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The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino acid metabolism

Archives of Microbiology volume 192, pages 691–702 (2010)Cite this article

Abstract

Small non-coding RNAs (sRNAs) are key players in prokaryotic metabolic circuits, allowing the cell to adapt to changing environmental conditions. Regulatory interference by sRNAs in cellular metabolism is often facilitated by the Sm-like protein Hfq. A search for novel sRNAs in A. baylyi intergenic regions was performed by a biocomputational screening. One candidate, Aar, encoded between trpS and sucD showed Hfq dependency in Northern blot analysis. Aar was expressed strongly during stationary growth phase in minimal medium; in contrast, in complex medium, strongest expression was in the exponential growth phase. Whereas over-expression of Aar in trans did not affect bacterial growth, seven mRNA targets predicted by two in silico approaches were upregulated in stationary growth phase. All seven mRNAs are involved in A. baylyi amino acid metabolism. A putative binding site for Lrp, the global regulator of branched-chain amino acids in E. coli, was observed within the aar gene. Both facts imply an Aar participation in amino acid metabolism.

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Acknowledgments

We would like to thank Björn Voss for his predictions of sRNA genes in Acinetobacter and Véronique de Berardinis for her effort to delete aar. Furthermore, we would like to thank Iris Steiner for her contribution. This work was supported by the German Federal Ministry of Education and Research (BMBF grant 0313921 FRISYS to A.S.R.); the German Research Foundation (DFG grant SPP1258 to S.F. STA850/7-1 and A.S.R. BA2168/2-1); and the state of Baden-Württemberg, Germany (personal LGFG grant to D.S.).

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Affiliations

  1. Institute of Microbiology and Biotechnology, University of Ulm, 89069, Ulm, Germany

    Dominik Schilling & Ulrike Gerischer

  2. Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, 01407, Leipzig, Germany

    Sven Findeiß

  3. Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110, Freiburg, Germany

    Andreas S. Richter

  4. Department of Microbiology, University of Georgia, Athens, GA, 30602-2605, USA

    Jennifer A. Taylor

  5. Department of Conservative Dentistry and Periodontology, University of Ulm, Albert-Einstein-Allee 11, 89069, Ulm, Germany

    Dominik Schilling

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  1. Dominik Schilling
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  2. Sven Findeiß
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Correspondence to Dominik Schilling.

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Communicated by Wolfgang Buckel.

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Schilling, D., Findeiß, S., Richter, A.S. et al. The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino acid metabolism. Arch Microbiol 192, 691–702 (2010). https://doi.org/10.1007/s00203-010-0592-6

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  • DOI: https://doi.org/10.1007/s00203-010-0592-6

Keywords

  • A. baylyi
  • Hfq
  • IntaRNA
  • RNAup
  • sRNAs