Biology subjects

Urlaub, H.

Publications and source records attributed to Urlaub, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Regulation of RNA maturation by the family of human G-patch proteins

The family of human G-patch proteins comprises more than 20 members, each characterized by a glycine-rich G-patch implicated in mediating interactions with RNA helicases. Here, we systematically identify the cognate RNA helicase of each G-patch protein, highlighting the association of DHX15 with a network of 20 G-patch cofactors. DHX35 and GPATCH1 represent a unique G-patch protein-RNA helicase pair, and we uncover a regulatory circuit between these partners. Comprehensive in vitro analyses of ATPase activity and RNA binding identify distinguishing features of DHX15- and non-DHX15-associated G-patch proteins, and demonstrate the roles of most G-patch proteins as bona fide stimulatory cofactors of DHX15. RNA interactome analyses of each G-patch protein and complementary transcriptome-wide alternative splicing analyses in cells lacking a G-patch protein reveal distinct modes of regulation of mRNA maturation by different G-patch proteins. For example, ZGPAT affects splicing indirectly through its requirement for efficient 2'-O-methylation of snRNAs, GPATCH8 exemplifies DHX15-associated alternative splicing modulation, whereas SUGP2 suppresses splicing in an RNA helicase-independent manner via direct binding to pre-mRNA introns.

molecular biology↗

bioRxiv2026

18S rRNA 3’ end cleavage by the phosphorylated endoribonuclease NOB1 is interconnected with early small subunit biogenesis

Processing of the precursor ribosomal RNAs (pre-rRNAs) is a key aspect of ribosomal subunit assembly that is closely coordinated with other maturation events. The ribonucleases that mediate pre-rRNA cleavages require regulation to ensure that their activities are exerted in a timely manner. Post-translational modifications can influence protein functions, and although many human ribosome assembly factors are reported to be post-translationally modified, most of these sites remain unconfirmed and functional insights are lacking. Here, we show that NOB1, the PIN domain endoribonuclease responsible for cleavage of the 3' end of the 18S rRNA, is phosphorylated within an evolutionarily conserved acidic tract that can be modified by casein kinase II in vitro. Association of NOB1 with pre-ribosomes is independent of these phosphorylations, and lack of NOB1 phosphorylation only mildly perturbs the efficiency of SSU maturation events upstream of 3' end cleavage of the 18S rRNA. Interestingly, our analyses of pre-rRNA levels in cells depleted of NOB1 or lacking its catalytic activity revealed not only accumulation of the 18SE precursor of the 18S rRNA, but also altered levels of pre-rRNAs containing 5' external transcribed spacer (ETS) sequences (43S, 26S and 30S). This suggests that lack of NOB1-mediated pre-rRNA cleavage impairs recycling of assembly factors required during early biogenesis steps, leading to altered kinetics of 5' ETS processing. Taken together these data provide new insights into the role of NOB1 during SSU biogenesis and the post-translational regulation of this ribonuclease.

Molecular Biology↗

bioRxiv2026

Cell-autonomous restoration of splicing homeostasis and RP11 phenotype in patient-derived RPE and retinal organoids by PRPF31.AAV gene therapy

Mutations in PRPF31 gene cause retinitis pigmentosa type 11 (RP11) through haploinsufficiency, impairing spliceosome assembly and triggering progressive retinal degeneration. While gene augmentation holds therapeutic promise, key questions remain regarding the mechanistic basis of rescue and its therapeutic efficacy across all primarily affected human retinal cell types and disease stages. Here, we utilised patient-specific induced pluripotent stem cells (iPSCs)-derived retinal pigment epithelium (RPE) cells and three-dimensional retinal organoids (ROs) to determine the therapeutic mechanism of AAV-mediated PRPF31 delivery. Using the ShH10(Y445F) serotype to ensure robust dual targeting of RPE and photoreceptors, we demonstrated that PRPF31 transduction restores nuclear localisation, reorganises SC35+ nuclear speckles and enhances p-SF3B1 active spliceosome foci. Transcriptomic and proteomic profiling revealed a global rescue of splicing activity and upregulation of phagocytosis, protein aggregate clearance pathways, and mitochondrial proteins. These molecular shifts facilitated the clearance of proteotoxic cytoplasmic aggregates and reversed key functional deficits; specifically, they reinforced RPE apical-basal polarity, restored phagocytic capacity and normal ciliary morphology and incidence, and boosted light-evoked activity in photoreceptors. Combining gene therapy with rapamycin-mediated-autophagy activation conferred no additive benefit, identifying the restoration of splicing homeostasis as the critical therapeutic driver. Notably, substantial phenotypic rescue is achievable in mature RPE, supporting a broad clinical window for intervention. Collectively, these data provide a systems-level validation of ShH10(Y445F)-PRPF31 gene therapy and establish a mechanistic framework for its clinical translation in RP11.

molecular biology↗

bioRxiv2026

Two components of the early ASH1 mRNA transport machinery undergo PUN motif-dependent liquid-liquid-phase separation

In eukaryotes, mRNA localization is a widespread mechanism of spatial gene regulation. Amongst the best-studied examples is the directional transport of ASH1 mRNA during mitosis of the budding yeast Saccharomyces cerevisiae. ASH1 mRNA is co-transcriptionally bound by the two RNA-binding proteins She2p and Loc1p and subsequently exported. In the cytoplasm, the adapter She3p binds to She2p forming an active transport complex with the myosin motor Myo4p to mediate actin-dependent transport into the daughter cell. Loc1p stays in the nucleus where it has a second function in ribosome biogenesis. In this study, we map the interaction surface of Loc1p on She2p and observe that it does not interfere with the RNA-binding interface of She2p. Analogous to a previous report on Loc1p and RNA, we could show that also Loc1p and She2p undergo liquid-liquid phase separation (LLPS). This event is caused by electrostatic interactions and can be regulated by the phosphorylation-driven alteration of She2ps oligomeric state. Furthermore, we observed that LLPS formation only requires the PUN motifs of Loc1p and that a ternary Loc1p-RNA-She2p complex also undergoes LLPS. In summary, our findings indicate that Loc1p co-transcriptionally recruits the nuclear ASH1 mRNA-She2p complex to LLPS, while the cytoplasmic Loc1p-lacking She2p-She3p-RNA transport complex does not form such LLPS.

biochemistry↗

bioRxiv2025

Structure of human cytoplasmic Pol II complex explains global transcription repression by Gdown1

RNA polymerase II (Pol II) is a 12-subunit enzyme crucial for gene transcription in the nucleus. However, its assembly in the cytoplasm, nuclear import, and nuclear function of assembly factors remain poorly understood. Here, we isolated Pol II from the cytoplasmic fraction of human cells (cfPol II) and determined its cryo-EM structure. The structure reveals that Pol II is fully assembled in the cytoplasm before nuclear import. We also found that Gdown1 binds Pol II through three distinct regions, indicating it may stabilize Pol II assembly intermediates. Notably, Gdown1 binding precludes the association of essential transcription factors IIB and IIF, rendering cfPol II inactive in promoter-dependent transcription in vitro. Our results provide a basis for Gdown1-dependent global transcription repression and suggest a model for the role of Gdown1 in Pol II assembly, import, and transcription regulation.

biochemistry↗

bioRxiv2025

High affinity cross-context cellular assays reveal novel protein-protein interactions of peripheral myelin protein of 22 kDa

Peripheral Myelin Protein 22 (PMP22) is a tetraspan membrane protein whose altered dosage causes the most common hereditary neuropathy, Charcot-Marie-Tooth disease type 1A (CMT1A). Despite its clinical significance, the physiological functions of PMP22 and the mechanism behind its tightly controlled gene dosage sensitivity remain unknown since over 30 years, in part due to limited knowledge of its protein-protein interactions (PPIs). In fact, integral membrane proteins such as PMP22 are significantly underrepresented in known cellular interactomes, likely due to limited suitability or technical challenges specific to these hydrophobic molecules in the major PPI discovery approaches. Here, we applied a rigorously optimized co-immunoprecipitation and mass spectrometry workflow using the mild detergent DDM and the high affinity ALFA-tag/anti-ALFA nanobody interaction to identify cellular PMP22-associated proteins. In a cross-context approach, we ran our standardized pipeline across multiple cell types including HEK293T, MDCKII epithelial cells, the Schwann cell line MSC80, and primary rat Schwann cells. We confirm known interactors, and uncover distinct, cell type-specific enrichment patterns following functional annotation analysis. Adhesion-related PPIs dominated in MDCKII cells (e.g., CD47, CLDN1, ATP1B1), while in Schwann cells myelin-associated PPIs were enriched. Importantly, we identified novel PPI candidates that may be highly relevant for PMP22 function including enzymes of the de novo sphingolipid biosynthesis pathway.

neuroscience↗

bioRxiv2025

Proteo-transcriptomic reprogramming and resource reallocation define the aging mammalian brain

Brain aging is a major risk for neurodegeneration, yet the underlying molecular mechanisms remain poorly understood. Here we performed an integrative proteo-transcriptomic analysis of the aging mouse brain, uncovering molecular signatures of aging through the assessment of protein aggregation, mRNA relocalization, and comparative proteomics across eight models of premature aging and neurodegeneration. We identified dynamic changes in physiological aging highlighting differences in synaptic maintenance and energy-allocation. These were linked to changes associated with fundamental protein biochemical properties such as size and net charge. Network analysis highlighted a decrease in mitochondrial complex I proteins not compensated at the mRNA level. Aggregation of 60S ribosome subunits indicated deteriorating translation efficiency and was accompanied by mitochondrial and proteasomal imbalance. The analysis of the nine models revealed key similarities and differences between physiological aging and pathology. Overall, our study provides an extensive resource on molecular aging, and offers insights into mechanisms predisposing to neurodegeneration, easily accessible at our Brain Aging and Molecular Atlas Project (BrainAging-MAP) website.

neuroscience↗

bioRxiv2025

Alphafold 3 guided insights into the Importin b / Importin 7 heterodimer interaction and its binding to Histone H1

The nuclear import of H1 linker histones is facilitated by a heterodimer of the transport receptors Importin{beta} (Imp{beta}) and Importin7 (Imp7). While both importins can individually interact with H1, only their preassembled hetero-dimer enables its proper binding for translocation through the nuclear pore. The interaction between Imp7 and Imp{beta} is mediated by a short stretch of residues in the C-terminal region of Imp7, which plays a key role in Imp7 activation by Imp{beta}. This interaction is allosterically regulated by Imp{beta}, finely tuning the activity of the Imp{beta}/Imp7 heterodimer. A complete model of the Imp{beta}:Imp7:H1 complex was predicted by Alphafold3 (AF3) and subsequently validated using cross-linking (X-link) data, isothermal titration calorimetry (ITC), and pull-down experiments, providing robust support for the models accuracy. This model positions the globular domain of H1 within the central cavity of Imp7, in agreement with cross-linking data. Refinement of this atomic model against a previously published cryo-EM map demonstrated significantly improved correspondence compared to the earlier interpretation, which placed the H1 globular domain within Imp{beta}. This enhanced structural consistency further substantiates the accuracy of the AI-driven prediction. Detailed analysis identified the nucleoporin-like binding (NlB) region of Imp7 as a short stretch interacting with the outer surface of Imp{beta}. This interaction mode implies that regulation of FG-binding site accessibility on Imp{beta}, mediated by the FXFG nucleoporin motives within the Imp7 NlB region, likely modulates transport pathways and/or enhances the efficiency of H1 nuclear import.

molecular biology↗

bioRxiv2025

Selective silencing of antibiotic-tethered ribosomes as a resistance mechanism against aminoglycosides

Antibiotic resistance is a growing threat, underscoring the need to understand the underlying mechanisms. Aminoglycosides kill bacteria by disrupting translation fidelity, leading to the synthesis of aberrant proteins. Surprisingly, mutations in fusA, a gene encoding translation elongation factor G (EF-G), frequently confer resistance, even though EF-G neither participates in mRNA decoding nor blocks aminoglycoside binding. Here, we show that EF-G resistance variants selectively slow ribosome movement along mRNA when aminoglycosides are bound. This delay increases the chance that the drug dissociates before misreading occurs. Over several elongation cycles, this selective silencing of drug-bound ribosomes prevents error cluster formation, preserving proteome and membrane integrity. As a result, fusA mutations confer resistance early in treatment by preventing self-promoted aminoglycoside uptake. Translation on drug-free ribosomes remains sufficiently rapid to sustain near-normal bacterial growth. This previously unrecognized resistance mechanism-- selective silencing of corrupted targets--reveals a novel antibiotic resistance strategy with potential therapeutic implications.

molecular biology↗

bioRxiv2025

Influence of ULK1 activity on the memory of ATG101 auto-activation dynamics

The initiation of autophagy is marked by the prompt convergence of initiation proteins to form super molecular complexes in spatially-defined autophagic hubs. The recruitment and activation of the ULK-kinase complex is a pivotal event in starting the initiation cascade. ULK complex-component ATG101 is required for initiating autophagy in mammalian cells, but its function is unknown. Its HORMA domain interacts with the HORMA domain of ATG13 and transmembrane protein ATG9A to collectively form the essential autophagy initiation complex ATG9A-ATG13-ATG101. ATG101 has structurally malleable elements, reminiscent of topological conversions used in related metamorphic HORMA domain proteins to control the rate of complex formation. To elucidate the function of ATG101, we monitored the interaction kinetics of ATG101 with ATG13 and ATG9A, and observed that the interaction of ATG101 with ATG9A and ATG13 is exceptionally slow. Dramatic acceleration of complex formation is observed upon a change in the fold of ATG101 induced by its transient homo-dimerization, which in turn is initiated by phosphorylation by the ULK1 kinase. In an auto-catalytic mechanism, ATG101 dimers create a positive feedback to propagate activation to further ATG101 molecules in the absence of ULK1 activity. Despite the competitive nature of the interaction interfaces, homo-dimerization of ATG101 surprisingly accelerates its association to ATG13. Memory of ATG101 activation persists for many hours after dephosphorylation and continues to accelerate the assembly of the ATG9A-ATG13-ATG101 complex. Overall, this work proposes an unusual regulatory mechanism where UKL1 initiates an ATG101 auto activation cascade, whose memory creates a responsive positive feedback that dictates the assembly rate of a key complex in autophagy initiation.

biochemistry↗

bioRxiv2025

Nanobinders for Synaptotagmin 1 enable the analysis of synapticvesicle dynamics in rodent and human models.

Synaptic neurotransmission is a critical hallmark of brain activity and one of the first processes to be affected in neural diseases. Monitoring this process, and in particular synaptic vesicle recycling, in living cells has been instrumental in unraveling mechanisms responsible for neurotransmitter release. However, currently available reporters suffer from major limitations such large probe size or lack of suitability for human neurons, hampering the understanding of human synaptic pathophysiology. Here we describe the NbLumSyt1 toolkit, a panel of nanobody-based affinity probes targeting the luminal domain of the synaptic vesicle protein Synaptotagmin 1 (Syt1). These new tools enable quantitative, non-invasive imaging and functional interrogation of synaptic transmission in human neurons, with unprecedented precision, versatility and cost efficiency, in technologies ranging from fixed-and live-cell super-resolution imaging to electron microscopy and mass spectrometry. Overall, NbLumSyt1 nanobinders provide a valuable platform for human synaptic physiology and pathophysiology, benefiting fundamental neuroscience and translational efforts to study and develop treatments for brain-related disorders.

neuroscience↗

bioRxiv2025

Molecular mechanisms of recruitment, function and regulation of UPF1 in histone mRNA decay

Animal replication-dependent histone mRNAs end in a conserved stem loop (SL) instead of the canonical poly(A) tail present in all other eukaryotic mRNAs. Degradation of the histone SL at the end of the S-phase is initiated by the stem-loop binding protein SLBP and its interplay with the RNA helicase UPF1 and the exoribonuclease 3hExo. We report direct interactions between SLBP and UPF1 and show that the unstructured SLBP N-terminus wraps around the UPF1 helicase core, contacting it at multiple sites. Although binding of SLBP to UPF1 impedes unwinding activity, it is critical for efficient histone mRNA decay in cells, as unwinding of the SL facilitates degradation by 3hExo. Here we show that the UPF1-activator, UPF2, binds 3hExo, and that UPF2-mediated activation of UPF1 overrides the inhibitory effect of SLBP. Our results highlight the intricate network of UPF1-centric protein-protein and protein/RNA interactions that fine-tunes its unwinding activity and orchestrates timely and efficient degradation of histone mRNA.

biochemistry↗

bioRxiv2025

Structural Basis of Lipid Membrane Binding by Human Ferlins

Ferlins, ancient membrane proteins with a unique architecture, are central to multiple essential, Ca2+-dependent vesicle fusion processes. Despite numerous functional studies and their link to burdening human diseases, a mechanistic understanding of how these multi-C2 domain proteins interact with lipid membranes to promote their remodeling and fusion is currently lacking. Here, we elucidate the near-complete cryo-electron microscopy structures of human myoferlin and dysferlin in their Ca2+ and lipid-bound states. We show that ferlins adopt compact, ring-like tertiary structures achieved upon membrane binding. The top arch of the ferlin ring, comprising the C2C-C2D region, is rigid and varies little across the observed functional states. In contrast, the N-terminal C2B and the C-terminal C2F-C2G domains cycle between alternative conformations and, in response to Ca2+, close the ferlin ring, promoting tight interaction with the target membrane. Probing key domain interfaces validates the observed architecture and informs a model of how ferlins engage lipid bilayers in a Ca2+- dependent manner. This work reveals the general principles of human ferlin structures and provides a framework for future analyses of ferlin-dependent cellular functions and disease mechanisms.

biochemistry↗

bioRxiv2025

Biocompatible sulfonium-based covalent probes for endogenous tubulin fluorescence nanoscopy in live and fixed cells

Fluorescent probes enable the visualization of dynamic cellular processes with high precision, particularly when coupled with super-resolution imaging techniques that surpass the diffraction limit. Traditional methods include fluorescent protein fusion (e.g., GFP) or organic fluorophores linked to ligands targeting the protein of interest. However, these approaches often introduce functional disruptions or ligand-associated biological effects. Herein, we address these challenges by developing covalent fluorescent probes for endogenous tubulin, a critical cytoskeletal protein involved in processes such as cell movement, division, and biomolecule trafficking. Using well-known tubulin binder cabazitaxel and cell permeable fluorophore silicon-rhodamine--as a basis, we introduce a novel biocompatible cleavable linker containing a sulfonium center. This allowed the construction of the optimized probe, 6-SiR-o-C9-CTX, demonstrating excellent cell permeability, fluorogenic properties, and the ability to covalently label tubulin across various human cell lines. Importantly, the targeting moiety could be washed out while preserving tubulin staining, ensuring minimal disruption of tubulin function. This labeling technique is compatible with STED nanoscopy in both live and fixed cells, offering a powerful high-resolution imaging tool.

biochemistry↗

bioRxiv2024

Molecular mechanism of co-transcriptional H3K36 methylation by SETD2

Tri-methylation of histone H3 at residue lysine-36 (H3K36me3) is a hallmark of actively and recently transcribed genes and contributes to cellular memory and identity. The deposition of H3K36me3 occurs co-transcriptionally when the methyltransferase SETD2 associates with RNA polymerase II (Pol II). Here we present three cryo-EM structures of SETD2 bound to Pol II elongation complexes at different states of nucleosome passage. Together with functional probing, our results suggest a 3-step mechanism of transcription-coupled H3K36me3 deposition. First, binding to the elongation factor SPT6 tethers the catalytic SET domain in proximity to the upstream DNA. Second, Pol II nucleosome passage leads to the transfer of a hexasome from downstream to upstream, poised for methylation. Finally, continued transcription leads to upstream nucleosome reassembly, partial dissociation of the histone chaperone FACT and sequential methylation of both H3 tails, completing H3K36me3 deposition of an upstream nucleosome after Pol II passage.

biochemistry↗

bioRxiv2024

Provirus deletion from Haloferax volcanii affects motility, stress resistance and CRISPR RNA expression

Haloferax volcanii harbours four putative proviruses: Halfvol1, Halfvol2, Halfvol3 and Halfvol4. In this study we successfully deleted all four provirus genomes, demonstrating, that they are not essential. Transcriptome comparison between this strain ({Delta}Halfvol1-4) and a wild type strain reveals an increase in archaella and chemotaxis gene expression, resulting in higher swarming motility in {Delta}Halfvol1-4. Furthermore, {Delta}Halfvol1-4 cells show an elongated cell shape and a higher resistance to H2O2 stress compared to the wild type. RNA-seq also revealed down-regulation of CRISPR arrays in the provirus-free strain. Circularised genomes of Halfvol1, Halfvol2 and Halfvol3 were found in the culture supernatant. This confirms excision of the proviruses from the chromosome, which seems to happen more efficiently at low temperature (30{degrees}C). Electron microscopy revealed potential viral particles in the supernatant, and mass spectrometry analysis confirmed the presence of structural viral proteins of Halfvol1 and Halfvol3 in the isolated virus sample. These observations suggest that these proviruses are active and cause a chronic infection in Hfx. volcanii.

molecular biology↗

bioRxiv2024

Structural basis of Nipah virus replication

Nipah virus (NiV) is a non-segmented negative-strand RNA virus (nsNSV) with high pandemic potential, as it frequently causes zoonotic outbreaks and can be transmitted from human to human. Its RNA-dependent RNA polymerase (RdRp) complex carries out viral genome replication and transcription and is therefore an attractive drug target. However, to date no structural data is available on the NiV RdRp complex. Here, we report cryo-EM structures of NiV RdRp in the apo and in an early elongation state with RNA and incoming substrate bound. The structure of the apo enzyme reveals the architecture of the NiV RdRp complex, which shows a high degree of similarity to other nsNSV RdRps. The structure of the RNA-bound NiV RdRp shows how the enzyme interacts with template and product RNA during early replication and how nucleoside triphosphates are bound in the active site. Comparisons show that RNA binding leads to rearrangements of key elements in the RdRp core and to ordering of the flexible C-terminal domains of NiV L required for RNA capping. Taken together, these results reveal the first structural snapshots of an actively replicating nsNSV RdRp and provide insights into the mechanisms of genome replication and transcription by NiV and related viruses.

biochemistry↗

bioRxiv2024

Internal in-frame translation generates Cas11b, which is important for effective interference in an archaeal CRISPR-Cas system

CRISPR-Cas is a sophisticated defence system used by bacteria and archaea to fend off invaders. CRISPR-Cas systems vary in their Cas protein composition and have therefore been divided into different classes and types. Type I systems of bacteria have been shown to contain the small Cas11 protein as part of the interference complex. Here we show for the first time that an archaeal CRISPR-Cas type I system also contains a Cas11 protein. In addition, we show for the first time an internal in-frame translation of an archaeal protein. The Cas11b protein from the Haloferax volcanii type I-B system is encoded in the cas8b gene. Translation initiation at an internal methionine of the cas8b open reading frame results in synthesis of Cas11b. Cas11b is required for an effective interference reaction and without Cas11b fewer Cascade complexes form. Comparison of transcriptomes from wild type and a Cas11b less strain show that the depletion of Cas11b results in differential regulation of many genes. Taken together Cas11b is important for the defence reaction of the type I-B CRISPR-Cas system and seems to play an additional cellular role.

molecular biology↗