RecA filament sliding on DNA facilitates homology search

Ragunathan, Kaushik; Liu, Cheng; Ha, Taekjip

doi:10.7554/elife.00067

Cited by 101 publications

(116 citation statements)

References 37 publications

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“…8). Several models have been proposed for the homology search by RecA (33)(34)(35). On the other hand, our overall model for the homology search is based upon the premise that the RecA presynaptic complex will rapidly engage duplex DNA and undergo an overall search process characterized by intersegmental transfer, which takes advantage of the polyvalent nature of the RecA presynaptic complex (Fig.…”

Section: Discussionmentioning

confidence: 99%

ATP hydrolysis Promotes Duplex DNA Release by the RecA Presynaptic Complex

Lee

Greene

2016

Journal of Biological Chemistry

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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...

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Section: Discussionmentioning

confidence: 99%

ATP hydrolysis Promotes Duplex DNA Release by the RecA Presynaptic Complex

Lee

Greene

2016

Journal of Biological Chemistry

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“…At the same time, one should notice that the intersegment transfer has been successfully accounted in other protein search systems (31), so our theoretical method can be extended in this direction. Another important process that was not taken into account in our theoretical model is the sliding of RecA filaments along the DNA chains (13). It is still unclear if this effect is relevant for the homology search, but the proposed discrete-state stochastic framework can be extended to take care of this question.…”

Section: Resultsmentioning

confidence: 99%

“…During this process a nucleotide sequence of another identical or similar DNA duplex is used for restoring the original sequence in the broken DNA molecule (8,9). Furthermore, the homologous recombination plays a fundamental role in the process of genetic diversity and reassembling of genetic information, which is important for living systems for adaption to changing environments (1,3,5,8,(11)(12)(13).…”

Section: Introductionmentioning

confidence: 99%

“…A different idea, which argues that the filament sliding is the source of the high efficiency of the homologous search process, has been also explored recently (13). Single-molecule fluorescent measurements with a high spatiotemporal resolution were employed, which, in contrast to earlier experiments that indicated no sliding (35), have observed multiple diffusional events for RecA filaments on DNA.…”

Section: Introductionmentioning

confidence: 99%

“…Single-molecule fluorescent measurements with a high spatiotemporal resolution were employed, which, in contrast to earlier experiments that indicated no sliding (35), have observed multiple diffusional events for RecA filaments on DNA. Using computer simulations, it was argued that sliding accelerates the homology search as much as 200 times (13). However, the degree of sliding was not significant: the observed sliding lengths were comparable or less than the size of the RecA filament.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

On the Mechanism of Homology Search by RecA Protein Filaments

Kochugaeva

Shvets

Kolomeisky

2017

Biophysical Journal

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Genetic stability is a key factor in maintaining, survival and reproduction of biological cells. It relies on many processes, but one of the most important is a homologous recombination, in which the repair of breaks in double-stranded DNA molecules is taking place with a help of several specific proteins. In bacteria this task is accomplished by RecA proteins that are active as nucleoprotein filaments formed on single-stranded segments of DNA. A critical step in the homologous recombination is a search for a corresponding homologous region on DNA, which is called a homology search. Recent single-molecule experiments clarified some aspects of this process, but its molecular mechanisms remain not well understood. We developed a quantitative theoretical approach to analyze the homology search. It is based on a discrete-state stochastic model that takes into account the most relevant physical-chemical processes in the system. Using a method of first-passage processes, a full dynamic description of the homology search is presented. It is found that the search dynamics depends on the degree of extension of DNA molecules and on the size of RecA nucleoprotein filaments, in agreement with experimental single-molecule measurements of DNA pairing by RecA proteins. Our theoretical calculations, supported by extensive Monte Carlo computer simulations, provide a molecular description of the mechanisms of the homology search.

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DNA Repair: The Search for Homology

2018

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The repair of chromosomal double-strand breaks (DSBs) by homologous recombination is essential to maintain genome integrity. The key step in DSB repair is the RecA/Rad51-mediated process to match sequences at the broken end to homologous donor sequences that can be used as a template to repair the lesion. Here, in reviewing research about DSB repair, I consider the many factors that appear to play important roles in the successful search for homology by several homologous recombination mechanisms. See also the video abstract here: https://youtu.be/vm7-X5uIzS8.

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RecA filament sliding on DNA facilitates homology search

Cited by 101 publications

References 37 publications

ATP hydrolysis Promotes Duplex DNA Release by the RecA Presynaptic Complex

ATP hydrolysis Promotes Duplex DNA Release by the RecA Presynaptic Complex

On the Mechanism of Homology Search by RecA Protein Filaments

DNA Repair: The Search for Homology

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