HOMOLOGOUS RECOMBINATION: FUNCTIONS, MECHANISM AND APPLICATIONS - BIOLOGY - 2025

The homologous recombination is a process that involves the exchange of DNA molecules between similar or identical sections of the genome. Cells use homologous recombination mainly to repair breaks in genetic material, generating genetic variation in populations.

In general, homologous recombination involves the physical pairing between homologous areas of the genetic material, followed by the breaking of the chains that are going to undergo the exchange, and finally the union of the new combined DNA molecules.

Recombination between two homologous chromosomes.

Source: Emw

Breaks in DNA must be repaired as quickly and efficiently as possible. When the damage is not repaired, the consequences can be serious and even lethal. In bacteria, the main function of homologous recombination is to repair these breaks in the genetic material.

Homologous recombination is considered one of the main mechanisms that allow the stability of the genome. It is present in all domains of life and even in viruses, so it is presumably a vital mechanism that appeared very early in the evolution of life.

Historical perspective

One of the most relevant principles proposed by Gregor Mendel consists of independence in the segregation of characters. According to this law, the different genes are passed from parent to child independently.

However, in 1900 the existence of very marked exceptions to this principle was evident. The English geneticists Bateson and Punnett showed that many times certain traits are inherited together, and for these traits the principle stated by Mendel is not valid.

Subsequent research managed to elucidate the existence of the recombination process, where cells were capable of exchanging genetic material. In cases where the genes inherited together, the DNA was not exchanged due to the physical closeness between the genes.

What is homologous recombination?

Homologous recombination is a cellular phenomenon that involves the physical exchange of DNA sequences between two chromosomes. Recombination involves a set of genes known as rec genes. These code for different enzymes that participate in the process.

DNA molecules are considered "homologous" when they share similar or identical sequences of more than 100 base pairs. DNA has small regions that can differ from each other, and these variants are known as alleles.

In living things, all DNA is considered recombinant DNA. The exchange of genetic material between chromosomes occurs continuously, mixing and rearranging the genes on the chromosomes.

This process occurs obviously in meiosis. Specifically in the phase where chromosomes pair up in the first cell division. In this stage, the exchange of genetic material between chromosomes occurs.

Historically, this process is designated in the literature using the Anglo-Saxon word crossing over. This event is one of the results of homologous recombination.

The frequency of crossing over between two genes of the same chromosome depends mainly on the distance that exists between them; the smaller the physical distance between them, the lower the frequency of exchange.

Functions and consequences of homologous recombination

Genetic material is constantly exposed to damage, caused by endogenous and exogenous sources, such as radiation, for example.

Human cells are estimated to have a significant number of DNA lesions, in the order of tens to hundreds per day. These lesions need to be repaired to avoid potential deleterious mutations, replication and transcription blocks, and damage at the chromosomal level.

From a medical point of view, DNA damage that is not repaired correctly results in the development of tumors and other pathologies.

Homologous recombination is an event that allows DNA repair, allowing the recovery of lost sequences, using the other (homologous) strand of DNA as a template.

This metabolic process is present in all forms of life, providing a high-fidelity mechanism that allows repairing "gaps" in DNA, double-stranded breaks and cross-links between DNA strands.

One of the most relevant consequences of recombination is the generation of new genetic variation. Along with mutations, they are the two processes that generate variation in living beings - remember that variation is the raw material for evolution.

In addition, it provides a mechanism to reset replication forks that have been corrupted.

In bacteria

In bacteria, there are frequent horizontal gene transfer events. These are classified as conjugation, transformation, and transduction. Here, prokaryotes take DNA from another organism, and even from different species.

During these processes, homologous recombination occurs between the recipient cell and the donor cell.

Mechanism

Homologous recombination begins with the break in one of the strands of the chromosomal DNA molecule. Following this, a series of steps catalyzed by multiple enzymes occur.

The 3 'end where the cut occurs is invaded by the homologous double strand of DNA. The invasion process is crucial. By "homologous chain" we mean the portions of the chromosomes that have the same genes in a linear order, although the nucleotide sequences do not have to be identical.

Synapse

This invasion of the strand places homologous chromosomes facing each other. This phenomenon of meeting threads is called synapse (not to be confused with the synapse in neurons, here the term is used with another meaning).

The synapse does not necessarily imply a direct contact between both homologous sequences, the DNA can continue to move for a while until it finds the homologous portion. This search process is called homologous alignment.

D-loop formation

Then, an event called "strand invasion" occurs. A chromosome is a double helix of DNA. In homologous recombination, two chromosomes look for their homologous sequences. In one of the helices, the strands separate and this strand "invades" the double helix structure, forming the structure called the D loop.

The D-loop strand has been displaced by the invasion of the breaking strand and pairs with the complementary strand of the original double helix.

Holliday junction formation

The next step is the formation of the Holliday unions. Here, the ends of the exchanged strands are tied together. This union has the ability to move in any direction. The joint can break and form multiple times.

The final process of recombination is the resolution of these unions and there are two ways or ways in which the cell achieves this. One of them is the cleavage of the union or by a process called dissolution, typical of eukaryotic organisms.

In the first mechanism, breaking the Holliday junction regenerates two chains. In the other "dissolution" event, a kind of collapse occurs in the union.

Proteins involved

A crucial protein in the recombination process is called Rad51 in eukaryotic cells, and RecA in Escherichia coli. It works in the different phases of recombination: before, during and after synapse.

The Rad51 protein facilitates the formation of the physical connection between the invading DNA and the tempered DNA. In this process the heteroduplex DNA is generated.

Rad51, and its RecA counterpart, catalyze the search for homologous DNA and the exchange of DNA strands. These proteins have the ability to cooperatively bind to single-band DNA.

There are also paralogue genes (originated from gene duplication events in a lineage of organisms) of Rad51, called Rad55 and Rad57. In humans, five Rad51 paralog genes called Rad51B, Rad51C, Rad51D, Xrcc2, and Xrcc3 have been identified.

Anomalies associated with recombination processes

Since recombination requires physical binding on chromosomes, it is a crucial step in proper segregation during meiosis. If proper recombination does not occur, the result can be major pathology.

Nondisjunction of chromosomes or errors in segregation is one of the most frequent causes of miscarriages and abnormalities of chromosomal origin, such as trisomy of chromosome 21, which causes Down syndrome.

Although recombination is usually a fairly precise process, regions of the genome that are repeated and genes that have multiple copies throughout the genome are prone to uneven crossover.

This interbreeding produces different clinically relevant traits, including common diseases such as thalassemia and autism.

Recombination applications

Molecular biologists have taken advantage of the knowledge of the mechanism of homologous recombination to create different technologies. One of these allows the creation of "knockout" organisms.

These genetically modified organisms make it possible to elucidate the function of a gene of interest.

One of the methodologies used for the creation of knockouts consists of the suppression of the expression of the specific gene by replacing the original gene with a modified or "damaged" version. The gene is exchanged for the mutated version by means of homologous recombination.

Other types of recombination

Besides homologous or legitimate recombination, there are other types of exchange of genetic material.

When the regions of DNA that exchange material are non-allelic (homologous chromosomes) the result is duplication or reduction of genes. This process is known as non-homologous recombination or unequal recombination.

Together, genetic material can also be exchanged between sister chromatids on the same chromosome. This process occurs in both the meiotic and mitotic division, and is called unequal exchange.

References

1. Baker, TA, Watson, JD, & Bell, SP (2003). Molecular biology of the gene. Benjamin-Cummings Publishing Company.
2. Devlin, TM (2004). Biochemistry: textbook with clinical applications. I reversed.
3. Jasin, M., & Rothstein, R. (2013). Repair of strand breaks by homologous recombination. Cold Spring Harbor perspectives in biology, 5 (11), a012740.
4. Li, X., & Heyer, WD (2008). Homologous recombination in DNA repair and DNA damage tolerance. Cell research, 18 (1), 99-113.
5. Murray, PR, Rosenthal, KS, & Pfaller, MA (2017). Medical microbiology. Elsevier Health Sciences.
6. Nussbaum, RL, McInnes, RR, & Willard, HF (2015). Thompson & Thompson genetics in medicine e-book. Elsevier Health Sciences.
7. Virgili, RO, & Taboada, JMV (2006). Human genome: new advances in research, diagnosis and treatment. Editions Universitat Barcelona.