Biology subjects

Steen, A.

Publications and source records attributed to Steen, A..

9 recordsLinked to original sources

bioRxiv2025

Conserved intrinsically disordered region of DNAJB6 dictates its surveillance of FG-Nup condensates

Molecular chaperones are known for their role in preventing protein aggregation and assisting proteins in reaching their structurally functional state. DNAJB6, a J-domain protein that partners with Hsp70s and nucleotide exchange factors, is very potent in preventing amyloid formation of proteins with large intrinsically disordered regions (IDRs), including several disease-associated proteins. Complementary to this, we recently demonstrated a role for DNAJB6 in surveilling FG-Nucleoporins (FG-Nups) phase transitions and highlighted its role in nuclear pore complex assembly. We expand on this by showing that this activity of phase state surveillance is directed to several FG-Nups and shared with the closely related DNAJB2 and DNAJB8. We demonstrate that the surveillance mechanism of DNAJB6 is encoded in an unusually highly conserved IDR that promotes the formation of stable, gel-like assemblies of the chaperone itself. These assemblies likely provide a stable environment that can outcompete stable homotypic FG-Nup interactions and instead favors multivalent heterotypic chaperone:FG-Nup interactions. The evolutionary conservation of the DNAJB6-IDR, mutant analyses from both experimental in vitro and in cell data, and multiscale molecular dynamics simulations suggest that the sequence space for encoding stable gel-like assemblies is narrow and optimized to avoid self-aggregation while providing potent anti-amyloidogenic capacity.

biochemistry↗

bioRxiv2025

Detecting Nuclear Pore Complex assembly in living cells

The formation of nuclear pore complexes (NPCs) -- vital gateways regulating nuclear-cytoplasmic transport -- is a highly orchestrated process requiring the integration of hundreds of nucleoporins into the nuclear envelope. A major challenge in studying this assembly process in living cells has been the difficulty to distinguish newly forming NPCs from their mature counterparts. Here, we present a powerful nanobody-based approach that overcomes this limitation. We demonstrate that a nanobody targeting the nucleoporin Nic96 from Saccharomyces cerevisiae selectively binds newly synthesized Nic96 subcomplexes prior to its incorporation into NPCs in vivo. Importantly, nanobody-bound Nic96 is incorporated in NPCs, and expression of the nanobody does not disrupt nuclear transport, cell growth, or lifespan, nor does it show genetic interactions with known NPC assembly surveillance pathways -- making it an ideal, non-perturbing tool to study NPC biogenesis in yeast. Illustrating the use of the Nic96 nanobody we report novel aspects of the early stages of assembly, including co-recruitment of Kap121 and VHH[Nic96] to putative assembly sites. In addition, we show local enrichment of newly synthesized nucleoporins on nuclear envelope proximal lipid droplets, including a specific subset of Pdr16- and Ldo16-positive lipid droplets near the nucleus-vacuole junction. When NPC assembly is delayed, association of Nic96 subcomplexes with lipid droplets increases. These findings illustrate how the strategy to pulse-label newly forming NPCs opens new avenues for dissecting the spatiotemporal regulation of NPC assembly and misassembly.

cell biology↗

bioRxiv2024

Imaging-Based Quantitative Assessment of Biomolecular Condensates in vitro and in Cells

The formation of biomolecular condensates contributes to intracellular compartmentalization, and plays an important role in many cellular processes. The characterization of condensates is however challenging, requiring advanced biophysical or biochemical methods that are often less suitable for in vivo studies. A particular need for easily accessible yet thorough methods that enable the characterization of condensates across different experimental systems thus remains. To address this, we present PhaseMetrics, a semi-automated FIJI-based image analysis pipeline tailored for quantifying particle properties from microscopy data. Tested using the FG-domain of yeast nucleoporin Nup100, PhaseMetrics accurately assesses particle properties across diverse experimental setups, including in vitro, Xenopus egg extracts, and cellular systems. It reliably detects changes induced by various conditions such as the presence of polyethylene glycol, 1,6-hexanediol, a salt gradient, and the molecular chaperone DNAJB6b. By enabling the accurate representation of the variability within the population and the detection of subtle changes at the single particle level, the method complements conventional biochemical assays. Combined, PhaseMetrics is an easily accessible, customizable pipeline that enables imaging-based quantitative assessment of biomolecular condensates in vitro and in cells, providing a valuable addition to the current toolbox.

biochemistry↗

bioRxiv2023

Nucleoporin Nsp1 surveils the phase state of FG-Nups

Transport through the NPC relies on intrinsically disordered FG-Nups forming a selective barrier. Away from the NPC, FG-Nups readily form condensates and aggregates, and we address how this behavior is surveilled in cells. FG-Nups, including Nsp1, together with nuclear transport receptor Kap95, form a native cytosolic condensate in yeast. In aged cells this condensate disappears as cytosolic Nsp1 levels decline. Biochemical assays and modeling show that Nsp1 is a modulator of FG-Nup liquid-liquid phase separation, promoting a liquid-like state. Nsp1s presence in the cytosol and condensates is critical, as a reduction of cytosolic levels in young cells induces NPC assembly and transport defects and a general decline in protein quality control, all quantitatively mimicking aging phenotypes. Excitingly, these phenotypes can be rescued by cytosolic Nsp1. We conclude that Nsp1 is a phase state regulator that surveils FG-Nups and impacts general protein homeostasis. HighlightsO_LINups form native cytosolic condensates C_LIO_LINsp1 reduction mimics NPC aging phenotypes C_LIO_LINsp1 acts as phase state modulator of FG-Nups C_LIO_LINsp1 shares surveillance function with classical chaperones C_LI

cell biology↗

bioRxiv2023

Specificity and mechanism of 1,6 hexanediol-induced disruption of nuclear transport

Selective transport through the nuclear pore complex (NPC) depends on the dynamic binding of the intrinsically disordered components of the NPC, the FG-nups, with each other and with nuclear transport receptors (NTRs). Hydrophobic interactions with the phenylalanines of FG-nups are critical for this dynamic binding. 1,6-hexanediol (1,6HD), is an aliphatic alcohol that interferes with hydrophobic interactions. Here we assessed the specificity and mechanism by which 1,6HD disrupts the permeability barrier of NPCs in live bakers yeast cells. Exposure to 1,6HD (10 min, 0-5%) leads to gradual loss of the NPC permeability. This is likely a direct effect on the nuclear transport machinery as cell viability, the pH and ATP levels in the cytosol, as well as the appearance of mitochondria, Golgi, peroxisomes, ER, vacuoles, plasma membrane, nucleolus, secretory pathway and stress granules are not notably changed. There are however effects on the cytoskeleton and Hsp104 to be noted. While 1,6HD treatment does not lead to dissociation or degradation of NPC subunits, a massive relocation of multiple NTRs from NPCs does occur. This displacement quantitatively correlates with the increased passive permeability of NPCs. The loss of NTRs and associated cargo will present a major change in the macromolecular crowding and composition and hence the physicochemical properties of the central channel. We conclude that 1,6HD provides a surprisingly specific intervention to temporarily permeate NPCs and we present evidence that the mechanism includes release of NTRs from the NPCs.

molecular biology↗

bioRxiv2022

Nuclear transport under stress phenocopies transport defects in models of C9Orf72 ALS

The nucleus is the hallmark of eukaryotic life and transport to and from the nucleus occurs through the nuclear pore complex (NPC). There is a multitude of data connecting the nuclear transport machinery - i.e. the NPCs and associated nuclear transport factors - to neurodegenerative diseases, but the mechanisms are not well understood. Using Saccharomyces cerevisiae, we systematically studied how the expression of polyPR and polyGA related to C9Orf72 amyotrophic lateral sclerosis impacts the nuclear transport machinery. We measured the abundance and localization of NPC components and transport factors, and assessed the kinetics of import and export by four transport receptors. PolyPR and polyGA cause distinct, and transport receptor dependent effects. We compared the specific changes in transport to those obtained when cells were exposed to different stress situations or mutations. This comparison showed similar patterns of transport defects in cells lacking specific NTRs and cells expressing polyPR. In contrast, polyGA expressing cells bear resemblance to stress conditions where energy maintenance is decreased. The similarity of the patterns of transport deficiencies suggests that polyPR has a direct effect on nuclear transport via NTRs, while polyGA impacts the energy state of the cell and subsequently changes transport.

cell biology↗

bioRxiv2021

The molecular chaperone DNAJB6 provides surveillance of FG-Nups and is required for interphase nuclear pore complex biogenesis

Biogenesis of nuclear pore complexes (NPCs) includes the formation of the permeability barrier composed of phenylalanine-glycine-rich nucleoporins (FG-Nups) that regulate the selective passage/crossing of biomolecules. The FG-Nups are intrinsically disordered and prone to liquid-liquid phase separate1,2 and aggregate when isolated3. It has remained largely unclear how FG-Nups are protected from making inappropriate interactions during NPC biogenesis. We found that DNAJB6, a molecular chaperone of the heat shock protein network, formed foci next to NPCs. The number of these foci decreases upon removal of proteins involved in the early steps of interphase NPC biogenesis. Reversely, when this process is stalled in the last steps, the number of DNAJB6-containing foci increases and they could be identified as herniations at the nuclear envelope (NE). Immunoelectron tomography showed that DNAJB6 localizes inside the lumen of the herniations arising at NPC biogenesis intermediates. Interestingly, loss of DNAJB6 results in annulate lamellae, which are structures containing partly assembled NPCs associated with disturbances in NPC biogenesis. We find that DNAJB6 binds to FG-Nups and can prevent the aggregation of the FG-region of several FG-Nups in cells and in vitro. Together, our data show that DNAJB6 provides quality control during NPC biogenesis and is the first molecular chaperone that is involved in the surveillance of native intrinsically disordered proteins, including FG-Nups.

molecular biology↗

bioRxiv2019

A physicochemical roadmap of yeast replicative aging

Cellular aging is a multifactorial process that is characterized by a decline in homeostatic capacity, best described at the molecular level. Physicochemical properties such as pH and macromolecular crowding, are essential to all molecular processes in cells and require maintenance. Whether a drift in physicochemical properties contributes to the overall decline of homeostasis in aging is not known. Here we show that the cytosol of yeast cells acidifies modestly in early aging and sharply after senescence. Using a macromolecular crowding sensor optimized for long-term FRET measurements, we show the macromolecular crowding changes less in longer-lived cells in contrast to shorter-lived cells. While the average pH and crowding levels change only modestly with aging, we observe drastic changes in organellar volume, leading to crowding on the {micro}m scale, which we term organellar crowding. Our measurements provide an initial framework of physicochemical parameters of replicatively-aged yeast cells.

biophysics↗

bioRxiv2018

Age-dependent deterioration of nuclear pore assembly in mitotic cells decreases transport dynamics

Nuclear transport is facilitated by the Nuclear Pore Complex (NPC) and is essential for life in eukaryotes. The NPC is a long-lived and exceptionally large structure. We asked whether NPC function is compromised in ageing mitotic cells. By imaging of single yeast cells during ageing, we show that the abundance of several NPC components and NPC assembly factors decreases while signs of misassembled NPCs appear. Consequently, nuclear permeability decreases, resulting in decreased dynamics of transcription factor shuttling and increased nuclear compartmentalisation. In support that declining NPC quality control is important in mitotic ageing, we find that the transport kinetics observed in ageing is mimicked in an NPC assembly mutant. Additionally, the single cell life histories reveal that cells that better maintain NPC function are longer lived. We conclude that assembly and quality control of NPCs are major challenges for ageing mitotic cells.

cell biology↗