Further characterization of these _dnaA_ mutants demonstrated a close connection between initiation of replication and cell cycle control: at a non-permissive temperature, a _dnaA_ mutant temporarily stops dividing and forms filamentous cells [2]; division later resumes towards one end of the filament to produce normal-sized cells that lack DNA [8]. The fact that the size of these anucleate cells is relatively constant (but see [9]) is consistent with the idea that DnaA is involved, directly or indirectly, in the positioning of the division site.  
In fact, the possibility that DnaA protein acts as a regulator of gene expression was raised by [PERSON] a few years after the isolation of the first mutant [10], and DnaA was subsequently shown to regulate many operons [11]. These observations, therefore, help make DnaA a candidate for the role of coordinator of the cell cycle.  
To explore this proposal, it is essential to characterise the biochemical properties of the DnaA protein. A large part of this was done by [PERSON] and his collaborators using genetic engineering only 20 years after the first isolation of a _dnaA_ mutant [12]. They found that the DnaA protein is an ATPase possessing a high affinity for the replication origin (_oriC_) via DnaA boxes constituted of nine bases. The consequence of this interaction is the opening of _oriC_, which allows the insertion of DNA helicase into _oriC_ in order to start DNA synthesis after the loading of DNA polymerase III. This interaction between DnaA and DnaA boxes seems to be important in most of the processes in which DnaA is involved [13;14]. DnaA has four domains [15;16] (Figure 1). Domain I binds both the helicase, DnaB, and the DiaA protein that may help link DnaA dimers and monomers; it also has a site for a low-affinity domain I-domain I interaction to generate dimers. Domain II is a linker. Domain III has an AAA+ motif that binds ATP or ADP; this binding of ATP leads to head-to-tail homo-oligomers in a helix; it also binds ssDNA and has a region that interacts with membrane. Domain IV is the dsDNA-binding domain that recognizes DnaA boxes (for references, see [11]).  
Hyperstructures are large assemblies of molecules and macromolecules that have particular functions; they constitute a level of organization intermediate between the macromolecule and the cell. We have refrained from defining the concept too precisely because it is still \"under development\" and a prematurely narrow definition might limit its usefulness. In doing this, we adopt the principle of using a \"generous Darwinian fog\" [17].  
Here, we raise questions that need to be addressed to clarify the roles of DnaA and related proteins in the cell cycle. We do this in the theoretical framework of hyperstructure dynamics and in the context of an origins-of-life scenario in which the early cells or _protocells_ had a cell cycle regulated by a cellular clock or timer based on physical chemistry. We consider the possibility that DnaA--and the hyperstructures with which it is associated--are the heirs to the original clock and that they integrate different sorts of information in order to coordinate the cell cycle with the environment.  
Figure 1: Functional structure of DnaA. The four domains (I, II, III and IV, blue, black, red and green, respectively) have different functions (see text for explanation). Not to scale.