Introduction to the Homologous and Site-Specific Recombination

Homologous recombination is an essential cellular process required for generating genetic diversity, ensuring proper chromosome segregation, and repairing certain types of DNA damage. Evolution could not happen efficiently without genetic recombination. If material could not be exchanged between homologous chromosomes, the content of each individual chromosome would be irretrievably fixed in its particular alleles, only changing in the event of a mutation. In the event of a mutation, it would then not be possible to separate favorable from unfavorable changes. The length of the target for mutation damage would effectively be increased from the gene to the chromosome. Ultimately, a chromosome would accumulate so many deleterious mutations that it would fail to function.
By shuffling the genes, recombination allows favorable and unfavorable mutations to be separated and tested as individual units in new assortments. It provides a means of escape and spreading for favorable alleles, as well as a means to eliminate an unfavorable allele without bringing down all the other genes with which this allele is associated. This is the basis for natural selection.
In addition to its role in genetic diversity, homologous recombination is also required in mitosis for repair of lesions at replication forks and for restarting replication that has stalled at these lesions. The importance of mitotic recombination events is highlighted by examples of human diseases that result from defects in recombination repair of DNA damage where altered activity of homologous recombination proteins is seen in some types of cancers. Homologous recombination is also essential for a process known as antigenic switching, which allows disease-causing parasites called trypanosomes to evade the human immune system.
Recombination occurs between precisely corresponding sequences so that not a single base pair is added to or lost from the recombinant chromosomes. Three types of recombination involve the physical exchange of material between duplex DNAs:
- Recombination involving a reaction between homologous sequences of DNA is called generalized or homologous recombination. In eukaryotes, it occurs at meiosis, usually both in males (during spermatogenesis) and females (during oogenesis). Recombination happens at the “four-strand” stage of meiosis and involves only two nonsister strands of the four strands (see the chapter titled Genes Are DNA and Encode RNAs and Polypeptides).
- Another type of event sponsors recombination between specific pairs of sequences. This was first characterized in prokaryotes where specialized recombination, also known as site-specific recombination, is responsible for the integration of phage genomes into the bacterial chromosome. The recombination event involves specific sequences of the phage DNA and the bacterial DNA, which include a short stretch of homology. The enzymes involved in this event act in an intermolecular reaction only on the particular pair of target sequences. Some related intramolecular reactions are responsible during bacterial division for regenerating two monomeric circular chromosomes when a dimer has been generated by generalized recombination. This latter class also includes recombination events that invert specific regions of the bacterial chromosome.
- In special circumstances, gene rearrangement is used to control expression. Rearrangement may create new genes, which are needed for expression in particular circumstances, as in the case of the immunoglobulins. This is an example of somatic recombination, which is discussed in the chapter titled Somatic Recombination and Hypermutation in the Immune System.Recombination events also may be responsible for switching expression from one preexisting gene to another, as in the example of yeast mating type, where the sequence at an active locus can be replaced by a sequence from a silent locus.
Rearrangements are also required to control expression of surface antigens in trypanosomes, in which silent alleles of surface antigen genes are duplicated into active expression sites. Some of these types of rearrangement share mechanistic similarities with transposition; in fact, they can be viewed as specially directed cases of transposition.
Let us consider the nature and consequences of the generalized and specialized recombination reactions. FIGURE .1 demonstrates that generalized recombination occurs between two homologous DNA duplexes and can occur at any point along their length. The crossover is the point at which each becomes joined to the other. The overall organization of the DNA does not change; the products have the same structure as the parents, and both parents and products are homologous.

FIGURE .1 No crossing over between the (a) and (b) genes gives rise to only nonrecombinant gametes. Crossing over between the A and B genes gives rise to the recombinant gametes Ab and aB and the nonrecombinant gametes AB and ab.
Specialized recombination occurs only between specific sites. The results depend on the locations of the two recombining sites. FIGURE .2 shows that an intermolecular recombination between a circular DNA and a linear DNA results in the insertion of the circular DNA into the linear DNA. Specialized recombination is often used to make changes such as this in the organization of DNA. The change in organization is a consequence of the locations of the recombining sites. We have a large amount of information about the enzymes that undertake specialized recombination, which are related to the topoisomerases that act to change the supercoiling of DNA in space .

FIGURE .2 Site-specific recombination occurs between the circular and linear DNAs at the boxed region (a). Integration results in an insertion of the A and B sequences between the X and Y sequences (b). The reaction is promoted by integrase enzymes. Reversal of the reaction results in a precise excision of the A and B sequences.
Data from B. Alberts, et al. Molecular Biology of the Cell, Fourth edition. Garland Science,
2002.