@article{MoellerOverloeperFoerstneretal.2014, author = {M{\"o}ller, Philip and Overl{\"o}per, Aaron and F{\"o}rstner, Konrad U. and Wen, Tuan-Nan and Sharma, Cynthia M. and Lai, Erh-Min and Narberhaus, Franz}, title = {Profound Impact of Hfq on Nutrient Acquisition, Metabolism and Motility in the Plant Pathogen Agrobacterium tumefaciens}, series = {PLOS ONE}, volume = {9}, journal = {PLOS ONE}, number = {10}, doi = {10.1371/journal.pone.0110427}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-114874}, pages = {e110427}, year = {2014}, abstract = {As matchmaker between mRNA and sRNA interactions, the RNA chaperone Hfq plays a key role in riboregulation of many bacteria. Often, the global influence of Hfq on the transcriptome is reflected by substantially altered proteomes and pleiotropic phenotypes in hfq mutants. Using quantitative proteomics and co-immunoprecipitation combined with RNA-sequencing (RIP-seq) of Hfq-bound RNAs, we demonstrate the pervasive role of Hfq in nutrient acquisition, metabolism and motility of the plant pathogen Agrobacterium tumefaciens. 136 of 2544 proteins identified by iTRAQ (isobaric tags for relative and absolute quantitation) were affected in the absence of Hfq. Most of them were associated with ABC transporters, general metabolism and motility. RIP-seq of chromosomally encoded Hfq 3xFlag revealed 1697 mRNAs and 209 non-coding RNAs (ncRNAs) associated with Hfq. 56 ncRNAs were previously undescribed. Interestingly, 55\% of the Hfq-bound ncRNAs were encoded antisense (as) to a protein-coding sequence suggesting that A. tumefaciens Hfq plays an important role in asRNA-target interactions. The exclusive enrichment of 296 mRNAs and 31 ncRNAs under virulence conditions further indicates a role for post-transcriptional regulation in A. tumefaciens-mediated plant infection. On the basis of the iTRAQ and RIP-seq data, we assembled a comprehensive model of the Hfq core regulon in A. tumefaciens.}, language = {en} } @article{RemesBerghoffFoerstneretal.2014, author = {Remes, Bernhard and Berghoff, Bork A. and F{\"o}rstner, Konrad U. and Klug, Gabriele}, title = {Role of oxygen and the OxyR protein in the response to iron limitation in Rhodobacter sphaeroides}, series = {BMC Genomics}, volume = {15}, journal = {BMC Genomics}, number = {794}, issn = {1471-2164}, doi = {10.1186/1471-2164-15-794}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-115357}, year = {2014}, abstract = {Background: High intracellular levels of unbound iron can contribute to the production of reactive oxygen species (ROS) via the Fenton reaction, while depletion of iron limits the availability of iron-containing proteins, some of which have important functions in defence against oxidative stress. Vice versa increased ROS levels lead to the damage of proteins with iron sulphur centres. Thus, organisms have to coordinate and balance their responses to oxidative stress and iron availability. Our knowledge of the molecular mechanisms underlying the co-regulation of these responses remains limited. To discriminate between a direct cellular response to iron limitation and indirect responses, which are the consequence of increased levels of ROS, we compared the response of the alpha-proteobacterium Rhodobacter sphaeroides to iron limitation in the presence or absence of oxygen. Results: One third of all genes with altered expression under iron limitation showed a response that was independent of oxygen availability. The other iron-regulated genes showed different responses in oxic or anoxic conditions and were grouped into six clusters based on the different expression profiles. For two of these clusters, induction in response to iron limitation under oxic conditions was dependent on the OxyR regulatory protein. An OxyR mutant showed increased ROS production and impaired growth under iron limitation. Conclusion: Some R. sphaeroides genes respond to iron limitation irrespective of oxygen availability. These genes therefore reflect a "core iron response" that is independent of potential ROS production under oxic, iron-limiting conditions. However, the regulation of most of the iron-responsive genes was biased by oxygen availability. Most strikingly, the OxyR-dependent activation of a subset of genes upon iron limitation under oxic conditions, including many genes with a role in iron metabolism, revealed that elevated ROS levels were an important trigger for this response. OxyR thus provides a regulatory link between the responses to oxidative stress and to iron limitation in R. sphaeroides.}, language = {en} } @article{SharmaDugarHerbigetal.2013, author = {Sharma, Cynthia M. and Dugar, Gaurav and Herbig, Alexander and F{\"o}rstner, Konrad U. and Heidrich, Nadja and Reinhardt, Richard and Nieselt, Kay}, title = {High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates}, series = {PLoS Genetics}, journal = {PLoS Genetics}, doi = {10.1371/journal.pgen.1003495}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-96610}, year = {2013}, abstract = {Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans. Comparison of multiple Campylobacter strains revealed a high genetic and phenotypic diversity. However, little is known about differences in transcriptome organization, gene expression, and small RNA (sRNA) repertoires. Here we present the first comparative primary transcriptome analysis based on the differential RNA-seq (dRNA-seq) of four C. jejuni isolates. Our approach includes a novel, generic method for the automated annotation of transcriptional start sites (TSS), which allowed us to provide genome-wide promoter maps in the analyzed strains. These global TSS maps are refined through the integration of a SuperGenome approach that allows for a comparative TSS annotation by mapping RNA-seq data of multiple strains into a common coordinate system derived from a whole-genome alignment. Considering the steadily increasing amount of RNA-seq studies, our automated TSS annotation will not only facilitate transcriptome annotation for a wider range of pro- and eukaryotes but can also be adapted for the analysis among different growth or stress conditions. Our comparative dRNA-seq analysis revealed conservation of most TSS, but also single-nucleotide-polymorphisms (SNP) in promoter regions, which lead to strain-specific transcriptional output. Furthermore, we identified strain-specific sRNA repertoires that could contribute to differential gene regulation among strains. In addition, we identified a novel minimal CRISPR-system in Campylobacter of the type-II CRISPR subtype, which relies on the host factor RNase III and a trans-encoded sRNA for maturation of crRNAs. This minimal system of Campylobacter, which seems active in only some strains, employs a unique maturation pathway, since the crRNAs are transcribed from individual promoters in the upstream repeats and thereby minimize the requirements for the maturation machinery. Overall, our study provides new insights into strain-specific transcriptome organization and sRNAs, and reveals genes that could modulate phenotypic variation among strains despite high conservation at the DNA level.}, language = {en} } @article{MietchenHagedornFoerstneretal.2011, author = {Mietchen, Daniel and Hagedorn, Gregor and F{\"o}rstner, Konrad U. and Kubke, M Fabiana and Koltzenburg, Claudia and Hahnel, Mark J. and Penev, Lyubomir}, title = {Wikis in scholarly publishing}, doi = {10.3233/ISU-2011-0621}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-87770}, year = {2011}, abstract = {Scientific research is a process concerned with the creation, collective accumulation, contextualization, updating and maintenance of knowledge. Wikis provide an environment that allows to collectively accumulate, contextualize, update and maintain knowledge in a coherent and transparent fashion. Here, we examine the potential of wikis as platforms for scholarly publishing. In the hope to stimulate further discussion, the article itself was drafted on Species-ID - a wiki that hosts a prototype for wiki-based scholarly publishing - where it can be updated, expanded or otherwise improved.}, subject = {Elektronisches Publizieren}, language = {en} } @phdthesis{Foerstner2008, author = {F{\"o}rstner, Konrad Ulrich}, title = {Computational analysis of metagenomic data: delineation of compositional features and screens for desirable enzymes}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-33577}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2008}, abstract = {The topic of my doctorial research was the computational analysis of metagenomic data. A metagenome comprises the genomic information from all the microorganisms within a certain environment. The currently available metagenomic data sets cover only parts of these usually huge metagenomes due to the high technical and financial effort of such sequencing endeavors. During my thesis I developed bioinformatic tools and applied them to analyse genomic features of different metagenomic data sets and to search for enzymes of importance for biotechnology or pharmaceutical applications in those sequence collections. In these studies nine metagenomic projects (with up to 41 subsamples) were analysed. These samples originated from diverse environments like farm soil, acid mine drainage, microbial mats on whale bones, marine water, fresh water, water treatment sludges and the human gut flora. Additionally, data sets of conventionally retrieved sequence data were taken into account and compared with each other}, subject = {Bioinformatik}, language = {en} } @inproceedings{FoerstnerHagedornKoltzenburgetal.2011, author = {F{\"o}rstner, Konrad and Hagedorn, Gregor and Koltzenburg, Claudia and Kubke, Fabiana and Mietchen, Daniel}, title = {Collaborative platforms for streamlining workflows in Open Science}, series = {Proceedings of the 6th Open Knowledge Conference}, booktitle = {Proceedings of the 6th Open Knowledge Conference}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-101678}, year = {2011}, abstract = {Despite the internet's dynamic and collaborative nature, scientists continue to produce grant proposals, lab notebooks, data files, conclusions etc. that stay in static formats or are not published online and therefore not always easily accessible to the interested public. Because of limited adoption of tools that seamlessly integrate all aspects of a research project (conception, data generation, data evaluation, peerreviewing and publishing of conclusions), much effort is later spent on reproducing or reformatting individual entities before they can be repurposed independently or as parts of articles. We propose that workflows - performed both individually and collaboratively - could potentially become more efficient if all steps of the research cycle were coherently represented online and the underlying data were formatted, annotated and licensed for reuse. Such a system would accelerate the process of taking projects from conception to publication stages and allow for continuous updating of the data sets and their interpretation as well as their integration into other independent projects. A major advantage of such work ows is the increased transparency, both with respect to the scientific process as to the contribution of each participant. The latter point is important from a perspective of motivation, as it enables the allocation of reputation, which creates incentives for scientists to contribute to projects. Such work ow platforms offering possibilities to fine-tune the accessibility of their content could gradually pave the path from the current static mode of research presentation into a more coherent practice of open science.}, language = {en} } @article{BabskiHaasNaetherSchindleretal.2016, author = {Babski, Julia and Haas, Karina A. and N{\"a}ther-Schindler, Daniela and Pfeiffer, Friedhelm and F{\"o}rstner, Konrad U. and Hammelmann, Matthias and Hilker, Rolf and Becker, Anke and Sharma, Cynthia M. and Marchfelder, Anita and Soppa, J{\"o}rg}, title = {Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)}, series = {BMC Genomics}, volume = {17}, journal = {BMC Genomics}, number = {629}, doi = {10.1186/s12864-016-2920-y}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164553}, year = {2016}, abstract = {Background Differential RNA-Seq (dRNA-Seq) is a recently developed method of performing primary transcriptome analyses that allows for the genome-wide mapping of transcriptional start sites (TSSs) and the identification of novel transcripts. Although the transcriptomes of diverse bacterial species have been characterized by dRNA-Seq, the transcriptome analysis of archaeal species is still rather limited. Therefore, we used dRNA-Seq to characterize the primary transcriptome of the model archaeon Haloferax volcanii. Results Three independent cultures of Hfx. volcanii grown under optimal conditions to the mid-exponential growth phase were used to determine the primary transcriptome and map the 5′-ends of the transcripts. In total, 4749 potential TSSs were detected. A position weight matrix (PWM) was derived for the promoter predictions, and the results showed that 64 \% of the TSSs were preceded by stringent or relaxed basal promoters. Of the identified TSSs, 1851 belonged to protein-coding genes. Thus, fewer than half (46 \%) of the 4040 protein-coding genes were expressed under optimal growth conditions. Seventy-two percent of all protein-coding transcripts were leaderless, which emphasized that this pathway is the major pathway for translation initiation in haloarchaea. A total of 2898 of the TSSs belonged to potential non-coding RNAs, which accounted for an unexpectedly high fraction (61 \%) of all transcripts. Most of the non-coding TSSs had not been previously described (2792) and represented novel sequences (59 \% of all TSSs). A large fraction of the potential novel non-coding transcripts were cis-antisense RNAs (1244 aTSSs). A strong negative correlation between the levels of antisense transcripts and cognate sense mRNAs was found, which suggested that the negative regulation of gene expression via antisense RNAs may play an important role in haloarchaea. The other types of novel non-coding transcripts corresponded to internal transcripts overlapping with mRNAs (1153 iTSSs) and intergenic small RNA (sRNA) candidates (395 TSSs). Conclusion This study provides a comprehensive map of the primary transcriptome of Hfx. volcanii grown under optimal conditions. Fewer than half of all protein-coding genes have been transcribed under these conditions. Unexpectedly, more than half of the detected TSSs belonged to several classes of non-coding RNAs. Thus, RNA-based regulation appears to play a more important role in haloarchaea than previously anticipated.}, language = {en} } @article{ČuklinaHahnImakaevetal.2016, author = {Čuklina, Jelena and Hahn, Julia and Imakaev, Maxim and Omasits, Ulrich and F{\"o}rstner, Konrad U. and Ljubimov, Nikolay and Goebel, Melanie and Pessi, Gabriella and Fischer, Hans-Martin and Ahrens, Christian H. and Gelfand, Mikhail S. and Evguenieva-Hackenberg, Elena}, title = {Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation}, series = {BMC Genomics}, volume = {17}, journal = {BMC Genomics}, doi = {10.1186/s12864-016-2602-9}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-164565}, pages = {302}, year = {2016}, abstract = {Background Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinformatics challenge. We performed dRNA-seq of Bradyrhizobium japonicum USDA 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map TSSs and promoters. Results A specialized machine learning procedure for TSS recognition allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4329 in symbiosis with soybean and 2766 in both conditions. Further, we provide proteomic evidence for 4090 proteins, among them 107 proteins corresponding to new genes and 178 proteins with N-termini different from the existing annotation (72 and 109 of them with TSS support, respectively). Guided by proteomics evidence, previously identified TSSs and TSSs experimentally validated here, we assign a score threshold to flag 14 \% of the mapped TSSs as a class of lower confidence. However, this class of lower confidence contains valid TSSs of low-abundant transcripts. Moreover, we developed a de novo algorithm to identify promoter motifs upstream of mapped TSSs, which is publicly available, and found motifs mainly used in symbiosis (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). Mapped TSSs and putative promoters, proteomic evidence and updated gene annotation were combined into an annotation file. Conclusions The genome-wide TSS and promoter maps along with the extended genome annotation of B. japonicum represent a valuable resource for future systems biology studies and for detailed analyses of individual non-coding transcripts and ORFs. Our data will also provide new insights into bacterial gene regulation during the agriculturally important symbiosis between rhizobia and legumes.}, language = {en} } @article{KrohnMoltAlawiFoerstneretal.2017, author = {Krohn-Molt, Ines and Alawi, Malik and F{\"o}rstner, Konrad U. and Wiegandt, Alena and Burkhardt, Lia and Indenbirken, Daniela and Thieß, Melanie and Grundhoff, Adam and Kehr, Julia and Tholey, Andreas and Streit, Wolfgang R.}, title = {Insights into microalga and bacteria interactions of selected phycosphere biofilms using metagenomic, transcriptomic, and proteomic approaches}, series = {Frontiers in Microbiology}, volume = {2017}, journal = {Frontiers in Microbiology}, number = {8}, doi = {10.3389/fmicb.2017.01941}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-173701}, year = {2017}, abstract = {Microalga are of high relevance for the global carbon cycling and it is well-known that they are associated with a microbiota. However, it remains unclear, if the associated microbiota, often found in phycosphere biofilms, is specific for the microalga strains and which role individual bacterial taxa play. Here we provide experimental evidence that \(Chlorella\) \(saccharophila\), \(Scenedesmus\) \(quadricauda\), and \(Micrasterias\) \(crux-melitensis\), maintained in strain collections, are associated with unique and specific microbial populations. Deep metagenome sequencing, binning approaches, secretome analyses in combination with RNA-Seq data implied fundamental differences in the gene expression profiles of the microbiota associated with the different microalga. Our metatranscriptome analyses indicates that the transcriptionally most active bacteria with respect to key genes commonly involved in plant-microbe interactions in the Chlorella (Trebouxiophyceae) and Scenedesmus (Chlorophyceae) strains belong to the phylum of the α-Proteobacteria. In contrast, in the Micrasterias (Zygnematophyceae) phycosphere biofilm bacteria affiliated with the phylum of the Bacteroidetes showed the highest gene expression rates. We furthermore show that effector molecules known from plant-microbe interactions as inducers for the innate immunity are already of relevance at this evolutionary early plant-microbiome level.}, language = {en} } @article{GomesWestermannSauerweinetal.2019, author = {Gomes, Sara F. Martins and Westermann, Alexander J. and Sauerwein, Till and Hertlein, Tobias and F{\"o}rstner, Konrad U. and Ohlsen, Knut and Metzger, Marco and Shusta, Eric V. and Kim, Brandon J. and Appelt-Menzel, Antje and Schubert-Unkmeir, Alexandra}, title = {Induced pluripotent stem cell-derived brain endothelial cells as a cellular model to study Neisseria meningitidis infection}, series = {Frontiers in Microbiology}, volume = {10}, journal = {Frontiers in Microbiology}, number = {1181}, doi = {10.3389/fmicb.2019.01181}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-201562}, year = {2019}, abstract = {Meningococcal meningitis is a severe central nervous system infection that occurs when Neisseria meningitidis (Nm) penetrates brain endothelial cells (BECs) of the meningeal blood-cerebrospinal fluid barrier. As a human-specific pathogen, in vivo models are greatly limited and pose a significant challenge. In vitro cell models have been developed, however, most lack critical BEC phenotypes limiting their usefulness. Human BECs generated from induced pluripotent stem cells (iPSCs) retain BEC properties and offer the prospect of modeling the human-specific Nm interaction with BECs. Here, we exploit iPSC-BECs as a novel cellular model to study Nm host-pathogen interactions, and provide an overview of host responses to Nm infection. Using iPSC-BECs, we first confirmed that multiple Nm strains and mutants follow similar phenotypes to previously described models. The recruitment of the recently published pilus adhesin receptor CD147 underneath meningococcal microcolonies could be verified in iPSC-BECs. Nm was also observed to significantly increase the expression of pro-inflammatory and neutrophil-specific chemokines IL6, CXCL1, CXCL2, CXCL8, and CCL20, and the secretion of IFN-γ and RANTES. For the first time, we directly observe that Nm disrupts the three tight junction proteins ZO-1, Occludin, and Claudin-5, which become frayed and/or discontinuous in BECs upon Nm challenge. In accordance with tight junction loss, a sharp loss in trans-endothelial electrical resistance, and an increase in sodium fluorescein permeability and in bacterial transmigration, was observed. Finally, we established RNA-Seq of sorted, infected iPSC-BECs, providing expression data of Nm-responsive host genes. Altogether, this model provides novel insights into Nm pathogenesis, including an impact of Nm on barrier properties and tight junction complexes, and suggests that the paracellular route may contribute to Nm traversal of BECs.}, language = {en} }