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. This proposal focuses on the novel mechanism for altering transcription by the RNA-regulator 6S RNA. A detailed understanding of the 6S RNA function and mechanism of action is instrumental for full comprehension of how appropriate cellular gene expression is maintained, particularly when nutrients are limiting. Cells with altered 6S RNA levels are decreased in their ability to survive starvation, 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. This proposal focuses on three questions regarding 6S RNA function and activity: 1. What is the mechanism of 6S RNA regulation of transcription? which will be addressed by a detailed examination of 6S RNA-RNA polymerase interactions;2. What other factors impact 6S RNA function? which will expand our understanding of how 6S RNA functions in the cellular environment. 3. What is the role of the 6S RNA-templated RNA synthesis? 6S RNA not only regulates RNA polymerase, but it is used as a template by the enzyme. All together, these experiments will not only address how, when and why 6S RNA is functioning, they are likely to elucidate additional insights into the transcriptional machinery.

Public Health Relevance

This work focuses on a novel mechanism of regulating gene expression, that ultimately contributes to survival of E. coli. Regulated transcription is one of the principle mechanisms underlying cellular responses to the environment, whether for survival of a single celled bacteria when nutrients are scarce, or in the environment of a whole organism such as a developing embryo. Therefore, basic understanding of how this important RNA works as a global regulator, will facilitate understanding another level of regulation of gene expression that is likely to exist in all organisms.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Prokaryotic Cell and Molecular Biology Study Section (PCMB)
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Sledjeski, Darren D
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University of Wisconsin Madison
Schools of Earth Sciences/Natur
United States
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Cavanagh, Amy T; Wassarman, Karen M (2014) 6S RNA, a global regulator of transcription in Escherichia coli, Bacillus subtilis, and beyond. Annu Rev Microbiol 68:45-60
Cabrera-Ostertag, Ignacio J; Cavanagh, Amy T; Wassarman, Karen M (2013) Initiating nucleotide identity determines efficiency of RNA synthesis from 6S RNA templates in Bacillus subtilis but not Escherichia coli. Nucleic Acids Res 41:7501-11
Cavanagh, Amy T; Wassarman, Karen M (2013) 6S-1 RNA function leads to a delay in sporulation in Bacillus subtilis. J Bacteriol 195:2079-86
Cavanagh, Amy T; Sperger, Jamie M; Wassarman, Karen M (2012) Regulation of 6S RNA by pRNA synthesis is required for efficient recovery from stationary phase in E. coli and B. subtilis. Nucleic Acids Res 40:2234-46
Storz, Gisela; Vogel, Jörg; Wassarman, Karen M (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 43:880-91
Klocko, Andrew D; Wassarman, Karen M (2009) 6S RNA binding to Esigma(70) requires a positively charged surface of sigma(70) region 4.2. Mol Microbiol 73:152-64
Cavanagh, Amy T; Klocko, Andrew D; Liu, Xiaochun et al. (2008) Promoter specificity for 6S RNA regulation of transcription is determined by core promoter sequences and competition for region 4.2 of sigma70. Mol Microbiol 67:1242-56
Wassarman, Karen M (2007) 6S RNA: a regulator of transcription. Mol Microbiol 65:1425-31
Wassarman, Karen M (2007) 6S RNA: a small RNA regulator of transcription. Curr Opin Microbiol 10:164-8
Trotochaud, Amy E; Wassarman, Karen M (2006) 6S RNA regulation of pspF transcription leads to altered cell survival at high pH. J Bacteriol 188:3936-43

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