11.0: Introduction

In which we consider how prokaryotes replicate asexually and how they can (under specific conditions) pass genetic information to one another and acquire such information from their environment.

The simplest types of biological (cellular as opposed to viral) reproduction are probably the asexual processes found in prokaryotes.^[402] In bacteria and archaea, the genome consists of a single large circular double-stranded DNA molecule, the bacterial chromosome. In some cases, the cell also contains smaller circular DNA molecules, known as plasmids. For the moment we will ignore plasmids and focus on the chromosome, although the replication processes are similar.^[403] The chromosome contains two important DNA sequence elements, the origin of replication (ORI) and the terminator region (TER). When conditions are appropriate, a cell will pass through a decision point, a molecular switch, known as "start" (→). This switch activates proteins that bind to the ORI region of the chromosome, initiating the assembly of the DNA replication complex. A replication bubble (a region of the DNA in which the two DNA strands have separated) forms, and replication forks begin to move in both directions around the molecule, making a copy. As the ORI sequence is replicated, the two ORI sites remain associated with the plasma membrane. The replication forks (↓) move around the DNA molecule, and collide in the TER region.The collision of the DNA replication forks generates a signal that indicates that DNA replication is complete. During this period the cell is growing, adding mass and volume. The division of one cell into two is mediated by the formation of a septum, an extension of the plasma membrane and the cell wall. Septum growth initiates between the two membrane-bound ORI sequences that ensures that each daughter cell receives one complete chromosome, one total genome.

In the chromosome the order of genes around the circular molecule is generally conserved between organisms of the same species. The genes along the chromosome constitute a syntenic linkage group, the same genes in the same order along a chromosome (discussed further below). In the standard asexual mode of replication, all of the alleles are inherited together, the result is that a mutation in any particular gene (generating a new allele) acts in concert with the other alleles (in the other genes) present. Over time, each organism produces a clone, and various clones interact with the environment and each other. Clones can display different levels of reproductive success; some clones can take over the population, while others may become extinct. In the case of studies on the evolution of bacterial antibiotic resistance (see below), each clone has to develop antibiotic resistance independently of every other clone; a similar situation was observed in long term bacterial evolution studies.^[404] There is no cross talk between lineages in such situations. Of course, if DNA is passed from clone to clone, as occurs within Griffith’s (previously considered) transformation experiments, things get more complex. The movement of genes between lineages is known as horizontal gene transfer. We consider the three versions of horizontal gene transfer found in prokaryotes.

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