Introduction to The Extrachromosomal Replicons

A bacterium can be a host for independently replicating genetic units in addition to its chromosome. These extrachromosomal genomes fall into two general types: plasmids and bacteriophages (phages). Some plasmids, and all phages, have the ability to transfer from a donor bacterium to a recipient by an infective process. An important distinction between them is that plasmids exist only as free DNA genomes, whereas bacteriophages are viruses that package a nucleic acid genome into a protein coat and are released from the bacterium at the end of an infective cycle.
Plasmids are self-replicating circular molecules of DNA that are maintained in the cell in a stable and characteristic number of copies; that is, the average number remains constant from generation to generation. Low-copy number plasmids are maintained at a constant quantity relative to the bacterial host chromosome, often between 1 and 10 per bacterium, depending on the plasmid. As with the host chromosome, they rely on a specific apparatus to be segregated equally at each bacterial division.

Multicopy plasmids exist in many copies per unit bacterium and can be segregated to daughter bacteria stochastically (meaning that there are enough copies to ensure that each daughter cell always gains some by a random distribution).
Plasmids and phages are defined by their ability to reside in a bacterium as independent genetic units. Certain plasmids, and some phages, can also exist as sequences integrated within the bacterial genome, though. In this case, the same sequence thatconstitutes the independent plasmid or phage genome is inherited like any other bacterial gene. Phages that are found as part of the bacterial chromosome are said to show lysogeny; plasmids that also have the ability to integrate into the chromosome are called episomes. All episomes are plasmids, but not all plasmids are episomes. Related processes are used by phages and episomes to insert into and excise from the bacterial chromosome.
A parallel between lysogenic phages and plasmids and episomes is that they maintain a selfish possession of their bacterium and often make it impossible for another element of the same type to become established. This effect is called immunity, although the molecular basis for plasmid immunity is different from lysogenic immunity, and is a consequence of the replication control system.

Several types of genetic units can be propagated in bacteria as independent genomes. Lytic phages can have genomes of any type of nucleic acid; they transfer between cells by release of infective particles. Lysogenic phages have double-stranded DNA genomes, as do plasmids and episomes. Some plasmids transfer between cells by a conjugative process (with direct contact between donor and recipient cells). A feature of the transfer process in both cases is that on occasion some bacterial host genes are transferred with the phage or plasmid DNA, so these events play a role in allowing exchange of genetic information between bacteria.
The key feature in determining the behavior of each type of unit is how its origin is used. An origin in a bacterial or eukaryotic chromosome is used to initiate a single replication event that
extends across the replicon. Replicons, however, can also be used to sponsor other forms of replication. The most common alternative is used by the small, independently replicating units of viruses. The objective of a viral replication cycle is to produce many copies of the viral genome before the host cell is lysed to release them.
Some viruses replicate in the same way as a host genome, with an initiation event leading to production of duplicate copies, each of which then replicates again, and so on. Others use a mode of replication in which many copies are produced as a tandem array following a single initiation event. A similar type of event is triggered by episomes when an integrated plasmid DNA ceases to be inert and initiates a replication cycle.
Many prokaryotic replicons are circular, and this indeed is a necessary feature for replication modes that produce multiple tandem copies. Some extrachromosomal replicons are linear, though, and in such cases researchers need to account for the ability to replicate the end of the replicon. (Of course, eukaryotic chromosomes are linear, so the same problem applies to the replicons at each end. These replicons, however, have a special system for resolving the problem.)