The architecture and conservation pattern of whole-cell control circuitry

Department of Developmental Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305, USA.
Journal of Molecular Biology (Impact Factor: 4.33). 02/2011; 409(1):28-35. DOI: 10.1016/j.jmb.2011.02.041
Source: PubMed

ABSTRACT The control circuitry that directs and paces Caulobacter cell cycle progression involves the entire cell operating as an integrated system. This control circuitry monitors the environment and the internal state of the cell, including the cell topology, as it orchestrates orderly activation of cell cycle subsystems and Caulobacter's asymmetric cell division. The proteins of the Caulobacter cell cycle control system and its internal organization are co-conserved across many alphaproteobacteria species, but there are great differences in the regulatory apparatus' functionality and peripheral connectivity to other cellular subsystems from species to species. This pattern is similar to that observed for the "kernels" of the regulatory networks that regulate development of metazoan body plans. The Caulobacter cell cycle control system has been exquisitely optimized as a total system for robust operation in the face of internal stochastic noise and environmental uncertainty. When sufficient details accumulate, as for Caulobacter cell cycle regulation, the system design has been found to be eminently rational and indeed consistent with good design practices for human-designed asynchronous control systems.

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    • "A recent review (McAdams & Shapiro, 2011) describes a fifth (Christen et al., 2011; Tan et al., 2010) regulator, SciP, a CtrA antagonist that inhibits the transcription of at least 58 CtrA-activated genes (Gora et al., 2010; Tan et al., 2010) in swarmer cells, limiting their expression to the predivisional stage of the cell cycle. SciP integrates with the oscillating core cell cycle regulators via CtrA and CcrM (Gora et al., 2010; Tan et al., 2010). "
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    ABSTRACT: The master regulator CtrA oscillates during the Caulobacter cell cycle due to temporally regulated proteolysis and transcription. It is proteolysed during the G1-S transition and reaccumulates in predivisional cells as a result of transcription from two sequentially activated promoters, P1 and P2. CtrA reinforces its own synthesis by directly mediating the activation of P2 concurrently with repression of P1. To explore the role of P1 in cell cycle control, we engineered a mutation into the native ctrA locus that prevents transcription from P1 but not P2. As expected, the ctrA P1 mutant exhibits striking growth, morphological and DNA replication defects. Unexpectedly, we found CtrA and its antagonist SciP, but not DnaA, GcrA or CcrM accumulation to be dramatically reduced in the ctrA P1 mutant. SciP levels closely paralleled CtrA accumulation, suggesting that CtrA acts as a rheostat to modulate SciP abundance. Furthermore, the reappearance of CtrA and CcrM in predivisional cells was delayed in the P1 mutant by 0.125 cell cycle unit in synchronized cultures. High levels of ccrM transcription despite low levels of CtrA and increased transcription of ctrA P2 in the ctrA P1 mutant are two examples of robustness in the cell cycle. Thus, Caulobacter can adjust regulatory pathways to partially compensate for reduced and delayed CtrA accumulation in the ctrA P1 mutant.
    Microbiology 07/2012; 158(Pt 10):2492-503. DOI:10.1099/mic.0.055285-0 · 2.84 Impact Factor
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    • "We have identified the Caulobacter crescentus essential genome to 8 bp resolution by performing ultrahigh-resolution transposon mutagenesis followed by high-throughput DNA sequencing to determine the transposon insertion sites. A notable feature of C. crescentus is that the regulatory events that control polar differentiation and cell-cycle progression are highly integrated, and they occur in a temporally restricted order (McAdams and Shapiro, 2011). Many components of the core regulatory circuit have been identified and simulation of the circuitry has been reported (Shen et al, 2008). "
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    ABSTRACT: Caulobacter crescentus is a model organism for the integrated circuitry that runs a bacterial cell cycle. Full discovery of its essential genome, including non-coding, regulatory and coding elements, is a prerequisite for understanding the complete regulatory network of a bacterial cell. Using hyper-saturated transposon mutagenesis coupled with high-throughput sequencing, we determined the essential Caulobacter genome at 8 bp resolution, including 1012 essential genome features: 480 ORFs, 402 regulatory sequences and 130 non-coding elements, including 90 intergenic segments of unknown function. The essential transcriptional circuitry for growth on rich media includes 10 transcription factors, 2 RNA polymerase sigma factors and 1 anti-sigma factor. We identified all essential promoter elements for the cell cycle-regulated genes. The essential elements are preferentially positioned near the origin and terminus of the chromosome. The high-resolution strategy used here is applicable to high-throughput, full genome essentiality studies and large-scale genetic perturbation experiments in a broad class of bacterial species.
    Molecular Systems Biology 08/2011; 7:528. DOI:10.1038/msb.2011.58 · 14.10 Impact Factor
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    Talanta 01/2011; 83(3):832-9. DOI:10.1016/j.talanta.2010.10.036 · 3.51 Impact Factor
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