ChIP-seq experiment: DnaA binding to E. coli chromosome before stress, during stress, and stress recovery

The ubiquitous protein DnaA is a chromosomal DNA replication initiator and transcription factor. It binds to 9-bp DNA sites called \"DnaA-boxes\" that are localized within the replication origin (oriC) and throughout chromosomal DNA, usually in the proximity of the promoter regions. During stress, bacteria undergo metabolic shifts that halt their growth and activate survival mechanisms. One outcome of these shifts is the accumulation of long chains of polyphosphate (polyP), an evolutionarily conserved linear polymer composed of up to 1,000 phosphate groups. It was previously identified that DnaA and the Lon protease bind to polyP, which stimulates Lon for the polyP-dependent DnaA proteolysis. We assumed that it have an impact not only on DnaA intracellular concentration but might also affect DNA binding pattern. To investigate this hypothesis and to analyze the DNA interaction profile of DnaA molecules remaining in stressed cells, we performed Chromatin Immunoprecipitation coupled with DNA sequencing (ChIP-seq).