Branch migration is the process by which base pairs on homologous DNA strands are consecutively exchanged at a Holliday junction, moving the branch point up or down the DNA sequence. Branch migration is the second step of genetic recombination, following the exchange of two single strands of DNA between two homologous chromosomes. The process is random, and the branch point can be displaced in either direction on the strand, influencing the degree of which the genetic material is exchanged. Branch migration can also be seen in

DNA repair DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as radiation can cause DNA da ...

and replication, when filling in gaps in the sequence. It can also be seen when a foreign piece of DNA invades the strand.

Mechanism

The mechanism for branch migration differs between

prokaryote A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Conne ...

s and eukaryotes.

Prokaryotes

The mechanism for prokaryotic branch migration has been studied many times in ''

Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Esc ...

''. In ''E. coli,'' the proteins RuvA and RuvB come together and form a complex that facilitates the process in a number of ways. RuvA is a tetramer and binds to the DNA at the Holliday junction when it is in the open X form. The protein binds in a way that the DNA entering/departing the junction is still free to rotate and slide through. RuvA has a domain with acidic

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha a ...

residues that interfere with the base pairs in the centre of the junction. This forces the base pairs apart so that they can re-anneal with base pairs on the homologous strands. In order for migration to occur, RuvA must be associated with RuvB and ATP. RuvB has the ability to

hydrolyze Hydrolysis (; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution, elimination, and solvation reactions in which water is the nucleophile. Biological hydrolysis ...

ATP, driving the movement of the branch point. RuvB is a hexamer with

helicase Helicases are a class of enzymes thought to be vital to all organisms. Their main function is to unpack an organism's genetic material. Helicases are motor proteins that move directionally along a nucleic acid phosphodiester backbone, separatin ...

activity, and also binds the DNA. As ATP is hydrolyzed, RuvB rotates the recombined strands while pulling them out of the junction, but does not separate the strands as helicase would. The final step in branch migration is called resolution and requires the protein RuvC. The protein is a dimer, and will bind to the Holliday junction when it takes on the stacked X form. The protein has endonuclease activity, and cleaves the strands at exactly the same time. The cleavage is symmetrical, and gives two recombined DNA molecules with single stranded breaks.Górecka KM, Komorowska W, Nowotny M. Crystal structure of RuvC resolvase in complex with Holliday junction substrate. Nucleic Acids Res. 2013 Nov;41(21):9945-55. doi: 10.1093/nar/gkt769. Epub 2013 Aug 25. PMID: 23980027; PMCID: PMC3834835

Eukaryotes

The eukaryotic mechanism is much more complex involving different and additional proteins, but follows the same general path. Rad54, a highly conserved eukaryotic protein, is reported to oligomerize on Holliday junctions to promote branch migration.

Archaea

A helicase (designated Saci-0814) isolated from the thermophilic crenarchaeon ''Sulfolobus acidocaldarius'' dissociated DNA Holliday junction structures, and showed branch migration activity ''in vitro''.Suzuki, S.; Kurosawa, N.; Yamagami, T.; Matsumoto, S.; Numata, T.; Ishino, S.; Ishino, Y. Genetic and Biochemical Characterizations of aLhr1 Helicase in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius. Catalysts 2022, 12, 34. https://doi.org/10.3390/catal12010034 In a ''S. acidocaldarius'' strain deleted for Saci-0814, the homologous recombination frequency was reduced five-fold compared to the parental strain indicating that Saci-0814 is involved in homologous recombination ''in vivo''. Based on this evidence it appears that Saci-0814 is employed in homologous recombination in ''S. acidocaldarius'' and functions as a branch migration helicase. Homologous recombination appears to be an important adaptation in hyperthermophiles, such as ''S. acidocaldarius'', for efficiently repairing DNA damage. Helicase Saci-0814 is classified as an aLhr1 (archaeal long helicase related 1) under superfamily 2 helicases, and its homologs are conserved among the archaea.

Control

The rate of branch migration is dependent on the amount of

divalent In chemistry, the valence (US spelling) or valency (British spelling) of an chemical element, element is the measure of its combining capacity with other atoms when it forms chemical compounds or molecules. Description The combining capacity, ...

ions, specifically magnesium ions (Mg²⁺), present during recombination. The ions determine which structure the Holliday junction will adopt, as they play a stabilizing role. When the ions are absent, the backbones repel each other and the junction takes on the open X structure. In this condition, migration is optimal and the junction will be free to move up and down the strands. When the ions are present, they neutralize the negatively charged backbone. This allows the strands to move closer together and the junction adopts the stacked X structure. It is during this state that resolution will be optimal, allowing RuvC to bind to the junction.

References

{{reflist Cellular processes Molecular genetics