Biology subjects

Szomek, M.

Publications and source records attributed to Szomek, M..

7 recordsLinked to original sources

bioRxiv2026

Host-derived lipids license proliferation of sterol-auxotrophic tick cells and promote flavivirus output

Sterol molecules play indispensable roles in the biology of cells and organisms. Yet, arthropods, including ticks, lack the capacity for de novo sterol biosynthesis and must rely on exogenous sources. How these organisms sense and utilise exogenous lipids at the cellular level remains poorly understood. Here, we show that host cholesterol and linoleic acid act as essential external signals that license proliferation of Ixodes ricinus tick cells. In lipid-depleted conditions, cells fail to proliferate despite retaining intracellular cholesterol, indicating that exogenous lipids function as regulatory cues rather than merely structural components. We further demonstrate that tick cells exhibit a non-canonical intracellular distribution of cholesterol, with predominant accumulation in lysosome-associated compartments, and that lipid availability induces a coordinated transcriptional program involving lipid uptake and trafficking machinery. Importantly, we find that limiting host lipid availability significantly reduces extracellular RNA output of tick-borne encephalitis virus (TBEV) from infected tick cells, indicating that viral production is affected by the metabolic state of the host cell. Together, our findings establish host-derived lipids as key regulators of cellular state in a sterol-auxotrophic organism and identify lipid availability as a determinant of flavivirus output. This work provides a conceptual framework linking nutrient sensing, cell proliferation, and vector-pathogen interactions.

microbiology↗

bioRxiv2025

Live-cell imaging and lipidomics of low density lipoprotein containing intrinsically fluorescent cholesteryl esters

Low density lipoprotein (LDL) delivers cholesterol to cells in the body in the form of cholesteryl esters (CEs), and dysfunction of this pathway is associated with various diseases. Due to the lack of suitable tools, our understanding of the intracellular transport and hydrolysis of CEs is limited. We present a novel approach for studying LDL-derived CEs in cells, using fatty acyl chain conjugates of the intrinsically fluorescent cholestatrienol (CTL). We demonstrate that CTL esters reconstituted into LDL particles are hydrolyzed in late endosomes and lysosomes (LE/LYSs) by acid lipase, while an LDL-derived CTL ether analog cannot leave LE/LYSs. Using live-cell imaging, lipidomics, and multimodal Bayesian modeling, we discover a sequential biphasic transport of LDL-derived CTL to LE/LYSs matching the kinetics of the lysosomal hydrolysis of LDL-associated CTL-ester with a half-time of 3.0 hours. Hydrolyzed CTL derived from LDL-associated CTL esters is rapidly re-esterified with a similar half-time and stored in lipid droplets, demonstrating efficient sterol transport to the endoplasmic reticulum (ER). The latter is supported by the detection of a faint CTL staining in the ER and by extensive contact formation between endo-lysosomes containing LDL and ER tubules. Using lipidomics and Bayesian kinetic modeling, we also track LDL-derived CEs and triacylglycerols in cells and determine the uptake kinetics for each lipid species individually. Our novel approach allows for precise measurement of post-endocytic trafficking and metabolism of LDL-derived cholesterol and other lipids in living cells.

biochemistry↗

bioRxiv2024

Structural and biochemical analysis of ligand binding in yeast Niemann-Pick type C1-related protein

In eukaryotes, integration of sterols into the vacuolar/lysosomal membrane is critically dependent on the Niemann-Pick type C (NPC) system. The system consists of an integral membrane protein, called NCR1 in yeast, and NPC2, a luminal soluble protein that transfers sterols to the N-terminal domain (NTD) of NCR1 before membrane integration. Both proteins have been implicated in sterol homeostasis of yeast and humans. Here, we investigate sterol and lipid binding of the NCR1/NPC2 transport system and determine crystal structures of the sterol-binding NTD. The NTD binds both ergosterol and cholesterol, with nearly identical conformations of the binding pocket. Apart from sterols, the NTD can also bind fluorescent analogs of phosphatidylinositol, phosphatidylcholine and phosphatidylserine as well as sphingosine and ceramide. We confirm the multi-lipid scope of the NCR1/NPC2 system using photo-crosslinkable and clickable lipid analogs, namely pac-cholesterol, pac-sphingosine and pac-ceramide. Finally, we reconstitute the transfer of pac-sphingosine from NPC2 to the NTD in vitro. Collectively, our results support that the yeast NPC system can work as versatile machinery for vacuolar homeostasis of structurally diverse lipids, besides ergosterol. Summary blurbResults of X-ray crystallography and binding assays with different lipids expand our knowledge of the substrate scope of the Niemann-Pick type C1-related proteins NCR1 and NPC2 in yeast. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/598172v2_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@102579borg.highwire.dtl.DTLVardef@c5be27org.highwire.dtl.DTLVardef@471096org.highwire.dtl.DTLVardef@191ee26_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Ratiometric fluorescence nanoscopy and lifetime imaging of novel Nile Red analogs for analysis of membrane packing in living cells

Subcellular membranes have complex lipid and protein compositions, which give rise to organelle-specific membrane packing, fluidity, and permeability. Due to its exquisite solvent sensitivity, the lipophilic fluorescence dye Nile Red has been used extensively to study membrane packing and polarity. Further improvement of Nile Red can be achieved by introducing electron-donating or withdrawing functional groups. Here, we compare the potential of derivatives of Nile Red with such functional substitutions for super-resolution fluorescence microscopy of lipid packing in model membranes and living cells. All studied Nile Red derivatives exhibit cholesterol-dependent fluorescence changes in model membranes, as shown by spectrally resolved stimulated emission depletion (STED) microscopy. STED imaging of Nile Red probes in cells reveals lower membrane packing in fibroblasts from healthy subjects compared to those from patients suffering from Niemann Pick type C1 (NPC1) disease, a lysosomal storage disorder with accumulation of cholesterol and sphingolipids in late endosomes and lysosomes. We also find small but consistent changes in the fluorescence lifetime of the Nile Red derivatives in NPC1 cells, suggesting altered hydrogen-bonding capacity in their membranes. All Nile Red derivatives are essentially non-fluorescent in water but increase their brightness in membranes, allowing for their use in MIN-FLUX single molecule tracking experiments. Our study uncovers the potential of Nile Red probes with functional substitutions for nanoscopic membrane imaging.

biophysics↗

bioRxiv2023

Ergosterol mediates aggregation of natamycin in the yeast plasma membrane

Polyene macrolides are antifungal substances, which interact with cells in a sterol-dependent manner. While being widely used, their mode of action is poorly understood. Here, we employ ultraviolet-sensitive (UV) microscopy to show that the antifungal polyene natamycin binds to the yeast plasma membrane (PM) and causes permeation of propidium iodide into cells. Right before membrane permeability becomes compromised, we observed clustering of natamycin in the PM that was independent of PM protein domains. Aggregation of natamycin was paralleled by cell deformation and membrane blebbing as revealed by soft X-ray microscopy. Substituting ergosterol for cholesterol decreased natamycin binding and resulted in reduced clustering of natamycin in the PM. Blocking of ergosterol synthesis necessitates sterol import via the ABC transporters Aus1/Pdr11 to ensure natamycin binding. Quantitative imaging of dehydroergosterol (DHE) and cholestatrienol (CTL), two analogs of ergosterol and cholesterol, respectively, revealed a largely homogeneous lateral sterol distribution in the PM, ruling out that natamycin binds to pre-assembled sterol domains. Depletion of sphingolipids using myriocin increased natamycin binding to yeast cells, likely by increasing the ergosterol fraction in the outer PM leaflet. We conclude that ergosterol-specific aggregation of natamycin in the yeast PM underlies its antifungal activity, which can be synergistically enhanced by inhibitors of sphingolipid synthesis. SignificanceErgosterol is the major sterol in the membranes of fungi and a major target for antifungal treatments. Polyene macrolides, such as natamycin, are known to target ergosterol but the underlying mechanisms for their preference for this yeast sterol compared to mammalian cholesterol is not understood. This study shows that natamycin forms aggregates when associated with yeast S. cerevisiae in an ergosterol-dependent manner. Cholesterol can only partially substitute for ergosterol with respect to natamycin binding and aggregation. Membrane-associated aggregation of natamycin is not the result of pre-formed sterol domains in the cell membrane, as we show by direct visualization of minimally modified ergosterol and cholesterol analogs. Inhibiting sphingolipid synthesis increased membrane association and antifungal activity of natamycin, suggesting that targeting sphingolipids in combination with polyene macrolides could lead to novel drug treatment approaches against fungal infections.

biophysics↗

bioRxiv2023

Automated quantification of lipophagy in Saccharomyces cerevisiae from fluorescence and cryo-soft X-ray microscopy data using deep learning

Lipophagy is a form of autophagy by which lipid droplets (LDs) become digested to provide nutrients as a cellular response to starvation. Lipophagy is often studied in yeast, Saccharomyces cerevisiae, in which LDs become internalized into the vacuole. There is a lack of tools to quantitatively assess lipophagy in intact cells with high resolution and throughput. Here, we combine soft X-ray tomography (SXT) with fluorescence microscopy and use a deep learning computational approach to visualize and quantify lipophagy in yeast. We focus on yeast homologs of mammalian Niemann Pick type C proteins, whose dysfunction leads to Niemann Pick type C disease in humans, i.e., NPC1 (named NCR1 in yeast) and NPC2. We developed a convolutional neural network (CNN) model which classifies ring-shaped versus lipid-filled or fragmented vacuoles containing ingested LDs in fluorescence images from wild-type yeast and from cells lacking NCR1 ({Delta}ncr1 cells) or NPC2 ({Delta}npc2 cells). Using a second CNN model, which performs automated segmentation of LDs and vacuoles from high-resolution reconstructions of X-ray tomograms, we can obtain 3D renderings of LDs inside and outside of the vacuole in a fully automated manner and additionally measure droplet volume, number, and distribution. We find that cells lacking functional NPC proteins can ingest LDs into vacuoles normally but show compromised degradation of LDs and accumulation of lipid vesicles inside vacuoles. This phenotype is most severe in{Delta} npc2 cells. Our new method is versatile and allows for automated high-throughput 3D visualization and quantification of lipophagy in intact cells.

bioinformatics↗

bioRxiv2018

Analysis of cholesterol export from endo-lysosomes by Niemann Pick C2 protein using combined fluorescence and X-ray microscopy

The Niemann-Pick C2 protein (NPC2) is a sterol transfer protein in late endosomes and lysosomes (LE/LYSs). How its capacity to transport cholesterol between membranes is linked to endo-lysosomal membrane trafficking is not known. Using quantitative fluorescence imaging combined with soft X-ray tomography (SXT); we show that NPC2 mediated sterol efflux is accompanied by large changes in distribution, size and ultrastructure of endocytic organelles. We observed clearance of intra-luminal lipid deposits, a decrease in number of autophagosomes, formation of membrane contact sites (MCSs) to the endoplasmic reticulum and extensive tubulation of LE/LYSs in three-dimensional SXT reconstructions of NPC2 treated human fibroblasts. The cells could recycle the cholesterol analog dehydroergosterol (DHE) from LE/LYSs slowly also in the absence of NPC2 protein but internalized NPC2 synchronized and accelerated this process significantly. Most fluorescent NPC2 was retained in LE/LYSs while DHE was selectively removed from these organelles, at least partially by non-vesicular exchange with other membranes. During sterol efflux LE/LYSs were reallocated to the cell periphery, where they could fuse with newly formed endosomes. Surface shedding of micro-vesicles was found, suggesting a pathway for cellular sterol release. We conclude that NPC2 mediated sterol efflux from LE/LYSs controls membrane traffic through the endo-lysosomal pathway.

cell biology↗