1. Introduction

12.1 Introduction

Key terms defined in this section

Replicon is a unit of the genome in which DNA is replicated; contains an origin for initiation of replication.

Whether a cell has only one chromosome (as in prokaryotes) or has many chromosomes (as in eukaryotes), the entire genome must be replicated precisely once for every cell division. How is the act of replication linked to the cell cycle?

Two general principles are used to compare the state of replication with the condition of the cell cycle:

• Initiation of DNA replication commits the cell (prokaryotic or eukaryotic) to a further division. From this standpoint, the number of descendants that a cell generates is determined by a series of decisions on whether or not to initiate DNA replication. Replication is controlled at the stage of initiation. Once replication has started, it continues until the entire genome has been duplicated.
  
• If replication proceeds, the consequent division cannot be permitted to occur until the replication event has been completed. Indeed, the completion of replication may provide a trigger for cell division. Then the duplicate genomes are segregated one to each daughter cell. The unit of segregation is the chromosome.

In prokaryotes, the initiation of replication is a single event involving a unique site on the bacterial chromosome, and the process of division is accomplished by the development of a septum. In eukaryotic cells, initiation of replication is identified by the start of S phase, a protracted period during which DNA synthesis occurs, and which involves many individual initiation events. The act of division is accomplished by the reorganization of the cell at mitosis. In this chapter, we are concerned with the regulation of DNA replication. How is a cycle of replication initiated? What controls its progress and how is its termination signaled? In 27 Cell cycle and growth regulation, we discuss the regulatory processes in eukaryotic cells that control entry into S phase and into mitosis, and also the "checkpoints" that postpone these actions until the appropriate conditions have been fulfilled.

The unit of DNA in which an individual act of replication occurs is called the replicon. Each replicon "fires" once and only once in each cell cycle. The replicon is defined by its possession of the control elements needed for replication. It has an origin at which replication is initiated. It may also have a terminus at which replication stops (Jacob et al., 1963).

Any sequence attached to an origin Xor, more precisely, not separated from an origin by a terminus Xis replicated as part of that replicon. The origin is a cis-acting site, able to affect only that molecule of DNA on which it resides.

(The original formulation of the replicon [in prokaryotes] viewed it as a unit possessing both the origin and the gene coding for the regulator protein. Now, however, "replicon" is usually applied to eukaryotic chromosomes to describe a unit of replication that contains an origin; trans-acting regulator protein(s) may be coded elsewhere.)

A genome in a prokaryotic cell constitutes a single replicon; so the units of replication and segregation coincide. The largest such replicon is the bacterial chromosome itself. Initiation at a single origin sponsors replication of the entire genome, once for every cell division. Each haploid bacterium has a single chromosome, so this type of replication control is called single copy.

Figure 11.2 Several types of independent genetic units exist in bacteria.

Bacteria may contain additional genetic information in the form of plasmids. A plasmid is an autonomous circular DNA genome that constitutes a separate replicon (see Figure 11.2). A plasmid replicon may show single-copy control, and replicate with the bacterial genome pari passu. Or it may be under multicopy control, when it is present in a greater number of copies than the bacterial chromosome. Each phage or virus DNA also constitutes a replicon, able to initiate many times during an infectious cycle. Perhaps a better way to view the prokaryotic replicon, therefore, is to reverse the definition: any DNA molecule that contains an origin can be replicated autonomously in the cell.

A major difference in the organization of bacterial and eukaryotic genomes is seen in their replication. Each eukaryotic chromosome contains a large number of replicons. So the unit of segregation includes many units of replication. This adds another dimension to the problem of control. All the replicons on a chromosome must be fired during one cell cycle, although they are not active simultaneously, but are activated over a fairly protracted period. Yet each of these replicons must be activated no more than once in each cell cycle.

Some signal must distinguish replicated from nonreplicated replicons, so that replicons do not fire a second time. And because many replicons are activated independently, another signal must exist to indicate when the entire process of replicating all replicons has been completed.

We have begun to collect information about the construction of individual replicons, but we still have little information about the relationship between replicons. We do not know whether the pattern of replication is the same in every cell cycle. Are all origins always used or are some origins sometimes silent? Do origins always fire in the same order? If there are different classes of origins, what distinguishes them?

In contrast with nuclear chromosomes, which have a single-copy type of control, the DNA of mitochondria and chloroplasts may be regulated more like plasmids that exist in multiple copies per bacterium. There are multiple copies of each organelle DNA per cell, and the control of organelle DNA replication must be related to the cell cycle.

In all these systems, the key question is to define the sequences that function as origins and to determine how they are recognized by the appropriate proteins of the apparatus for replication. We start by considering the basic construction of replicons and the various forms that they take; following the consideration of the origin, we turn to the question of how replication of the genome is coordinated with bacterial division, and what is responsible for segregating the genomes to daughter bacteria.

Research

Jacob, F., Brenner, S., and Cuzin, F. (1963). On the regulation of DNA replication in bacteria. Cold Spring Harbor Symp. Quant. Biol. 28, 329-348.