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

Verification of CtrA and DnaA binding site prediction. A. Number of genes putatively controlled by CtrA (dark gray) and DnaA (light gray) across alpha-proteobacteria. B. Distribution of p-values assigned to each gene with respect to the CtrA binding and DnaA binding for three alpha-proteobacteria (CCRE = C. crescentus, BABO = B. abortus, SMELI = S. meliloti) and species, possessing only DnaA (ECOLI = E. coli, BSUB = B. subtilis). The distributions of CCRE, BABO, SMELI for CtrA start to diverge from the 'background' distributions represented by organisms not possessing CtrA at a p < 0.05, while for DnaA this distribution is uniform among all five organisms. C. Consensus sequences of DnaA and CtrA in different bacteria found experimentally elsewhere (see references near the sequences) compared with our PMWs. M = T or G, W = A or T.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Verification of CtrA and DnaA binding site prediction. A. Number of genes putatively controlled by CtrA (dark gray) and DnaA (light gray) across alpha-proteobacteria. B. Distribution of p-values assigned to each gene with respect to the CtrA binding and DnaA binding for three alpha-proteobacteria (CCRE = C. crescentus, BABO = B. abortus, SMELI = S. meliloti) and species, possessing only DnaA (ECOLI = E. coli, BSUB = B. subtilis). The distributions of CCRE, BABO, SMELI for CtrA start to diverge from the 'background' distributions represented by organisms not possessing CtrA at a p < 0.05, while for DnaA this distribution is uniform among all five organisms. C. Consensus sequences of DnaA and CtrA in different bacteria found experimentally elsewhere (see references near the sequences) compared with our PMWs. M = T or G, W = A or T.

Mentions: The prediction of CtrA and DnaA binding sites across alphas is based on Caulobacter data and we have already discussed how, from previous studies, it is possible to hypothesize that CtrA and DnaA (and also CcrM) binding sites are conserved across the alpha-proteobacteria. However our prediction ability might be accurate only for bacteria closely related to Caulobacter, but, going farther, this confidence could decrease. To evaluate this bias in binding site prediction, we counted the number of genes in each genome putatively controlled by CtrA and DnaA, normalized for the genome size. We found (Figure 6A) that the number of predicted genes is fairly constant and depends only on the genome size (or number of genes), suggesting that our prediction confidence is not biased by the phylogenetic distance. This result also explains the success of the complementations of ctrA deletion in Caulobacter by orthologs from other alpha proteobacteria, as discussed in the previous sections [46,52]. We also evaluated whether the presence of CtrA and DnaA predicted genes depended on the presence of CtrA and DnaA themselves in the genomes or if it was an artifact of bioinformatic analysis. We therefore plotted the fraction of genes controlled by CtrA and DnaA at small p-values in three alpha proteobacteria possessing CtrA and DnaA and in E. coli and B. subtilis, which possess only DnaA (Figure 6B). From this analysis it is evident that, at lower p-values, only organisms with CtrA keep a consistent fraction of genes controlled by CtrA, while for DnaA, which is present and active in all, every organism maintains a similar fraction of putatively controlled genes--even at lower p-values.


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)

Verification of CtrA and DnaA binding site prediction. A. Number of genes putatively controlled by CtrA (dark gray) and DnaA (light gray) across alpha-proteobacteria. B. Distribution of p-values assigned to each gene with respect to the CtrA binding and DnaA binding for three alpha-proteobacteria (CCRE = C. crescentus, BABO = B. abortus, SMELI = S. meliloti) and species, possessing only DnaA (ECOLI = E. coli, BSUB = B. subtilis). The distributions of CCRE, BABO, SMELI for CtrA start to diverge from the 'background' distributions represented by organisms not possessing CtrA at a p < 0.05, while for DnaA this distribution is uniform among all five organisms. C. Consensus sequences of DnaA and CtrA in different bacteria found experimentally elsewhere (see references near the sequences) compared with our PMWs. M = T or G, W = A or T.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Verification of CtrA and DnaA binding site prediction. A. Number of genes putatively controlled by CtrA (dark gray) and DnaA (light gray) across alpha-proteobacteria. B. Distribution of p-values assigned to each gene with respect to the CtrA binding and DnaA binding for three alpha-proteobacteria (CCRE = C. crescentus, BABO = B. abortus, SMELI = S. meliloti) and species, possessing only DnaA (ECOLI = E. coli, BSUB = B. subtilis). The distributions of CCRE, BABO, SMELI for CtrA start to diverge from the 'background' distributions represented by organisms not possessing CtrA at a p < 0.05, while for DnaA this distribution is uniform among all five organisms. C. Consensus sequences of DnaA and CtrA in different bacteria found experimentally elsewhere (see references near the sequences) compared with our PMWs. M = T or G, W = A or T.
Mentions: The prediction of CtrA and DnaA binding sites across alphas is based on Caulobacter data and we have already discussed how, from previous studies, it is possible to hypothesize that CtrA and DnaA (and also CcrM) binding sites are conserved across the alpha-proteobacteria. However our prediction ability might be accurate only for bacteria closely related to Caulobacter, but, going farther, this confidence could decrease. To evaluate this bias in binding site prediction, we counted the number of genes in each genome putatively controlled by CtrA and DnaA, normalized for the genome size. We found (Figure 6A) that the number of predicted genes is fairly constant and depends only on the genome size (or number of genes), suggesting that our prediction confidence is not biased by the phylogenetic distance. This result also explains the success of the complementations of ctrA deletion in Caulobacter by orthologs from other alpha proteobacteria, as discussed in the previous sections [46,52]. We also evaluated whether the presence of CtrA and DnaA predicted genes depended on the presence of CtrA and DnaA themselves in the genomes or if it was an artifact of bioinformatic analysis. We therefore plotted the fraction of genes controlled by CtrA and DnaA at small p-values in three alpha proteobacteria possessing CtrA and DnaA and in E. coli and B. subtilis, which possess only DnaA (Figure 6B). From this analysis it is evident that, at lower p-values, only organisms with CtrA keep a consistent fraction of genes controlled by CtrA, while for DnaA, which is present and active in all, every organism maintains a similar fraction of putatively controlled genes--even at lower p-values.

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