@article{YuVogelFoerstner2018,
  author    = {Yu, Sung-Huan and Vogel, J{\"o}rg and F{\"o}rstner, Konrad U.},
  title     = {ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes},
  series = {GigaScience},
  volume    = {7},
  journal   = {GigaScience},
  doi       = {10.1093/gigascience/giy096},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-178942},
  year      = {2018},
  abstract  = {To understand the gene regulation of an organism of interest, a comprehensive genome annotation is essential. While some features, such as coding sequences, can be computationally predicted with high accuracy based purely on the genomic sequence, others, such as promoter elements or noncoding RNAs, are harder to detect. RNA sequencing (RNA-seq) has proven to be an efficient method to identify these genomic features and to improve genome annotations. However, processing and integrating RNA-seq data in order to generate high-resolution annotations is challenging, time consuming, and requires numerous steps. We have constructed a powerful and modular tool called ANNOgesic that provides the required analyses and simplifies RNA-seq-based bacterial and archaeal genome annotation. It can integrate data from conventional RNA-seq and differential RNA-seq and predicts and annotates numerous features, including small noncoding RNAs, with high precision. The software is available under an open source license (ISCL) at https://pypi.org/project/ANNOgesic/.},
  language  = {en}
}
@article{WestermannVenturiniSellinetal.2019,
  author    = {Westermann, Alexander J. and Venturini, Elisa and Sellin, Mikael E. and F{\"o}rstner, Konrad U. and Hardt, Wolf-Dietrich and Vogel, J{\"o}rg},
  title     = {The major RNA-binding protein ProQ impacts virulence gene expression in Salmonella enterica serovar Typhimurium},
  series = {mBio},
  volume    = {10},
  journal   = {mBio},
  number    = {1},
  doi       = {10.1128/mBio.02504-18},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-177722},
  pages     = {e02504-18},
  year      = {2019},
  abstract  = {FinO domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts, including mRNAs from many virulence regions, but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis, and virulence genes which is accompanied by altered MAPK (mitogen-activated protein kinase) signaling in the host. Comparison with the other major RNA chaperone in Salmonella, Hfq, reinforces the notion that these two global RNA-binding proteins work in parallel to ensure full virulence. Of newly discovered infection-associated ProQ-bound small noncoding RNAs (sRNAs), we show that the 3′UTR-derived sRNA STnc540 is capable of repressing an infection-induced magnesium transporter mRNA in a ProQ-dependent manner. Together, this comprehensive study uncovers the relevance of ProQ for Salmonella pathogenesis and highlights the importance of RNA-binding proteins in regulating bacterial virulence programs. IMPORTANCE The protein ProQ has recently been discovered as the centerpiece of a previously overlooked "third domain" of small RNA-mediated control of gene expression in bacteria. As in vitro work continues to reveal molecular mechanisms, it is also important to understand how ProQ affects the life cycle of bacterial pathogens as these pathogens infect eukaryotic cells. Here, we have determined how ProQ shapes Salmonella virulence and how the activities of this RNA-binding protein compare with those of Hfq, another central protein in RNA-based gene regulation in this and other bacteria. To this end, we apply global transcriptomics of pathogen and host cells during infection. In doing so, we reveal ProQ-dependent transcript changes in key virulence and host immune pathways. Moreover, we differentiate the roles of ProQ from those of Hfq during infection, for both coding and noncoding transcripts, and provide an important resource for those interested in ProQ-dependent small RNAs in enteric bacteria.},
  language  = {en}
}