Refine
Has Fulltext
- yes (31) (remove)
Is part of the Bibliography
- yes (31)
Year of publication
Document Type
- Journal article (29)
- Conference Proceeding (1)
- Doctoral Thesis (1)
Language
- English (31)
Keywords
- RNA-seq (4)
- escherichia coli (4)
- gene expression (3)
- transcriptomics (3)
- Antisense RNA (2)
- Rhodobacter sphaeroides (2)
- bacteria (2)
- dRNA-Seq (2)
- genome annotation (2)
- identification (2)
- messenger RNA (2)
- transcriptome (2)
- 5-bromodeoxyuridine (1)
- Archaea (1)
- Bacteriaophage AR9 (1)
- Bioinformatik (1)
- Bradyrhizobium (1)
- CRISPR-Cas system (1)
- CRISPRs (1)
- DNA glycosation (1)
- DNA methylation (1)
- DNA methylferase homolog (1)
- Dictyostelium discoideum (1)
- E. coli Nissle 1917 (1)
- EHEC (1)
- Elektronisches Publizieren (1)
- Enyzme (1)
- Erwinia amylovora (1)
- GC-Wert (1)
- GC-value (1)
- Genome re-annotation (1)
- Haloferax volcanii (1)
- Hfq (1)
- Internal transcription start site (1)
- K279a (1)
- LamB (1)
- Leaderless transcript (1)
- Metagenomics (1)
- Metagenomomanalyse (1)
- Methanosarcina mazei (1)
- NHase (1)
- Neisseria meningitidis (1)
- Nitrilase (1)
- Nodule (1)
- Non-coding RNAs (1)
- Open Science (1)
- OxyR (1)
- PKS (1)
- ProQ (1)
- Promoter (1)
- Promoter prediction (1)
- Proteogenomics (1)
- RNA CHAPERONE HFQ (1)
- RNA expression (1)
- RNA sequencing (1)
- RNA sequencing (RNA-Seq) (1)
- RNA-binding proteins (1)
- RNA-polymerase-II (1)
- RNAseq (1)
- RNase E (1)
- RbdB (1)
- SEQ (1)
- SWI2/SNF2-like protein (1)
- Shiga toxin producing E. coli (1)
- Sinorhizobium fredii (1)
- Staphylococci (1)
- Stenotrophomonas maltophilia (1)
- Streptomyces (1)
- TRNA(ASP) (1)
- Transcription profiling (1)
- Transcription start site (1)
- Transcriptome (1)
- Virtual Research Environment (1)
- adaptation phase (1)
- anti-sigma factor (1)
- antibiotic resistance (1)
- antisense RNA (1)
- antisense RNAs (1)
- archaea (1)
- automation (1)
- bacillus subtilis (1)
- bacterial genomics (1)
- bacterial pathogen (1)
- beta-lactamases (1)
- binding (1)
- binding protein HFQ (1)
- bioassay-guided fractionation (1)
- biofilms (1)
- biology (1)
- blood-brain barrier (1)
- blood-cerebrospinal fluid barrier (1)
- brain endothelial cells (1)
- brucei genome (1)
- burkholderia cenocepacia (1)
- campylobacter (1)
- casposon (1)
- cepedia complex (1)
- characterization (1)
- collaboratories (1)
- colony morphotypes (1)
- dependent gene-expression (1)
- device-related infections (1)
- distance-dependent decay (1)
- drospophila (1)
- dsRNA binding protein (1)
- emotional behavior (1)
- enterica serovar thphimurium (1)
- enzymes (1)
- flagellar basal body (1)
- genome (1)
- genome architecture (1)
- genome-wide analysis (1)
- genomic islands (1)
- genomic libraries (1)
- genomic library construction (1)
- genomics (1)
- global gene expression (1)
- gram-negative bacteria (1)
- hela cells (1)
- histone variants (1)
- hydrogen regulation (1)
- hydrogen-peroxide (1)
- hyperthermophile (1)
- in-vivo (1)
- iron limitation (1)
- lambda-phages (1)
- lambdoid prophage (1)
- listeria monocytogenes (1)
- marine sponges (1)
- mass spectrometry (1)
- maternal separation (1)
- mechanism (1)
- membrane vesicles (1)
- meningococcus (1)
- messenger-RNA (1)
- metagenomics (1)
- metaproteomics (1)
- metatranscriptomics (1)
- methanoarchaea (1)
- microalga-bacteria interaction (1)
- microbiology (1)
- microprocessor (1)
- mouse (1)
- mycobacterium tuberculosis (1)
- noncoding RNA (1)
- nosocomial pathogen (1)
- organohalide respiration (1)
- oxidative stress (1)
- pathogen (1)
- persistence (1)
- persister cells (1)
- phenotypic heterogeneity (1)
- photooxidative stress (1)
- photosynthesis genes (1)
- phototrophic growth (1)
- phycosphere biofilm (1)
- plant symbioses (1)
- plasmid copy number (1)
- polycistronic transcription (1)
- posttranscriptional control (1)
- probiotic (1)
- promoters (1)
- protein HFQ (1)
- pseudomas aeruginosa (1)
- quanititative proteomics (1)
- quorum sensing (QS) (1)
- red fluorescent protein (1)
- regulatory small RNAs (1)
- reputation (1)
- resistance (1)
- rhodobacter sphaeroides (1)
- riboswitch (1)
- sRNA (1)
- scholarly publishing (1)
- scientific publishing (1)
- sequence motif analysis (1)
- serotonin (1)
- single molecule real time (SMRT) (1)
- singlet oxygen stress (1)
- sinorhizobium fredii NGR234 (1)
- small RNAs (1)
- small non-coding RNAs (1)
- small regulatory RNAs (1)
- stem cells (1)
- streptococcus pneumoniae (1)
- stress resistance (1)
- stx-phages (1)
- subtilis genome (1)
- tetrachloroethene (1)
- transcription start site (1)
- transcriptional landscape (1)
- transcriptional regulation (1)
- transcriptome analysis (1)
- translation initiation (1)
- transport systems (1)
- two‐component system (1)
- variant surface glycoprotein (1)
- version control (1)
- wikis (1)
- workflow platform (1)
- xanthomonas maltophilia (1)
Institute
- Institut für Molekulare Infektionsbiologie (27)
- Medizinische Fakultät (3)
- Institut für Hygiene und Mikrobiologie (1)
- Institut für Pharmazie und Lebensmittelchemie (1)
- Julius-von-Sachs-Institut für Biowissenschaften (1)
- Klinik und Poliklinik für Psychiatrie, Psychosomatik und Psychotherapie (1)
- Lehrstuhl für Tissue Engineering und Regenerative Medizin (1)
- Theodor-Boveri-Institut für Biowissenschaften (1)
Sonstige beteiligte Institutionen
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.
Role of oxygen and the OxyR protein in the response to iron limitation in Rhodobacter sphaeroides
(2014)
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.
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.
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.
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
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.
Energy conservation via organohalide respiration (OHR) in dehalogenating Sulfurospirillum species is an inducible process. However, the gene products involved in tetrachloroethene (PCE) sensing and signal transduction have not been unambiguously identified. Here, genome sequencing of Sulfurospirillum strains defective in PCE respiration and comparative genomics, which included the PCE‐respiring representatives of the genus, uncovered the genetic inactivation of a two‐component system (TCS) in the OHR gene region of the natural mutants. The assumption that the TCS gene products serve as a PCE sensor that initiates gene transcription was supported by the constitutive low‐level expression of the TCS operon in fumarate‐adapted cells of Sulfurospirillum multivorans. Via RNA sequencing, eight transcriptional units were identified in the OHR gene region, which includes the TCS operon, the PCE reductive dehalogenase operon, the gene cluster for norcobamide biosynthesis, and putative accessory genes with unknown functions. The OmpR‐family response regulator (RR) encoded in the TCS operon was functionally characterized by promoter‐binding assays. The RR bound a cis‐regulatory element that contained a consensus sequence of a direct repeat (CTATW) separated by 17 bp. Its location either overlapping the −35 box or 50 bp further upstream indicated different regulatory mechanisms. Sequence variations in the regulator binding sites identified in the OHR gene region were in accordance with differences in the transcript levels of the respective gene clusters forming the PCE regulon. The results indicate the presence of a fine‐tuned regulatory network controlling PCE metabolism in dehalogenating Sulfurospirillum species, a group of metabolically versatile organohalide‐respiring bacteria.
RNA-binding proteins (RBPs) have been established as core components of several post-transcriptional gene regulation mechanisms. Experimental techniques such as cross-linking and co-immunoprecipitation have enabled the identification of RBPs, RNA-binding domains (RBDs) and their regulatory roles in the eukaryotic species such as human and yeast in large-scale. In contrast, our knowledge of the number and potential diversity of RBPs in bacteria is poorer due to the technical challenges associated with the existing global screening approaches. We introduce APRICOT, a computational pipeline for the sequence-based identification and characterization of proteins using RBDs known from experimental studies. The pipeline identifies functional motifs in protein sequences using position-specific scoring matrices and Hidden Markov Models of the functional domains and statistically scores them based on a series of sequence-based features. Subsequently, APRICOT identifies putative RBPs and characterizes them by several biological properties. Here we demonstrate the application and adaptability of the pipeline on large-scale protein sets, including the bacterial proteome of Escherichia coli. APRICOT showed better performance on various datasets compared to other existing tools for the sequence-based prediction of RBPs by achieving an average sensitivity and specificity of 0.90 and 0.91 respectively. The command-line tool and its documentation are available at https://pypi.python.org/pypi/bio-apricot.
We identified the dsRNA binding protein RbdB as an essential component in miRNA processing in Dictyostelium discoideum. RbdB is a nuclear protein that accumulates, together with Dicer B, in nucleolar foci reminiscent of plant dicing bodies. Disruption of rbdB results in loss of miRNAs and accumulation of primary miRNAs. The phenotype can be rescued by ectopic expression of RbdB thus allowing for a detailed analysis of domain function. The lack of cytoplasmic dsRBD proteins involved in miRNA processing, suggests that both processing steps take place in the nucleus thus resembling the plant pathway. However, we also find features e.g. in the domain structure of Dicer which suggest similarities to animals. Reduction of miRNAs in the rbdB- strain and their increase in the Argonaute A knock out allowed the definition of new miRNAs one of which appears to belong to a new non-canonical class.
Bacteriophage AR9 is a recently sequenced jumbo phage that encodes two multisubunit RNA polymerases. Here we investigated the AR9 transcription strategy and the effect of AR9 infection on the transcription of its host, Bacillus subtilis. Analysis of whole-genome transcription revealed early, late, and continuously expressed AR9 genes. Alignment of sequences upstream of the 5′ ends of AR9 transcripts revealed consensus sequences that define early and late phage promoters. Continuously expressed AR9 genes have both early and late promoters in front of them. Early AR9 transcription is independent of protein synthesis and must be determined by virion RNA polymerase injected together with viral DNA. During infection, the overall amount of host mRNAs is significantly decreased. Analysis of relative amounts of host transcripts revealed notable differences in the levels of some mRNAs. The physiological significance of up- or downregulation of host genes for AR9 phage infection remains to be established. AR9 infection is significantly affected by rifampin, an inhibitor of host RNA polymerase transcription. The effect is likely caused by the antibiotic-induced killing of host cells, while phage genome transcription is solely performed by viral RNA polymerases.