Biology subjects

Schulte, U.

Publications and source records attributed to Schulte, U..

8 recordsLinked to original sources

bioRxiv2026

Super-resolution complexome of human mitochondria elucidates translocase, morphology and OXPHOS networks

Mitochondria function as cellular powerhouses and central hubs in metabolism, redox and stress reactions, signaling and apoptosis1-5. Defects of mitochondria lead to numerous human diseases1,6-8. The integration of mitochondrial proteins into complexes and networks is crucial for their function. Whereas the composition of the human mitochondrial proteome has been studied8,9, only limited information is available on the organization of the proteome into protein complexes and assemblies. Here we present a systematic mapping of the human mitochondrial complexome from HEK293T cells at super-resolution, resolving more than 7,000 abundance profile peaks of mitochondrial proteins. Proteins functioning in signaling, cell stress, protein biogenesis, turnover and membrane dynamics display particularly high complexities. High resolution and precise quantification enable discrimination between canonical constituents and non-stoichiometric regulatory interactors of the ATP synthase, major metabolite channels and import translocases. The complexome reveals membrane-spanning networks of protein insertase and morphology machinery, and co-assembly of protein import and export components at the major respiratory supercomplex, unraveling a multifunctional organization of mitochondrial machineries. This complexome represents a fully interactive resource for the systematic analysis of human mitochondrial machineries and interaction networks.

biochemistry↗

bioRxiv2025

Structural basis of ClC-3 inhibition by TMEM9 and PI(3,5)P2

The trafficking and activity of endosomes relies on the exchange of chloride ions and protons by members of the CLC family of chloride channels and transporters, whose mutations are associated with numerous diseases. Despite their critical roles, the mechanisms by which CLC transporters are regulated are poorly understood. Here, we show that two related accessory {beta}-subunits, TMEM9 and TMEM9B, directly interact with ClC-3, -4 and -5. Cryo-EM structures reveal that TMEM9 inhibits ClC-3 by sealing the cytosolic entrance to the Cl- ion pathway. Unexpectedly, we find that PI(3,5)P2 stabilizes the interaction between TMEM9 and ClC-3 and is required for proper regulation of ClC-3 by TMEM9. Collectively, our findings reveal that TMEM9 and PI(3,5)P2 collaborate to regulate endosomal ion homeostasis by modulating the activity of ClC-3.

cell biology↗

bioRxiv2024

A ternary Neurexin-T178-PTPR complex represents a core-module of neuronal synapse organization

The organization of cell-cell contacts is fundamental for multi-cellular life and operation of organs. Synapses, prototypic contact sites for neuronal communication, are key to brain function and work over the last decades identified multiple synaptic cell adhesion molecules (sCAMs) that drive their organization. Whether these sCAMs operate independently or in coordination through yet unknown linker proteins remained elusive. Here, we used a systematic large-scale multi-epitope affinity-purification approach combined with quantitative mass spectrometry and immuno-EM to comprehensively map trans-synaptic protein networks in the mouse brain. We discover a presynaptic core-module assembled from the two major sCAM families, Neurexins1-3 and LAR-type receptor protein tyrosine phosphatases (PTPRD,S,F), and the previously uncharacterized tetraspanin proteins T178A, B. These ternary Neurexin-T178-PTPR complexes form through their trans-membrane domains and assemble during biogenesis in the ER. Loss of T178B results in module dissociation, strong reduction of LAR-PTPRs and re-distribution of synaptic Neurexins. At synapses, the Neurexin-T178-PTPR module recruits stable and extended trans-synaptic protein networks with defined pre- and post-synaptic partners and secreted extracellular linkers. The network architecture robustly interlinks the distinct functional modules/machineries of the presynaptic active zone and establishes tight associations with XKR-type lipid scramblases and postsynaptic GABAergic and glutamatergic neurotransmitter receptors. Our data identify a universal presynaptic core-module for synaptic adhesion and trans-synaptic signaling in the mammalian brain.

neuroscience↗

bioRxiv2023

Role of the small protein Mco6 in the mitochondrial sorting and assembly machinery

The majority of mitochondrial precursor proteins are imported through the Tom40 {beta}-barrel channel of the translocase of the outer membrane (TOM). The sorting and assembly machinery (SAM) is essential for {beta}-barrel membrane protein insertion into the outer membrane and thus required for the assembly of the TOM complex. Here we demonstrate that the a-helical outer membrane protein Mco6 forms a complex with the mitochondrial distribution and morphology protein Mdm10 as part of the SAM machinery. Moreover, Mco6 also interacts with the subunit Mim1 of the mitochondrial import complex (MIM), which is itself required for the biogenesis of a-helical outer membrane proteins. MCO6 and MDM10 display a negative genetic interaction and a MCO6-MDM10 yeast double mutant contains reduced levels of TOM complex. Cells lacking Mco6 affect the levels of Mdm10 and MIM-subunits associated with assembly defects of the TOM complex. Thus, this work reveals a role of the SAMMco6 complex for the biogenesis of the mitochondrial outer membrane.

cell biology↗

bioRxiv2022

Erythrocyte invasion-neutralising antibodies prevent Plasmodium falciparum RH5 from binding to basigin-containing membrane protein complexes

Basigin is an essential host receptor for invasion of Plasmodium falciparum into human erythrocytes, interacting with parasite surface protein PfRH5. PfRH5 is a leading blood-stage malaria vaccine candidate and a target of growth-inhibitory antibodies. However, basigin is not alone on the erythrocyte surface. Instead, we show that it is exclusively found in one of two macromolecular complexes, bound predominantly to either plasma membrane Ca2+-ATPase 1/4, PMCA1/4, or monocarboxylate transporter 1, MCT1. PfRH5 binds to either of these complexes with a higher affinity than to isolated basigin ectodomain, making it likely that these are the physiological targets of PfRH5. PMCA-mediated Ca2+ export is not affected by PfRH5, ruling this out as the mechanism underlying changes in calcium flux at the interface between an erythrocyte and the invading parasite. However, our studies rationalise the function of the most effective growth inhibitory antibodies targeting PfRH5. While these antibodies do not reduce the binding of PfRH5 to monomeric basigin, they do reduce its binding to basigin-PMCA and basigin-MCT complexes. This indicates that the most effective PfRH5-targeting antibodies inhibit growth by sterically blocking the essential interaction of PfRH5 with basigin in its physiological context.

microbiology↗

bioRxiv2022

Conformational dynamics and target-dependent myristoyl switch of calcineurin B homologous protein 3

Calcineurin B homologous protein 3 (CHP3) is an EF-hand Ca2+-binding protein involved in regulation of cancerogenesis, cardiac hypertrophy and neuronal development via interactions with sodium/proton exchangers (NHEs) and signalling proteins. CHP3 binds Ca2+ with micromolar affinity providing the basis to respond to intracellular Ca2+ signals. Ca2+ binding and myristoylation are important for CHP3 function but the underlying molecular mechanism remained elusive. Here, we show that Ca2+ binding and myristoylation independently affect conformational dynamics and functions of human CHP3. Ca2+ binding increased flexibility and hydrophobicity of CHP3 indicative of an open conformation. CHP3 in open Ca2+-bound conformation had higher affinity for NHE1 and associated stronger with lipid membranes compared to the closed Mg2+-bound conformation. Myristoylation enhanced flexibility of CHP3 and decreased its affinity to NHE1 independently of the bound ion, but did not affect its binding to lipid membranes. The data exclude the proposed Ca2+-myristoyl switch for CHP3. Instead, they document a Ca2+-independent exposure of the myristoyl moiety induced by binding of the target peptide to CHP3 enhancing its association to lipid membranes. We name this novel regulatory mechanism "target-dependent myristoyl switch". Taken together, the interplay of Ca2+ binding, myristoylation and target binding allows for a context-specific regulation of CHP3 functions.

biochemistry↗

bioRxiv2021

Population genomics of wall lizards reflects the dynamic history of the Mediterranean Basin

The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an "Out-of-Italy" expansion following the Messinian salinity crisis (~5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian and Balkan peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flow have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.

evolutionary biology↗

bioRxiv2020

CEDAR, an online resource for the reporting and exploration of complexome profiling data

Complexome profiling is an emerging omics approach that systematically interrogates the composition of protein complexes (the complexome) of a sample, by combining biochemical separation of native protein complexes with mass-spectrometry based quantitation proteomics. The resulting fractionation profiles hold comprehensive information on the abundance and composition of the complexome, and have a high potential for reuse by experimental and computational researchers. However, the lack of a central resource that provides access to these data, reported with adequate descriptions and an analysis tool, has limited their reuse. Therefore, we established the ComplexomE profiling DAta Resource (CEDAR, www3.cmbi.umcn.nl/cedar/), an openly accessible database for depositing and exploring mass spectrometry data from complexome profiling studies. Compatibility and reusability of the data is ensured by a standardized data and reporting format containing the "minimum information required for a complexome profiling experiment" (MIACE). The data can be accessed through a user-friendly web interface, as well as programmatically using the REST API portal. Additionally, all complexome profiles available on CEDAR can be inspected directly on the website with the profile viewer tool that allows the detection of correlated profiles and inference of potential complexes. In conclusion, CEDAR is a unique, growing and invaluable resource for the study of protein complex composition and dynamics across biological systems.

bioinformatics↗