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  • GO1 (1)
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  • RNA-seq (1)
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  • methanol methyltransferase isozymes (1)
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  • Pernitzsch, Sandy R. (2)
  • Sharma, Cynthia M. (2)
  • Backofen, Rolf (1)
  • Jäger, Dominik (1)
  • Richter, Andreas S. (1)
  • Schmitz, Ruth A. (1)

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Transcriptome Complexity and Riboregulation in the Human Pathogen Helicobacter pylori (2012)
Pernitzsch, Sandy R. ; Sharma, Cynthia M.
An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains (2012)
Jäger, Dominik ; Pernitzsch, Sandy R. ; Richter, Andreas S. ; Backofen, Rolf ; Sharma, Cynthia M. ; Schmitz, Ruth A.
We report on the characterization and target analysis of the small (s) RNA\(_{162}\) in the methanoarchaeon Methanosarcina mazei. Using a combination of genetic approaches, transcriptome analysis and computational predictions, the bicistronic MM2441-MM2440 mRNA encoding the transcription factor MM2441 and a protein of unknown function was identified as a potential target of this sRNA, which due to processing accumulates as three stabile 5' fragments in late exponential growth. Mobility shift assays using various mutants verified that the non-structured single-stranded linker region of sRNA\(_{162}\) (SLR) base-pairs with the MM2440-MM2441 mRNA internally, thereby masking the predicted ribosome binding site of MM2441. This most likely leads to translational repression of the second cistron resulting in dis-coordinated operon expression. Analysis of mutant RNAs in vivo confirmed that the SLR of sRNA\(_{162}\) is crucial for target interactions. Furthermore, our results indicate that sRNA\(_{162}\)-controlled MM2441 is involved in regulating the metabolic switch between the carbon sources methanol and methylamine. Moreover, biochemical studies demonstrated that the 50 end of sRNA\(_{162}\) targets the 5'-untranslated region of the cis-encoded MM2442 mRNA. Overall, this first study of archaeal sRNA/mRNA-target interactions unraveled that sRNA\(_{162}\) acts as an antisense (as) RNA on cis- and trans-encoded mRNAs via two distinct domains, indicating that cis-encoded asRNAs can have larger target regulons than previously anticipated.
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