Abstract
Replication of the bacterial chromosome initiates at a single origin of replication that is called oriC. This occurs via the concerted action of numerous proteins, including DnaA, which acts as an initiator. The origin sequences vary across species, but all bacterial oriCs contain the information necessary to guide assembly of the DnaA protein complex at oriC, triggering the unwinding of DNA and the beginning of replication. The requisite information is encoded in the unique arrangement of specific sequences called DnaA boxes, which form a framework for DnaA binding and assembly. Other crucial sequences of bacterial origin include DNA unwinding element (DUE, which designates the site at which oriC melts under the influence of DnaA) and binding sites for additional proteins that positively or negatively regulate the initiation process. In this review, we summarize our current knowledge and understanding of the information encoded in bacterial origins of chromosomal replication, particularly in the context of replication initiation and its regulation. We show that oriC encoded instructions allow not only for initiation but also for precise regulation of replication initiation and coordination of chromosomal replication with the cell cycle (also in response to environmental signals). We focus on Escherichia coli, and then expand our discussion to include several other microorganisms in which additional regulatory proteins have been recently shown to be involved in coordinating replication initiation to other cellular processes (e.g., Bacillus, Caulobacter, Helicobacter, Mycobacterium, and Streptomyces). We discuss diversity of bacterial oriC regions with the main focus on roles of individual DNA recognition sequences at oriC in binding the initiator and regulatory proteins as well as the overall impact of these proteins on the formation of initiation complex.
Highlights
In contrast to the situation in Eukaryotes, chromosomal replication in bacteria begins at a single site on the chromosome: the origin of replication (Leonard and Méchali, 2013)
We show that oriC encoded instructions allow for initiation and for precise regulation of replication initiation and coordination of chromosomal replication with the cell cycle
We focus on Escherichia coli, and expand our discussion to include several other microorganisms in which additional regulatory proteins have been recently shown to be involved in coordinating replication initiation to other cellular processes (e.g., Bacillus, Caulobacter, Helicobacter, Mycobacterium, and Streptomyces)
Summary
In contrast to the situation in Eukaryotes, chromosomal replication in bacteria begins at a single site on the chromosome: the origin of replication (oriC) (Leonard and Méchali, 2013). The oriBPs can be classified by their sequence specificity and/or function: they may or non- interact with oriC to positively or negatively influence the unwinding of the origin They confer their direct effects by binding to DnaA (or other oriBPs) binding sites, and exert their indirect effects by changing the DNA structure of the origin to modulate the binding of additional oriBPs. The proteins that regulate replication initiation have been best described for E. coli, in which ∼11 oriC binding proteins have been identified (Table 2). This sequestration mechanism appears to be exclusive to a few DamMT-specifying proteobacteria, as homologs of the seqA gene have been identified only in this subset of Gram-negative bacteria (Brézellec et al, 2006) Another negative regulator of initiation in E. coli, the Fis protein, associates with oriC throughout most of the cell cycle; similar to SeqA, Fis negatively influences replication initiation by regulating the occupation of DnaA on low-affinity sites (Cassler et al, 1995; Ryan et al, 2004). The release of SeqA reveals the IHF binding site; displacement of Fis promotes IHF binding; and IHF binding leads to bending of the DNA (Polaczek, 1990; Cassler et al, 1995; Rice et al, 1996; Weisberg et al, 1996; Table 2 | OriBP (origin binding protein) regulators
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