A5076640513- Legume Nitrogen Fixing Symbiosis
- RNA and protein synthesis mechanisms
- Bacteriophages and microbial interactions
- RNA modifications and cancer
- RNA Research and Splicing
- Bacterial Genetics and Biotechnology
- Plant nutrient uptake and metabolism
- Genomics and Phylogenetic Studies
- Mechanical stress and fatigue analysis
- Plant-Microbe Interactions and Immunity
- Microbial Community Ecology and Physiology
- Nuclear Materials and Properties
- DNA Repair Mechanisms
- Enterobacteriaceae and Cronobacter Research
- CRISPR and Genetic Engineering
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Pediatric Hepatobiliary Diseases and Treatments
- Plant Pathogenic Bacteria Studies
- RNA Interference and Gene Delivery
- Plant and Fungal Interactions Research
- Yersinia bacterium, plague, ectoparasites research
- Advanced Electron Microscopy Techniques and Applications
- Microbial Fuel Cells and Bioremediation
- Cancer Research and Treatments
Justus-Liebig-Universität Gießen
2015-2025
Universität Greifswald
2022
Czech Academy of Sciences, Institute of Microbiology
2012-2019
Giessen School of Theology
2009-2019
Institut für Medizinische Informatik, Biometrie und Epidemiologie
1999
University of Bayreuth
1994-1997
Endoribonuclease E, a key enzyme involved in RNA decay and processing bacteria, organizes protein complex called degradosome. In Escherichia coli, Rhodobacter capsulatus, Streptomyces coelicolor, RNase E interacts with the phosphate-dependent exoribonuclease polynucleotide phosphorylase, DEAD-box helicase(s), additional factors an RNA-degrading complex. To characterize degradosome of psychrotrophic bacterium Pseudomonas syringae Lz4W, was enriched by cation exchange chromatography...
Abstract Background Small untranslated RNAs (sRNAs) are widespread regulators of gene expression in bacteria. This study reports on a comprehensive screen for sRNAs the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti applying deep sequencing cDNAs and microarray hybridizations. Results A total 1,125 sRNA candidates that were classified as trans-encoded (173), cis-encoded antisense (117), mRNA leader transcripts (379), sense overlapping coding regions (456) identified...
Bacterial quorum sensing molecules not only grant the communication within bacterial communities, but also influence eukaryotic hosts. N-acyl-homoserine lactones (AHLs) produced by pathogenic or beneficial bacteria were shown to induce diverse reactions in animals and plants. In plants, reaction AHLs depends on length of lipid side chain. Here we investigated impact two Arabidopsis thaliana, which usually enter a close symbiosis with plants from Fabaceae (legumes) family produce long-chain...
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 a bioinformatics challenge. We performed Bradyrhizobium japonicum USDA 110, the nitrogen-fixing symbiont soybean, developed algorithms TSSs promoters. A specialized machine learning procedure TSS recognition allowed us 15,923 TSSs: 14,360 in free-living bacteria, 4329 symbiosis with soybean 2766...
The Gram-negative, soil-dwelling plant symbiont Sinorhizobium meliloti shares its free-living habitat with antibiotic producers. To learn about early steps of adaptation to antibiotics, we analyzed transcriptome changes after 10 min exposure subinhibitory amount tetracycline (Tc). RNA-seq revealed 297 differentially expressed genes. Besides ten upregulated ribosomal genes, there was no recognizable functional pattern in the observed changes. Instead, genes were mostly first operons and often...
Abstract The soil-dwelling plant symbiont Sinorhizobium meliloti is a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) largely missing, because sORFs are poorly annotated and SEPs hard to detect experimentally. However, given that can fulfill important functions, identification translated critical for analyzing their roles in bacterial physiology. Ribosome profiling (Ribo-seq) with...
Small RNAs (sRNAs) play a pivotal role in bacterial gene regulation. However, the sRNAs of vast majority bacteria with sequenced genomes still remain unknown since sRNA genes are usually difficult to recognize and thus not annotated. Here, expression seven (BjrC2a, BjrC2b, BjrC2c, BjrC68, BjrC80, BjrC174 BjrC1505) predicted by genome comparison Bradyrhizobium Rhodopseudomonas members, was verified RNA gel blot hybridization, microarray deep sequencing analyses from soybean symbiont japonicum...
Quorum sensing is a cell density-dependent communication system of bacteria relying on autoinducer molecules. During the analysis post-transcriptional regulation quorum in nitrogen fixing plant symbiont Sinorhizobium meliloti, we predicted and verified direct interaction between 5'-UTR sinI mRNA encoding synthase small RNA (sRNA), which named RcsR1. In vitro, RcsR1 prevented cleavage by RNase E impaired translation. line with low ribosomal occupancy transcript destabilization upon binding to...
Proteins encoded by small open reading frames (sORFs) have a widespread occurrence in diverse microorganisms and can be of high functional importance. However, due to annotation biases their technically challenging direct detection, these proteins been overlooked for long time were only recently rediscovered. The currently rapidly growing number such requires efficient methods investigate structure-function relationship. Herein, method is presented fast determination the conformational...
Summary The eukaryotic exosome is a protein complex with essential functions in processing and degradation of RNA. Exosome‐like complexes were recently found Archaea. Here we characterize the Sulfolobus solfataricus . Two fractions can be discriminated by density gradient centrifugation. We show that Cdc48 associated from 30S−50S fraction but not 11.3S fraction. While only some contain Cdc48, archaeal DnaG‐like was to core subunit addition Rrp4, Rrp41, Rrp42 Csl4. Assays depleted extracts...
Sinorhizobium meliloti harbours genes encoding orthologs of ribonuclease (RNase) E and RNase J, the principle endoribonucleases in Escherichia coli Bacillus subtilis , respectively. To analyse role J S. RNA from a mutant with miniTn5‐insertion J‐encoding gene was compared to wild‐type difference length 5.8S‐like ribosomal (rRNA) observed. Complementation mutant, Northern blotting primer extension revealed that is necessary for 5′‐end maturation 16S rRNA two 23S fragments, but not 5S rRNA.
Quorum sensing of Sinorhizobium meliloti relies on N-acyl-homoserine lactones (AHLs) as autoinducers. AHL production increases at high population density, and this depends the synthase SinI two transcriptional regulators, SinR ExpR. Our study demonstrates that ectopic expression gene rne, coding for RNase E, an endoribonuclease is probably essential growth, prevents accumulation AHLs detectable levels. The rne led to a higher level mRNA lower sinI independently presence ExpR, receptor, AHLs....
Ribosome-mediated transcription attenuation is a basic posttranscriptional regulation mechanism in bacteria. Liberated attenuator RNAs arising this process are generally considered nonfunctional. In Sinorhizobium meliloti, the tryptophan (Trp) biosynthesis genes organized into three operons, trpE(G), ppiD-trpDC-moaC-moeA, and trpFBA-accD-folC, of which only first one, contains short ORF (trpL) 5'-UTR regulated by attenuation. Under conditions Trp sufficiency, terminated between trpL small...
A 130-nucleotide-long rRNA species corresponding to the 5' end of 23S gene was found in 96 strains belonging different Rhizobium, Bradyrhizobium, and Agrobacterium species. Additional fragmentation central region large-subunit occurred all agrobacteria, except vitis, most Rhizobium leguminosarum etli but did not occur any other rhizobia bradyrhizobia studied.
The conserved Sm and Sm-like proteins are involved in different aspects of RNA metabolism. Here, we explored the interactome SmAP1 SmAP2 crenarchaeon Sulfolobus solfataricus (Sso) to shed light on their physiological function(s). Both, co-purified with several RNA-processing/modification, translation protein turnover as well components exosome 3΄ 5΄ degradation RNA. In follow-up studies a direct interaction poly(A) binding accessory exosomal subunit DnaG was demonstrated. Moreover, elevated...
ABSTRACT We provide experimental evidence for RNase III-dependent processing in helix 9 of the 23S rRNA as a general feature many species alpha subclass Proteobacteria (alpha- ). investigated 12 Rhodobacter , Rhizobium Sinorhizobium Rhodopseudomonas and Bartonella strains. The processed region is characterized by presence intervening sequences (IVSs). rDNA between positions 109 205 ( Escherichia coli numbering) were determined, potential secondary structures are proposed. Comparison IVSs...