Genes VII

Without genetic recombination, the content of each individual chromosome would be irretrievably fixed in its particular alleles, changeable only by mutation. The length of the target for mutation damage would be increased from the gene to the chromosome. Deleterious mutations would accumulate, eliminating each chromosome (and thereby removing any favorable mutations that have occurred).

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, and a means to eliminate an unfavorable allele without bringing down all the other genes with which this allele is associated.

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 share the feature that the process involves physical exchange of material between duplex DNAs, but differ in the circumstances:

• Recombination involving 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). We recall that it happens at the "four strand" stage of meiosis, and involves only two of the four strands (see 1 Genes are DNA).
• Another type of event sponsors recombination between specific pairs of sequences, and has been best characterized in prokaryotes. 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 bacterial DNA, which include a short stretch of homology. The enzymes involved in this event act only on the particular pair of target sequences. Related reactions are responsible for inverting specific regions of the bacterial chromosome.
• A different type of event allows one DNA sequence to be inserted into another without reliance on sequence homology. Transposition provides a means by which certain elements move from one chromosomal location to another. The mechanisms involved in transposition depend upon breakage and reunion of DNA strands, and thus are related to the processes of recombination. Transposition is the subject of Chapters 15 V16.
• Another type of recombination is used by RNA viruses, in which the polymerase switches from one template to another while it is synthesizing RNA. As a result, the newly synthesized molecule joins sequence information from two different parents. This type of mechanism for recombination is called copy choice, and is discussed briefly in 16 Retroviruses and retroposons. It is not used for recombination between duplex DNA substrates.

Homologous recombination is a reaction between two duplexes of DNA. Its critical feature is that the enzymes responsible can use any pair of homologous sequences as substrates (although some types of sequences may be favored over others). The frequency of recombination is not constant throughout the genome, but is influenced by both global and local effects. The overall frequency may be different in oocytes and in sperm; recombination occurs twice as frequently in female as in male humans. And within the genome its frequency depends upon chromosome structure; for example, crossing-over is suppressed in the vicinity of the condensed and inactive regions of heterochromatin.

Figure 14.1 compares the visible progress of chromosomes through meiosis with the molecular interactions that are involved in exchanging material between duplexes of DNA. Meiosis starts with a protracted prophase whose 5 stages are summarized in the figure.

The beginning of meiosis is marked by the point at which individual chromosomes become visible. Each of these chromosomes has replicated previously, and consists of two sister chromatids, each of which contains a duplex DNA. The homologous chromosomes approach one another and begin to pair in one or more regions, forming bivalents. Pairing extends until the entire length of each chromosome is apposed with its homolog. The process is called synapsis or chromosome pairing. When the process is completed, the chromosomes are laterally associated in the form of a synaptonemal complex, which has a characteristic structure in each species, although there is wide variation in the details between species.

Recombination between chromosomes involves a physical exchange of parts, usually represented as a breakage and reunion, in which two nonsister chromatids (each containing a duplex of DNA) have been broken and then linked each with the other. When the chromosomes begin to separate, they can be seen to be held together at discrete sites, the chiasmata. The number and distribution of chiasmata parallel the features of genetic crossing-over. Traditional analysis holds that a chiasma represents the crossing-over event (see Figure 1.22). The chiasmata remain visible when the chromosomes condense and all four chromatids become evident.

What is the molecular basis for these events? Each sister chromatid contains a single DNA duplex, so each bivalent contains 4 duplex molecules of DNA. Recombination requires a mechanism that allows the duplex DNA of one sister chromatid to interact with the duplex DNA of a sister chromatid from the other chromosome. It must be possible for this reaction to occur between any pair of corresponding sequences in the two molecules in a highly specific manner that allows material to be exchanged with precision at the level of the individual base pair.

We know of only one mechanism for nucleic acids to recognize one another on the basis of sequence: complementarity between single strands. The figure shows a general model for the involvement of single strands in recombination. The first step in providing single strands is to make a break in each DNA duplex. Then one or both of the strands of that duplex can be released. If (at least) one strand displaces the corresponding strand in the other duplex, the two duplex molecules will be specifically connected at corresponding sequences. If the strand exchange is extended, there can be more extensive connection between the duplex. And by exchanging both strands and later cutting them, it is possible to connect the parental duplex molecules by means of a crossover that corresponds to the demands of a breakage and reunion.

We cannot at this juncture relate these molecular events rigorously with the changes that are observed at the level of the chromosomes. There is no detailed information about the molecular events involved in recombination in higher eukaryotic cells (in which meiosis has been most closely observed). However, recently the isolation of mutants in yeast has made it possible to correlate some of the molecular steps with approximate stages of meiosis. Detailed information about the recombination process is available in bacteria, in which molecular activities are known that cause genetic exchange between duplex molecules. However, the bacterial reaction involves interaction between restricted regions of the genome, rather than an entire pairing of genomes. The synapsis of eukaryotic chromosomes remains the most difficult stage to explain at the molecular level.