Center for Integrated Protein Science Munich

Alzheimer´s disease is a neurodegenerative disease with high global prevalence and no cure available. It is known that the microbiota-gut-brain-axis plays a role in the pathogenesis, but the pathways are not fully understood yet. To elucidate the role of dietary fibre supplementation on this axis in a 5xFAD mouse model of Alzheimer´s disease, a feeding trial with an inulin supplement was conducted. At the start (Basis, n = 11) and after 7 weeks with (AD + F; n = 15) and without (AD; n = 15) supplementation, the mice were sacrificed and the following samples were taken: ingesta for 16 S rRNA sequencing and short-chain fatty acid (SCFA) analysis, and brain tissue for amyloid-beta staining and proteome analysis. The microbiota patterns in stomach, small intestine, caecum and colon differed between AD and AD + F. SCFA concentrations were significantly higher in group AD + F as compared to AD and Basis. In the AD mice, plaque load was significantly increased as compared to Basis, while a reduction in AD + F as compared to AD was observed. The brain proteome also differed between AD + F and AD, indicating a beneficial effect of the inulin supplementation, possibly mediated in part by microbial acetate. Since prebiotic substances like inulin are also part of human diets, this should be investigated further in the translational context.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-20986-8.

Abstract The RNA-binding protein hangover is essential for several stress responses in Drosophila melanogaster . Here, we discover a novel function of hangover in the regulation of gene expression. Hangover binds to more than 2.000 genes in the Drosophila genome and modulates transcription. We identify a diverse set of chromatin regulators as hangover interactors, including NSL, dMec, Sin3A, dREAM and Ino80. Among these, the non-specific lethal complex (NSL) is the most prominent one. We show that hangover attenuates NSL-mediated H4K16 acetylation at transcriptional start sites to downregulate gene expression. Our work uncovers novel roles for hangover in epigenetic gene regulation and suggests that it coordinates the function of multiple chromatin regulators. Abstract Figure

Excess double-stranded RNA (dsRNA) is present in the cytoplasm of human cells, usually following viral infections. Recognition of dsRNAs activates innate immune pathways, leading to cellular inflammation and inhibition of cell growth. Here, we show that an effective dsRNA response may occur without the onset of inflammation. Pro-inflammatory [RLR (retinoic acid-inducible gene I-like receptor)-dependent pathway] and cell growth inhibitory mechanisms [oligoadenylate synthetase (OAS)/ribonuclease L (RNase L)- and dsRNA-activated protein kinase (PKR)-dependent pathways] can act independently. We found that the 5' ends of dsRNA direct the onset of cellular inflammation, whereas the RNA duplex activates the OAS/RNase L and PKR pathways. Unexpectedly, three of the most common human RNA epitranscriptomic marks-i.e., N6-methyladenosine, 5-methylcytosine, and pseudouridine-had almost no influence on the immunogenicity of dsRNA; however, the presence of N6-methyladenosine inhibited the OAS/RNase L pathway. Our observations demonstrate how precisely innate immunity is fine tuned in cells to take appropriate countermeasures when a specific threat arises.

Living cells can adapt their shape in response to their environment, a process driven by the interaction between their flexible membrane and the activity of the underlying cytoskeleton. However, the precise physical mechanisms of this coupling remain unclear. Here we show how cytoskeletal forces acting on a biomimetic membrane affect its deformations. Using a minimal cell model that consists of an active network of microtubules and molecular motors encapsulated inside lipid vesicles, we observe large shape fluctuations and travelling membrane deformations. Quantitative analysis of membrane and microtubule dynamics demonstrates how active forces set the temporal scale of vesicle fluctuations, giving rise to fluctuation spectra that differ in both their spatial and temporal decays from their counterparts in thermal equilibrium. Using simulations, we extend the classical framework of membrane fluctuations to active cytoskeleton-driven vesicles, demonstrating how correlated activity governs membrane dynamics and the roles of confinement, membrane material properties and cytoskeletal forces. Our findings provide a quantitative foundation for understanding the shape-morphing abilities of living cells.

Accurate chromosome segregation requires the attachment of microtubules to centromeres, epigenetically defined by the enrichment of CENP-A nucleosomes. During DNA replication, CENP-A nucleosomes undergo dilution. To preserve centromere identity, correct amounts of CENP-A must be restored in a cell cycle-controlled manner orchestrated by the Mis18 complex (Mis18α-Mis18β-Mis18BP1). We demonstrate here that PLK1 interacts with the Mis18 complex by recognizing self-primed phosphorylations of Mis18α (Ser54) and Mis18BP1 (Thr78 and Ser93) through its Polo-box domain. Disrupting these phosphorylations perturbed both centromere recruitment of the CENP-A chaperone HJURP and new CENP-A loading. Biochemical and functional analyses showed that phosphorylation of Mis18α and PLK1 binding were required to activate Mis18α-Mis18β and promote Mis18 complex-HJURP interaction. Thus, our study reveals key molecular events underpinning the licensing role of PLK1 in ensuring accurate centromere inheritance.

Molecular gearing systems are technomimetic nanoscale analogues to complex geared machinery in the macroscopic world. They are defined as systems incorporating intermeshed movable parts which perform correlated rotational motions by mechanical engagement. Only recently, new methods to actively drive molecular gearing motions instead of relying on passive thermal activation have been developed. Further progress in this endeavor will pave the way for unidirectional molecular gearing devices with a distinct type of molecular machine awaiting its realization. Within this work an essential step towards this goal is achieved by evidencing directional biases for the light-induced rotations in our molecular photogear system. Using a custom-designed LED-coupled chiral cryo-HPLC setup for the in situ irradiation of enantiomeric analytes, an intrinsic selectivity for clockwise or counterclockwise rotations was elucidated experimentally. Significant directional biases in the photogearing processes and light-induced single bond rotations (SBRs) are observed for our photogear with directional preferences of up to 4.8 : 1. Harnessing these effects will allow to rationally design and construct a fully directional molecular gearing motor in the future.

Pancreatic ductal adenocarcinoma (PDAC) poses a significant threat due to its tendency to evade early detection, frequent metastasis, and the subsequent challenges in devising effective treatments. Processes that govern epithelial-mesenchymal transition (EMT) in PDAC hold promise for advancing novel therapeutic strategies. SAMD1 (SAM domain-containing protein 1) is a CpG island-binding protein that plays a pivotal role in the repression of its target genes. Here, we revealed that SAMD1 acts as a repressor of genes associated with EMT. Upon deletion of SAMD1 in PDAC cells, we observed significantly increased migration rates. SAMD1 exerts its effects by binding to specific genomic targets, including CDH2, encoding N-cadherin, which emerged as a driver of enhanced migration upon SAMD1 knockout. Furthermore, we discovered the FBXO11-containing E3 ubiquitin ligase complex as an interactor and negative regulator of SAMD1, which inhibits SAMD1 chromatin-binding genome-wide. High FBXO11 expression in PDAC is associated with poor prognosis and increased expression of EMT-related genes, underlining an antagonistic relationship between SAMD1 and FBXO11. In summary, our findings provide insights into the regulation of EMT-related genes in PDAC, shedding light on the intricate role of SAMD1 and its interplay with FBXO11 in this cancer type.

ABSTRACTProtamine 2 (Prm2/PRM2), together with Protamine 1 (Prm1/PRM1), constitute the two protamines found in both murine and human sperm. During spermiogenesis in haploid male germ cells, chromatin undergoes significant condensation, a phase in which most histones are replaced by a species-specific ratio of these two protamines. Altered PRM1/PRM2 ratios are associated with subfertility and infertility in both male mice and men. Notably, during histone-to-protamine exchange a small fraction of histones remains (ranging from 1% to 15%) bound to DNA. The regulatory roles of these residual histones, governed by post-translational modifications (PTMs), play a pivotal role in spermatogenesis, particularly in chromatin remodeling and epigenetic regulation of genes during sperm differentiation or even in early embryogenesis.In this study, utilizing aPrm2-deficient mouse model and conducting an analysis of sperm samples from men exhibiting either normozoospermia or atypical spermiograms, we observed alterations in the methylation and acetylation profiles of histones H3 and H4. Subsequent in-depth analysis revealed that discrepancies in protamine ratios do not significantly influence the post-translational modifications (PTMs) of histones in testicular sperm. In epididymal sperm these altered protamine ratios are associated with a reduction in the acetylation levels of histone H4 (H4ac), a phenomenon consistent across both murine and human samples. In particular, H4K5ac and H4K12ac were identified as the two modifications that appear to decrease as a result of reducedPrm2/PRM2levels. Our findings reveal that Protamine 2 is necessary for the maintenance of specific histone PTMs, such as acetylation, which is essential for proper spermatogenesis and particularly for chromatin remodeling.