bacteria. The last one (green) contains polC and is composed of genes essentially specific to Firmicutes. The computing and visualization of the clusters was performed using the JMP® software (SAS Institute, Cary, NC).
Mentions: To get a first crude view of the processes underlying this replication-associated bias we used the JMP® software (SAS Institute, Cary, NC) to compute a hierarchical clustering of the B. subtilis essential genes [34] according to their occurrence proportion in different Bacteria clades (Figure 4). Three main clusters were obtained. Unexpectedly, they were all related to DNA replication. This substantiated the conjecture that the way replication is organized was indeed at the core of some important functional variation specific to bacteria forming a given clade.

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.

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