Escherichia coli DnaA interacts with HU in initiation at the E. coli replication origin

Abstract

SummaryEscherichia coli HU protein is a dimer encoded by two closely related genes whose expression is growth phase-dependent. As a major component of the bacterial nucleoid, HU binds to DNA non-specifically, but acts at the chromosomal origin (oriC) during initiation by stimulating strand opening in vitro. We show that the a dimer of HU is more active than other forms of HU in initiation of an oriC-containing plasmid because it more effectively promotes strand opening of oriC. Other results demonstrate that HU stabilizes the DnaA oligomer bound to oriC, and that the a subunit of HU interacts with the N-terminal region of DnaA. These observations support a model whereby DnaA interacts with the a dimer or the ab heterodimer, depending on their cellular abundance, to recruit the respective form of HU to oriC. The greater activity of the a dimer of HU at oriC may stimulate initiation during early log phase compared with the lesser activity of the ab heterodimer or the b dimer.

The structure of a DnaA/HobA complex from Helicobacter pylori provides insight into regulation of DNA replication in bacteria

“…Its modular architecture allows for interactions with different binding partners during the various steps of the formation of the active replication forks and coupling to other cellular events (3,15,17,20,22,29,30). In E. coli, DnaA III interactions with itself, Hda, or DnaC are important for the spatial positioning of the ATP-DnaA molecules and their recycling (13,17,31,32).…”

“…These two proteins facilitate the hydrolysis of ATP by DnaA which would lead to a disassembly of the helical arrangement and hence to the inactivation of DnaA. In E. coli, the formation of the orisome is assisted by several accessory factors such as IHF, SeqA, HU, and DiaA [reviewed in (3)], with the latter two binding directly to DnaA (15,16). The DnaA paralogue DnaC is necessary to load the DnaB helicase.…”

Roles of Nucleoid-Associated Proteins in Stress-Induced Mutagenic Break Repair in StarvingEscherichia coli

“…Thus, four of these five NAPs appear to promote MBR via stress-response regulation. Because of their essential nature, IciA and DnaA (Chodavarapu et al 2008a) were not included in this study. CbpB, which, like IciA and DnaA, binds the replication origin (Skarstad et al 1993), also was not studied.…”

Helicase Loading at Chromosomal Origins of Replication

“…The interaction with RNA polymerase correlates with the role of DnaA as a transcriptional activator in stabilizing the binding of RNA polymerase at the gidA and lP R promoters (Szalewska-Pałasz et al 1998;Flåtten et al 2009), and possibly at the glpD and fliC promoters (Mizushima et al 1994;Messer and Weigel 1997). With HU or DiaA, their respective binding stabilizes DnaA oligomerized at oriC to stimulate initiation in vitro (Keyamura et al 2007(Keyamura et al , 2009Chodavarapu et al 2008a). By comparison, L2 inhibits initiation by impairing the formation of a DnaA oligomer at oriC (Chodavarapu et al 2011).…”

“…These interactions are critical for helicase loading and are described in more detail below. Other proteins that interact with domain 1 are HU (Chodavarapu et al 2008a), DiaA (Keyamura et al 2007, Dps (Chodavarapu et al 2008b), ribosomal protein L2 (Chodavarapu et al 2011), and RNA polymerase (Flåtten et al 2009). The interaction with RNA polymerase correlates with the role of DnaA as a transcriptional activator in stabilizing the binding of RNA polymerase at the gidA and lP R promoters (Szalewska-Pałasz et al 1998;Flåtten et al 2009), and possibly at the glpD and fliC promoters (Mizushima et al 1994;Messer and Weigel 1997).…”