DnaA binding locus datA promotes DnaA-ATP hydrolysis to enable cell cycle-coordinated replication initiation

• Published in: Proceedings of the National Academy of Sciences - PNAS 2013-01, Vol.110 (3), p.936-941
• Main Authors: Kasho, Kazutoshi, Katayama, Tsutomu
• Format: Article
• Language: English
• Subjects: Adenosine triphosphatase; Adenosine Triphosphate - metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Base Sequence; Binding Sites - genetics; Biological Sciences; Cell Cycle; Cell growth; Chromosomes; Chromosomes, Bacterial - genetics; Chromosomes, Bacterial - metabolism; DNA; DNA replication; DNA Replication - genetics; DNA Replication - physiology; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; E coli; Escherichia coli; Escherichia coli - cytology; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Gene expression regulation; Genes, Bacterial; Genetic loci; Hydrolysis; Integration Host Factors - chemistry; Integration Host Factors - genetics; Integration Host Factors - metabolism; Models, Biological; Molecules; Origin Recognition Complex - chemistry; Origin Recognition Complex - genetics; Origin Recognition Complex - metabolism; Protein Interaction Domains and Motifs; Sensors
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1212070110

The initiation of chromosomal DNA replication is rigidly regulated to ensure that it occurs in a cell cycle-coordinated manner. To ensure this in Escherichia coli , multiple systems regulate the activity of the replication initiator ATP-DnaA. The level of ATP-DnaA increases before initiation after which it drops via DnaA-ATP hydrolysis, yielding initiation-inactive ADP-DnaA. DnaA-ATP hydrolysis is crucial to regulation of initiation and mainly occurs by a replication-coupled feedback mechanism named RIDA (regulatory inactivation of DnaA). Here, we report a second DnaA-ATP hydrolysis system that occurs at the chromosomal site datA . This locus has been annotated as a reservoir for DnaA that binds many DnaA molecules in a manner dependent upon the nucleoid-associated factor IHF (integration host factor), resulting in repression of untimely initiations; however, there is no direct evidence for the binding of many DnaA molecules at this locus. We reveal that a complex consisting of datA and IHF promotes DnaA-ATP hydrolysis in a manner dependent on specific inter-DnaA interactions. Deletion of datA or the ihf gene increased ATP-DnaA levels to the maximal attainable levels in RIDA-defective cells. Cell-cycle analysis suggested that IHF binds to datA just after replication initiation at a time when RIDA is activated. We propose a model in which cell cycle-coordinated ATP-DnaA inactivation is regulated in a concerted manner by RIDA and datA .