@Article{Jager_Pernitzsch_Richter-archa_sRNA_targe-NAR2012,
  author =	 {J{\"a}ger, Dominik and Pernitzsch, Sandy R. and Richter, 
                  Andreas S. and Backofen, Rolf and Sharma, Cynthia M. and 
                  Schmitz, Ruth A.},
  title =	 {An archaeal {sRNA} targeting \textit{cis}- and \textit{trans}-
                  encoded {mRNAs} via two distinct domains},
  journal =	 NAR,
  year =	 {2012},
  volume =	 {40},
  number =	 {21},
  pages =	 {10964-79},
  user =	 {arichter},
  pmid =	 {22965121},
  doi = 	 {10.1093/nar/gks847},
  issn = 	 {1362-4962},
  issn = 	 {0305-1048},
  abstract =	 {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 5' 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.}
}