RecA-mediated sequence homology recognition as an example of how searching speed in self-assembly systems can be optimized by balancing entropic and enthalpic barriers

Jiang, Lili; Prentiss, Mara

doi:10.1103/physreve.90.022704

Cited by 19 publications

(31 citation statements)

References 37 publications

(38 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…‘Curtains’ of either Rad51- or RecA-coated ssDNA were tethered between nanofabricated barriers, and short fluorescently-labeled duplex oligonucleotides were incubated with the filaments (Figure 4D and Figure 4E). This approach allowed the authors to measure the kinetic lifetimes of the pairing intermediates, and thereby test the model for homology recognition described by Mara Prentiss and colleagues [93, 94]. Interestingly, when dsDNA substrates containing seven nucleotides or less of microhomology were used, the authors saw only transiently paired complexes; however, adding an eighth homologous nucleotide resulted in a dramatic increase in both pairing efficiency and binding energy.…”

Section: Recognition Of Dna Sequence Homology: Testing Involves Concementioning

confidence: 99%

RecA: Regulation and Mechanism of a Molecular Search Engine

Bell

Kowalczykowski

2016

Trends in Biochemical Sciences

185

164

View full text Add to dashboard Cite

Homologous recombination maintains genomic integrity by repairing broken chromosomes. The broken chromosome is partially resected to produce single-stranded DNA that is used to search for homologous dsDNA. This homology-driven ‘search and rescue’ is catalyzed by a class of DNA strand exchange proteins that are defined in relation to Escherichia coli RecA, which forms a filament on single-stranded DNA. Here, we review the regulation of RecA filament assembly and the mechanism by which RecA quickly and efficiently searches for and identifies a unique homologous sequence amongst a vast excess of heterologous DNA. Given that RecA is the prototypic DNA strand exchange protein, its behavior affords insight into the actions of eukaryotic RAD51 orthologs and their regulators, BRCA2 and other tumor suppressors.

show abstract

Section: Recognition Of Dna Sequence Homology: Testing Involves Concementioning

confidence: 99%

RecA: Regulation and Mechanism of a Molecular Search Engine

Bell

Kowalczykowski

2016

Trends in Biochemical Sciences

185

164

View full text Add to dashboard Cite

show abstract

“…Interestingly, previous theoretical studies have suggested that the net change in binding free energy for each correctly paired triplet should be on the order of thermal energy (42)(43)(44) and that the fidelity of base triplet pairing during DNA strand exchange would benefit from relatively low changes in binding free energy for each triplet step (42)(43)(44). These studies have also suggested that the structural deformation necessary to extend B-DNA to match the much longer extension of RS-DNA may enhance the ability of the presynaptic complex to reject nonhomologous sequences during the homology search (44 -46).…”

Section: Discussionmentioning

confidence: 99%

ATP hydrolysis Promotes Duplex DNA Release by the RecA Presynaptic Complex

Lee

Greene

2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

Homologous recombination is an important DNA repair pathway that plays key roles in maintaining genome stability. Escherichia coli RecA is an ATP-dependent DNA-binding protein that catalyzes the DNA strand exchange reactions in homologous recombination. RecA assembles into long helical filaments on single-stranded DNA, and these presynaptic complexes are responsible for locating and pairing with a homologous duplex DNA. Recent single molecule studies have provided new insights into RecA behavior, but the potential influence of ATP in the reactions remains poorly understood. Here we examine how ATP influences the ability of the RecA presynaptic complex to interact with homologous dsDNA. We demonstrate that over short time regimes, RecA presynaptic complexes sample heterologous dsDNA similarly in the presence of either ATP or ATP␥S, suggesting that initial interactions do not depend on ATP hydrolysis. In addition, RecA stabilizes pairing intermediates in three-base steps, and stepping energetics is seemingly unaltered in the presence of ATP. However, the overall dissociation rate of these paired intermediates with ATP is ϳ4-fold higher than with ATP␥S. These experiments suggest that ATP plays an unanticipated role in promoting the turnover of captured duplex DNA intermediates as RecA attempts to align homologous sequences during the early stages of recombination.Homologous recombination allows for the regulated exchange of genetic information between two different DNA molecules of identical or nearly identical sequence composition (1-4). Homologous recombination contributes to double-strand DNA break repair, the rescue of stalled or collapsed replication forks, programmed and aberrant chromosomal rearrangements, horizontal gene transfer, and meiosis (5-9). The importance of homologous recombination is underscored by its broad conservation across all kingdoms of life and 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 in eukaryotes.Many of the key reactions in homologous recombination are catalyzed by the Rad51/RecA family of DNA recombinases (1-4). These recombinases are broadly conserved, and prominent family members include bacterial RecA, the archeal 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 (10), and much of our current understanding of recombination mechanisms can be attributed to studies of bacterial RecA (4).During recombination, RecA bound to the presynaptic ssDNA must first locate a homologous duplex DNA template. This process is referred to as the homology search, and it is conceptually similar to the target searches of other site-specific DNA-binding proteins (11)(12)(13)(14). Once aligned, the presynaptic ssDNA can be paired with the complementary strand of a homologous dsDNA, resulting in the displacement of the noncomplementary s...

show abstract

“…The importance of length-dependent sequence recognition as a means for rapidly rejecting incorrect sequences was first recognized by Charles Thomas, Jr. (60), who in 1966 suggested that it would be beneficial for recombination to take place between nonrepetitive minimal recognition lengths composed of "words" that can be uniquely identified within the genome, and these original concepts have been further elaborated by several groups (55,(61)(62)(63). Simply put, longer sequences are less common than shorter sequences, so there is a benefit to search for these longer sequences, which will also have a higher probability of being the correct homologous target (Fig.…”

Section: Theoretical Considerationsmentioning

confidence: 99%

DNA Sequence Alignment during Homologous Recombination

Greene

2016

Journal of Biological Chemistry

View full text Add to dashboard Cite

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...

show abstract

RecA-mediated sequence homology recognition as an example of how searching speed in self-assembly systems can be optimized by balancing entropic and enthalpic barriers

Cited by 19 publications

References 37 publications

RecA: Regulation and Mechanism of a Molecular Search Engine

RecA: Regulation and Mechanism of a Molecular Search Engine

ATP hydrolysis Promotes Duplex DNA Release by the RecA Presynaptic Complex

DNA Sequence Alignment during Homologous Recombination

Contact Info

Product

Resources

About