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Complete set of the Atg8–E1–E2–E3 conjugation machinery forms an interaction web that mediates membrane shaping

Nature Structural & Molecular Biology volume 31, pages 170–178 (2024)Cite this article

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Abstract

Atg8, a ubiquitin-like protein, is conjugated with phosphatidylethanolamine (PE) via Atg7 (E1), Atg3 (E2) and Atg12–Atg5–Atg16 (E3) enzymatic cascade and mediates autophagy. However, its molecular roles in autophagosome formation are still unclear. Here we show that Saccharomyces cerevisiae Atg8–PE and E1–E2–E3 enzymes together construct a stable, mobile membrane scaffold. The complete scaffold formation induces an in-bud in prolate-shaped giant liposomes, transforming their morphology into one reminiscent of isolation membranes before sealing. In addition to their enzymatic roles in Atg8 lipidation, all three proteins contribute nonenzymatically to membrane scaffolding and shaping. Nuclear magnetic resonance analyses revealed that Atg8, E1, E2 and E3 together form an interaction web through multivalent weak interactions, where the intrinsically disordered regions in Atg3 play a central role. These data suggest that all six Atg proteins in the Atg8 conjugation machinery control membrane shaping during autophagosome formation.

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Fig. 1: Atg8 conjugation machinery possesses membrane invagination activity.
Fig. 2: Atg8–PE and E1, E2 and E3 enzymes assemble on the membrane.
Fig. 3: Coiled-coil domain in Atg16 mediates a scaffold formation.
Fig. 4: NTD in Atg7 homodimer mediates scaffold formation.
Fig. 5: FR and HR in Atg3 mediate scaffold formation.
Fig. 6: Membrane shaping by Atg8–PE and E1–E2–E3 conjugation machinery.

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Data availability

Microscopic data are deposited online at https://doi.org/10.6084/m9.figshare.24165963. NMR data are deposited online at https://doi.org/10.6084/m9.figshare.23939424. Source data are provided with this paper.

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Acknowledgements

We thank Y. Ishii for assistance with protein preparation. This work was supported in part by JSPS KAKENHI grant nos. JP19H05707 (to N.N.N.), JP21K15045 (to T.M.), JP19K16344 (to D.N.), JP19H05708 (to H.N.), JP19K16071 and JP22K06123 (to T.K.), CREST, Japan Science and Technology Agency grant nos. JPMJCR13M7 (to N.N.N. and H.N.) and JPMJCR20E3 (to N.N.N.), AMED-CREST, Japan Agency for Medical Research and Development grant no. JP21gm1410004s0102 (to H.N.) and grants from the Takeda Science Foundation (to N.N.N., T.M. and D.N.), and from the Tokyo Biochemical Research foundation (to N.N.N. and J.M.A.).

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Author notes

  1. These authors contributed equally: Jahangir Md. Alam, Tatsuro Maruyama.

Authors and Affiliations

  1. Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan

    Jahangir Md. Alam, Tatsuro Maruyama & Nobuo N. Noda

  2. Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan

    Daisuke Noshiro & Nobuo N. Noda

  3. Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan

    Chika Kakuta, Tetsuya Kotani & Hitoshi Nakatogawa

  4. School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan

    Hitoshi Nakatogawa

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Contributions

J.M.A., T.M. and N.N.N. designed the research. J.M.A. and T.M. performed GUV experiments. D.N. performed HS-AFM experiments. T.M. performed NMR experiments. C.K., T.K. and H.N. performed budding yeast experiments. J.M.A., T.M., D.N., T.K., H.N. and N.N.N. analyzed data. T.M. and N.N.N. wrote the paper with the inputs from all the authors. N.N.N. supervised the work.

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Correspondence to Nobuo N. Noda.

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Nature Structural & Molecular Biology thanks Helen Walden and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available. Primary Handling Editor: Katarzyna Ciazynska, in collaboration with the Nature Structural & Molecular Biology team.

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Extended data

Extended Data Fig. 1 Non-enzymatic effect of conjugation machinery on Atg8-conjugated membrane morphology.

Atg7 (a), Atg3 (b), Atg12–Atg5–Atg16 (c), Atg7 and Atg3 (d), and Atg7 and Atg12–Atg5–Atg16 (e) are applied to Atg8R117C chemically conjugated to PE MCC lipid in a prolate GUV. In (b) and (d), a prolate GUV is tattered by the additions of Atg3 or Atg7 and Atg3, respectively. Experiments were repeated independently five times or more with similar results. DIC, differential interference contrast. Scale bars, 10 μm.

Extended Data Fig. 2 Estimation of area density of Atg8–PE on GUV.

NBD-DOPE in LUV and Alexa Fluor 488-Atg8 in bulk are used for the calibration in fluorescence sensitivity. NBD-DOPE is supposed to be incorporated into GUV stoichiometrically. For area density measurement of Atg8–PE on GUV, Alexa Fluor 488-Atg8 (5.0 μM), Atg7 (2.5 μM), Atg3 (2.5 μM) and Atg12–Atg5–Atg16 (1.25 μM) are introduced to the vicinity of GUV in the presence of MgATP via micropipette. Lipid composition is POPC:POPE:PI:Liss Rhod PE = 59:30:10:1 (mol%). The areal fraction of Atg8–PE at a plateau is estimated to be 6.2% from the fluorescence, corresponding to one Atg8–PE molecule per 161 nm2. Experiments were repeated independently three times with similar results. Scale bar, 10 μm.

Source data

Extended Data Fig. 3 NMR analyses of Atg7C, Atg3FR and Atg3HR.

a, 1H-15N HSQC spectral changes of [u-15N]-Atg7C with the titration of Atg8 (left), Atg12–Atg5–Atg16N (middle) and Atg7NTD (right). b, 1H-15N HSQC spectral changes of [u-15N]-Atg3FR with the titration of Atg8 (left), Atg12–Atg5–Atg16N (middle) and Atg7NTD (right). c, 1H-15N HSQC spectral changes of [u-15N]-Atg3HR with the titration of Atg8 (left), Atg12–Atg5–Atg16N (right). Insets show amide signal derived from the side chain in Trp. The protein ratios in the titrations are indicated in each panel, respectively.

Extended Data Fig. 4 Mutational analyses on Atg7 and Atg16.

a, Membrane-bound model of Atg16 predicted by the PPM server38 using the monomeric AlphaFold2 structure of Atg16. Ala mutations denoted as mut 1 and mut 2 were introduced into membrane-facing residues. b, c, Yeast cells were grown to mid-log phase, treated with rapamycin for 4 h, and examined for autophagic activity and the production of Atg8–PE by immunoblotting using anti-myc, anti-GFP, anti-Ape1, anti-Atg8, and anti-HA antibodies. The production of Atg8–PE was examined by urea-SDS-PAGE and immunoblotting. mApe1, mature Ape1; prApe1, Ape1 proform; GFP’, GFP fragment generated by vacuolar degradation of Pgk1-GFP. Experiments were repeated independently twice with similar results. b, Atg16 mutants or truncates at the coiled-coil that showed defects in autophagy activity (Pgk1-GFP procession and Ape1 maturation) also showed defects in Atg8-PE formation. c, The role of Atg7NTD in autophagy activity besides Atg8-PE formation could not be studied since Atg7CTD alone failed to form Atg8-PE even under overexpressing conditions. d, Localization analyses of Atg proteins after lipidation reaction using Atg16 mutants. Data are mean with plots for n = 5 (Atg16D101A E102A), 4 (Atg16mut 1) and 7 (Atg16mut 1+mut 2) GUVs.

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Supplementary Video 1

Shape changes of prolate GUV along with Atg8–PE conjugation reaction. This video was used to generate the images shown in Fig. 1b.

Supplementary Video 2

Another example of shape changes of prolate GUV along with Atg8–PE conjugation reaction.

Supplementary Video 3

HS-AFM observation of the Atg8 conjugation machinery shown in Fig. 4d. Scale bar, 100 nm. Height scale, 0–17 nm.

Supplementary Video 4

HS-AFM observation of the Atg8 conjugation machinery on lipid bilayers shown in Fig. 4e. Scale bar, 30 nm. Height scale, 0–8 nm.

Supplementary Video 5

HS-AFM observation of the glutaraldehyde-treated Atg8 conjugation machinery on lipid bilayers shown in Fig. 4f, left. Scale bar, 50 nm.

Supplementary Video 6

HS-AFM observation of the glutaraldehyde-treated Atg8 conjugation machinery on lipid bilayers shown in Fig. 4f, right. Scale bar, 50 nm.

Source data

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Source Data Extended Data Fig. 2

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Source Data Extended Data Fig. 4

Unprocessed western blots.

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Alam, J.M., Maruyama, T., Noshiro, D. et al. Complete set of the Atg8–E1–E2–E3 conjugation machinery forms an interaction web that mediates membrane shaping. Nat Struct Mol Biol 31, 170–178 (2024). https://doi.org/10.1038/s41594-023-01132-2

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