1
|
Ballesteros U, Iriondo MN, Varela YR, Goñi FM, Alonso A, Montes LR, Etxaniz A. The N-terminal region of the ATG8 autophagy protein LC3C is essential for its membrane fusion properties. Int J Biol Macromol 2024; 262:129835. [PMID: 38302024 DOI: 10.1016/j.ijbiomac.2024.129835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/03/2024]
Abstract
Autophagy is a catabolic process in which a double-membrane organelle, the autophagosome (AP), engulfs cellular components that will be degraded in the lysosomes. ATG8 protein family members participate at various stages of AP formation. The present study compares the capacity to induce lipid-vesicle tethering and fusion of two ATG8 family members, LC3B and LC3C, with model membranes. LC3B is the most thoroughly studied ATG8 protein. It is generally considered as an autophagosomal marker and a canonical representative of the LC3 subfamily. LC3C is less studied, but recent data have reported its implication in various processes, crucial to cellular homeostasis. The results in this paper show that LC3C induces higher levels of tethering and of intervesicular lipid mixing than LC3B. As the N-terminus of LC3C is different from that of the other family members, various mutants of the N-terminal region of both LC3B and LC3C were designed, and their activities compared. It was concluded that the N-terminal region of LC3C was responsible for the enhanced vesicle tethering, membrane perturbation and vesicle-vesicle fusion activities of LC3C as compared to LC3B. The results suggest a specialized function of LC3C in the AP expansion process.
Collapse
Affiliation(s)
- Uxue Ballesteros
- Department of Biochemistry and Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940 Leioa, Spain
| | - Marina N Iriondo
- Department of Biochemistry and Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940 Leioa, Spain
| | - Yaiza R Varela
- Department of Biochemistry and Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940 Leioa, Spain
| | - Félix M Goñi
- Department of Biochemistry and Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940 Leioa, Spain
| | - Alicia Alonso
- Department of Biochemistry and Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940 Leioa, Spain
| | - L Ruth Montes
- Department of Biochemistry and Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940 Leioa, Spain.
| | - Asier Etxaniz
- Department of Biochemistry and Instituto Biofisika (CSIC, UPV/EHU), University of the Basque Country, 48940 Leioa, Spain.
| |
Collapse
|
2
|
Varela YR, Iriondo MN, Goñi FM, Alonso A, Montes LR. Ceramide regulation of autophagy: A biophysical approach. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159444. [PMID: 38056762 DOI: 10.1016/j.bbalip.2023.159444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023]
Abstract
Specific membrane lipids play unique roles in (macro)autophagy. Those include phosphatidylethanolamine, to which LC3/GABARAP autophagy proteins become covalently bound in the process, or cardiolipin, an important effector in mitochondrial autophagy (or mitophagy). Ceramide (Cer), or N-acyl sphingosine, is one of the simplest sphingolipids, known as a stress signal in the apoptotic pathway. Moreover, Cer is increasingly being recognized as an autophagy activator, although its mechanism of action is unclear. In the present review, the proposed Cer roles in autophagy are summarized, together with some biophysical properties of Cer in membranes. Possible pathways for Cer activation of autophagy are discussed, including specific protein binding of the lipid, and Cer-dependent perturbation of bilayer properties. Cer generation of lateral inhomogeneities (domain formation) is given special attention. Recent biophysical results, including fluorescence and atomic force microscopy data, show Cer-promoted enhanced binding of LC3/GABARAP to lipid bilayers. These observations could be interpreted in terms of the putative formation of Cer-rich nanodomains.
Collapse
Affiliation(s)
- Yaiza R Varela
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
| | - Marina N Iriondo
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
| | - Félix M Goñi
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
| | - Alicia Alonso
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain.
| | - L Ruth Montes
- Instituto Biofisika (UPV/EHU, CSIC) and Departamento de Bioquímica, Universidad del País Vasco, 48940 Leioa, Spain
| |
Collapse
|
3
|
Varela YR, Alonso A. LC3/GABARAP binding to fluid membranes is potentiated by ceramide. Autophagy 2023; 19:1371-1373. [PMID: 36251508 PMCID: PMC10012933 DOI: 10.1080/15548627.2022.2136821] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2022] [Accepted: 10/12/2022] [Indexed: 11/02/2022] Open
Abstract
LC3/GABARAP constitute a macroautophagy/autophagy-related protein family derived from yeast Atg8. The involvement of specific lipids in LC3/GABARAP function is poorly understood. Exploring the interaction of LC3/GABARAP proteins with phosphatidylcholine- or sphingomyelin-based bilayers has revealed that cardiolipin is essential for the protein-bilayer interaction, and that ceramide markedly increases binding. Giant unilamellar vesicles examined under confocal fluorescence microscopy reveal that ceramide segregates laterally into very rigid domains, while GABARAP binds only the more fluid regions, suggesting that the enhancing role of ceramide is exerted by the minority of ceramide molecules dispersed in the fluid phase.Abbreviations: Atg8: autophagy-related 8; Cer: ceramide; CL: cardiolipin; eCer: egg ceramide; GABARAP: gamma-aminobutyric acid receptor associated protein; GUV: giant unilamellar vesicle; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; Rho-PE: lissamine rhodamine phosphatidylethanolamine; SM: sphingomyelin.
Collapse
Affiliation(s)
- Yaiza R Varela
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| | - Alicia Alonso
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa, Spain
| |
Collapse
|
4
|
Lipids in Mitochondrial Macroautophagy: Phase Behavior of Bilayers Containing Cardiolipin and Ceramide. Int J Mol Sci 2023; 24:ijms24065080. [PMID: 36982156 PMCID: PMC10049649 DOI: 10.3390/ijms24065080] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023] Open
Abstract
Cardiolipin (CL) is a key lipid for damaged mitochondrial recognition by the LC3/GABARAP human autophagy proteins. The role of ceramide (Cer) in this process is unclear, but CL and Cer have been proposed to coexist in mitochondria under certain conditions. Varela et al. showed that in model membranes composed of egg sphingomyelin (eSM), dioleoyl phosphatidylethanolamine (DOPE), and CL, the addition of Cer enhanced the binding of LC3/GABARAP proteins to bilayers. Cer gave rise to lateral phase separation of Cer-rich rigid domains but protein binding took place mainly in the fluid continuous phase. In the present study, a biophysical analysis of bilayers composed of eSM, DOPE, CL, and/or Cer was attempted to understand the relevance of this lipid coexistence. Bilayers were studied by differential scanning calorimetry, confocal fluorescence microscopy, and atomic force microscopy. Upon the addition of CL and Cer, one continuous phase and two segregated ones were formed. In bilayers with egg phosphatidylcholine instead of eSM, in which the binding of LC3/GABARAP proteins hardly increased with Cer in the former study, a single segregated phase was formed. Assuming that phase separation at the nanoscale is ruled by the same principles acting at the micrometer scale, it is proposed that Cer-enriched rigid nanodomains, stabilized by eSM:Cer interactions formed within the DOPE- and CL-enriched fluid phase, result in structural defects at the rigid/fluid nanointerfaces, thus hypothetically facilitatingLC3/GABARAP protein interaction.
Collapse
|
5
|
Iriondo MN, Etxaniz A, Varela YR, Ballesteros U, Lázaro M, Valle M, Fracchiolla D, Martens S, Montes LR, Goñi FM, Alonso A. Effect of ATG12-ATG5-ATG16L1 autophagy E3-like complex on the ability of LC3/GABARAP proteins to induce vesicle tethering and fusion. Cell Mol Life Sci 2023; 80:56. [PMID: 36729310 PMCID: PMC9894987 DOI: 10.1007/s00018-023-04704-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 02/03/2023]
Abstract
In macroautophagy, the autophagosome (AP) engulfs portions of cytoplasm to allow their lysosomal degradation. AP formation in humans requires the concerted action of the ATG12 and LC3/GABARAP conjugation systems. The ATG12-ATG5-ATG16L1 or E3-like complex (E3 for short) acts as a ubiquitin-like E3 enzyme, promoting LC3/GABARAP proteins anchoring to the AP membrane. Their role in the AP expansion process is still unclear, in part because there are no studies comparing six LC3/GABARAP family member roles under the same conditions, and also because the full human E3 was only recently available. In the present study, the lipidation of six members of the LC3/GABARAP family has been reconstituted in the presence and absence of E3, and the mechanisms by which E3 and LC3/GABARAP proteins participate in vesicle tethering and fusion have been investigated. In the absence of E3, GABARAP and GABARAPL1 showed the highest activities. Differences found within LC3/GABARAP proteins suggest the existence of a lipidation threshold, lower for the GABARAP subfamily, as a requisite for tethering and inter-vesicular lipid mixing. E3 increases and speeds up lipidation and LC3/GABARAP-promoted tethering. However, E3 hampers LC3/GABARAP capacity to induce inter-vesicular lipid mixing or subsequent fusion, presumably through the formation of a rigid scaffold on the vesicle surface. Our results suggest a model of AP expansion in which the growing regions would be areas where the LC3/GABARAP proteins involved should be susceptible to lipidation in the absence of E3, or else a regulatory mechanism would allow vesicle incorporation and phagophore growth when E3 is present.
Collapse
Affiliation(s)
- Marina N. Iriondo
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain ,Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Asier Etxaniz
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain ,Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Yaiza R. Varela
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain ,Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Uxue Ballesteros
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain ,Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Melisa Lázaro
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia Spain
| | - Mikel Valle
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Bizkaia Spain
| | - Dorotea Fracchiolla
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Sascha Martens
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - L. Ruth Montes
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain ,Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Félix M. Goñi
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain ,Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940 Leioa, Spain
| | - Alicia Alonso
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940, Leioa, Spain. .,Department of Biochemistry and Molecular Biology, University of the Basque Country, 48940, Leioa, Spain.
| |
Collapse
|