Regulated transcription is one of the principle mechanisms to alter gene expression in response to environmental stimuli. Intensive study over more than 3 decades has provided a detailed understanding of the transcriptional machinery as well as many of the signals to which it responds. A novel mechanism for altering transcription, which uses the RNA-regulator 6S RNA, recently has been discovered. Therefore, a detailed understanding of the role of 6S RNA in transcriptional regulation is instrumental for full comprehension of how appropriate cellular gene expression is maintained. Cells with altered 6S RNA levels are decreased in their ability to survive in stationary phase, indicating 6S RNA has a major impact on cell physiology. Many small RNAs in bacteria are utilized to optimize cellular responses to unfavorable nutritional or chemical environments through post-transcriptional regulation of gene expression. 6S RNA expands this list to include regulation in response to late stationary phase, as well as to include a unique method of regulation at the level of transcription. This proposal focuses on answering three questions regarding 6S RNA function and activity: 1. How global are 6S RNA effects on gene expression which will be addressed by identification of the 6S RNA regulon; 2. What are the physiological consequences of 6S RNA mediated changes in gene expression which will be addressed through genetic analysis of phenotypes associated with loss of 6S RNA; 3. How 6S RNA changes the transcriptional machinery and its activity, which will be addressed through biochemical approaches.
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