Recombination | 20 | v4 | BIOS Instant Notes in Genetics

ABSTRACT

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Overview

Recombination is a process which makes new combinations of genetic information on a DNA molecule (a chromosome) by cutting and splicing between existing DNA molecules (chromosomes) to form a crossover called a chiasma in meiosis.

General recombination

General recombination is a process of exchange between chromosomes (or DNA double helices) which share a long region (usually hundreds of base pairs) of homology. Two homologous double-stranded DNA molecules align, break, and rejoin by splicing to exchange their ends.

Holliday structure

A Holliday structure, or half chiasma, is an important intermediate in recombination. Two homologous (same sequence) double helices exchange nicked single strands of the same polarity, so that there is a partner switch. If the double helices rotate (rotary diffusion) the exchanged strands can wind across between the helices, and the branch point migrates. The four ends around the exchange point are structurally identical, and the Holliday structure can isomerize so that either the two 5′→3′ strands or the two 3′→5′ strands cross over. The two helices are eventually separated (resolved) by cutting and differently rejoining the crossedover single-stranded DNA strands, either the two 3′→5′ or the two 5′→3′ strands. The ends of the helices are only exchanged (recombined) if the strands cut to resolve the structure are the ones which were not cut to create the Holliday structure in the first place (i.e. to achieve recombination, all four strands are eventually cut and swapped). The favored model for generating a Holliday structure by nicking single strands was the Aviemore (Meselson-Radding) model, where the strands to be exchanged are not nicked at identical points. Instead, one single nicked strand may transfer first and displace the identical strand from the other double helix. The displaced strand is then nicked and transferred further along. Degradation by exonuclease and synthesis by DNA polymerase can then make the ends meet. Ligation then restores continuity.

The double-strand break model

Recombination in the yeast Saccharomyces cerevisiae is initiated by a double-strand break in one chromatid (double helix). The 5′ ends are cut back by about 500 bases by exonuclease, and the remaining 3′ ends invade the homologous chromatid (double helix), generating two half- Holliday structures, one each side of the break. The gap is filled by synthesis, and further strand exchange completes the two Holliday structures. If these are resolved differently (one by cutting 5′→3′ strands, the other by cutting 3′→5′ strands) then recombination (exchange) of the ends of the chromatids will occur.

Conversion

The splicing of DNA molecules between chromatids with sequence differences (say one has AT where the other has CG) can generate hybrid (heteroduplex) DNA with mismatches (AG, CT). These may be corrected by mismatch repair pathways, converting the sequence on one chromosome to be like the sequence on the other. This gives a non- Mendelian ratio, three chromatids can have one sequence, one chromatid still has the other sequence. If the mismatch is not repaired before the next DNA replication phase, the mismatched bases will act as templates, generating different sequences in the two daughter cells after mitosis. This is called postmeiotic segregation (pms). Gap-filling synthesis in the double-strand break-repair model also converts the sequence in the gap.

Recombination enzymes

Most of the enzymes involved in the repair of DNA damage, both excision repair (ultraviolet-light-induced damage) and double-strand break repair (ionizing radiation, X-ray- and ?-ray-induced damage) also function in recombination in meiosis. There are several enzymes specific to meiosis as well. Deficiencies in some recombination-related enzymes are associated with human disease (e.g. breast cancer 1 gene product and ataxia telangiectasia).

Site-specific recombination

Bacteriophage lambda integrates into the host (E. coli) recombination genome at a specific 15 bp sequence (att or ‘O’) found on both the bacteriophage and host chromosome. The bacteriophage gene int coding for integrase is necessary for this. Excision is also by recombination catalyzed by excisionase.