Biology subjects

Körner, C.

Publications and source records attributed to Körner, C..

6 recordsLinked to original sources

bioRxiv2026

Lipid Droplet Targeting Drives Substrate Access during Very Long Chain Fatty Acid Activation by Fat1

Fatty acids, the most abundant building blocks for lipid synthesis, require conjugation with Coenzyme A (CoA) for their incorporation into membrane lipids. Of those, very long chain fatty acids (VLCFAs), the precursors of yeast ceramides, are particularly hydrophobic. Yet it remains unresolved where and how the sole VLCFA-CoA synthetase Fat1 activates them. Here we show that lipid droplets (LDs) are both the site of free VLCFAs storage, as well as their place of activation. Free VLCFAs preferentially partition into LDs in molecular simulations and in vitro reconstitutions, whereas Fat1 targets the LD surface in cells via a N-terminal amphipathic helix. Structural predictions identify an essential hydrophobic cavity in Fat1 that connects the active site to the membrane, suggesting that VLCFAs directly shuttle from the LD core into the enzymatic pocket. Our model explains how the organelle targeting of a fatty acid activator evolved to match the biophysical properties and consequently the subcellular localization of its highly hydrophobic substrate.

biochemistry↗

bioRxiv2024

The promoter mutation paucity as part of the dark matter of the cancer genome

Cancer is a heterogeneous disease caused by genetic alterations. Computational analysis of cancer genomes led to the expansion of the catalog of driver mutations. While individual high-impact mutations have been discovered also in gene promoters, frequency-based approaches have only characterized a few novel candidates. To investigate the promoter mutation paucity in cancer, we developed the REMIND-Cancer workflow to predict activating promoter mutations in silico, irrespective of their recurrence frequency, and applied it to the PCAWG dataset. We positively validated 7 candidates by luciferase assay including mutations within the promoters of ANKRD53 and MYB. Our analysis indicates that particular mutational signatures and necessary co-alterations constrain the creation and positive selection of functional promoter mutations. We conclude that activating promoter mutations are more frequent in the PCAWG dataset than previously observed, which has potential implications for personalized oncology.

bioinformatics↗

bioRxiv2024

The structure of the Orm2-containing serine palmitoyltransferase complex reveals distinct inhibitory potentials of yeast Orm proteins.

The levels of sphingolipids are crucial determinants of neurodegenerative disorders. Therefore, sphingolipid levels have to be tightly regulated. The Orm protein family and ceramides act as inhibitors in the rate-limiting step of sphingolipid biosynthesis - the condensation of L-serine and palmitoyl-CoA. The two yeast isoforms Orm1 and Orm2 form a complex with the serine palmitoyltransferase (SPT). While the sequences of the Orm proteins are highly similar, however, Orm1 and Orm2 are differentially regulated in yeast cells. The mechanistic details of the differential regulation remain elusive. To elucidate the regulatory mechanism, we determined the cryo-electron microscopy structure of the SPT complex containing Orm2. Through in vitro activity assays and a newly developed plasmid coverage assay combined with targeted lipidomics, we demonstrate that the SPT complex with Orm2 exhibits lower activity in comparison to the complex containing Orm1. This collectively suggests a higher inhibitory potential of Orm2, despite the remarkably similar structures of the Orm1- and Orm2 containing complexes. The high conservation of the SPT from yeast to man implies that the three human ORMDL isoforms could also have different regulatory capacities, which might be essential to understanding their role in sphingolipid-mediated neurodegenerative disorders. HighlightsO_LICryo-EM structures of serine palmitoyltransferase with Orm2 from S. cerevisiae C_LIO_LICeramide-mediated inhibition on SPT activity is conserved amongst SPTs C_LIO_LIThe two yeast Orm isoforms have different regulatory capacity C_LI

biochemistry↗

bioRxiv2023

Structure of the yeast ceramide synthase

Ceramides play a pivotal role as essential lipids, serving as foundational components for complex sphingolipids and potent signaling molecules. Ceramides are the products of the N-acylation of a sphingoid base and a CoA-activated fatty acid. This reaction is catalyzed by the enzymes of the evolutionarily conserved ceramide synthase (CerS) family. Yet, the precise structural details and catalytic mechanisms of CerSs have remained elusive. Here, we employed cryo-EM single particle analysis to unravel the structure of the yeast ceramide synthase complex in both an active and a fumonisin B1 inhibited state. Our findings shed light on the complexs architecture, revealing a dimer of Lip1 subunits bound to the two catalytic subunits, Lag1 and Lac1. Each catalytic subunit forms a hydrophobic crevice that is accessible from both the cytosolic site as well as from the intermembrane space of the endoplasmic reticulum (ER). Within this cavity, we identify amino acids forming the active center and a sphingoid base, one of the substrates of the complex. Together, this suggests a pre-loaded state of the CerS. Additionally, the fumonisin B1 bound structure reveals the inhibitory mechanism by blocking the cytosolic acyl-CoA binding site.

biochemistry↗

bioRxiv2021

Cell atlas of the regenerating human liver after portal vein embolization

The liver has the remarkable capacity to regenerate. In the clinic, this capacity can be induced by portal vein embolization (PVE), which redirects portal blood flow resulting in liver hypertrophy in locations with increased blood supply, and atrophy of embolized segments. Here we apply single-cell and single-nucleus transcriptomics on healthy, hypertrophied, and atrophied patient-derived liver samples to explore cell states in the liver during regeneration. We first establish an atlas of cell subtypes from the healthy human liver using fresh and frozen tissues, and then compare post-PVE samples with their reference counterparts. We find that PVE alters portal-central zonation of hepatocytes and endothelial cells. Embolization upregulates expression programs associated with development, cellular adhesion and inflammation across cell types. Analysis of interlineage crosstalk revealed key roles for immune cells in modulating regenerating tissue responses. Altogether, our data provides a rich resource for understanding homeostatic mechanisms arising during human liver regeneration and degeneration.

genomics↗

bioRxiv2021

Coordinated regulation of WNT/β-catenin, c-Met, and Integrin signalling pathways by miR-193b controls triple negative breast cancer metastatic traits

BackgroundTriple Negative Breast Cancer (TNBC) is the most aggressive subtype of Breast Cancer (BC). Treatment options for TNBC patients are limited and further insights into disease aetiology are needed to develop better therapeutic approaches. microRNAs ability to regulate multiple targets could hold a promising discovery approach to pathways relevant for TNBC aggressiveness. Thus, we address the role of miRNAs in controlling signalling pathways and phenotypes relevant to the biology of TNBC. MethodsTo identify miRNAs regulating WNT/{beta}-catenin, c-Met, and integrin signalling pathways, we performed a high-throughput targeted proteomic approach, investigating the effect of 800 miRNAs on the expression of 62 proteins in the MDA-MB-231 TNBC cell line. We then developed a novel network analysis, Pathway Coregulatory (PC) score, to detect miRNAs regulating the three pathways. Using in vitro assays for cell growth, migration, apoptosis, and stem-cell content, we validated the function of candidate miRNAs. Bioinformatic analyses using BC patients datasets were employed to assess expression of miRNAs as well as their pathological relevance in TNBC patients. ResultsWe identified six candidate miRNAs coordinately regulating the three signalling pathways. Quantifying cell growth of three TNBC cell lines upon miRNA gain-of-function experiments, we characterised miR-193b as a strong and consistent repressor of this phenotype. Importantly, the effects of miR-193b were stronger than chemical inhibition of the individual pathways. We further demonstrated that miR-193b induced apoptosis, repressed migration, and regulated stem-cell markers in MDA-MB-231 cells. Furthermore, miR-193b expression was the lowest in patients classified as TNBC or Basal compared to other subtypes when classified by PAM50 signatures. Gene Set Enrichment Analysis showed that miR-193b expression was significantly associated with reduced activity of of WNT/{beta}-catenin and c-Met signalling pathways in TNBC patients. ConclusionsIntegrating miRNA-mediated effects and protein functions on networks, we show that miRNAs predominantly act in a coordinated fashion to activate or repress signalling pathways responsible for metastatic traits in TNBC. We further demonstrate that our top candidate, miR-193b, regulates these phenotypes to an extent stronger than individual pathway inhibition, thus proving that its effect on TNBC aggressiveness is mediated by repressing multiple interconnected pathways.

cancer biology↗