The ability to degrade mRNA and re-use its component nucleotides is essential to viability of all living cells. There is increasing evidence that mRNA decay is a coordinated multistep process that is dynamically regulated in response to changes in cell physiology. However, limited information currently is available about the features of ribonucleases that determine their mode of action, their relative activities, and their response to physiological events. Similarly there is incomplete knowledge of the proteins and non-coding RNAs that can interact with ribonucleases and/or their substrates to modulate ribonucleolytic activity and specificity. The long-term objective of the proposed research is to achieve a better understanding of the mechanisms that regulate RNA decay in bacteria.
The specific aims for the next project period are: 1) to elucidate the structural features of the RNase E and RNase G proteins that determine their specificity and mode of action, 2) to identify and investigate the effects of other cellular proteins that interact with these ribonucleases, regulate their actions, and allow them to respond to changes in cell physiology, and 3) to identify transcripts whose degradation by these ribonucleases is differentially affected by physiological changes, identify the regulatory proteins and/or small RNAs that mediate these effects, and elucidate the mechanisms of action of selected regulators. The research is multifaceted and will employ a combination of genetic and biochemical approaches--including mutational analysis of ribonuclease structure/function relationships, microarray-based investigations of changes in RNA decay in response to physiological events, protein purification and analysis, and biochemical study of the effects of regulator proteins and/or RNAs on ribonuclease action. While these investigations are intended to elucidate fundamental aspects of bacterial RNA decay, the information obtained is likely to facilitate the more efficient use of microorganisms to express biologically and medically important proteins and also to further the development of novel antimicrobial drugs that target RNA decay mechanisms in bacteria. ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM054158-08
Application #
7035749
Study Section
Special Emphasis Panel (ZRG1-MBC-2 (01))
Program Officer
Rhoades, Marcus M
Project Start
1996-07-01
Project End
2010-03-31
Budget Start
2006-04-01
Budget End
2010-03-31
Support Year
8
Fiscal Year
2006
Total Cost
$372,221
Indirect Cost
Name
Stanford University
Department
Genetics
Type
Schools of Medicine
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305
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Manasherob, Robert; Miller, Christine; Kim, Kwang-sun et al. (2012) Ribonuclease E modulation of the bacterial SOS response. PLoS One 7:e38426
Tamura, Masaru; Kers, Johan A; Cohen, Stanley N (2012) Second-site suppression of RNase E essentiality by mutation of the deaD RNA helicase in Escherichia coli. J Bacteriol 194:1919-26
Go, Hayoung; Moore, Christopher J; Lee, Minho et al. (2011) Upregulation of RNase E activity by mutation of a site that uncompetitively interferes with RNA binding. RNA Biol 8:1022-34
Xu, Weijing; Huang, Jianqiang; Lin, Richard et al. (2010) Regulation of morphological differentiation in S. coelicolor by RNase III (AbsB) cleavage of mRNA encoding the AdpA transcription factor. Mol Microbiol 75:781-91
Xu, Weijing; Huang, Jianqiang; Cohen, Stanley N (2008) Autoregulation of AbsB (RNase III) expression in Streptomyces coelicolor by endoribonucleolytic cleavage of absB operon transcripts. J Bacteriol 190:5526-30
Kim, Kwang-sun; Manasherob, Robert; Cohen, Stanley N (2008) YmdB: a stress-responsive ribonuclease-binding regulator of E. coli RNase III activity. Genes Dev 22:3497-508
Tamura, Masaru; Lee, Kangseok; Miller, Christine A et al. (2006) RNase E maintenance of proper FtsZ/FtsA ratio required for nonfilamentous growth of Escherichia coli cells but not for colony-forming ability. J Bacteriol 188:5145-52
Gao, Junjun; Lee, Kangseok; Zhao, Meng et al. (2006) Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome. Mol Microbiol 61:394-406
Caruthers, Jonathan M; Feng, Yanan; McKay, David B et al. (2006) Retention of core catalytic functions by a conserved minimal ribonuclease E peptide that lacks the domain required for tetramer formation. J Biol Chem 281:27046-51

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