RUI: The Function and Molecular Mechanisms of Novel RNAs in E. Coli

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When they enter new environments, for example the human body or the water supply, bacteria quickly adapt by altering their gene expression patterns. This project will analyze a poorly understood class of regulators that may be important for such changes in gene expression in many if not most bacterial species. The research in this study will be divided into discrete projects for training undergraduate and Master's level students. The outcomes of the research will be conveyed to the community through specific outreach programs associated with the University of Colorado at Colorado Springs' Center for Science, Technology, Engineering and Mathematics Education. This Center is dedicated to promoting science education and hands-on experiences for economically disadvantaged and minority-serving Colorado public school districts.Gene transcription is a highly regulated process, ensuring that only the genes necessary in a particular situation are expressed. Transcription was thought to occur exclusively at genes producing protein-coding mRNAs, ribosomal RNAs, and transfer RNAs. However, in the past decade, non-coding regulatory RNAs have emerged as a new class of transcribed genetic elements. More recently, large portions of the genome have been observed to be transcribed; this genome-wide transcription was termed pervasive transcription. Pervasive transcription was initially considered to be non-functional noise; however, there is now evidence suggesting that pervasive transcripts are functional. The objective of this project is to elucidate the function and molecular mechanisms of gene regulation by pervasive transcripts in the well-studied and genetically tractable model organism Escherichia coli. Traditional loss-of-function reverse genetic assays are challenging to perform on these RNAs because they overlap (or are complementary to) annotated genes. Therefore innovative methods to construct deletions of pervasive transcripts will be employed. These deletion strains will allow us to probe the role of pervasive RNAs in gene regulation and to dissect the molecular mechanisms of their regulation. Understanding the regulatory roles of pervasive transcripts, and the mechanisms they employ, in gene expression in E. coli will also offer insight into the gene regulation strategies of other bacteria, as well as eukaryotes, due to the widespread nature of pervasive transcription across all domains of life.