Data from: Extrusion-modulated DnaA activity oscillations coordinate DNA replication with biomass growth

Robust control of DNA replication is fundamental to bacterial
proliferation. In Escherichia coli, replication initiation is thought to
be regulated by oscillations in DnaA activity, driven by DnaA-chromosome
interactions that differ among leading models. However, direct evidence
linking these oscillations to replication initiation has been lacking, and
existing models fail to explain the observed decoupling of replication
initiation from dnaA expression. Here, we establish a direct link between
DnaA activity and replication initiation by demonstrating robust
oscillations in DnaA activity, which peak precisely at replication
initiation across diverse growth conditions and genetic perturbations.
Notably, these oscillations persist even when dnaA transcription remains
constant, suggesting a regulatory mechanism that modulates DnaA activity
independently of its expression. Additionally, we propose an extrusion
model in which DNA-binding proteins sense biomass-DNA imbalance and
extrude DnaA from the chromosome to trigger replication, overcoming
limitations of existing models. Consistent with this model, perturbation
of the nucleoid-associated protein H-NS modulates DnaA activity and
replication timing, supporting its mechanistic validity.