A5024743312- RNA and protein synthesis mechanisms
- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Plant-Microbe Interactions and Immunity
- Cytomegalovirus and herpesvirus research
- Ubiquitin and proteasome pathways
- Clostridium difficile and Clostridium perfringens research
- Vibrio bacteria research studies
- Probiotics and Fermented Foods
- Glycosylation and Glycoproteins Research
- Advanced biosensing and bioanalysis techniques
- RNA Research and Splicing
- Viral gastroenteritis research and epidemiology
- RNA Interference and Gene Delivery
- Viral Infections and Immunology Research
- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Toxoplasma gondii Research Studies
- Veterinary medicine and infectious diseases
Weizmann Institute of Science
2022-2024
University of Würzburg
2016-2022
Furtwangen University
2017
Plant growth can be affected by soil bacteria. In turn, plants are known to influence bacteria through rhizodeposits and changes in abiotic conditions. We aimed quantify the phylotype richness relative abundance of rhizosphere that actually influenced a plant species-specific manner determine role disproportionately large diversity low-abundance belonging rare biosphere (<0.1 abundance) this process. addition, we whether phylogeny has an on bacterial community. For purpose, 19 herbaceous...
RNA-protein interactions are the crucial basis for many steps of bacterial gene expression, including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast to recent progress in analysis Gram-negative bacteria, knowledge about complexes Gram-positive species remains scarce. Here, we used Grad-seq approach draft a comprehensive landscape such Streptococcus pneumoniae, total determining sedimentation profiles ~ 88% transcripts and 62% proteins this important human...
ABSTRACT Much of our current knowledge about cellular RNA–protein complexes in bacteria is derived from analyses gram-negative model organisms, with the discovery RNA-binding proteins (RBPs) generally lagging behind Gram-positive species. Here, we have applied Grad-seq analysis native to a major human pathogen, Clostridioides difficile, whose RNA biology remains largely unexplored. Our resolves in-gradient distributions for ∼88% all annotated transcripts and ∼50% proteins, thereby providing...
Abstract Bacterial anti-phage defense systems are frequently clustered in microbial genomes, forming islands. This genomic property enabled the recent discovery of multiple based on their co-localization with known systems, but full arsenal mechanisms bacteria is still unknown. In this study we report 21 new that protect from phages, computational analyses and phage infection experiments. We find protein domains to be involved eukaryotic anti-viral immunity, including ISG15-like proteins,...
Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading bacterial organism respect to global protein-protein networks. Yet, there no census RNA/protein complexes in this model species microbiology. Here, we performed Grad-seq establish an complexome, reconstructing sedimentation profiles a glycerol gradient for ∼85% all E. transcripts and ∼49% proteins. These include majority small noncoding RNAs (sRNAs)...
Abstract Multiple immune pathways in humans conjugate ubiquitin-like proteins to virus and host molecules as a means of antiviral defense. Here we studied an anti-phage defense system bacteria, comprising protein, ubiquitin-conjugating enzymes E1 E2, deubiquitinase. We show that during phage infection, this specifically conjugates the protein central tail fiber, at tip is essential for assembly well recognition target receptor. Following cells encoding release mixture partially assembled,...
New methods for the global identification of RNA-protein interactions have led to greater recognition abundance and importance RNA-binding proteins (RBPs) in bacteria. Here, we expand this tool kit by developing SEC-seq, a method based on similar concept as established Grad-seq approach. In Grad-seq, cellular RNA protein complexes bacterium interest are separated glycerol gradient, followed high-throughput RNA-sequencing mass spectrometry analyses individual gradient fractions. predicted...
Ribosome profiling (Ribo-seq) is a powerful method for the transcriptome-wide assessment of protein synthesis rates and study translational control mechanisms. Yet, Ribo-seq also has limitations. These include difficulties with analysis translation-modulating molecules such as antibiotics, which are often toxic or challenging to deliver into living cells. Here, we have developed in vitro (INRI-seq), cell-free analyze landscape fully customizable synthetic transcriptome. Using Escherichia...
ABSTRACT Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading bacterial organism respect to global protein-protein networks. Yet, there no census RNA/protein complexes in this model species microbiology. Here, we performed Grad-seq establish an complexome, reconstructing sedimentation profiles a glycerol gradient for ~85% all E. transcripts and ~49% proteins. These include majority small noncoding...
ABSTRACT New methods for the global identification of RNA-protein interactions have led to greater recognition abundance and importance RNA-binding proteins (RBPs) in bacteria. Here, we expand this tool kit by developing SEC-seq, a method based on similar concept as established Grad-seq approach. In Grad-seq, cellular RNA protein complexes bacterium interest are separated glycerol gradient, followed high-throughput RNA-sequencing mass spectrometry analyses individual gradient fractions....
ABSTRACT Ribosome profiling (Ribo-seq) is a powerful method for the transcriptome-wide assessment of protein synthesis rates and study translational control mechanisms. Yet, Ribo-seq also has limitations. These include difficulties with detection low abundance transcripts analysis translation-modulating molecules such as antibiotics, which are often toxic or challenging to deliver into living cells. Here, we have developed in vitro (INRI-seq), cell-free analyze landscape fully customizable...