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Oshidari R, Strecker J, Chung DKC, Abraham KJ, Chan JNY, Damaren CJ, Mekhail K. Nuclear microtubule filaments mediate non-linear directional motion of chromatin and promote DNA repair. Nat Commun 2018; 9:2567. [PMID: 29967403 PMCID: PMC6028458 DOI: 10.1038/s41467-018-05009-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 06/07/2018] [Indexed: 12/19/2022] Open
Abstract
Damaged DNA shows increased mobility, which can promote interactions with repair-conducive nuclear pore complexes (NPCs). This apparently random mobility is paradoxically abrogated upon disruption of microtubules or kinesins, factors that typically cooperate to mediate the directional movement of macromolecules. Here, we resolve this paradox by uncovering DNA damage-inducible intranuclear microtubule filaments (DIMs) that mobilize damaged DNA and promote repair. Upon DNA damage, relief of centromeric constraint induces DIMs that cooperate with the Rad9 DNA damage response mediator and Kar3 kinesin motor to capture DNA lesions, which then linearly move along dynamic DIMs. Decreasing and hyper-inducing DIMs respectively abrogates and hyper-activates repair. Accounting for DIM dynamics across cell populations by measuring directional changes of damaged DNA reveals that it exhibits increased non-linear directional behavior in nuclear space. Abrogation of DIM-dependent processes or repair-promoting factors decreases directional behavior. Thus, inducible and dynamic nuclear microtubule filaments directionally mobilize damaged DNA and promote repair. Following DNA damage, different processes come to action to aid repair. The authors here find that microtubule filaments within the cell nucleus capture and non-randomly mobilize damaged chromatin to mediate DNA repair.
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Affiliation(s)
- Roxanne Oshidari
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, University of Toronto, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Jonathan Strecker
- Department of Molecular Genetics, MaRS Centre, University of Toronto, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada.,Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, 02142, USA
| | - Daniel K C Chung
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, University of Toronto, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Karan J Abraham
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, University of Toronto, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Janet N Y Chan
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, University of Toronto, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada
| | - Christopher J Damaren
- Institute for Aerospace Studies, University of Toronto, 4925 Dufferin Street, Toronto, ON, M3H 5T6, Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, University of Toronto, West Tower, 661 University Avenue, Toronto, ON, M5G 1M1, Canada. .,Canada Research Chairs Program, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
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Nair DB, Chung DKC, Schneider J, Uchida K, Aizawa SI, Jarrell KF. Identification of an additional minor pilin essential for piliation in the archaeon Methanococcus maripaludis. PLoS One 2013; 8:e83961. [PMID: 24386316 PMCID: PMC3875500 DOI: 10.1371/journal.pone.0083961] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/11/2013] [Indexed: 11/19/2022] Open
Abstract
Methanococcus maripaludis is an archaeon with two studied surface appendages, archaella and type IV-like pili. Previously, the major structural pilin was identified as MMP1685 and three additional proteins were designated as minor pilins (EpdA, EpdB and EpdC). All of the proteins are likely processed by the pilin-specific prepilin peptidase EppA. Six other genes were identified earlier as likely encoding pilin proteins processed also by EppA. In this study, each of the six genes (mmp0528, mmp0600, mmp0601, mmp0709, mmp0903 and mmp1283) was deleted and the mutants examined by electron microscopy to determine their essentiality for pili formation. While mRNA transcripts of all genes were detected by RT-PCR, only the deletion of mmp1283 led to nonpiliated cells. This strain could be complemented back to a piliated state by supplying a wildtype copy of the mmp1283 gene in trans. This study adds to the complexity of the type IV pili system in M. maripaludis and raises questions about the functions of the remaining five pilin-like genes and whether M. maripaludis under other growth conditions may be able to assemble additional pili-like structures.
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Affiliation(s)
- Divya B Nair
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Daniel K C Chung
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - James Schneider
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Kaoru Uchida
- Department of Life Sciences, Prefectural University of Hiroshima, 562 Nanatsuka, Shobara, Hiroshima, Japan
| | - Shin-Ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, 562 Nanatsuka, Shobara, Hiroshima, Japan
| | - Ken F Jarrell
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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