Computational and Genetic Reduction of a Cell Cycle to Its Simplest, Primordial Components

Abstract

Mathematical modelling and genetics in the bacterium Caulobacter crescentus identified redundancy in asymmetric cell cycle regulation through the dispensability of key transcription factor GcrA and methyltransferase CcrM, which together form a genetic module.

Abstract

What are the minimal requirements to sustain an asymmetric cell cycle? Here we use mathematical modelling and forward genetics to reduce an asymmetric cell cycle to its simplest, primordial components. In the Alphaproteobacterium Caulobacter crescentus, cell cycle progression is believed to be controlled by a cyclical genetic circuit comprising four essential master regulators. Unexpectedly, our in silico modelling predicted that one of these regulators, GcrA, is in fact dispensable. We confirmed this experimentally, finding that Δ gcrA cells are viable, but slow-growing and elongated, with the latter mostly due to an insufficiency of a key cell division protein. Furthermore, suppressor analysis showed that another cell cycle regulator, the methyltransferase CcrM, is similarly dispensable with simultaneous gcrA/ ccrM disruption ameliorating the cytokinetic and growth defect of Δ gcrA cells. Within the Alphaproteobacteria, gcrA and ccrM are consistently present or absent together, rather than either gene being present alone, suggesting that gcrA/ ccrM constitutes an independent, dispensable genetic module. Together our approaches unveil the essential elements of a primordial asymmetric cell cycle that should help illuminate more complex cell cycles.

Author Summary

Cell cycle regulation is remarkably complex and the fundamental principles difficult to understand, even in simple cells. The bacterium Caulobacter crescentus is a popular model organism to study cell cycle regulation due to the two different daughter cells resulting from cell division: a mobile “swarmer” cell and a “stalked” cell that adheres to surfaces. Here, we use mathematical modelling and genetic experiments to identify the core components of the asymmetric cell cycle of these bacteria. Using our mathematical model we predicted and confirmed experimentally that the transcription factor and cell cycle regulator, GcrA, hitherto thought to be essential, is in fact dispensable. We also identified another master regulator, the methyltransferase, CcrM as dispensable. Furthermore, simultaneous deletion of both GcrA and CcrM removes the severe cell division defects observed on either single deletion, returning cells to near wild-type morphology. We found that GcrA and CcrM constitute an independent, dispensable, genetic module that regulates transcription of cytokinetic proteins during the cell cycle. Phylogenetically, the module is conserved in Alphaproteobacteria, the class of Caulobacter, but is not present in the tree root of the class, suggesting that we have identified the primordial core of the asymmetric cell cycle regulatory circuit in the Alphaproteobacteria.