A5020497562- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Mechanical stress and fatigue analysis
- Circular RNAs in diseases
- Legume Nitrogen Fixing Symbiosis
- Probiotics and Fermented Foods
- RNA modifications and cancer
- Viral Infections and Vectors
- Microbial Community Ecology and Physiology
- Enzyme Structure and Function
- Mycobacterium research and diagnosis
- Machine Learning in Bioinformatics
- Methane Hydrates and Related Phenomena
- Transgenic Plants and Applications
- Bioinformatics and Genomic Networks
- Oral microbiology and periodontitis research
- Evolution and Genetic Dynamics
- Vector-borne infectious diseases
- Genomics and Chromatin Dynamics
- interferon and immune responses
- RNA Research and Splicing
- Vector-Borne Animal Diseases
- Chromosomal and Genetic Variations
Philipps University of Marburg
2015-2025
Loewe Center for Synthetic Microbiology
2020-2023
Orthology analysis is an important part of data in many areas bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood sequence data, hence the rapidly increasing number genomes that can be compared simultaneously, calls for efficient software tools brute-force approaches with quadratic memory requirements become infeasible practise. rapid pace at which new available, furthermore, makes it desirable to compute genome-wide orthology relations a given...
The elucidation of orthology relationships is an important step both in gene function prediction as well towards understanding patterns sequence evolution. Orthology assignments are usually derived directly from similarities for large data because more exact approaches exhibit too high computational costs. Here we present PoFF, extension the standalone tool Proteinortho, which enhances detection by combining clustering, similarity, and synteny. In course this work, FFAdj-MCS, a heuristic...
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance has to be detected and removed. We show here this severe restriction the is not necessary. Building upon recent advances in mathematical phylogenetics we demonstrate gene duplications convey meaningful phylogenetic information allow inference plausible trees, provided orthologs paralogs can distinguished with degree...
The study of enterococcal genomes has grown considerably in recent years. While special attention is paid to comparative genomic analysis among clinical relevant isolates, this we performed an exhaustive food origin and/or with potential be used as probiotics. Beyond common genetic features, especially aimed identify those that are specific strains isolated from a certain food-related source well features present species-specific manner. Thus, the genome sequences 25 Enterococcus strains, 7...
Significance RNase P is a tRNA-processing enzyme of unique architectural diversity: either catalytic RNA plus one or more (up to 10) proteins, (or three) unrelated proteins only. We identified yet another form in the bacterium Aquifex aeolicus , 23-kDa protein and smallest known P. Apparently, it was acquired by horizontal gene transfer from Archaea. In some other bacteria many archaea, simultaneously present with presumably ancient RNA-based form. Bacteria both activities may represent...
RNA has been proposed as an important scaffolding factor in the nucleus, aiding protein complex assembly dense intracellular milieu. Architectural contributions of to cytosolic signaling pathways, however, remain largely unknown. Here, we devised a multidimensional gradient approach, which systematically locates components within cellular networks. Among subset noncoding RNAs (ncRNAs) cosedimenting with ubiquitin-proteasome system, our approach unveiled ncRNA MaIL1 critical structural...
Abstract Endogenous retroviruses (ERVs) are an integral part of the mammalian genome. The role immune control ERVs in general is poorly defined as their function anti-cancer targets or drivers autoimmune disease. Here, we generate mouse-strains where Moloney-Murine Leukemia Virus tagged with GFP (ERV-GFP) infected mouse germline. This enables us to analyze genetic, epigenetic and cell intrinsic restriction factors ERV activation control. We identify autoreactive B response against...
Proteinortho is a widely used tool to predict (co)-orthologous groups of genes for any set species. It finds application in comparative and functional genomics, phylogenomics, evolutionary reconstructions. With rapidly increasing number available genomes, the demand large-scale predictions also growing. In this contribution, we evaluate implement major algorithmic improvements that significantly enhance speed analysis without reducing precision. Graph-based detection (co-)orthologs typically...
Bacterial RNA polymerases (RNAP) utilize 6S RNAs as templates to synthesize ultrashort transcripts (up ~ 14 nt), termed product (pRNAs), that play a key role in reversing the blockage of RNAP by RNA. Here we resolved pRNA length profile 6 S-1 from Bacillus subtilis, major model system for study biology, during outgrowth cells extended stationary phase. 9-mers were found be particularly abundant species, followed 8/10/11-mers and 13/14-mers. Consistent with vitro data Escherichia coli system,...
Bacterial 6S RNAs bind to the housekeeping RNA polymerase (σ(A)-RNAP in Bacillus subtilis) regulate transcription a growth phase-dependent manner. B. subtilis expresses two RNAs, 6S-1 and 6S-2 RNA, with different expression profiles. We show vitro that shares hallmark features RNA: Both (1) are able serve as templates for pRNA transcription; (2) comparable affinity σ(A)-RNAP; (3) specifically inhibit from DNA promoters, (4) can form stable RNA:pRNA hybrid structures (5) abolish binding...
Abstract The guanosine nucleotide‐based second messengers ppGpp and pppGpp (collectively: (p)ppGpp) enable adaptation of microorganisms to environmental changes stress conditions. In contrast, the closely related adenosine nucleotides (p)ppApp are involved in type VI secretion system (T6SS)‐mediated killing during bacterial competition. Long R elA‐ S poT H omolog (RSH) enzymes regulate synthesis degradation (p)ppGpp (and potentially also (p)ppApp) through their synthetase hydrolase domains,...
Abstract Stressosomes are stress-sensing protein complexes widely conserved among bacteria. Although a role in the regulation of general stress response is well documented Gram-positive bacteria, activating signals still unclear, and little known about physiological function stressosomes Gram-negative Here we investigated stressosome marine pathogen Vibrio vulnificus . We demonstrate that it senses oxygen identified its modulating iron-metabolism. determined cryo-electron microscopy...
The honeybee (Apis mellifera) represents a model organism for social insects displaying behavioral plasticity. This is reflected by an age-dependent task allocation. most protruding tasks are performed young nurse bees and older forager that take care of the brood inside hive collect food from outside hive, respectively. molecular mechanism leading to transition foragers currently under intense research. Circular RNAs, however, were not considered in this context so far. As today, group...
Sinorhizobium meliloti is an alphaproteobacterium belonging to the Rhizobiales Bacteria from this order elongate their cell wall at new pole, generated by division. Screening for protein interaction partners of previously characterized polar growth factors RgsP and RgsM, we identified inner membrane components Tol-Pal system (TolQ TolR) novel Rgs (rhizobial septation) proteins with unknown functions. TolQ, Pal, all proteins, except RgsE, were indispensable S. growth. Six Pal localized...
The RNase P family comprises structurally diverse endoribonucleases ranging from complex ribonucleoproteins to single polypeptides. We show that the organellar (AtPRORP1) and two nuclear (AtPRORP2,3) single-polypeptide isoenzymes Arabidopsis thaliana confer viability Escherichia coli cells with a lethal knockdown of its endogenous RNA-based P. RNA-Seq revealed AtPRORP1, compared bacterial or AtPRORP3, cleaves several precursor tRNAs (pre-tRNAs) aberrantly in E. coli. Aberrant cleavage by...
The Aquificales are a diverse group of thermophilic bacteria that thrive in terrestrial and marine hydrothermal environments. They can be divided into the families Aquificaceae, Desulfurobacteriaceae Hydrogenothermaceae. Although eleven fully sequenced assembled genomes available, only little is known about this taxonomic order terms RNA metabolism. In work, we compare available genomes, extend their protein annotation, identify regulatory sequences, annotate non-coding RNAs (ncRNAs)...
Reassortment of their segmented genomes allows influenza A viruses (IAV) to gain new characteristics, which potentially enable them cross the species barrier and infect hosts. Improved replication was observed for reassortants strictly avian IAV A/FPV/Rostock/34 (FPV, H7N1) containing NS segment from A/Goose/Guangdong/1/1996 (GD, H5N1), but not A/Mallard/NL/12/2000 (MA, H7N3). The NS1 GD MA differ only in 8 aa positions. Here, we show that efficient FPV-NSMA-derived mutants linked presence a...
Cell division and cell wall synthesis mechanisms are similarly conserved among bacteria. Consequently some bacterial species have comparable sets of genes organized in the dcw (division wall) gene cluster. Dcw genes, their regulation relative order within cluster outstandingly rod shaped gram negative bacteria to ensure an efficient coordination growth division. A well studied representative is E. coli. The first promoter (mraZ1p) gives rise polycistronic transcripts containing a 38 nt long...
The function of 6S RNA, a global regulator transcription, was studied in the photosynthetic α-proteobacterium Rhodobacter sphaeroides. cellular levels R. sphaeroides RNA peak toward transition to stationary phase and strongly decrease during extended phase. synthesis so-called product transcripts (mainly 12-16-mers) on as template by polymerase found be highest late exponential Product ≥ 13-mers are expected trigger dissociation RNA:RNA complexes. A deletion had no impact growth under...
The global transcriptional regulator 6S RNA is abundant in a broad range of bacteria. competes with DNA promoters for binding to the housekeeping polymerase (RNAP) holoenzyme. When bound RNAP, serves as transcription template RNAP an RNA-dependent polymerization reaction. resulting short transcripts (so-called product RNAs = pRNAs) can induce stable structural rearrangement when reaching certain length. This leads release and thus recovery at promoters. While most bacteria express single...
Bacterial 6S RNA regulates transcription via binding to the active site of polymerase holoenzymes. has been identified in majority bacteria, most cases encoded by a single gene. Firmicutes including Bacillus subtilis encode two paralogs, 6S-1 and 6S-2 RNA. Hypothesizing that regulatory role RNAs may be particularly important under natural, constantly changing environmental conditions, we constructed deletion mutants undomesticated B. wild-type strain NCIB 3610. We observed strong phenotype...