What Interests Us: How Do Organisms Respond to Stress?
At its simplest level, the living cell can be thought of as a compartmentalized microreactor that constantly senses its environment, including stress signals, and through a series of well-coordinated unit operations, generates an output that leads to adaptation, and ensures survival even under adverse conditions. Given the extraordinary complexity of the environment, the stress response is, not surprisingly, equally complicated. The overarching goal of the Deaconescu Laboratory is to unravel basic mechanisms of stress response using an integrative approach, combining protein engineering, structural biology and biochemistry in bulk with single-molecule biophysics, molecular genetics and functional studies in cells and animal models. Our current focus lies on cellular responses elicited by DNA damage.
Interplay of DNA Repair and Transcription: From Structures to Mechanisms
The double-helical nature of DNA, the length of genes, and the ubiquitous presence of endogenous and exogenous DNA-damaging agents pose significant topological and information processing challenges to the cell. DNA serves as a track for a variety of essential cellular machines, including the DNA replication and transcription machineries that scan or read the chromosome. Our overall goal is to understand how DNA repair pathways interface with other cellular processes. To this end, we are focusing on a specialized subpathway of nucleotide excision repair (NER) called transcription-coupled DNA repair (TCR). TCR is triggered by the stalling of RNA polymerase molecules at certain DNA lesions, such as UV-induced damage. In TCR, as in NER, repair is achieved through a "cut and patch" mechanism, in which excision of a short oligonucleotide containing the DNA damage is followed by resynthesis and gap filling. Unlike in genome-wide NER, the initial recognition of the DNA damage is mediated by RNA polymerase itself (rather than dedicated repair machinery), which stalls and serves as a beacon for recruitment of transcription-repair coupling factors. These, in turn, remodel or dissociate RNA polymerase transcription complexes and preferentially recruit NER proteins to the damaged site.
TCR exists in both prokaryotes and eukaryotes, and, in humans, has been associated with a variety of syndromes, such as UV-sensitive syndrome, DeSantis Cacchione, and the better-known progeroid (accelerated-aging) Cockayne syndrome, characterized by severe, multi-systemic developmental and neurological defects. In ongoing experiments, we are dissecting the complicated mechanochemistry of transcription-repair coupling factors with the overall goal of understanding how these proteins, part of a large family of dsDNA translocases, utilize the energy of ATP hydrolysis to exert mechanical work to remodel their substrates and recruit NER proteins.
The General Stress Response and Regulation of RpoS Turnover by the ClpXP Machine
Dorothee Kern Group (HHMI and Brandeis University)
Antonina Roll-Mecak Group (NIH and NINDS)
Michelle Wang Group (HHMI and Cornell University)
Susan Gottesman Group (National Cancer Institute)
Sue Wickner Group (National Cancer Institute)