Sphingolipids integrate TORC2 with TORC1 through vacuolar liquid-ordered domain formation

DENDA, H.; ETO, K.; NISHIYAMA, K.; HAGIWARA, R.; OKANO, T.; YOSHIZUMI, S.; HIROTA, A.; NAKAZONO, K.; YABUKI, Y.; OKANO, A.; SEKIKAWA, Y.; SHIMAMOTO, T.; HANAOKA, K.; SAKURAGI, K.; SCHLARMANN, P.; IKEDA, A.; MASUMURA, K.; MIZUNUMA, M.; ISE, N.; KANAI, M.; IEFUJI, H.; SRIVATSAV, A.; ADHYAPAK, P.; MATHEW, L.; KAPOOR, S.; FUNATO, K.

doi:10.64898/2026.06.03.729730

Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.06.03.729730

Sphingolipids integrate TORC2 with TORC1 through vacuolar liquid-ordered domain formation

View original source ↗Export metadata ↓

Abstract

The coordination of multiple signaling pathways across different compartments of the endomembrane system is essential for cellular adaptation to the environment; however, the underlying mechanisms remain poorly understood. Previous studies have described the existence of sterol-enriched liquid-ordered (Lo) domains in the vacuole membrane of yeast, which act as platforms for signal initiation. Here, we demonstrate that vacuolar Lo domains serve as signaling platforms for the evolutionarily conserved Target of Rapamycin Complex 1 (TORC1) kinase complex. Notably, we show that TORC2, which is functionally distinct from TORC1 and localized to the plasma membrane, regulates TORC1 activity through sphingolipid metabolism and subsequent vacuolar Lo domain formation. Collectively, our findings reveal a lipid domain-mediated network that integrates two signaling pathways originating from spatially different cellular sites. HIGHLIGHTSO_LIDecreased sphingolipid levels cause characteristic phenotypes that reflect low TORC1 activity. C_LIO_LISphingolipid-enriched vacuolar Lo domains are required for the EGO complex-mediated activation of TORC1. C_LIO_LISphingolipids integrate TORC2 and TORC1 through vacuolar Lo domain formation. C_LIO_LIVacuole fusion and acidification control TORC1 activity via sphingolipid metabolism. C_LI

Explore related subjects

cell biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

DENDA, H., ETO, K., NISHIYAMA, K., HAGIWARA, R., OKANO, T., YOSHIZUMI, S., HIROTA, A., NAKAZONO, K., YABUKI, Y., OKANO, A., SEKIKAWA, Y., SHIMAMOTO, T., HANAOKA, K., SAKURAGI, K., SCHLARMANN, P., IKEDA, A., MASUMURA, K., MIZUNUMA, M., ISE, N., KANAI, M., IEFUJI, H., SRIVATSAV, A., ADHYAPAK, P., MATHEW, L., KAPOOR, S., FUNATO, K.. 2026-06-06. Sphingolipids integrate TORC2 with TORC1 through vacuolar liquid-ordered domain formation. https://doi.org/10.64898/2026.06.03.729730

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Deep generative embeddings of gene expression and splicing reposition the interpretation of single-cell transcriptomic signatures

Single-cell transcriptomic analysis predominantly derives cell identity from gene expression analysis, while alternative splicing is processed separately despite its fundamental role for cell homeostasis. To overcome the limits of separate investigations, we developed a probabilistic deep learning framework, Crecerelle, enabling resolution of the contributions of gene expression and alternative splicing in each cell. Crecerelle learns cell embeddings from gene expressions and alternative splicing isoforms, to decipher their mutually dependent impact on the functional characterisation of cells in a data-driven manner, exemplified for the Tabula Muris dataset. This is enabled through a zero-and-N-inflated Dirichlet-Multinomial for a variational autoencoder that learns cell embeddings solely from splicing profiles, as well as a bi-modal variational autoencoder with a relevance-weighted mixture-of-experts variational posterior to consolidate the modality-specific contribution at single-cell level. Crecerelle reveals cell-type-specific isoform markers as well as subpopulations with unique isoforms and uncovers regulatory and disease-associated pathways not detected by gene expression analyses alone. This scalable and interpretable framework thus allows a more holistic study of transcriptomic regulation and will open a route to modality-relevance-weighted investigations across single-cell multiomics datasets and their influence on cellular homeostasis, tissue development and disease phenotypes.

cell biology↗

bioRxiv2026

MHC Molecules on B Cell Microvilli Are Spatially Associated with IL-15Rα

Interleukin-15 (IL-15) trans-presentation (TP) by B cells is an important mechanism of T-cell activation; however, the spatial organisation of interleukin-15 receptor (IL-15R) relative to major histocompatibility complex (MHC) molecules on B-cell microvilli remains poorly understood. As microvilli protrude from the B-cell surface and may serve as sites of initial B cell-T-cell contact, the distribution of IL-15R and MHC molecules within these structures may be important during the earliest stages of T-cell recognition and activation. Here, we investigated the spatial association and molecular proximity of IL-15R with MHC class I and class II molecules on B-cell microvilli before immunological synapse formation, using confocal microscopy, stimulated emission depletion (STED) microscopy, stochastic optical reconstruction microscopy (STORM), and fluorescence lifetime imaging microscopy-based Forster resonance energy transfer (FLIM-FRET). Both MHC class I and class II molecules showed significant spatial association with IL-15R; however, the extent of colocalisation decreased as spatial resolution increased. STED microscopy revealed significant colocalisation between IL-15R and MHC class I, whereas STORM did not detect this association. In contrast, IL-15R and MHC class II remained significantly colocalised at both resolutions. FLIM-FRET further demonstrated molecular proximity between IL-15R and both MHC class I and class II molecules, with higher FRET efficiency observed for MHC class II. Collectively, these findings indicate that IL-15R is spatially organised in proximity to both MHC class I and class II molecules on B-cell microvilli before immunological synapse formation. This arrangement at potential sites of initial B-cell-T-cell contact may facilitate the coordination of IL-15 trans-presentation and antigen presentation during the earliest stages of B-cell-T-cell interactions.

cell biology↗

bioRxiv2026

Pulsed-SILAC in single mouse embryos reveals early embryonic protein synthesis dynamics and phosphosite regulation

Early embryogenesis relies extensively on maternally deposited products until zygotic genome activation, yet the dynamics for the synthesis of new proteins in mammalian embryos remains poorly characterized. To address this, we applied pulsed stable isotope labelling by amino acids in cell culture (pSILAC) combined with narrow-window data-independent acquisition mass spectrometry to single mouse oocytes and embryos to resolve de novo protein synthesis during early embryogenesis. This revealed that the maternal proteome is not a static reservoir, with components of the subcortical maternal complex and amino acid transporters SLC7A1/2 being actively synthesized during the earliest developmental stages. Furthermore, phosphoproteomic analysis identified hundreds of previously unreported phosphosites and extensive regulation during the oocyte-to-embryo transition. Notably, phosphorylation of the PRC2-interacting KLP motif of EZHIP emerged as a potential regulatory mechanism, with modification of this region reducing EZHIP-PRC2 interaction and coinciding with H3K27me3 remodelling. Together, single embryo pSILAC revealed a maternal proteome that is continuously synthesized, recycled, and post-translationally regulated during early embryogenesis.

cell biology↗