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Kim Y, Lizana L, Jeon JH. Fractal and Knot-Free Chromosomes Facilitate Nucleoplasmic Transport. PHYSICAL REVIEW LETTERS 2022; 128:038101. [PMID: 35119884 DOI: 10.1103/physrevlett.128.038101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Chromosomes in the nucleus assemble into hierarchies of 3D domains that, during interphase, share essential features with a knot-free condensed polymer known as the fractal globule (FG). The FG-like chromosome likely affects macromolecular transport, yet its characteristics remain poorly understood. Using computer simulations and scaling analysis, we show that the 3D folding and macromolecular size of the chromosomes determine their transport characteristics. Large-scale subdiffusion occurs at a critical particle size where the network of accessible volumes is critically connected. Condensed chromosomes have connectivity networks akin to simple Bernoulli bond percolation clusters, regardless of the polymer models. However, even if the network structures are similar, the tracer's walk dimension varies. It turns out that the walk dimension depends on the network topology of the accessible volume and dynamic heterogeneity of the tracer's hopping rate. We find that the FG structure has a smaller walk dimension than other random geometries, suggesting that the FG-like chromosome structure accelerates macromolecular diffusion and target-search.
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Affiliation(s)
- Yeonghoon Kim
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Ludvig Lizana
- Integrated Science Lab, Department of Physics, Umeå University, Umeå 90187, Sweden
| | - Jae-Hyung Jeon
- Department of Physics, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
- Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
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2
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Muster B, Rapp A, Cardoso MC. Systematic analysis of DNA damage induction and DNA repair pathway activation by continuous wave visible light laser micro-irradiation. AIMS GENETICS 2017; 4:47-68. [PMID: 31435503 PMCID: PMC6690239 DOI: 10.3934/genet.2017.1.47] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/16/2017] [Indexed: 01/19/2023]
Abstract
Laser micro-irradiation can be used to induce DNA damage with high spatial and temporal resolution, representing a powerful tool to analyze DNA repair in vivo in the context of chromatin. However, most lasers induce a mixture of DNA damage leading to the activation of multiple DNA repair pathways and making it impossible to study individual repair processes. Hence, we aimed to establish and validate micro-irradiation conditions together with inhibition of several key proteins to discriminate different types of DNA damage and repair pathways using lasers commonly available in confocal microscopes. Using time-lapse analysis of cells expressing fluorescently tagged repair proteins and also validation of the DNA damage generated by micro-irradiation using several key damage markers, we show that irradiation with a 405 nm continuous wave laser lead to the activation of all repair pathways even in the absence of exogenous sensitization. In contrast, we found that irradiation with 488 nm laser lead to the selective activation of non-processive short-patch base excision and single strand break repair, which were further validated by PARP inhibition and metoxyamine treatment. We conclude that these low energy conditions discriminated against processive long-patch base excision repair, nucleotide excision repair as well as double strand break repair pathways.
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Affiliation(s)
- Britta Muster
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Alexander Rapp
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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3
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Chaudhary N, Nakka KK, Chavali PL, Bhat J, Chatterjee S, Chattopadhyay S. SMAR1 coordinates HDAC6-induced deacetylation of Ku70 and dictates cell fate upon irradiation. Cell Death Dis 2014; 5:e1447. [PMID: 25299772 PMCID: PMC4237237 DOI: 10.1038/cddis.2014.397] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 08/11/2014] [Accepted: 08/14/2014] [Indexed: 11/30/2022]
Abstract
Acetylation status of DNA end joining protein Ku70 dictates its function in DNA repair and Bax-mediated apoptosis. Despite the knowledge of HDACs and HATs that are reported to modulate the acetylation dynamics of Ku70, very little is known about proteins that critically coordinate these key modifications. Here, we demonstrate that nuclear matrix-associated protein scaffold/matrix-associated region-binding protein 1 (SMAR1) is a novel interacting partner of Ku70 and coordinates with HDAC6 to maintain Ku70 in a deacetylated state. Our studies revealed that knockdown of SMAR1 results in enhanced acetylation of Ku70, which leads to impaired recruitment of Ku70 in the chromatin fractions. Interestingly, ionizing radiation (IR) induces the expression of SMAR1 and its redistribution as distinct nuclear foci upon ATM-mediated phosphorylation at serine 370. Furthermore, SMAR1 regulates IR-induced G2/M cell cycle arrest by facilitating Chk2 phosphorylation. Alternatively, SMAR1 provides radioresistance by modulating the association of deacetylated Ku70 with Bax, abrogating the mitochondrial translocation of Bax. Thus, we provide mechanistic insights of SMAR1-mediated regulation of repair and apoptosis via a complex crosstalk involving Ku70, HDAC6 and Bax.
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Affiliation(s)
- N Chaudhary
- Chromatin and Disease Biology Laboratory, National Centre for Cell Science, Pune University Campus, Pune, India
| | - K K Nakka
- Chromatin and Disease Biology Laboratory, National Centre for Cell Science, Pune University Campus, Pune, India
| | - P L Chavali
- Chromatin and Disease Biology Laboratory, National Centre for Cell Science, Pune University Campus, Pune, India
| | - J Bhat
- Department of Biophysics, Bose Institute, Kolkata, India
| | - S Chatterjee
- Department of Biophysics, Bose Institute, Kolkata, India
| | - S Chattopadhyay
- Chromatin and Disease Biology Laboratory, National Centre for Cell Science, Pune University Campus, Pune, India
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4
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Cabrero J, Bakkali M, Navarro-Domínguez B, Ruíz-Ruano FJ, Martín-Blázquez R, López-León MD, Camacho JPM. The Ku70 DNA-repair protein is involved in centromere function in a grasshopper species. Chromosome Res 2013; 21:393-406. [PMID: 23797468 DOI: 10.1007/s10577-013-9367-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/07/2013] [Accepted: 06/09/2013] [Indexed: 01/05/2023]
Abstract
The Ku70 protein is involved in numerous cell functions, the nonhomologous end joining (NHEJ) DNA repair pathway being the best known. Here, we report a novel function for this protein in the grasshopper Eyprepocnemis plorans. We observed the presence of large Ku70 foci on the centromeres of meiotic and mitotic chromosomes during the cell cycle stages showing the highest centromeric activity (i.e., metaphase and anaphase). The fact that colchicine treatment prevented centromeric location of Ku70, suggests a microtubule-dependent centromeric function for Ku70. Likewise, the absence of Ku70 at metaphase-anaphase centromeres from three males whose Ku70 gene had been knocked down using interference RNA, and the dramatic increase in the frequency of polyploid spermatids observed in these males, suggest that the centromeric presence of Ku70 is required for normal cytokinesis in this species. The centromeric function of Ku70 was not observed in 14 other grasshopper and locust species, or in the mouse, thus suggesting that it is an autapomorphy in E. plorans.
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Affiliation(s)
- Josefa Cabrero
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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5
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Tobias F, Löb D, Lengert N, Durante M, Drossel B, Taucher-Scholz G, Jakob B. Spatiotemporal dynamics of early DNA damage response proteins on complex DNA lesions. PLoS One 2013; 8:e57953. [PMID: 23469115 PMCID: PMC3582506 DOI: 10.1371/journal.pone.0057953] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 01/29/2013] [Indexed: 11/18/2022] Open
Abstract
The response of cells to ionizing radiation-induced DNA double-strand breaks (DSB) is determined by the activation of multiple pathways aimed at repairing the injury and maintaining genomic integrity. Densely ionizing radiation induces complex damage consisting of different types of DNA lesions in close proximity that are difficult to repair and may promote carcinogenesis. Little is known about the dynamic behavior of repair proteins on complex lesions. In this study we use live-cell imaging for the spatio-temporal characterization of early protein interactions at damage sites of increasing complexity. Beamline microscopy was used to image living cells expressing fluorescently-tagged proteins during and immediately after charged particle irradiation to reveal protein accumulation at damaged sites in real time. Information on the mobility and binding rates of the recruited proteins was obtained from fluorescence recovery after photobleaching (FRAP). Recruitment of the DNA damage sensor protein NBS1 accelerates with increasing lesion density and saturates at very high damage levels. FRAP measurements revealed two different binding modalities of NBS1 to damage sites and a direct impact of lesion complexity on the binding. Faster recruitment with increasing lesion complexity was also observed for the mediator MDC1, but mobility was limited at very high damage densities due to nuclear-wide binding. We constructed a minimal computer model of the initial response to DSB based on known protein interactions only. By fitting all measured data using the same set of parameters, we can reproduce the experimentally characterized steps of the DNA damage response over a wide range of damage densities. The model suggests that the influence of increasing lesion density accelerating NBS1 recruitment is only dependent on the different binding modes of NBS1, directly to DSB and to the surrounding chromatin via MDC1. This elucidates an impact of damage clustering on repair without the need of invoking extra processing steps.
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Affiliation(s)
- Frank Tobias
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
| | - Daniel Löb
- TU Darmstadt, Institut für Festkörperphysik, Darmstadt, Germany
| | - Nicor Lengert
- TU Darmstadt, Institut für Festkörperphysik, Darmstadt, Germany
| | - Marco Durante
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
- TU Darmstadt, Institut für Festkörperphysik, Darmstadt, Germany
| | - Barbara Drossel
- TU Darmstadt, Institut für Festkörperphysik, Darmstadt, Germany
| | | | - Burkhard Jakob
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt, Germany
- * E-mail:
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Shao B, Yago T, Coghill PA, Klopocki AG, Mehta-D'souza P, Schmidtke DW, Rodgers W, McEver RP. Signal-dependent slow leukocyte rolling does not require cytoskeletal anchorage of P-selectin glycoprotein ligand-1 (PSGL-1) or integrin αLβ2. J Biol Chem 2012; 287:19585-98. [PMID: 22511754 DOI: 10.1074/jbc.m112.361519] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In inflamed venules, neutrophils roll on P- or E-selectin, engage P-selectin glycoprotein ligand-1 (PSGL-1), and signal extension of integrin α(L)β(2) in a low affinity state to slow rolling on intercellular adhesion molecule-1 (ICAM-1). Cytoskeleton-dependent receptor clustering often triggers signaling, and it has been hypothesized that the cytoplasmic domain links PSGL-1 to the cytoskeleton. Chemokines cause rolling neutrophils to fully activate α(L)β(2), leading to arrest on ICAM-1. Cytoskeletal anchorage of α(L)β(2) has been linked to chemokine-triggered extension and force-regulated conversion to the high affinity state. We asked whether PSGL-1 must interact with the cytoskeleton to initiate signaling and whether α(L)β(2) must interact with the cytoskeleton to extend. Fluorescence recovery after photobleaching of transfected cells documented cytoskeletal restraint of PSGL-1. The lateral mobility of PSGL-1 similarly increased by depolymerizing actin filaments with latrunculin B or by mutating the cytoplasmic tail to impair binding to the cytoskeleton. Converting dimeric PSGL-1 to a monomer by replacing its transmembrane domain did not alter its mobility. By transducing retroviruses expressing WT or mutant PSGL-1 into bone marrow-derived macrophages from PSGL-1-deficient mice, we show that PSGL-1 required neither dimerization nor cytoskeletal anchorage to signal β(2) integrin-dependent slow rolling on P-selectin and ICAM-1. Depolymerizing actin filaments or decreasing actomyosin tension in neutrophils did not impair PSGL-1- or chemokine-mediated integrin extension. Unlike chemokines, PSGL-1 did not signal cytoskeleton-dependent swing out of the β(2)-hybrid domain associated with the high affinity state. The cytoskeletal independence of PSGL-1-initiated, α(L)β(2)-mediated slow rolling differs markedly from the cytoskeletal dependence of chemokine-initiated, α(L)β(2)-mediated arrest.
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Affiliation(s)
- Bojing Shao
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, USA
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7
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Arbuckle JL, Rahman NS, Zhao S, Rodgers W, Rodgers KK. Elucidating the domain architecture and functions of non-core RAG1: the capacity of a non-core zinc-binding domain to function in nuclear import and nucleic acid binding. BMC BIOCHEMISTRY 2011; 12:23. [PMID: 21599978 PMCID: PMC3124419 DOI: 10.1186/1471-2091-12-23] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 05/20/2011] [Indexed: 12/19/2022]
Abstract
Background The repertoire of the antigen-binding receptors originates from the rearrangement of immunoglobulin and T-cell receptor genetic loci in a process known as V(D)J recombination. The initial site-specific DNA cleavage steps of this process are catalyzed by the lymphoid specific proteins RAG1 and RAG2. The majority of studies on RAG1 and RAG2 have focused on the minimal, core regions required for catalytic activity. Though not absolutely required, non-core regions of RAG1 and RAG2 have been shown to influence the efficiency and fidelity of the recombination reaction. Results Using a partial proteolysis approach in combination with bioinformatics analyses, we identified the domain boundaries of a structural domain that is present in the 380-residue N-terminal non-core region of RAG1. We term this domain the Central Non-core Domain (CND; residues 87-217). Conclusions We show how the CND alone, and in combination with other regions of non-core RAG1, functions in nuclear localization, zinc coordination, and interactions with nucleic acid. Together, these results demonstrate the multiple roles that the non-core region can play in the function of the full length protein.
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Affiliation(s)
- Janeen L Arbuckle
- Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73190, USA
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8
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Chen CC, Yang YC, Wang WH, Chen CS, Chang LK. Enhancement of Zta-activated lytic transcription of Epstein-Barr virus by Ku80. J Gen Virol 2010; 92:661-8. [DOI: 10.1099/vir.0.026302-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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9
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KOIKE M, KOIKE A, SUGASAWA J, TOYOOKA T, IBUKI Y. Dynamics of Ku80 in Living Hamster Cells with DNA Double-Strand Breaks Induced by Chemotherapeutic Drugs. J Vet Med Sci 2010; 72:1405-12. [DOI: 10.1292/jvms.10-0185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Manabu KOIKE
- DNA Repair Gene Res., National Institute of Radiological Sciences
| | - Aki KOIKE
- DNA Repair Gene Res., National Institute of Radiological Sciences
| | - Jun SUGASAWA
- DNA Repair Gene Res., National Institute of Radiological Sciences
| | - Tatsushi TOYOOKA
- Laboratory of Radiation Biology, Graduate School of Nutritional and Environmental Sciences, University of Shizuoka
| | - Yuko IBUKI
- Laboratory of Radiation Biology, Graduate School of Nutritional and Environmental Sciences, University of Shizuoka
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10
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Fang L, Wang Y, Du D, Yang G, Tak Kwok T, Kai Kong S, Chen B, Chen DJ, Chen Z. Cell polarity protein Par3 complexes with DNA-PK via Ku70 and regulates DNA double-strand break repair. Cell Res 2007; 17:100-16. [PMID: 17287830 DOI: 10.1038/sj.cr.7310145] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The partitioning-defective 3 (Par3), a key component in the conserved Par3/Par6/aPKC complex, plays fundamental roles in cell polarity. Herein we report the identification of Ku70 and Ku80 as novel Par3-interacting proteins through an in vitro binding assay followed by liquid chromatography-tandem mass spectrometry. Ku70/Ku80 proteins are two key regulatory subunits of the DNA-dependent protein kinase (DNA-PK), which plays an essential role in repairing double-strand DNA breaks (DSBs). We determined that the nuclear association of Par3 with Ku70/Ku80 was enhanced by gamma-irradiation (IR), a potent DSB inducer. Furthermore, DNA-PKcs, the catalytic subunit of DNA-PK, interacted with the Par3/Ku70/Ku80 complex in response to IR. Par3 over-expression or knockdown was capable of up- or downregulating DNA-PK activity, respectively. Moreover, the Par3 knockdown cells were found to be defective in random plasmid integration, defective in DSB repair following IR, and radiosensitive, phenotypes similar to that of Ku70 knockdown cells. These findings identify Par3 as a novel component of the DNA-PK complex and implicate an unexpected link of cell polarity to DSB repair.
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Affiliation(s)
- Longhou Fang
- Key Laboratory of Proteomics and Laboratory of Molecular Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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11
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Mari PO, Florea BI, Persengiev SP, Verkaik NS, Brüggenwirth HT, Modesti M, Giglia-Mari G, Bezstarosti K, Demmers JAA, Luider TM, Houtsmuller AB, van Gent DC. Dynamic assembly of end-joining complexes requires interaction between Ku70/80 and XRCC4. Proc Natl Acad Sci U S A 2006; 103:18597-602. [PMID: 17124166 PMCID: PMC1693708 DOI: 10.1073/pnas.0609061103] [Citation(s) in RCA: 297] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA double-strand break (DSB) repair by nonhomologous end joining (NHEJ) requires the assembly of several proteins on DNA ends. Although biochemical studies have elucidated several aspects of the NHEJ reaction mechanism, much less is known about NHEJ in living cells, mainly because of the inability to visualize NHEJ repair proteins at DNA damage. Here we provide evidence that a pulsed near IR laser can produce DSBs without any visible alterations in the nucleus, and we show that NHEJ proteins accumulate in the irradiated areas. The levels of DSBs and Ku accumulation diminished in time, showing that this approach allows us to study DNA repair kinetics in vivo. Remarkably, the Ku heterodimers on DNA ends were in dynamic equilibrium with Ku70/80 in solution, showing that NHEJ complex assembly is reversible. Accumulation of XRCC4/ligase IV on DSBs depended on the presence of Ku70/80, but not DNA-PK(CS). We detected a direct interaction between Ku70 and XRCC4 that could explain these requirements. Our results suggest that this assembly constitutes the core of the NHEJ reaction and that XRCC4 may serve as a flexible tether between Ku70/80 and ligase IV.
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Affiliation(s)
- Pierre-Olivier Mari
- Departments of *Cell Biology and Genetics
- Pathology, Erasmus MC, University Medical Center, 3000 CA, Rotterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | - Dik C. van Gent
- Departments of *Cell Biology and Genetics
- To whom correspondence should be addressed at:
Department of Cell Biology and Genetics, Erasmus MC, University Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands. E-mail:
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12
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Lacroix B, Li J, Tzfira T, Citovsky V. Will you let me use your nucleus? How Agrobacterium gets its T-DNA expressed in the host plant cell. Can J Physiol Pharmacol 2006; 84:333-45. [PMID: 16902581 DOI: 10.1139/y05-108] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Agrobacterium is the only known bacterium capable of natural DNA transfer into a eukaryotic host. The genes transferred to host plants are contained on a T-DNA (transferred DNA) molecule, the transfer of which begins with its translocation, along with several effector proteins, from the bacterial cell to the host-cell cytoplasm. In the host cytoplasm, the T-complex is formed from a single-stranded copy of the T-DNA (T-strand) associated with several bacterial and host proteins and it is imported into the host nucleus via interactions with the host nuclear import machinery. Once inside the nucleus, the T-complex is most likely directed to the host genome by associating with histones. Finally, the chromatin-associated T-complex is uncoated from its escorting proteins prior to the conversion of the T-strand to a double-stranded form and its integration into the host genome.
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Affiliation(s)
- Benoît Lacroix
- Department of Biochemistry and Cell Biology, State University of NY, Stony Brook, 11794-5212, USA.
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13
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Mortusewicz O, Rothbauer U, Cardoso MC, Leonhardt H. Differential recruitment of DNA Ligase I and III to DNA repair sites. Nucleic Acids Res 2006; 34:3523-32. [PMID: 16855289 PMCID: PMC1524911 DOI: 10.1093/nar/gkl492] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2006] [Revised: 06/22/2006] [Accepted: 06/27/2006] [Indexed: 12/30/2022] Open
Abstract
DNA ligation is an essential step in DNA replication, repair and recombination. Mammalian cells contain three DNA Ligases that are not interchangeable although they use the same catalytic reaction mechanism. To compare the recruitment of the three eukaryotic DNA Ligases to repair sites in vivo we introduced DNA lesions in human cells by laser microirradiation. Time lapse microscopy of fluorescently tagged proteins showed that DNA Ligase III accumulated at microirradiated sites before DNA Ligase I, whereas we could detect only a faint accumulation of DNA Ligase IV. Recruitment of DNA Ligase I and III to repair sites was cell cycle independent. Mutational analysis and binding studies revealed that DNA Ligase I was recruited to DNA repair sites by interaction with PCNA while DNA Ligase III was recruited via its BRCT domain mediated interaction with XRCC1. Selective recruitment of specialized DNA Ligases may have evolved to accommodate the particular requirements of different repair pathways and may thus enhance efficiency of DNA repair.
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Affiliation(s)
- Oliver Mortusewicz
- Department of Biology II, Ludwig Maximilians University Munich82152 Planegg-Martinsried, Germany
- Max Delbrück Center for Molecular Medicine13125 Berlin, Germany
| | - Ulrich Rothbauer
- Department of Biology II, Ludwig Maximilians University Munich82152 Planegg-Martinsried, Germany
- Max Delbrück Center for Molecular Medicine13125 Berlin, Germany
| | | | - Heinrich Leonhardt
- To whom correspondence should be addressed. Tel: +49 89 2180 74232; Fax: +49 89 2180 74236; E-mail:
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14
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Takahagi M, Tatsumi K. Aggregative organization enhances the DNA end-joining process that is mediated by DNA-dependent protein kinase. FEBS J 2006; 273:3063-75. [PMID: 16759233 DOI: 10.1111/j.1742-4658.2006.05317.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The occurrence of DNA double-strand breaks in the nucleus provokes in its structural organization a large-scale alteration whose molecular basis is still mostly unclear. Here, we show that double-strand breaks trigger preferential assembly of nucleoproteins in human cellular fractions and that they mediate the separation of large protein-DNA aggregates from aqueous solution. The interaction among the aggregative nucleoproteins presents a dynamic condition that allows the effective interaction of nucleoproteins with external molecules like free ATP and facilitates intrinsic DNA end-joining activity. This aggregative organization is functionally coacervate-like. The key component is DNA-dependent protein kinase (DNA-PK), which can be characterized as a DNA-specific aggregation factor as well as a nuclear scaffold/matrix-interactive factor. In the context of aggregation, the kinase activity of DNA-PK is essential for efficient DNA end-joining. The massive and functional concentration of nucleoproteins on DNA in vitro may represent a possible status of nuclear dynamics in vivo, which probably includes the DNA-PK-dependent response to multiple double-strand breaks.
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Affiliation(s)
- Masahiko Takahagi
- Research Center for Radiation Safety, National Institute of Radiological Sciences, Chiba, Japan
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15
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Sibani S, Price GB, Zannis-Hadjopoulos M. Ku80 binds to human replication origins prior to the assembly of the ORC complex. Biochemistry 2005; 44:7885-96. [PMID: 15910003 DOI: 10.1021/bi047327n] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Ku heterodimer, an abundant nuclear protein, binds DNA replication origins in a sequence-specific manner and promotes initiation. In this study, using HCT116 Ku80+/- haplo-insufficient and Orc2(delta/-) hypomorphic cells, the order of binding of Ku and the human origin recognition complex (HsORC) was determined. The nuclear expression of Ku80 was found to be decreased by 60% in Ku80+/- cells, while its general association with chromatin was decreased by 33%. Coimmunoprecipitation studies indicated that the Ku heterodimer associates specifically with the human HsOrc-2, -3, -4, and -6 subunits. Chromatin immunoprecipitation (ChIP) experiments, using cells synchronized to late G1, showed that the association of Ku80 with the lamin B2, beta-globin, and c-myc origins in vivo was decreased by 1.5-, 2.3-, and 2.5-fold, respectively, in Ku80+/- cells. The association of HsOrc-3, -4, and -6 was consistently decreased in all three origins examined in Ku80+/- cells, while that of HsOrc-2 showed no significant variation, indicating that the HsOrc-3, -4, and -6 subunits bind to the origins after Ku80. In Orc2(delta/-) cells, the association of HsOrc-2 with the lamin B2, beta-globin, and c-myc origins was decreased by 2.8-, 4.9-, and 2.8-fold, respectively, relative to wild-type HCT116 cells. Furthermore, nascent strand abundance at these three origins was decreased by 4.5-, 2.3-, and 2.6-fold in Orc2(delta/-) relative to HCT116 cells, respectively. Interestingly, the association of Ku80 with these origins was not affected in this hypomorphic cell line, indicating that Ku and HsOrc-2 bind to origins independently of each other.
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Affiliation(s)
- Sahar Sibani
- McGill Cancer Center and Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 1Y6
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16
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Abstract
The latest development of imaging technology and fluorescent proteins has enabled us to visualize the dynamics of chromatin proteins in living cells. Particularly, photobleaching techniques like fluorescence recovery after photobleaching (FRAP) revealed the mobility of many nuclear proteins including histones. Although most nucleosomal histones are maintained over cell generations to maintain epigenetic marks on their tails, some exhibit dynamic exchange. In general, histone H3-H4 tetramers stably bind to DNA once assembled during DNA replication; in contrast, the H2A-H2B dimers exchange slowly in euchromatin and are evicted during transcription. Recent data further indicate that different histone variants have different localization and kinetics. The replacement H3 variant, H3.3, is incorporated into transcriptionally active chromatin independently of DNA replication, and the centromeric variant, CENP-A, appears to assemble into nucleosomes in centromeres during G2 phase by replacing canonical H3. Different behaviors of H2A variants are also demonstrated. Importantly, the mobility of histones, and other nuclear proteins, is altered in response to changes in cellular physiology and various stimuli. Whereas we know little about how these dynamics are regulated, distinct complexes that mediate assembly and exchange of specific variants have been isolated, thus future analyses will reveal the molecular mechanisms underlying the phenomena in living cells.
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Affiliation(s)
- Hiroshi Kimura
- Nuclear Function and Dynamics Unit, HMRO, School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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Drouet J, Delteil C, Lefrançois J, Concannon P, Salles B, Calsou P. DNA-dependent protein kinase and XRCC4-DNA ligase IV mobilization in the cell in response to DNA double strand breaks. J Biol Chem 2004; 280:7060-9. [PMID: 15520013 DOI: 10.1074/jbc.m410746200] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Repair of DNA double strand breaks (DSBs) by the non-homologous end joining (NHEJ) pathway in mammals requires at least the DNA-dependent protein kinase (DNA-PK) and the DNA ligase IV-XRCC4 protein complexes. DNA-PK comprises the Ku70/Ku80 heterodimer and the catalytic subunit DNA-PKcs. Here we report the first description of the nuclear mobilization of endogenous NHEJ proteins after exposure of human cells to double strand-breaking agents. DSB infliction specifically induced a dose- and time-dependent mobilization of Ku70/80, DNA-PKcs, XRCC4, and DNA ligase IV proteins from a soluble nucleoplasmic compartment to a less extractable nuclear fraction. XRCC4 recruitment was accompanied by its DNA-PK-dependent phosphorylation. The recruited proteins co-immunoprecipitated, indicating that they had assembled into complexes. However, DNA-PK was attached to chromatin, whereas XRCC4-ligase IV resisted solubilization by DNase I. The rates of appearance and dissolution of NHEJ proteins paralleled that of histone variant H2AX phosphorylation and dephosphorylation. We established that under conditions of genomic DSB infliction 1) Ku recruitment was not dependent on the co-recruitment of the other NHEJ proteins, 2) DNA-PKcs was physically required for the mobilization of the XRCC4-ligase IV complex, 3) DNA ligase IV was physically necessary for stable recruitment of XRCC4, and 4) phosphorylation of either H2AX or XRCC4 was unnecessary for DNA-PK or XRCC4-ligase IV recruitment. Altogether these results offer insights into the interplay between key NHEJ proteins during this repair process in the cell.
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Affiliation(s)
- Jérôme Drouet
- Institut de Pharmacologie et de Biologie Structurale, CNRS UMR 5089, 205 route de Narbonne, 31077 Toulouse, Cedex 4, France
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18
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Gordy C, Mishra S, Rodgers W. Visualization of antigen presentation by actin-mediated targeting of glycolipid-enriched membrane domains to the immune synapse of B cell APCs. THE JOURNAL OF IMMUNOLOGY 2004; 172:2030-8. [PMID: 14764667 DOI: 10.4049/jimmunol.172.4.2030] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Glycolipid-enriched membrane (GEM) domains, or lipid rafts, function in signaling in immune cells, but their properties during Ag presentation are less clear. To address this question, GEM domains were studied using fluorescence cell imaging of mouse CH27 B cells presenting Ag to D10 T cells. Our experiments showed that APCs were enriched with GEM domains in the immune synapse, and this occurred in an actin-dependent manner. This enrichment was specific to GEM domains, because a marker for non-GEM regions of the membrane was excluded from the immune synapse. Furthermore, fluorescence photobleaching experiments showed that protein in the immune synapse was dynamic and rapidly exchanged with that in other compartments of CH27 cells. To identify the signals for targeting GEM domains to the immune synapse in APCs, capping of the domains was measured in cells after cross-linking surface molecules. This showed that co-cross-linking CD48 with MHC class II was required for efficient capping and intracellular signaling. Capping of GEM domains by co-cross-linking CD48 and MHC class II occurred with co-capping of filamentous actin, and both domain capping and T cell-CH27 cell conjugation were inhibited by pretreating CH27 cells with latrunculin B. Furthermore, disruption of the actin cytoskeleton of the CH27 cells also inhibited formation of a mature immune synapse in those T cells that did conjugate to APCs. Thus, Ag presentation and efficient T cell stimulation occur by an actin-dependent targeting of GEM domains in the APC to the site of T cell engagement.
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Affiliation(s)
- Claire Gordy
- Molecular Immunogenetics Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
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19
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Byrum J, Jordan S, Safrany ST, Rodgers W. Visualization of inositol phosphate-dependent mobility of Ku: depletion of the DNA-PK cofactor InsP6 inhibits Ku mobility. Nucleic Acids Res 2004; 32:2776-84. [PMID: 15150344 PMCID: PMC419599 DOI: 10.1093/nar/gkh592] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Repair of DNA double-strand breaks (DSBs) in mammalian cells by nonhomologous end-joining (NHEJ) is initiated by the DNA-PK protein complex. Recent studies have shown inositol hexakisphosphate (InsP6) is a potent cofactor for DNA-PK activity in NHEJ. Specifically, InsP6 binds to the Ku component of DNA-PK, where it induces a conformational change and a corresponding increase in DNA end-joining activity. However, the effect of InsP6 on the dynamics of Ku, such as its mobility in the nucleus, is unknown. Importantly, these dynamics reflect the character of Ku's interactions with other molecules. To address this question, the diffusion of Ku was measured by fluorescence photobleaching experiments using cells expressing green fluorescent protein (GFP)-labeled Ku. InsP6 was depleted by treating cells with calmodulin inhibitors, which included the compounds W7 and chlorpromazine. These treatments caused a 50% reduction in the mobile fraction of Ku-GFP, and this could be reversed by replenishing cells with InsP6. By expressing deletion mutants of Ku-GFP, it was determined that its W7-sensitive region occurred at the N-terminus of the dimerization domain of Ku70. These results therefore show that InsP6 enhances Ku mobility through a discrete region of Ku70, and modulation of InsP6 levels in cells represents a potential avenue for regulating NHEJ by affecting the dynamics of Ku and hence its interaction with other nuclear proteins.
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Affiliation(s)
- Jennifer Byrum
- Molecular Immunogenetics Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, MS 17, Oklahoma City, OK 73104, USA
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Affiliation(s)
- Jessica A Downs
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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21
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Carrero G, Crawford E, Th'ng J, de Vries G, Hendzel MJ. Quantification of Protein–Protein and Protein–DNA Interactions In Vivo, Using Fluorescence Recovery after Photobleaching. Methods Enzymol 2003; 375:415-42. [PMID: 14870681 DOI: 10.1016/s0076-6879(03)75026-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Gustavo Carrero
- Department of Mathematical and Statistical Sciences, Faculty of Science, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
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22
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Carrero G, McDonald D, Crawford E, de Vries G, Hendzel MJ. Using FRAP and mathematical modeling to determine the in vivo kinetics of nuclear proteins. Methods 2003; 29:14-28. [PMID: 12543068 DOI: 10.1016/s1046-2023(02)00288-8] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Fluorescence recovery after photobleaching (FRAP) has become a popular technique to investigate the behavior of proteins in living cells. Although the technique is relatively old, its application to studying endogenous intracellular proteins in living cells is relatively recent and is a consequence of the newly developed fluorescent protein-based living cell protein tags. This is particularly true for nuclear proteins, in which endogenous protein mobility has only recently been studied. Here we examine the experimental design and analysis of FRAP experiments. Mathematical modeling of FRAP data enables the experimentalist to extract information such as the association and dissociation constants, distribution of a protein between mobile and immobilized pools, and the effective diffusion coefficient of the molecule under study. As experimentalists begin to dissect the relative influence of protein domains within individual proteins, this approach will allow a quantitative assessment of the relative influences of different molecular interactions on the steady-state distribution and protein function in vivo.
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Affiliation(s)
- Gustavo Carrero
- Department of Mathematical and Statistical Sciences, University of Alberta, Alberta, Canada
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23
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Koike M. Dimerization, translocation and localization of Ku70 and Ku80 proteins. JOURNAL OF RADIATION RESEARCH 2002; 43:223-236. [PMID: 12518983 DOI: 10.1269/jrr.43.223] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The Ku protein is a complex of two subunits, Ku70 and Ku80, and was originally identified as an autoantigen recognized by the sera of patients with autoimmune diseases. The Ku protein plays a key role in multiple nuclear processes, e.g., DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in nuclei. On the other hand, several studies have reported cytoplasmic or cell surface localization of Ku in various cell types. To clarify the fundamental characteristics of Ku, we have examined the expression, heterodimerization, subcellular localization, chromosome location, and molecular mechanisms of the nuclear transport of Ku70 and Ku80. The mechanism that regulates for nuclear localization of Ku70 and Ku80 appears to play, at least in part, a key role in regulating the physiological function of Ku in vivo.
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Affiliation(s)
- Manabu Koike
- Radiation Hazards Research Group, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan.
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