The Caulobacter crescentus Homolog of DnaA (HdaA) Also Regulates the Proteolysis of the Replication Initiator Protein DnaA

Abstract

It is not known how diverse bacteria regulate chromosome replication. Based on Escherichia coli studies, DnaA initiates replication and the homolog of DnaA (Hda) inactivates DnaA using the RIDA (regulatory inactivation of DnaA) mechanism that thereby prevents extra chromosome replication cycles. RIDA may be widespread, because the distantly related Caulobacter crescentus homolog HdaA also prevents extra chromosome replication (J. While most bacteria use the DnaA protein to initiate chromosome replication (1-3), bacteria responding to diverse environmental pressures probably evolved many different mechanisms to regulate DnaA and thereby adjust replication control to their specific needs (3-5). The model Gram-negative bacterium Caulobacter crescentus is found in nutrient-poor freshwater lakes and streams (6). C. crescentus evolved to divide asymmetrically, and it produces a motile "swarmer cell" and a nonmotile "stalked cell" after each cell division (6-8). Chromosome replication is coupled to this dimorphic cell division since only the stalked cells initiate chromosome replication, and the swarmer cells differentiate into stalked cells before they replicate their chromosomes (9-13). CtrA is a global response regulator protein that binds to and represses the C. crescentus origin of chromosome replication in the swarmer cells (10,(14)(15)(16). Competitive binding between CtrA and DnaA is a key mechanism of replication control that blocks replication in swarmer cells while allowing replication in the stalked cells (10,17). In addition to this dimorphic control, C. crescentus chromosome replication occurs once and only once per cell division cycle (18). However, CtrA activity does not block extra rounds of chromosome replication prior to cell division (16,19).Escherichia coli uses at least three mechanisms to block extra rounds of chromosome replication. As reviewed by Katayama and coworkers (20), E. coli possesses two mechanisms that restrict DnaA binding to the origin of replication (oriC) and one mechanism, termed RIDA (regulatory inactivation of DnaA), that inactivates DnaA. Of these three mechanisms, RIDA is the dominant mechanism in E. coli (20,21). E. coli DnaA binds ATP or ADP, but only the active DnaA-ATP form can initiate oriC replication. RIDA prevents overreplication by producing the inactive DnaA-ADP form. This is essentially a negative-feedback mechanism that Citation Wargachuk R, Marczynski GT. 2015. The Caulobacter crescentus homolog of DnaA (HdaA) also regulates the proteolysis of the replication initiator protein DnaA.

Lon recognition of the replication initiator DnaA requires a bipartite degron

“…Our in vitro results indicate a need for the ATPase domain III and N‐terminal 22 amino acids of DnaA as Lon recognition elements, and we hypothesized that mutations in these regions would also affect DnaA degradation in the cell. The role of the AAA+ ATPase domain in DnaA degradation has been explored in prior work with mutations in the ATPase domain (R357A) resulting in variants of DnaA that are poorly degraded in vivo and in vitro (Wargachuk and Marczynski, ; Liu et al ., ), a result that we verified again (Fig. B).…”

“…In our work, we show how different regions of DnaA contribute to post‐translational regulation by the Lon protease. We find that the AAA+ ATPase domain of DnaA is critical for Lon binding, providing support for prior observations that the nucleotide‐bound state of DnaA affects its stability in vivo (Wargachuk and Marczynski, ; Liu et al ., ). Our work also suggests that DnaA recognition by Lon occurs through different means than those already characterized for Lon substrates.…”

The role of Helicobacter pylori DnaA domain I in orisome assembly on a bipartite origin of chromosome replication

“…For example, the E. coli DnaA domains I and III interact with the DnaB helicase (Sakiyama et al, ; Seitz, Weigel, & Messer, ; Sutton, Carr, Vicente, & Kaguni, ). Domains I and III of E. coli DnaA and possibly domain III of Caulobacter crescentus DnaA interact with the Hda‐β‐clamp complex (Su’etsugu, ; Wargachuk & Marczynski, ). In addition, the Bacillus subtilis domain III interacts with Soj and YabA (Scholefield, Errington, & Murray, ; Scholefield & Murray, ).…”

HdaB: a novel and conserved DnaA-related protein that targets the RIDA process to stimulate replication initiation

“…This Regulated Inactivation of DnaA (RIDA) process ensures that cells start the replication of their chromosome once and only once per cell cycle. In C. crescentus, the Lon ATP-dependent protease degrades DnaA-ADP more efficiently than DnaA-ATP [11][12][13] , so that the RIDA process not only inactivates DnaA but also destabilizes it, providing a robust control system 4 .…”