scholarly journals Computational Analysis of Retrovirus-Inducedscid Cell Death

2001 ◽  
Vol 75 (7) ◽  
pp. 3121-3128 ◽  
Author(s):  
René Daniel ◽  
Samuel Litwin ◽  
Richard A. Katz ◽  
Anna Marie Skalka
Keyword(s):  
Cell Death ◽  
Nonhomologous End Joining ◽  
End Joining ◽  
Dependent Protein Kinase ◽  
Retroviral Infection ◽  
Dna Integration ◽  
Modeling Approach ◽  
Dependent Protein ◽  
A Cell ◽  
Pass Through

ABSTRACT It was shown recently that retroviral infection induces integrase-dependent apoptosis (programmed cell death) in DNA-dependent protein kinase (DNA-PK)-deficient scid pre-B cell lines, and it has been proposed that retroviral DNA integration is perceived as DNA damage that is repairable by the DNA-PK-dependent nonhomologous end-joining pathway (R. Daniel, R. A. Katz, and A. M. Skalka, Science 284:644–647, 1999). Very few infectious virions seem to be necessary to induce scid cell death. In this study, we used a modeling approach to estimate the number of integration events necessary to induce cell death of DNA-PK-deficient scid cells. Several models for integration-mediated cell killing were considered. Our analyses indicate that a single hit (integration event) is sufficient to kill a scid cell. Moreover, the closest fit between the experimental data and our computational simulations was achieved with a model in which the infectedscid cell must pass through S phase to trigger apoptosis. This model is consistent with the findings that a single double-strand DNA break is sufficient to kill a cell deficient in DNA repair and illustrates the potential of a modeling approach to address quantitative aspects of virus-cell interactions.

scholarly journals Cryo-EM structure of the DNA-PK holoenzyme

2017 ◽  
Vol 114 (28) ◽  
pp. 7367-7372 ◽  
Author(s):  
Humayun Sharif ◽  
Yang Li ◽  
Yuanchen Dong ◽  
Liyi Dong ◽  
Wei Li Wang ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Interaction ◽  
Kinase Domain ◽  
Nonhomologous End Joining ◽  
Globular Domain ◽  
End Joining ◽  
Large Protein ◽  
Dependent Protein Kinase ◽  
Cryo Electron Microscopy ◽  
Dependent Protein

DNA-dependent protein kinase (DNA-PK) is a large protein complex central to the nonhomologous end joining (NHEJ) DNA-repair pathway. It comprises the DNA-PK catalytic subunit (DNA-PKcs) and the heterodimer of DNA-binding proteins Ku70 and Ku80. Here, we report the cryo-electron microscopy (cryo-EM) structures of human DNA-PKcs at 4.4-Å resolution and the DNA-PK holoenzyme at 5.8-Å resolution. The DNA-PKcs structure contains three distinct segments: the N-terminal region with an arm and a bridge, the circular cradle, and the head that includes the kinase domain. Two perpendicular apertures exist in the structure, which are sufficiently large for the passage of dsDNA. The DNA-PK holoenzyme cryo-EM map reveals density for the C-terminal globular domain of Ku80 that interacts with the arm of DNA-PKcs. The Ku80-binding site is adjacent to the previously identified density for the DNA-binding region of the Ku70/Ku80 complex, suggesting concerted DNA interaction by DNA-PKcs and the Ku complex.

scholarly journals DNA-dependent protein kinase in nonhomologous end joining: a lock with multiple keys?

2007 ◽  
Vol 179 (2) ◽  
pp. 183-186 ◽  
Author(s):  
Eric Weterings ◽  
David J. Chen
Keyword(s):  
Protein Kinase ◽  
Strand Break ◽  
Nonhomologous End Joining ◽  
End Joining ◽  
Dsb Repair ◽  
Dependent Protein Kinase ◽  
Dna Molecule ◽  
Dna Double Strand Break ◽  
Dependent Protein ◽  
Multiple Keys

The DNA-dependent protein kinase (DNA-PK) is one of the central enzymes involved in DNA double-strand break (DSB) repair. It facilitates proper alignment of the two ends of the broken DNA molecule and coordinates access of other factors to the repair complex. We discuss the latest findings on DNA-PK phosphorylation and offer a working model for the regulation of DNA-PK during DSB repair.

scholarly journals DNA-dependent protein kinase promotes DNA end processing by MRN and CtIP

2020 ◽  
Vol 6 (2) ◽  
pp. eaay0922 ◽  
Author(s):  
Rajashree A. Deshpande ◽  
Logan R. Myler ◽  
Michael M. Soniat ◽  
Nodar Makharashvili ◽  
Linda Lee ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Homologous Recombination ◽  
Single Molecule ◽  
Strand Break ◽  
Nonhomologous End Joining ◽  
End Joining ◽  
Dependent Protein Kinase ◽  
Mrn Complex ◽  
Dependent Protein ◽  
Dna Ends

The repair of DNA double-strand breaks occurs through nonhomologous end joining or homologous recombination in vertebrate cells—a choice that is thought to be decided by a competition between DNA-dependent protein kinase (DNA-PK) and the Mre11/Rad50/Nbs1 (MRN) complex but is not well understood. Using ensemble biochemistry and single-molecule approaches, here, we show that the MRN complex is dependent on DNA-PK and phosphorylated CtIP to perform efficient processing and resection of DNA ends in physiological conditions, thus eliminating the competition model. Endonucleolytic removal of DNA-PK–bound DNA ends is also observed at double-strand break sites in human cells. The involvement of DNA-PK in MRN-mediated end processing promotes an efficient and sequential transition from nonhomologous end joining to homologous recombination by facilitating DNA-PK removal.

scholarly journals Fixing DNA breaks during class switch recombination

2008 ◽  
Vol 205 (3) ◽  
pp. 509-513 ◽  
Author(s):  
Christopher J. Jolly ◽  
Adam J.L. Cook ◽  
John P. Manis
Keyword(s):  
Dna Sequences ◽  
Class Switch Recombination ◽  
Nonhomologous End Joining ◽  
Repair Pathway ◽  
Dna Breaks ◽  
End Joining ◽  
Dependent Protein Kinase ◽  
Class Switch ◽  
Dependent Protein

Immunoglobulin (Ig) class switch recombination (CSR) involves the breakage and subsequent repair of two DNA sequences, known as switch (S) regions, which flank IgH constant region exons. The resolution of CSR-associated breaks is thought to require the nonhomologous end-joining (NHEJ) DNA repair pathway, but the role of the NHEJ factor DNA-dependent protein kinase catalytic subunit (DNA-PKcs) in this process has been unclear. A new study, in which broken IgH-containing chromosomes in switching B cells were visualized directly, clearly demonstrated that DNA-PKcs and, unexpectedly, the nuclease Artemis are involved in the resolution of switch breaks.

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