Ceramides bind VDAC2 to trigger mitochondrial apoptosis

Shashank Dadsena; Svenja Bockelmann; John G M Mina; Dina G Hassan; Sergei Korneev; Guilherme Razzera; Helene Jahn; Patrick Niekamp; Dagmar Müller; Markus Schneider; Fikadu G Tafesse; Siewert J Marrink; Manuel N Melo; Joost C M Holthuis

doi:10.1038/s41467-019-09654-4

Ceramides bind VDAC2 to trigger mitochondrial apoptosis

Nat Commun. 2019 Apr 23;10(1):1832. doi: 10.1038/s41467-019-09654-4.

Authors

Shashank Dadsena¹, Svenja Bockelmann¹, John G M Mina^{2

3}, Dina G Hassan^{1

4}, Sergei Korneev¹, Guilherme Razzera^{5

6}, Helene Jahn¹, Patrick Niekamp¹, Dagmar Müller¹, Markus Schneider^{1

7

8}, Fikadu G Tafesse⁹, Siewert J Marrink¹⁰, Manuel N Melo^{11

12}, Joost C M Holthuis^{13

14

15}

Affiliations

¹ Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076, Osnabrück, Germany.
² Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076, Osnabrück, Germany. j.mina@tees.ac.uk.
³ School of Science, Engineering and Design, Teesside University, Middlesbrough, TS1 3BX, UK. j.mina@tees.ac.uk.
⁴ Institute of Environmental Studies and Research, Ain Shams University, Cairo, Egypt.
⁵ Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
⁶ Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Florianópolis, Brazil.
⁷ Plant Physiology Division, Department of Biology/Chemistry, University of Osnabrück, 49076, Osnabrück, Germany.
⁸ Center for Cellular Nanoanalytics, Osnabrück University, Artilleriestraße 77, 49076, Osnabrück, Germany.
⁹ Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, 97239, USA.
¹⁰ Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
¹¹ Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal. m.n.melo@itqb.unl.pt.
¹² Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands. m.n.melo@itqb.unl.pt.
¹³ Molecular Cell Biology Division, Department of Biology/Chemistry, University of Osnabrück, 49076, Osnabrück, Germany. holthuis@uos.de.
¹⁴ Center for Cellular Nanoanalytics, Osnabrück University, Artilleriestraße 77, 49076, Osnabrück, Germany. holthuis@uos.de.
¹⁵ Membrane Biochemistry and Biophysics, Bijvoet Center and Institute of Biomembranes, Utrecht University, 3584 CH, Utrecht, The Netherlands. holthuis@uos.de.

Abstract

Ceramides draw wide attention as tumor suppressor lipids that act directly on mitochondria to trigger apoptotic cell death. However, molecular details of the underlying mechanism are largely unknown. Using a photoactivatable ceramide probe, we here identify the voltage-dependent anion channels VDAC1 and VDAC2 as mitochondrial ceramide binding proteins. Coarse-grain molecular dynamics simulations reveal that both channels harbor a ceramide binding site on one side of the barrel wall. This site includes a membrane-buried glutamate that mediates direct contact with the ceramide head group. Substitution or chemical modification of this residue abolishes photolabeling of both channels with the ceramide probe. Unlike VDAC1 removal, loss of VDAC2 or replacing its membrane-facing glutamate with glutamine renders human colon cancer cells largely resistant to ceramide-induced apoptosis. Collectively, our data support a role of VDAC2 as direct effector of ceramide-mediated cell death, providing a molecular framework for how ceramides exert their anti-neoplastic activity.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Apoptosis*
Binding Sites / genetics
Ceramides / chemistry
Ceramides / metabolism*
Gene Knockout Techniques
Glutamic Acid / chemistry
Glutamic Acid / genetics
Glutamic Acid / metabolism
HCT116 Cells
HEK293 Cells
HeLa Cells
Humans
Mitochondria / physiology*
Molecular Dynamics Simulation
RNA, Small Interfering / metabolism
Recombinant Proteins / chemistry
Recombinant Proteins / genetics
Recombinant Proteins / isolation & purification
Recombinant Proteins / metabolism
Voltage-Dependent Anion Channel 1 / chemistry
Voltage-Dependent Anion Channel 1 / genetics
Voltage-Dependent Anion Channel 1 / isolation & purification
Voltage-Dependent Anion Channel 1 / metabolism
Voltage-Dependent Anion Channel 2 / chemistry
Voltage-Dependent Anion Channel 2 / genetics
Voltage-Dependent Anion Channel 2 / isolation & purification
Voltage-Dependent Anion Channel 2 / metabolism*

Substances

Ceramides
RNA, Small Interfering
Recombinant Proteins
VDAC1 protein, human
VDAC2 protein, human
Voltage-Dependent Anion Channel 2
Glutamic Acid
Voltage-Dependent Anion Channel 1

Abstract

Publication types

MeSH terms

Substances

Grants and funding