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| 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
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| 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.
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| 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.
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| 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(s) |
ulrike.maeder@uni-greifswald.de
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| Organization name |
University Medicine Greifswald
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| Department |
Functional Genomics
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| Street address |
F.-L.-Jahn-Str. 15A
|
| City |
Greifswald |
| ZIP/Postal code |
D-17489 |
| Country |
Germany |
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| Platforms (1) |
| GPL10901 |
Bacillus subtilis Custom Agilent 44k v2 |
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| Samples (6)
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| GSM754762 |
B. subtilis_RNaseY depletion_replicate A_hyb1 |
| GSM754763 |
B. subtilis_RNaseY depletion_replicate A_hyb2 |
| GSM754765 |
B. subtilis_RNaseY depletion_replicate B_hyb1 |
| GSM754766 |
B. subtilis_RNaseY depletion_replicate B_hyb2 |
| GSM754767 |
B. subtilis_RNaseY depletion_replicate C_hyb1 |
| GSM754769 |
B. subtilis_RNaseY depletion_replicate C_hyb2 |
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| Relations |
| BioProject |
PRJNA143531 |
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