A single-molecule approach to unravel the molecular mechanism of the action of Deinococcus radiodurans RecD2 and its interaction with SSB and RecA in DNA repair

Purkait, Debayan; Islam, Farhana; Mishra, Padmaja P.

doi:10.1016/j.ijbiomac.2022.09.043

Cited by 3 publications

(5 citation statements)

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“…During the binding process, this protein carries the ability to resolve secondary DNA structures like hairpins or G-quadruplexes. The translocation rate of RecD2 on single-stranded (ss) and double-stranded (ds) DNA was found to be 3.1 nucleotides and 1.4 nucleotides per second, respectively . The dsDNA unwinding activity of RecD2 has been studied even in the absence of ATP, but a fast and iterative mode of unwinding is achieved in the presence of ATP, and it follows the “Switch and Translocation Model”’.…”

Section: Single-molecule Fluorescence Resonance Energy Transfer (Smfret)mentioning

confidence: 99%

“…The translocation rate of RecD2 on single-stranded (ss) and doublestranded (ds) DNA was found to be 3.1 nucleotides and 1.4 nucleotides per second, respectively. 36 The dsDNA unwinding activity of RecD2 has been studied even in the absence of ATP, but a fast and iterative mode of unwinding is achieved in the presence of ATP, and it follows the "Switch and Translocation Model"'. RecD2 has been found to interact with other DNAbinding proteins such as RecA and SSB.…”

Section: ■ Single-molecule Fluorescence Resonance Energy Transfer (Sm...mentioning

confidence: 99%

“…As recent studies on RecD2 have indicated the recruitment of SSB by RecD2 for efficient loading on the DNA, 36 the interaction of RecD or RecD2 with DNA and other accessory proteins in the DNA repair pathway may also be visualized by AFM. This method may provide exclusive proficiency in revealing the structural and functional relationship of the specificity of the protein binding complex of the fork DNA, the binding affinity, and the DNA conformational changes through bend angle analysis during the DNA repair pathways to relate to the biological context of its functions.…”

Section: ■ Atomic Force Microscopymentioning

confidence: 99%

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Insights into the Dynamics and Helicase Activity of RecD2 of Deinococcus radiodurans during DNA Repair: A Single-Molecule Perspective

2023

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While the double helix is the most stable conformation of DNA inside cells, its transient unwinding and subsequent partial separation of the two complementary strands yields an intermediate single-stranded DNA (ssDNA). The ssDNA is involved in all major DNA transactions such as replication, transcription, recombination, and repair. The process of DNA unwinding and translocation is shouldered by helicases that transduce the chemical energy derived from nucleotide triphosphate (NTP) hydrolysis to mechanical energy and utilize it to destabilize hydrogen bonds between complementary base pairs. Consequently, a comprehensive understanding of the molecular mechanisms of these enzymes is essential. In the last few decades, a combination of single-molecule techniques (force-based manipulation and visualization) have been employed to study helicase action. These approaches have allowed researchers to study the single helicase−DNA complex in real-time and the free energy landscape of their interaction together with the detection of conformational intermediates and molecular heterogeneity during the course of helicase action. Furthermore, the unique ability of these techniques to resolve helicase motion at nanometer and millisecond spatial and temporal resolutions, respectively, provided surprising insights into their mechanism of action. This perspective outlines the contribution of single-molecule methods in deciphering molecular details of helicase activities. It also exemplifies how each technique was or can be used to study the helicase action of RecD2 in recombination DNA repair.

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Section: Single-molecule Fluorescence Resonance Energy Transfer (Smfret)mentioning

confidence: 99%

Section: ■ Single-molecule Fluorescence Resonance Energy Transfer (Sm...mentioning

confidence: 99%

Section: ■ Atomic Force Microscopymentioning

confidence: 99%

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Insights into the Dynamics and Helicase Activity of RecD2 of Deinococcus radiodurans during DNA Repair: A Single-Molecule Perspective

2023

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“…Compared to E. coli , the RecD helicase in Ant6 and R1 has a long N terminal region and is termed RecD2. This protein is typically found in bacterial systems lacking the RecBCD complex which plays a major role in the repair of DNA double-strand breaks ( Cox and Battista, 2005 ; Purkait et al, 2022 ). Moreover, D. radiodurans recD mutants are sensitive to IR, UV, and H 2 O 2 stress.…”

Section: Interpretation Of Data Setmentioning

confidence: 99%

“…The present study identifies nearly all the "Fts" proteins and the "Min" system like E. coli in both Ant6 and R1 genome (Supplementary Table S6), however, the regulatory mechanism associated with cell division in Deinococcus has not yet been fully elucidated. Mishra et al (2022) reported that FtsK plays an important role in the genome separation, and septum formation and cell division in D. radiodurans. This protein was also identified in the Ant6 and K12 genome (Supplementary Table S6).…”

Section: Dna Repair and Associated Systemsmentioning

confidence: 99%