Living with the Quick Fix


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(l-r) Omer Ziv and Prof. Zvi Livneh
Our DNA is thought to get damaged at the staggering rate of 50,000 times a day, mostly from byproducts of our metabolism and such external agents as sunlight and tobacco smoke. If left unmended, this damage can eventually lead to cancer, immunodeficiency, premature aging and neurodegeneration. Fortunately, organisms have evolved a whole array of DNA repair mechanisms – different kinds for every type of damage.
Among them are various “quick fix” mechanisms; these have been the focus of research in Prof. Zvi Livneh’s lab in the Weizmann Institute’s Biological Chemistry Department. In a new study published in Nature Communications, Livneh and his colleagues have now revealed how one of these mechanisms, called translesion DNA synthesis (TLS), is regulated in mammalian cells. These findings may have potential applications for cancer prevention and therapy, especially for certain cancers that have mutations in the TLS genes.

Bridge over troubled DNA

“Fixes” may come at a price. The methodical routine that accurately restores the damaged DNA to its original code is time- and energy-consuming. So the cell may turn to “fast,” but error-prone methods, which, in the case of TLS, merely tolerate the damage, “bridging” the damaged section and allowing DNA replication to bypass the hurdle and continue on its way. The cost of this fast mechanism lies in the possible introduction of a wrong DNA code – a gamble that carries risks of the onset of disease and even death. In previous research, Livneh’s lab discovered that at the heart of the TLS mechanism is a group of DNA polymerases – enzymes that assemble the DNA strand. With no fewer than 10 of these polymerases, all “sloppy” workers, one might expect a host of problems, yet, surprisingly, the error rate is relatively low. The research of Livneh and others offered an explanation: Each of these polymerases is finely tuned to deal with a specific type of DNA damage, thus lowering the chance of a mistake. The question now was: What keeps all these polymerases in check – ensuring their action at the right place and time?

Unique genes revealed

To identify the genes that regulate TLS, Livneh and PhD student Omer Ziv, in collaboration with Prof. Eytan Domany and former PhD student Amit Zeisel of the Physics of Complex Systems Department, developed a novel two-stage screening approach: First, they took human cells with a specific defect – in the repair of UV-induced DNA damage. One by one, they “turned off” 1000 different genes, winnowing out those cells that had either reduced or increased survival rates after being exposed to damaging UV light. These cells then went through a second round of more refined screening developed by the team; this time, to determine whether the cells’ survival was specifically dependent on TLS. Of the 1000 genes screened, the scientists discovered 17 new ones involved in TLS, six of which appear to be unique to mammals.
NPM1 interacts with DNA polymerase eta and regulates polymerase eta-promoted TLS. Assay of polymerase eta and NPM1 in unirradiated (l) and ultraviolet irradiated cells ((c) after one hour, (r) after 18 hours). Blue: DNA in the nucleus; green: polymerase eta–NPM1 interaction

New regulatory system, old cancer mystery

The scientists chose to further investigate one of the novel TLS genes they identified; this gene encodes a multifunctional protein, nucleophosmin (NPM1), which is involved in the biogenesis of ribosomes and cell proliferation, among its many roles. The team discovered that NPM1 regulates TLS by physically interacting with one of the “sloppy” polymerases – called DNA polymerase eta – in the nucleus of the cell. NPM1 binds to polymerase eta as long as there is no damage, thus “locking” it away to protect it against degradation while maintaining a functional pool for fast action when needed. In the meantime, the polymerase is prevented from acting on any intact DNA and introducing needless errors. When damage does occur, i.e., following exposure to UV radiation, NPM1 releases its hold on the polymerase. The team traced the effect experimentally: NPM1 deficiency resulted in decreased DNA polymerase eta levels, leading to defective TLS.
Domany: “NPM1 is essentially the ‘guardian’ of DNA polymerase eta.” The scientists think that the multiple new TLS genes uncovered in this research might play a similar role for the other “sloppy” polymerases, thus providing a tightly controlled system that works in harmony, with minimal error.
For a specific cancer – acute myeloid leukemia (AML) – these findings may provide an explanation to a longstanding mystery: NPM1 has been found to be mutated in approximately 30% of AML patients; and patients harboring such mutations puzzlingly tend to have a better response to chemotherapy. Studies have shown that TLS is involved in resistance to chemotherapy, which damages DNA. The Weizmann team’s research suggests that AML cells carrying the mutated NPM1 gene have lower TLS rates, as their DNA polymerase eta degrades without its “guardian,” and they thus are more easily killed by the treatment.
Livneh: “Plans are currently under way to test these observations in AML patients, and if evidence supports these findings, it could indicate that NPM1 and DNA polymerase eta, and in particular their interaction, could be potential targets for AML drugs.”
Also participating in the study were Nataly Mirlas-Neisberg, Dr. Umakanta Swain, Dr. Reinat Nevo and Nir Ben-Chetrit of the Weizmann Institute, as well as Prof. Brunangelo Falini, Dr. Maria Paola Martelli and Roberta Rossi of the University of Perugia, Italy; Prof. Nicholas Geacintov of New York University, USA; Prof. Thomas Carell and Stefan Schiesser of Ludwig Maximilians University, Germany; and Prof. Christine E. Canman of the University of Michigan, USA.
Prof. Eytan Domany’s research is supported by the Leir Charitable Foundations; Mordechai Segal, Israel; and the Louis and Fannie Tolz Collaborative Research Project. Prof. Domany is the incumbent of the Henry J. Leir Professorial Chair.

Prof. Zvi Livneh’s research is supported by the Y. Leon Benoziyo Institute for Molecular Medicine, which he heads; the Dr. Erhard, Emmi and Fred Loewinsohn Center for Pediatric Health, which he heads; the Leona M. and Harry B. Helmsley Charitable Trust; the David M. Polen Charitable Trust; the Mike and Valeria Rosenbloom through the Mike Rosenbloom Foundation; and the Sergio Lombroso Award for Cancer Research. Prof. Livneh is the incumbent of the Maxwell Ellis Professorial Chair of Biomedical Research.