TMEM41B

TMEM41B is an ER-resident multispanning membrane protein containing a DedA/VTT domain that functions as both a phospholipid scramblase and a Ca²⁺ release channel, thereby maintaining ER bilayer lipid equilibrium and Ca²⁺ homeostasis (PMID:35044051, PMID:40038246). It forms a physical complex with VMP1 and localizes to mitochondria-associated ER membranes, where it facilitates membrane curvature events essential for autophagosome phagophore maturation, lipid droplet metabolism, VLDL lipoprotein biogenesis, and GPI-anchored protein trafficking from the ER to the Golgi (PMID:30093494, PMID:30352685, PMID:37279648). These same membrane-remodeling activities are co-opted by flaviviruses and coronaviruses, which require TMEM41B for the formation of double-membrane vesicle replication organelles (PMID:33338421, PMID:35536318). Constitutive knockout causes embryonic lethality in mice, and postnatal depletion leads to rapid lethality and proliferation arrest, underscoring its essential role in cellular and organismal viability (PMID:30352685, PMID:38640735).

1. 2018 High

   Three independent CRISPR screens converged on TMEM41B as an ER membrane protein required at an early step of autophagosome formation, establishing it as a core autophagy factor and revealing an additional role in lipid droplet homeostasis.

   Evidence Genome-wide CRISPR screens with autophagy reporters, KO cell characterization, fluorescence and electron microscopy across multiple labs

   PMID:30093494 PMID:30126924

   Open questions at the time

   • Molecular mechanism by which TMEM41B promotes phagophore elongation was unknown
   • Relationship to VMP1 was only partially characterized
   • Whether lipid droplet accumulation was a direct or indirect consequence was unclear
2. 2018 High

   Discovery that TMEM41B and VMP1 physically interact and that VMP1 overexpression rescues TMEM41B-KO autophagy defects established them as a functional unit, while interactome analysis placed TMEM41B at mitochondria-associated ER membranes and showed that constitutive KO in mice is embryonic lethal.

   Evidence Reciprocal co-immunoprecipitation, in vitro binding, autophagic flux rescue, IP-MS interactome, subcellular fractionation, knockout mice

   PMID:30093494 PMID:30352685 PMID:30773971

   Open questions at the time

   • Whether TMEM41B and VMP1 have identical or distinct biochemical activities was unknown
   • The enzymatic activity of the DedA domain had not been determined
3. 2019 High

   Further reporter-based studies confirmed TMEM41B acts at the phagophore maturation stage and clarified that it plays related but not fully overlapping roles with VMP1 in autophagosome biogenesis.

   Evidence CRISPR screen with multiple autophagy reporters, quantitative microscopy, biochemical analyses

   PMID:30933966

   Open questions at the time

   • The biochemical basis for the non-overlapping functions of TMEM41B and VMP1 remained undefined
4. 2020 High

   Genome-wide screens for host dependency factors revealed TMEM41B as essential for flavivirus and SARS-CoV-2 replication, connecting its membrane-remodeling function to viral double-membrane vesicle formation and identifying population-level SNPs that reduce infection susceptibility.

   Evidence Full-genome CRISPR loss-of-function screens, virology stage-specific assays, SNP functional analysis

   PMID:33338421

   Open questions at the time

   • Whether TMEM41B directly shapes membranes or acts indirectly through lipid composition changes was unresolved
   • Structural basis for membrane curvature activity was unknown
5. 2021 High

   Mechanistic dissection showed TMEM41B acts at an early, post-entry stage of coronavirus replication by mobilizing cholesterol and lipids for membrane expansion, distinguishing its role from receptor-mediated viral entry.

   Evidence CRISPR KO screens, viral lifecycle stage assays, lipid mobilization studies

   PMID:34043740 PMID:34871328

   Open questions at the time

   • Direct lipid transfer or scramblase activity had not yet been demonstrated biochemically
6. 2022 High

   In vitro reconstitution demonstrated that TMEM41B (and VMP1) possess phospholipid scramblase activity, providing the first direct biochemical function for the DedA/VTT domain and explaining how it equilibrates ER bilayer leaflets.

   Evidence Fluorescent liposome-based phospholipid scrambling assay with purified protein, in vivo metabolic labeling

   PMID:35044051 PMID:35496801

   Open questions at the time

   • Structural basis for scramblase activity was not resolved
   • Whether scramblase activity alone accounts for all membrane-remodeling phenotypes was unclear
7. 2022 High

   Epistatic ordering of TMEM41B and VMP1 during β-coronavirus DMV biogenesis showed that TMEM41B facilitates nsp3–nsp4 interaction and ER zippering, while VMP1 is needed for subsequent DMV closure — placing them at sequential steps.

   Evidence KO cells expressing nsp3/4, interaction assays, electron microscopy of DMV intermediates

   PMID:35536318 PMID:35900889

   Open questions at the time

   • Whether the same sequential relationship applies to autophagosome formation was not tested
   • Direct interaction between TMEM41B and viral nsps was not demonstrated
8. 2022 Medium

   Metabolomic profiling revealed that TMEM41B and VMP1 have distinct effects on cellular lipid and energy metabolism during dengue virus replication, with TMEM41B deficiency uniquely rescuable by exogenous fatty acids.

   Evidence TMEM41B/VMP1 KO cells, viral replication assays, fatty acid supplementation, metabolomics

   PMID:35939522

   Open questions at the time

   • The specific lipid species or metabolic pathway directly regulated by TMEM41B was not identified
   • Single-lab finding without independent replication
9. 2023 Medium

   TMEM41B's scramblase activity was linked to ER-to-Golgi trafficking of GPI-anchored proteins: TMEM41B loss stabilized PGAP1 by slowing its ERAD and delayed cargo export, broadening the functional scope beyond autophagy.

   Evidence TMEM41B-KO cells, PI-PLC sensitivity assay, PGAP1 turnover assay, GPI-AP trafficking assay

   PMID:37279648

   Open questions at the time

   • Whether TMEM41B directly scrambles specific phospholipids required for GPI-AP sorting was not shown
   • Single-lab study
10. 2024 Medium

    Postnatal ubiquitous depletion of TMEM41B in adult mice caused rapid lethality within weeks, and MEFs showed severe proliferation defects, demonstrating that TMEM41B is essential not only during embryogenesis but throughout postnatal life.

    Evidence Tamoxifen-inducible conditional KO mice, cell proliferation assays in MEFs

    PMID:38640735

    Open questions at the time

    • Which specific tissue(s) or cellular process failure causes postnatal lethality was not determined
    • Single-lab finding
11. 2024 Medium

    VMP1 and TMEM41B scramblase activity was shown to control plasma membrane delivery of the WNT receptor FZD2, linking their function to primitive endoderm specification in mouse ESCs.

    Evidence ESC gene KO, cell surface proteomics, differentiation assays, transgenic FZD2 rescue

    PMID:39695329

    Open questions at the time

    • Whether TMEM41B acts directly on FZD2 maturation or indirectly through global ER lipid remodeling was not resolved
    • Single-lab study in ESC model
12. 2025 High

    Single-channel electrophysiology with purified recombinant TMEM41B demonstrated it forms a Ca²⁺-permeable channel, revealing a second intrinsic activity beyond scramblase function; TMEM41B deficiency caused ER Ca²⁺ overload that altered T cell signaling and maintained an aberrant naive-but-metabolically-activated state.

    Evidence Single-channel electrophysiology with purified protein, cellular Ca²⁺ imaging, T cell phenotyping and signaling assays

    PMID:40038246

    Open questions at the time

    • Whether the Ca²⁺ channel and scramblase activities are structurally separable is unknown
    • Whether Ca²⁺ channel activity contributes to the autophagy or lipid metabolism phenotypes was not tested
13. 2025 Medium

    TMEM41B was found to stabilize FASN by inhibiting its ubiquitination in vascular smooth muscle cells, promoting lipid synthesis and pro-inflammatory cytokine release; silencing TMEM41B reduced atherosclerotic plaques in ApoE⁻/⁻ mice.

    Evidence VSMC TMEM41B knockdown/overexpression, ubiquitination assay, in vivo ApoE⁻/⁻ mouse model

    PMID:41297878

    Open questions at the time

    • Whether FASN stabilization is a direct interaction or secondary to altered ER lipid homeostasis is unclear
    • Single-lab finding

• Key unresolved questions include the high-resolution structure of TMEM41B, the structural relationship between its scramblase and Ca²⁺ channel activities, the identity of specific lipid substrates it scrambles in vivo, and whether its diverse cellular phenotypes (autophagy, lipid droplets, VLDL secretion, viral DMVs, T cell quiescence) all derive from a unified scramblase/channel mechanism or require additional activities.
• No high-resolution structure of TMEM41B is available
• Whether scramblase and Ca²⁺ channel represent one pore or two distinct activities is unknown
• In vivo lipid substrate specificity has not been determined