The genetic recombination it is the process by which nucleic acid molecules exchange fragments, generating a new molecule. It is very common in DNA, but RNA is also a substrate for recombination. Recombination is, after mutation, the most important source of generation of genetic variability.
DNA participates in different biochemical processes. During replication, it serves as a template for the generation of two new DNA molecules. In transcription, it allows the generation of RNA molecules from specific regions controlled by a promoter.
But in addition to that, DNA is also capable of exchanging fragments. Through this process it generates new combinations that are not the product of the two previous processes, nor of fertilization..
All recombination process involves breaking and joining of the DNA molecules that participate in the process. This mechanism varies depending on the recombination substrate, the enzymes that participate in the process, and the mechanism of its execution..
Recombination generally depends on the existence of complementary, similar (if not identical), or homologous regions between the recombining molecules. In the case that molecules recombine in processes not guided by homology, the recombination is said to be non-homologous.
If the homology involves a very short region present in both molecules, the recombination is said to be site-specific..
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What we call homology in recombination does not necessarily refer to the evolutionary origin of the participating molecules. We are talking more about the degree of similarity in the nucleotide sequence.
Non-reparative recombination, for example, occurs in eukaryotes during the meiosis process. Undoubtedly, there can be no greater homology than between pairs of chromosomes in the same cell.
That is why they are called homologous chromosomes. However, there are cases in which the DNA of a cell exchanges material with a foreign DNA. These DNAs must be very similar to recombine, but they do not necessarily have to share the same ancestor (homology) to achieve this..
The site of attachment and exchange between two DNA molecules is called the chiasm, and the process itself is called crosslinking. During the crossover, an exchange of bands is verified between the participating DNAs..
This generates a cointegrate, which are two DNA molecules physically joined into one. When "solving" the cointegration, two molecules are generated, generally changed (recombinant).
To "solve", in the context of recombination, is to separate the component DNA molecules of a cointegrate.
In site-specific recombination, two DNA molecules, generally not homologous, have a short sequence common to both. This sequence is the target of a specific splicing enzyme.
The enzyme, capable of recognizing this sequence and not another, cuts it at a particular site in both molecules. With the help of some other factors, it exchanges the DNA bands of the two participating molecules and forms a cointegrate.
This is the basis for the formation of the cointegrate between the genome of the bacterium. Escherichia coli and that of the bacteriophage lambda. A bacteriophage is a virus that infects bacteria.
The formation of this cointegrate is carried out by an enzyme encoded in the virus genome: lambda integrase. It recognizes a common sequence called attP in the circular genome of the virus, and attB in that of the bacteria.
By cutting both sequences in both molecules, it generates free segments, swaps the bands, and joins the two genomes. A larger, or cointegrated circle is then formed.
In cointegration, the virus genome is passively carried by the bacterial genome, with which it replicates. In this state, it is said that the virus is in the provirus state, and that the bacterium is lysogenic for it..
The reverse process, that is, the resolution of the cointegrate, can take many generations - or even not occur. However, doing so is enzymatically mediated by another protein encoded by the virus genome called excisionase. When this occurs, the virus separates from the cointegrate, reactivates and causes cell lysis..
Homologous recombination occurs between DNA molecules that share at least about 40 nucleotides of complete or near complete similarity. In order to carry out the recombination process, at least one endonuclease must participate.
Endonucleases are enzymes that make internal cuts in DNA. Some do it to proceed to degrade DNA. Others, as in the case of recombination, do it to generate a dent in the DNA.
This unique nick allows processing of a single band DNA with a free end. This free end, oriented by a recombinase, allows a single band to invade a double DNA, displacing the resident band identical to it..
This is the cross-over point, between a donor ("invader") DNA molecule and another receptor..
The enzyme (recombinase) that carries out the process of band invasion and exchange in Escherichia coli it is called RecA. There are other homologous proteins in prokaryotes, such as RadA in archaea. In eukaryotes the equivalent enzyme is called RAD51.
Once the invasive band displaces the resident, it interacts with the band that was left simple in the donor molecule. Both sites are sealed by the action of a ligase.
Now we have a DNA of hybrid bands (a donor band and a recipient band, of different origins) flanked by donor DNA and recipient DNA. The crossover points (chiasmata) move in both directions by at least 200 bp.
Each point of crossover forms what is known as the Holliday structure (cruciform DNA product of a recombination event).
This cruciform DNA must be resolved by other endonucleases. Chimeric or hybrid DNA of this structure can be resolved in two ways. If the second endonucleotide cut occurs in the same band in which the first occurred, no recombination occurs. If the second cut occurs in the other band, the resulting products are recombinant.
This is a type of somatic recombination (not meiotic) that contributes to the generation in the enormous variability of antibodies of the immune system.
This recombination takes place in particular fragments of the genes that code for the polypeptide chains that define them. It is carried out by B cells and involves different genetic regions.
Interestingly, there are parasites like Trypanosoma brucei that employ a similar recombination mechanism to create variability in a surface antigen. In this way, they can evade the host's response if it fails to generate the antibody capable of recognizing the "new" antigen..
Finally, there are recombination processes that do not depend on the sequence similarity of the participating molecules. In eukaryotes, for example, the recombination of non-homologous ends is very important.
This occurs with DNA fragments that show double band breaks in the DNA. These are "repaired" by the cell joining them to other fragments, also with double band breaks..
However, these molecules do not necessarily have to be similar to participate in this recombination process. That is, by repairing the damage, the cell can join unrelated DNAs, thus creating a really new (recombinant) molecule.
Recombination ensures the fidelity of DNA information during and after the replication process. Recombination detects DNA damage during the new banding process in this extremely long macromolecule.
As each band has its own information, and that of its complementary, recombination ensures that none is lost. Each acts as a witness to the other. Similarly, in diploid organisms, a homologous chromosome witnesses its sibling, and vice versa.
On the other hand, once DNA has been replicated, the damage repair mechanisms of this molecule are varied. Some are direct (the injury is directly acted upon) and others are indirect.
Indirect repair mechanisms depend on recombination to take place. That is, to repair the damage in a DNA molecule, another homologous molecule is used. This would act in reparative recombination as a template from which it has suffered damage..
Recombination is capable of creating enormous chromosomal variability during meiosis. Somatic recombination also generates variability, as in the case of antibodies in vertebrates.
In many organisms meiosis is gametic. In sexually reproducing organisms, recombination is one of the most powerful ways to generate variability.
That is, to spontaneous mutation and chromosome segregation, recombination must be added as another element that generates gametic variability..
The integration of bacteriophage genomes by site-specific recombination, on the other hand, has contributed to the remodeling of the genome of their host bacteria..
This has contributed to the generation of genomic variability, and evolution, of this important group of living beings..
We have already seen that DNA can be repaired, but not what damages it. In reality, almost anything can damage DNA, starting with faulty replication that goes uncorrected..
But beyond that, DNA can be damaged by UV light, ionizing radiation, free oxygen radicals produced by cellular respiration, and what we eat, smoke, breathe, ingest or touch..
Fortunately, you don't have to give up living to protect DNA. You have to give up certain things, but the big work is done by the cell itself. These mechanisms for detecting DNA damage, and its repair, obviously have a genetic basis, and their deficiency, enormous consequences.
Diseases related to defects in homologous recombination include, for example, Bloom and Werner syndromes, familial breast and ovarian cancer, etc..
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