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

Jager, D., Pernitzsch, S. R., Richter, A. S., Backofen, R., Sharma, C. M. and Schmitz, Ruth A. (2012) An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains Nucleic Acids Research, 40 (21). pp. 10964-10979.

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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 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.

Document Type: Article
Additional Information: Univ Kiel, Inst Allgemeine Mikrobiol, D-24118 Kiel, Germany. Univ Wurzburg, Zentrum Infekt Forsch, D-97080 Wurzburg, Germany. Univ Freiburg, Inst Informat, D-79110 Freiburg, Germany. Schmitz, RA (reprint author), Univ Kiel, Inst Allgemeine Mikrobiol, Bot Garten 1-9, D-24118 Kiel, Germany. rschmitz@ifam.uni-kiel.de
Keywords: methanosarcina-mazei go1 methanol methyltransferase isozymes small nucleolar rnas acetivorans c2a antisense rnas strain go1 transcriptional regulator translational initiation pyrococcus-furiosus escherichia-coli
Research affiliation: Kiel University
OceanRep > The Future Ocean - Cluster of Excellence
Kiel University > Kiel Marine Science
Refereed: Yes
ISSN: 0305-1048
Projects: Future Ocean
Date Deposited: 14 May 2014 10:00
Last Modified: 14 May 2014 10:00
URI: http://eprints.uni-kiel.de/id/eprint/24049

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