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Becker, S.

Publications and source records attributed to Becker, S..

At least 55 records · Page 3Linked to original sources

Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression

Some transcription factors (TFs) can form liquid-liquid phase separated (LLPS) condensates. However, the functions of these TF condensates in 3D genome organization and gene regulation remain elusive. In response to methionine (met) starvation, budding yeast TF Met4 and a few co-activators, including Met32, induce a set of genes involved in met biosynthesis. Here, we show that the endogenous Met4 and Met32 form co-localized puncta-like structures in yeast nuclei upon met depletion. Recombinant Met4 and Met32 form mixed droplets with LLPS properties in vitro. In relation to chromatin, Met4 puncta co-localize with target genes, and at least a subset of these target genes is clustered in 3D in a Met4-dependent manner. A MET3pr-GFP reporter inserted near several native Met4 binding sites becomes co-localized with Met4 puncta and displays enhanced transcriptional activity. A Met4 variant with a partial truncation of an intrinsically disordered region (IDR) shows less puncta formation, and this mutant selectively reduces the reporter activity near Met4 binding sites to the basal level. Overall, these results support a model where Met4 and co-activators form condensates to bring multiple target genes into a vicinity with higher local TF concentrations, which facilitates a strong response to methionine depletion.

genetics↗

Purine nucleosides replace cAMP in allosteric regulation of PKA in trypanosomatid pathogens

Cyclic nucleotide binding domains (CNB) confer allosteric regulation by cAMP or cGMP to many signalling proteins, including PKA and PKG. PKA of phylogenetically distant Trypanosoma is the first exception as it is cyclic nucleotide-independent and responsive to nucleoside analogues (Bachmaier et al. 2019). Here we show that natural nucleosides inosine, guanosine and adenosine are nanomolar affinity CNB ligands and activators of PKA orthologs of the important tropical pathogens T. brucei, T. cruzi and Leishmania. The sequence and structural determinants of binding affinity, -specificity and kinase activation of PKAR were established by structure-activity relationship (SAR) analysis, co-crystal structures and mutagenesis. Substitution of 2-3 amino acids in the binding sites is sufficient for conversion of CNB domains from nucleoside to cyclic nucleotide specificity. In addition, a trypanosomatid-specific C-terminal helix (D) is required for high affinity binding to CNB-B. The D helix functions as a lid of the binding site that shields ligands from solvent. Selectivity of guanosine for CNB-B and of adenosine for CNB-A results in synergistic kinase activation at low nanomolar concentration. PKA pulldown from rapid lysis establishes guanosine as the predominant ligand in vivo in T. brucei bloodstream forms, whereas guanosine and adenosine seem to synergize in the procyclic developmental stage in the insect vector. We discuss the versatile use of CNB domains in evolution and recruitment of PKA for novel nucleoside-mediated signalling.

biochemistry↗

Direct Antigen Presentation is the Canonical Pathway of Cytomegalovirus CD8 T-cell Priming Regulated by Balanced Immune Evasion Mounting a Strong Antiviral Response

CD8 T cells are the main antiviral effectors of the adaptive immune response to cytomegaloviruses (CMVs) in confining acute infection and in long-term surveillance of latent infection. An unresolved issue of debate, with diametrically opposite conclusions, is the mechanism by which CMV-specific naive CD8 T cells are primed. The idea of priming by antigen cross-presentation through uninfected professional antigen presenting cells taking up viral proteins derived from infected cells was based on the observation that the net response is not improved when direct presentation is enhanced by deletion of viral immune evasion genes affecting the classical MHC class-I pathway of antigen presentation. Redundance of priming mechanisms has been demonstrated by experimental models in which either pathway has been rendered inaccessible, so that both pathways are, in principle, capable of priming CD8 T cells. For studying CMV-specific priming in the normal host competent in both antigen presentation pathways, we took the novel approach to enhance instead of delete immune evasion protein expression. Surprisingly, the net magnitude of the CD8 T-cell response in the regional lymph node draining a local site of infection was identical for the contrasts of reduced or enhanced direct antigen presentation. At first glance, this may lead one to conclude that direct presentation plays no role in priming. This interpretation, however, is incompatible with the finding that an intermediate extent of direct antigen presentation, as it exists for wild-type virus, resulted in the best CD8 T-cell response. Our findings thus revealed an essential positive role of a balanced viral immune evasion in mounting a strong antiviral immune response. This novel insight sheds a completely new light on the acquisition of viral immune evasion genes during virus-host co-evolution.

immunology↗

Immunotherapy of cytomegalovirus infection by low-dose adoptive transfer of antiviral CD8 T cells relies on substantial post-transfer expansion of central memory cells but not effector-memory cells

Cytomegaloviruses (CMVs) are host species-specific in their replication. It is a hallmark of all CMVs that productive primary infection is controlled by concerted innate and adaptive immune responses in the immunocompetent host. As a result, the infection usually passes without overt clinical symptoms and develops into latent infection, referred to as latency. During latency, the virus is maintained in a non-replicative state from which it can reactivate to productive infection under conditions of waning immune surveillance. In contrast, infection of an immunocompromised host causes CMV disease with viral multiple-organ histopathology resulting in organ failure. Primary or reactivated CMV infection of hematopoietic cell transplantation (HCT) recipients in a "window of risk" between therapeutic hematoablative leukemia therapy and immune system reconstitution remains a clinical challenge. Studies in the mouse model of experimental HCT and infection with murine CMV (mCMV), followed by clinical trials in HCT patients with human CMV (hCMV) reactivation, have revealed a protective function of virus-specific CD8 T cells upon adoptive cell transfer (AT). Memory CD8 T cells derived from latently infected hosts are a favored source for immunotherapy by AT. Strikingly low numbers of these cells were found to prevent CMV disease, suggesting either an immediate effector function of few transferred cells or a clonal expansion generating high numbers of effector cells. In the murine model, the memory population consists of resting central memory T cells (TCM), as well as of conventional effector-memory T cells (cTEM) and inflationary effector-memory T cells (iTEM). iTEM, increase in numbers over time in the latently infected host, a phenomenon known as memory inflation (MI). They thus appeared to be a promising source for use in immunotherapy. However, we show here that iTEM contribute little to the control of infection after AT, which rests almost exclusively on a superior proliferation potential of TCM. Author SummaryImmunotherapy of reactivated cytomegalovirus infection in immunocompromised HCT recipients by adoptive transfer (AT) of antiviral CD8 T cells is the last resort to fight virus variants that have acquired resistance to standard antiviral drugs. Provision of cell numbers high enough for clearance of productive infection remains a logistical limitation for AT to become clinical routine. Although use of donor memory CD8 T cells has become the standard in clinical AT, little is known about the relative antiviral efficacies of memory CD8 T-cell activation subsets, such as central memory cells (TCM) and different populations of effector-memory cells (TEM). A reliable quantitative comparison of the antiviral efficacies of memory CD8 T-cell subsets is precluded in clinical investigation, because independent cohorts of AT donors and AT recipients unavoidably differ in many genetical, immunological, and virological variables. Therefore, this is a question for which a preclinical animal model is predestined. We show here in the well-established mouse model of low-dose AT that CMV infection is by far most efficiently controlled by virus-specific TCM, based on a superior potential to proliferate even in extra-lymphoid tissue to prevent virus spread. For clinical AT, our data provide an argument to favor transfer of sorted TCM rather than TEM.

immunology↗

Transcription factors operate on a limited vocabulary of binding motifs in Arabidopsis thaliana

Predicting gene expression from promoter sequence requires understanding of the different signal integration points within a promoter. Sequence-specific transcription factors (TFs) binding to their cognate TF binding motifs control gene expression in eukaryotes by activating and repressing transcription. Their interplay generates complex expression patterns in reaction to environmental conditions and developmental cues. We hypothesized that signals are not only integrated by different TFs binding various positions in a promoter, but also by single TF binding motifs onto which multiple TFs can bind. Analyzing 2,190 binding motifs, we identified only 76 core TF binding motifs in plants. Twenty-one TF protein families act highly specific and bind a single conserved motif. Four TF families are classified as semi-conserved as they bind up to four motifs within a family, with divisions along phylogenetic groups. Five TF families bind diverse motifs. Expression analyses revealed high competition within TF families for the same binding motif. The results show that singular binding motifs act as signal integrators in plants where a combination of binding affinity and TF abundance likely determine the output.

systems biology↗

Autoinhibition in the Signal Transducer CIN85 Modulates B Cell Activation

Signal transduction by the ligated B cell antigen receptor (BCR) depends on the pre-organization of its intracellular components, such as the effector proteins SLP65 and CIN85 within phase-separated condensates. These liquid-like condensates are based on the interaction between three Src homology 3 (SH3) domains and corresponding proline-rich recognition motifs (PRM) in CIN85 and SLP65, respectively. However, detailed information on the protein conformation and how it impacts on the capability of SLP65/CIN85 condensates to orchestrate BCR signal transduction is still lacking. This study identifies a hitherto unknown intramolecular SH3:PRM interaction between the C-terminal SH3 domain (SH3C) of CIN85 and an adjacent PRM. We used high-resolution nuclear magnetic resonance (NMR) experiments to study the flexible linker region containing the PRM and determined the extent of the interaction in multidomain constructs of the protein. Moreover, we observed that the phosphorylation of a serine residue located in the immediate vicinity of the PRM regulates this intramolecular interaction. This allows for a dynamic modulation of CIN85s valency towards SLP65, regulating the extent of liquid-liquid phase separation. B cell culture experiments further revealed that the PRM/SH3C interaction is crucial for maintaining the physiological level of SLP65/CIN85 condensate formation, activation-induced membrane recruitment of CIN85, and subsequent mobilization of Ca2+. Our findings therefore suggest that the intramolecular interaction to the adjacent disordered linker is effective in modulating CIN85s valency both in vitro and in vivo. This therefore constitutes a powerful way for the modulation of SLP65/CIN85 condensate formation and subsequent B cell signaling processes within the cell.

biophysics↗

Quantitative description of the phase separation behavior of the multivalent SLP65-CIN85 complex

Biomolecular condensates play a major role in cell compartmentalization, besides membrane-enclosed organelles. The multivalent SLP65 and CIN85 proteins are downstream B cell receptor (BCR)-signaling effectors, required for a proper immune response. Both proteins phase separate together with vesicles to form pre-signaling clusters. Within this tripartite system, six PRMs of SLP65 interact promiscuously with three SH3 domains of the CIN85 monomer, establishing 18 individual SH3-PRM interactions whose individual dissociation constants we determined. Based on these 18 dissociation constants, we measured the phase separation properties of the natural SLP65/CIN85 system as well as designer constructs that emphasize the strongest SH3/PRM interactions. By modelling these various SLP65/CIN85 constructs with the program LASSI (LAttice simulation engine for Sticker and Spacer Interactions) we reproduced the observed phase separation properties. In addition, LASSI revealed a deviation in the experimental measurement, which was independently identified as a previously unknown intramolecular interaction. Thus, thermodynamic properties of the individual PRM/SH3 interactions allow to model the phase separation behavior of the SLP65/CIN85 system faithfully.

biophysics↗

Extracellular release of a disintegrin and metalloproteinases orchestrates periodontal disease severity

Periodontal diseases are amongst the most common pathologies worldwide with a high risk for the development of systemic complications. Periodontal disease is driven by oral pathogens such as Porphyromonas gingivalis and the release of inflammatory cytokines. These cytokines (e.g. TNF) or their receptors (IL-1R) are substrates of a disintegrin and metalloproteinases (ADAMs). In a comparative approach, we observed an increase of ADAM8 protein expression and activity in the sulcus fluid of periodontal disease patients correlating with the disease stage. In contrast, the induced ADAM10 expression was decreased. In vitro mechanistic studies revealed that both Porphyromonas gingivalis infection and the resulting cytokine release orchestrated the release of soluble ADAM8 by keratinocytes and neutrophils as soluble ectodomain and on exosomes, respectively. Furthermore, ADAM8 regulated the release of ADAM10 and MMP9, thereby potentially influencing wound healing and tissue destruction. Thus, the dysregulation of the cell-associated and extracellular ADAM proteolytic activity mainly driven by ADAM8 may be an essential regulatory element in periodontal disease onset and progression. This potential as novel local treatment option should be addressed in future translational studies.

immunology↗

Direct optical measurement of intra-molecular distances down to the Angstrom scale

Optical investigations of nanometer distances between proteins, their subunits, or other biomolecules have been the exclusive prerogative of Forster Resonance Energy Transfer (FRET) microscopy for decades. Here we show that MINFLUX fluorescence nanoscopy measures intra-molecular distances down to 1 nm - and in planar projections down to 1 Angstrom - directly, linearly, and with Angstrom precision. Our method is validated by quantifying well-characterized 1-to-10 nm distances in polypeptides and proteins. Moreover, we visualize the orientations of immunoglobulin subunits and reveal specific configurations of a histidine kinase domain dimer. Our results open the door for examining proximities and interactions of macromolecules under physiological conditions.

biophysics↗

Cryo-EM structures of lipidic fibrils of amyloid-β (1-40)

Alzheimers disease (AD) is a progressive and incurable neurodegenerative disease characterized by the extracellular deposition of amyloid plaques. Investigation into the composition of these plaques revealed a high amount of amyloid-{beta} (A{beta}) fibrils and a high concentration of lipids, suggesting that fibril-lipid interactions may also be relevant for the pathogenesis of AD. Therefore, we grew A{beta}40 fibrils in the presence of lipid vesicles and determined their structure by cryo-electron microscopy (cryo-EM) to high resolution. The fold of the major polymorph is similar to the structure of brain-seeded fibrils reported previously. The majority of the lipids are bound to the fibrils as we show by cryo-EM and NMR spectroscopy. This apparent lipid extraction from vesicles observed here in vitro provides structural insights into potentially disease-relevant fibril-lipid interactions.

molecular biology↗

Real-time tracking of drug binding to Influenza A M2 reveals a high energy barrier

The drug Rimantadine binds to two different sites in the M2 protein from influenza A, a peripheral site and a pore site that is the primary site of efficacy. It remained enigmatic that pore binding did not occur in certain detergent micelles, and in particular incomplete binding was observed in a mixture of lipids selected to match the viral membrane. Here we show that two effects are responsible, namely changes in the protein upon pore binding that prevented detergent solubilization, and slow binding kinetics in the lipid samples. Using 55-100 kHz magic-angle spinning NMR, we characterize kinetics of drug binding in three different lipid environments: DPhPC, DPhPC with cholesterol and viral mimetic membrane lipid bilayers. Slow pharmacological binding kinetics allowed the characterization of spectral changes associated with non-specific binding to the protein periphery in the kinetically trapped pore-apo state. Resonance assignments were determined from a set of proton-detected 3D spectra. Chemical shift changes associated with functional binding in the pore of M2 were tracked in real time in order to estimate the activation energy. The binding kinetics are affected by pH and the lipid environment and in particular cholesterol. We found that the imidazole-imidazole hydrogen bond at residue histidine 37 is a stable feature of the protein across several lipid compositions. Pore binding breaks the imidazole-imidazole hydrogen bond and limits solubilization in DHPC detergent. Highlights5 {degrees}C kinetically traps Influenza A M2 (as dimer of dimers) in the apo form in vitro. Kinetic control allows characterization of non-specific chemical shift perturbation. Pore-bound M2 loses dissolvability in DHPC micelles, suggesting structural change. M2, residues 18-60, forms a dimer-of-dimers structure in several bilayer compositions.

biophysics↗

Post-infection treatment with the E protein inhibitor BIT225 reduces disease severity and increases survival of k18-hACE2 transgenic mice infected with a lethal dose of SARS-CoV-2

The Coronavirus envelope (E) protein is a small structural protein with ion channel activity that plays an important role in virus assembly, budding, immunopathogenesis and disease severity. The viroporin E is also located in Golgi and ER membranes of infected cells and is associated with inflammasome activation and immune dysregulation. Here we evaluated in vitro antiviral activity, mechanism of action and in vivo efficacy of BIT225 for the treatment of SARS-CoV-2 infection. BIT225 showed broad-spectrum direct-acting antiviral activity against SARS-CoV-2 in Calu3 and Vero cells with similar potency across 6 different virus strains. BIT225 inhibited ion channel activity of E-protein but did not inhibit endogenous calcium-induced ion channel activity or TMEM16A in Xenopus oocytes. BIT225 administered by oral gavage for 12 days starting 12 h before infection completely prevented body weight loss and mortality in SARS-CoV-2 infected K18 mice (100% survival, n=12), while all vehicle-dosed animals reached a mortality endpoint by day 9 across two studies (n=12). When treatment started at 24 h after infection, body weight loss, and mortality were also prevented (100% survival, n=5), while 4 of 5 mice maintained and increased body weight and survived when treatment started 48 hours after infection. Treatment efficacy was dependent on BIT225 dose and was associated with significant reductions in lung viral load (3.5 log10), virus titer (4000 pfu/ml) and lung and serum cytokine levels. These results validate viroporin E as a viable antiviral target and support the clinical study of BIT225 for treatment and prophylaxis of SARS-CoV-2 infection. AUTHORS SUMMARYAntiviral agents are highly important for the management of COVID-19. We need new antivirals, because available drugs have major drawbacks that limit their use and are threatened by drug resistance. This study demonstrates that the small molecule drug BIT225 is an inhibitor of an important viral ion channel (E-protein). E-protein is required for virus replication and is involved in eliciting inflammatory response to infection. Exacerbated inflammation is a hallmark of severe COVID-19 in mice and in humans. In a mouse model of severe SARS-CoV-2 infection, BIT225 treatment starting before or 24 hours after infection could protect all treated mice from developing disease, from experiencing weight loss and from death (100%, n=17), while all untreated mice developed severe disease, started to lose body weight from day 3 onwards and died within 9 days after infection. BIT225 treatment was associated with potent suppression of virus load, and reduced inflammation markers, consistent with effective clearance of the virus. These results are remarkable for the exceptionally high efficacy achieved with a new mechanism of action. BIT225 is a clinical stage drug candidate with an established human safety profile. These results support clinical evaluation of BIT225 for the treatment of human SARS-CoV-2 infection.

molecular biology↗

Mechanism of sensor kinase CitA transmembrane signaling

Membrane bound histidine kinases (HKs) are ubiquitous sensors of extracellular stimuli in bacteria. Here, we used solid-state NMR in conjunction with crystallography, solution NMR and distance measurements to investigate the transmembrane signaling mechanism of a paradigmatic citrate sensing membrane embedded HK, CitA. Citrate binding in the sensory extracytoplasmic PAS domain (PASp) causes the linker to transmembrane helix 2 (TM2) to adopt a helical conformation. This triggers a piston-like pulling of TM2 and a quaternary structure rearrangement in the cytosolic PAS domain (PASc). Crystal structures of PASc reveal both anti-parallel and parallel dimer conformations. An anti-parallel to parallel transition upon citrate binding agrees with interdimer distances measured in the lipid embedded protein using a site-specific 19F label in PASc. These data show how Angstrom scale structural changes in the sensor domain are transmitted across the membrane to be converted and amplified into a nm scale shift in the linker to the phosphorylation subdomain of the kinase. One-Sentence SummaryTransmembrane signal transduction of a PAS-domain containing histidine kinase occurs via a piston-like pulling of a transmembrane helix, and amplification by cytoplasmic PAS domain dimer rearrangement.

molecular biology↗

Now you see it: fixation-related electrical potentials during a free visual search task reveal the timing of visual awareness

It has been repeatedly claimed that emotional faces capture attention readily, and that they are processed without awareness. Yet some observations cast doubt on these assertions. Part of the problem may lie in the experimental paradigms employed. Here, we used a free viewing visual search task and simultaneously recorded electroencephalography and eye-movements. Fixation-related potentials were computed for fearful and neutral facial expressions, and the electrical response compared when participants were aware or unaware of the fixated stimulus. We showed that the P300 increased across repeated fixations on the unseen targets, culminating in a conscious report, likely reflecting evidence accumulation. Awareness of the stimulus was associated with electrical changes emerging at around 130 ms, with emotions of the stimulus being dissociated only after awareness had arisen. These results suggest that the earliest electrical correlate of awareness emerges at around 130 ms in visual search and that emotion processing requires visual awareness.

neuroscience↗

Modeling Single-Cell Dynamics Using Unbalanced Parameterized Monge Maps

Optimal Transport (OT) has proven useful to infer single-cell trajectories of developing biological systems by aligning distributions across time points. Recently, Parameterized Monge Maps (PMM) were introduced to learn the optimal map between two distributions. Here, we apply PMM to model single-cell dynamics and show that PMM fails to account for asymmetric shifts in cell state distributions. To alleviate this limitation, we propose Unbalanced Parameterised Monge Maps (UPMM). We first describe the novel formulation and show on synthetic data how our method extends discrete unbalanced OT to the continuous domain. Then, we demonstrate that UPMM outperforms well-established trajectory inference methods on real-world developmental single-cell data.

bioinformatics↗

Endogenous modulation of pain relief: evidence for dopaminergic but not opioidergic involvement

Relief of ongoing pain is a potent motivator of behavior, directing actions to escape from or reduce potentially harmful stimuli. Whereas endogenous modulation of pain events is well characterized, relatively little is known about the modulation of pain relief and its corresponding neurochemical basis. Here we studied pain modulation during a probabilistic relief-seeking task (a wheel of fortune gambling task), in which people actively or passively received reduction of a tonic thermal pain stimulus. We found that relief perception was enhanced by active decisions and unpredictability, and greater in high novelty-seeking trait individuals, consistent with a model in which relief is tuned by its informational content. We then probed the roles of dopaminergic and opioidergic signaling, both of which are implicated in relief processing, by embedding the task in a double-blinded cross-over design with administration of the dopamine precursor levodopa and the opioid receptor antagonist naltrexone. We found that levodopa, but not naltrexone, enhanced each of these information-specific aspects of relief modulation. These results show that dopaminergic signaling has a key role in modulating the perception of pain relief to optimize motivation and behavior.

neuroscience↗

The 3D structure of lipidic fibrils of α-synuclein

-synuclein (Syn) is abundant in neurons, but its misfolding and abnormal fibrillization are associated with severe neurodegenerative diseases. Although interactions between Syn and phospholipid membranes are relevant during Syn fibril assembly, insights into the interactions of Syn fibrils with phospholipids have remained elusive. Here, we present six novel polymorphic atomic structures of Syn fibrils aggregated in the presence of phospholipids. The structures reveal that phospholipids favor a novel protofilament fold, mediate an unusual arrangement of protofilaments, and fill the central cavities between the protofilaments. These findings provide a structural rationale for fibril-induced lipid extraction, a mechanism likely to be involved in the development of -synucleinopathies.

molecular biology↗

No substantial pre-existing B cell immunity against SARS-CoV-2 in healthy adults

Pre-existing immunity against SARS-CoV-2 may have critical implications for our understanding of COVID-19 susceptibility and severity. Various studies recently provided evidence of pre-existing T cell immunity against SARS-CoV-2 in unexposed individuals. In contrast, the presence and clinical relevance of a pre-existing B cell immunity remains to be fully elucidated. Here, we provide a detailed analysis of the B cell response to SARS-CoV-2 in unexposed individuals. To this end, we extensively investigated the memory B cell response to SARS-CoV-2 in 150 adults sampled pre-pandemically. Comprehensive screening of donor plasma and purified IgG samples for binding and neutralization in various functional assays revealed no substantial activity against SARS-CoV-2 but broad reactivity to endemic betacoronaviruses. Moreover, we analyzed antibody sequences of 8,174 putatively SARS-CoV-2-reactive B cells on a single cell level and generated and tested 158 monoclonal antibodies. None of the isolated antibodies displayed relevant binding or neutralizing activity against SARS-CoV-2. Taken together, our results show no evidence of relevant pre-existing antibody and B cell immunity against SARS-CoV-2 in unexposed adults.

immunology↗