Biology subjects

Neumann-Schaal, M.

Publications and source records attributed to Neumann-Schaal, M..

17 recordsLinked to original sources

bioRxiv2026

From Magnetosomes to Vesicles: LemA Proteins as Drivers of Bacterial Membrane Reorganization

The cellular machineries that remodel bacterial membranes during organelle and vesicle formation remain poorly defined. Herein, we report MamQ as a key determinant of the lipid invaginations that enclose the magnetosome. MamQ belongs to the broadly conserved LemA protein family, whose members localize to either the inner or outer membrane. Heterologous overproduction of 13 different LemA proteins in Escherichia coli induced extensive membrane restructuring and vesiculation, indicating a conserved membrane-remodelling activity. In Pseudomonas aeruginosa, overproduction of the inner membrane protein LemA1 (PaLemA1) promoted cytoplasmic membrane vesicle (CMV) formation, whereas the periplasmic-located outer membrane-anchored LemA2 (PaLemA2) drove the formation of bacterial outer-membrane vesicles (OMVs). Conversely, deletion of the corresponding genes reduced extracellular vesicle production. Interactome analyses identified 256 protein partners of PaLemA1 and PaLemA2, including multiple components of the cellular divisome, such as CpoB, FtsE, FtsI, FtsK, FtsN, FtsW, MinE, ParB, ZapG, ZipA. Bacterial two-hybrid assays confirmed interactions between both LemA proteins and the cell division regulator CpoB, whose perturbation markedly altered vesicle formation. Additional interaction partners included PspA, an ESCRT-III-like protein implicated in membrane remodelling. Proteins involved in cell wall metabolism, membrane turnover, lipopolysaccharide (LPS) biogenesis, protein export and maturation, energy metabolism, and stress-responsive gene regulation were also enriched, suggesting a supporting role for PaLemA proteins in coordinating membrane-associated processes. Consistent with this, LemA deletion mutants displayed altered vesicle composition and global changes in gene expression. Furthermore, PalemA2 expression was induced in stationary phase and under envelope stress via the extracytoplasmic sigma factor AlgU, itself an interaction partner of the LemA proteins. Together, our findings indicate the LemA family act as a conserved membrane-remodelling system that, in conjunction with PspA, CpoB and divisome components, organises membrane-localized protein complexes required for bacterial organelle biogenesis and vesicle formation while executing a controlled, protein-machinery-driven mechanism that operates independently of passive chemical blebbing (such as hydrophobic PQS intercalation) or lytic membrane fragmentation.

microbiology↗

bioRxiv2026

Interspecies transfer of giant virulence-factor-like proteins in a bacterial symbiosis

The transfer of virulence factors into eukaryotic cells is a hallmark of bacterial pathogenesis. We report the expression, interspecies transfer, subcellular localization, and potential functions of three unusually large virulence factor-like proteins that underlie a bipartite mutualistic bacterial symbiosis. These proteins are synthesized by green sulfur bacterial epibionts surrounding a central motile chemoheterotroph in the multicellular phototrophic consortium Chlorochromatium aggregatum. While symbiosis-proteins remain intracellular during axenic epibiont growth, they are transferred to the partner bacterium in the association. An RTX-like protein secreted towards the central bacterium is capable of degrading its alginate capsule, thereby promoting direct cell-to-cell contact. Two gigantic hemagglutinin-like proteins are predicted to fold when binding extracellular Ca2+ to form Type 6-like auto injection needles, explaining their observed transfer into the central bacterium. These functionalities extend far beyond the known pathogenic interactions of bacteria with eukaryotes and provide new perspectives on the evolution of bacterial virulence factors.

microbiology↗

bioRxiv2025

Viral infection collapses intracytoplasmic membrane integrity and autotrophic metabolism in ammonia-oxidizing Nitrosomonas europaea

Ammonia-oxidizing bacteria (AOB) catalyze the first and rate-limiting step of nitrification. They are essential for nitrogen cycling in engineered and natural environments, yet little is known about their viruses or the consequences of phage infection for host physiology. Here, we report the isolation and characterization of a novel lytic bacteriophage, vB_NeuP-Nir1 (Nir1), infecting the model AOB Nitrosomonas europaea. Phage Nir1 was highly virulent, ceased ammonia oxidation within hours, and caused complete lysis of host populations even at multiplicities of infection as low as 10-6. Electron microscopy revealed drastic host cell remodeling during infection, including pronounced cell bloating and large-scale disintegration of intracytoplasmic membranes. Integrated transcriptomic and metabolomic analyses showed that loss of these ATP and reducing equivalent generating membrane systems was accompanied by signatures of compromised lipid homeostasis and collapse of autotrophic CO2 fixation. In parallel, Nir1 infection induced metabolic rewiring of the host, including upregulation of uptake systems for nucleic acids, amino acids, and small organic compounds, increased expression of iron acquisition and putative iron-dependent respiratory components, as well as accumulation of metabolites associated with membrane breakdown and stabilization of viral DNA. Together, these results provide the first detailed mechanistic insight into phage-induced host modulation in a chemolithoautotrophic nitrifier. Our study establishes the Nir1-N. europaea system as a model for investigating virus-host interactions in AOB and lays the foundation for assessing the role of phages in shaping nitrification and nitrogen cycling in engineered and natural ecosystems.

microbiology↗

bioRxiv2025

Itaconate is metabolized to 2-hydroxymethylsuccinate through a CoA-independent degradation pathway in mitochondria

The immunometabolite itaconate modulates cellular metabolism and is converted into structurally similar C5 dicarboxylates that require advanced analytics to decipher their metabolic fate. Here, we employ high-resolution mass spectrometry and tracing approaches and identify 2-hydroxymethylsuccinate (2HMS) as a previously unrecognized C5 dicarboxylate derived from itaconate. 2HMS synthesis occurs during inflammatory responses and upon itaconate treatment, as detected by 13C itaconate tracing. Pathway analysis reveals that methylglutaconyl-CoA hydratase (AUH) drives 2HMS synthesis through a CoA-independent conversion (CIC) pathway. This pathway is distinct from the CoA-dependent conversion (CDC) pathway that generates mesaconate and itaconyl-CoA influencing B12-dependent processes. In vivo inflammation studies reveal that adipose tissue prefers CIC to produce 2HMS and liver favors CDC-mediated mesaconate synthesis, highlighting tissue-specific itaconate degradation routes. This study identifies a new branch of itaconate metabolism, provides an analytical framework to resolve C5 dicarboxylate networks, and links 2HMS to inflammation and mitochondrial metabolism that might be targeted therapeutically.

cell biology↗

bioRxiv2025

Metabolites produced by gut bacteria under anoxic conditions drive the suppression of Acinetobacter baumannii

Multidrug-resistant (MDR) bacteria pose a significant global health threat. Among these, Acinetobacter baumannii, particularly carbapenem-resistant A. baumannii, is a leading cause of healthcare-associated infections. Emerging evidence links gut colonization to systemic infections, highlighting opportunities for new control strategies. We demonstrate that A. baumannii can survive under anaerobic conditions ([≤]1%) and shows limited growth under low oxygen conditions ([≥]1%), underscoring its adaptation to niches in the intestine. However, specific carbohydrates, including maltose, provide the gut bacteria Klebsiella oxytoca with a competitive advantage under anoxic conditions, enabling it to actively suppress A. baumannii through its metabolism. Notably, maltose induces this suppressive capacity in other commensals and complex gut microbiomes as well. Force-feeding experiments in Galleria mellonella larvae corroborate that K. oxytoca in combination with maltose significantly reduces A. baumannii recovery in gut environments. These findings suggest that targeted carbohydrate supplementation could enhance probiotic strategies, creating an environment unfavorable to A. baumannii.

microbiology↗

bioRxiv2025

Ablation of polysaccharide breakdown in Bacteroides thetaiotaomicron prevents cross-feeding and growth of Salmonella Typhimurium in the mouse gut

Pathogens invading the intestine compete for nutrients with the resident microbiota. However, there is evidence that commensal members of the gut also provide nutritional resources to enteropathogens and thus promote their outgrowth. In this study, we investigated metabolic cross-feeding mechanisms between the abundant gut commensal Bacteroides thetaiotaomicron and the model enteropathogen Salmonella enterica serovar Typhimurium. We discovered that the processing of various dietary and host-derived glycans by B. thetaiotaomicron liberated building blocks available to Salmonella and identified a range of cross-fed metabolites. Interfering with polysaccharide degradation in B. thetaiotaomicron by genetic manipulation of specific polysaccharide utilization loci (PUL) inhibited pathogenic cross-feeding, both in vitro and in a gnotobiotic mouse model. Our findings highlight the complex metabolic commensal-pathogen interaction in the intestine and propose the disruption of polysaccharide breakdown as a potential microbiota-centric strategy to intervene in intestinal infections.

microbiology↗

bioRxiv2024

Comparative analysis of the treatment-naive microbiome across rheumatic diseases to predict MTX treatment response

The human gut microbiota is recognized as a modulator of inflammatory diseases and has been linked to interindividual differences in therapy responsiveness. However, the robustness of disease-specific microbiome signatures across closely related diseases is rarely compared. Here, we compared treatment-naive microbiota composition and functional potential across rheumatic diseases, including rheumatoid arthritis (RA) and spondyloarthritis subforms, to identify disease-specific biomarkers. While we failed to define robust disease-specific microbiota signatures, we identified microbial signatures linked to methotrexate (MTX) responsiveness for the two rheumatic diseases RA and psoriatic arthritis (PsA), for which MTX is the first-line treatment. Notably, the signatures were distinct, i.e., we could define a signature based on the relative abundance of microbial species for RA, yet the signature for PsA was based on the relative abundance of microbial pathways. Together this supports the previously recognized value of microbiota to predict treatment responses to MTX in RA and identifies distinct signatures predicting MTX responsiveness for PsA.

microbiology↗

bioRxiv2024

Bacterial membrane vesicles of Pseudomonas aeruginosa activate AMPK signaling through inhibition of mitochondrial complex III

Bacterial membrane vesicles (BMVs) are secreted by many pathogenic bacteria and known to stimulate various host responses upon infection, thereby contributing to the pathogenicity of bacterial pathogens like Pseudomonas aeruginosa. While the effects of BMVs on host immune responses are well studied, little is known about their impact on cell metabolism and mitochondrial respiration. Here, we show that P. aeruginosa BMVs (1) reprogram cell metabolism of human lung cells, (2) negatively affect mitochondrial respiration by (3) specifically inhibiting complex III of the electron transport chain leading to (4) the activation of AMP-activated protein kinase (AMPK) signaling which in turn results in (5) AMPK-dependent inhibition of global protein synthesis.

cell biology↗

bioRxiv2024

Succession of bacteria and archaea within the soil micro-food web

Bacterivorous nematodes represent numerically abundant bacterial grazers in the soil micro-food web. Their trophic regulation shapes the soil microbiome, but the underlying population dynamics of bacteria and archaea are poorly understood. Here, we followed bulk soil respiration and time-resolved population dynamics (32 days) of bacterial and archaeal species in response to top-down control by a common bacterivorous soil nematode, Acrobeloides buetschlii, bottom-up control by resource amendment via maize litter as well as the combination of both. Addition of maize litter significantly increased soil respiration rates, while bacterivorous nematodes shifted the maximum rate of soil respiration from day 12 to day 6. Underlying bacterial and archaeal abundance changes could be separated into five major response types, dominating in different top-down and bottom-up control scenarios. Individual microbial species switched between response types depending on the different scenarios. In-depth analysis of these differential abundance patterns revealed a broad feeding behavior for A. buetschlii on dominating populations of gram-negative bacteria (Acidobacteriota, Bacteroidota, Gemmatimonatoda, Pseudomonadota) and ammonia-oxidizing archaea (Nitrososphaerota), while discriminating against dominant populations of gram-positive bacteria (Actinobacteriota, Bacillota). Combined bottom-up control by maize litter and top-down control by nematode grazing caused a succession of soil microbiota, which was driven by population changes first in the Bacteroidota, then in the Pseudomonadota, and last in the Acidobacteriota and Nitrososphaerota. This mechanistic understanding of nematode grazing on soil microbiota population dynamics is essential to inform predictive models of the soil food web.

microbiology↗

bioRxiv2023

Formation of the pyruvoyl-dependent proline reductase Prd from Clostridioides difficile requires the maturation enzyme PrdH

Stickland fermentation, the coupled oxidation and reduction of amino acid pairs, is a major pathway for obtaining energy in the nosocomial bacterium Clostridioides difficile. D-proline is the preferred substrate for the reductive path, making it not only a key component of the general metabolism but also impacting on the expression of the clostridial toxins TcdA and TcdB. D-proline reduction is catalyzed by the proline reductase Prd, which belongs to the pyruvoyl-dependent enzymes. These enzymes are translated as inactive proenzymes and require subsequent processing to install the covalently bound pyruvate. Whereas pyruvoyl formation by intramolecular serinolysis has been studied in unrelated enzymes, details about pyruvoyl generation by cysteinolysis such as in Prd are lacking. Here we show that Prd maturation requires a small dimeric protein that we have named PrdH. PrdH is co-encoded with the PrdA and PrdB subunits of Prd and also found in species producing similar reductases. By producing stable variants of PrdA and PrdB, we demonstrate that PrdH-mediated cleavage and pyruvoyl formation in the PrdA subunit require PrdB, which can be harnessed to produce active recombinant Prd for subsequent analyses. We further created PrdA- and PrdH-mutants to get insight into the interaction of the components and into the processing reaction itself. Finally, we show that deletion of prdH in C. difficile renders the corresponding mutant blind to proline, suggesting that this processing factor is essential for proline utilization. Due to the link between Stickland fermentation and pathogenesis, we suggest PrdH may be an attractive target for drug development. Significance StatementEnergy conservation via Stickland fermentation was first described in the 1930s, yet information about the key enzyme of this process, Prd, is scarce, despite the fact that its central role in both metabolism and toxin production make it a promising potential drug target. Here we show how a small, previously overlooked protein that we named PrdH mediates the formation of the catalytically essential pyruvoyl-group in the active center of Prd. In vivo studies in C. difficile emphasize its critical importance in the utilization of proline. The known interplay between proline reduction and toxin production leads us to suggest PrdH as a potential drug target. Moreover, our findings open the door for further structural and functional studies with recombinantly produced active Prd.

biochemistry↗

bioRxiv2023

Isolation and quantification of bacterial membrane vesicles for quantitative metabolic studies using mammalian cell cultures

Bacterial membrane vesicles (BMVs) are produced by most bacteria and participate in various cellular processes, such as intercellular communication, nutrient exchange, and pathogenesis. Notably, these vesicles can contain virulence factors, including toxic proteins, DNA, and RNA. Such factors can contribute to the harmful effects of bacterial pathogens on host cells and tissues. Although the general effects of BMVs on host cellular physiology are well known, the underlying molecular mechanisms are less understood. In this study, we introduce a vesicle quantification method, leveraging the membrane dye FM4-64. We utilize a linear regression model to analyze the fluorescence emitted by stained vesicle membranes to ensure consistent and reproducible vesicle-host interaction studies using cultured cells. This method is particularly valuable for identifying host cellular processes impacted by vesicles and their specific cargo. Moreover, it outcompetes clearly unreliable protein concentration-based methods. We (1) show a linear correlation between the quantity of vesicles and the fluorescence signal emitted from the FM4-64 dye, (2) introduce the "vesicle load" as a new semi-quantitative unit, facilitating more reproducible vesicle-cell culture interaction experiments (3) show that a stable vesicle load yields consistent host responses when studying vesicles from Pseudomonas aeruginosa mutants (4) demonstrate that typical vesicle isolation contaminants, such as flagella, do not significantly skew the metabolic response of lung epithelial cells to P. aeruginosa vesicles, and (5) identify inositol-1-monophosphatase (SuhB) as a pivotal regulator in the vesicle-mediated pathogenesis of P. aeruginosa.

cell biology↗

bioRxiv2023

COMPLETE GENOME SEQUENCE OF VIBRIO SYNGNATHI SP. NOV., A FISH PATHOGEN, ISOLATED FROM THE KIEL FJORD

A new Vibrio strain K08M4T was isolated from the broad-nosed pipefish Syngnathus typhle in the Kiel Fjord. Infection experiments revealed that K08M4T is highly virulent for juvenile pipefish. Cells of strain K08M4T are Gram-stain-negative, curved rod-shaped and motile by means of a single polar flagellum. The strain can grow aerobically at 9 to 40{degrees}C, at pH 4 to 10.5 and tolerates up to 12% (w/v) NaCl. The most prevalent (> 10%) cellular fatty acids of K08M4T were C16:1{omega} 7c and C16:0. Whole-genome comparisons revealed that K08M4T represents a separate evolutionary lineage which is distinct from other Vibrio species and falls within the Vibrio Splendidus clade. The genome is 4,886,292 bp in size, consists of two circular chromosomes (3,298,328 bp, 1,587,964 bp), and comprises 4,178 protein-coding genes and 175 RNA genes. In this study, we describe the phenotypic features of the new isolate and present the annotation and analysis of its complete genome sequence. Based on these data, the new isolate represents a new species for which we propose the name Vibrio syngnathi. The type strain is K08M4T (=DSM 109818T). Supplementary materialOne supplementary figure and six supplementary table are available with the online version of the Manuscript.

microbiology↗

bioRxiv2023

Genomics of the "tumorigenes" clade of the family Rhizobiaceae and description of Rhizobium rhododendri sp. nov.

Tumorigenic members of the family Rhizobiaceae, known as agrobacteria, are responsible for crown and cane gall diseases of various agricultural crops worldwide. Tumorigenic agrobacteria are commonly found in the genera Agrobacterium, Allorhizobium, and Rhizobium. In this study, we analyzed a distinct "tumorigenes" clade of the genus Rhizobium, which includes the tumorigenic species Rhizobium tumorigenes, as well as strains causing crown gall disease on rhododendron. Here, high quality, closed genomes of representatives of the "tumorigenes" clade were generated, followed by comparative genomic and phylogenomic analyses. Additionally, phenotypic characteristics of representatives of the "tumorigenes" clade were analyzed. Our results showed that the tumorigenic strains isolated from rhododendron represent a novel species of the genus Rhizobium for which the name Rhizobium rhododendri sp. nov. is proposed. This species also includes additional strains originating from blueberry and Himalayan blackberry in USA, whose genome sequences were retrieved from GenBank. Both R. tumorigenes and R. rhododendri contain multipartite genomes, including a chromosome, putative chromids, and megaplasmids. Synteny and phylogenetic analyses indicated that a large putative chromid of R. rhododendri resulted from the cointegration of an ancestral megaplasmid and two putative chromids, following its divergence from R. tumorigenes. Moreover, gene clusters specific for both species of the "tumorigenes" clade were identified, and their biological functions and roles in ecological diversification of R. rhododendri and R. tumorigenes were predicted and discussed.

microbiology↗

bioRxiv2022

Evolution of resilience against heat stress in a red-tide dinoflagellate

"Red tides" are harmful algal blooms (HABs) caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. Increasingly frequent, HABs are driven by a combination of environmental factors including nutrient enrichment, particularly in warm waters. Here, we present the de novo assembled genome (~4.75 Gbp), transcriptome, proteome, and metabolome from Prorocentrum cordatum, a globally abundant, bloom-forming dinoflagellate. Using axenic algal cultures, we studied the molecular mechanisms that underpin response to temperature stress, which is relevant to current ocean warming trends. We discovered a complementary interplay between RNA editing and exon usage that regulates the expression and functional diversity of biomolecules, reflected by reduction in photosynthesis, central metabolism, and protein synthesis. Our multi-omics analyses uncover the molecular response to heat stress in an important HAB species, which is driven by complex gene structures in a large, high-G+C genome, combined with multi-level transcriptional regulation.

genomics↗

bioRxiv2022

Two new Rhizobiales species isolated from root nodules of common sainfoin (Onobrychis viciifolia) show different plant colonization strategies

Root nodules of legume plants are primarily inhabited by rhizobial nitrogen-fixing bacteria. Here we propose two new Rhizobiales species isolated from root nodules of common sainfoin (Onobrychis viciifolia), as shown by core-gene phylogeny, overall genome relatedness indices and pan-genome analysis. Mesorhizobium onobrychidis sp. nov., actively induces nodules, and achieves atmospheric nitrogen and carbon dioxide fixation. This species appears to be depleted in motility genes, and is enriched in genes for direct effects on plant growth performance. Its genome reveals functional and plant growth-promoting signatures like a large unique chromosomal genomic island with high density of symbiotic genetic traits. Onobrychidicola muellerharveyae gen. nov. sp. nov., is described as type species of the new genus Onobrychidicola in Rhizobiaceae. This species comprises unique genetic features and plant growth-promoting traits (PGPTs), which strongly indicate its function in biotic stress reduction and motility. We applied a newly developed bioinformatics approach for in silico prediction of PGPTs (PGPT-Pred), which supports the different lifestyles of the two new species and the plant growth-promoting performance of M. onobrychidis in the greenhouse trial.

microbiology↗

bioRxiv2020

Functional diversity of isoprenoidal lipids in Methylobacterium extorquens PA1

Hopanoids and carotenoids are two of the major isoprenoid-derived lipid classes in prokaryotes that have been proposed to have similar membrane ordering properties as sterols. Methylobacterium extorquens contains hopanoids and carotenoids in their outer membrane, making them an ideal system to investigate whether isoprenoid lipids play a complementary role in outer membrane ordering and cellular fitness. By genetically knocking out hpnE, and crtB we disrupted the production of squalene, and phytoene in Methylobacterium extorquens PA1, which are the presumed precursors for hopanoids and carotenoids, respectively. Deletion of hpnE unexpectedly revealed that carotenoid biosynthesis utilizes squalene as a precursor resulting in a pigmentation with a C30 backbone, rather than the previously predicted C40 phytoene-derived pathway. We demonstrate that hopanoids but not carotenoids are essential for growth at high temperature. However, disruption of either carotenoid or hopanoid synthesis leads to opposing effects on outer membrane lipid packing. These observations show that hopanoids and carotenoids may serve complementary biophysical roles in the outer membrane. Phylogenetic analysis suggests that M. extorquens may have acquired the C30 pathway through lateral gene transfer with Planctomycetes. This suggests that the C30 carotenoid pathway may have provided an evolutionary advantage to M. extorquens. ImportanceAll cells have a membrane that delineates the boundary between life and its environment. To function properly, membranes must maintain a delicate balance of physical and chemical properties. Lipids play a crucial role in tuning membrane properties. In eukaryotic organisms from yeast to mammals, sterols are essential for assembling a cell surface membrane that can support life. However, bacteria generally do not make sterols, so how do they solve this problem? Hopanoids and carotenoids are two major bacterial lipids, that are proposed as sterol surrogates. In this study we explore the bacterium M. extorquens for studying the role of hopanoids and carotenoids in surface membrane properties and cellular growth. Our findings suggest that hopanoids and carotenoids may serve complementary roles balancing outer membrane properties, and provide a foundation for elucidating the principles of surface membrane adaptation.

microbiology↗

bioRxiv2019

Dinoroseobacter shibae outer membrane vesicles are enriched for the chromosome dimer resolution site dif

Outer membrane vesicles (OMVs) of Gram-negative bacteria have key roles in pathogenesis. However, little is known about their biogenesis and cargo in marine bacteria. In Dinoroseobacter shibae, a marine member of the Rhodobacteraceae, OMVs were produced throughout exponential growth, and DNA could be detected by fluorescence microscopy inside appr. 65% of vesicles. Single cell analysis using time-lapse microscopy showed that individual cells secreted multiple OMVs, preferentially at the septum during cell division. OMVs were enriched for saturated fatty acids, thus their secretion likely increases the fluidity of the membrane of the releasing cell locally. DNA was isolated from the vesicle lumen and sequenced; it was up to 40fold enriched for the region around the terminus of replication (ter). Within this region, the peak of coverage of vesicle DNA was located at dif, a conserved 28 bp palindromic sequence required for binding of the site specific tyrosine recombinases XerCD which are activated by the divisome protein FtsK immediately prior to septum formation. Some of the most abundant proteins of the vesicle proteome were predicted to be required for direct interaction with peptidoglycan during cell division. Single cell analysis, electron microscopy, proteome and DNA cargo show that constitutive OMV secretion in D. shibae occurs mainly prior to septum formation. The footprint of the FtsK/XerCD molecular machinery which resolves chromosome dimers suggests a novel highly conserved route for incorporation of DNA into OMVs. Clearing the division site from small DNA fragments might be an important function of this type of vesicles.

microbiology↗