Biology subjects

Prasse, D.

Publications and source records attributed to Prasse, D..

4 recordsLinked to original sources

bioRxiv2025

Transcription profiling and functional analysis of spRNAs and their corresponding asRNAs in Methanosarcina mazei

Small proteins (sPs) encoded by small RNAs (sRNAs), the so-called small protein RNAs (spRNAs), and their corresponding antisense RNAs (asRNAs) have emerged as important regulatory elements in microbial stress adaptation, yet remain poorly characterized in archaea. In this study, we identified and characterized five sRNA/asRNA pairs in the methanoarchaeon Methanosarcina mazei. Expression analysis revealed condition-specific regulation of two of those pairs, spRNA23/asRNA93 and spRNA24/asRNA94, under oxidative, temperature, and osmotic stress. Overexpression of the corresponding small proteins, sP23 and sP24, revealed distinct physiological effects: both enhanced growth under high-salt conditions, while sP24 in addition supported cell size maintenance during osmotic stress, as confirmed by transmission electron microscopy. Consistently, overexpression of asRNA94 let to impaired growth under salt stress, suggesting its negative regulatory role towards sP24. The results also imply that the antisense RNA might be crucial for controlling sP24 expression under non-stress conditions. Bioinformatic analysis predicted one transmembrane domain in sP24. Membrane-association of sP24 was experimentally validated in vitro using a cell-free expression system, demonstrating sP24s integration into lipid bilayers. Conservation analysis showed that spRNA24 appears specific for M. mazei strains potentially reflecting niche adaptation, while spRNA23 is widespread within Methanosarcina. These findings demonstrate that archaeal sRNAs can encode functional small proteins, often encoded together with their respective regulatory asRNA, that contribute to environmental stress responses, overall offering new insights into the role of sRNA-derived small proteins in archaea.

microbiology↗

bioRxiv2022

Bacterial colonizers of Nematostella vectensis are initially selected by the host before interactions between bacteria determine further succession

The microbiota of multicellular organisms undergoes considerable changes during development but the general mechanisms that control community assembly and succession are poorly understood. Here, we use bacterial recolonization experiments in Nematostella vectensis as a model to understand general mechanisms determining bacterial establishment and succession. We compared the dynamic establishment of the microbiome on the germfree host and on inert silica. Following the dynamic reconstruction of microbial communities on both substrates, we show that the initial colonization events are strongly influenced by the host but not by the tube, while the subsequent bacteria-bacteria interactions are the main cause of bacterial succession. Interestingly, the recolonization pattern on adult hosts resembles the ontogenetic colonization succession. This process occurs independently of the bacterial composition of the inoculum and can be followed at the level of individual bacteria, suggesting that priority effects are neglectable for early colonization events in Nematostella. To identify potential metabolic traits associated with initial colonization success and potential metabolic interactions among bacteria associated with bacterial succession, we reconstructed the metabolic networks of bacterial colonizers based on their genomes. These analyses revealed that bacterial metabolic capabilities reflect the recolonization pattern, and the degradation of chitin might be a selection factor during early colonization of the animal. Concurrently, transcriptomic analyses revealed that Nematostella possesses two chitin synthase genes, one of which is upregulated during early recolonization. Our results show that early colonization events are strongly controlled by the host while subsequent colonization depends on metabolic bacteria-bacteria interactions largely independent of host development.

microbiology↗

bioRxiv2020

Microbial regulation of hexokinase 2 links mitochondrial metabolism and cell death in colitis

Hexokinases (HK) catalyze the first step of glycolysis and thereby limit its pace. HK2 is highly expressed in the gut epithelium, plays a role in immune responses and is upregulated in inflammation and ulcerative colitis 1-3. Here, we examined the microbial regulation of HK2 and its impact on intestinal inflammation by generating mice lacking HK2 specifically in intestinal epithelial cells (Hk2{Delta}IEC). Hk2{Delta}IEC mice were less susceptible to acute intestinal inflammation upon challenge with dextran sodium sulfate (DSS). Analyzing the epithelial transcriptome from Hk2{Delta}IEC mice during acute colitis revealed downregulation of cell death signaling and mitochondrial dysfunction dependent on loss of HK2. Using intestinal organoids derived from Hk2{Delta}IEC mice and Caco-2 cells lacking HK2, we identified peptidyl-prolyl cis-trans isomerase (PPIF) as a key target of HK2-mediated regulation of mitochondrial permeability and repression of cell-death during intestinal inflammation. The microbiota strongly regulated HK2 expression and activity. The microbially-derived short-chain fatty acid (SCFA) butyrate repressed HK2 expression and oral supplementation protected wildtype but not Hk2{Delta}IEC mice from DSS colitis. Our findings define a novel mechanism how butyrate may act as a protective factor for intestinal barrier homeostasis and suggest targeted HK2 inhibition as a promising therapeutic avenue in intestinal inflammation.

immunology↗

bioRxiv2019

Evaluating the quorum quenching potential of bacteria associated to Aurelia aurita and Mnemiopsis leidyi

The associated microbiota of marine invertebrates plays an important role to the host in relation to fitness, health and homeostasis of the metaorganism. As one key chemically-mediated interaction, Quorum sensing (QS) and interference with QS among colonizing bacteria ultimately affects the establishment and dynamics of the microbial community on the host. Aiming to address interspecies competition of cultivable microbes associated to merging model species of the basal animal phyla Cnidaria (Aurelia aurita) and Ctenophora (Mnemiopsis leidyi) as well as to evaluate their potential to shape the associated community by interfering with QS, we performed a classical isolation approach. Overall, 84 bacteria were isolated from A. aurita medusae and polyps, 64 bacteria from M. leidyi, and 83 bacteria from the ambient seawater, followed by taxonomically classification by full length 16S rRNA gene analysis. The results show that the moon jellyfish A. aurita and the comb jelly M. leidyi harbor a cultivable core microbiota consisting of typical marine and ubiquitously found bacteria (e.g. Chryseobacter, Microbacterium, Micrococcus, Olleya, Phaeobacter, Pseudoalteromonas, Pseudomonas, Rhodococcus, Shewanella, Staphylococcus, and Vibrio) which can also be found in the ambient seawater. However, several bacteria were restricted to one host (e.g. for A. aurita: Bacillus, Glaciecola, Ruegeria, Luteococcus; for M. leidyi: Acinetobacter, Aeromonas, Colwellia, Exiguobacterium, Marinomonas, Pseudoclavibacter, Psychrobacter, Sagittula, Thalassomonas) suggesting host-specific microbial community patterns. Evaluating QQ activities, out of 231 isolates, 121 showed QS-interfering activity. They mainly interfered with the acyl homoserine lactone (AHL) based communication, whereas 21 showed simultaneous quorum quenching activities against AHL and autoinducer-2. Overall, this study provides insights into the cultivable part of the microbiota associated to two environmentally important marine non-model organisms and discloses their potential in synthesizing QS interfering compounds, potentially important in shaping a healthy and resilient microbiota.

microbiology↗