In the 1960s and 1970s, we began to learn about specialized recombination processes independent of genetic homology: chiefly, virus insertion and excision by site-specific recombination and transposition (Bukhari 1977). These were different from the familiar homology-dependent recombination used to establish genetic maps. Because they were new, there was a tendency to name homology-independent processes "illegitimate recombination," implying they were very specialized and not of general importance. Today, of course, we know that the movement of mobile genetic elements by "illegitimate recombination" is ubiquitous and of major evolutionary importance.
We have also learned that cells can use "legitimate" recombination in many different ways. It begins with a double-strand (DS) break in one of two homologous DNA molecules. When such breaks occur accidentally, they trigger homologous recombination for DNA repair.
In many situations, cells need recombination when no accidents have occurred. They possess special enzymes, endonucleases, that make DS breaks to initiate the process. For example, homologous recombination holds chromosome pairs together in meiosis. My University of Chicago colleague, Rochelle Esposito, and her students discovered that there is a special endonuclease, Spo11, that makes the essential DS breaks. Without Spo11, yeast and other organisms cannot carry out a normal meiotic process to produce haploid spores or gametes.
Spo11, like all endonucleases, cleaves preferred sequences. So there is a non-random pattern to the sites where homologous recombination occurs preferentially ("hotspots") in yeasts, plants, and animals.
A very recent paper illustrates another kind of hotspot control. Mouse cells have a special chromatin-binding protein that alters recombination hotspots: it binds to highly evolved genome expression signals in mouse DNA and protects them from disruption by homologous recombination. Without the protective binding protein, they become recombination hotspots.
The ability to target homologous recombination by DS breaks has also been utilized by different kinds of cells as a means of altering the proteins they express. In this way, some cells use "legitimate" recombination in the way other cells use "illegitimate" recombination. The first example of this specialized use of homologous recombination was in yeast sex change operations.
When yeast cells undergo meiosis, they produce four haploid spores. Haploids have one copy of each chromosome, not two. Spores can reproduce as haploid cells but are more sensitive to DNA damage. Diploid cells with two copies of every chromosome are less sensitive because damage to one copy can be repaired by recombination using the second copy. Thus, yeasts benefit by propagating as diploids, and most yeast in nature are diploid.
Haploid yeasts become diploids by fusing with cells of opposite sex, or "mating type." Sometimes this occurs between adjacent spores of opposite mating type following meiosis. But if one spore becomes isolated, it only has single mating type. How can it become diploid? The answer is to undergo a sex-change operation or "mating-type switching." The switch produces haploid cells of the opposite mating type so that fusion and diploid formation can proceed among the descendants of a single haploid spore.
In both budding yeast and fission yeast, sex change occurs when copies of epigenetically silent mating type information replace expressed mating type information. The substitution occurs by a directional form of homologous recombination called "gene conversion," where information at one site is copied into another homologous site. Although the sequences for the two mating types must be different, the silent region and the expressed region to be replaced are located within homologous cassettes, which allow gene conversion to proceed.
The sex change operation is initiated by a DS break at a special site in the expressed cassette. This break and other recombination control functions target the gene conversion event so mating type changes with high probability. Interestingly, the DS break mechanisms in budding yeast and fission yeast are different. Budding yeast use a typical endonuclease called HO or SceI. But fission yeast use a modified transposase protein, normally associated with the "illegitimate" process of transposition. Thus, we know that this purposeful specialization of "legitimate" recombination has undergone at least two completely independent parallel evolutionary steps.
A somewhat different use of gene conversion between silent and expressed cassettes takes place in numerous disease microbes (pathogens), both bacteria and eukaryotes. These pathogens use gene conversion to alter the structure of their surface proteins to avoid recognition by the host immune system ("antigenic variation").
In the best-studied cases, the bacterial Lyme disease spirochaete Borrelia, and the sleeping sickness protist Trypanosoma brucei, the genome sequence evidence for cassette recombination is strong, but the process is not as well understood as the yeast mating-type switches. The reason is that rather than two silent and one expressed cassette, as in the yeasts, these pathogens use dozens or hundreds of cassettes to keep ahead of the immune system.
"Legitimate recombination" was assumed to be reasonably uniform in the early days of genetics. That was the basis of constructing genetic maps. We now know homologous recombination can be used "illegitimately" (i.e. targeted either positively or negatively). I think the molecular studies are remarkable in uncovering a striking variety of ways cells have adapted homologous recombination for diverse purposes. As the recent mouse paper shows, we have only begun to scratch the surface of what promises to be a rich vein of cellular inventiveness.
Bukhari, A. I., J.A. Shapiro, and S. L. Adhya (Eds.) (1977). DNA insertion elements, plasmids and episomes Cold Spring Harbor, New York, Cold Spring Harbor Press.