Background: There is a considerable amount of evidence documenting the importance of ubiquitin conjugation and deconjugation in DNA repair mechanisms, as well as the identity of some the ubiquitin ligases and some of the deubiquitinating enzymes involved. However, the substrates of ubiquitination are still largely controversial and the heterogeneity of the ubiquitin chains involved has not been clearly defined. Recently, unanchored ubiquitin chains have emerged as functional regulators of innate immunity and kinase regulation, however they have not yet been addressed in DNA repair mechanisms. It is important to understand the complete picture of the """"""""ubiquitin architecture"""""""" of DNA repair mechanisms and exploring the functional importance of unanchored ubiquitin chains presents a hitherto overlooked opportunity. Objective: The goal of this proposal is to further characterize the """"""""ubiquitin architecture"""""""" of DNA repair mechanisms in order to be able to exploit them for more successful therapeutic strategies. On the one hand, the possibility of free, unanchored ubiquitin chains will be assessed, as well as the effect of sustained ubiquitin chain formation on DNA repair mechanisms, both of which will underscore the importance of deubiquitinating enzymes (DUBs) as crucial regulators of DNA repair pathways.
Specific Aims : (1) Determine the existence and abundance of unanchored ubiquitin chains during DNA damage responses, (2) Determine the effect of sustained ubiquitin chain formation on DNA damage responses, (3) Identify functionally important interacting proteins of alternative ubiquitin-linkages within DNA damage foci. Study Design: At first, polyubiquitin conjugates will be purified from cells treated by DNA damaging agents and ubiquitin conjugates will be assessed for their free ubiquitin chain content. Then, the effect of a conjugation- competent but deconjugation-deficient mutant of ubiquitin that I have recently developed will be tested to initiate a DNA repair response mechanism in the absence of DNA damage. Additionally, the effect of the mutant in making ubiquitin chains of a defined linkage will be tested under DNA damaging conditions to see if sustained ubiquitin chain formation sensitizes cells to DNA damage or inhibits the response. Finally, ubiquitin chain binding proteins will be purified by affinity purification from DNA damage induced cells to identify novel interacting proteins of alternative ubiquitin chains involved in DNA damage by mass spectrometry.

Public Health Relevance

The genetic material in cells, DNA, is constantly subjected to various damaging conditions, which cause mutations if they are left uncorrected, leading to cancer development and progression. The research I am proposing in this proposal is basic in nature, i.e., the mechanistic understanding of DNA repair mechanisms, however, the project is global in scope because it fundamentally applies to every dividing cell of the human body that each must guard their genome against deleterious mutations. Understanding the mechanisms of DNA repair will ultimately lead to better strategies to utilize this pathway for successful cancer therapies.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Postdoctoral Individual National Research Service Award (F32)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-F08-E (20))
Program Officer
Janes, Daniel E
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
New York University
Schools of Medicine
New York
United States
Zip Code
Békés, Miklós; van der Heden van Noort, Gerbrand J; Ekkebus, Reggy et al. (2016) Recognition of Lys48-Linked Di-ubiquitin and Deubiquitinating Activities of the SARS Coronavirus Papain-like Protease. Mol Cell 62:572-85
Békés, Miklós; Rut, Wioletta; Kasperkiewicz, Paulina et al. (2015) SARS hCoV papain-like protease is a unique Lys48 linkage-specific di-distributive deubiquitinating enzyme. Biochem J 468:215-26
Békés, Miklós; Okamoto, Keiji; Crist, Sarah B et al. (2013) DUB-resistant ubiquitin to survey ubiquitination switches in mammalian cells. Cell Rep 5:826-38
Cotto-Rios, Xiomaris M; Békés, Miklós; Chapman, Jessica et al. (2012) Deubiquitinases as a signaling target of oxidative stress. Cell Rep 2:1475-84