(Toronto – February 23, 2012) Imagine an incident where smoke alludes to a five-alarm fire, drawing fire engines to quell the damage and suppress the flames through a series of coordinated events. But what if that emergency response is hindered? And just how finely tuned is each step in the response?
A cell’s answer to DNA damage is like that five-alarm response, and researchers worldwide are working to understand how it is initiated, communicated and inhibited once the fire subsides, since this is our primary defense against diseases such as cancer.
In the first study of its kind, Mount Sinai Hospital researchers in the labs of Drs. Daniel Durocher and Frank Sicheri, as well as colleagues in Seattle, have uncovered the structural mechanism by which a protein called OTUB1 inhibits the DNA damage response in the cell—a discovery that deepens understanding of genetic “protection” responses, and which opens the door to new, more sophisticated cancer therapies.
The study was published in a February issue of the journal Molecular Cell, and follows earlier work by senior scientist Dr. Durocher and colleagues in August 2010, in which they reported that OTUB1 interferes with the DNA damage response by blocking addition of ubiquitin to proteins by an E2 enzyme.
Ubiquitin-conjugating enzymes, or E2s, are important targets for drug discovery. Through a process called ubiquitination, E2s attach ubiquitin tags to proteins and, in so doing, influence their stability or binding to other proteins to trigger cellular signals. The E2 family of enzymes controls the levels and signaling behaviour of many key proteins that are important for cell proliferation and other cellular processes. The response to DNA damage is an example of a cellular process that relies extensively on protein ubiquination, where an amplification of the ubiquitin response triggers recruitment of other proteins involved in DNA repair.
“These E2 enzymes are beginning to yield an exciting new class of therapeutic targets,” said Dr. Yu-Chi Juang, a post-doctoral researcher in the lab of senior scientist Dr. Sicheri, and co-first author of the study. “But until now, we did not understand the exact means by which OTUB1 works to interfere with ubiquitin recognition and to suppress E2 function.”
In the present study, the teams of Drs. Durocher and Sicheri uncovered the structural mechanism by which OTUB1, a deubiquitinase enzyme, binds to E2 to interrupt ubiquitin transfer and dampen the DNA damage response.
“The DNA damage response is very highly regulated. Molecular ‘gatekeepers’ exist to either enhance or inhibit the capacity of the cell to communicate the presence of DNA damage and then repair DNA defects,” said Dr. Marie-Claude Landry, a post-doctoral researcher in the lab of Dr. Durocher and co-first author on this paper. “This is the first study to uncover the specific mechanism of action of OTUB1, which is different from the one used by the majority of deubiquitinase enzymes and does not involve cleavage of ubiquitin itself.”
Using a combination of yeast genetics and cellular assays, Dr. Landry identified several key amino acids on OTUB1 that, when mutated, abolish its capacity to inhibit E2s. Those mutations were then positioned on critical and functional domains of the OTUB1-E2 complex that had been solved by Dr. Juang using sophisticated x-ray imaging techniques (x-ray crystallography).
“Our study reveals how OUTB1 suppresses E2 function through an unconventional mechanism,” said Dr. Landry, noting that OTUB1 binds preferentially to ubiquitin-charged E2 (E2~Ub) through contacts with both conjugated ubiquitin and the E2 enzyme. “Our biggest surprise was that an extra free ubiquitin molecule was found as part of the OTUB1-E2~Ub complex, and this free ubiquitin is required for promoting formation of the inhibited E2 complex,” echoed Dr. Juang. “The presence of these ubiquitin molecules explains perfectly how OTUB1 inhibits ubiquitin transfer by the E2, and also how OTUB1 cleaves a specific type of polyubiquitin chain.”
Mutations in genes involved in the DNA damage response frequently contribute to cancer formation and are also involved in infertility and immune deficiency. Therefore, targeting the proteins that regulate DNA repair could lead to new types of therapeutics for these diseases.
“Our next steps will be to understand how OTUB1 activity is regulated following DNA damage as well as after the DNA has been repaired. This information, in combination with the known structure of the OTUB1-E2 complex, will be very useful for the development of drugs that specifically target OTUB1 activity,” said Dr. Juang.
The study was supported by the Canadian Institutes of Health Research and the Canadian Breast Cancer Foundation (Ontario Region).
Earlier work by Dr. Durocher identified RNF8 and RNF168, two key players in the DNA damage response mediated by ubiquitin signaling. RNF168 has also been shown to be mutated in RIDDLE syndrome, an immunodeficiency and radiosensitivity disorder. Dr. Durocher and his colleagues found how the deubiquitylase enzyme OTUB1 inhibits UBC13, a protein that acts with RNF168 to amplify the RNF8-dependent ubiquitination. That discovery also improved understanding of familial breast and ovarian cancer, as the research showed that OTUB1 inhibits the action of BRCA1, a DNA repair protein often mutated in these cancers.