Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.
Subscribe

Sci. Signal., 7 December 2010
Vol. 3, Issue 151, p. rs3
[DOI: 10.1126/scisignal.2001034]

RESEARCH RESOURCES

ATM-Dependent and -Independent Dynamics of the Nuclear Phosphoproteome After DNA Damage

Ariel Bensimon1*{dagger}, Alexander Schmidt2,3*, Yael Ziv1, Ran Elkon4, Shih-Ya Wang5, David J. Chen5, Ruedi Aebersold2,6,7{ddagger}, and Yosef Shiloh1{ddagger}

1 David and Inez Myers Laboratory for Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
2 Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zurich, Zurich 8093, Switzerland.
3 Biozentrum, University of Basel, Basel 4056, Switzerland.
4 Division of Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, Netherlands.
5 Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390–9187, USA.
6 Competence Center for Systems Physiology and Metabolic Diseases, Eidgenössische Technische Hochschule Zurich, Zurich 8093, Switzerland.
7 Faculty of Science, University of Zurich, Zurich 8057, Switzerland.

* These authors contributed equally to this work.

{dagger} Present address: Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zurich, Zurich 8093, Switzerland.

Abstract: The double-strand break (DSB) is a cytotoxic DNA lesion caused by oxygen radicals, ionizing radiation, and radiomimetic chemicals. Cells cope with DNA damage by activating the DNA damage response (DDR), which leads either to damage repair and cellular survival or to programmed cell death. The main transducer of the DSB response is the nuclear protein kinase ataxia telangiectasia mutated (ATM). We applied label-free quantitative mass spectrometry to follow the dynamics of DSB-induced phosphoproteome in nuclear fractions of the human melanoma G361 cells after radiomimetic treatment. We found that these dynamics are complex, including both phosphorylation and dephosphorylation events. In addition to identifying previously unknown ATM-dependent phosphorylation and dephosphorylation events, we found that about 40% of DSB-induced phosphorylations were ATM-independent and that several other kinases are potentially involved. Sustained activity of ATM was required to maintain many ATM-dependent phosphorylations. We identified an ATM-dependent phosphorylation site on ATM itself that played a role in its retention on damaged chromatin. By connecting many of the phosphorylated and dephosphorylated proteins into functional networks, we highlight putative crosstalks between proteins pertaining to several cellular biological processes. Our study expands the DDR phosphorylation landscape and identifies previously unknown ATM-dependent and -independent branches. It reveals insights into the breadth and complexity of the cellular responses involved in the coordination of many DDR pathways, which is in line with the critical importance of genomic stability in maintenance of cellular homeostasis.

{ddagger} To whom correspondence should be addressed. E-mail: yossih{at}post.tau.ac.il (Y.S.); rudolf.aebersold{at}imsb.biol.ethz.ch (R.A.)

Citation: A. Bensimon, A. Schmidt, Y. Ziv, R. Elkon, S.-Y. Wang, D. J. Chen, R. Aebersold, Y. Shiloh, ATM-Dependent and -Independent Dynamics of the Nuclear Phosphoproteome After DNA Damage. Sci. Signal. 3, rs3 (2010).

Read the Full Text

THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Brain and induced pluripotent stem cell-derived neural stem cells as an in vitro model of neurodegeneration in ataxia-telangiectasia.
L. Carlessi, E. F. Poli, and D. Delia (2013)
Exp Biol Med 238, 301-307
   Abstract »    Full Text »    PDF »
Mechanism of DNA resection during intrachromosomal recombination and immunoglobulin class switching.
A. Bothmer, P. C. Rommel, A. Gazumyan, F. Polato, C. R. Reczek, M. F. Muellenbeck, S. Schaetzlein, W. Edelmann, P.-L. Chen, R. M. Brosh Jr., et al. (2013)
J. Exp. Med. 210, 115-123
   Abstract »    Full Text »    PDF »
RNF4-Dependent Hybrid SUMO-Ubiquitin Chains Are Signals for RAP80 and Thereby Mediate the Recruitment of BRCA1 to Sites of DNA Damage.
C. M. Guzzo, C. E. Berndsen, J. Zhu, V. Gupta, A. Datta, R. A. Greenberg, C. Wolberger, and M. J. Matunis (2012)
Science Signaling 5, ra88
   Abstract »    Full Text »    PDF »
Protein abundance is key to distinguish promiscuous from functional phosphorylation based on evolutionary information.
E. D. Levy, S. W. Michnick, and C. R. Landry (2012)
Phil Trans R Soc B 367, 2594-2606
   Abstract »    Full Text »    PDF »
Charting the Landscape of Tandem BRCT Domain-Mediated Protein Interactions.
N. T. Woods, R. D. Mesquita, M. Sweet, M. A. Carvalho, X. Li, Y. Liu, H. Nguyen, C. E. Thomas, E. S. Iversen Jr., S. Marsillac, et al. (2012)
Science Signaling 5, rs6
   Abstract »    Full Text »    PDF »
Loss of ATM kinase activity leads to embryonic lethality in mice.
J. A. Daniel, M. Pellegrini, B.-S. Lee, Z. Guo, D. Filsuf, N. V. Belkina, Z. You, T. T. Paull, B. P. Sleckman, L. Feigenbaum, et al. (2012)
J. Cell Biol. 198, 295-304
   Abstract »    Full Text »    PDF »
The ATM protein: The importance of being active.
Y. Shiloh and Y. Ziv (2012)
J. Cell Biol. 198, 273-275
   Abstract »    Full Text »    PDF »
Computational Approaches for Analyzing Information Flow in Biological Networks.
B. Kholodenko, M. B. Yaffe, and W. Kolch (2012)
Science Signaling 5, re1
   Abstract »    Full Text »    PDF »
INT6/EIF3E Interacts with ATM and Is Required for Proper Execution of the DNA Damage Response in Human Cells.
C. Morris, N. Tomimatsu, D. J. Richard, D. Cluet, S. Burma, K. K. Khanna, and P. Jalinot (2012)
Cancer Res. 72, 2006-2016
   Abstract »    Full Text »    PDF »
Global Phosphoproteome Profiling Reveals Unanticipated Networks Responsive to Cisplatin Treatment of Embryonic Stem Cells.
A. Pines, C. D. Kelstrup, M. G. Vrouwe, J. C. Puigvert, D. Typas, B. Misovic, A. de Groot, L. von Stechow, B. van de Water, E. H. J. Danen, et al. (2011)
Mol. Cell. Biol. 31, 4964-4977
   Abstract »    Full Text »    PDF »
ATM Protein-dependent Phosphorylation of Rad50 Protein Regulates DNA Repair and Cell Cycle Control.
M. Gatei, B. Jakob, P. Chen, A. W. Kijas, O. J. Becherel, N. Gueven, G. Birrell, J.-H. Lee, T. T. Paull, Y. Lerenthal, et al. (2011)
J. Biol. Chem. 286, 31542-31556
   Abstract »    Full Text »    PDF »
Investigation of the Functional Link between ATM and NBS1 in the DNA Damage Response in the Mouse Cerebellum.
I. Dar, G. Yosha, R. Elfassy, R. Galron, Z.-Q. Wang, Y. Shiloh, and A. Barzilai (2011)
J. Biol. Chem. 286, 15361-15376
   Abstract »    Full Text »    PDF »
Inhibition of Homologous Recombination by DNA-Dependent Protein Kinase Requires Kinase Activity, Is Titratable, and Is Modulated by Autophosphorylation.
J. A. Neal, V. Dang, P. Douglas, M. S. Wold, S. P. Lees-Miller, and K. Meek (2011)
Mol. Cell. Biol. 31, 1719-1733
   Abstract »    Full Text »    PDF »
Autophosphorylation and ATM Activation: ADDITIONAL SITES ADD TO THE COMPLEXITY.
S. V. Kozlov, M. E. Graham, B. Jakob, F. Tobias, A. W. Kijas, M. Tanuji, P. Chen, P. J. Robinson, G. Taucher-Scholz, K. Suzuki, et al. (2011)
J. Biol. Chem. 286, 9107-9119
   Abstract »    Full Text »    PDF »
Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications.
S. E. Polo and S. P. Jackson (2011)
Genes & Dev. 25, 409-433
   Abstract »    Full Text »    PDF »

To Advertise     Find Products

Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882