bims-mecosi Biomed News
on Membrane contact sites
Issue of 2021–07–11
six papers selected by
Verena Kohler, Stockholm University
  1. Cubic spline-based depth-dependent localization of mitochondria-endoplasmic reticulum contacts by three-dimensional light-sheet super-resolution microscopy.
  2. Insights into VPS13 properties and function reveal a new mechanism of eukaryotic lipid transport.
  3. zapERtrap: A light-regulated ER release system reveals unexpected neuronal trafficking pathways.
  4. Junctional ER Organization Affects Mechanotransduction at Cadherin-Mediated Adhesions.
  5. Degradation of lipid droplets by chimeric autophagy-tethering compounds.
  6. Membrane perturbation by lipidated Atg8 underlies autophagosome biogenesis.
  1. Analyst. 2021 Jul 06.
    Cubic spline-based depth-dependent localization of mitochondria-endoplasmic reticulum contacts by three-dimensional light-sheet super-resolution microscopy.
    Yucheng Sun, Seungah Lee, Seong Ho Kang.
      The contact distance between mitochondria (Mito) and endoplasmic reticulum (ER) has received considerable attention owing to their crucial function in maintaining lipid and calcium homeostasis. Herein, cubic spline algorithm-based depth-dependent fluorescence-free three-dimensional light-sheet super-resolution microscopy (3D LSRM) with dual-wavelength illumination sources was investigated to study the distance of Mito-ER contacts in various live cells. To detect wavelength-dependent scattering, 12 nm gold nanoparticles (AuNPs) and 20 nm silver nanoparticles (AgNPs) as fluorescence-free nanoprobes were conjugated with Mito and ER. The cubic spline algorithm-based method showed improved localization precision in lateral and axial directions compared with that for previously used least squares and least cubic algorithms. The cubic spline-based depth-dependent localization was applied to the spatial localization of nanoprobes in super-resolution images, in which the average distance of Mito and ER was 22.4 nm in HeLa cells, 22.2 nm in RAW264.7 macrophage cells, 21.9 nm in AGS cells, 21.4 nm in HT29 cells, and 21.3 nm in HEK293 cells. The distances were ∼12% larger than those previously determined by electron microscopy, which demonstrated that this method was accessible and reliable for studying the intracellular structures of various live cells at the subdiffraction limit resolution.
    DOI:  https://doi.org/10.1039/d1an00852h
  2. Biochim Biophys Acta Mol Cell Biol Lipids. 2021 Jun 30. pii: S1388-1981(21)00131-1. [Epub ahead of print] 159003
    Insights into VPS13 properties and function reveal a new mechanism of eukaryotic lipid transport.
    Marianna Leonzino, Karin M Reinisch, Pietro De Camilli.
      The occurrence of protein mediated lipid transfer between intracellular membranes has been known since the late 1960's. Since these early discoveries, numerous proteins responsible for such transport, which often act at membrane contact sites, have been identified. Typically, they comprise a lipid harboring module thought to shuttle back and forth between the two adjacent bilayers. Recently, however, studies of the chorein domain protein family, which includes VPS13 and ATG2, has led to the identification of a novel mechanism of lipid transport between organelles in eukaryotic cells mediated by a rod-like protein bridge with a hydrophobic groove through which lipids can slide. This mechanism is ideally suited for bulk transport of bilayer lipids to promote membrane growth. Here we describe how studies of VPS13 led to the discovery of this new mechanism, summarize properties and known roles of VPS13 proteins, and discuss how their dysfunction may lead to disease.
    Keywords:  Chorein domain; Lipid channels; Membrane expansion
    DOI:  https://doi.org/10.1016/j.bbalip.2021.159003
  3. J Cell Biol. 2021 Sep 06. pii: e202103186. [Epub ahead of print]220(9):
    zapERtrap: A light-regulated ER release system reveals unexpected neuronal trafficking pathways.
    Ashley M Bourke, Samantha L Schwartz, Aaron B Bowen, Mason S Kleinjan, Christina S Winborn, Dean J Kareemo, Amos Gutnick, Thomas L Schwarz, Matthew J Kennedy.
      Here we introduce zapalog-mediated endoplasmic reticulum trap (zapERtrap), which allows one to use light to precisely trigger forward trafficking of diverse integral membrane proteins from internal secretory organelles to the cell surface with single cell and subcellular spatial resolution. To demonstrate its utility, we use zapERtrap in neurons to dissect where synaptic proteins emerge at the cell surface when processed through central (cell body) or remote (dendrites) secretory pathways. We reveal rapid and direct long-range trafficking of centrally processed proteins deep into the dendritic arbor to synaptic sites. Select proteins were also trafficked to the plasma membrane of the axon initial segment, revealing a novel surface trafficking hotspot. Proteins locally processed through dendritic secretory networks were widely dispersed before surface insertion, challenging assumptions for precise trafficking at remote sites. These experiments provide new insights into compartmentalized secretory trafficking and showcase the tunability and spatiotemporal control of zapERtrap, which will have broad applications for regulating cell signaling and function.
    DOI:  https://doi.org/10.1083/jcb.202103186
  4. Front Cell Dev Biol. 2021 ;9 669086
    Junctional ER Organization Affects Mechanotransduction at Cadherin-Mediated Adhesions.
    Michelle Joy-Immediato, Manuel J Ramirez, Mauricio Cerda, Yusuke Toyama, Andrea Ravasio, Pakorn Kanchanawong, Cristina Bertocchi.
      Cadherin-mediated adhesions (also known as adherens junctions) are adhesive complexes that connect neighboring cells in a tissue. While the role of the actin cytoskeleton in withstanding tension at these sites of contact is well documented, little is known about the involvement of microtubules and the associated endoplasmic reticulum (ER) network in cadherin mechanotransduction. Therefore, we investigated how the organization of ER extensions in close proximity of cadherin-mediated adhesions can affect such complexes, and vice versa. Here, we show that the extension of the ER to cadherin-mediated adhesions is tension dependent and appears to be cadherin-type specific. Furthermore, the different structural organization of the ER/microtubule network seems to affect the localization of ER-bound PTP1B at cadherin-mediated adhesions. This phosphatase is involved in the modulation of vinculin, a molecular clutch which enables differential engagement of the cadherin-catenin layer with the actomyosin cytoskeleton in response to tension. This suggests a link between structural organization of the ER/microtubule network around cadherin-specific adhesions, to control the mechanotransduction of adherens junctions by modulation of vinculin conformational state.
    Keywords:  cadherin-mediated adhesion; endoplasmic reticulum; mechanotransduction; microtubules; vinculin
    DOI:  https://doi.org/10.3389/fcell.2021.669086
  5. Cell Res. 2021 Jul 08.
    Degradation of lipid droplets by chimeric autophagy-tethering compounds.
    Yuhua Fu, Ningxie Chen, Ziying Wang, Shouqing Luo, Yu Ding, Boxun Lu.
      Degrading pathogenic proteins by degrader technologies such as PROTACs (proteolysis-targeting chimeras) provides promising therapeutic strategies, but selective degradation of non-protein pathogenic biomolecules has been challenging. Here, we demonstrate a novel strategy to degrade non-protein biomolecules by autophagy-tethering compounds (ATTECs), using lipid droplets (LDs) as an exemplar target. LDs are ubiquitous cellular structures storing lipids and could be degraded by autophagy. We hypothesized that compounds interacting with both the LDs and the key autophagosome protein LC3 may enhance autophagic degradation of LDs. We designed and synthesized such compounds by connecting LC3-binding molecules to LD-binding probes via a linker. These compounds were capable of clearing LDs almost completely and rescued LD-related phenotypes in cells and in two independent mouse models with hepatic lipidosis. We further confirmed that the mechanism of action of these compounds was mediated through LC3 and autophagic degradation. Our proof-of-concept study demonstrates the capability of degrading LDs by ATTECs. Conceptually, this strategy could be applied to other protein and non-protein targets.
    DOI:  https://doi.org/10.1038/s41422-021-00532-7
  6. Nat Struct Mol Biol. 2021 Jul 08.
    Membrane perturbation by lipidated Atg8 underlies autophagosome biogenesis.
    Tatsuro Maruyama, Jahangir Md Alam, Tomoyuki Fukuda, Shun Kageyama, Hiromi Kirisako, Yuki Ishii, Ichio Shimada, Yoshinori Ohsumi, Masaaki Komatsu, Tomotake Kanki, Hitoshi Nakatogawa, Nobuo N Noda.
      Autophagosome biogenesis is an essential feature of autophagy. Lipidation of Atg8 plays a critical role in this process. Previous in vitro studies identified membrane tethering and hemi-fusion/fusion activities of Atg8, yet definitive roles in autophagosome biogenesis remained controversial. Here, we studied the effect of Atg8 lipidation on membrane structure. Lipidation of Saccharomyces cerevisiae Atg8 on nonspherical giant vesicles induced dramatic vesicle deformation into a sphere with an out-bud. Solution NMR spectroscopy of Atg8 lipidated on nanodiscs identified two aromatic membrane-facing residues that mediate membrane-area expansion and fragmentation of giant vesicles in vitro. These residues also contribute to the in vivo maintenance of fragmented vacuolar morphology under stress in fission yeast, a moonlighting function of Atg8. Furthermore, these aromatic residues are crucial for the formation of a sufficient number of autophagosomes and regulate autophagosome size. Together, these data demonstrate that Atg8 can cause membrane perturbations that underlie efficient autophagosome biogenesis.
    DOI:  https://doi.org/10.1038/s41594-021-00614-5
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