Relative Distribution of DnaA and DNA in Escherichia coli Cells as a Factor of Their Phenotypic Variability

Phenotypic variability in isogenic bacterial populations helps them to cope with external stress. This variability can stem from gene expression noise and/or unequal partitioning of low-copy-number freely diffusing proteins during cell division. Some high-copy-number components are transiently associated with almost immobile large assemblies (hyperstructures) and thereby may not be distributed equally. We hypothesize that hyperstructure organization of bacterial cells can contribute to bacterial phenotypic variability. We focus on nucleoid hyperstructure containing many DNA-associated proteins. Our previous findings suggested that replication initiation timing may be the main source of variability for nucleoid segregation events. To uncover the role of the initiator DnaA in phenotypic variability in E. coli , we followed its intra- and intercellular distribution using chromosomally encoded fluorescently tagged DnaA and histone-like HU under their native promoters. The mobility of DnaA is low, corresponding to a diffusion-binding mode, but still one order faster than that of HU. The intracellular distribution of DnaA concentration is homogeneous in contrast to the significant asymmetry in the distribution of HU; the latter leading to unequal DNA content of nucleoids in future daughter compartments. The intercellular variability of HU (CV=26%), DnaA, and their ratio (both with CV=18%) is high. The variable DnaA/DNA may cause a variable replication initiation time (initiation noise). Asynchronous initiation at different oriCs may be, in turn, a plausible origin of the asymmetric DNA distribution. We specify that the DnaA/DNA ratio may be a more rigorous feature in determining the variability of initiation time in E. coli than each of them separately.