Genes VII

The entire chromosome is replicated once for every cell division cycle. Initiation of replication commits the cell to a cycle of division; completion of replication may provide a trigger for the actual division process. The bacterial chromosome consists of a single replicon, but a eukaryotic chromosome is divided into many replicons that function over the protracted period of S phase. The problem of replicating the ends of a linear replicon is solved in a variety of ways, most often by converting the replicon to a circular form. Some viruses have special proteins that recognize ends. Eukaryotic chromosomes encounter the problem at their terminal replicons.

Eukaryotic replication is (at least) an order of magnitude slower than bacterial replication. Origins sponsor bidirectional replication, and are probably used in a fixed order during S phase. The only eukaryotic origins identified at the sequence level are those of S. cerevisiae, which have a core consensus sequence consisting of 11 base pairs, mostly A PT.

The minimal E. coli origin consists of ~245 bp and initiates bidirectional replication. Any DNA molecule with this sequence can replicate in E. coli. Two replication forks leave the origin and move around the chromosome, apparently until they meet, although ter sequences that would cause the forks to terminate after meeting have been identified. Transcription units are organized so that transcription usually proceeds in the same direction as replication.

The rolling circle is an alternative form of replication for circular DNA molecules in which an origin is nicked to provide a priming end. One strand of DNA is synthesized from this end, displacing the original partner strand, which is extruded as a tail. Multiple genomes can be produced by continuing revolutions of the circle.

Rolling circles are used to replicate some phages. The A protein that nicks the φX174 origin has the unusual property of cis-action. It acts only on the DNA from which it was synthesized. It remains attached to the displaced strand until an entire strand has been synthesized, and then nicks the origin again, releasing the displaced strand and starting another cycle of replication.

Rolling circles also are involved in bacterial conjugation, when an F plasmid is transferred from a donor to a recipient cell, following the initiation of contact between the cells by means of the F-pili. A free F plasmid infects new cells by this means; an integrated F factor creates an Hfr strain that may transfer chromosomal DNA. In the case of conjugation, replication is used to synthesize complements to the single strand remaining in the donor and to the single strand transferred to the recipient, but does not provide the motive power.

A fixed time of 40 minutes is required to replicate the E. coli chromosome and a further 20 minutes is required before the cell can divide. When cells divide more rapidly than every 60 minutes, a replication cycle is initiated before the end of the preceding division cycle. This generates multiforked chromosomes. The initiation event depends on titration of cell mass, probably by accumulating an initiator protein. Initiation may occur at the cell membrane, since the origin is associated with the membrane for a short period after initiation.

Segregation involves additional sequences that have not yet been characterized. Most mutations that prevent proper segregation lie in ancillary functions, such as the enzymes needed for the two daughter chromosomes to disentangle. One mutation that directly affects segregation may identify a motor or a protein that connects the chromosome to the envelope. The septum that divides the cell grows at a location defined by the pre-existing periseptal annulus; a locus of three genes codes for products that regulate whether the midcell periseptal annulus or the polar sites derived from previous annuli are used for septum formation. Absence of septum formation generates multinucleated filaments; excess of septum formation generates anucleate minicells. Some bacteria have systems related to those involved in plasmid partition, in which a pair of proteins binds to a DNA sequence near the origin and causes the origin to be localized to the poles.

Plasmids have a variety of systems that ensure or assist partition, and an individual plasmid may carry systems of several types. The copy number of a plasmid describes whether it is present at the same level as the bacterial chromosome (one per unit cell) or in greater numbers. Plasmid incompatibility can be a consequence of the mechanisms involved in either replication or partition (for single-copy plasmids). Two plasmids that share the same control system for replication are incompatible because the number of replication events ensures that there is only one plasmid for each bacterial genome.