Deciphering fundamental biological processes involving protein-nucleic acid interactions at the molecular level

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ABSTRACT The central focus of the Schumacher laboratory is to deduce molecular principles that govern fundamental biological processes involving protein-nucleic acid interactions. Our recent work has honed in on transcription networks and DNA segregation in microbes. The latter studies have uncovered key insights into the molecular mechanisms utilized by simplified systems employing actin-like and tubulin-like NTPases to segregate bacterial plasmids. However, the molecular mechanism(s) controlling the most common bacterial segregation systems, the Walker-box based systems, remain unclear and represent a major focus of our research. Strikingly, our recent studies characterizing the first archaeal segregation system revealed that it utilizes a bacterial-like Walker-box NTPase to drive DNA segregation, indicating that Walker-box segregation machineries may be the most ubiquitous type of DNA segregation modules in biology. These investigations also revealed that the archaeal segregation ParB protein harbors a fold similar to CenpA, the histone homolog that mediates DNA segregation in eukaryotes. Thus, these studies uncovered possible evolutionary linkages in segregation machineries between the 3 domains of life. Our most recent work has provided the first molecular views of Walker-box NTPases bound to DNA and ParB. These data combined with cellular and biochemical studies have allowed us to propose a general, non-polymer based model for Walker-box segregation that we will test using cellular and molecular approaches. Our work on the nitrogen regulatory circuitry in B. subtilis has revealed new DNA binding modalities and a novel regulatory mechanism involving the direct enzyme of nitrogen homeostasis, glutamine synthetase. A new direction for the lab is to deduce the molecular mechanisms controlling Streptomyces development, which coincides with their production of antibiotics (secondary metabolites). Indeed, Streptomyces generate most of our current antibiotics as well as a plethora of biomedically important compounds. In the next 5 years we will expand on these efforts, but also add cellular, genetic and cryo-EM microscopy approaches to provide a more complete picture of these systems. These investigations notably intersect with the lab's interests in microbial multidrug resistance and multidrug tolerance. Indeed, while the overall goals of these studies are to determine fundamental biological principles these ongoing studies will also provide novel targets for the development of antimicrobial therapeutics, which are urgently needed given the alarming rise of multidrug resistant microbes and the scarcity of new antimicrobials in the pipeline.