Biology subjects

Stahl, K.

Publications and source records attributed to Stahl, K..

6 recordsLinked to original sources

bioRxiv2024

Molecular insights into dynamic protein structures by high-contrast crosslinking mass spectrometry

Proteins are comprised of structured domains and dynamic regions, and both are essential for biological function. However, studying dynamic regions is challenging using most structural biology methods, including crosslinking mass spectrometry. Here, we dramatically improve the usefulness of distance restraints from crosslinking MS by taking advantage of short-lived reactive species generated from diazirine-based photo-crosslinking. This leads to a clear view of complex topologies and conformational changes, including in dynamic regions. We demonstrate that photo-crosslinking MS data can be used to model flexible regions and conformational changes in the DNA repair complexes; Fanconi Anemia core complex and FANCD2-FANCI. In addition, we obtain new insights into the architecture and arrangement of the highly flexible CCR4-NOT mRNA deadenylation complex. The improved contrast of photo-crosslinking empowers structural biology by providing clearer structural insights into dynamic biological systems that have eluded other structural biology approaches.

molecular biology↗

bioRxiv2024

Forest dieback in drinking water protection areas - a hidden threat to water quality

For centuries, forests have been considered a natural safeguard for drinking water quality. We challenge this view in light of the rising frequency of climate extremes, such as droughts coinciding with high temperatures, which have caused unprecedented pulses of forest dieback globally. Drought-induced forest diebacks may jeopardize the crucial role of forests in protecting water quality, potentially even turning forests into sources of contamination. To underscore the critical importance of the topic, here we provide the first comprehensive assessment of forest cover, type, and dieback (assessed as canopy cover loss) across drinking Water Protection Areas (WPAs) in Germany, one of the countries hit most severely by the unprecedented Central European drought of 2018-2020. Our findings reveal a high forest cover of 43% in WPAs, from which a substantial amount of 5% canopy cover got lost within only three years as a direct or indirect consequence of the drought. Spruce-dominated forests, constituting 28% of all forests in WPAs, were particularly susceptible, but other dominant tree species also experienced anomalously high mortality rates. Combining this assessment with exemplary records of nitrate concentrations in the groundwater of WPAs revealed that forest dieback can significantly impair drinking quality. On average, nitrate concentrations more than doubled in WPAs with severe forest dieback, whereas nitrate concentrations did not significantly change in undisturbed WPAs. However, we also found pronounced differences between WPAs affected by forest dieback, underlining the need for further data and research to derive a generalizable understanding of the underlying mechanisms and controls. Based on this assessment, we deduce critical data and knowledge gaps essential to developing well-informed prediction, adaptation, and mitigation strategies. We call for interdisciplinary research addressing the hidden threat forest dieback poses for our drinking water resources.

biochemistry↗

bioRxiv2023

Control of iron homeostasis by a regulatory protein-protein interaction in Bacillus subtilis: The FurA (YlaN) acts as an antirepressor to the ferric uptake regulator Fur

Iron is essential for most organisms. However, two problems are associated with the use of iron for aerobically growing organisms: (i) its accumulation leads to the formation of toxic reactive oxygen species and (ii) it is present mainly as the highly insoluble ferric iron which makes the access to iron difficult. As a consequence, a tight regulation of iron homeostasis is required. This regulation is achieved in many bacteria by the ferric uptake repressor Fur. The way how the activity of Fur is controlled, has so far remained elusive. Here, we have identified the Fur antirepressor FurA (previously YlaN) in the model bacterium Bacillus subtilis and describe its function to release Fur from the DNA under conditions of iron limitation. The FurA protein physically interacts with Fur, and this interaction prevents Fur from binding to its target sites due to a complete re-orientation of the protein. Both in vivo and in vitro experiments using a reporter fusion and Fur-DNA binding assays, respectively, demonstrate that the Fur-FurA interaction prevents Fur from binding DNA and thus from repressing the genes required for iron uptake. Accordingly, the lack of FurA results in the inability of the cell to express the genes for iron uptake under iron-limiting conditions. This explains why the furA gene was identified as being essential under standard growth conditions in B. subtilis. Phylogenetic analysis suggests that the control of Fur activity by the antirepressor FurA is confined to, but very widespread in bacteria of the class Bacilli. IMPORTANCEIron is essential for most bacteria since it is required for many redox reactions. Under aerobic conditions, iron is both essential and toxic due to radical formation. Thus, iron homeostasis must be faithfully controlled. The transcription factor Fur is responsible for this regulation in many bacteria; however, the control of Fur activity has remained open. Here we describe the FurA protein, a so far unknown protein which acts as an antirepressor to Fur in Bacillus subtilis. This mechanism seems to be widespread in B. subtilis and several important pathogens and might be a promising target for drug development.

microbiology↗

bioRxiv2023

Modelling protein complexes with crosslinking mass spectrometry and deep learning

Scarcity of structural and evolutionary information on protein complexes poses a challenge to deep learning-based structure modelling. We integrated experimental distance restraints obtained by crosslinking mass spectrometry (MS) into AlphaFold-Multimer, by extending AlphaLink to protein complexes. Integrating crosslinking MS data substantially improves modelling performance on challenging targets, by helping to identify interfaces, focusing sampling, and improving model selection. This extends to single crosslinks from whole-cell crosslinking MS, opening the possibility of whole-cell structural investigations driven by experimental data. We demonstrate this by revealing the molecular basis of iron homeostasis in Bacillus subtilis.

bioinformatics↗

bioRxiv2022

Development and application of a computable genotype model in the GA4GH Variation Representation Specification

As the diversity of genomic variation data increases with our growing understanding of the role of variation in health and disease, it is critical to develop standards for precise inter-system exchange of these data for research and clinical applications. The Global Alliance for Genomics and Health (GA4GH) Variation Representation Specification (VRS) meets this need through a technical terminology and information model for disambiguating and concisely representing variation concepts. Here we discuss the recent Genotype model in VRS, which may be used to represent the allelic composition of a genetic locus. We demonstrate the use of the Genotype model and the constituent Haplotype model for the precise and interoperable representation of pharmacogenomic diplotypes, HGVS variants, and VCF records using VRS and discuss how this can be leveraged to enable interoperable exchange and search operations between assayed variation and genomic knowledgebases.

bioinformatics↗

bioRxiv2019

Heparanase-2 protects from endothelial injury by inhibiting TLR4 signaling

ObjectiveThe endothelial glycocalyx and the regulation of its shedding are important to vascular health. Endo-{beta}-D-glucuronidase heparanase-1 (HPSE1) is the only enzyme that can shed heparan sulfate. However, the mechanisms are not well understood.\n\nApproach and resultsTo investigate HPSE1 and its endogenous inhibitor, heparanase-2 (HPSE2), we used cell culture, lentiviral protein overexpression, a microfluidic chip model of cell culture under shear stress conditions, and lipopolysaccharide (LPS) injections in mice. We show that HPSE1 activity aggravated Toll-like receptor 4 (TLR4)-mediated response of endothelial cells to LPS. On the contrary, HPSE2 overexpression was protective. The microfluidic chip flow model confirmed that HPSE2 prevented heparan sulfate shedding by HPSE1. Furthermore, heparan sulfate did not interfere with cluster of differentiation-14 (CD14)-dependent LPS binding, but instead reduced the presentation of the LPS-CD14 complex to TLR4. HPSE2 reduced LPS-mediated TLR4 activation by LPS, subsequent cell signaling, and cytokine expression. Moreover, HPSE2-overexpressing endothelial cells remained protected against LPS-mediated loss of cell-cell contacts. In vivo, expression of HPSE2 in plasma and kidney medullary capillaries was decreased in mouse sepsis model. We next applied purified HPSE2 in mice and observed decreases in TNF and IL-6 plasma concentrations after intravenous LPS injections.\n\nConclusionsOur data demonstrate the important role of heparan sulfate and the glycocalyx in endothelial cell activation and suggest a protective role of HPSE2 in microvascular inflammation. HPSE2 offers new options for protection against HPSE1-mediated endothelial damage and preventing microvascular disease.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC=\"FIGDIR/small/705939v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (50K):\norg.highwire.dtl.DTLVardef@1bae526org.highwire.dtl.DTLVardef@11a6039org.highwire.dtl.DTLVardef@a36deforg.highwire.dtl.DTLVardef@1869ea8_HPS_FORMAT_FIGEXP M_FIG Graphical abstract\n\nC_FIG O_TBL View this table:\norg.highwire.dtl.DTLVardef@11a3deborg.highwire.dtl.DTLVardef@1d71919org.highwire.dtl.DTLVardef@b0c8a3org.highwire.dtl.DTLVardef@4477f3org.highwire.dtl.DTLVardef@11f1588_HPS_FORMAT_FIGEXP M_TBL O_TABLECAPTIONNon standard abbreviations\n\nC_TABLECAPTION C_TBL

cell biology↗