@Article{Daume_Uhl_Backofen-RIP_Sugge_Trans-2017,
  author =	 {Daume, Michael and Uhl, Michael and Backofen, Rolf and 
                  Randau, Lennart},
  title =	 {{RIP}-{Seq} {Suggests} {Translational} {Regulation} by 
                  {L7Ae} in {Archaea}},
  journal =	 {MBio},
  year =	 {2017},
  volume =	 {8},
  number =	 {4},
  pages =	 {},
  user =	 {uhlm},
  pmid =	 {28765217},
  doi = 	 {10.1128/mBio.00730-17},
  issn = 	 {2150-7511},
  abstract =	 {L7Ae is a universal archaeal protein that recognizes and 
                  stabilizes kink-turn (k-turn) motifs in RNA substrates. 
                  These structural motifs are widespread in nature and are 
                  found in many functional RNA species, including ribosomal 
                  RNAs. Synthetic biology approaches utilize L7Ae/k-turn 
                  interactions to control gene expression in eukaryotes. Here, 
                  we present results of comprehensive RNA immunoprecipitation 
                  sequencing (RIP-Seq) analysis of genomically tagged L7Ae 
                  from the hyperthermophilic archaeon Sulfolobus 
                  acidocaldarius A large set of interacting noncoding RNAs was 
                  identified. In addition, several mRNAs, including the l7ae 
                  transcript, were found to contain k-turn motifs that 
                  facilitate L7Ae binding. In vivo studies showed that L7Ae 
                  autoregulates the translation of its mRNA by binding to a 
                  k-turn motif present in the 5' untranslated region (UTR). A 
                  green fluorescent protein (GFP) reporter system was 
                  established in Escherichia coli and verified conservation of 
                  L7Ae-mediated feedback regulation in Archaea Mobility shift 
                  assays confirmed binding to a k-turn in the transcript of 
                  nop5-fibrillarin, suggesting that the expression of all C/D 
                  box sRNP core proteins is regulated by L7Ae. These studies 
                  revealed that L7Ae-mediated gene regulation evolved in 
                  archaeal organisms, generating new tools for the modulation 
                  of synthetic gene circuits in bacteria.IMPORTANCE L7Ae is an 
                  essential archaeal protein that is known to structure 
                  ribosomal RNAs and small RNAs (sRNAs) by binding to their 
                  kink-turn motifs. Here, we utilized RIP-Seq methodology to 
                  achieve a first global analysis of RNA substrates for L7Ae. 
                  Several novel interactions with noncoding RNA molecules 
                  (e.g., with the universal signal recognition particle RNA) 
                  were discovered. In addition, L7Ae was found to bind to 
                  mRNAs, including its own transcript's 5' untranslated 
                  region. This feedback-loop control is conserved in most 
                  archaea and was incorporated into a reporter system that was 
                  utilized to control gene expression in bacteria. These 
                  results demonstrate that L7Ae-mediated gene regulation 
                  evolved originally in archaeal organisms. The 
                  feedback-controlled reporter gene system can easily be 
                  adapted for synthetic biology approaches that require strict 
                  gene expression control.}
}