Damage Sensing by the Bacterial Nucleotide Excision Repair Pathway

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Intellectual Merits. Duplex DNA, the information repository of the cell, is easily damaged. Cells have evolved several pathways that mount biochemical responses to the presence of such damage. One of these is the nucleotide excision repair (NER) pathway, which is distinguished by the ability to process a chemically diverse set of damage. In bacteria, the first steps in NER are performed by three proteins: UvrA, UvrB, and UvrC. A large body of work has described the components that mediate NER and details of how they operate. The UvrA/UvrB ensemble recognizes damage and cooperates with UvrC and other factors to restore the original sequence. The structure of this large ~300 kDa UvrA/UvrB damage sensor and processor is unknown and this has stymied experiments to understand its mechanism of action. The goal of this project is to obtain a structure-based understanding of nucleotide excision repair. The specific aims address the following questions: 1) How does UvrA employ ATP to sense damaged DNA? and 2) How do UvrA and UvrB cooperate to process DNA damage? This work extends on the structure of UvrA and the first-ever view of the UvrA/UvrB ensemble. Understanding the structure and function of the NER pathway is important because of its central role in maintaining the integrety genetic information against damage and its role in DNA replication, gene expression, evolution and cellular processes such as apoptosis, senescence and tumorigenesis.Broader Impacts. The investigator developed an integrated multi-disciplinary teaching and research program in biochemistry, cell biology and structural biology targeting juniors, seniors and doctoral students. Lecture materials include elements from current and past research. In addition, the investigator tutors undergraduate biochemistry majors. A large group of talented undergraduates has trained in the investigators laboratory. The science is interdisciplinary and involves molecular biological, biochemical, biophysical, and structural approaches. Results are published in peer-reviewed journals. Research materials are made available to the scientific community in several ways, including depositions in the Protein Data Bank.