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Nucleic Acids Res. 2012 Nov;40(21):10964-79. doi: 10.1093/nar/gks847. Epub 2012 Sep 10.

An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains.

Author information

1
Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany.

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.

PMID:
22965121
PMCID:
PMC3510493
DOI:
10.1093/nar/gks847
[Indexed for MEDLINE]
Free PMC Article

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