Direct single-cell observation of a key E. coli cell cycle oscillator

Abstract

A long-standing hypothesis sees DNA replication control in E. coli as a central cell cycle os-cillator at whose core is the DnaA protein. The consensus is that the activity of the DnaA protein, which is dependent on its nucleotide bound state, is an effector of initiation of DNA replication and a sensor of cell size. However, while several processes are known to regulate DnaA activity as a function of the cell cycle, the oscillations in DnaA expression and DnaA ac-tivity have never been observed at the single cell level, and their correlation with cell volume has yet to be established. In this study, we measured the volume-specific production rate of a reporter protein under control of the dnaAP2 promoter in single cells. By a careful dissection of the effects of DnaA-ATP-and SeqA-dependent regulation, two distinct cell cycle oscilla-tors emerge. The first oscillator, driven by gene dosage, DnaA activity and SeqA repression oscillates synchronously, and shows a causal relationship, with cell size and divisions, sim-ilarly to initiation events. The second one, a reporter of dosage and DnaA activity only, is strongly coupled to cell size, but loses the synchrony and causality properties, suggesting that DnaA activity peaks do not correspond directly to initiation events. These findings suggest that while transcription regulation by DnaA activity performs volume sensing, transient in-hibition of gene expression by SeqA following replication fork passage keeps DnaA activity oscillations in phase with initiation events.