PolyP inhibits CobB deacetylase triggering a regulatory coupling to prevent DNA replication initiation

Abstract

Polyphosphate (polyP) is considered having regulatory functions in both procaryotic and eucaryotic cells. Under certain stress conditions, bacteria accumulate polyP, which results in liquid-liquid phase separation and polyP granules formation with not fully uncovered functions. We demonstrate that in starved Escherichia coli cells, replication initiator DnaA protein fails to form defined foci and does not bind to the origin of DNA replication (oriC), while to some extent interacts other sites on the chromosome. This is because polyP interacts with a long variant of CobB deacetylase and inhibits its activity, which results in an increased DnaA acetylation level preventing the DnaA interaction with oriC and consequently the initiation of DNA replication. This constitutes a polyP-dependent regulatory coupling targeting deacetylase for the inhibition of DNA replication initiation. Our experiments also demonstrate the importance of the multiplicity of regulatory mechanisms for the complete inhibition of initiation of DNA replication in stressed bacterial cells.