Institut für Biologie

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Concerning the photophysics of fluorophores towards tailored bioimaging compounds: A case study involving S100A9 inflammation markers
(2023) Steiner, Simon T.; Maisuls, Iván; Junker, Anna; Fritz, Günter; Faust, Andreas; Strassert, Cristian A.; Steiner, Simon T.; European Institute for Molecular Imaging, Westfälische Wilhelms-Universität Münster, Münster, Germany; Maisuls, Iván; Center for Nanotechnology, Westfälische Wilhelms-Universität Münster, Münster, Germany; Junker, Anna; European Institute for Molecular Imaging, Westfälische Wilhelms-Universität Münster, Münster, Germany; Fritz, Günter; Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany; Faust, Andreas; European Institute for Molecular Imaging, Westfälische Wilhelms-Universität Münster, Münster, Germany; Strassert, Cristian A.; Center for Nanotechnology, Westfälische Wilhelms-Universität Münster, Münster, Germany
A full understanding concerning the photophysical properties of a fluorescent label is crucial for a reliable and predictable performance in biolabelling applications. This holds true not only for the choice of a fluorophore in general, but also for the correct interpretation of data, considering the complexity of biological environments. In the frame of a case study involving inflammation imaging, we report the photophysical characterization of four fluorescent S100A9-targeting compounds in terms of UV–vis absorption and photoluminescence spectroscopy, fluorescence quantum yields (ΦF) and excited state lifetimes (τ) as well as the evaluation of the radiative and non-radiative rate constants (kr and knr, respectively). The probes were synthesized based on a 2-amino benzimidazole-based lead structure in combination with commercially available dyes, covering a broad color range from green (6-FAM) over orange (BODIPY-TMR) to red (BODIPY-TR) and near-infrared (Cy5.5) emission. The effect of conjugation with the targeting structure was addressed by comparison of the probes with their corresponding dye-azide precursors. Additionally, the 6-FAM and Cy5.5 probes were measured in the presence of murine S100A9 to determine whether protein binding influences their photophysical properties. An interesting rise in ΦF upon binding of 6-FAM-SST177 to murine S100A9 enabled the determination of its dissociation equilibrium constant, reaching up to KD = 324 nM. This result gives an outlook for potential applications of our compounds in S100A9 inflammation imaging and fluorescence assay developments. With respect to the other dyes, this study demonstrates how diverse microenvironmental factors can severely impair their performance while rendering them poor performers in biological media, showing that a preliminary photophysical screening is key to assess the suitability of a particular luminophore.
Haemosporidian parasite infections of Malagasy Philepittidae and Nectariniidae are driven by phylogeny rather than ecology
(2023) Barbon, Hannah; Berthoud, Jean-Louis; Woog, Friederike; Musa, Sandrine
The nectarivorous common sunbird asity (Neodrepanis coruscans) is phylogenetically closely related to the frugivorous velvet asity (Philepitta castanea), yet it shares similar habitat and foraging behaviour as the Malagasy sunbirds (Cinnyris spp.). As ecological factors have been shown to influence blood parasite prevalence, it should be tested whether parasite abundance, prevalence and diversity of N. coruscans are more similar to the sunbirds than to its relative. Therefore, blood samples (n = 156) and smears (n = 60) were tested for different blood parasites (Haemosporida, trypanosomes, filarioid nematodes) using molecular and microscopic methods. High prevalence of haemosporidian parasites was observed in all bird taxa, with rates ranging from 23% in N. coruscans to 84.6% in C. notatus. The Malagasy Cinnyris spp. exhibited a high occurrence of mixed haemosporidian infections (>76%) with various specialized lineages. Within the Philepittidae family, no Haemoproteus infection was detected and just a few cases of mixed infections. Nectariniidae species predominantly had specialized haemosporidian lineages, while Philepittidae had infections mainly caused by generalist lineages. These findings emphasize the diverse range of blood parasites in Nectariniidae, while additionally highlighting the high diversity of trypanosomes and filarioid nematodes in Philepittidae. Additionally, several newly discovered haemosporidian lineages, Trypanosoma isolates and filarioid nematode isolates were identified. Notably, Philepittidae exhibited a lower prevalence of avian haemosporidian parasites compared to Nectariniidae, possibly due to potential resistance mechanisms. Despite N. coruscans sharing similar habitat and behavioural ecology with both Cinnyris spp., it closely resembles its relative, P. castanea, in all aspects of haemosporidian parasitism.
High genetic diversity of Echinococcus canadensis G10 in northeastern Asia: Is it the region of origin?
(2023) Wassermann, Marion; Addy, Francis; Kokolova, Ludmila; Okhlopkov, Innokentiy; Leibrock, Sarah; Oberle, Jenny; Oksanen, Antti; Romig, Thomas
Echinococcus canadensis consists of 4 genotypes: G6, G7, G8 and G10. While the first 2 predominantly infect domestic animals, the latter are sylvatic in nature involving mainly wolves and cervids as hosts and can be found in the northern temperate to Arctic latitudes. This circumstance makes the acquisition of sample material difficult, and little information is known about their genetic structure. The majority of specimens analysed to date have been from the European region, comparatively few from northeast Asia and Alaska. In the current study, Echinococcus spp. from wolves and intermediate hosts from the Republic of Sakha in eastern Russia were examined. Echinococcus canadensis G10 was identified in 15 wolves and 4 cervid intermediate hosts. Complete mitochondrial cytochrome c oxidase subunit 1 (cox1) sequences were obtained from 42 worm and cyst specimens from Sakha and, for comparison, from an additional 13 G10 cysts from Finland. For comparative analyses of the genetic diversity of G10 of European and Asian origin, all available cox1 sequences from GenBank were included, increasing the number of sequences to 99. The diversity found in northeast Asia was by far higher than in Europe, suggesting that the geographic origin of E. canadensis (at least of G10) might be northeast Asia.
Prostaglandin E2 signaling through prostaglandin E receptor subtype 2 and Nurr1 induces fibroblast growth factor 23 production
(2024) Feger, Martina; Hammerschmidt, Katharina; Liesche, lona; Rausch, Steffen; Alber, Jana; Föller, Michael
Bone cells produce fibroblast growth factor 23 (FGF23), a hormone regulating renal phosphate and vitamin D homeostasis, and a paracrine factor produced in further tissues. Chronic kidney disease and cardiovascular disorders are associated with early elevations of plasma FGF23 levels associated with clinical outcomes. FGF23 production is dependent on many conditions including inflammation. Prostaglandin E2 (PGE2) is a major eicosanoid with a broad role in pain, inflammation, and fever. Moreover, it regulates renal blood flow, renin secretion, natriuresis as well as bone formation through prostaglandin E receptor 2 (EP2). Here, we studied the role of PGE2 and its signaling for the production of FGF23. Osteoblast-like UMR-106 cells were exposed to EP receptor agonists, antagonists or RNAi. Wild type and EP2 knockout mice were treated with stable EP2 agonist misoprostol. Fgf23 or Nurr1 gene expression was determined by quantitative real-time PCR, hormone and further blood parameters by enzyme-linked immunosorbent assay and colorimetric methods. PGE2 and EP2 agonists misoprostol and butaprost enhanced FGF23 production in UMR-106 cells, effects mediated by EP2 and transcription factor Nurr1. A single dose of misoprostol up-regulated bone Fgf23 expression and FGF23 serum levels in wild type mice with subtle effects on parameters of mineral metabolism only. Compared to wild type mice, the FGF23 effect of misoprostol was significantly lower in EP2-deficient mice. To conclude, PGE2 signaling through EP2 and Nurr1 induces FGF23 production. Given the broad physiological and pathophysiological implications of PGE2 signaling, this effect is likely of clinical relevance.
Ecosystem services and insect decline: The role of parasitoid Hymenoptera
(2024) Haas-Renninger, Maura; Krogmann, Lars
Parasitoid Hymenoptera provide essential ecosystem services, as they consume their arthropod hosts during their development, controlling host populations and thus contributing to the resilience of ecosystems. However, information on their taxonomic diversity, distribution and population trends are scarce even in well-studied regions such as Central Europe, making it difficult to understand how they are affected by insect decline. Reasons for this knowledge gap are the enormous diversity in contrast to their small size (microhymenoptera), which is why they are referred to as ‘dark taxa’. In recent years, many monitoring projects have been launched to study insect population trends in the context of insect decline and climate change, with a focus on well-studied target groups, such as wild bees, butterflies or beetles. However, parasitoid wasps, which are probably the most species rich group of all insects, are totally neglected although Malaise traps, which are widely used in monitoring studies, catch large numbers of parasitoid Hymenoptera and can therefore serve as a starting point to assess diversity and abundance of this important group. The present work aims to establish a baseline for parasitoid Hymenoptera diversity and abundance in semi-arid meadows in southwestern Germany in a conservational and applied context. It consists of three research papers, each of which contribute to fulfil this goal. The first research paper deals with the efficiency of the fractionator to separate microhymenoptera families from Malaise trap samples and discusses its potential for long-term monitoring studies. The fractionator is an affordable and user-friendly apparatus based on a plastic tub with a sieve that is placed on an orbital shaker. When the complete sample is poured in, it can be separated by shaking into two size fractions. In this study it was used to separate microhymenoptera families from a Malaise trap sample. The results show that 24 out of 34 Hymenoptera families (71 %) were separated into one of the two size fractions, which proves that the fractionator can be a helpful tool to make microhymenoptera from bulk samples accessible for further taxonomic work. In the second research paper, Malaise trap samples from an ongoing insect monitoring program were used to study the relationship of total insect biomass to abundance and diversity of microhymenoptera, as well as to assess the phenology of microhymenoptera families. Microhymenoptera abundance and diversity were positively correlated with total insect biomass, suggesting that insect biomass can be a valuable proxy for abundance trends even for small-sized insects such as microhymenoptera. Further, 90,452 specimens from 26 families belonging to 10 superfamilies of Hymenoptera were counted in total. Microhymenoptera showed two main activity periods during the year, reaching a first peak between June and July and a second between July and August. We could not find any evidence for a negative impact of mowing or grazing on the abundance of microhymenoptera. The families showed different phenological patterns, with varying numbers of activity peaks, and with some families being abundant very early (e.g. Platygastridae) or very late in the season (e.g. Figitidae, Trichogrammatidae). This is the first baseline for microhymenoptera occurrence patterns in Central Europe. The third research paper assesses the effect of mowing on microhymenoptera and how this effect can be reduced through arthropod-friendly mowing techniques, such as an adapted mowing head and a flushing bar. The results show that mowing with a conventional mulching mower has a detrimental effect on microhymenoptera with a loss of up to 64 % of individuals. The adapted mowing head had an effect only on Chalcidoidea, sparing 38 % of individuals compared to the conventional mower. The flushing bar had only a limited positive impact, because it showed a significant effect on total number of microhymenoptera with a significant reduction of 30 % on Chalcidoidea and a tendency for Ichneumonoidea with a reduction of 47 %. This shows that the conventional mowing head can have serious effects on microhymenoptera and that the effect can only be partially mitigated by insect-friendly mowing techniques. I presented the benefits and the limitations of implementing the fractionator in a monitoring workflow. As a positive example, using the fractionator enabled me to create the dataset of research paper 2, which together with research paper 3 can be a valuable reference for adapting schedules for plant protection measures and mowing dates. Insect biomass is strongly correlated with microhymenoptera abundance (research paper 2), which implies that microhymenoptera follow similar negative trends as other insects, but more meadows would need to be included to support our findings. I sorted microhymenoptera from Malaise trap samples as well as suction samples, resulting in different dominating families. Therefore a variety of collecting methods are necessary to assess the whole diversity of parasitoid Hymenoptera. All 103,312 specimens that I processed during my doctoral work are assessed in a digital database, and available for further morphological and molecular work. By linking an insect monitoring initiative with the taxonomically focused GBOLIII: Dark Taxa project, I was able to bring together the best of two worlds, and these combined efforts supported the discovery of a new wasp species. In conclusion, this work lays the foundation for the long-term assessment of parasitoid Hymenoptera in meadow ecosystems and thus contributes to a better understanding of how they are affected by insect decline. It highlights the ecological importance of parasitoid Hymenoptera and serves as a resource for their conservation. In the future, focus must be laid on studying the complex species interaction networks of parasitoid Hymenoptera and associated species. Automated systems such as the DiversityScanner using AI in combination with molecular techniques can help to gain knowledge on this highly important insect group.
The low mutational flexibility of the EPSP synthase in Bacillus subtilis is due to a higher demand for shikimate pathway intermediates
(2023) Schwedt, Inge; Schöne, Kerstin; Eckert, Maike; Pizzinato, Manon; Winkler, Laura; Knotkova, Barbora; Richts, Björn; Hau, Jann-Louis; Steuber, Julia; Mireles, Raul; Noda‐Garcia, Lianet; Fritz, Günter; Mittelstädt, Carolin; Hertel, Robert; Commichau, Fabian M.
Glyphosate (GS) inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase that is required for aromatic amino acid, folate and quinone biosynthesis in Bacillus subtilis and Escherichia coli. The inhibition of the EPSP synthase by GS depletes the cell of these metabolites, resulting in cell death. Here, we show that like the laboratory B. subtilis strains also environmental and undomesticated isolates adapt to GS by reducing herbicide uptake. Although B. subtilis possesses a GS-insensitive EPSP synthase, the enzyme is strongly inhibited by GS in the native environment. Moreover, the B. subtilis EPSP synthase mutant was only viable in rich medium containing menaquinone, indicating that the bacteria require a catalytically efficient EPSP synthase under nutrient-poor conditions. The dependency of B. subtilis on the EPSP synthase probably limits its evolvability. In contrast, E. coli rapidly acquires GS resistance by target modification. However, the evolution of a GS-resistant EPSP synthase under non-selective growth conditions indicates that GS resistance causes fitness costs. Therefore, in both model organisms, the proper function of the EPSP synthase is critical for the cellular viability. This study also revealed that the uptake systems for folate precursors, phenylalanine and tyrosine need to be identified and characterized in B. subtilis.
Recombinant production and characterization of metalloproteins from bacterial pathogens and the innate immune response
(2024) Göbel, Katharina; Fritz, Günter
The challenges and potential solutions of drug development are highlighted by discussing the identification, production and characterization of potential new drug targets in this study. The successful development of new and specific pharmaceuticals requires that the target for the respective new drug is available as a pure and homogenous molecule in its native state. Typically, the target molecule is a protein. E.g. antibacterial drugs target proteins from a bacterial pathogen or in human diseases pharmaceuticals predominantly target proteins of signaling pathways or receptors. These proteins are usually not available directly from the organism itself and have to be produced in an expression host and purified to homogeneity. Despite the advances in the field of recombinant protein expression and purification many proteins are very difficult to produce and thus represent the major bottleneck in the development of new pharmaceuticals. In particular demanding is the expression of metalloproteins, which make up to 30% of all proteins coded in the human genome and represent a major challenge in recombinant protein production. Metalloproteins are a diverse class of proteins that is crucial for various biological processes. They play an important role in the regulation, catalysis, and maintenance of biomolecular structure. Alone, 10% of all human proteins contain zinc ions and 2% contain iron, and both metal ions are often inserted by specific but so far unknown chaperones impeding the recombinant production of correctly folded and active proteins. The challenges in studying these metalloproteins arise from their complex structures and the difficulty of their expression and isolation. To overcome these problems new approaches and solutions are highlighted and exemplified by the production and characterization of potential new drug targets in this study. The focus lies particularly on metalloproteins that play a role in infectious diseases. Global health challenges include the persistent threat of infectious diseases despite advances in healthcare, hygiene and therapeutics. The COVID-19 pandemic and rising antibiotic resistance are prime examples of the ongoing risks. This research focuses on three different proteins: (1) the maturation factor NqrM from the bacterial pathogen Vibrio cholerae, (2) the human regulator of the interferon response ubiquitin-specific protease 18 (USP18) and its interaction partners, as well as (3) the viral Papain-like protease (PLpro) from the pathogenic virus SARS-CoV-2. All three proteins belong to the class of metalloproteins and bind either iron as in the case of NqrM or zinc as for USP18 and PLpro. New methods and strategies were developed to produce, isolate and investigate these metalloproteins and since all three proteins represent potential drug targets the results presented here provide the basis for future drug development. The production of proteins requires the selection of appropriate expression host systems such as bacteria, yeast, mammalian cells, etc., depending on the desired application. The study emphasizes the versatility of expression host E. coli due to its well-studied genetics, rapid growth kinetics and ease of handling. However, challenges such as the lack of post-translational modifications can lead to the production of non-functional proteins. Optimization of expression strategies is crucial, and the study describes various factors affecting protein production, including protein engineering, growth conditions, media composition and induction parameters expanding and enhancing the well-established E.coli expression system also for very challenging target proteins. The successful isolation of the proteins formed the fundamental basis for a detailed functional and structural characterization of the proteins. The research presented here takes a forward approach and encompasses the new strategies in cloning, recombinant expression and purification of proteins from bacteria, viruses and humans, emphasizing the advantages and disadvantages of homo- and heterologous recombinant expression. The results obtained highlight also the need for extensive experimental testing to establish optimal conditions, particularly for challenging proteins such as the metalloproteins studied here.
Limitations of soil-applied non-microbial and microbial biostimulants in enhancing soil P turnover and recycled P fertilizer utilization: A study with and without plants
(2024) Herrmann, Michelle Natalie; Griffin, Lydia Grace; John, Rebecca; Mosquera-Rodríguez, Sergio F.; Nkebiwe, Peteh Mehdi; Chen, Xinping; Yang, Huaiyu; Müller, Torsten
Introduction: Phosphorus recovery from waste streams is a global concern due to open nutrient cycles. However, the reliability and efficiency of recycled P fertilizers are often low. Biostimulants (BS), as a potential enhancer of P availability in soil, could help to overcome current barriers using recycled P fertilizers. For this, a deeper understanding of the influence of BSs on soil P turnover and the interaction of BSs with plants is needed. Methods: We conducted an incubation and a pot trial with maize in which we testednon-microbial (humic acids and plant extracts) and microbial BSs (microbial consortia) in combination with two recycled fertilizers for their impact on soil P turnover, plant available P, and plant growth. Results and discussion: BSs could not stimulate P turnover processes (phosphatase activity, microbial biomass P) and had a minor impact on calcium acetate-lactate extractable P (CAL-P) in the incubation trial. Even though stimulation of microbial P turnover by the microbial consortium and humic acids in combination with the sewage sludge ash could be identified in the plant trial with maize, this was not reflected in the plant performance and soil P turnover processes. Concerning the recycled P fertilizers, the CAL-P content in soil was not a reliable predictor of plant performance with both products resulting in competitive plant growth and P uptake. While this study questions the reliability of BSs, it also highlights the necessity toimprove our understanding and distinguish the mechanisms of P mobilization in soil and the stimulation of plant P acquisition to optimize future usage.
Identification of ZBTB26 as a novel risk factor for congenital hypothyroidism
(2021) Vick, Philipp; Eberle, Birgit; Choukair, Daniela; Weiss, Birgit; Roeth, Ralph; Schneider, Isabelle; Paramasivam, Nagarajan; Bettendorf, Markus; Rappold, Gudrun A.
Congenital primary hypothyroidism (CH; OMIM 218700) is characterized by an impaired thyroid development, or dyshormonogenesis, and can lead to intellectual disability and growth retardation if untreated. Most of the children with congenital hypothyroidism present thyroid dysgenesis, a developmental anomaly of the thyroid. Various genes have been associated with thyroid dysgenesis, but all known genes together can only explain a small number of cases. To identify novel genetic causes for congenital hypothyroidism, we performed trio whole-exome sequencing in an affected newborn and his unaffected parents. A predicted damaging de novo missense mutation was identified in the ZBTB26 gene (Zinc Finger A and BTB Domain containing 26). An additional cohort screening of 156 individuals with congenital thyroid dysgenesis identified two additional ZBTB26 gene variants of unknown significance. To study the underlying disease mechanism, morpholino knock-down of zbtb26 in Xenopus laevis was carried out, which demonstrated significantly smaller thyroid anlagen in knock-down animals at tadpole stage. Marker genes expressed in thyroid tissue precursors also indicated a specific reduction in the Xenopus ortholog of human Paired-Box-Protein PAX8, a transcription factor required for thyroid development, which could be rescued by adding zbtb26. Pathway and network analysis indicated network links of ZBTB26 to PAX8 and other genes involved in thyroid genesis and function. GWAS associations of ZBTB26 were found with height. Together, our study added a novel genetic risk factor to the list of genes underlying congenital primary hypothyroidism and provides additional support that de novo mutations, together with inherited variants, might contribute to the genetic susceptibility to CH.
Up-regulation of fibroblast growth factor 23 gene expression in UMR106 osteoblast-like cells with reduced viability
(2021) Münz, Sina; Feger, Martina; Edemir, Bayram; Föller, Michael
Fibroblast growth factor 23 (FGF23) controls vitamin D and phosphate homeostasis in the kidney and has additional paracrine effects elsewhere. As a biomarker, its plasma concentration is associated with progression of inflammatory, renal, and cardiovascular diseases. Major stimuli of FGF23 synthesis include active vitamin D and inflammation. Antineoplastic chemotherapy treats cancer by inducing cellular damage ultimately favoring cell death (apoptosis and necrosis) and causing inflammation. Our study explored whether chemotherapeutics and other apoptosis inducers impact on Fgf23 expression. Experiments were performed in osteoblast-like UMR106 cells, Fgf23 gene expression and protein synthesis were determined by qRT-PCR and ELISA, respectively. Viability was assessed by MTT assay and NFκB activity by Western Blotting. Antineoplastic drugs cisplatin and doxorubicin as well as apoptosis inducers procaspase-activating compound 1 (PAC-1), a caspase 3 activator, and serum depletion up-regulated Fgf23 transcripts while reducing cell proliferation and viability. The effect of cisplatin on Fgf23 transcription was paralleled by Il-6 up-regulation and NFκB activation and attenuated by Il-6 and NFκB signaling inhibitors. To conclude, cell viability-decreasing chemotherapeutics as well as apoptosis stimulants PAC-1 and serum depletion up-regulate Fgf23 gene expression. At least in part, Il-6 and NFκB may contribute to this effect.
Tachysterol2 increases the synthesis of fibroblast growth factor 23 in bone cells
(2022) Ewendt, Franz; Kotwan, Julia; Ploch, Stefan; Feger, Martina; Hirche, Frank; Föller, Michael; Stangl, Gabriele I.
Tachysterol2 (T2) is a photoisomer of the previtamin D2 found in UV-B-irradiated foods such as mushrooms or baker’s yeast. Due to its structural similarity to vitamin D, we hypothesized that T2 can affect vitamin D metabolism and in turn, fibroblast growth factor 23 (FGF23), a bone-derived phosphaturic hormone that is transcriptionally regulated by the vitamin D receptor (VDR). Initially, a mouse study was conducted to investigate the bioavailability of T2 and its impact on vitamin D metabolism and Fgf23 expression. UMR106 and IDG-SW3 bone cell lines were used to elucidate the effect of T2 on FGF23 synthesis and the corresponding mechanisms. LC-MS/MS analysis found high concentrations of T2 in tissues and plasma of mice fed 4 vs. 0 mg/kg T2 for 2 weeks, accompanied by a significant decrease in plasma 1,25(OH)2D and increased renal Cyp24a1 mRNA abundance. The Fgf23 mRNA abundance in bones of mice fed T2 was moderately higher than that in control mice. The expression of Fgf23 strongly increased in UMR106 cells treated with T2. After Vdr silencing, the T2 effect on Fgf23 diminished. This effect is presumably mediated by single-hydroxylated T2-derivatives, since siRNA-mediated silencing of Cyp27a1, but not Cyp27b1, resulted in a marked reduction in T2-induced Fgf23 gene expression. To conclude, T2 is a potent regulator of Fgf23 synthesis in bone and activates Vdr. This effect depends, at least in part, on the action of Cyp27a1. The potential of oral T2 to modulate vitamin D metabolism and FGF23 synthesis raises questions about the safety of UV-B-treated foods.
Low-input high-molecular-weight DNA extraction for long-read sequencing from plants of diverse families
(2022) Russo, Alessia; Mayjonade, Baptiste; Frei, Daniel; Potente, Giacomo; Kellenberger, Roman T.; Frachon, Léa; Copetti, Dario; Studer, Bruno; Frey, Jürg E.; Grossniklaus, Ueli; Schlüter, Philipp M.
Long-read DNA sequencing technologies require high molecular weight (HMW) DNA of adequate purity and integrity, which can be difficult to isolate from plant material. Plant leaves usually contain high levels of carbohydrates and secondary metabolites that can impact DNA purity, affecting downstream applications. Several protocols and kits are available for HMW DNA extraction, but they usually require a high amount of input material and often lead to substantial DNA fragmentation, making sequencing suboptimal in terms of read length and data yield. We here describe a protocol for plant HMW DNA extraction from low input material (0.1 g) which is easy to follow and quick (2.5 h). This method successfully enabled us to extract HMW from four species from different families (Orchidaceae, Poaceae, Brassicaceae, Asteraceae). In the case of recalcitrant species, we show that an additional purification step is sufficient to deliver a clean DNA sample. We demonstrate the suitability of our protocol for long-read sequencing on the Oxford Nanopore Technologies PromethION® platform, with and without the use of a short fragment depletion kit.
Regulatory modules of metabolites and protein phosphorylation in arabidopsis genotypes with altered sucrose allocation
(2022) Stefan, Thorsten; Wu, Xu Na; Zhang, Youjun; Fernie, Alisdair; Schulze, Waltraud X.
Multi-omics data sets are increasingly being used for the interpretation of cellular processes in response to environmental cues. Especially, the posttranslational modification of proteins by phosphorylation is an important regulatory process affecting protein activity and/or localization, which, in turn, can have effects on metabolic processes and metabolite levels. Despite this importance, relationships between protein phosphorylation status and metabolite abundance remain largely underexplored. Here, we used a phosphoproteomics–metabolomics data set collected at the end of day and night in shoots and roots of Arabidopsis to propose regulatory relationships between protein phosphorylation and accumulation or allocation of metabolites. For this purpose, we introduced a novel, robust co-expression measure suited to the structure of our data sets, and we used this measure to construct metabolite-phosphopeptide networks. These networks were compared between wild type and plants with perturbations in key processes of sugar metabolism, namely, sucrose export (sweet11/12 mutant) and starch synthesis (pgm mutant). The phosphopeptide–metabolite network turned out to be highly sensitive to perturbations in sugar metabolism. Specifically, KING1, the regulatory subunit of SnRK1, was identified as a primary candidate connecting protein phosphorylation status with metabolism. We additionally identified strong changes in the fatty acid network of the sweet11/12 mutant, potentially resulting from a combination of fatty acid signaling and metabolic overflow reactions in response to high internal sucrose concentrations. Our results further suggest novel protein-metabolite relationships as candidates for future targeted research.
tsCRISPR based identification of Rab proteins required for the recycling of Drosophila TRPL ion channel
(2024) Zeger, Matthias; Stanisławczyk, Lena Sarah; Bulić,Marija; Binder, Andrea Maria; Huber, Armin
In polarized cells, the precise regulation of protein transport to and from the plasma membrane is crucial to maintain cellular function. Dysregulation of intracellular protein transport in neurons can lead to neurodegenerative diseases such as Retinitis Pigmentosa, Alzheimer’s and Parkinson’s disease. Here we used the light-dependent transport of the TRPL (transient receptor potential-like) ion channel in Drosophila photoreceptor cells to study the role of Rab proteins in TRPL recycling. TRPL is located in the rhabdomeric membrane of dark-adapted flies, but it is transported out of the rhabdomere upon light exposure and localizes at the Endoplasmatic Reticulum within 12 h. Upon subsequent dark adaptation, TRPL is recycled back to the rhabdomeric membrane within 90 min. To screen for Rab proteins involved in TRPL recycling, we established a tissue specific (ts) CRISPR/Cas9-mediated knock- out of individual Rab genes in Drosophila photoreceptors and assessed TRPL localization using an eGFP tagged TRPL protein in the intact eyes of these mutants. We observed severe TRPL recycling defects in the knockouts of Rab3, Rab4, Rab7, Rab32, and RabX2. Using immunohistochemistry, we further showed that Rab3 and RabX2 each play a significant role in TRPL recycling and also influence TRPL transport. We localized Rab3 to the late endosome in Drosophila photoreceptors and observed disruption of TRPL transport to the ER in Rab3 knock-out mutants. TRPL transport from the ER to the rhabdomere ensues from the trans-Golgi where RabX2 is located. We observed accumulated TRPL at the trans-Golgi in RabX2 knock-out mutants. In summary, our study reveals the requirement of specific Rab proteins for different steps of TRPL transport in photoreceptor cells and provides evidence for a unique retrograde recycling pathway of TRPL from the ER via the trans-Golgi
Metabolic rewiring enables ammonium assimilation via a non‐canonical fumarate‐based pathway
(2024) Mardoukhi, Mohammad Saba Yousef; Rapp, Johanna; Irisarri, Iker; Gunka, Katrin; Link, Hannes; Marienhagen, Jan; de Vries, Jan; Stülke, Jörg; Commichau, Fabian M.
Glutamate serves as the major cellular amino group donor. In Bacillus subtilis, glutamate is synthesized by the combined action of the glutamine synthetase and the glutamate synthase (GOGAT). The glutamate dehydrogenases are devoted to glutamate degradation in vivo. To keep the cellular glutamate concentration high, the genes and the encoded enzymes involved in glutamate biosynthesis and degradation need to be tightly regulated depending on the available carbon and nitrogen sources. Serendipitously, we found that the inactivation of the ansR and citG genes encoding the repressor of the ansAB genes and the fumarase, respectively, enables the GOGAT-deficient B. subtilis mutant to synthesize glutamate via a non-canonical fumarate-based ammonium assimilation pathway. We also show that the de-repression of the ansAB genes is sufficient to restore aspartate prototrophy of an aspB aspartate transaminase mutant. Moreover, in the presence of arginine, B. subtilis mutants lacking fumarase activity show a growth defect that can be relieved by aspB overexpression, by reducing arginine uptake and by decreasing the metabolic flux through the TCA cycle.
Taeniidae in Namibian wildlife with emphasis on lion, cheetah, and African wild dog
(2024) Aschenborn, Ortwin; Mackenstedt, Ute
An opportunic survey for Echinococcus spp. in wild mammals was conducted in seven distinct stuy areas throughout Namibia, representing all major ecosystems, between 2012 and 2021. In total, 184 individually attributable faeces and 40 intestines were collected from eight species of carnivores, and 300 carcasses or organs of thirteen species of ungulates were examined for Echinococcus cysts. Nested PCR and sequencing of the mitochondrial nad1 gene led to the identification of five species of the Echinococcus granulosus sensu lato complex. Echinococcus canadensis G6/7 was found throughout Namibia at low frequency in lions, cheetahs, African wild dogs, black-backed jackals and oryx antelopes. Echinococcus equinus was present only in northern Namibia, locally at high frequency in lions, black-backed jackals and plains zebras. Echinococcus felidis was found only in one small area in the north-east of Namibia, but with high frequency in lions and warthogs. Echinococcus granulosus sensu stricto was identified only in two African wild dogs in the north-east of Namibia, and Echinococcus ortleppi occurred in central and southern Namibia in black-backed jackals and oryx antelopes. The development of fertile cysts indicated active intermediate host roles of oryx antelopes for E. canadensis and E. ortleppi, of warthogs for E. felidis, and of plains zebras for E. equinus. Our data support earlier hypotheses of exclusive or predominant wildlife life-cycles for E. felidis involving lions and warthogs, and – in Namibia – for E. equinus involving lions and/or black-backed jackals and plains zebras. Our data further support an interlink of wild and domestic transmission for E. ortleppi. A possible involvement of livestock and domestic dogs in transmission of E. canadensis G6/7 and E. granulosus s.s., the two parasite species with highest zoonotic potential, is uncertain for Namibia and needs further investigation. The present study was conducted in the isolated desert town of Oranjemund in the far south of Namibia. It is an extremely arid region where no livestock husbandry is practiced and only animals adapted to the desert can be found. However, in and around the city, artifi cial irrigation maintains lush green patches of grass that attract wild animals, in particular oryx antelopes (Oryx gazella). In 2015 four oryx antelopes were euthanised due to poor conditions and a post-mortem examination was conducted. Two were found positive for cystic echinococcosis and 16 cysts were collected for molecular analyses. In addition, faecal samples from black-backed jackals (n=5) and domestic dogs (n=9), which were regularly observed to feed on oryx carcasses, were collected and taeniid eggs isolated. Parasite species identifi cation of the cysts and eggs was done by amplifying and se- quencing the mitochondrial nad1 gene. Both oryx antelopes were found infected with E. ortleppi and one co-infected with E. canadensis G6/7. Both Echinococcus species were able to develop fertile cysts in oryx, making oryx antelopes competent hosts for these parasites. Therefore, the analysis of faecal samples was of high interest and although the numbers were quite small, taeniid eggs were found in three out of fi ve faecal samples of jackals and in all nine dog samples. However, species determination was only successful with two jackal and one dog sample. All three were positive for E. canadensis G6/7. The absence of E. ortleppi may be due to the low number of faecal samples examined. In our small study, we discovered a rather unique lifecycle of Echinococcus spp. between jackals and domestic dogs as defi nitive hosts and oryx antelopes as intermediate hosts. Here, the presence of E. canadensis G6/7 is of particular concern, as it is the second most important causative agent of CE in humans.
The emergence and dynamics of tick-borne Encephalitis Virus in a new endemic region in Southern Germany
(2022) Lang, Daniel; Chitimia-Dobler, Lidia; Bestehorn-Willmann, Malena; Lindau, Alexander; Drehmann, Marco; Stroppel, Gabriele; Hengge, Helga; Mackenstedt, Ute; Kaier, Klaus; Dobler, Gerhard; Borde, Johannes
Tick-borne encephalitis (TBE) is the most important viral tick-borne infection in Europe and Asia. It is emerging in new areas. The mechanisms of emergence are fairly unknown or speculative. In the Ravensburg district in southern Germany, TBE emerged, mainly over the last five years. Here, we analyzed the underlying epidemiology in humans. The resulting identified natural foci of the causal TBE virus (TBEV) were genetically characterized. We sampled 13 potential infection sites at these foci and detected TBEV in ticks (Ixodes ricinus) at eight sites. Phylogenetic analysis spurred the introduction of at least four distinct TBEV lineages of the European subtype into the Ravensburg district over the last few years. In two instances, a continuous spread of these virus strains over up to 10 km was observed.
Central carbon metabolism, sodium-motive electron ransfer, and ammonium formation by the vaginal pathogen Prevotella bivia
(2021) Schleicher, Lena; Herdan, Sebastian; Fritz, Günter; Trautmann, Andrej; Seifert, Jana; Steuber, Julia
Replacement of the Lactobacillus dominated vaginal microbiome by a mixed bacterial population including Prevotella bivia is associated with bacterial vaginosis (BV). To understand the impact of P. bivia on this microbiome, its growth requirements and mode of energy production were studied. Anoxic growth with glucose depended on CO2 and resulted in succinate formation, indicating phosphoenolpyruvate carboxylation and fumarate reduction as critical steps. The reductive branch of fermentation relied on two highly active, membrane-bound enzymes, namely the quinol:fumarate reductase (QFR) and Na+-translocating NADH:quinone oxidoreductase (NQR). Both enzymes were characterized by activity measurements, in-gel fluorography, and VIS difference spectroscopy, and the Na+-dependent build-up of a transmembrane voltage was demonstrated. NQR is a potential drug target for BV treatment since it is neither found in humans nor in Lactobacillus. In P. bivia, the highly active enzymes L-asparaginase and aspartate ammonia lyase catalyze the conversion of asparagine to the electron acceptor fumarate. However, the by-product ammonium is highly toxic. It has been proposed that P. bivia depends on ammonium-utilizing Gardnerella vaginalis, another typical pathogen associated with BV, and provides key nutrients to it. The product pattern of P. bivia growing on glucose in the presence of mixed amino acids substantiates this notion.
Na+-coupled respiration and reshaping of extracellular polysaccharide layer counteract monensin-induced cation permeability in Prevotella bryantii B14
(2021) Trautmann, Andrej; Schleicher, Lena; Pfirrmann, Jana; Boldt, Christin; Steuber, Julia; Seifert, Jana
Monensin is an ionophore for monovalent cations, which is frequently used to prevent ketosis and to enhance performance in dairy cows. Studies have shown the rumen bacteria Prevotella bryantii B14 being less affected by monensin. The present study aimed to reveal more information about the respective molecular mechanisms in P. bryantii, as there is still a lack of knowledge about defense mechanisms against monensin. Cell growth experiments applying increasing concentrations of monensin and incubations up to 72 h were done. Harvested cells were used for label-free quantitative proteomics, enzyme activity measurements, quantification of intracellular sodium and extracellular glucose concentrations and fluorescence microscopy. Our findings confirmed an active cell growth and fermentation activity of P. bryantii B14 despite monensin concentrations up to 60 µM. An elevated abundance and activity of the Na+-translocating NADH:quinone oxidoreductase counteracted sodium influx caused by monensin. Cell membranes and extracellular polysaccharides were highly influenced by monensin indicated by a reduced number of outer membrane proteins, an increased number of certain glucoside hydrolases and an elevated concentration of extracellular glucose. Thus, a reconstruction of extracellular polysaccharides in P. bryantii in response to monensin is proposed, which is expected to have a negative impact on the substrate binding capacities of this rumen bacterium.
Application of fluorescent proteins for functional dissection of the drosophila visual system
(2021) Smylla, Thomas; Wagner, Krystina; Huber, Armin
The Drosophila eye has been used extensively to study numerous aspects of biological systems, for example, spatio-temporal regulation of differentiation, visual signal transduction, protein trafficking and neurodegeneration. Right from the advent of fluorescent proteins (FPs) near the end of the millennium, heterologously expressed fusion proteins comprising FPs have been applied in Drosophila vision research not only for subcellular localization of proteins but also for genetic screens and analysis of photoreceptor function. Here, we summarize applications for FPs used in the Drosophila eye as part of genetic screens, to study rhodopsin expression patterns, subcellular protein localization, membrane protein transport or as genetically encoded biosensors for Ca2+ and phospholipids in vivo. We also discuss recently developed FPs that are suitable for super-resolution or correlative light and electron microscopy (CLEM) approaches. Illustrating the possibilities provided by using FPs in Drosophila photoreceptors may aid research in other sensory or neuronal systems that have not yet been studied as well as the Drosophila eye.

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