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Biology subjects

Fuchs, M.

Publications and source records attributed to Fuchs, M..

At least 19 recordsLinked to original sources

Molecular logics in dual sensor regulation of enzyme activity: Phosphorylation OR blue-light activation of cyanobacterial diguanylate cyclases

Bacterial cells use multiple environmental cues to regulate levels of the second messenger cyclic dimeric GMP. This compound influences key lifestyle decisions such as motility, biofilm formation, or virulence. Although many diguanylate cyclases (DGCs) combined with various sensory domains have been studied previously, how distinct inputs are integrated within a single enzyme remains incompletely understood. Here, we investigate a cyanobacterial family of dual-sensor DGCs that combine an N-terminal receiver (Rec) domain followed by a light-oxygen-voltage (LOV) domain upstream of a diguanylate cyclase (GGDEF) domain. Using in vivo activity screening and in vitro characterisation, we determined how phosphorylation and blue light, individually and jointly, regulate enzyme activity. By measuring kinetic parameters across four defined functional states, unphosphorylated or phosphorylated, in combination with dark or light states, we reveal logic gate-like behaviours. One representative, LaRldC, integrates both signals with pronounced fold-changes in activity-, consistent with overall OR-type logic and with light acting as the dominant input. Our results demonstrate its function as a molecular gate coupling phosphorylation and illumination sensing to cyclic-di-GMP formation. These findings provide valuable insights into multi-signal decision-making in cyanobacteria and establish further understanding of how modular sensory domains are wired to control bacterial second-messenger signalling.

biochemistry↗

High-throughput transposon mutagenesis defines the essential genome of diverse phages

Phages are important drivers of bacterial evolution with therapeutic potential as antimicrobials. However, gaps in our understanding of phages and our inability to rapidly engineer them with new genetic cargo hinders progress towards phage-based therapies. To address the lack of unbiased, genome-wide mutational tools for phages, we developed transposon mutagenesis employing CRISPR-anti-CRISPR (Acr)-based selection and deep-sequencing (Phage Tn-seq). Transposon mutagenesis was effective for phages with unmodified or hypermodified genomes and a jumbo phage that protects its DNA within a nucleus. Phage Tn-seq enabled phage gene essentiality assignment consistent with structural proteomics and core gene conservation. Insertion biases allowed prediction of transcriptional direction and early injected phage DNA regions. We exploited the method to rapidly deliver new cargo to phage genomes in just a few days and used an AI-designed Acr to expand the phage transposon toolbox. Phage Tn-seq is a versatile tool to advance our understanding and applications of phages.

microbiology↗

Directed cortico-limbic dialogue in the human brain

How can one trace the brains orderly directed signals amid a tangle of nerve fibers? Because direct access to actual brain signaling is rare in humans, the precise wiring diagrams for cortico-limbic communication during sleep and wake remain essentially unmapped, hampering progress in neuroscience. Now, a unique neurosurgical window on the human brain allows for electrically mapping cortical connections at the hospital, but studies so far have relied on average signals, masking the dynamic nature of signal flow across brain regions. To causally estimate signaling dynamics, we repeatedly probed cortico-limbic networks with short-lived electrical pulses over days and assessed the variable fate of each transmitted signal on a single-trial basis. In the resulting openly available dataset, we characterized signaling probabilities and directionality across thousands local and long-range cortico-limbic connections over days. Challenging established views, we found that limbic structures send twice as many signals as they receive, in both wakefulness and sleep. Our findings provide a fundamental framework for causally interpreting signal flow in the brain and formulating therapeutic strategies for brain networks disorders.

neuroscience↗

STED/AFM as a tool to investigate mechanical and adhesive properties of migrating keratinocytes

E-cadherin is a central junctional molecule of adherens junctions that regulates epithelial integrity. In keratinocytes, wound healing critically depends on dynamic modulation of adhesion and cytoskeletal organization. Here, we applied wound healing assay and the combination of the stimulated emission depletion (STED) microscopy with the atomic force microscopy (AFM) (STED/AFM hybrid technique), to study E-cadherin binding properties during keratinocyte migration. Wound closure occurred within 6 h, an effect associated with E-cadherin accumulation at the leading edge. For location-specific binding measurements with the STED/AFM technique, we overexpressed E-cadherin in mouse keratinocytes and performed single molecule force spectroscopy measurements. Inhibition of actin polymerization abolished E-cadherin binding and further reduced overall cellular stiffness. To study adhesion mechanics during migration, we used the STED/AFM technique and performed single-molecule force spectroscopy at the leading edge of keratinocytes migrating into cell-free areas, generated by removal of two-well inserts. This approach enabled, for the first time, simultaneous measurements of single-molecule binding properties and cellular mechanistic properties in actively migrating keratinocytes. Our results revealed that E-Cad molecules present during migration exhibit binding properties comparable to those of E-Cad in stable AJs. This suggests that these molecules remain functional competent and may be readily available for rapid re-engagement in cell-cell adhesion when required. We introduce a powerful methodology to investigate single molecule binding properties in migrating cells, offering new opportunities to analyze epithelial repair at molecular resolution.

cell biology↗

Cell-to-cell mobility of the stem cell inducing WUSCHEL transcription factor is controlled by a balance of transport and retention

Non-cell autonomous induction of stem cell fate is a shared feature across multicellular organisms, however the underlying mechanisms diverge substantially between the kingdoms of live. In plants, cell to cell mobility of transcription factors has emerged as a key paradigm. For the shoot apical meristem of the reference plant Arabidopsis thaliana it has been described that the translocation of the WUSCHEL homeodomain transcription factor from niche cells to stem cells is essential for their maintenance. Here we systematically investigate the function of diverse WUS alleles and leverage multispectral live cell imaging coupled to computational analysis and mechanistic mathematical modelling to show that WUSCHEL protein mobility is the result of balance between active transport and retention in niche cells and likely independent of the stem cell signal CLAVATA3. Importantly, we show that diffusion across cell layers of the meristem is not symmetrical, suggesting that there is unexpected complexity in cellular connections.

plant biology↗

Supramolecular Enzyme-Peptide Gels for Localized Therapeutic Biocatalysis

Enzyme therapeutics are often compromised by poor accumulation within target tissues, necessitating repeated systemic dosing that can exacerbate side-effects like immunogenicity. We report an injectable supramolecular enzyme-peptide gel platform for prolonged local enzyme retention in vivo. The gel is based on CATCH(+/-) (Co-Assembling Tags based on CHarge-complementarity), cationic and anionic peptide pairs that form {beta}-sheet fibrillar gels upon mixing. Five disparate enzymes recombinantly fused to CATCH(-) peptide integrate into CATCH(+/-) fibrils during assembly, resulting in five single-enzyme and three dual-enzyme catalytically-active enzyme-peptide gels. CATCH gels enable titratable catalytic activity and prolonged localized retention. Gels of uricase, an FDA-approved but systemically-ineffective enzyme therapy for gout, rapidly dissolve gout crystals, with low risk of anaphylaxis after repeat dosing. Dual-enzyme gels of uricase and anti-inflammatory indoleamine 2,3-dioxygenase outperformed either single-enzyme formulation by concomitantly dissolving the crystals and suppressing pro-inflammatory neutrophil functions. Modular and tunable enzyme content, coupled with prolonged retention, establish CATCH enzyme-peptide gels as a generalizable vehicle for effective local therapeutic biocatalysis.

bioengineering↗

SGLT2 inhibitors attenuate endothelial to mesenchymal transition and cardiac fibroblast activation

Beneficial effects of sodium glucose co-transporter 2 inhibitors (SGLT2is) in cardiovascular diseases have been extensively reported leading to the inclusion of these drugs in the treatment guidelines for heart failure. However, molecular actions especially on non-myocyte cells remain uncertain. We observed dose-dependent inhibitory effects of two SGLT2is, dapagliflozin (DAPA) and empagliflozin (EMPA), on inflammatory signaling in human umbilical vein endothelial cells (HUVECs). Proteomics analyses and subsequent enrichment analyses discovered profound effects of these SGLT2is on proteins involved in mitochondrial respiration and actin cytoskeleton. Validation in functional oxygen consumption measurements as well as tube formation and migration assays revealed strong impacts of DAPA. Considering that most influenced parameters played central roles in endothelial to mesenchymal transition (EndMT), we performed in vitro EndMT assays and identified substantial reduction of mesenchymal and fibrosis marker expression as well as changes in cellular morphology upon treatment with SGLT2is. In line, human cardiac fibroblasts (HCFs) exposed to DAPA showed less proliferation, reduced ATP production, and decelerated migration capacity while less extensive impacts were observed upon EMPA. Mechanistically, sodium proton exchanger 1 (NHE1) as well as sodium-myoinositol cotransporter (SMIT) and sodium-multivitamin cotransporter (SMVT) could be identified as relevant targets of SGLT2is in non-myocyte cardiovascular cells as validated by individual siRNA-knockdown experiments. In summary, we found comprehensive beneficial effects of SGLT2is on human endothelial cells and cardiac fibroblasts. The results of this study therefore support a distinct effect of selected SGLT2i on non-myocyte cardiovascular cells and grant further insights into potential molecular mode of action of these drugs.

pharmacology and toxicology↗

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↗

ASBAR: an Animal Skeleton-Based Action Recognition framework. Recognizing great ape behaviors in the wild using pose estimation with domain adaptation.

The study and classification of animal behaviors have traditionally relied on direct human observation or video analysis, processes that are labor-intensive, time-consuming, and prone to human bias. Advances in machine learning for computer vision, particularly in pose estimation and action recognition, offer transformative potential to enhance the understanding of animal behaviors. However, the integration of these technologies for behavior recognition remains underexplored, particularly in natural settings. We introduce ASBAR (Animal Skeleton-Based Action Recognition), a novel framework that integrates pose estimation and behavior recognition into a cohesive pipeline. To demonstrate its utility, we tackled the challenging task of classifying natural behaviors of great apes in the wild. Our approach leverages the OpenMonkeyChallenge dataset, one of the largest open-source primate pose datasets, to train a robust pose estimation model using DeepLabCut. Subsequently, we extracted skeletal motion data from the PanAf500 dataset, a collection of in-the-wild videos of gorillas and chimpanzees annotated with nine behavior categories. Using PoseConv3D from MMAction2, we trained a skeleton-based action recognition model, achieving a Top-1 accuracy of 75.3%. This performance is comparable to previous video-based methods while reducing input data size by approximately 20-fold, offering significant advantages in computational efficiency and storage. To support further research, we provide an open-source, terminal-based GUI for training and evaluation, along with a dataset of 5,440 annotated keypoints for replication and extension to other species and behaviors. All models, code, and data are publicly available at: https://github.com/MitchFuchs/asbar

animal behavior and cognition↗

Increased beta2-adrenergic signaling is a targetable stimulus essential for bone healing by promoting callus neovascularization

Traumatic brain injury (TBI) is associated with a hyperadrenergic state and paradoxically causes systemic bone loss while accelerating fracture healing. Here, we identify the beta2-adrenergic receptor (Adrb2) as a central mediator of these skeletal manifestations. While the negative effects of TBI on the unfractured skeleton can be explained by the established impact of Adrb2 signaling on bone formation, Adrb2 promotes neovascularization of the fracture callus under conditions of high sympathetic tone, including TBI and advanced age. Mechanistically, norepinephrine stimulates the expression of Vegfa and Cgrp primarily in periosteal cells via Adrb2, both of which synergistically promote the formation of osteogenic type-H vessels in the fracture callus. Accordingly, the beneficial effect of TBI on bone repair is abolished in mice lacking Adrb2 or Cgrp, and aged Adrb2-deficient mice without TBI develop fracture nonunions despite high bone formation in uninjured bone. Pharmacologically, the Adrb2 antagonist propranolol impairs, and the agonist formoterol promotes fracture healing in aged mice by regulating callus neovascularization. Clinically, intravenous beta-adrenergic sympathomimetics are associated with improved callus formation in trauma patients with long bone fractures. Thus, Adrb2 is a novel target for promoting bone healing, and widely used beta-blockers may cause fracture nonunion under conditions of increased sympathetic tone. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/548550v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@cea57corg.highwire.dtl.DTLVardef@d29642org.highwire.dtl.DTLVardef@186ea5aorg.highwire.dtl.DTLVardef@83eaae_HPS_FORMAT_FIGEXP M_FIG Artwork was created in BioRender. C_FIG

cell biology↗

Characterization of cotton virus A, a novel and distinct member of the genus Caulimovirus with endogenous viral elements in Gossypium spp.

The complete genome sequence of cotton virus A, a new virus infecting cotton (Gossypium spp.), was determined using high-throughput sequencing, PCR and rolling circle amplification. The 7,482-nt genome is a circular dsDNA molecule that codes for six open reading frames similar to other members of the Caulimovirus genus (family Caulimoviridae) but presenting key genome organization differences. P3, P5 and P6 are presumed movement, coat, and reverse transcriptase proteins, respectively. P1, P2 and P4 showed no homology to virus proteins. Endogenous viral elements were found in G. hirsutum and G. tomentosum, but not in G. barbadense, G. arboreum, or G. herbaceum.

plant biology↗

A network of small RNAs regulates sporulation initiation in C. difficile

The obligate anaerobic, enteric pathogen Clostridioides difficile persists in the intestinal tract by forming antibiotic resistant endospores that contribute to relapsing and recurrent infections. Despite the importance of sporulation for C. difficile pathogenesis, environmental cues, and molecular mechanisms regulating sporulation initiation remain ill defined. Here, using RIL-seq to capture the Hfq-dependent RNA-RNA interactome, we discovered a network of small RNAs that bind to mRNAs encoding sporulation-related genes. We show that two of these small RNAs, SpoX and SpoY, regulate translation of the master regulator of sporulation, Spo0A, in an opposing manner, which ultimately leads to altered sporulation rates. Infection of antibiotic-treated mice with SpoX and SpoY deletion mutants revealed a global effect on gut colonization and intestinal sporulation. Our work uncovers an elaborate RNA-RNA interactome controlling the physiology and virulence of C. difficile and identifies a complex post-transcriptional layer in the regulation of spore formation in this important human pathogen.

molecular biology↗

VPRBP functions downstream of the androgen receptor and OGT to restrict p53 activation in prostate cancer

A comprehensive understanding of androgen receptor (AR) signalling mechanisms during prostate carcinogenesis is instrumental in developing novel therapies. Studies have shown glycosylation as a key androgen regulated process and that O-GlcNAc transferase (OGT), the enzyme that catalyses the covalent addition of UDP-N-acetylglucosamine (UDP-GlcNAc) to serine and threonine residues of proteins, is often up-regulated in prostate cancer (PCa) with its expression correlated with high Gleason score. In this study we have identified an AR and OGT co-regulated factor, VPRBP also known as DCAF1. We show that VPRBP is regulated by the AR at the transcript level, and stabilized by OGT at the protein level. VPRBP knockdown in PCa cells led to a significant decrease in cell proliferation, p53 stabilization, nucleolar fragmentation and increased p53 recruitment to the chromatin. In human prostate tumor samples, VPRBP protein overexpression correlated with AR amplification, OGT overexpression, early biochemical relapse and poor clinical outcome. Analysis of TCGA datasets found a positive correlation of VPRBP with AR mRNA expression. Furthermore, AR activity gene signature analysis revealed a positive correlation of VPRBP with a subset of AR target genes implying that VPRBP has a preferential regulatory impact on part of the AR regulome. In conclusion, we have shown that VPRBP/DCAF1 promotes PCa cell proliferation by restraining p53 activation under the influence of the AR and OGT as well as uncovered a unique subset of AR activity gene signature that correlates with VPRBP expression with the potential for new avenues for patient stratification and treatment.

cancer biology↗

Probing cortical excitability under GABAergic modulation

Cortical excitability, the variable response to a given cortical input, is widely studied in neuroscience, from slice experiments and in silico modeling work to human clinical settings. However, a unifying definition and a translational approach to the phenomenon are currently lacking. For example, at the onset of epileptic seizures, cortical excitability may impair resilience to perturbations (external or endogenous). In this study, we tested in vivo whether changes in cortical excitability quantified as evoked response to small perturbation corresponded to changes in resilience to larger perturbations. To do so, we used both cell-type circuit specific optogenetic stimulation in mice and direct intracranial stimulation in one human subject and quantified 1) evoked cortical responses to single pulses of varying intensity, and 2) evoked cortical facilitation and suppression to paired pulses at varying intervals. In the presence of a gamma-Aminobutyric acid (GABA) agonist or antagonist, we found that 1) cortical response to single pulses and 2) cortical facilitation decreased and increased, respectively. Additionally, using trains of opto-pulses in mice in the presence of a GABA agonist, we found increased resilience to the induction of seizures. With this study, we provide evidence for a tight correlation between cortical excitability and resilience, exploring a range of cortical dynamics, from physiological excitability, to pathological discharges. Our study carried out with two different stimulation methods in two species suggests that varying cortical excitability can be tracked with simple protocols involving minute short-lived perturbative stimuli.

neuroscience↗

Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking

The SARS-CoV-2 macrodomain (Mac1) within the non-structural protein 3 (Nsp3) counteracts host-mediated antiviral ADP-ribosylation signalling. This enzyme is a promising antiviral target because catalytic mutations render viruses non-pathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of diverse fragment libraries resulted in 214 unique macrodomain-binding fragments, out of 2,683 screened. An additional 60 molecules were selected from docking over 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several crystallographic and docking fragment hits were validated for solution binding using three biophysical techniques (DSF, HTRF, ITC). Overall, the 234 fragment structures presented explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.

biochemistry↗

An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important Gram-positive bacterium

The Gram-positive human pathogen Clostridioides difficile has emerged as the leading cause of antibiotic-associated diarrhea. Despite growing evidence for a role of Hfq in RNA-based gene regulation in C. difficile, little is known about the bacteriums transcriptome architecture and mechanisms of post-transcriptional control. Here, we have applied a suite of RNA-centric techniques, including transcription start site mapping, transcription termination mapping and Hfq RIP-seq, to generate a single-nucleotide resolution RNA map of C. difficile 630. Our transcriptome annotation provides information about 5 and 3 untranslated regions, operon structures and non-coding regulators, including 42 sRNAs. These transcriptome data are accessible via an open-access browser called Clost-Base. Our results indicate functionality of many conserved riboswitches and predict novel cis-regulatory elements upstream of MDR-type ABC transporters and transcriptional regulators. Recent studies have revealed a role of sRNA-based regulation in several Gram-positive bacteria but their involvement with the RNA-binding protein Hfq remains controversial. Here, sequencing the RNA ligands of Hfq reveals in vivo association of many sRNAs along with hundreds of potential target mRNAs in C. difficile providing evidence for a global role of Hfq in post-transcriptional regulation in a Gram-positive bacterium. Through integration of Hfq-bound transcripts and computational approaches we predict regulated target mRNAs for the novel sRNA AtcS encoding several adhesins and the conserved oligopeptide transporter oppB that influences sporulation initiation in C. difficile. Overall, these findings provide a potential mechanistic explanation for increased biofilm formation and sporulation in an hfq deletion strain and lay the foundation for understanding clostridial ribo regulation with implications for the infection process.

microbiology↗

Metformin rescues muscle function in BAG3 myofibrillar myopathy models

Dominant de novo mutations in the co-chaperone BAG3 cause a severe form of myofibrillar myopathy, exhibiting progressive muscle weakness, muscle structural failure, and protein aggregation.\n\nTo identify therapies we generated two zebrafish models, one conditionally expressing BAG3P209L and one with a nonsense mutation in bag3. Whilst transgenic BAG3P209L expressing fish display protein aggregation, modelling the early phase of the disease, bag3-/- fish demonstrate impaired autophagic activity, exercise dependent fibre disintegration, and reduced swimming activity, consistent with later stages.\n\nWe confirmed the presence of impaired autophagy in patient samples and screened autophagy promoting compounds for their effectiveness at removing protein aggregates, identifying nine including Metformin. Further evaluation demonstrated Metformin is not only able to remove the protein aggregates in zebrafish and human myoblasts but is also able to rescue the fibre disintegration and swimming deficit observed in the bag3-/- fish. Therefore, repurposing Metformin provides a promising therapy for BAG3 myopathy.

genetics↗

Altered resting state functional connectivity in a thalamo-cortico-cerebellar network in patients with schizophrenia

Schizophrenia is described as a disease in which complex psychopathology together with cognitive and behavioral impairments are related to widely disrupted brain circuitry causing a failure in coordinating information across multiple brain sites. This led to the hypothesis of schizophrenia as a network disease e.g. in the cognitive dysmetria model and the dysconnectivity theory. Nevertheless, there is no consensus regarding localized mechanisms, namely dysfunction of certain networks underlying the multifaceted symptomatology.\n\nIn this study, we investigated potential functional disruptions in 35 schizophrenic patients and 41controls using complex cerebral network analysis, namely network-based statistic (NBS) and graph theory in resting state fMRI. NBS can reveal locally impaired subnetworks whereas graph analysis characterizes whole brain network topology.\n\nUsing NBS we observed a local hyperconnected thalamo-cortico-cerebellar subnetwork in the schizophrenia group. Furthermore, nodal graph measures retrieved from the thalamo-cortico-cerebellar subnetwork revealed that the total number of connections from/to (degree) of the thalamus is higher in patients with schizophrenia. Interestingly, graph analysis on the whole brain functional networks did not reveal group differences. Together, our results suggest that disruptions in the brain networks of schizophrenia patients are situated at the local level of the hyperconnected thalamo-cortico-cerebellar rather than globally spread in brain.\n\nOur results provide further evidence for the importance of the thalamus and cerebellum in schizophrenia and to the notion that schizophrenia is a network disease in line with the dysconnectivity theory and cognitive dysmetria model.

neuroscience↗