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○ Wiley

Preprints posted in the last 90 days, ranked by how well they match Traffic's content profile, based on 20 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.

1
Systematic Analysis of GARP- and EARP-Mediated Trafficking Pathways Using Lysosomal Proteomics

Sivalingam, B.; Altuzar, J.; Walter, S.; Holthuis, J.; Esch, B. M.; Fröhlich, F.

2026-10-09 biochemistry 10.64898/2026.10.08.757561 medRxiv
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Eukaryotic cells utilize tethering complexes for sorting of proteins within the endo-lysosomal system. The GARP complex and the EARP complex both function in endosomal recycling. Both complexes share three common subunits (VPS51, VPS52, and VPS53), with each relying on one specific subunit: VPS54 for GARP and VPS50 for EARP. Mutations in both complexes are linked to various neurodegenerative disorders. While model cargoes have been described, the cargo spectrum of both complexes remains largely elusive. Here, we combined lysosomal proteomics with knockdowns of GARP and EARP to analyze their cargo spectra. Using the lysosome as a terminal reference point for mis-sorted proteins, we show that GARP depletion causes a loss in lysosomal hydrolases and accumulation of non-lysosomal cargo. EARP depletion results in lysosomal accumulation of secreted proteins. Our findings serve as a reference to study GARP and EARP complexes. We demonstrate that a systematic phenotypic analysis of GARP and EARP mutants is necessary to understand the pathological consequences of their dysfunction.

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Vacuolar type H+ ATPase is involved in stress responses in Leishmania mexicana by regulating the lysosomal pH

Gluenz, E.; Alagoez, C.; Wendt, A.

2026-08-21 cell biology 10.64898/2026.08.21.746154 medRxiv
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Vacuolar H+ ATPases (v-ATPases) are conserved proton pumps that support diverse biological functions through acidification of cellular organelles. The protozoan parasite Leishmania requires its v-ATPase for survival in the sand fly vector and mammalian host, but genetic mutants remain viable in vitro. To gain further insight into this conditionally lethal phenotype, we first mapped organellar localization of the v-ATPase by co-localisation imaging of fluorescently tagged v-ATPase subunits and organelle markers. The v-ATPase signal was strongest in the flagellar pocket region, consistent with enrichment in the contractile vacuole complex (CVC). To define the conditions that require a functional v-ATPase, deletion mutants were exposed to different stresses (pH, temperature, osmolality, dense culture). All tested deviations from standard culture conditions affected the mutants' growth rate, viability or both. Despite differences in phenotype severity, all stressors triggered the formation of a large autolysosome, positive for the autophagy marker protein ATG8 and the lysosomal enzyme cysteine peptidase A, indicating an arrest at the final step of autophagy. Measurements with the pH sensor pHLuorin2 showed that the luminal pH of the lysosomes was 5.6 in unperturbed promastigotes and 7.1 in v-ATPase mutants. These data support a canonical function for the Leishmania v-ATPase in lysosome acidification and autophagy, which is essential for parasite differentiation, and identify the poorly characterized Leishmania CVC as another major site of v-ATPase concentration.

3
In vitro characterization of the baker's yeast deubiquitinase Ubp3

Bostelmann-Arp, L.; Khosa, S.; Reiners, J.; Mayor Voeltzke, K.; Smits, S. H. J.; Reichert, A. S.; Schmitt, L.

2026-08-20 biochemistry 10.64898/2026.08.19.745719 medRxiv
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Ubp3 is one of about 20 deubiquitinases (DUBs) in S. cerevisiae. The current view generally assumes that Ubp3 requires its interaction partner Bre5, which is proposed to function as a positive regulator. Accordingly, the Ubp3/Bre5 complex has been implicated in a broad range of cellular processes for example trafficking between ER and Golgi, stress granule formation and selective autophagy. However, the molecular basis of this proposed Bre5-dependent activity remains unclear. To address this at a molecular level, Ubp3, Bre5, and related constructs were heterologously expressed in E. coli, purified to homogeneity, and characterized in vitro. Both proteins contain folded domains as well as extensive intrinsically disordered regions (IDRs). Despite this structural complexity, the Ubp3/Bre5 complex could be isolated following either co-expression in vivo or after in vitro assembly. Unexpectedly, complex formation with Bre5 was not required for the catalytic activity of full length Ubp3. Furthermore, even the isolated catalytic domain of Ubp3 was fully active against two distinct substrates in the absence of Bre5, demonstrating that its deubiquitinating activity is intrinsically independent of Bre5. These findings indicate that the catalytic domain alone is sufficient for substrate cleavage, whereas the extensive IDRs of Ubp3 and its cofactor Bre5 might contribute to substrate recognition or specificity. Overall, this study challenges the prevailing model of Bre5-dependent activation of Ubp3 and provides new insights into the molecular organization of the Ubp3/Bre5 system. More broadly, it highlights the importance of intrinsically disordered regions in regulating deubiquitinase function and cellular signaling networks.

4
Copine-6 integrates calcium, phosphoinositide and Rab11 signals to coordinate glutamate receptor recycling

Tan, J. Z. A.; Batallas-Borja, A.; Chandra, M.; Nguyen, T.-B.; Jang, S. E.; Gu, G.; Zhang, L.; Chen, K.-E.; Weeratunga, S.; Ascher, D.; Widagdo, J.; Collins, B.; Anggono, V.

2026-08-27 cell biology 10.64898/2026.08.26.747421 medRxiv
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Endosomal trafficking is a major pathway that delivers cell-surface proteins, including glutamate receptors, to support neurotransmission and normal brain functions. Activity-dependent insertion of glutamate receptors is essential for synaptic plasticity, learning and memory. Copine-6 is a neuronal-specific calcium (Ca2+) binding protein that mediates activity-induced exocytosis of -amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-type glutamate receptors. The activation of N-methyl-D-aspartate (NMDA) receptors triggers Ca2+-dependent translocation of Copine-6 to intracellular endosomal compartments. However, the mechanisms underlying the activity-dependent accumulation of Copine-6 in endosomes remain unknown. Here, we show that Copine-6 exhibits Ca2+-dependent binding to phosphatidylinositol-3-phosphate (PI(3)P) through the C2B domain and displays enhanced interaction with active Rab11a in a Ca2+-independent manner via the vWA domain. Mutations in the C2B that inhibit binding to PI(3)P not only block the activity-induced translocation of Copine-6 to early endosomes, but it also causes an aberrant accumulation of Copine-6 in recycling endosomes. Consequently, loss of Copine-6 expression impairs the efficient coupling of early and recycling endosomes and blocks activity-dependent delivery of both AMPA and NMDA receptors onto the neuronal plasma membrane. These defects can be restored by re-expressing wild-type Copine-6, but not the C2B phospholipid-binding mutant. Together, our findings establish Copine-6 as a molecular bridge that enhances coupling between the early and recycling endosomal membranes, thereby facilitating the activity-dependent forward trafficking of glutamate receptors to the neuronal plasma membrane to maintain synaptic potentiation.

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TSPAN3 defines a distinct intracellular trafficking route to secretory multivesicular bodies

Van den Bor, J.; Bobeldijk, M. L.; Zala, C. A.; Sanchez, C. T.; Lalo, C.; Adem, B.; Maaijen, J. A.; Bundock, E. M.; Weijers, N. A.; Soltani, Z. E.; de Heus, C.; Jansen, P. W.; Zheng, W.; Andaloussi, S. E.; Liv, N.; van Spriel, A.; Stecker, K. E.; Smal, I. V.; van Mierlo, G.; Verweij, F. J.

2026-08-26 cell biology 10.64898/2026.08.26.747209 medRxiv
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Extracellular vesicles (EVs) comprise molecularly diverse populations generated through multiple membrane-trafficking pathways, yet the intracellular basis of this heterogeneity remains poorly understood. Here, we identify the EV-associated tetraspanin TSPAN3 as a marker of a secretory multivesicular body (MVB) population that is molecularly and functionally distinct from canonical CD63-positive compartments. Using endogenous genome editing, live-cell and super-resolution microscopy, electron microscopy, quantitative EV secretion assays, and complementary proteomic approaches, we show that TSPAN3 localizes to fusion-competent MVBs but exhibits limited overlap with CD63 during secretion. Unlike CD63, which extensively traffics through the plasma membrane and depends on YXX{Phi}-mediated endocytic retrieval, TSPAN3 reaches secretory MVBs predominantly through an intracellular trafficking route that relies on a dileucine-containing sorting region. Orthogonal proximity-labeling and affinity-purification proteomics revealed that TSPAN3-positive compartments are associated with a selective LC3/ATG8-related membrane network, including GABARAPL2 and proteins involved in endosomal membrane remodeling and fusion. Perturbation of residues required for this association impaired localization to LC3-positive compartments and reduced secretory MVB fusion. Consistent with these findings, pharmacological disruption of autophagy- and endolysosomal-associated pathways differentially altered TSPAN3-positive EV secretion. Finally, proximity-labeled EV proteomics demonstrated that TSPAN3-associated EVs possess cargo signatures distinct from CD63-associated EVs, with greater representation of endosomal and endolysosomal proteins suggesting that tetraspanin-associated membrane nanodomains retain molecular signatures consistent with their intracellular trafficking history. Together, our findings identify TSPAN3 as a marker of a previously unrecognized secretory MVB population distinguished by its intracellular trafficking, molecular interactions, and EV composition, supporting a model in which distinct tetraspanin-organized membrane nanodomains are associated with different intracellular trafficking routes and molecularly distinct EV populations.

6
Melanophilin, a Myosin Va Adapter Protein, Biases Track Selection of Myosin Va-and Kinesin-1-Transported Liposomes at Actin-Microtubule Intersections In Vitro

Bensel, B. M.; Fagnant, P. M.; Macfarlane, J. E.; Previs, M. J.; Trybus, K. M.; Warshaw, D. M.

2026-09-02 biophysics 10.64898/2026.09.01.748553 medRxiv
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Secretory vesicle transport from the Golgi to the cell membrane involves kinesin and myosin Va motors on the vesicle surface cooperatively navigating their shared cargo through numerous actin-microtubule (MT) intersections. How the track on which the cargo exits the intersection is selected so that vesicles are delivered to their destination with spatial and temporal fidelity remains unclear. Here we hypothesized that melanophilin -- the adapter that links myosin Va to pigmented melanosomes and can bind to both actin and MTs -- acts as a phosphorylation-dependent switch to bias track preference at actin-MT intersections. To test this, we modeled melanosome transport in vitro using 350-nm liposomes with ~5 surface-bound molecules each of constitutively active myosin Va, kinesin-1, and full-length melanophilin with varying phosphorylation levels. Liposomes were then challenged with actin-MT intersections. Regardless of the track the liposomes entered the intersection on, liposomes with phosphorylated melanophilin were biased towards exiting the intersection on actin filaments while those with dephosphorylated melanophilin were biased to exit on MTs. Consistent with this, phosphorylated melanophilin showed a 2-fold preference to bind actin over MTs, and slowed liposome transport by myosin Va along actin filaments by ~40% by effectively acting as an anchor. Conversely, dephosphorylated melanophilin preferentially bound (2-fold) MTs over actin and, by acting as a tether, increased the kinesin-1 liposome transport distance on MTs. Therefore, melanophilin, based on its phosphorylation state, can bias track selection of cargo transported by kinesin-1 and myosin Va through the cell's complex cytoskeletal network with its numerous actin-MT intersections.

7
Dynamin proline-rich domain isoform abundance, not identity, determines synaptic vesicle recycling efficiency in Drosophila

Silveira, A. M.; De Leon Gonzalez, K. M.; Scalera, A. L.; Westhoff, L. J.; Roytman, K. A.; Del Signore, S. J.; Goode, B. L.; Rodal, A. A.

2026-08-25 cell biology 10.64898/2026.08.24.746809 medRxiv
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During neurotransmission, synaptic vesicle exocytosis adds membrane and proteins to the cell surface. To sustain further release, this material must be retrieved, via several distinct endocytic modes matched to the level of exocytosis. The GTPase dynamin plays a central role in endocytosis, but it has remained unclear which endocytic modes it supports. In mammals, distinct dynamin gene products with different proline-rich domains (PRDs) are proposed to mediate particular modes of endocytosis; however, the function of each PRD isoform has not been tested in an organism. Drosophila dynamin is encoded by one gene (shibire) that produces long and short PRD isoforms (Shi-L and Shi-S), which differ by a 48 amino acid C-terminal extension. Using isoform-specific knockin and knockdown tools, we found that loss of the more abundant Shi-S isoform disrupted bulk endocytosis and vesicle reformation under high exocytic demand, reduced evoked transmission at moderate levels of activity, and enhanced spontaneous release at rest. These functions did not depend on the PRD extension, as either isoform could rescue these phenotypes when re-expressed. Our results indicate that dynamin contributes to vesicle recycling across multiple endocytic retrieval modes and that PRD specialization is not required for these functions.

8
Tag-stabilized fluorescent protein binders for endogenous cell type-specific protein labelling

Schnider, S. T.; Kring, C.; Maggi, L.; Vigano, A. M.; Affolter, M.; Aguilar, G.; Kempf, A.

2026-09-29 cell biology 10.64898/2026.09.29.754891 medRxiv
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Protein labelling using genetically encoded fluorescent protein fusions has revolutionized the study of protein localization and function. However, visualizing endogenous proteins in specific cell types remains challenging, as existing approaches often require overexpression or laborious genetic engineering. To address these limitations, we developed a library of fluorescent protein binders using existing nanobodies and single-chain variable fragments that recognize fluorescent proteins and short peptide tags, allowing for modular, cell type-specific labelling of genetically tagged endogenous proteins. We found that fluorescent protein binders generate background fluorescence in the absence of the target protein, reducing signal specificity. To overcome this limitation, we generated destabilized fluorescent protein binders directed against GFP, ALFA, GCN4 peptide and V5. These binders display increased antigen-dependent stability and reduced background fluorescence, thereby improving the signal-to-noise ratio of endogenous protein visualization. We demonstrate the detection of endogenous proteins in drosophila larvae and embryos, zebrafish embryos, as well as in specific neuronal populations of the adult drosophila brain. In the brain, tissue-specific labelling revealed previously unknown protein expression and subcellular localization in sleep-regulatory neurons. Together, our panel of tag-stabilized fluorescent protein binders provides a versatile, ready-to-use toolkit for background-free, cell type-specific visualization of endogenous proteins.

9
The Z-shaped N-terminal Domain of Atg11 Coordinates Atg9 Recruitment in Selective Autophagy

Najera, S. I.; Andhare, D.; Hill, A. E.; Bekkhozhin, Z.; Ragusa, M. J.

2026-08-19 biochemistry 10.64898/2026.08.17.744853 medRxiv
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Macroautophagy is a conserved catabolic process that facilitates the degradation of cellular material by capturing it in double membrane vesicles termed autophagosomes. In Saccharomyces cerevisiae, selective macroautophagy is initiated by the scaffolding protein Atg11. Atg11 recruits the transmembrane protein Atg9, which resides in small vesicles, to autophagic cargo. Atg9 vesicles then fuse, forming the initial membrane sheet that expands into the autophagosomal membrane. While it is known that Atg9 interacts with Atg11 via a set of hydrophobic amino acids in the disordered N-terminus of Atg9, it is unclear how Atg11 mediates this interaction. To gain insight into this unknown aspect of autophagy initiation we utilized a combination of biochemical, structural, and cellular approaches. We demonstrate that the N-terminal domain (NTD) of Atg11 is the primary interaction site for Atg9, but the NTD requires clustering by the C-terminal region of Atg11 for its complete interaction with Atg9. We investigated the structure of the Atg11-NTD using cryo-EM which, in combination with AlphaFold modeling, revealed a positively charged binding pocket within the Atg11-NTD that is essential for Atg9 binding. Mutation of this conserved binding pocket leads to a loss of Atg9 binding in yeast and a reduction in the selective autophagy of mitochondria. Taken together, our results demonstrate the mechanism by which Atg11 recruits Atg9 to autophagy initiation sites.

10
A cleavable signal peptide controls the topology and Golgi targeting of the membrane protein TMEM165

Velings, M.-O.; Simar, R.; Bleret, A.; Tevel, V.; Boonen, M.; Morsomme, P.

2026-08-20 cell biology 10.64898/2026.08.19.745746 medRxiv
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TMEM165 is a Golgi-resident multi-pass membrane protein involved in divalent cation homeostasis and associated with congenital disorders of glycosylation, yet its N-terminal biogenesis has remained unresolved. Here, we demonstrate that TMEM165 contains a functional cleavable signal peptide required for correct Golgi targeting and membrane topology. Loss of this signal peptide causes protein mislocalization, and altered topology with N-terminal cytosolic exposure, whereas extended N-terminal deletion restores both Golgi localization and overall membrane topology, consistent with insertion mediated by the first transmembrane domain as commonly described for multi-pass membrane proteins. Importantly, this N-terminally truncated form remains responsive to manganese-induced degradation and partially restores glycosylation defects associated with TMEM165 deficiency, indicating that the extended N-terminal region is dispensable for core TMEM165 function. Together, these findings identify the signal peptide as a key determinant of TMEM165 biogenesis and suggest that its conservation may contribute not only to membrane targeting, but also to maintaining the proper luminal environment of the N-terminus during early biogenesis.

11
Transfected plasmids have reduced expression in cells deficient in SEPTIN 9 or ESCRT proteins

Ngwoke, E.; Hollien, J.

2026-08-24 cell biology 10.64898/2026.08.21.746337 medRxiv
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Transfection of cells with DNA plasmids typically involves the uptake of lipoparticles by endocytosis, followed by the inefficient escape of these particles from endosomes into the cytoplasm. We found that the expression of transfected plasmids was reduced in cells depleted of either SEPTIN 9 or proteins in the endosomal sorting complexes required for transport (ESCRT) pathway. The reduction in plasmid expression could not be fully explained by effects on endocytosis. SEPTIN 9 depletion appeared to reduce the acidification of plasmid-containing compartments, suggesting that it primarily affects the pH-sensitive escape of plasmids from endosomes. Depletion of the ESCRT proteins VPS36 or ALIX resulted in especially dramatic reductions in transfected plasmid expression, which were accompanied by reduced colocalization between the transfected DNA and CHMP4, an ESCRT protein important for endosomal membrane remodeling during intraluminal vesicle formation. Finally, transfected plasmid DNA was strongly colocalized with LC3B, suggesting that the default pathway for transfected material is autophagy.

12
Ire1 membrane stress responses support cell growth upon disruptions in inter-organelle contacts

Hewlett, B. R.; Esch, B. M.; Thomas, F. B.; Araki, M.; Ikeda, A.; Hanaoka, K.; Funato, K.; Fröhlich, F.; Stefan, C. J.

2026-07-31 cell biology 10.64898/2026.07.27.740907 medRxiv
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Disruptions in inter-organelle contacts result in membrane lipid homeostasis defects that ultimately impair cellular function and viability. Yet, essential responses to membrane lipid imbalances remain poorly understood. In this study, we demonstrate that Ire1-dependent Membrane Stress Responses (MSR), distinct from the canonical Unfolded Protein Response (UPR), sustain the growth of yeast cells lacking inter-organelle contacts. Comprehensive lipidomics reveal that the Ire1-mediated MSR compensates for glycerophospholipid synthesis defects by modulating sphingolipid metabolism. Quantitative imaging further indicates that Ire1 mediates these effects, at least in part, by elevating cytoplasmic Ca2+ which in turn stimulates calcineurin activity necessary for cellular homeostasis. Accordingly, inhibition of calcineurin results in severe endoplasmic reticulum stress in yeast cells depleted of inter-organelle contacts. Thus, the Ire1 MSR directs Ca2+-dependent calcineurin activity and lipid metabolism upon disruptions in membrane contact sites to maintain cellular homeostasis. Alterations in inter-organelle contacts are associated with several diseases, including neurodegenerative disorders. Our findings in yeast suggest that evoking the MSR may be a means to ameliorate neuronal degeneration and delay the progression of neurodegenerative disorders.

13
Single-shot light-field microscopy captures delivery-dependent dye and autofluorescence patterns in Caenorhabditis elegans

Markus, R.; Rea, E.; Berfi, N. A.; Taresco, V.; Hudson, C.; White, D. R. A.; Chauhan, V. M.

2026-09-10 biophysics 10.64898/2026.09.07.749827 medRxiv
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Three-dimensional imaging of live Caenorhabditis elegans commonly relies on sequential z-stack acquisition, which can be slow and susceptible to movement and photobleaching. Here, we used light-field microscopy to capture dye and delivery-dependent fluorescence patterns across intact adult worms in a single exposure per channel. With a 40x/1.20 NA water-immersion objective, each reconstructed dataset contained 121 axial slices spanning 109 {micro}m at 0.91 {micro}m spacing. In a representative adult, nematode signal extended from 40.88 to 85.4 {micro}m, corresponding to approximately 44.5 {micro}m of captured axial depth without sequential z scanning. Three fluorescence channels were acquired with a summed exposure time of 112 ms across a 685 x 1010 {micro}m field of view. FM1-43 labelled intestinal, cuticular and vesicular structures, FM4-64 highlighted ingested bacteria and intestinal compartments, and Nile Red revealed vesicular and broader whole-organism fluorescence. Intrinsic blue and green autofluorescence signals were also resolved. These observations demonstrate rapid single-shot acquisition of whole-organism three-dimensional fluorescence information and show how delivery route influences the spatial distribution of commonly used fluorescent probes in C. elegans.

14
Rab11-exosome biogenesis regulators mediate Aβ-induced intercellular propagation of endolysosomal trafficking defects and neurodegeneration

Cording, A.; Verma, B.; Arous, A.; Rice, S.; Vine, H.; Blincowe, L.; Wainwright, S. M.; Singh, P. J.; Goberdhan, D. C. I.; Wilson, C.

2026-09-20 neuroscience 10.64898/2026.09.17.752336 medRxiv
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Alzheimer's Disease (AD) is characterised by two histopathological hallmarks, intracellular tau-containing neurofibrillary tangles and extracellular amyloid plaques containing {beta}-amyloid (A{beta}), a specific cleavage product of Amyloid Precursor Protein (APP). Initiation of A{beta}-induced neuronal pathology, however, has been postulated to involve intracellular events affecting endolysosomal trafficking that can propagate between cells. Recent studies in non-neuronal Drosophila secondary cells (SCs) have revealed that A{beta} interferes with APP-regulated protein aggregation events, which package signalling molecules into insoluble dense-core granules (DCGs) during normal regulated secretion, inducing endolysosomal defects that are transferred to other cells. Here, using SCs, we show that knockdown of the gene encoding accessory ESCRT-III protein Chmp5, which selectively regulates the formation of intraluminal vesicles (ILVs) inside SC DCG compartments that are subsequently released as Rab11-exosomes, inhibits propagation of A{beta}-induced endolysosomal trafficking defects. Furthermore, knocking down Chmp5 or other accessory ESCRT-III genes also suppresses A{beta}-induced, neurodegeneration-dependent morphological defects in the Drosophila eye. We conclude that genes controlling the Rab11-exosome biogenesis pathway play a key role in both A{beta}-induced endolysosomal trafficking defects associated with aberrant regulated secretion and cellular events leading to neurodegeneration. Our findings indicate these processes are linked and may suggest new target pathways for future development of AD therapeutics.

15
Ktd1 is a phospho-regulated member of the Dup240 family that mediates defence against killer toxin K28

Nadir, H. H.; Pembery, A.; Laidlaw, K. M.; Milburn, A.; Leake, M. C.; MacDonald, C.

2026-08-10 cell biology 10.64898/2026.08.07.743514 medRxiv
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The DUP240 gene family in Saccharomyces cerevisiae encodes ten proteins containing two transmembrane domains (TMDs). Despite decades of interest driven by their high sequence similarity, little functional information exists regarding whether Dup240 family members share redundant or distinct roles. In this study, we combined computational modelling, subcellular localisation, and functional assays across the family to identify shared and unique features. Computational modelling revealed that Ktd1 possesses a unique structural element adjacent to its TMD region. Out of six successfully localised family members, Ktd1 was the only protein predominantly targeted to the vacuolar membrane and the sole Dup240 required for defence against the K28 killer toxin. Computational predictions further indicated that Ktd1 undergoes extensive post-translational regulation, containing multiple validated phosphorylation sites. Screening potential regulatory kinases and phosphatases identified several enzymes required for K28 defence, which were independently validated using liquid-based toxin sensitivity assays. A multicopy suppressor screen demonstrated that KTD1 overexpression rescued K28 sensitivity across most enzyme mutant backgrounds, confirming Ktd1 acts downstream or in parallel to many factors. However, the phosphatase Sit4 and the kinase Hog1 scored as most likely co-factors in Ktd1 mediated defence. Live-cell fluorescence imaging of these two enzymes revealed no dramatic spatial re-localisation during K28 exposure, suggesting that phospho-dependent regulation of Ktd1-mediated defence may occur through transient signalling events. Together, these findings identify Ktd1 as the central effector of the Dup240 family in toxin defence and provide a mechanistic framework for understanding Dup240 regulation.

16
Direct visualization of lysosome-mediated intracellular transport and membrane anchoring of TNF-α in human T cells

Burgess, A.; Gunasekara, H.; Xie, J.; Hu, Y. S.

2026-10-09 biophysics 10.64898/2026.10.07.757379 medRxiv
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Tumor necrosis factor-alpha (TNF-) represents a major pro-inflammatory cytokine associated with chronic inflammation. Enhanced understanding of intracellular trafficking of TNF- enables the identification of drug targets that modulate TNF- secretion at the cellular source. However, conventional cytokine assays provide only bulk measurements of secreted TNF- or static measurements in fixed cells and therefore cannot provide mechanistic information. Here, we report a fluorescence imaging platform to visualize and quantify intracellular TNF- trafficking in human T cells. Using a Jurkat T cell line stably expressing TNF- fused to mStayGold as a model system, we revealed through single-particle tracking (SPT) that T cell activation increased the motility of TNF- vesicles and that microtubule perturbation disrupted this increased motility. 3D structured illumination microscopy uncovered spatial associations between TNF- vesicles and lysosomes, and SPT further demonstrated their coordinated transport. Using total internal reflection fluorescence microscopy, we captured the sub-second splitting of single TNF- vesicles into multiple puncta that subsequently separated, suggesting delivery of TNF- from the vesicle to the plasma membrane. Confocal-based super-resolution microscopy further resolved TNF- vesicles fusing with the plasma membrane and transmembrane TNF-. Together, these imaging capabilities for tracking and super-resolving the intracellular transport and membrane delivery of TNF- in live T cells enable mechanistic studies of TNF- trafficking and release.

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A Kiss-and-Ride Mechanism for Lipid Exchange at Membrane Contact Sites

Ballekov, A.; Eisenreichov, A.; Holic, R.; Griac, P.; Boura, E.; Humpolickova, J.

2026-10-04 biophysics 10.64898/2026.09.29.755298 medRxiv
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Lipid transfer proteins (LTPs) mediate non-vesicular lipid transport at membrane contact sites, yet how transient membrane tethering contributes to lipid transfer remains poorly understood. Here, we use the single-domain yeast phosphatidylserine transporter Osh6, a member of the oxysterol-binding protein-related protein family, to investigate tethering-dependent lipid transport. We show that Osh6 can access two transport modes depending on membrane composition: conventional shuttling between membranes and a tethering-dependent mode in which the opposing membrane facilitates cargo extraction from the donor membrane. Combining lipid transport and membrane-tethering measurements with kinetic analysis, lipid partitioning, and in vivo complementation, we provide evidence for a transient membrane-bridged intermediate during lipid transfer. Productive phosphatidylinositol 4-phosphate (PI4P) extraction destabilizes this bridged state, allowing cargo-loaded Osh6 to disengage and continue the transport cycle. We term this mechanism kiss-and-ride, in which transient membrane contact facilitates cargo extraction ("kiss") before the cargo-loaded protein disengages ("ride"). Consistent with this model, PI4P transport is preserved in a lidless Osh6 mutant with impaired membrane dissociation, whereas phosphatidylserine transport is strongly reduced, revealing distinct mechanistic requirements for the two cargoes. Together, our findings reveal a tethering-dependent transport mode in a cup-like LTP and suggest that membrane contact sites can actively shape the mechanism of lipid transport rather than merely bringing donor and acceptor membranes into proximity.

18
Overexpressing FLP Recombinase Can Cause Synaptic Trafficking Defects in C. elegans

Lenninger, Z. A.; Hoerndli, F. J.

2026-10-06 neuroscience 10.64898/2026.10.01.756008 medRxiv
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Site-specific recombinases, such as Cre recombinase (Cre) and FLP recombinase (FLPase), are popular tools that enable precise spatiotemporal control over fluorescent reporter genes. However, studies show that increased Cre expression can lead to cytotoxic phenotypes including DNA damage, cell cycle arrest, cell death, and aneuploidy. In contrast, there is little-to-no known cytotoxicity associated with FLPase. FLPase is considered to be the safer, if less efficient, recombinase. To compensate for decreased efficiency, researchers will often increase expression of the FLPase to ensure a complete gene edit. Despite previous evidence that FLPase is nontoxic at high doses, we report that high expression of FLPase from multi-copy extrachromosomal arrays can disrupt synaptic protein trafficking in C. elegans. We discovered several off-target effects of high FLPase expression including mislocalization of the pre-synaptic marker FLPon::mScarlet::SYD-2 and decreased synaptic abundance, transport, and expression of the ionotropic glutamate receptor subunit GLR-1. Neither overexpression of an inactive FLPase, low activity FLPase, nor mCherry under the same promoter elicited these effects. However, single-copy expression of the FLPase construct reliably tags FLPon::mScarlet::SYD-2 and does not lead to these off-target effects. This work supports growing awareness that tyrosine recombinases can become cytotoxic at high doses.

19
Human ORFeome expression in S. cerevisiae to better understand extracellular vesicle biology

Trani, J.; Daneshi, S.; Kachroo, A. H.; Brett, C. L.

2026-09-09 synthetic biology 10.64898/2026.09.05.749614 medRxiv
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Extracellular vesicles (EVs) mediate intercellular communication by all organisms studied, from bacteria to yeast to man. Yet evolutionarily conserved mechanisms governing aspects of fundamental EV biology remain enigmatic. To address this, we sought to establish Saccharomyces cerevisiae (bakers yeast) as a model by identifying ectopically expressed human proteins sorted into yeast EVs. Using an optimized pooled cloning method, we inserted >13,000 human open reading frames (ORFs) upstream of an GFP tag within yeast expression plasmids. After transformation into S. cerevisiae, we confirmed expression of 3,288 GFP-tagged human proteins with diverse cellular expression levels and subcellular localizations. Heat stress triggered release of intact, lipid-bound, EGFP-positive small EVs from all transformant pools. Proteomic analysis identified 292 human proteins within EV samples, including canonical human EV biomarkers. Over 70% had yeast orthologs also found in yeast EVs suggesting conserved sorting mechanisms. Protein-protein interaction network analysis linked these EV cargoes to ESCRT-associated pathways. Finally, validation of seven candidates showed that DEF3A, ANXA2 and CLIC1 were enriched in yeast EVs. This study establishes an omics-compatible synthetic biology framework to humanize yeast EVs, begins to uncover conserved cargo sorting mechanisms, and supports future engineering of designer EVs.

20
Contact of mobile cis-Golgi network with ER exit sites executes COPI-mediated receptor recycling

Rodriguez-Prieto, R.; Suda, Y.; Tojima, T.; Sabido-Bozo, S.; Kurokawa, K.; Nakano, A.; Muniz, M.

2026-10-07 cell biology 10.64898/2026.10.06.756745 medRxiv
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COPI-mediated retrograde transport is essential for maintaining homeostasis between the endoplasmic reticulum (ER) and the Golgi in eukaryotic cells. However, its spatiotemporal dynamics remain unclear. In budding yeast, ER export occurs through a hug-and-kiss mechanism, wherein mobile cis-Golgi network (CGN) elements transiently approach ER exit sites (ERES) to capture cargo before departing to deliver it to the Golgi. Here, using high-resolution 3D and 4D live imaging, we show that the COPI-mediated recycling of a cargo receptor from the CGN back to the ER occurs during the hug-and-kiss event. Furthermore, this recycling is complete before the CGN detaches from the ERES, suggesting that COPI-mediated retrograde transport is spatiotemporally coupled to ER export during a single and transient CGN-ERES association. Consistent with this model, when COPI function is impaired, the receptor fails to return efficiently to the ER and instead remains in the CGN after separation from the ERES. Additionally, COPI impairment prolonged CGN-ERES association, suggesting that COPI function also facilitates CGN detachment from ERES. Thus, we propose that rapid COPI-mediated recycling drives CGN maturation directly at the ERES interface, enabling the CGN to detach and proceed along the secretory pathway.