Identification of small-molecule inhibitors of the DNA repair proteins RuvAB from Pseudomonas aeruginosa

Dai, Lin; Lu, Lian; Zhang, Xu; Wu, Jian; Li, Jinyu; Lin, Zhonghui

doi:10.1016/j.bmc.2022.117022

Cited by 3 publications

(3 citation statements)

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“…Recently, small molecule inhibitors (corilagin, bardoxolone methyl (BM), and 10-(6′-plastoquinonyl)decyltriphenylphosphonium (SKQ1)) targeting P. aeruginosa RuvAB (PaRuvAB) have been identified. These discoveries were made in conjunction with a FRET-based HJ branch migration assay and studies based on high-throughput small-molecule screening . In particular, corilagin directly binds PaRuvB at the ATPase site, inhibiting ATP hydrolysis whereas BM and SKQ1 hinder the PaRuvA and HJ interaction.…”

Section: Holliday Junction and Resolvasomes As Therapeutic Targetsmentioning

confidence: 99%

“…These discoveries were made in conjunction with a FRET-based HJ branch migration assay and studies based on high-throughput small-molecule screening. 248 In particular, corilagin directly binds PaRuvB at the ATPase site, inhibiting ATP hydrolysis whereas BM and SKQ1 hinder the PaRuvA and HJ interaction. The cryoelectron microscopy (cryo-EM) analysis of the intermediate complex between RuvAB and the HJ in P. aeruginosa illustrates that eight RuvA subunits arrange into two tetramers, surrounding the HJ.…”

Section: Holliday Junction and Resolvasomes As Therapeutic Targetsmentioning

confidence: 99%

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Prokaryotic DNA Crossroads: Holliday Junction Formation and Resolution

Nautiyal,

Thakur

2024

ACS Omega

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Cells are continually exposed to a multitude of internal and external stressors, which give rise to various types of DNA damage. To protect the integrity of their genetic material, cells are equipped with a repertoire of repair proteins that engage in various repair mechanisms, facilitated by intricate networks of protein−protein and protein−DNA interactions. Among these networks is the homologous recombination (HR) system, a molecular repair mechanism conserved in all three domains of life. On one hand, HR ensures high-fidelity, template-dependent DNA repair, while on the other hand, it results in the generation of combinatorial genetic variations through allelic exchange. Despite substantial progress in understanding this pathway in bacteria, yeast, and humans, several critical questions remain unanswered, including the molecular processes leading to the exchange of DNA segments, the coordination of protein binding, conformational switching during branch migration, and the resolution of Holliday Junctions (HJs). This Review delves into our current understanding of the HR pathway in bacteria, shedding light on the roles played by various proteins or their complexes at different stages of HR. In the first part of this Review, we provide a brief overview of the end resection processes and the strand-exchange reaction, offering a concise depiction of the mechanisms that culminate in the formation of HJs. In the latter half, we expound upon the alternative methods of branch migration and HJ resolution more comprehensively and holistically, considering the historical research timelines. Finally, when we consolidate our knowledge about HR within the broader context of genome replication and the emergence of resistant species, it becomes evident that the HR pathway is indispensable for the survival of bacteria in diverse ecological niches.

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Section: Holliday Junction and Resolvasomes As Therapeutic Targetsmentioning

confidence: 99%

Section: Holliday Junction and Resolvasomes As Therapeutic Targetsmentioning

confidence: 99%

Prokaryotic DNA Crossroads: Holliday Junction Formation and Resolution

Nautiyal,

Thakur

2024

ACS Omega

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“…Therefore, the RuvAB proteins have been recognized as attractive targets to combat P. aeruginosa infections. We recently reported that the small-molecule inhibitors of PaRuvAB could increase the susceptibility of P. aeruginosa to UV-C irradiation ( Dai et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Cryo-EM structure of the RuvAB-Holliday junction intermediate complex from Pseudomonas aeruginosa

et al. 2023

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Holliday junction (HJ) is a four-way structured DNA intermediate in homologous recombination. In bacteria, the HJ-specific binding protein RuvA and the motor protein RuvB together form the RuvAB complex to catalyze HJ branch migration. Pseudomonas aeruginosa (P. aeruginosa, Pa) is a ubiquitous opportunistic bacterial pathogen that can cause serious infection in a variety of host species, including vertebrate animals, insects and plants. Here, we describe the cryo-Electron Microscopy (cryo-EM) structure of the RuvAB-HJ intermediate complex from P. aeruginosa. The structure shows that two RuvA tetramers sandwich HJ at the junction center and disrupt base pairs at the branch points of RuvB-free HJ arms. Eight RuvB subunits are recruited by the RuvA octameric core and form two open-rings to encircle two opposite HJ arms. Each RuvB subunit individually binds a RuvA domain III. The four RuvB subunits within the ring display distinct subdomain conformations, and two of them engage the central DNA duplex at both strands with their C-terminal β-hairpins. Together with the biochemical analyses, our structure implicates a potential mechanism of RuvB motor assembly onto HJ DNA.

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