SPP 1258:  Sensory and Regulatory RNAs in Prokaryotes

• Subject Area: Medicine ; Biology ; Chemistry ; Physics
• Term: from 2007 to 2013
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 22465846

One of the most fascinating discoveries in recent biology has been the regulatory potential of regulatory RNAs. Recent estimates suggest that a typical microbial genome may encode hundreds of small regulatory RNAs. Such sRNAs are generally untranslated, and most often range from 50 to 250 nucleotides in length. Where characterised in detail, some sRNAs were found to regulate target genes by binding to (regulatory) proteins, whilst most of them turned out as antisense RNAs that act on trans-encoded mRNAs.
Most bacterial mRNAs contain a 5'-untranslated region (5'-UTR) with more than the Shine-Dalgarno (SD) sequence required for interaction with the 30S ribosomal particle. Such extended 5'-UTRs can fold into complex structures with regulatory properties. RNA thermometers, for example, acquire a structure that blocks translation at low temperatures. Riboswitches control gene expression by ligand-induced conformational changes that control transcription termination, translation initiation or RNA processing.
The goal of the Priority Programme is to bring together scientists to explore the regulatory potential of RNA in diverse prokaryotic systems. That is apart from the standard model bacteria, Escherichia coli and Bacillus subtilis, several other microbes including cyanobacteria, Rhizobiaceae, several pathogens and halophilic as well as methanogenic Archaea will be studied.

• DFG Programme: Priority Programmes
• International Connection: Austria, Poland

Projects

• A conserved small RNA in the RpoS regulon (Applicant Vogel, Jörg )
• Central project: Deep sequencing as a tool for prokaryotic RNA research (Applicant Vogel, Jörg )
• Characterization of small regulatory RNAs with a putative function in the virulence of Xanthomonas campestris pv. vesicatoria (Applicant Bonas, Ulla )
• Computational Detection of Bacterial ncRNAs and their Targets (Applicants Backofen, Rolf ;  Stadler, Peter Florian )
• Elucidation of novel regulatory mechanisms employed by small noncoding RNAs from B. subtilis and identification of RNA chaperones involved in these mechanisms (Applicant Brantl, Sabine )
• Folding of the FMN dependent riboswitch (Applicant Müller, Sabine )
• Functional analysis of selected sRNAs potentially involved in nitrogen and / or general stress response in the archaeon Methanosarcina mazei Gö1 (Applicant Schmitz-Streit, Ruth Anne )
• GlmY and GlmZ: A regulatory cascade composed of two small RNAs (Applicant Görke, Boris )
• Identification and function of regulatory RNA in the phototropic model organism Synechocystis sp. PCC 6803 (Applicants Hess, Wolfgang R. ;  Wilde, Annegret )
• Influence of sensory and regulatory RNAs on the biological fitness and pathogenity of Yersinia pseudotuberculosis (Applicant Dersch, Petra )
• Ligand recognition and discrimation in the S-adenosylhomocysteine (SAH) sensing riboswitch (Applicant Wöhnert, Jens )
• Mittel zur Durchführung von Kolloquien, Koordinationsbesprechungen und Koordinierung des Schwerpunkts (Applicant Narberhaus, Franz )
• Multiple target regulation by GcvB sRNA (Applicant Vogel, Jörg )
• NMR Investigation of the Regulation of Gene Expression by RNA Thermometers (Applicant Schwalbe, Harald )
• Processing and degradation of regulatory RNAs in Escherichia coli (Applicant Klug, Gabriele )
• Regulatory RNAs in the hfq-deficient oxyphototroph Prochlorococcus sp. (Applicant Steglich, Claudia )
• Riboswitches and small RNAs in Bacilli under different thermal conditions (Applicant Stülke, Jörg )
• Role of an sRNA repeat in general stress response of alpha-proteobacteria and mechanisms of regulation (Applicant Klug, Gabriele )
• Role of Hfq-binding aptamers in antisense transcripts opposite to start and stop sites of protein coding genes in E. coli (Applicant Schroeder, Renée )
• Single-molecule fluorescence analysis of the temperature dependent structure and dynamics of an RNA thermometer: consequences for its molecular function (Applicants Müller, Sabine ;  Seidel, Claus )
• Small non-coding RNAs in Streptomyces coelicolor (Applicant Süß, Beatrix )
• Small regulatory RNAs from the halophilic archaeon Haloferax volcanii (Applicants Marchfelder, Anita ;  Soppa, Jörg )
• Structural analysis of regulatory RNAs: Hfq-mediated gene regulation by small trans-acting RNAs (Applicant Weichenrieder, Oliver )
• Structural and functional aspects of the small riboregulator 6S RNA (Applicant Hartmann, Roland K. )
• Structure and function of RNA thermometers (Applicant Narberhaus, Franz )
• Studies on the structure and function of bacterial 6S RNA, a putative transcriptional regulator (Applicant Wagner, Rolf )
• Target identification and functional analysis of regulatory small RNAs in Sinorhizobium meliloti and related alpha-proteobacteria (Applicants Becker, Anke ;  Giegerich, Robert )
• The regulatory role of five small noncoding RNAs in Streptococcus pneumoniae (Applicant Brückner, Reinhold )
• The role of small RNAs in physiology and virulence of Agrobacterium tumefaciens (Applicant Narberhaus, Franz )
• X-ray crystallographic structure analysis of the RNA thermometer ROSE and the preQ1-specific riboswitch (Applicant Ficner, Ralf )

• Spokesperson: Professor Dr. Franz Narberhaus