Genetic diversity in a species is maintained through both mutation and recombination. Mutation alters single genes or small groups of genes in an individual, whereas recombination redistributes the contents of a genome among various individuals during reproduction. In classical biology, recombination is the outcome of crossing over between paired sister chromosomes during meiosis in eukaryotes. Strictly speaking, recombination is any process that creates end-to-end joining from two different DNA molecules. Thus, the daughter-strand gap repair process (see here) is a form of recombination.

Meiotic recombination in diploid organisms requires extensive sequence homology between the recombining partners and is called homologous recombination. This term also describes certain recombinational events between bacterial chromosomes. Most bacterial homologous recombination processes share a common requirement for the RecA protein or its counterpart.

New DNA can be introduced into a bacterial cell by the following processes:

1. Conjugation during bacterial mating;

2. Transformation, when DNA is taken up by cells; and

3. Transduction, when bacterial DNA that was accidentally packaged into a phage particle is introduced by infection.

Site-specific recombination, by contrast, involves only limited sequence homology between recombining partners. Sites of breaking and joining are determined by specific DNA--protein interactions. Integration of bacteriophage into the host bacterial chromosome occurs by a site-specific recombination mechanism (Figure 25.17). The RecA protein of E. coli is not required for this process. Rather, the virus makes a site-specific enzyme, called integrase, and specific DNA - protein interactions between the enzyme and the recombining partners (rather than extensive DNA - DNA sequence homology) determine the site of recombination.

Two other forms of recombination are the following:

1. Transposition, which involves neither sequence homology nor the RecA protein, but does require a special sequence on the donor DNA.

2. Illegitimate recombination, an extremely rare event that may occur by chance, involves neither sequence homology nor the action of any known protein. Table 25.3 summarizes the main distinctions among the four major types of recombination.