title: An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains.
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.
authors.affiliation: Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany.
authors.forename: Dominik
authors.initials: D
authors.lastname: Jäger
authors.forename: Sandy R
authors.initials: SR
authors.lastname: Pernitzsch
authors.forename: Andreas S
authors.initials: AS
authors.lastname: Richter
authors.forename: Rolf
authors.initials: R
authors.lastname: Backofen
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Sharma
authors.forename: Ruth A
authors.initials: RA
authors.lastname: Schmitz
mesh_terms: D020121:5' Untranslated Regions; D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D020869:Gene Expression Profiling; D019848:Gene Expression Regulation, Archaeal; D017020:Methanosarcina / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D019642:RNA, Archaeal / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D020121:5' Untranslated Regions; D019843:Archaeal Proteins; D019642:RNA, Archaeal; D012333:RNA, Messenger; D058727:RNA, Small Untranslated