Limits...
The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis.

Brilli M, Fondi M, Fani R, Mengoni A, Ferri L, Bazzicalupo M, Biondi EG - BMC Syst Biol (2010)

Bottom Line: The regulatory cell cycle architecture was identified in all representative alpha-proteobacteria, revealing a high diversification of circuits but also a conservation of logical features.An evolutionary model was proposed where ancient alphas already possessed all modules found in Caulobacter arranged in a variety of connections.Two schemes appeared to evolve: a complex circuit in Caulobacterales and Rhizobiales and a simpler one found in Rhodobacterales.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Evolutionary Biology, University of Florence, via Romana, 17, Florence, Italy.

ABSTRACT

Background: In the bacterium Caulobacter crescentus, CtrA coordinates DNA replication, cell division, and polar morphogenesis and is considered the cell cycle master regulator. CtrA activity varies during cell cycle progression and is modulated by phosphorylation, proteolysis and transcriptional control. In a phosphorylated state, CtrA binds specific DNA sequences, regulates the expression of genes involved in cell cycle progression and silences the origin of replication. Although the circuitry regulating CtrA is known in molecular detail in Caulobacter, its conservation and functionality in the other alpha-proteobacteria are still poorly understood.

Results: Orthologs of Caulobacter factors involved in the regulation of CtrA were systematically scanned in genomes of alpha-proteobacteria. In particular, orthologous genes of the divL-cckA-chpT-ctrA phosphorelay, the divJ-pleC-divK two-component system, the cpdR-rcdA-clpPX proteolysis system, the methyltransferase ccrM and transcriptional regulators dnaA and gcrA were identified in representative genomes of alpha-proteobacteria. CtrA, DnaA and GcrA binding sites and CcrM putative methylation sites were predicted in promoter regions of all these factors and functions controlled by CtrA in all alphas were predicted.

Conclusions: The regulatory cell cycle architecture was identified in all representative alpha-proteobacteria, revealing a high diversification of circuits but also a conservation of logical features. An evolutionary model was proposed where ancient alphas already possessed all modules found in Caulobacter arranged in a variety of connections. Two schemes appeared to evolve: a complex circuit in Caulobacterales and Rhizobiales and a simpler one found in Rhodobacterales.

Show MeSH

Related in: MedlinePlus

Functions controlled by CtrA among alpha-proteobacteria. Enrichment of genes controlled by CtrA in COG categories (see also Additional file 8, Table S5). The scale corresponds to the p-value of the functional enrichment calculated as described in the Material and Methods. The p-value is inversely correlated to the strength of the functional enrichment of each regulon, i.e. a lower p-value indicates stronger enrichment.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2877005&req=5

Figure 4: Functions controlled by CtrA among alpha-proteobacteria. Enrichment of genes controlled by CtrA in COG categories (see also Additional file 8, Table S5). The scale corresponds to the p-value of the functional enrichment calculated as described in the Material and Methods. The p-value is inversely correlated to the strength of the functional enrichment of each regulon, i.e. a lower p-value indicates stronger enrichment.

Mentions: Two kinds of results from this analysis are shown here: (i) CtrA target genes belonging to our starting dataset of cell cycle related genes (Figure 3) and (ii) enrichment of COG (clusters of orthologous groups of proteins) categories of genome-wide CtrA regulons for each genome analyzed (Figure 4).


The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis.

Brilli M, Fondi M, Fani R, Mengoni A, Ferri L, Bazzicalupo M, Biondi EG - BMC Syst Biol (2010)

Functions controlled by CtrA among alpha-proteobacteria. Enrichment of genes controlled by CtrA in COG categories (see also Additional file 8, Table S5). The scale corresponds to the p-value of the functional enrichment calculated as described in the Material and Methods. The p-value is inversely correlated to the strength of the functional enrichment of each regulon, i.e. a lower p-value indicates stronger enrichment.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2877005&req=5

Figure 4: Functions controlled by CtrA among alpha-proteobacteria. Enrichment of genes controlled by CtrA in COG categories (see also Additional file 8, Table S5). The scale corresponds to the p-value of the functional enrichment calculated as described in the Material and Methods. The p-value is inversely correlated to the strength of the functional enrichment of each regulon, i.e. a lower p-value indicates stronger enrichment.
Mentions: Two kinds of results from this analysis are shown here: (i) CtrA target genes belonging to our starting dataset of cell cycle related genes (Figure 3) and (ii) enrichment of COG (clusters of orthologous groups of proteins) categories of genome-wide CtrA regulons for each genome analyzed (Figure 4).

Bottom Line: The regulatory cell cycle architecture was identified in all representative alpha-proteobacteria, revealing a high diversification of circuits but also a conservation of logical features.An evolutionary model was proposed where ancient alphas already possessed all modules found in Caulobacter arranged in a variety of connections.Two schemes appeared to evolve: a complex circuit in Caulobacterales and Rhizobiales and a simpler one found in Rhodobacterales.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Evolutionary Biology, University of Florence, via Romana, 17, Florence, Italy.

ABSTRACT

Background: In the bacterium Caulobacter crescentus, CtrA coordinates DNA replication, cell division, and polar morphogenesis and is considered the cell cycle master regulator. CtrA activity varies during cell cycle progression and is modulated by phosphorylation, proteolysis and transcriptional control. In a phosphorylated state, CtrA binds specific DNA sequences, regulates the expression of genes involved in cell cycle progression and silences the origin of replication. Although the circuitry regulating CtrA is known in molecular detail in Caulobacter, its conservation and functionality in the other alpha-proteobacteria are still poorly understood.

Results: Orthologs of Caulobacter factors involved in the regulation of CtrA were systematically scanned in genomes of alpha-proteobacteria. In particular, orthologous genes of the divL-cckA-chpT-ctrA phosphorelay, the divJ-pleC-divK two-component system, the cpdR-rcdA-clpPX proteolysis system, the methyltransferase ccrM and transcriptional regulators dnaA and gcrA were identified in representative genomes of alpha-proteobacteria. CtrA, DnaA and GcrA binding sites and CcrM putative methylation sites were predicted in promoter regions of all these factors and functions controlled by CtrA in all alphas were predicted.

Conclusions: The regulatory cell cycle architecture was identified in all representative alpha-proteobacteria, revealing a high diversification of circuits but also a conservation of logical features. An evolutionary model was proposed where ancient alphas already possessed all modules found in Caulobacter arranged in a variety of connections. Two schemes appeared to evolve: a complex circuit in Caulobacterales and Rhizobiales and a simpler one found in Rhodobacterales.

Show MeSH
Related in: MedlinePlus