Replication fork passage drives asymmetric dynamics of a critical nucleoid‐associated protein in Caulobacter

In bacteria, chromosome dynamics and gene expression are modulated by nucleoid‐associated proteins (NAPs), but little is known about how NAP activity is coupled to cell cycle progression. Using genomic techniques, quantitative cell imaging, and mathematical modeling, our study in Caulobacter crescentus identifies a novel NAP (GapR) whose activity over the cell cycle is shaped by DNA replication. GapR activity is critical for cellular function, as loss of GapR causes severe, pleiotropic defects in growth, cell division, DNA replication, and chromosome segregation. GapR also affects global gene expression with a chromosomal bias from origin to terminus, which is associated with a similar general bias in GapR binding activity along the chromosome. Strikingly, this asymmetric localization cannot be explained by the distribution of GapR binding sites on the chromosome. Instead, we present a mechanistic model in which the spatiotemporal dynamics of GapR are primarily driven by the progression of the replication forks. This model represents a simple mechanism of cell cycle regulation, in which DNA‐binding activity is intimately linked to the action of DNA replication. Synopsis Nucleoid‐associated proteins (NAPs) regulate chromosome organization and global gene expression in bacteria. Experiments and modeling reveal a simple mechanism by which DNA replication can control the spatiotemporal dynamics of NAPs and other DNA‐binding proteins. GapR is an α‐proteobacterial NAP that affects growth, division, DNA replication, and global gene expression in Caulobacter crescentus . DNA‐binding and transcriptional activities of GapR are biased from origin to terminus regions of the chromosome despite uniformly distributed binding sites. GapR binds strongly to DNA in vivo , and dissociation is primarily driven by replication fork progression. Modeling shows that the directionality of DNA replication causes the origin‐to‐terminus asymmetry in DNA‐binding activity. Graphical Abstract Experiments and modeling reveal a simple mechanism by which DNA replication can control spatiotemporal dynamics of bacterial DNA‐binding proteins involved in chromosome organization and global gene expression.