Origins of DNA Replication in the Three Domains of Life Nicholas P

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Origins of DNA Replication in the Three Domains of Life Nicholas P REVIEW ARTICLE Origins of DNA replication in the three domains of life Nicholas P. Robinson and Stephen D. Bell MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, Cambridge, UK Keywords Replication of DNA is essential for the propagation of life. It is somewhat Cdc6; DnaA; DNA Replication; MCM; ORC surprising then that, despite the vital nature of this process, cellular organ- isms show a great deal of variety in the mechanisms that they employ to Correspondence ensure appropriate genome duplication. This diversity is manifested along S. D. Bell, MRC Cancer Cell Unit, Hutchison MRC Research Centre, Hills Road, classical evolutionary lines, with distinct combinations of replicon architec- Cambridge, CB2 2XZ, UK ture and replication proteins being found in the three domains of life: the Fax: +44 1223 763296 Bacteria, the Eukarya and the Archaea. Furthermore, although there are Tel: +44 1223 763311 mechanistic parallels, even within a given domain of life, the way origins of E-mail: sb419@hutchison-mrc.cam.ac.uk replication are defined shows remarkable variation. (Received 8 April 2005, revised 11 May 2005, accepted 13 May 2005) doi:10.1111/j.1742-4658.2005.04768.x mosome [2]. In Escherichia coli, oriC is located The origin of origins between the gldA and mioC genes. The 250 bp oriC In a now classic 1963 paper, Jacob, Brenner & Cuzin region contains multiple repeated sequences containing proposed that, in a manner analogous to the inter- a nine base pair consensus element termed the DnaA action of trans-acting regulators with cis-acting opera- box [3]. Other bacteria also possess single origins of tors in control of gene expression, an initiator factor replication with multiple DnaA boxes although both would act at a replicator sequence in the chromosome the precise number and distribution of these boxes to control and facilitate DNA replication [1]. However, vary between species [4]. Interestingly, in many bac- in contrast to the then prevalent models for negative teria the origin of replication is found adjacent to the regulation of gene expression, it was proposed that the gene for DnaA itself, suggesting a mechanism for the replication initiator factor would act positively to pro- coordinate control of origin activity and levels of initi- mote replication at the replicator, or as it is now ator proteins [4]. An individual consensus DnaA box named, origin of replication. In the following 40 years is bound by a monomer of the DnaA protein and this much has been learnt about the nature of initiators interaction induces a sharp bend in the binding site [5]. and origins of replication, particularly in simple model However, in natural bacterial origins there are multiple systems. However, many of the molecular details of DnaA boxes and these orchestrate complex cooper- the basis of origin selection remain poorly understood, ative binding events to DnaA boxes with varying particularly in higher eukaryotes. degrees of conformity to the consensus sequence. A particularly interesting ramification of this is that a DnaA box with poor conservation to the consensus Bacteria may not be able to bind DnaA on its own. However, In bacteria the origin of replication is termed oriC, binding to this ‘weak’ site can be facilitated by binding and typically a single origin exists per bacterial chro- of DnaA to an adjacent high affinity consensus site [4]. Abbreviations ACS, ARS-consensus sequence; ARS, autonomously replicating sequences; DBD, DNA binding domain; MCM, minichromosomal maintenance; ORB, origin recognition box; ORC, origin recognition complex; pre-RC, prereplicative complex. FEBS Journal 272 (2005) 3757–3766 ª 2005 FEBS 3757 Origins of DNA replication N. P. Robinson and S. D. Bell Bacterial origins of replication also possess a second by extending so-called arginine fingers into the ATP conserved element, a highly AT rich region. The binding subunit of a neighbour [7]. Thus, there is the unwinding of this intrinsically meltable DNA is a key capacity to transduce the effects of ATP to ADP step in replication initiation at origins. Under highly hydrolysis in one subunit through a network of inter- defined in vitro conditions, DnaA is capable of medi- acting proteins. It has been found that although ADP– ating partial unwinding of this region on its own DnaA and ATP–DnaA have similar affinities for con- (Fig. 1). It appears therefore, that the combination of sensus DnaA boxes [8], the ATP bound form is able to DNA bending induced by DnaA and the cooperative recognize an additional six base pair element, provi- interactions between DnaA monomers on DNA result ding a consensus ‘strong’ DnaA box is present in the in local topological tension that manifests itself by vicinity. In addition, single stranded versions of these unwinding of this intrinsically less stable region of ‘ATP–DnaA box’ hexameric sequences can also be duplex [6]. recognized by ATP–DnaA. Six of these ATP–DnaA A further level of complexity arises from the fact boxes are found in the AT rich region of E. coli oriC. that DnaA is a member of the AAA+ family of ATP- Thus, once the topological tension induced by DnaA ases. This class of protein possess a nucleotide-binding binding has melted this region, the exposed single domain that can bind ATP and catalyse its hydrolysis. stranded ATP–DnaA boxes can be bound by ATP– The conformation of the AAA+ domain alters DnaA stabilizing the DNA in the melted form [4,8]. depending on the phosphorylation status of the bound It is apparent therefore, that the combination of nucleotide. Furthermore, AAA+ proteins often exist multiple DNA recognition sites, distortion of duplex as multimers and neighbouring subunits communicate DNA, and cooperative interactions between DNA bound initiator proteins at bacterial origins leads to a complex nucleoprotein architecture, the precise stoichio- metry of which remains unclear, that both mediates the DnaA AT-rich region initial melting and stabilizes the resultant single stranded box DNA. It therefore comes as no surprise that bacterial architectural chromatin proteins such as HU and IHF play important roles in facilitating the assembly of this complex [9]. DnaA Once the melted origin–DnaA complex has formed, the replicative helicase DnaB can be loaded. Although DnaA interacts physically with DnaB [4], this reaction DnaB requires the action of another protein, DnaC [10–13]. Interestingly DnaC, like DnaA, is a member of the DnaC AAA+ family of ATPases, however, the role of ATP appears to be rather more subtle than simply being required as an energy source to facilitate loading of the ring shaped DnaB helicase. Indeed, ATP hydrolysis by DnaC is not required for DnaB loading as this reaction can be performed by ATP–DnaC, ADP– DnaC or even nucleotide free forms of DnaC [14]. Rather the role of ATP in the reaction is to serve as a switch that controls the activity of the helicase. The ATP bound form of DnaC severely inhibits the heli- case activity of DnaB and also increases the affinity of DnaC for single stranded DNA. In contrast ADP– DnaC does not inhibit DnaB helicase and has lower DNA binding affinity. Thus, it has been proposed that Fig. 1. Cartoon of the assembly of the DNA replication machinery ATP–DnaC interacts with DnaB and facilitates load- on the E. coli oriC region. Binding of DnaA (green ovals) to the ing of the helicase onto the single stranded region of DnaA boxes (blue boxes) is shown. This leads to local DNA distor- tion and facilitates binding of DnaA to melted DNA in an AT-rich the melted origin. However, the high affinity of ATP– region (purple region). DnaB (blue), in a complex with DnaC (peach) DnaC for DNA effectively glues DnaB to the origin, is recruited to the melted region, followed by disassociation of preventing its translocation and therefore suppressing DnaC as detailed in the text. its helicase activity. Subsequently, the hydrolysis of 3758 FEBS Journal 272 (2005) 3757–3766 ª 2005 FEBS N. P. Robinson and S. D. Bell Origins of DNA replication ATP to ADP by DnaC releases DnaB allowing it to 1 act as the replicative helicase [14]. 2 3 ORC 4 6 Complex 5 Eukaryotic origins The identification of initiation sites in eukaryotic Origin organisms has been an arduous task. In contrast to the single, clearly defined sites of bacterial replication, eukaryotic DNA synthesis commences from hundreds or even thousands of origins, which rarely contain Cdt1 obvious sequence motifs, and are often difficult to characterize (reviewed in [15–19]). This complexity is MCM compounded by the fact that eukaryotic origin activa- Cdc6 2-7 tion is asynchronous. In addition, initiation site usage displays considerable flexibility under varying growth conditions, or throughout different stages of develop- ment. In more recent years, it has become increasingly apparent that epigenetic factors govern the regulation of eukaryotic origin activity (reviewed in [15,16]). These modulations provide the elasticity necessary for coordinated initiation from multiple sites. Lessons from budding yeast Although eukaryotic replication initiation is inevitably Fig. 2. Model for recruitment of the eukaryotic minichromosomal more complicated than the bacterial process, some par- maintenance (MCM) complex to an origin of replication. The origin is first bound by the heterohexameric ORC (light blue). Cdc6 (red) allels can be drawn between the two systems. These is then recruited and, in conjunction with Cdt1 (orange), recruits the similarities are perhaps most obvious in the budding MCM complex (dark blue) to the origin. yeast Saccharomyces cerevisiae, where conserved sequence motifs have been identified at the origins. Budding yeast initiation sites, or autonomously replica- Mcm2–7, is the most probable candidate for this role. ting sequences (ARS), are noncoding regions of DNA, As in bacteria, this recruitment requires supplementary approximately 100–200 bp in length.
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