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  • Title: An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains.
    Author: Jäger D, Pernitzsch SR, Richter AS, Backofen R, Sharma CM, Schmitz RA.
    Journal: Nucleic Acids Res; 2012 Nov; 40(21):10964-79. PubMed ID: 22965121.
    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.
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