Abstract
Homologous recombination is a fundamental process in all living organisms that allows the faithful repair of DNA double strand breaks, through the exchange of DNA strands between homologous regions of the genome. Results of three decades of investigation and recent fruitful observations have unveiled key elements of the reaction mechanism, which proceeds along nucleofilaments of recombinase proteins of the RecA family. Yet, one essential aspect of homologous recombination has largely been overlooked when deciphering the mechanism: while ATP is hydrolyzed in large quantity during the process, how exactly hydrolysis influences the DNA strand exchange reaction at the structural level remains to be elucidated. In this study, we build on a previous geometrical approach that studied the RecA filament variability without bound DNA to examine the putative implication of ATP hydrolysis on the structure, position, and interactions of up to three DNA strands within the RecA nucleofilament. Simulation results on modeled intermediates in the ATP cycle bring important clues about how local distortions in the DNA strand geometries resulting from ATP hydrolysis can aid sequence recognition by promoting local melting of already formed DNA heteroduplex and transient reverse strand exchange in a weaving type of mechanism.
Highlights
Homologous recombination (HR) is a fundamental biological process common to all living organisms
In order to explore the structural implication of isolated hydrolysis events occurring within RecA filaments, we considered filaments where at a given moment one unique hydrolysis event occurs within a helical turn and two consecutive hydrolysis spots are separated along the filament by at least five monomers with bound ATP
We concentrate on the case where the duplex DNA resulting from strand exchange is in site I during the elongation stage where ATP hydrolysis influences the course of the reaction
Summary
Homologous recombination (HR) is a fundamental biological process common to all living organisms It enables both the faithful repair of DNA double strand breaks, necessary for cell survival, and the crossover of endogenous genes or insertion of exogenous genes, which promotes diversification and species survival in the long term [1,2,3]. These functions are performed in the cell within long helical nucleoprotein filaments formed by the polymerization of recombinase proteins (RecA for prokaryotes) on a single-stranded DNA (ssDNA, called incoming strand) resulting from the processing of damaged DNA [4]. While ATP hydrolysis influences the kinetics of subsequent steps [6], hydrolysis is not necessary for the whole HR reaction to successfully go to completion in vitro on limited lengths of homologous DNA up to few kilobases [10]
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