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

Dataset DOI: [10.5061/dryad.bvq83bkp4](https://doi.org/10.5061/dryad.bvq83bkp4)

## Description of the data and file structure

To analyze the cell cycle-dependent changes in dnaA transcription levels and DnaA activity, this study employed the mRNA FISH method to quantitatively analyze dnaA mRNA and lacZ mRNA—which is driven by the reporter construct Psyn66/Pcon-lacZ—under different growth conditions and genetic perturbations. For the acquired bright-field and fluorescence images, the parameters provided here, including cell morphology and fluorescence intensity, were extracted using MicrobeJ software (DOI: 10.1038/nmicrobiol 2016.77).

This dataset comprises various MATLAB .mat files in each subfolder for DnaA-activity reporter host cells cultivated under various growth conditions.

### Files and variables

#### File: Fish_data_extracted_from_microscopic_images_via_MicrobeJ.zip

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