DNA Sequence Alignment during Homologous Recombination

Abstract

Homologous recombination allows for the regulated exchange of genetic information between two different DNA molecules of identical or nearly identical sequence composition, and is a major pathway for the repair of double-stranded DNA breaks. A key facet of homologous recombination is the ability of recombination proteins to perfectly align the damaged DNA with homologous sequence located elsewhere in the genome. This reaction is referred to as the homology search and is akin to the target searches conducted by many different DNA-binding proteins. Here I briefly highlight early investigations into the homology search mechanism, and then describe more recent research. Based on these studies, I summarize a model that includes a combination of intersegmental transfer, short-distance one-dimensional sliding, and length-specific microhomology recognition to efficiently align DNA sequences during the homology search. I also suggest some future directions to help further our understanding of the homology search. Where appropriate, I direct the reader to other recent reviews describing various issues related to homologous recombination. Homologous RecombinationHomologous recombination enables the exchange of genetic information between different DNA molecules and is a major driving force in evolution. Homologous recombination contributes to double-strand DNA break (DSB) 2 repair, the rescue of stalled or collapsed replication forks, programmed and aberrant chromosomal rearrangements, horizontal gene transfer, and meiosis (1-5). The importance of homologous recombination is underscored by the findings that defects in key recombination proteins can result in a loss of genome integrity and lead to gross chromosomal rearrangements that are a hallmark of cancer. During recombination, a presynaptic ssDNA is paired with the complementary strand of a homologous dsDNA, resulting in the displacement of the noncomplementary strand from the duplex to generate a D-loop intermediate ( Fig. 1) (6 -8). This intermediate can be channeled through a number of alternative pathways, any of which can allow for the repair of the originally broken DNA molecule using information derived from the template (1, 9, 10).Key reactions in homologous recombination are catalyzed by the Rad51/RecA family DNA recombinases, which are ATP-dependent proteins that form helical filaments on DNA (6 -8, 11). These recombinases are broadly conserved, and prominent family members include bacterial RecA, the archaeal protein RadA, and the eukaryotic recombinases Rad51 and Dmc1. RecA is the archetypal recombinase originally identified in genetic screens for Escherichia coli mutants defective in recombination by Clark and Margulies in 1965 (12). This discovery set the stage for years of investigation into the RecA protein, including its biochemical purification and characterization by the Radding, Howard-Flanders, Lehman, and Roberts laboratories (13)(14)(15)(16)(17)(18)(19)(20).The importance of this early work on bacterial recombination was underscored by studies in...

Dynamic interactions of the homologous pairing 2 (Hop2)–meiotic nuclear divisions 1 (Mnd1) protein complex with meiotic presynaptic filaments in budding yeast

“…These nucleoprotein filaments, referred to as presynaptic complexes, are responsible for promoting key DNA transactions during the early stages of HR (7,21,26). The presynaptic complex first locates a homologous dsDNA template through a process referred to as the homology search (17, [27][28][29][30]. The presynaptic complex then pairs the bound ssDNA with the complementary strand from the homologous dsDNA template (7,17,21,24,(31)(32)(33).…”

Rad51-mediated double-strand break repair and mismatch correction of divergent substrates

“… The RecA/Rad51 family of recombinases execute the critical step in homologous recombination (HR): the search for homologous DNA to serve as the template during DNA double-strand break (DSB) repair 1–7 . Although budding yeast Rad51 has been extensively characterized in vitro 3,4,6–9 , the stringency of its search and sensitivity to mismatched sequences in vivo remain poorly defined.…”

A change of view: homologous recombination at single-molecule resolution

“…The homology search has been the subject of a number of in-depth reviews 86,101–103 , and thus here we only briefly highlight the key areas where progress has been made using a combination of bulk biochemical studies and SM studies. For instance, these types of studies are beginning to present a more unified picture of the basic principles that guide sequence alignment during the homology search.…”