Die Genexpressionsmaschinerie in Chloroplasten und Mitochondrien und die ihrer prokaryotischen Vorläufer sind konserviert. Innerhalb eines bakteriellen Grundgerüsts entwickelte sich darüber hinaus ein komplexer RNA-Metabolismus. In der vorliegenden Arbeit wird eine neue Klasse kleiner RNAs (15-50nt) mit plastidärem und mitochondrialen Ursprung beschrieben. Diese kurzen RNAs überlappen mit Bindestellen von RNA-bindenden Proteinen, die mRNAs gegen exonukleolytischen Verdau beschützen. Diese stabilisierende Funktion wird vermutlich hauptsächlich von PPR (Pentatricopeptid repeat) Proteinen und verwandten Proteine bewerkstelligt. Die kleinen RNAs repräsentieren dabei minimale nuklease-resistente Bereiche, sogenannte RNA-Bindeprotein footprints. Solche footprints finden sich in fast jedem intergenischen Bereich, der Prozessierung aufweist. Durch transkriptomweite Untersuchungen von kleinen RNAs in Mutanten von RNA-Bindeproteinen konnte für diese eine Reihe von Bindestellen identifiziert werden. Nuklease-resistente kleine RNAs fehlen in entsprechenden Mutanten. Der Vergleich neu identifizierter Ziele einzelner RNA-Bindeproteine führte dabei zu neuen Erkenntnissen über den Mechanismus der RNA-Erkennung durch PPR Proteine. Im Gegensatz zu Plastiden befinden sich kleine RNAs in Mitochondrien überwiegend an den 3‘ Enden von Transkripten, deren Stabilität vermutlich maßgeblich von diesen RNA-Bindeproteinen beeinflusst wird. Für das chloroplastidäre Ribonukleoprotein CP31A konnte gezeigt werden, dass es an der Stabilisierung der ndhF mRNA beteiligt ist. Die Interaktion mit der ndhF mRNA, die eine zentrale Komponente des NDH-Komplexes kodiert, wird dabei über die 3‘ untranslatierte Region vermittelt. Zusätzlich konnte gezeigt werden, dass CP31A die Stabilität einiger antisense Transkripte beeinflusst. Weiterhin wurden zehn neue Cytidin Desaminierungungen durch die Analyse von RNA-Seq Datensätzen in der Modellpflanze Arabidopsis thaliana identifiziert. / Chloroplasts and mitochondria are of endosymbiotic origin. Their basic gene expression machineries are retained from their free-living prokaryotic progenitors. On top of this bacterial scaffold, a number of organelle-specific RNA processing steps evolved. In this thesis, a novel class of organelle-specific short (15-50nt) RNAs is described on a transcriptome-wide scale. The small RNAs are found at binding sites of PPR (Pentatricopeptide repeat) and PPR-like proteins, which protect mRNAs against exonucleolytic decay. The small RNAs represent minimal nuclease resistant RNAs, so called PPR footprints. Small RNAs were identified in almost every intergenic region subjected to intergenic processing. This finding suggests that accumulation of processed transcripts in plastids is mostly due to protection by highly specific RNA-binding proteins. Small RNA sequencing identified a number of nuclease insensitive sites missing in mutants of RNA-binding proteins. Analysis of multiple small RNAs representing target sites of single PPR proteins expands the knowledge of target specificity. In mitochondria, accumulations of small RNAs predicts that at least two thirds of mitochondrial mRNAs are stabilized by RNA-binding proteins binding in their 3’UTR. In sum, small organellar RNAs turned out to be instrumental in elucidating the hitherto enigmatic intercistronic processing of organellar RNAs and allowed novel insights into the function of the dominant family of organellar RNA binding proteins, the PPR proteins. A chloroplast ribonucleoprotein CP31A is shown to be involved in stabilization of an mRNA for a central component of the NDH-complex by interaction with its 3’UTR. In addition, CP31A represents the first factor described that influences the accumulation of chloroplast antisense transcripts. Finally, ten novel plastid C to U RNA-editing sites were identified in the model plant Arabidopsis thaliana, using a novel RNA-Seq based approach.

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In Enterobacteriaceae, the transcriptional regulator AmpR, a member of the LysR family, regulates the expression of a chromosomal β-lactamase AmpC. The regulatory repertoire of AmpR is broader in Pseudomonas aeruginosa, an opportunistic pathogen responsible for numerous acute and chronic infections including cystic fibrosis. Previous studies showed that in addition to regulating ampC, P. aeruginosa AmpR regulates the sigma factor AlgT/U and production of some quorum sensing (QS)-regulated virulence factors. In order to better understand the ampR regulon, the transcriptional profiles generated using DNA microarrays and RNA-Seq of the prototypic P. aeruginosa PAO1 strain with its isogenic ampR deletion mutant, PAO∆ampR were analyzed. Transcriptome analysis demonstrates that the AmpR regulon is much more extensive than previously thought influencing the differential expression of over 500 genes. In addition to regulating resistance to β-lactam antibiotics via AmpC, AmpR also regulates non-β-lactam antibiotic resistance by modulating the MexEF-OprN efflux pump. Virulence mechanisms including biofilm formation, QS-regulated acute virulence, and diverse physiological processes such as oxidative stress response, heat-shock response and iron uptake are AmpR-regulated. Real-time PCR and phenotypic assays confirmed the transcriptome data. Further, Caenorhabditis elegans model demonstrates that a functional AmpR is required for full pathogenicity of P. aeruginosa. AmpR, a member of the core genome, also regulates genes in the regions of genome plasticity that are acquired by horizontal gene transfer. The extensive AmpR regulon included other transcriptional regulators and sigma factors, accounting for the extensive AmpR regulon. Gene expression studies demonstrate AmpR-dependent expression of the QS master regulator LasR that controls expression of many virulence factors. Using a chromosomally tagged AmpR, ChIP-Seq studies show direct AmpR binding to the lasR promoter. The data demonstrates that AmpR functions as a global regulator in P. aeruginosa and is a positive regulator of acute virulence while negatively regulating chronic infection phenotypes. In summary, my dissertation sheds light on the complex regulatory circuit in P. aeruginosa to provide a better understanding of the bacterial response to antibiotics and how the organism coordinately regulates a myriad of virulence factors.