The hemimethylated replication origin of Escherichia coli can be initiated in vitro

The Escherichia coli SeqA protein

The Escherichia coli SeqA protein contributes to regulation of chromosome replication by preventing re-initiation at newly replicated origins. SeqA protein binds to new DNA which is hemimethylated at the adenine of GATC sequences. Most of the cellular SeqA is found complexed with the new DNA at the replication forks. In vitro the SeqA protein binds as a dimer to two GATC sites and is capable of forming a helical fiber of dimers through interactions of the N-terminal domain. SeqA can also bind, with less affinity, to fully methylated origins and affect timing of "primary" initiations. In addition to its roles in replication, the SeqA protein may also act in chromosome organization and gene regulation.

Regulatory Network of the Initiation of Chromosomal Replication inEscherichia coli

The bacterial chromosome is replicated once during the division cycle, a process ensured by the tight regulation of initiation at oriC. In prokaryotes, the initiator protein DnaA plays an essential role at the initiation step, and feedback control is critical in regulating initiation. Three systems have been identified that exert feedback control in Escherichia coli, all of which are necessary for tight strict regulation of the initiation step. In particular, the ATP-dependent control of DnaA activity is essential. A missing link in initiator activity regulation has been identified, facilitating analysis of the reaction mechanism. Furthermore, key components of this regulatory network have also been described. Because the eukaryotic initiator complex, ORC, is also regulated by ATP, the bacterial system provides an important model for understanding initiation in eukaryotes. This review summarizes recent studies on the regulation of initiator activity.

DnaA: controlling the initiation of bacterial DNA replication and more

Escherichia coli is a model system to study the mechanism of DNA replication and its regulation during the cell cycle. One regulatory pathway ensures that initiation of DNA replication from the chromosomal origin, oriC, is synchronous and occurs at the proper time in the bacterial cell cycle. A major player in this pathway is SeqA protein and involves its ability to bind preferentially to oriC when it is hemi-methylated. The second pathway modulates DnaA activity by stimulating the hydrolysis of ATP bound to DnaA protein. The regulatory inactivation of DnaA function involves an interaction with Hda protein and the beta dimer, which functions as a sliding clamp for the replicase, DNA polymerase III holoenzyme. The datA locus represents a third mechanism, which appears to influence the availability of DnaA protein in supporting rifampicin-resistant initiations.

Compartmentalization of prokaryotic DNA replication

It becomes now apparent that prokaryotic DNA replication takes place at specific intracellular locations. Early studies indicated that chromosomal DNA replication, as well as plasmid and viral DNA replication, occurs in close association with the bacterial membrane. Moreover, over the last several years, it has been shown that some replication proteins and specific DNA sequences are localized to particular subcellular regions in bacteria, supporting the existence of replication compartments. Although the mechanisms underlying compartmentalization of prokaryotic DNA replication are largely unknown, the docking of replication factors to large organizing structures may be important for the assembly of active replication complexes. In this article, we review the current state of this subject in two bacterial species, Escherichia coli and Bacillus subtilis, focusing our attention in both chromosomal and extrachromosomal DNA replication. A comparison with eukaryotic systems is also presented.

Excess SeqA prolongs sequestration of oriC and delays nucleoid segregation and cell division

Following initiation of chromosomal replication in Escherichia coli, newly initiated origins (oriCs) are prevented from further initiations by a mechanism termed sequestration. During the sequestration period (which lasts about one-third of a cell cycle), the origins remain hemimethylated. The SeqA protein binds hemimethylated oriC in vitro. In vivo, the absence of SeqA causes overinitiation and strongly reduces the duration of hemimethylation. The pattern of immunostained SeqA complexes in vivo suggests that SeqA has a role in organizing hemimethylated DNA at the replication forks. We have examined the effects of overexpressing SeqA under different cellular conditions. Our data demonstrate that excess SeqA significantly increases the time oriC is hemimethylated following initiation of replication. In some cells, sequestration continued for more than one generation and resulted in inhibition of primary initiation. SeqA overproduction also interfered with the segregation of sister nucleoids and caused a delay in cell division. These results suggest that SeqA's function in regulation of replication initiation is linked to chromosome segregation and possibly cell division.

The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication

The initiation of replication is the central event in the bacterial cell cycle. Cells control the rate of DNA synthesis by modulating the frequency with which new chains are initiated, like all macromolecular synthesis. The end of the replication cycle provides a checkpoint that must be executed for cell division to occur. This review summarizes recent insight into the biochemistry, genetics and control of the initiation of replication in bacteria, and the central role of the initiator protein DnaA.

Limiting DNA replication to once and only once

In Escherichia coli cells, the origin of chromosomal replication is temporarily inactivated after initiation has occurred. Origin sequestration is the first line of defence against over-initiation, providing a time window during which the initiation potential can be reduced by: (i) titration of DnaA proteins to newly replicated chromosomal elements; (ii) regulation of the activity of the DnaA initiator protein; and (iii) sequestration of the dnaA gene promoter. This review represents the first attempt to consider together older and more recent data on such inactivation mechanisms in order to analyze their contributions to the overall tight replication control observed in vivo. All cells have developed mechanisms for origin inactivation, but those of other bacteria and eukaryotic cells are clearly distinct from those of E. coli. Possible differences and similarities are discussed.

The eclipse period of Escherichia coli

The minimal time between successive initiations on the same origin (the eclipse) in Escherichia coli was determined to be approximately 25-30 min. An inverse relationship was found between the length of the eclipse and the amount of Dam methyltransferase in the cell, indicating that the eclipse corresponds to the period of origin hemimethylation. The SeqA protein was absolutely required for the eclipse, and DnaA titration studies suggested that the SeqA protein prevented the binding of multiple DnaA molecules on oriC (initial complex formation). No correlation between the amount of SeqA and eclipse length was revealed, but increased SeqA levels affected chromosome partitioning and/or cell division. This was corroborated further by an aberrant nucleoid distribution in SeqA-deficient cells. We suggest that the SeqA protein's role in maintaining the eclipse is tied to a function in chromosome organization.

The Escherichia coli SeqA protein binds specifically and co-operatively to two sites in hemimethylated and fully methylated oriC

The Escherichia coli SeqA protein has been found to affect initiation of replication negatively, both in vivo and in vitro. The mechanism of inhibition is, however, not known. SeqA has been suggested to affect the formation and activity of the initiation complex at oriC, either by binding to DNA or by interacting with the DnaA protein. We have investigated the binding of SeqA to oriC by electron microscopy and found that SeqA binds specifically to two sites in oriC, one on each side of the DnaA binding site R1. Specific binding was found for fully and hemimethylated but not unmethylated oriC in good agreement with earlier mobility shift studies. The affinity of SeqA for hemi-methylated oriC was higher than for fully methylated oriC. The binding was in both cases strongly cooperative. We suggest that SeqA binds to two nucleation sites in oriC, and by the aid of protein-protein interaction spreads to adjacent regions in the same oriC as well as recruiting additional oriC molecules and/or complexes into larger aggregates.

Evidence of two levels of control of P1 oriR and host oriC replication origins by DNA adenine methylation

A mutant mini-P1 plasmid with increased copy number can be established in Dam- strains of Escherichia coli, where mini-P1 plasmid replication is normally blocked. Comparison of this plasmid and a plasmid driven by the host oriC replication origin showed that both origins are subject to control by methylation at two different levels. First, both origins appear to be subject to negative regulation acting at the level of hemimethylation. This probably involves the sequestration of the hemimethylated DNA produced by replication, as has been previously described for oriC. Second, both origins show a positive requirement for adenine methylation for efficient function in vivo. This conclusion is supported by the behavior of the P1 origin in an improved in vitro replication system. In vitro, where sequestration of hemimethylated DNA is not expected to occur, the hemimethylated P1 origin DNA was fully functional as a template. However, the activity of fully unmethylated DNA was severely restricted in comparison with that of either of the methylated forms. This in vitro uncoupling of the two effects of origin methylation suggests that two separate mechanisms are involved.

Chromosome partition in Escherichia coli

The past year has seen important genetic and biochemical advances in our understanding of the mechanisms that are involved in chromosome partition into two daughter cells in Escherichia coli. Topoisomerase IV and XerCD recombinase have been shown to be required for the unlinking of replicated chromosomes. MukB, an alpha-helical coiled-coil protein, has been shown to be involved in chromosome partition, and this is the first candidate for a bacterial motor protein. Another protein, FtsZ, has been shown to form a constriction ring in cell division and may also relate to chromosome partition.

Participation of the bacterial membrane in DNA replication and chromosome partition

The concept that the bacterial membrane plays an active role in the regulation of DNA replication and in segregation, or 'partition', of the bacterial chromosome at cell division was proposed in 1963. Membrane participation offered a relatively simple way to coordinate replication and partition. Some of the details of this model have been confirmed, while others have been changed. In fact, it appears that the membrane may play several distinct roles in these processes, and recent experiments have begun to identify the complexity of membrane involvement.

Presence of methylated adenine in GATC sequences in chromosomal DNAs from Campylobacter species

We digested chromosomal DNAs from 12 Campylobacter strains (C. jejuni, 4 strains; C. coli, 2 strains; C. fetus subsp. fetus, 2 strains; C. hyointestinalis, 2 strains; and C. upsaliensis, 2 strains) and from 4 Helicobacter strains (H. pylori, 2 strains; and H. mustelae, 2 strains) with HindIII, SstI, BamHI, DpnI, MboI, and Sau3AI. Restriction fragments were then separated by electrophoresis in 1% agarose or 10% polyacrylamide gels. Only DNAs from three Campylobacter species (C. jejuni, C. coli, and C. upsaliensis) were digested with DpnI (an enzyme that recognizes only methylated adenine in GATC sequences). We used MboI and Sau3AI to confirm these findings.

Escherichia coli cells lacking methylation-blocking factor (leucine-responsive regulatory protein) have precise timing of initiation of DNA replication in the cell cycle

A protein that is required for specific methylation inhibition of two GATC sites in the papBA pilin promoter region, known as methylation-blocking factor (Mbf) and recently shown to be identical to the leucine-responsive regulatory protein (Lrp), is not responsible for the delayed methylation at oriC implicated in an eclipse period following initiation of DNA replication. Cells containing a transposon mutation within the mbf (lrp) gene initiate DNA replication at the correct time during the cell cycle, whereas cells with increased amounts of the Dam methyltransferase initiate DNA replication randomly throughout the cell cycle.

DNA replication, the bacterial cell cycle, and cell growth

The coupling of replication to the cell cycle and cell growth involves events that occur at oriC. Immediately after initiation, there is an eclipse phase during which reinitiation from the newly synthesized origins is prevented. GATC sites in oriC remain in a hemimethylated state longer than other sites because of their association with the outer membrane, which prevents DnaA from binding and activating additional rounds of initiation. After the origins are methylated and released from the outer membrane, the concentration of newly synthesized DnaA and the activation of oriC by transcription from the nearby mioC and gid promoters determine when the next rounds of replication initiate. If growth rate is reduced, the synthesis of (p)ppGpp will increase, and this will lead to a decrease in dnaA, mioC, and gid transcription. On the other hand, if growth rate is increased by access to a tasty meal, synthesis of (p)ppGpp will decrease, expression of dnaA, mioC, and gid genes will increase, and a shortening of the interinitiation time will result. The participation of all these control features ensures rapid and precise coordination of DNA replication with cell growth.

A turnstile for initiation of DNA replication

The progress of a cell through its growth cycle is a multifaceted process; so far we have seen only a glimpse of the complex interplay between the macromolecules performing and regulating the different steps involved. In most organisms, control mechanisms ensure that all chromosomal DNA sequences are replicated once, and only once, between two cell divisions. This enables each division to produce two daughter cells with a genetic content identical to that of their mother. Although the biochemical synthetic processes involved in replicating DNA have been described in detail, our knowledge of the regulatory mechanisms of DNA replication remains scant. In recent experiments with Escherichia coli, new light has been shed on these elusive control mechanisms, and evidence has emerged that may signal an end to our ignorance about this important biological problem.