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Series GSE30430 Query DataSets for GSE30430
Status Public on Sep 01, 2011
Title RNA processing in Bacillus subtilis: Identification of targets of the essential RNase Y
Organism Bacillus subtilis subsp. subtilis str. 168
Experiment type Expression profiling by array
Summary RNA processing and degradation is initiated by endonucleolytic cleavage of the target RNAs. In many bacteria, this activity is performed by RNase E which is not present in Bacillus subtilis and other Gram-positive bacteria. Recently, the essential endoribonuclease RNase Y has been discovered in B. subtilis. This RNase is involved in the degradation of bulk mRNA suggesting a major role in mRNA metabolism. However, only a few targets of RNase Y have been identified so far. In order to assess the global impact of RNase Y, we compared the transcriptomes of strains expressing RNase Y or depleted for RNase Y. Our results indicate that processing by RNase Y results in accumulation of about 80 mRNAs. Some of these targets were substantially stabilized by RNase Y depletion, resulting in half-lives in the range of an hour. Moreover, about 40 mRNAs were less abundant when RNase Y was depleted among them the mRNAs of the operons required for biofilm formation. Interestingly, overexpression of RNase Y was sufficient to induce biofilm formation. The results emphasize the importance of RNase Y for B. subtilis and are in support of the idea that RNase Y is the functional equivalent of RNase E.
 
Overall design To study the global function of RNase Y, a microarray analysis was performed with a B. subtilis strain allowing controlled depletion of RNase Y. Strain GP193 (Commichau et al., 2009, Mol. Cell. Proteomics 8: 1350-1360) expressing the rny gene under the control of a xylose-inducible promoter was cultivated in CSE minimal medium in the presence or absence of the inducer xylose. The transcriptomes of the two cultures (i.e. expressing RNase Y and depleted for RNase Y) were compared at a timepoint at which the reduced RNase Y amounts already affected the mRNA turnover whereas the growth rates of the two cultures were still almost identical.
 
Contributor(s) Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Rothe FM, Herzberg C, Stülke J
Citation(s) 21815947
Submission date Jul 06, 2011
Last update date Apr 06, 2016
Contact name Ulrike Mäder
E-mail ulrike.maeder@uni-greifswald.de
Organization name University Medicine Greifswald
Department Functional Genomics
Street address F.-L.-Jahn-Str. 15A
City Greifswald
ZIP/Postal code D-17489
Country Germany
 
Platforms (1)
GPL10901 Bacillus subtilis Custom Agilent 44k v2
Samples (6)
GSM754762 B. subtilis_RNaseY depletion_replicate A_hyb1
GSM754763 B. subtilis_RNaseY depletion_replicate A_hyb2
GSM754765 B. subtilis_RNaseY depletion_replicate B_hyb1
Relations
BioProject PRJNA143531

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE30430_RAW.tar 78.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data provided as supplementary file
Processed data included within Sample table

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