Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification on biology

Zheng, Fengwei; Georgescu, Roxana E.; Yao, Nina Y.; O'Donnell, Mike; H, Li

doi:10.1016/j.celrep.2023.112694

Cited by 8 publications

(2 citation statements)

References 73 publications

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“…In further support of this hypothesis, the T4 bacteriophage sliding clamp (in the presence of p/t-DNA) is opened into a right-handed spiral by its cognate clamp loader 16 , and MD simulations show that the free T4 clamp prefers to adopt a right-handed spiral in the open form 59 . We also note that Rad24-RFC, which shares four out of five subunits with the RFC loader, opens the 9-1-1 clamp into a planar conformation 23,24,60 . Accordingly, we predict that the free 9-1-1 clamp prefers planar opening, even without the presence of the Rad24-RFC loader.…”

Section: Discussionmentioning

confidence: 77%

Differences in clamp loader mechanism between bacteria and eukaryotes

Landeck,

Pajak,

Norman

et al. 2023

Preprint

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SUMMARYClamp loaders are pentameric ATPases that place circular sliding clamps onto DNA, where they function in DNA replication and genome integrity. The central activity of a clamp loader is the opening of the ring-shaped sliding clamp, and the subsequent binding to primer-template (p/t)-junctions. The general architecture of clamp loaders is conserved across all life, suggesting that their mechanism is retained. Recent structural studies of the eukaryotic clamp loader Replication Factor C (RFC) revealed that it functions using a crab-claw mechanism, where clamp opening is coupled to a massive conformational change in the loader. Here we investigate the clamp loading mechanism of theE. coliclamp loader at high resolution using cryo-electron microscopy (cryo-EM). We find that theE. coliclamp loader opens the clamp using a crab-claw motion at a single pivot point, whereas the eukaryotic RFC loader uses motions distributed across the complex. Furthermore, we find clamp opening occurs in multiple steps, starting with a partly open state with a spiral conformation, and proceeding to a wide open clamp in a surprising planar geometry. Finally, our structures in the presence of p/t-junctions illustrate how clamp closes around p/t-junctions and how the clamp loader initiates release from the loaded clamp. Our results reveal mechanistic distinctions in a macromolecular machine that is conserved across all domains of life.

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Section: Discussionmentioning

confidence: 77%

Differences in clamp loader mechanism between bacteria and eukaryotes

Landeck,

Pajak,

Norman

et al. 2023

Preprint

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“…Junctional MHs formed by A-EJ involve limited resection and fill-in processes. Implicated factors include, among others, CtIP (13), Mre11 and associated RAD50-NBS1 (MRN) (14)(15)(16)(17), and loaders of DNA clamps to tether polymerases, such as polymerase theta (Polθ) and polymerase lambda (Polλ) (11,(18)(19)(20)(21)(22). Ataxiatelangiectasia mutated (ATM)-mediated phosphorylation of CtIP stimulates sequential Mre11 endo-and exonuclease activity to remove protein-bound or -adducted 5′ ends (23)(24)(25)(26), whereas DNA2 promotes resection of clean ends (27).…”

Section: Introductionmentioning

confidence: 99%

ATM and 53BP1 regulate alternative end joining–mediated V(D)J recombination

Wang,

Sadeghi,

et al. 2024

Sci. Adv.

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G 0 -G 1 phase alternative end joining (A-EJ) is a recently defined mutagenic pathway characterized by resected deletion and translocation joints that are predominantly direct and are distinguished from A-EJ in cycling cells that rely much more on microhomology-mediated end joining (MMEJ). Using chemical and genetic approaches, we systematically evaluate potential A-EJ factors and DNA damage response (DDR) genes to support this mechanism by mapping the repair fates of RAG1/2-initiated double-strand breaks in the context of Igκ locus V-J recombination and chromosome translocation. Our findings highlight a polymerase theta–independent Parp1-XRCC1/LigIII axis as central A-EJ components, supported by 53BP1 in the context of an Ataxia-telangiectasia mutated (ATM)–activated DDR. Mechanistically, we demonstrate varied changes in short-range resection, MMEJ, and translocation, imposed by compromising specific DDR activities, which include polymerase alpha, Ataxia-telangiectasia and Rad3-related (ATR), DNA2, and Mre11. This study advances our understanding of DNA damage repair within the 53BP1 regulatory domain and the RAG1/2 postcleavage complex.

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