Read-through transcription of tRNA underlies the cell cycle-dependent dissociation of IHF from the DnaA-inactivating sequence .

Timely initiation of chromosomal DNA replication in is achieved by cell cycle-coordinated regulation of the replication origin, , and the replication initiator, ATP-DnaA. Cellular levels of ATP-DnaA increase and peak at the time for initiation at , after which hydrolysis of DnaA-bound ATP causes those to fall, yielding initiation-inactive ADP-DnaA. This hydrolysis is facilitated by the chromosomal locus located downstream of the tRNA-Gly () operon, which possesses a cluster of DnaA-binding sequences and a single binding site (IBS) for the DNA bending protein IHF (integration host factor). While IHF binding activates the function and is regulated to occur specifically at post-initiation time, the underlying regulatory mechanisms remain obscure. Here, we demonstrate that -IHF binding at pre-initiation time is down-regulated depending on the read-through transcription of IBS initiated at the promoter. During the cell cycle, the level of read-through transcription, but not promoter activity, fluctuated in a manner inversely related to -IHF binding. Transcription from the promoter was predominantly interrupted at IBS by IHF binding. The terminator/attenuator sequence of the operon, as well as DnaA binding within overall, contributed to attenuation of transcription upstream of IBS, preserving the timely fluctuation of read-through transcription. These findings provide a mechanistic insight of tRNA transcription-dependent -IHF regulation, in which an unidentified factor is additionally required for the timely -IHF dissociation, and support the significance of for controlling the cell cycle progression as a connecting hub of tRNA production and replication initiation.