15. General (homologous) recombination. Molecular mechanisms of crossing over

Recombination

• Definition: Recombination is the process by which DNA molecules are cut and rejoined in new configurations, leading to the generation of new combinations of genetic information. This process occurs during meiosis and can result in an entirely new set of genetic material in offspring.

• Mechanisms:

  • Directed vs. Random: Recombination can be a regulated, directed process, such as during meiosis, or it can occur as a random mutation. Directed recombination is often controlled by the cell’s machinery to ensure proper genetic diversity and function.

• Types of Recombination:

  • General Recombination: Also known as homologous recombination, this involves the exchange of genetic material between homologous chromosomes during meiosis. It contributes to genetic diversity by mixing genetic information from the two parent organisms.

  • Site-Specific Recombination: This type of recombination occurs at specific locations in the genome and is mediated by recombinase enzymes. It is crucial for processes such as the integration of viral DNA into the host genome and the rearrangement of gene segments.

• Recombination in Prokaryotes:

  • Transformation: The uptake of free DNA from the environment by a bacterial cell.

  • Conjugation: The direct transfer of DNA from one bacterial cell to another through a physical connection called a pilus.

  • Transduction: The transfer of DNA from one bacterium to another by a bacteriophage (a virus that infects bacteria).

• Recombination in Eukaryotes:

  • Sexual Recombination: In eukaryotes, sexual recombination occurs during meiosis. This involves the exchange of genetic material between homologous chromosomes, leading to genetic variation in gametes (sperm and eggs) and contributing to genetic diversity in offspring

Recombination in Bacteria

• Conjugation:

  • Description: In conjugation, a piece of DNA is transferred directly from one bacterial cell to another through a physical connection known as a pilus. This process is often mediated by plasmids, which are small, circular DNA molecules separate from the bacterial chromosome.

  • Requirement: Direct cell-to-cell contact is necessary for conjugation to occur.

• Transformation:

  • Description: During transformation, a bacterial cell takes up free DNA from its surrounding environment. This DNA can be from lysed (dead) bacterial cells or other sources.

  • Process: The taken-up DNA may be integrated into the bacterial genome or exist as a plasmid.

• Transduction:

  • Description: In transduction, new DNA is introduced into a bacterial cell by a bacteriophage (a virus that infects bacteria). The bacteriophage injects its genetic material into the host cell, which can then incorporate this DNA into its own genome.

  • Types: Transduction can be classified into generalized transduction (where any bacterial gene can be transferred) and specialized transduction (where only specific genes are transferred)

General Recombination - Principles

• Scope:

  • Affects Large Regions: General recombination, also known as homologous recombination, involves the exchange of genetic material over large regions of the genome.

• Base-Pairing Interactions:

  • Homologous Sequences: This process is guided by base-pairing interactions between long, homologous DNA sequences. The participating DNA sequences generally need to be homologous, meaning they share a similar sequence and structure.

• Chromosomal Location:

  • Two Chromosomes: The sequences involved in general recombination are typically located on two copies of the same chromosome (homologous chromosomes) or between chromatids of a duplicated chromosome.

• Exchange Site:

  • Not Strictly Defined: The exact site of genetic exchange is not strictly defined, allowing for flexible regions of recombination along the chromosomes.

• Heteroduplex Formation:

  • Heteroduplex Joint: At the site of exchange, one strand of DNA is base-paired with a strand from the opposite DNA molecule, forming a heteroduplex joint. This joint connects the two double helices and can span thousands of base pairs.

• Crossing Over:

  • Homologous Recombination: The process of crossing over, where segments of DNA are exchanged between homologous chromosomes, is a key example of homologous recombination.

Proteins Involved in General Recombination

• Endonucleases:

  • Function: Endonucleases are enzymes that introduce double-strand breaks into DNA at specific sites. These breaks are crucial for initiating recombination. Some endonucleases also possess helicase activity, unwinding the DNA to facilitate the recombination process.

• Helicases:

  • Function: Helicases are enzymes that unwind the DNA double helix ahead of the recombination machinery. This unwinding is necessary to allow the recombination proteins access to the single-stranded DNA.

• Single-Strand DNA-Binding Proteins (SSBs):

  • Function: These proteins stabilize single-stranded DNA (ssDNA) that forms during the recombination process. They prevent ssDNA from re-annealing or being degraded.

• Ligases:

  • Function: Ligases are enzymes responsible for sealing nicks in the DNA backbone after the recombination process is completed. They rejoin the DNA strands to complete the formation of the recombinant molecules.

• Proteins for Energy Supply:

  • Function: Various proteins provide the energy required for the recombination process. This energy is usually supplied in the form of ATP, which is needed for the activity of helicases, endonucleases, and ligases.

• Synaptonemal Complex Proteins:

  • Function: During meiosis, proteins that form the synaptonemal complex facilitate the pairing (synapsis) of homologous chromosomes. This complex helps align the chromosomes accurately for crossover and recombination to occur

Functions of General Recombination

• Generation of Genetic Diversity:

  • New Allele Combinations: General recombination (homologous recombination) facilitates the exchange of genetic material between homologous chromosomes during meiosis. This results in gametes (sperm and eggs) with new combinations of alleles, contributing to genetic diversity in offspring.

• DNA Repair:

  • Recombinative Repair: Recombination also plays a critical role in the repair of damaged DNA. After DNA replication, recombinative repair processes can fix double-strand breaks or other forms of DNA damage by using homologous sequences as templates for accurate repair.

• Side Effects:

  • Uneven Crossing Over: While generally beneficial, recombination can sometimes lead to uneven crossing over, which may result in the duplication or deletion of DNA sequences along chromosomes. This can cause genomic imbalances and contribute to genetic disorders.

• Bloom Syndrome:

  • Description: Bloom syndrome is a genetic disorder characterized by increased frequency of homologous recombination events. This condition is caused by mutations in the BLM gene, which encodes a helicase essential for proper DNA replication and repair. The increased recombination can lead to genomic instability and a higher risk of cancer.

• DNA Damage Response:

  • Repair Activation: When cells detect DNA damage, repair systems are activated to address the issues. These systems work intensively to correct errors and maintain genomic integrity, utilizing processes like homologous recombination to repair damaged or broken DNA.

Crossing-Over During Meiosis

• Occurrence:

  • Phase: Crossing-over occurs during meiosis specifically in Prophase I.

• Homologous Chromosome Pairing:

  • Chromosome Alignment: During Prophase I, homologous chromosomes come together and align closely in a process called synapsis. This alignment sets the stage for crossing-over.

• Crossing-Over Process:

  • Pachytene Stage: In the pachytene stage of Prophase I, crossing-over occurs between non-sister chromatids of homologous chromosomes. This exchange of genetic material is mediated by the synaptonemal complex.

  • Synaptonemal Complex Structure: The synaptonemal complex is a protein structure that facilitates crossing-over and consists of:

    • Central Element: A central protein layer.

    • Lateral Protein Axes: Two parallel protein structures that run along the length of the chromosomes.

    • Recombination Nodules: Structures where crossing-over occurs.

    • Transverse Filaments: Connect the central element and the lateral axes, stabilizing the synapsis and facilitating recombination.

• Synapsis Formation:

  • Non-Sister Chromatid Interaction: Synapses are formed between the non-sister chromatids of homologous chromosomes, allowing for the exchange of genetic material.

• Genetic Diversity:

  • Unique Gametes: The process of crossing-over contributes to genetic diversity by producing new combinations of alleles. This is a key reason why each gamete is genetically unique