1
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Cheung YWS, Nam SE, Fairlie GMJ, Scheu K, Bui JM, Shariati HR, Gsponer J, Yip CK. Structure of the human autophagy factor EPG5 and the molecular basis of its conserved mode of interaction with Atg8-family proteins. Autophagy 2025; 21:1173-1191. [PMID: 39809444 PMCID: PMC12087653 DOI: 10.1080/15548627.2024.2447213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 12/19/2024] [Accepted: 12/22/2024] [Indexed: 01/16/2025] Open
Abstract
The multi-step macroautophagy/autophagy process ends with the cargo-laden autophagosome fusing with the lysosome to deliver the materials to be degraded. The metazoan-specific autophagy factor EPG5 plays a crucial role in this step by enforcing fusion specificity and preventing mistargeting. How EPG5 exerts its critical function and how its deficiency leads to diverse phenotypes of the rare multi-system disorder Vici syndrome are not fully understood. Here, we report the first structure of human EPG5 (HsEPG5) determined by cryo-EM and AlphaFold2 modeling. Our structure revealed that HsEPG5 is constructed from helical bundles analogous to tethering factors in membrane trafficking pathways but contains a unique protruding thumb domain positioned adjacent to the atypical tandem LIR motifs involved in interaction with the GABARAP subfamily of Atg8-family proteins. Our NMR spectroscopic, molecular dynamics simulations and AlphaFold modeling studies showed that the HsEPG5 tandem LIR motifs only bind the canonical LIR docking site (LDS) on GABARAP without engaging in multivalent interaction. Our co-immunoprecipitation analysis further indicated that full-length HsEPG5-GABARAP interaction is mediated primarily by LIR1. Finally, our biochemical affinity isolation, X-ray crystallographic analysis, affinity measurement, and AlphaFold modeling demonstrated that this mode of binding is observed between Caenorhabditis elegans EPG-5 and its Atg8-family proteins LGG-1 and LGG-2. Collectively our work generated novel insights into the structural properties of EPG5 and how it potentially engages with the autophagosome to confer fusion specificity.ABBREVIATIONS: ATG: autophagy related; CSP: chemical shift perturbation; eGFP: enhanced green fluoresent protein; EM: electron microscopy; EPG5: ectopic P-granules 5 autophagy tethering factor; GST: glutathione S-transferase; HP: hydrophobic pocket; HSQC: heteronuclear single-quantum correlation; ITC: isothermal titration calorimetry; LDS: LC3 docking site; LIR: LC3-interacting region; MD: molecular dynamics; NMR: nuclear magnetic resonance; TEV: tobacco etch virus.
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Affiliation(s)
- Yiu Wing Sunny Cheung
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Sung-Eun Nam
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Gage M. J. Fairlie
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Karlton Scheu
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Jennifer M. Bui
- Michael Smith Laboratories, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Hannah R. Shariati
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Jörg Gsponer
- Michael Smith Laboratories, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Calvin K. Yip
- Life Sciences Institute, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
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2
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Song JZ, Li H, Yang H, Liu R, Zhang W, He T, Xie MX, Chen C, Cui L, Wu S, Rong Y, Pan LF, Zhu J, Gong Q, Wang J, Qin Z, Xie Z. Recruitment of Atg1 to the phagophore by Atg8 orchestrates autophagy machineries. Nat Struct Mol Biol 2025:10.1038/s41594-025-01546-0. [PMID: 40295771 DOI: 10.1038/s41594-025-01546-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 03/24/2025] [Indexed: 04/30/2025]
Abstract
Autophagy-related (Atg) proteins catalyze autophagosome formation at the phagophore assembly site (PAS). The assembly of Atg proteins at the PAS follows a semihierarchical order, in which Atg8 is thought to be quite downstream but still able to control the size of autophagosomes. Yet, how Atg8 coordinates multiple branches of autophagy machinery to regulate autophagosomal size is not clear. Here, we show that, in yeast, Atg8 positively regulates the autophagy-specific phosphatidylinositol 3-OH kinase complex and the retrograde trafficking of Atg9 vesicles through interaction with Atg1. Mechanistically, Atg8 does not enhance the kinase activity of Atg1; instead, it recruits Atg1 to the surface of the phagophore likely to orient Atg1's activity toward select substrates, leading to efficient phagophore expansion. Artificial tethering of Atg1 kinase domains to Atg8s enhanced autophagy in yeast, human and plant cells and improved muscle performance in worms. We propose that Atg8-mediated relocation of Atg1 from the PAS scaffold to the phagophore is a critical step in positive autophagy regulation.
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Affiliation(s)
- Jing-Zhen Song
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hui Li
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Haiyan Yang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Rui Liu
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenting Zhang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Tianlong He
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Meng-Xi Xie
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Chen
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Li Cui
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shian Wu
- School of Life Sciences, Nankai University, Tianjin, China
| | - Yueguang Rong
- School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Li-Feng Pan
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Jing Zhu
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingqiu Gong
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Juan Wang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China.
| | - Zhao Qin
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, School of Medicine, Tongji University, Shanghai, China.
- Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, China.
| | - Zhiping Xie
- State Key Laboratory of Microbial Metabolism and Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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3
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Cillo M, Buonomo V, Vainshtein A, Grumati P. Autophagy, ER-phagy and ER Dynamics During Cell Differentiation. J Mol Biol 2025:169151. [PMID: 40222412 DOI: 10.1016/j.jmb.2025.169151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2024] [Revised: 04/07/2025] [Accepted: 04/08/2025] [Indexed: 04/15/2025]
Abstract
The endoplasmic reticulum (ER) is a multifunctional organelle essential for protein and lipid synthesis, ion transport and inter-organelle communication. It comprises a highly dynamic network of membranes that continuously reshape to support a wide range of cellular processes. During cellular differentiation, extensive remodelling of both ER architecture and its proteome is required to accommodate alterations in cell morphology and function. Autophagy, and ER-phagy in particular, plays a pivotal role in reshaping the ER, enabling cells to meet their evolving needs and adapt to developmental cues. Despite the ER's critical role in cellular differentiation, the mechanisms responsible for regulating its dynamics are not fully understood. Emerging evidence suggests that transcriptional and post-translational regulation play a role in fine-tuning ER-phagy and the unfolded protein response (UPR). This review explores the molecular basis of autophagy and ER-phagy, highlighting their role in ER remodelling during cellular differentiation. A deeper understanding of these processes could open new avenues for targeted therapeutic approaches in conditions where ER remodelling is impaired.
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Affiliation(s)
- Michele Cillo
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy; Department of Clinical Medicine and Surgery, Federico II University, 80131 Naples, Italy
| | - Viviana Buonomo
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy; Department of Clinical Medicine and Surgery, Federico II University, 80131 Naples, Italy
| | | | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy; Department of Clinical Medicine and Surgery, Federico II University, 80131 Naples, Italy.
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4
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Campisi D, Hawkins N, Bonjour K, Wollert T. The Role of WIPI2, ATG16L1 and ATG12-ATG5 in Selective and Nonselective Autophagy. J Mol Biol 2025:169138. [PMID: 40221132 DOI: 10.1016/j.jmb.2025.169138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2024] [Revised: 02/24/2025] [Accepted: 04/07/2025] [Indexed: 04/14/2025]
Abstract
Autophagy is a conserved cellular recycling pathway that delivers damaged or superfluous cytoplasmic material to lysosomes for degradation. In response to cytotoxic stress or starvation, autophagy can also sequester bulk cytoplasm and deliver it to lysosomes to regenerate building blocks. In macroautophagy, a membrane cisterna termed phagophore that encloses autophagic cargo is generated. The formation of the phagophore depends on a conserved machinery of autophagy related proteins. The phosphatidylinositol(3)-phosphate binding protein WIPI2 facilitates the transition from phagophore initiation to phagophore expansion by recruiting the ATG12-ATG5-ATG16L1 complex to phagophores. This complex functions as an E3-ligase to conjugate ubiquitin-like ATG8 proteins to phagophore membranes, which promotes tethering of cargo to phagophore membranes, phagophore expansion, maturation and the fusion of autophagosomes with lysosomes. ATG16L1 also has important functions independently of ATG12-ATG5 in autophagy and beyond. In this review, we will summarize the functions of WIPI2 and ATG16L1 in selective and nonselective autophagy.
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Affiliation(s)
- Daniele Campisi
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
| | - N'Toia Hawkins
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
| | - Kennedy Bonjour
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France
| | - Thomas Wollert
- Membrane Biochemistry and Transport, Institut Pasteur, Université de Paris, UMR3691 CNRS, 75015 Paris, France.
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5
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North BJ, Ohnstad AE, Ragusa MJ, Shoemaker CJ. The LC3-interacting region of NBR1 is a protein interaction hub enabling optimal flux. J Cell Biol 2025; 224:e202407105. [PMID: 39928048 PMCID: PMC11809422 DOI: 10.1083/jcb.202407105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 12/05/2024] [Accepted: 01/07/2025] [Indexed: 02/11/2025] Open
Abstract
During autophagy, toxic cargo is encapsulated by autophagosomes and trafficked to lysosomes for degradation. NBR1, an autophagy receptor targeting ubiquitinated aggregates, serves as a model for studying the multivalent, heterotypic interactions of cargo-bound receptors. Here, we find that three critical NBR1 partners-ATG8-family proteins, FIP200, and TAX1BP1-each bind to distinct, overlapping determinants within a short linear interaction motif (SLiM). To explore whether overlapping SLiMs extend beyond NBR1, we analyzed >100 LC3-interacting regions (LIRs), revealing that FIP200 and/or TAX1BP1 binding to LIRs is a common phenomenon and suggesting LIRs as protein interaction hotspots. Phosphomimetic peptides demonstrate that phosphorylation generally enhances FIP200 and ATG8-family binding but not TAX1BP1, indicating differential regulation. In vivo, LIR-mediated interactions with TAX1BP1 promote optimal NBR1 flux by leveraging additional functionalities from TAX1BP1. These findings reveal a one-to-many binding modality in the LIR motif of NBR1, illustrating the cooperative mechanisms of autophagy receptors and the regulatory potential of multifunctional SLiMs.
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Affiliation(s)
- Brian J. North
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Amelia E. Ohnstad
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | | | - Christopher J. Shoemaker
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
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6
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Leveille A, Schwarzrock T, Brown H, True B, Plasencia J, Neudecker P, Üffing A, Weiergräber OH, Willbold D, Kritzer JA. Exploring Arylidene-Indolinone Ligands of Autophagy Proteins LC3B and GABARAP. ACS Med Chem Lett 2025; 16:271-277. [PMID: 39967642 PMCID: PMC11831563 DOI: 10.1021/acsmedchemlett.4c00517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 12/17/2024] [Accepted: 12/18/2024] [Indexed: 02/20/2025] Open
Abstract
We report the first structure-activity studies of arylidene-indolinone compound GW5074, which was reported as a ligand of autophagy-related protein LC3B. The literature has conflicting information on the binding affinity of this compound, and there is some debate regarding its use as a component of autophagy-dependent degrader compounds. We developed an AlphaScreen assay to measure competitive inhibition of the binding of known peptide ligands to LC3B and its paralog GABARAP. Eighteen analogs were synthesized and tested against both proteins. Inhibitory potencies were found to be in the mid- to high-micromolar range. 2D-NMR data revealed the binding site on GABARAP as hydrophobic pocket 1, where native peptide ligands bind with an aromatic side chain. Our results suggest that GW5074 binds LC3B and GABARAP with micromolar affinity. These affinities could support further exploration in targeted protein degradation, but only if off-target effects and poor solubility can be appropriately addressed.
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Affiliation(s)
- Alexandria
N. Leveille
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Thomas Schwarzrock
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Hawley Brown
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Bennett True
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Joanet Plasencia
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Philipp Neudecker
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225Düsseldorf, Germany
- Institut
für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany
| | - Alina Üffing
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225Düsseldorf, Germany
- Institut
für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany
| | - Oliver H. Weiergräber
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225Düsseldorf, Germany
- Institut
für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany
| | - Dieter Willbold
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225Düsseldorf, Germany
- Institut
für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Forschungszentrum Jülich, 52425Jülich, Germany
| | - Joshua A. Kritzer
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
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7
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Begar E, Seyrek E, Firat‐Karalar EN. Navigating centriolar satellites: the role of PCM1 in cellular and organismal processes. FEBS J 2025; 292:688-708. [PMID: 38825736 PMCID: PMC11839937 DOI: 10.1111/febs.17194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/20/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024]
Abstract
Centriolar satellites are ubiquitous membrane-less organelles that play critical roles in numerous cellular and organismal processes. They were initially discovered through electron microscopy as cytoplasmic granules surrounding centrosomes in vertebrate cells. These structures remained enigmatic until the identification of pericentriolar material 1 protein (PCM1) as their molecular marker, which has enabled their in-depth characterization. Recently, centriolar satellites have come into the spotlight due to their links to developmental and neurodegenerative disorders. This review presents a comprehensive summary of the major advances in centriolar satellite biology, with a focus on studies that investigated their biology associated with the essential scaffolding protein PCM1. We begin by exploring the molecular, cellular, and biochemical properties of centriolar satellites, laying the groundwork for a deeper understanding of their functions and mechanisms at both cellular and organismal levels. We then examine the implications of their dysregulation in various diseases, particularly highlighting their emerging roles in neurodegenerative and developmental disorders, as revealed by organismal models of PCM1. We conclude by discussing the current state of knowledge and posing questions about the adaptable nature of these organelles, thereby setting the stage for future research.
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Affiliation(s)
- Efe Begar
- Department of Molecular Biology and GeneticsKoç UniversityIstanbulTurkey
| | - Ece Seyrek
- Department of Molecular Biology and GeneticsKoç UniversityIstanbulTurkey
| | - Elif Nur Firat‐Karalar
- Department of Molecular Biology and GeneticsKoç UniversityIstanbulTurkey
- School of MedicineKoç UniversityIstanbulTurkey
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8
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Kolapalli SP, Beese CJ, Reid SE, Brynjólfsdóttir SH, Jørgensen MH, Jain A, Cuenco J, Lewinska M, Abdul-Al A, López AR, Jäättelä M, Sakamoto K, Andersen JB, Maeda K, Rusten TE, Lund AH, Frankel LB. Pellino 3 E3 ligase promotes starvation-induced autophagy to prevent hepatic steatosis. SCIENCE ADVANCES 2025; 11:eadr2450. [PMID: 39823344 PMCID: PMC11740972 DOI: 10.1126/sciadv.adr2450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 12/18/2024] [Indexed: 01/30/2025]
Abstract
Nutrient deprivation is a major trigger of autophagy, a conserved quality control and recycling process essential for cellular and tissue homeostasis. In a high-content image-based screen of the human ubiquitome, we here identify the E3 ligase Pellino 3 (PELI3) as a crucial regulator of starvation-induced autophagy. Mechanistically, PELI3 localizes to autophagic membranes, where it interacts with the ATG8 proteins through an LC3-interacting region (LIR). This facilitates PELI3-mediated ubiquitination of ULK1, driving ULK1's subsequent proteasomal degradation. PELI3 depletion leads to an aberrant accumulation and mislocalization of ULK1 and disrupts the early steps of autophagosome formation. Genetic deletion of Peli3 in mice impairs fasting-induced autophagy in the liver and enhances starvation-induced hepatic steatosis by reducing autophagy-mediated clearance of lipid droplets. Notably, PELI3 expression is decreased in the livers of patients with metabolic dysfunction-associated steatotic liver disease (MASLD), suggesting its role in hepatic steatosis development in humans. The findings suggest that PELI3-mediated control of autophagy plays a protective role in liver health.
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Affiliation(s)
- Srinivasa P. Kolapalli
- Cellular Homeostasis and Recycling, Danish Cancer Institute, DK-2100 Copenhagen, Denmark
| | - Carsten J. Beese
- Cellular Homeostasis and Recycling, Danish Cancer Institute, DK-2100 Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Steven E. Reid
- Cellular Homeostasis and Recycling, Danish Cancer Institute, DK-2100 Copenhagen, Denmark
| | | | - Maria H. Jørgensen
- Cellular Homeostasis and Recycling, Danish Cancer Institute, DK-2100 Copenhagen, Denmark
| | - Ashish Jain
- Center for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Joyceline Cuenco
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Monika Lewinska
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Gubra, DK-2970 Hørsholm, Denmark
| | - Ahmad Abdul-Al
- Cellular Homeostasis and Recycling, Danish Cancer Institute, DK-2100 Copenhagen, Denmark
| | - Aida R. López
- Cellular Homeostasis and Recycling, Danish Cancer Institute, DK-2100 Copenhagen, Denmark
| | - Marja Jäättelä
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, DK-2100 Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kei Sakamoto
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jesper B. Andersen
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kenji Maeda
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Institute, DK-2100 Copenhagen, Denmark
| | - Tor E. Rusten
- Center for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anders H. Lund
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Lisa B. Frankel
- Cellular Homeostasis and Recycling, Danish Cancer Institute, DK-2100 Copenhagen, Denmark
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
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9
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Aponte-Diaz D, Harris JM, Kang TE, Korboukh V, Sotoudegan MS, Gray JL, Yennawar NH, Moustafa IM, Macadam A, Cameron CE. Non-lytic spread of poliovirus requires the nonstructural protein 3CD. mBio 2025; 16:e0327624. [PMID: 39665531 PMCID: PMC11708018 DOI: 10.1128/mbio.03276-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Accepted: 11/14/2024] [Indexed: 12/13/2024] Open
Abstract
Non-enveloped viruses like poliovirus (PV) have evolved the capacity to spread by non-lytic mechanisms. For PV, this mechanism exploits the host secretory autophagy pathway. Virions are selectively incorporated into autophagosomes, double-membrane vesicles that travel to the plasma membrane, fuse, and release single-membrane vesicles containing virions. Loading of cellular cargo into autophagosomes relies on direct or indirect interactions with microtubule-associated protein 1B-light chain 3 (LC3) that are mediated by motifs referred to as LC3-interaction regions (LIRs). We have identified a PV mutant with a severe defect in non-lytic spread. An F-to-Y substitution in a putative LIR of the nonstructural protein 3CD prevented virion incorporation into LC3-positive autophagosomes and virion trafficking to the plasma membrane for release. Using high-angle annular dark-field scanning transmission electron microscopy to monitor PV-induced autophagosome biogenesis, for the first time, we show that virus-induced autophagic signals yield normal autophagosomes, even in the absence of virions. The F-to-Y derivative of PV 3CD was unable to support normal autophagosome biogenesis. Together, these studies make a compelling case for the direct role of a viral nonstructural protein in the formation and loading of the vesicular carriers used for non-lytic spread that may depend on the proper structure, accessibility, and/or dynamics of its LIR. The studies of PV 3CD protein reported here will hopefully provoke a more deliberate look at the presence and function of LIR motifs in viral proteins of viruses known to use autophagy as the basis for non-lytic spread. IMPORTANCE Poliovirus (PV) and other enteroviruses hijack the cellular secretory autophagy pathway for non-lytic virus transmission. While much is known about the cellular factors required for non-lytic transmission, much less is known about viral factors contributing to transmission. We have discovered a PV nonstructural protein required for multiple steps of the pathway leading to vesicle-enclosed virions. This discovery should facilitate the identification of the specific steps of the cellular secretory autophagy pathway and corresponding factors commandeered by the virus and may uncover novel targets for antiviral therapy.
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Affiliation(s)
- David Aponte-Diaz
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jayden M. Harris
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Tongjia Ella Kang
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Victoria Korboukh
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Mohamad S. Sotoudegan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer L. Gray
- Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Neela H. Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ibrahim M. Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Andrew Macadam
- Division of Vaccines, Medicines and Healthcare Products Regulatory Agency, Potters Bar, Herts., United Kingdom
| | - Craig E. Cameron
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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10
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Alizadeh J, da Silva Rosa SC, Cordani M, Ghavami S. Evaluation of Mitochondrial Phagy (Mitophagy) in Human Non-small Adenocarcinoma Tumor Cells. Methods Mol Biol 2025; 2879:261-273. [PMID: 38607594 DOI: 10.1007/7651_2024_532] [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] [Indexed: 04/13/2024]
Abstract
Non-small cell lung cancer (NSCLC) is a predominant form of lung cancer characterized by its aggressive nature and high mortality rate, primarily due to late-stage diagnosis and metastatic spread. Recent studies underscore the pivotal role of mitophagy, a selective form of autophagy targeting damaged or superfluous mitochondria, in cancer biology, including NSCLC. Mitophagy regulation may influence cancer cell survival, proliferation, and metastasis by modulating mitochondrial quality and cellular energy homeostasis. Herein, we present a comprehensive methodology developed in our laboratory for the evaluation of mitophagy in NSCLC tumor cells. Utilizing a combination of immunoblotting, immunocytochemistry, and fluorescent microscopy, we detail the steps to quantify early and late mitophagy markers and mitochondrial dynamics. Our findings highlight the potential of targeting mitophagy pathways as a novel therapeutic strategy in NSCLC, offering insights into the complex interplay between mitochondrial dysfunction and tumor progression. This study not only sheds light on the significance of mitophagy in NSCLC but also establishes a foundational approach for its investigation, paving way for future research in this critical area of cancer biology.
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Affiliation(s)
- Javad Alizadeh
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Simone C da Silva Rosa
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Marco Cordani
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.
- Faculty of Medicine in Zabrze, University of Technology in Katowice, Zabrze, Poland.
- Research Institute of Oncology and Hematology, Cancer Care Manitoba, University of Manitoba, Winnipeg, MB, Canada.
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11
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Schwalm MP, Knapp S, Rogov VV. Toward effective Atg8-based ATTECs: Approaches and perspectives. J Cell Biochem 2024; 125:e30380. [PMID: 36780422 DOI: 10.1002/jcb.30380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/15/2023]
Abstract
Induction of Atg8-family protein (LC3/GABARAP proteins in human) interactions with target proteins of interest by proximity-inducing small molecules offers the possibility for novel targeted protein degradation approaches. However, despite intensive screening campaigns during the last 5 years, no potent ligands for LC3/GABARAPs have been developed, rendering this approach largely unexplored and unsuitable for therapeutic exploitation. In this Viewpoint, we analyze the reported attempts identifying LC3/GABARAP inhibitors and provide our own point of view why no potent inhibitors have been found. Additionally, we designate reasonable directions for the identification of potent and probably selective LC3/GABARAP inhibitors for alternative therapeutic applications.
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Affiliation(s)
- Martin P Schwalm
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Stefan Knapp
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
| | - Vladimir V Rogov
- Department of Biochemistry, Chemistry and Pharmacy, Institute for Pharmaceutical Chemistry, Goethe University, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt, Germany
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12
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Baral K, Joshi S, Lopez A, Mugon G, Chanda A, Chandrasheker AA, Hinton C, Thapa K, Mercer A, Spade L, Liu G, Bhetwal BP, Fang J, Khambu B. Transcriptional changes impact hepatic proteome in autophagy-impaired liver. FEBS Open Bio 2024; 14:1851-1863. [PMID: 39284785 PMCID: PMC11532973 DOI: 10.1002/2211-5463.13898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 08/09/2024] [Accepted: 09/09/2024] [Indexed: 11/05/2024] Open
Abstract
Hepatic proteomes are intricately controlled through biosynthesis, extracellular secretion, and intrahepatic degradation. Autophagy governs lysosome-mediated intrahepatic degradation and the hepatic proteome. When autophagy is impaired, it leads to the accumulation of intrahepatic proteins, causing proteinopathy. This study investigates whether autophagy can modulate the hepatic proteome non-degradatively. Utilizing conditional, inducible, and hepatotoxin models of hepatic autophagy impairment, we assessed the overall hepatic proteome expression using Coomassie brilliant blue (CBB) staining and liquid chromatography-tandem mass spectrometry (LC/MS). We pinpointed and confirmed four specific hepatic proteins-Cps1, Ahcy, Ca3, and Gstm1-that were selectively modified in autophagy-deficient livers. Expression of Cps1, Ahcy, and Ca3 were significantly reduced, while Gstm1 expression increased in livers with autophagy impairment. Interestingly, these changes in hepatic protein levels were not due to defective autophagic degradation but were associated with alterations in mRNA transcript levels. Moreover, as a result of autophagic dysfunction, sustained activation of the nuclear erythroid-derived 2-like 2 (Nrf2) transcription factor, transcriptionally regulated the mRNA levels of these proteins. Our findings indicate that autophagy can influence hepatic proteins not solely via traditional degradative routes but also through non-degradative transcriptional processes by modulating Nrf2.
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Affiliation(s)
- Kamal Baral
- Department of Pathology and Laboratory MedicineTulane University School of MedicineNew OrleansLAUSA
| | | | - Adriana Lopez
- Department of Pathology and Laboratory MedicineTulane University School of MedicineNew OrleansLAUSA
| | - Gavisha Mugon
- Department of Biochemistry and Molecular BiologyTulane University School of MedicineNew OrleansLAUSA
| | - Aroma Chanda
- Department of Pathology and Laboratory MedicineTulane University School of MedicineNew OrleansLAUSA
| | - Arya A. Chandrasheker
- Department of Pathology and Laboratory MedicineTulane University School of MedicineNew OrleansLAUSA
| | - Cameron Hinton
- Department of Pathology and Laboratory MedicineTulane University School of MedicineNew OrleansLAUSA
| | - Kapil Thapa
- Department of Cell and Molecular BiologySchool of Science and EngineeringNew OrleansLAUSA
| | - Arissa Mercer
- Department of Pathology and Laboratory MedicineTulane University School of MedicineNew OrleansLAUSA
| | - Leah Spade
- Department of Pathology and Laboratory MedicineTulane University School of MedicineNew OrleansLAUSA
| | - Gang Liu
- Department of Pathology and Laboratory MedicineTulane University School of MedicineNew OrleansLAUSA
| | | | - Jia Fang
- Department of Biochemistry and Molecular BiologyTulane University School of MedicineNew OrleansLAUSA
| | - Bilon Khambu
- Department of Pathology and Laboratory MedicineTulane University School of MedicineNew OrleansLAUSA
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13
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Üffing A, Weiergräber OH, Schwarten M, Hoffmann S, Willbold D. GABARAP interacts with EGFR - supporting the unique role of this hAtg8 protein during receptor trafficking. FEBS Lett 2024; 598:2656-2669. [PMID: 39160442 DOI: 10.1002/1873-3468.14997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/02/2024] [Accepted: 07/24/2024] [Indexed: 08/21/2024]
Abstract
The human Atg8 family member GABARAP is involved in numerous autophagy-related and -unrelated processes. We recently observed that specifically the deficiency of GABARAP enhances epidermal growth factor receptor (EGFR) degradation upon ligand stimulation. Here, we report on two putative LC3-interacting regions (LIRs) within EGFR, the first of which (LIR1) is selected as a GABARAP binding site in silico. Indeed, in vitro interaction studies reveal preferential binding of LIR1 to GABARAP and GABARAPL1. Our X-ray data demonstrate interaction of core LIR1 residues FLPV with both hydrophobic pockets of GABARAP suggesting canonical binding. Although LIR1 occupies the LIR docking site, GABARAP Y49 and L50 appear dispensable in this case. Our data support the hypothesis that GABARAP affects the fate of EGFR at least in part through direct binding.
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Affiliation(s)
- Alina Üffing
- Heinrich-Heine-Universität Düsseldorf, Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, Düsseldorf, Germany
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
| | - Oliver H Weiergräber
- Heinrich-Heine-Universität Düsseldorf, Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, Düsseldorf, Germany
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
| | - Melanie Schwarten
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
| | - Silke Hoffmann
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
| | - Dieter Willbold
- Heinrich-Heine-Universität Düsseldorf, Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, Düsseldorf, Germany
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), Jülich, Germany
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14
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Chen Y, Barylko B, Eichorst J, Mueller J, Albanesi J. Identification of the GABARAP binding determinant in PI4K2A. Biosci Rep 2024; 44:BSR20240200. [PMID: 39344512 PMCID: PMC11499380 DOI: 10.1042/bsr20240200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 09/17/2024] [Accepted: 09/26/2024] [Indexed: 10/01/2024] Open
Abstract
GABARAP is a member of the ATG8 family of ubiquitin-like autophagy related proteins. It was initially discovered as a facilitator of GABA-A receptor translocation to the plasma membrane and has since been shown to promote the intracellular transport of a variety of other proteins under non-autophagic conditions. We and others have shown that GABARAP interacts with the Type II phosphatidylinositol 4-kinase, PI4K2A, and that this interaction is important for autophagosome-lysosome fusion. Here, we identify a 7-amino acid segment within the PI4K2A catalytic domain that contains the GABARAP interaction motif (GIM). This segment resides in an exposed loop that is not conserved in the other mammalian Type II PI 4-kinase, PI4K2B, explaining the specificity of GABARAP binding to the PI4K2A isoform. Mutation of the PI4K2A GIM inhibits GABARAP binding and PI4K2A-mediated recruitment of cytosolic GABARAP to subcellular organelles. We further show that GABARAP binds to mono-phosphorylated phosphoinositides, PI3P, PI4P, and PI5P, raising the possibility that these lipids contribute to the binding energies that drive GABARAP-protein interactions on membranes.
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Affiliation(s)
- Yan Chen
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, U.S.A
| | - Barbara Barylko
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, U.S.A
| | - John P. Eichorst
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, U.S.A
| | - Joachim D. Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, U.S.A
| | - Joseph P. Albanesi
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, U.S.A
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15
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Leveille AN, Schwarzrock T, Brown H, True B, Plasencia J, Neudecker P, Üffing A, Weiergräber OH, Willbold D, Kritzer JA. Exploring Arylidene-Indolinone Ligands of Autophagy Proteins LC3B and GABARAP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.25.581879. [PMID: 39554136 PMCID: PMC11565829 DOI: 10.1101/2024.02.25.581879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
We report the first structure-activity studies of arylidene-indolinone compound GW5074 which was reported as a ligand of autophagy-related protein LC3B. The literature has conflicting information on the binding affinity of this compound and there is some debate regarding its use as a component of autophagy-dependent degrader compounds. We developed an AlphaScreen assay to measure competitive inhibition of the binding of known peptide ligands to LC3B and its paralog GABARAP. 18 analogs were synthesized and tested against both proteins. Inhibitory potencies were found to be in the mid- to high micromolar range. 2D-NMR data revealed the binding site on GABARAP as hydrophobic pocket 1, where native peptide ligands bind with an aromatic side chain. Our results suggest that GW5074 binds LC3B and GABARAP with micromolar affinity. These affinities could support further exploration in targeted protein degradation, but only if off-target effects and poor solubility can be appropriately addressed.
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Affiliation(s)
| | - Thomas Schwarzrock
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford MA, USA
| | - Hawley Brown
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford MA, USA
| | - Bennett True
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford MA, USA
| | - Joanet Plasencia
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford MA, USA
| | - Philipp Neudecker
- Heinrich-Heine-Universität Düsseldorf, Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, 40225 Düsseldorf, Germany
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), 52425 Jülich, Germany
| | - Alina Üffing
- Heinrich-Heine-Universität Düsseldorf, Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, 40225 Düsseldorf, Germany
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), 52425 Jülich, Germany
| | - Oliver H. Weiergräber
- Heinrich-Heine-Universität Düsseldorf, Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, 40225 Düsseldorf, Germany
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), 52425 Jülich, Germany
| | - Dieter Willbold
- Heinrich-Heine-Universität Düsseldorf, Mathematisch-Naturwissenschaftliche Fakultät, Institut für Physikalische Biologie, 40225 Düsseldorf, Germany
- Forschungszentrum Jülich, Institut für Biologische Informationsprozesse: Strukturbiochemie (IBI-7), 52425 Jülich, Germany
| | - Joshua A. Kritzer
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford MA, USA
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16
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Aponte-Diaz D, Harris JM, Kang TE, Korboukh V, Sotoudegan MS, Gray JL, Yennawar NH, Moustafa IM, Macadam A, Cameron CE. Non-lytic spread of poliovirus requires the nonstructural protein 3CD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.18.619132. [PMID: 39464037 PMCID: PMC11507938 DOI: 10.1101/2024.10.18.619132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
Non-enveloped viruses like poliovirus (PV) have evolved the capacity to spread by non-lytic mechanisms. For PV, this mechanism exploits the host secretory autophagy pathway. Virions are selectively incorporated into autophagosomes, double-membrane vesicles that travel to the plasma membrane, fuse, and release single-membrane vesicles containing virions. Loading of cellular cargo into autophagosomes relies on direct or indirect interactions with microtubule-associated protein 1B-light chain 3 (LC3) that are mediated by motifs referred to as LC3-interaction regions (LIRs). We have identified a PV mutant with a severe defect in non-lytic spread. An F-to-Y substitution in a putative LIR of the nonstructural protein 3CD prevented virion incorporation into LC3-positive autophagosomes and virion trafficking to the plasma membrane for release. Using high-angle annular dark-field scanning transmission electron microscopy to monitor PV-induced autophagosome biogenesis, for the first time, we show that virus-induced autophagic signals yield normal autophagosomes, even in the absence of virions. The F-to-Y derivative of PV 3CD was unable to support normal autophagosome biogenesis. Together, these studies make a compelling case for a direct role of a viral nonstructural protein in the formation and loading of the vesicular carriers used for non-lytic spread that may depend on the proper structure, accessibility, and/or dynamics of its LIR. The studies of PV 3CD protein reported here will hopefully provoke a more deliberate look at the presence and function of LIR motifs in viral proteins of viruses known to use autophagy as the basis for non-lytic spread.
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Affiliation(s)
- David Aponte-Diaz
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jayden M Harris
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tongjia Ella Kang
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Victoria Korboukh
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Present address: Strategic Alliances and Program Management, C4 Therapeutics, Inc., Watertown, MA 02472, USA
| | - Mohamad S Sotoudegan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jennifer L Gray
- Materials Research Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew Macadam
- Division of Vaccines, Medicines and Healthcare Products Regulatory Agency, Herts. EN6 3QG, UK
| | - Craig E Cameron
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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17
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Yeung SHS, Lee RHS, Cheng GWY, Ma IWT, Kofler J, Kent C, Ma F, Herrup K, Fornage M, Arai K, Tse KH. White matter hyperintensity genetic risk factor TRIM47 regulates autophagy in brain endothelial cells. FASEB J 2024; 38:e70059. [PMID: 39331575 DOI: 10.1096/fj.202400689rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 08/27/2024] [Accepted: 09/05/2024] [Indexed: 09/29/2024]
Abstract
White matter hyperintensity (WMH) is strongly correlated with age-related dementia and hypertension, but its pathogenesis remains obscure. Genome-wide association studies identified TRIM47 at the 17q25 locus as a top genetic risk factor for WMH formation. TRIM family is a class of E3 ubiquitin ligase with pivotal functions in autophagy, which is critical for brain endothelial cell (ECs) remodeling during hypertension. We hypothesize that TRIM47 regulates autophagy and its loss-of-function disturbs cerebrovasculature. Based on transcriptomics and immunohistochemistry, TRIM47 is found highly expressed by brain ECs in human and mouse, and its transcription is upregulated by artificially induced autophagy while downregulated in hypertension-like conditions. Using in silico simulation, immunocytochemistry and super-resolution microscopy, we predicted a highly conserved binding site between TRIM47 and the LIR (LC3-interacting region) motif of LC3B. Importantly, pharmacological autophagy induction increased Trim47 expression on mouse ECs (b.End3) culture, while silencing Trim47 significantly increased autophagy with ULK1 phosphorylation induction, transcription, and vacuole formation. Together, we demonstrate that TRIM47 is an endogenous inhibitor of autophagy in brain ECs, and such TRIM47-mediated regulation connects genetic and physiological risk factors for WMH formation but warrants further investigation.
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Affiliation(s)
- Sunny Hoi-Sang Yeung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Ralph Hon-Sun Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Gerald Wai-Yeung Cheng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Iris Wai-Ting Ma
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Julia Kofler
- Division of Neuropathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Candice Kent
- Department of Neurobiology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Fulin Ma
- Department of Neurobiology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Karl Herrup
- Department of Neurobiology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Myriam Fornage
- Human Genetics Center, Division of Epidemiology, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ken Arai
- Neuroprotection Research Laboratories, Departments of Radiology and Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, USA
| | - Kai-Hei Tse
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong
- Brain and Mind Centre, University of Sydney, Camperdown, New South Wales, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
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18
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Hushmandi K, Einollahi B, Aow R, Suhairi SB, Klionsky DJ, Aref AR, Reiter RJ, Makvandi P, Rabiee N, Xu Y, Nabavi N, Saadat SH, Farahani N, Kumar AP. Investigating the interplay between mitophagy and diabetic neuropathy: Uncovering the hidden secrets of the disease pathology. Pharmacol Res 2024; 208:107394. [PMID: 39233055 PMCID: PMC11934918 DOI: 10.1016/j.phrs.2024.107394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 08/18/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024]
Abstract
Mitophagy, the cellular process of selectively eliminating damaged mitochondria, plays a crucial role in maintaining metabolic balance and preventing insulin resistance, both key factors in type 2 diabetes mellitus (T2DM) development. When mitophagy malfunctions in diabetic neuropathy, it triggers a cascade of metabolic disruptions, including reduced energy production, increased oxidative stress, and cell death, ultimately leading to various complications. Thus, targeting mitophagy to enhance the process may have emerged as a promising therapeutic strategy for T2DM and its complications. Notably, plant-derived compounds with β-cell protective and mitophagy-stimulating properties offer potential as novel therapeutic agents. This review highlights the intricate mechanisms linking mitophagy dysfunction to T2DM and its complications, particularly neuropathy, elucidating potential therapeutic interventions for this debilitating disease.
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Affiliation(s)
- Kiavash Hushmandi
- Nephrology and Urology Research Center, Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Behzad Einollahi
- Nephrology and Urology Research Center, Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Rachel Aow
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Suhana Binte Suhairi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amir Reza Aref
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, Long School of Medicine, San Antonio, TX, USA
| | - Pooyan Makvandi
- Department of Biomaterials, Saveetha Dental College and Hospitals, SIMATS, Saveetha University, Chennai 600077, India; University Centre for Research & Development, Chandigarh University, Mohali, Punjab 140413, India
| | - Navid Rabiee
- Department of Biomaterials, Saveetha Dental College and Hospitals, SIMATS, Saveetha University, Chennai 600077, India
| | - Yi Xu
- Department of Science & Technology, Department of Urology, NanoBioMed Group, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, China
| | - Noushin Nabavi
- Independent Researcher, Victoria, British Columbia V8V 1P7, Canada
| | - Seyed Hassan Saadat
- Nephrology and Urology Research Center, Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Najma Farahani
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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19
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Jones RA, Cooper F, Kelly G, Barry D, Renshaw MJ, Sapkota G, Smith JC. Zebrafish reveal new roles for Fam83f in hatching and the DNA damage-mediated autophagic response. Open Biol 2024; 14:240194. [PMID: 39437839 PMCID: PMC11495952 DOI: 10.1098/rsob.240194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 10/25/2024] Open
Abstract
The FAM83 (Family with sequence similarity 83) family is highly conserved in vertebrates, but little is known of the functions of these proteins beyond their association with oncogenesis. Of the family, FAM83F is of particular interest because it is the only membrane-targeted FAM83 protein. When overexpressed, FAM83F activates the canonical Wnt signalling pathway and binds to and stabilizes p53; it therefore interacts with two pathways often dysregulated in disease. Insights into gene function can often be gained by studying the roles they play during development, and here we report the generation of fam83f knock-out (KO) zebrafish, which we have used to study the role of Fam83f in vivo. We show that endogenous fam83f is most strongly expressed in the hatching gland of developing zebrafish embryos, and that fam83f KO embryos hatch earlier than their wild-type (WT) counterparts, despite developing at a comparable rate. We also demonstrate that fam83f KO embryos are more sensitive to ionizing radiation than WT embryos-an unexpected finding, bearing in mind the previously reported ability of FAM83F to stabilize p53. Transcriptomic analysis shows that loss of fam83f leads to downregulation of phosphatidylinositol-3-phosphate (PI(3)P) binding proteins and impairment of cellular degradation pathways, particularly autophagy, a crucial component of the DNA damage response. Finally, we show that Fam83f protein is itself targeted to the lysosome when overexpressed in HEK293T cells, and that this localization is dependent upon a C' terminal signal sequence. The zebrafish lines we have generated suggest that Fam83f plays an important role in autophagic/lysosomal processes, resulting in dysregulated hatching and increased sensitivity to genotoxic stress in vivo.
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Affiliation(s)
- Rebecca A. Jones
- Department of Molecular Biology, Princeton University, Princeton, NJ08544, USA
| | - Fay Cooper
- School of Biosciences, University of Sheffield, SheffieldS10 2TN, UK
- Neuroscience Institute, University of Sheffield, SheffieldS10 2TN, UK
| | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, LondonNW1 1AT, UK
| | - David Barry
- The Francis Crick Institute, 1 Midland Road, LondonNW1 1AT, UK
| | | | - Gopal Sapkota
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, DundeeDD1 5EH, UK
| | - James C. Smith
- The Francis Crick Institute, 1 Midland Road, LondonNW1 1AT, UK
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20
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Ali MG, Wahba HM, Igelmann S, Cyr N, Ferbeyre G, Omichinski JG. Structural and functional characterization of the role of acetylation on the interactions of the human Atg8-family proteins with the autophagy receptor TP53INP2/DOR. Autophagy 2024; 20:1948-1967. [PMID: 38726830 PMCID: PMC11346521 DOI: 10.1080/15548627.2024.2353443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 04/20/2024] [Accepted: 05/05/2024] [Indexed: 05/29/2024] Open
Abstract
The Atg8-family proteins (MAP1LC3/LC3A, LC3B, LC3C, GABARAP, GABARAPL1 and GABARAPL2) play a pivotal role in macroautophagy/autophagy through their ability to help form autophagosomes. Although autophagosomes form in the cytoplasm, nuclear levels of the Atg8-family proteins are significant. Recently, the nuclear/cytoplasmic shuttling of LC3B was shown to require deacetylation of two Lys residues (K49 and K51 in LC3B), which are conserved in Atg8-family proteins. To exit the nucleus, deacetylated LC3B must bind TP53INP2/DOR (tumor protein p53 inducible nuclear protein 2) through interaction with the LC3-interacting region (LIR) of TP53INP2 (TP53INP2LIR). To examine their selectivity for TP53INP2 and the role of the conserved Lys residues in Atg8-family proteins, we prepared the six human Atg8-family proteins and acetylated variants of LC3A and GABARAP for biophysical and structural characterization of their interactions with the TP53INP2LIR. Isothermal titration calorimetry (ITC) experiments demonstrate that this LIR binds preferentially to GABARAP subfamily proteins, and that only acetylation of the second Lys residue reduces binding to GABARAP and LC3A. Crystal structures of complexes with GABARAP and LC3A (acetylated and deacetylated) define a β-sheet in the TP53INP2LIR that determines the GABARAP selectivity and establishes the importance of acetylation at the second Lys. The in vitro results were confirmed in cells using acetyl-mimetic variants of GABARAP and LC3A to examine nuclear/cytoplasmic shuttling and colocalization with TP53INP2. Together, the results demonstrate that TP53INP2 shows selectivity to the GABARAP subfamily and acetylation at the second Lys of GABARAP and LC3A disrupts key interactions with TP53INP2 required for their nuclear/cytoplasmic shuttling.
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Affiliation(s)
- Mohamed G. Ali
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Department of Biochemistry, Beni-Suef University, Beni-Suef, Egypt
| | - Haytham M. Wahba
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Department of Biochemistry, Beni-Suef University, Beni-Suef, Egypt
| | - Sebastian Igelmann
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Normand Cyr
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Gerardo Ferbeyre
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - James G. Omichinski
- Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, Canada
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21
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Wu Y, Chen Y, Yan X, Dai X, Liao Y, Yuan J, Wang L, Liu D, Niu D, Sun L, Chen L, Zhang Y, Xiang L, Chen A, Li S, Xiang W, Ni Z, Chen M, He F, Yang M, Lian J. Lopinavir enhances anoikis by remodeling autophagy in a circRNA-dependent manner. Autophagy 2024; 20:1651-1672. [PMID: 38433354 PMCID: PMC11210930 DOI: 10.1080/15548627.2024.2325304] [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: 06/12/2023] [Revised: 02/15/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024] Open
Abstract
Macroautophagy/autophagy-mediated anoikis resistance is crucial for tumor metastasis. As a key autophagy-related protein, ATG4B has been demonstrated to be a prospective anti-tumor target. However, the existing ATG4B inhibitors are still far from clinical application, especially for tumor metastasis. In this study, we identified a novel circRNA, circSPECC1, that interacted with ATG4B. CircSPECC1 facilitated liquid-liquid phase separation of ATG4B, which boosted the ubiquitination and degradation of ATG4B in gastric cancer (GC) cells. Thus, pharmacological addition of circSPECC1 may serve as an innovative approach to suppress autophagy by targeting ATG4B. Specifically, the circSPECC1 underwent significant m6A modification in GC cells and was subsequently recognized and suppressed by the m6A reader protein ELAVL1/HuR. The activation of the ELAVL1-circSPECC1-ATG4B pathway was demonstrated to mediate anoikis resistance in GC cells. Moreover, we also verified that the above pathway was closely related to metastasis in tissues from GC patients. Furthermore, we determined that the FDA-approved compound lopinavir efficiently enhanced anoikis and prevented metastasis by eliminating repression of ELAVL1 on circSPECC1. In summary, this study provides novel insights into ATG4B-mediated autophagy and introduces a viable clinical inhibitor of autophagy, which may be beneficial for the treatment of GC with metastasis.
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Affiliation(s)
- Yaran Wu
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing, China
- Department of Clinical Biochemistry, Faculty of Pharmacy and Laboratory Medicine, Army Medical University, Chongqing, China
| | - Yang Chen
- Department of Clinical Biochemistry, Faculty of Pharmacy and Laboratory Medicine, Army Medical University, Chongqing, China
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xiaojing Yan
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Xufang Dai
- College of Education and Science, Chongqing Normal University, Chongqing, China
| | - Yaling Liao
- Department of Clinical Biochemistry, Faculty of Pharmacy and Laboratory Medicine, Army Medical University, Chongqing, China
| | - Jing Yuan
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Liting Wang
- Biomedical Analysis Center, Army Medical University, Chongqing, China
| | - Dong Liu
- Department of Clinical Biochemistry, Faculty of Pharmacy and Laboratory Medicine, Army Medical University, Chongqing, China
| | - Dun Niu
- Department of Clinical Biochemistry, Faculty of Pharmacy and Laboratory Medicine, Army Medical University, Chongqing, China
| | - Liangbo Sun
- Department of Clinical Biochemistry, Faculty of Pharmacy and Laboratory Medicine, Army Medical University, Chongqing, China
| | - Lingxi Chen
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Yang Zhang
- Department of Clinical Biochemistry, Faculty of Pharmacy and Laboratory Medicine, Army Medical University, Chongqing, China
| | - Li Xiang
- Department of Clinical Biochemistry, Faculty of Pharmacy and Laboratory Medicine, Army Medical University, Chongqing, China
| | - An Chen
- Department of Clinical Biochemistry, Faculty of Pharmacy and Laboratory Medicine, Army Medical University, Chongqing, China
| | - Shuhui Li
- Department of Clinical Biochemistry, Faculty of Pharmacy and Laboratory Medicine, Army Medical University, Chongqing, China
| | - Wei Xiang
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Rehabilitation Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Zhenhong Ni
- State Key Laboratory of Trauma, Burns and Combined Injury, Department of Rehabilitation Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Ming Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing, China
| | - Fengtian He
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Mingzhen Yang
- Department of Clinical Biochemistry, Faculty of Pharmacy and Laboratory Medicine, Army Medical University, Chongqing, China
| | - Jiqin Lian
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing, China
- Department of Clinical Biochemistry, Faculty of Pharmacy and Laboratory Medicine, Army Medical University, Chongqing, China
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22
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Li S, Sun J, Li Y, Lv X, Wang L, Song L. CgPHB2 involved in the haemocyte mitophagy in response to Vibrio splendidus stimulation in Pacific oyster Crassostrea gigas. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 156:105168. [PMID: 38522715 DOI: 10.1016/j.dci.2024.105168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/05/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024]
Abstract
Prohibitin2 (PHB2) is recently identified as a novel inner membrane mitophagy receptor to mediate mitophagy. In the present study, the function of CgPHB2 in mediating mitophagy in response to Vibrio splendidus stimulation was investigated in Crassostrea gigas. CgPHB2 protein was mainly distributed in the cytoplasm of three subpopulations of haemocytes. After V. splendidus stimulation, the expressions of CgPHB2 mRNA in haemocytes were up-regulated significantly at 6, 12 and 24 h, and the abundance of CgPHB2 protein was also enhanced at 12-24 h compared to control group. Furthermore, the green signals of CgPHB2 were colocalized respectively with the red signals of mitochondria and CgLC3 in the haemocytes at 12 h after V. splendidus stimulation, and the co-localization value of CgPHB2 and mtphagy Dye was significantly increased. The direct interaction between CgPHB2 and CgLC3 was simulated by molecular docking. In PHB2-inhibitor Fluorizoline-treated oysters, the mRNA expressions of mitophagy-related genes and the ratio of mitophagy were significantly decreased in haemocytes of oysters after V. splendidus stimulation. All the results collectively suggested that CgPHB2 participated in mediating the haemocyte mitophagy in the antibacterial immune response of oysters.
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Affiliation(s)
- Shurong Li
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Jiejie Sun
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Control, Dalian Ocean University, Dalian, 116023, China.
| | - Yinan Li
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Xiaoqian Lv
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Control, Dalian Ocean University, Dalian, 116023, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology & Disease Control, Dalian Ocean University, Dalian, 116023, China; Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Control, Dalian Ocean University, Dalian, 116023, China
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23
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Pandey A, Kakani P, Shukla S. CTCF and BORIS-mediated autophagy regulation via alternative splicing of BNIP3L in breast cancer. J Biol Chem 2024; 300:107416. [PMID: 38810696 PMCID: PMC11254729 DOI: 10.1016/j.jbc.2024.107416] [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: 10/18/2023] [Revised: 05/09/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Autophagy is a pivotal regulatory and catabolic process, induced under various stressful conditions, including hypoxia. However, little is known about alternative splicing of autophagy genes in the hypoxic landscape in breast cancer. Our research unravels the hitherto unreported alternative splicing of BNIP3L, a crucial hypoxia-induced autophagic gene. We showed that BNIP3L, under hypoxic condition, forms two isoforms, a full-length isoform (BNIP3L-F) and a shorter isoform lacking exon 1 (BNIP3L-Δ1). The hypoxia-induced BNIP3L-F promotes autophagy, while under normoxia, the BNIP3L-Δ1 inhibits autophagy. We discovered a novel dimension of hypoxia-mediated epigenetic modification that regulates the alternative splicing of BNIP3L. Here, we showed differential DNA methylation of BNIP3L intron 1, causing reciprocal binding of epigenetic factor CCCTC-binding factor (CTCF) and its paralog BORIS. Additionally, we highlighted the role of CTCF and BORIS impacting autophagy in breast cancer. The differential binding of CTCF and BORIS results in alternative splicing of BNIP3L forming BNIP3L-F and BNIP3L-Δ1, respectively. The binding of CTCF on unmethylated BNIP3L intron 1 under hypoxia results in RNA Pol-II pause and inclusion of exon 1, promoting BNIP3L-F and autophagy. Interestingly, the binding of BORIS on methylated BNIP3L intron 1 under normoxia also results in RNA Pol-II pause but leads to the exclusion of exon 1 from BNIP3L mRNA. Finally, we reported the critical role of BORIS-mediated RNA Pol-II pause, which subsequently recruits SRSF6, redirecting the proximal splice-site selection, promoting BNIP3L-Δ1, and inhibiting autophagy. Our study provides novel insights into the potential avenues for breast cancer therapy by targeting autophagy regulation, specifically under hypoxic condition.
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Affiliation(s)
- Anchala Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Parik Kakani
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India.
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24
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North BJ, Ohnstad AE, Ragusa MJ, Shoemaker CJ. The LC3-interacting region of NBR1 is a protein interaction hub enabling optimal flux. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593318. [PMID: 38766171 PMCID: PMC11100792 DOI: 10.1101/2024.05.09.593318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
During autophagy, potentially toxic cargo is enveloped by a newly formed autophagosome and trafficked to the lysosome for degradation. Ubiquitinated protein aggregates, a key target for autophagy, are identified by multiple autophagy receptors. NBR1 is an archetypal autophagy receptor and an excellent model for deciphering the role of the multivalent, heterotypic interactions made by cargo-bound receptors. Using NBR1 as a model, we find that three critical binding partners - ATG8-family proteins, FIP200, and TAX1BP1 - each bind to a short linear interaction motif (SLiM) within NBR1. Mutational peptide arrays indicate that these binding events are mediated by distinct overlapping determinants, rather than a single, convergent, SLiM. AlphaFold modeling underlines the need for conformational flexibility within the NBR1 SLiM, as distinct conformations mediate each binding event. To test the extent to which overlapping SLiMs exist beyond NBR1, we performed peptide binding arrays on >100 established LC3-interacting regions (LIRs), revealing that FIP200 and/or TAX1BP1 binding to LIRs is a common phenomenon and suggesting LIRs as protein interaction hotspots. Comparative analysis of phosphomimetic peptides highlights that while FIP200 and Atg8-family binding are generally augmented by phosphorylation, TAX1BP1 binding is nonresponsive, suggesting differential regulation of these binding events. In vivo studies confirm that LIR-mediated interactions with TAX1BP1 enhance NBR1 activity, increasing autophagosomal delivery by leveraging an additional LIR from TAX1BP1. In sum, these results reveal a one-to-many binding modality in NBR1, providing key insights into the cooperative mechanisms among autophagy receptors. Furthermore, these findings underscore the pervasive role of multifunctional SLiMs in autophagy, offering substantial avenues for further exploration into their regulatory functions.
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Affiliation(s)
- Brian J North
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Amelia E Ohnstad
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | | | - Christopher J Shoemaker
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
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25
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Wallace NS, Gadbery JE, Cohen CI, Kendall AK, Jackson LP. Tepsin binds LC3B to promote ATG9A trafficking and delivery. Mol Biol Cell 2024; 35:ar56. [PMID: 38381558 PMCID: PMC11064669 DOI: 10.1091/mbc.e23-09-0359-t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024] Open
Abstract
Tepsin is an established accessory protein found in Adaptor Protein 4 (AP-4) coated vesicles, but the biological role of tepsin remains unknown. AP-4 vesicles originate at the trans-Golgi network (TGN) and target the delivery of ATG9A, a scramblase required for autophagosome biogenesis, to the cell periphery. Using in silico methods, we identified a putative LC3-Interacting Region (LIR) motif in tepsin. Biochemical experiments using purified recombinant proteins indicate tepsin directly binds LC3B preferentially over other members of the mammalian ATG8 family. Calorimetry and structural modeling data indicate this interaction occurs with micromolar affinity using the established LC3B LIR docking site. Loss of tepsin in cultured cells dysregulates ATG9A export from the TGN as well as ATG9A distribution at the cell periphery. Tepsin depletion in a mRFP-GFP-LC3B HeLa reporter cell line using siRNA knockdown increases autophagosome volume and number, but does not appear to affect flux through the autophagic pathway. Reintroduction of wild-type tepsin partially rescues ATG9A cargo trafficking defects. In contrast, reintroducing tepsin with a mutated LIR motif or missing N-terminus drives diffuse ATG9A subcellular distribution. Together, these data suggest roles for tepsin in cargo export from the TGN; ensuring delivery of ATG9A-positive vesicles; and in overall maintenance of autophagosome structure.
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Affiliation(s)
- Natalie S. Wallace
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - John E. Gadbery
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Cameron I. Cohen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
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26
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Petraccione K, Ali MGH, Cyr N, Wahba HM, Stocker T, Akhrymuk M, Akhrymuk I, Panny L, Bracci N, Cafaro R, Sastre D, Silberfarb A, O’Maille P, Omichinski J, Kehn-Hall K. An LIR motif in the Rift Valley fever virus NSs protein is critical for the interaction with LC3 family members and inhibition of autophagy. PLoS Pathog 2024; 20:e1012093. [PMID: 38512999 PMCID: PMC10986958 DOI: 10.1371/journal.ppat.1012093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/02/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024] Open
Abstract
Rift Valley fever virus (RVFV) is a viral zoonosis that causes severe disease in ruminants and humans. The nonstructural small (NSs) protein is the primary virulence factor of RVFV that suppresses the host's antiviral innate immune response. Bioinformatic analysis and AlphaFold structural modeling identified four putative LC3-interacting regions (LIR) motifs (NSs 1-4) in the RVFV NSs protein, which suggest that NSs interacts with the host LC3-family proteins. Using, isothermal titration calorimetry, X-ray crystallography, co-immunoprecipitation, and co-localization experiments, the C-terminal LIR motif (NSs4) was confirmed to interact with all six human LC3 proteins. Phenylalanine at position 261 (F261) within NSs4 was found to be critical for the interaction of NSs with LC3, retention of LC3 in the nucleus, as well as the inhibition of autophagy in RVFV infected cells. These results provide mechanistic insights into the ability of RVFV to overcome antiviral autophagy through the interaction of NSs with LC3 proteins.
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Affiliation(s)
- Kaylee Petraccione
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Mohamed G. H. Ali
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
- Department of Biochemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Normand Cyr
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Haytham M. Wahba
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
- Department of Biochemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Timothy Stocker
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Maryna Akhrymuk
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Ivan Akhrymuk
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Lauren Panny
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Nicole Bracci
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Raphaël Cafaro
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
- Department of Biochemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Danuta Sastre
- Biosciences Division, SRI International, Menlo Park, California, United States of America
| | - Andrew Silberfarb
- Artificial Intelligence Center, SRI International, Menlo Park, California, United States of America
| | - Paul O’Maille
- Biosciences Division, SRI International, Menlo Park, California, United States of America
| | - James Omichinski
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Kylene Kehn-Hall
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
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27
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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.
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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.
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Zeke A, Gibson TJ, Dobson L. Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents. PLoS Comput Biol 2024; 20:e1011902. [PMID: 38363808 PMCID: PMC10903960 DOI: 10.1371/journal.pcbi.1011902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 02/29/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024] Open
Abstract
The pathogenic, tropical Leishmania flagellates belong to an early-branching eukaryotic lineage (Kinetoplastida) with several unique features. Unfortunately, they are poorly understood from a molecular biology perspective, making development of mechanistically novel and selective drugs difficult. Here, we explore three functionally critical targeting short linear motif systems as well as their receptors in depth, using a combination of structural modeling, evolutionary sequence divergence and deep learning. Secretory signal peptides, endoplasmic reticulum (ER) retention motifs (KDEL motifs), and autophagy signals (motifs interacting with ATG8 family members) are ancient and essential components of cellular life. Although expected to be conserved amongst the kinetoplastids, we observe that all three systems show a varying degree of divergence from their better studied equivalents in animals, plants, or fungi. We not only describe their behaviour, but also build models that allow the prediction of localization and potential functions for several uncharacterized Leishmania proteins. The unusually Ala/Val-rich secretory signal peptides, endoplasmic reticulum resident proteins ending in Asp-Leu-COOH and atypical ATG8-like proteins are all unique molecular features of kinetoplastid parasites. Several of their critical protein-protein interactions could serve as targets of selective antimicrobial agents against Leishmaniasis due to their systematic divergence from the host.
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Affiliation(s)
- Andras Zeke
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Budapest, Hungary
| | - Toby J. Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Laszlo Dobson
- Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Budapest, Hungary
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
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29
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Xue VW, Liu S, Sun Q, Ning J, Li H, Wang W, Sayed S, Zhao X, Fu L, Lu D. CK1δ/ε inhibition induces ULK1-mediated autophagy in tumorigenesis. Transl Oncol 2024; 40:101863. [PMID: 38185060 PMCID: PMC10808987 DOI: 10.1016/j.tranon.2023.101863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024] Open
Abstract
INTRODUCTION Autophagy is an important mechanism of cell homeostasis maintenance. As essential serine/threonine-protein kinases, casein kinase I family members affect tumorigenesis by regulating a variety of cellular progression. However, the mechanism by which they regulate autophagy remains unclear. MATERIALS AND METHODS We silenced CK1δ/ε in cancer cells and observed cell morphology, the expression of autophagy-related genes, and its impact on cancer cell growth and viability. By inhibiting CK1δ/ε-induced upregulation of autophagy genes, we profiled the regulatory mechanism of CK1δ/ε on autophagy and cancer cell growth. The impact of CK1δ/ε inhibition on tumor cell growth was also assessed in vivo. RESULTS Here, we found that CK1δ/ε played an important role in ULK1-mediated autophagy regulation in both lung cancer and melanoma cells. Mechanically, silencing CK1δ/ε increased ULK1 expression with enhanced autophagic flux and suppressed cancer cell proliferation, while ULK1 knockdown blocked the activation of autophagy caused by CK1δ/ε inhibition. By silencing CK1δ/ε in syngeneic mouse model bearing LLC1 murine lung cancer cells in vivo, we observed tumor growth suppression mediated by CK1δ/ε inhibition. CONCLUSION Our results provide evidence for the role of CK1δ/ε in the regulation of tumorigenesis via the ULK1-mediated autophagy, and also suggest the impact of CK1δ/ε inhibition on tumor growth and its significance as a potential therapeutic target.
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Affiliation(s)
- Vivian Weiwen Xue
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, No. 1066 Xueyuan Avenue, Nanshan District, Shenzhen 518060, China; College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China
| | - Shanshan Liu
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, No. 1066 Xueyuan Avenue, Nanshan District, Shenzhen 518060, China
| | - Qi Sun
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, No. 1066 Xueyuan Avenue, Nanshan District, Shenzhen 518060, China
| | - Jiong Ning
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, No. 1066 Xueyuan Avenue, Nanshan District, Shenzhen 518060, China; Center for Molecular Biomedicine, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Huan Li
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, No. 1066 Xueyuan Avenue, Nanshan District, Shenzhen 518060, China
| | - Weilan Wang
- Center for Healthy Longevity, National University of Singapore, Singapore
| | - Sapna Sayed
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, No. 1066 Xueyuan Avenue, Nanshan District, Shenzhen 518060, China
| | - Xibao Zhao
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, No. 1066 Xueyuan Avenue, Nanshan District, Shenzhen 518060, China
| | - Li Fu
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, No. 1066 Xueyuan Avenue, Nanshan District, Shenzhen 518060, China.
| | - Desheng Lu
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Marshall Laboratory of Biomedical Engineering, Shenzhen University Health Science Center, No. 1066 Xueyuan Avenue, Nanshan District, Shenzhen 518060, China.
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Veluthakal R, Esparza D, Hoolachan JM, Balakrishnan R, Ahn M, Oh E, Jayasena CS, Thurmond DC. Mitochondrial Dysfunction, Oxidative Stress, and Inter-Organ Miscommunications in T2D Progression. Int J Mol Sci 2024; 25:1504. [PMID: 38338783 PMCID: PMC10855860 DOI: 10.3390/ijms25031504] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Type 2 diabetes (T2D) is a heterogenous disease, and conventionally, peripheral insulin resistance (IR) was thought to precede islet β-cell dysfunction, promoting progression from prediabetes to T2D. New evidence suggests that T2D-lean individuals experience early β-cell dysfunction without significant IR. Regardless of the primary event (i.e., IR vs. β-cell dysfunction) that contributes to dysglycemia, significant early-onset oxidative damage and mitochondrial dysfunction in multiple metabolic tissues may be a driver of T2D onset and progression. Oxidative stress, defined as the generation of reactive oxygen species (ROS), is mediated by hyperglycemia alone or in combination with lipids. Physiological oxidative stress promotes inter-tissue communication, while pathological oxidative stress promotes inter-tissue mis-communication, and new evidence suggests that this is mediated via extracellular vesicles (EVs), including mitochondria containing EVs. Under metabolic-related stress conditions, EV-mediated cross-talk between β-cells and skeletal muscle likely trigger mitochondrial anomalies leading to prediabetes and T2D. This article reviews the underlying molecular mechanisms in ROS-related pathogenesis of prediabetes, including mitophagy and mitochondrial dynamics due to oxidative stress. Further, this review will describe the potential of various therapeutic avenues for attenuating oxidative damage, reversing prediabetes and preventing progression to T2D.
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Affiliation(s)
- Rajakrishnan Veluthakal
- Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope Beckman Research Institute, 1500 E. Duarte Rd, Duarte, CA 91010, USA; (D.E.); (J.M.H.); (R.B.); (M.A.); (E.O.); (C.S.J.)
| | | | | | | | | | | | | | - Debbie C. Thurmond
- Department of Molecular and Cellular Endocrinology, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope Beckman Research Institute, 1500 E. Duarte Rd, Duarte, CA 91010, USA; (D.E.); (J.M.H.); (R.B.); (M.A.); (E.O.); (C.S.J.)
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Yeung SHS, Lee RHS, Cheng GWY, Ma IWT, Kofler J, Kent C, Ma F, Herrup K, Fornage M, Arai K, Tse KH. White matter hyperintensity genetic risk factor TRIM47 regulates autophagy in brain endothelial cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.18.566359. [PMID: 38187529 PMCID: PMC10769267 DOI: 10.1101/2023.12.18.566359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
White matter hyperintensity (WMH) is strongly correlated with age-related dementia and hypertension, but its pathogenesis remains obscure. GWAS identified TRIM47 at 17q25 locus as a top genetic risk factor for WMH formation. TRIM family is a class of E3 ubiquitin ligase with pivotal functions in autophagy, which is critical for brain endothelial cell (ECs) remodeling during hypertension. We hypothesize that TRIM47 regulates autophagy and its loss-of-function disturbs cerebrovasculature. Based on transcriptomics and immunohistochemistry, TRIM47 is found selectively expressed by brain ECs in human and mouse, and its transcription is upregulated by artificially-induced autophagy while downregulated in hypertension-like conditions. Using in silico simulation, immunocytochemistry and super-resolution microscopy, we identified the highly conserved binding site between TRIM47 and the LIR (LC3-interacting region) motif of LC3B. Importantly, pharmacological autophagy induction increased Trim47 expression on mouse ECs (b.End3) culture, while silencing Trim47 significantly increased autophagy with ULK1 phosphorylation induction, transcription and vacuole formation. Together, we confirm that TRIM47 is an endogenous inhibitor of autophagy in brain ECs, and such TRIM47-mediated regulation connects genetic and physiological risk factors for WMH formation but warrants further investigation. SUMMARY STATEMENT TRIM47, top genetic risk factor for white matter hyperintensity formation, is a negative regulator of autophagy in brain endothelial cells and implicates a novel cellular mechanism for age-related cerebrovascular changes.
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Aguilera MO, Delgui LR, Reggiori F, Romano PS, Colombo MI. Autophagy as an innate immunity response against pathogens: a Tango dance. FEBS Lett 2024; 598:140-166. [PMID: 38101809 DOI: 10.1002/1873-3468.14788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 12/17/2023]
Abstract
Intracellular infections as well as changes in the cell nutritional environment are main events that trigger cellular stress responses. One crucial cell response to stress conditions is autophagy. During the last 30 years, several scenarios involving autophagy induction or inhibition over the course of an intracellular invasion by pathogens have been uncovered. In this review, we will present how this knowledge was gained by studying different microorganisms. We intend to discuss how the cell, via autophagy, tries to repel these attacks with the objective of destroying the intruder, but also how some pathogens have developed strategies to subvert this. These two fates can be compared with a Tango, a dance originated in Buenos Aires, Argentina, in which the partner dancers are in close connection. One of them is the leader, embracing and involving the partner, but the follower may respond escaping from the leader. This joint dance is indeed highly synchronized and controlled, perfectly reflecting the interaction between autophagy and microorganism.
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Affiliation(s)
- Milton O Aguilera
- Laboratorio de Mecanismos Moleculares Implicados en el Tráfico Vesicular y la Autofagia-Instituto de Histología y Embriología (IHEM), Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina
- Facultad de Odontología, Microbiología, Parasitología e Inmunología, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Laura R Delgui
- Instituto de Histología y Embriología de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro Universitario M5502JMA, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
| | - Fulvio Reggiori
- Department of Biomedicine, Aarhus University, Denmark
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Denmark
| | - Patricia S Romano
- Laboratorio de Biología de Trypanosoma cruzi y la célula hospedadora - Instituto de Histología y Embriología de Mendoza, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Centro Universitario M5502JMA, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
- Facultad de Ciencias Médicas, Centro Universitario M5502JMA, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
| | - María I Colombo
- Laboratorio de Mecanismos Moleculares Implicados en el Tráfico Vesicular y la Autofagia-Instituto de Histología y Embriología (IHEM), Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina
- Facultad de Ciencias Médicas, Centro Universitario M5502JMA, Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
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Schwalm MP, Dopfer J, Knapp S, Rogov VV. High-Throughput Screening for LC3/GABARAP Binders Utilizing the Fluorescence Polarization Assay. Methods Mol Biol 2024; 2845:203-218. [PMID: 39115669 DOI: 10.1007/978-1-0716-4067-8_17] [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] [Indexed: 09/18/2024]
Abstract
The characterization of interactions between autophagy modifiers (Atg8-family proteins) and their natural ligands (peptides and proteins) or small molecules is important for a detailed understanding of selective autophagy mechanisms and for the design of potential Atg8 inhibitors that affect the autophagy processes in cells. The fluorescence polarization (FP) assay is a rapid, cost-effective, and robust method that provides affinity and selectivity information for small molecules and peptide ligands targeting human Atg8 proteins.This chapter introduces the basic principles of FP assays. In addition, a case study on peptide interaction with human Atg8 proteins (LC3/GABARAPs) is described. Finally, data analysis and quality control of FP assays are discussed for the proper calculation of Ki values for the measured compounds.
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Affiliation(s)
- Martin P Schwalm
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt, Germany
| | - Johannes Dopfer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt, Germany
| | - Vladimir V Rogov
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt, Germany.
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34
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Rogov VV, Nezis IP, Tsapras P, Zhang H, Dagdas Y, Noda NN, Nakatogawa H, Wirth M, Mouilleron S, McEwan DG, Behrends C, Deretic V, Elazar Z, Tooze SA, Dikic I, Lamark T, Johansen T. Atg8 family proteins, LIR/AIM motifs and other interaction modes. AUTOPHAGY REPORTS 2023; 2:27694127.2023.2188523. [PMID: 38214012 PMCID: PMC7615515 DOI: 10.1080/27694127.2023.2188523] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
The Atg8 family of ubiquitin-like proteins play pivotal roles in autophagy and other processes involving vesicle fusion and transport where the lysosome/vacuole is the end station. Nuclear roles of Atg8 proteins are also emerging. Here, we review the structural and functional features of Atg8 family proteins and their protein-protein interaction modes in model organisms such as yeast, Arabidopsis, C. elegans and Drosophila to humans. Although varying in number of homologs, from one in yeast to seven in humans, and more than ten in some plants, there is a strong evolutionary conservation of structural features and interaction modes. The most prominent interaction mode is between the LC3 interacting region (LIR), also called Atg8 interacting motif (AIM), binding to the LIR docking site (LDS) in Atg8 homologs. There are variants of these motifs like "half-LIRs" and helical LIRs. We discuss details of the binding modes and how selectivity is achieved as well as the role of multivalent LIR-LDS interactions in selective autophagy. A number of LIR-LDS interactions are known to be regulated by phosphorylation. New methods to predict LIR motifs in proteins have emerged that will aid in discovery and analyses. There are also other interaction surfaces than the LDS becoming known where we presently lack detailed structural information, like the N-terminal arm region and the UIM-docking site (UDS). More interaction modes are likely to be discovered in future studies.
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Affiliation(s)
- Vladimir V. Rogov
- Institute for Pharmaceutical Chemistry, Department of Biochemistry, Chemistry and Pharmacy, Goethe University, 60438 Frankfurt, am Main, and Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Ioannis P. Nezis
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | | | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China and College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yasin Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo 060-0815, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Martina Wirth
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Stephane Mouilleron
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | | | - Christian Behrends
- Munich Cluster of Systems Neurology, Ludwig-Maximilians-Universität München, München, Germany
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM and Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Zvulun Elazar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Ivan Dikic
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt am Main, and Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Trond Lamark
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Terje Johansen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
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Dwivedi R, Baindara P. Differential Regulation of TFEB-Induced Autophagy during Mtb Infection and Starvation. Microorganisms 2023; 11:2944. [PMID: 38138088 PMCID: PMC10746089 DOI: 10.3390/microorganisms11122944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Through the promotion of phagolysosome formation, autophagy has emerged as a crucial mechanism to eradicate intracellular Mycobacterium tuberculosis (Mtb). A cell-autonomous host defense mechanism called lysosome biogenesis and autophagy transports cytoplasmic cargos and bacterial phagosomes to lysosomes for destruction during infection. Similar occurrences occurred in stressful or starvation circumstances and led to autophagy, which is harmful to the cell. It is interesting to note that under both hunger and infection states, the transcription factor EB (TFEB) acts as a master regulator of lysosomal activities and autophagy. This review highlighted recent research on the multitier regulation of TFEB-induced autophagy by a variety of host effectors and Mtb sulfolipid during Mtb infection and starvation. In general, the research presented here sheds light on how lysosome biogenesis and autophagy are differentially regulated by the TFEB during Mtb infection and starvation.
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Affiliation(s)
- Richa Dwivedi
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Piyush Baindara
- Radiation Oncology, NextGen Precision Health, School of Medicine, University of Missouri, Columbia, MO 65211, USA
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36
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Quadir N, Shariq M, Sheikh JA, Singh J, Sharma N, Hasnain SE, Ehtesham NZ. Mycobacterium tuberculosis protein MoxR1 enhances virulence by inhibiting host cell death pathways and disrupting cellular bioenergetics. Virulence 2023; 14:2180230. [PMID: 36799069 PMCID: PMC9980616 DOI: 10.1080/21505594.2023.2180230] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Mycobacterium tuberculosis (M. tb) utilizes the multifunctionality of its protein factors to deceive the host. The unabated global incidence and prevalence of tuberculosis (TB) and the emergence of multidrug-resistant strains warrant the discovery of novel drug targets that can be exploited to manage TB. This study reports the role of M. tb AAA+ family protein MoxR1 in regulating host-pathogen interaction and immune system functions. We report that MoxR1 binds to TLR4 in macrophage cells and further reveal how this signal the release of proinflammatory cytokines. We show that MoxR1 activates the PI3K-AKT-MTOR signalling cascade by inhibiting the autophagy-regulating kinase ULK1 by potentiating its phosphorylation at serine 757, leading to its suppression. Using autophagy-activating and repressing agents such as rapamycin and bafilomycin A1 suggested that MoxR1 inhibits autophagy flux by inhibiting autophagy initiation. MoxR1 also inhibits apoptosis by suppressing the expression of MAPK JNK1/2 and cFOS, which play critical roles in apoptosis induction. Intriguingly, MoxR1 also induced robust disruption of cellular bioenergetics by metabolic reprogramming to rewire the citric acid cycle intermediates, as evidenced by the lower levels of citric acid and electron transport chain enzymes (ETC) to dampen host defence. These results point to a multifunctional role of M. tb MoxR1 in dampening host defences by inhibiting autophagy, apoptosis, and inducing metabolic reprogramming. These mechanistic insights can be utilized to devise strategies to combat TB and better understand survival tactics by intracellular pathogens.
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Affiliation(s)
- Neha Quadir
- National Institute of Pathology, ICMR, Safdarjung Hospital Campus, New Delhi, India,Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, India
| | - Mohd. Shariq
- National Institute of Pathology, ICMR, Safdarjung Hospital Campus, New Delhi, India
| | | | - Jasdeep Singh
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Neha Sharma
- National Institute of Pathology, ICMR, Safdarjung Hospital Campus, New Delhi, India
| | - Seyed Ehtesham Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India,Department of Life Science,School of Basic Science and Research, Sharda University, Greater Noida, India,CONTACT Seyed Ehtesham Hasnain
| | - Nasreen Zafar Ehtesham
- National Institute of Pathology, ICMR, Safdarjung Hospital Campus, New Delhi, India,Nazreen Zafar Ehtesham
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Körschgen H, Baeken M, Schmitt D, Nagel H, Behl C. Co-chaperone BAG3 enters autophagic pathway via its interaction with microtubule associated protein 1 light chain 3 beta. Traffic 2023; 24:564-575. [PMID: 37654251 DOI: 10.1111/tra.12916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 07/20/2023] [Accepted: 08/18/2023] [Indexed: 09/02/2023]
Abstract
The co-chaperone BAG3 is a hub for a variety of cellular pathways via its multiple domains and its interaction with chaperones of the HSP70 family or small HSPs. During aging and under cellular stress conditions in particular, BAG3, together with molecular chaperones, ensures the sequestration of aggregated or aggregation-prone ubiquitinated proteins to the autophagic-lysosomal system via ubiquitin receptors. Accumulating evidence for BAG3-mediated selective autophagy independent of cargo ubiquitination led to analyses predicting a direct interaction of BAG3 with LC3 proteins. Phylogenetically, BAG3 comprises several highly conserved potential LIRs, LC3-interacting regions, which might allow for the direct targeting of BAG3 including its cargo to autophagosomes and drive their autophagic degradation. Based on pull-down experiments, peptide arrays and proximity ligation assays, our results provide evidence of an interaction of BAG3 with LC3B. In addition, we could demonstrate that disabling all predicted LIRs abolished the inducibility of a colocalization of BAG3 with LC3B-positive structures and resulted in a substantial decrease of BAG3 levels within purified native autophagic vesicles compared with wild-type BAG3. These results suggest an autophagic targeting of BAG3 via interaction with LC3B. Therefore, we conclude that, in addition to being a key co-chaperone to HSP70, BAG3 may also act as a cargo receptor for client proteins, which would significantly extend the role of BAG3 in selective macroautophagy and protein quality control.
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Affiliation(s)
- Hagen Körschgen
- The Autophagy Lab, Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Marius Baeken
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Daniel Schmitt
- The Autophagy Lab, Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Heike Nagel
- The Autophagy Lab, Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Christian Behl
- The Autophagy Lab, Institute of Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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38
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Bunker EN, Le Guerroué F, Wang C, Strub M, Werner A, Tjandra N, Youle RJ. Nix interacts with WIPI2 to induce mitophagy. EMBO J 2023; 42:e113491. [PMID: 37621214 PMCID: PMC10646555 DOI: 10.15252/embj.2023113491] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/13/2023] [Accepted: 07/15/2023] [Indexed: 08/26/2023] Open
Abstract
Nix is a membrane-anchored outer mitochondrial protein that induces mitophagy. While Nix has an LC3-interacting (LIR) motif that binds to ATG8 proteins, it also contains a minimal essential region (MER) that induces mitophagy through an unknown mechanism. We used chemically induced dimerization (CID) to probe the mechanism of Nix-mediated mitophagy and found that both the LIR and MER are required for robust mitophagy. We find that the Nix MER interacts with the autophagy effector WIPI2 and recruits WIPI2 to mitochondria. The Nix LIR motif is also required for robust mitophagy and converts a homogeneous WIPI2 distribution on the surface of the mitochondria into puncta, even in the absence of ATG8s. Together, this work reveals unanticipated mechanisms in Nix-induced mitophagy and the elusive role of the MER, while also describing an interesting example of autophagy induction that acts downstream of the canonical initiation complexes.
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Affiliation(s)
- Eric N Bunker
- Surgical Neurology BranchNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - François Le Guerroué
- Surgical Neurology BranchNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - Chunxin Wang
- Surgical Neurology BranchNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
| | - Marie‐Paule Strub
- Biochemistry and Biophysics CenterNational Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaMDUSA
| | - Achim Werner
- Stem Cell Biochemistry UnitNational Institute of Dental and Craniofacial Research, National Institutes of HealthBethesdaMDUSA
| | - Nico Tjandra
- Biochemistry and Biophysics CenterNational Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaMDUSA
| | - Richard J Youle
- Surgical Neurology BranchNational Institute of Neurological Disorders and Stroke, National Institutes of HealthBethesdaMDUSA
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39
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Mei L, Chen X, Wei F, Huang X, Liu L, Yao J, Chen J, Luo X, Wang Z, Yang A. Tethering ATG16L1 or LC3 induces targeted autophagic degradation of protein aggregates and mitochondria. Autophagy 2023; 19:2997-3013. [PMID: 37424101 PMCID: PMC10549199 DOI: 10.1080/15548627.2023.2234797] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) based on the ubiquitin-proteasome system have made great progress in the field of drug discovery. There is mounting evidence that the accumulation of aggregation-prone proteins or malfunctioning organelles is associated with the occurrence of various age-related neurodegenerative disorders and cancers. However, PROTACs are inefficient for the degradation of such large targets due to the narrow entrance channel of the proteasome. Macroautophagy (hereafter referred to as autophagy) is known as a self-degradative process involved in the degradation of bulk cytoplasmic components or specific cargoes that are sequestered into autophagosomes. In the present study, we report the development of a generalizable strategy for the targeted degradation of large targets. Our results suggested that tethering large target models to phagophore-associated ATG16L1 or LC3 induced targeted autophagic degradation of the large target models. Furthermore, we successfully applied this autophagy-targeting degradation strategy to the targeted degradation of HTT65Q aggregates and mitochondria. Specifically, chimeras consisting of polyQ-binding peptide 1 (QBP) and ATG16L1-binding peptide (ABP) or LC3-interacting region (LIR) induced targeted autophagic degradation of pathogenic HTT65Q aggregates; and the chimeras consisting of mitochondria-targeting sequence (MTS) and ABP or LIR promoted targeted autophagic degradation of dysfunctional mitochondria, hence ameliorating mitochondrial dysfunction in a Parkinson disease cell model and protecting cells from apoptosis induced by the mitochondrial stress agent FCCP. Therefore, this study provides a new strategy for the selective proteolysis of large targets and enrich the toolkit for autophagy-targeting degradation.Abbreviations: ABP: ATG16L1-binding peptide; ATG16L1: autophagy related 16 like 1; ATTEC: autophagy-tethering compound; AUTAC: autophagy-targeting chimera; AUTOTAC: autophagy-targeting chimera; Baf A1: bafilomycin A1; BCL2: BCL2 apoptosis regulator; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CASP3: caspase 3; CPP: cell-penetrating peptide; CQ: chloroquine phosphate; DAPI: 4',6-diamidino-2-phenylindole; DCM: dichloromethane; DMF: N,N-dimethylformamide; DMSO: dimethyl sulfoxide; EBSS: Earle's balanced salt solution; FCCP: carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone; FITC: fluorescein-5-isothiocyanate; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; HEK293: human embryonic kidney 293; HEK293T: human embryonic kidney 293T; HPLC: high-performance liquid chromatography; HRP: horseradish peroxidase; HTT: huntingtin; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MFF: mitochondrial fission factor; MTS: mitochondria-targeting sequence; NBR1: NBR1 autophagy cargo receptor; NLRX1: NLR family member X1; OPTN: optineurin; P2A: self-cleaving 2A peptide; PB1: Phox and Bem1p; PBS: phosphate-buffered saline; PE: phosphatidylethanolamine; PINK1: PTEN induced kinase 1; PRKN: parkin RBR E3 ubiquitin protein ligase; PROTACs: proteolysis-targeting chimeras; QBP: polyQ-binding peptide 1; SBP: streptavidin-binding peptide; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SPATA33: spermatogenesis associated 33; TIMM23: translocase of inner mitochondrial membrane 23; TMEM59: transmembrane protein 59; TOMM20: translocase of outer mitochondrial membrane 20; UBA: ubiquitin-associated; WT: wild type.
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Affiliation(s)
- Ligang Mei
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xiaorong Chen
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Fujing Wei
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xue Huang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lu Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jia Yao
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jing Chen
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xunguang Luo
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Zhuolin Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, China
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40
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Nieto-Torres JL, Zaretski S, Liu T, Adams PD, Hansen M. Post-translational modifications of ATG8 proteins - an emerging mechanism of autophagy control. J Cell Sci 2023; 136:jcs259725. [PMID: 37589340 PMCID: PMC10445744 DOI: 10.1242/jcs.259725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Autophagy is a recycling mechanism involved in cellular homeostasis with key implications for health and disease. The conjugation of the ATG8 family proteins, which includes LC3B (also known as MAP1LC3B), to autophagosome membranes, constitutes a hallmark of the canonical autophagy process. After ATG8 proteins are conjugated to the autophagosome membranes via lipidation, they orchestrate a plethora of protein-protein interactions that support key steps of the autophagy process. These include binding to cargo receptors to allow cargo recruitment, association with proteins implicated in autophagosome transport and autophagosome-lysosome fusion. How these diverse and critical protein-protein interactions are regulated is still not well understood. Recent reports have highlighted crucial roles for post-translational modifications of ATG8 proteins in the regulation of ATG8 functions and the autophagy process. This Review summarizes the main post-translational regulatory events discovered to date to influence the autophagy process, mostly described in mammalian cells, including ubiquitylation, acetylation, lipidation and phosphorylation, as well as their known contributions to the autophagy process, physiology and disease.
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Affiliation(s)
- Jose L. Nieto-Torres
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
- Department of Biomedical Sciences, School of Health Sciences and Veterinary, Universidad Cardenal Herrera-CEU, CEU Universities, 46113 Moncada, Spain
| | - Sviatlana Zaretski
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Tianhui Liu
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Peter D. Adams
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
| | - Malene Hansen
- Sanford Burnham Prebys Medical Discovery Institute, Program of Development, Aging, and Regeneration, La Jolla, CA 92037, USA
- The Buck Institute for Aging Research, Novato, CA 94945, USA
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41
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Wallace NS, Gadbery JE, Cohen CI, Kendall AK, Jackson LP. Tepsin binds LC3B to promote ATG9A export and delivery at the cell periphery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549521. [PMID: 37502979 PMCID: PMC10370099 DOI: 10.1101/2023.07.18.549521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Tepsin is an established accessory protein found in Adaptor Protein 4 (AP-4) coated vesicles, but the biological role of tepsin remains unknown. AP-4 vesicles originate at the trans -Golgi network (TGN) and target the delivery of ATG9A, a scramblase required for autophagosome biogenesis, to the cell periphery. Using in silico methods, we identified a putative L C3-Interacting R egion (LIR) motif in tepsin. Biochemical experiments using purified recombinant proteins indicate tepsin directly binds LC3B, but not other members, of the mammalian ATG8 family. Calorimetry and structural modeling data indicate this interaction occurs with micromolar affinity using the established LC3B LIR docking site. Loss of tepsin in cultured cells dysregulates ATG9A export from the TGN as well as ATG9A distribution at the cell periphery. Tepsin depletion in a mRFP-GFP-LC3B HeLa reporter cell line using siRNA knockdown increases autophagosome volume and number, but does not appear to affect flux through the autophagic pathway. Re-introduction of wild-type tepsin partially rescues ATG9A cargo trafficking defects. In contrast, re-introducing tepsin with a mutated LIR motif or missing N-terminus does not fully rescue altered ATG9A subcellular distribution. Together, these data suggest roles for tepsin in cargo export from the TGN; delivery of ATG9A-positive vesicles at the cell periphery; and in overall maintenance of autophagosome structure.
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42
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Vo MT, Choi CY, Choi YB. The mitophagy receptor NIX induces vIRF-1 oligomerization and interaction with GABARAPL1 for the promotion of HHV-8 reactivation-induced mitophagy. PLoS Pathog 2023; 19:e1011548. [PMID: 37459327 PMCID: PMC10374065 DOI: 10.1371/journal.ppat.1011548] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/27/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023] Open
Abstract
Recently, viruses have been shown to regulate selective autophagy for productive infections. For instance, human herpesvirus 8 (HHV-8), also known as Kaposi's sarcoma-associated herpesvirus (KSHV), activates selective autophagy of mitochondria, termed mitophagy, thereby inhibiting antiviral innate immune responses during lytic infection in host cells. We previously demonstrated that HHV-8 viral interferon regulatory factor 1 (vIRF-1) plays a crucial role in lytic replication-activated mitophagy by interacting with cellular mitophagic proteins, including NIX and TUFM. However, the precise molecular mechanisms by which these interactions lead to mitophagy activation remain to be determined. Here, we show that vIRF-1 binds directly to mammalian autophagy-related gene 8 (ATG8) proteins, preferentially GABARAPL1 in infected cells, in an LC3-interacting region (LIR)-independent manner. Accordingly, we identified key residues in vIRF-1 and GABARAPL1 required for mutual interaction and demonstrated that the interaction is essential for mitophagy activation and HHV-8 productive replication. Interestingly, the mitophagy receptor NIX promotes vIRF-1-GABARAPL1 interaction, and NIX/vIRF-1-induced mitophagy is significantly inhibited in GABARAPL1-deficient cells. Moreover, a vIRF-1 variant defective in GABARAPL1 binding substantially loses the ability to induce vIRF-1/NIX-induced mitophagy. These results suggest that NIX supports vIRF-1 activity as a mitophagy mediator. In addition, we found that NIX promotes vIRF-1 aggregation and stabilizes aggregated vIRF-1. Together, these findings indicate that vIRF-1 plays a role as a viral mitophagy mediator that can be activated by a cellular mitophagy receptor.
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Affiliation(s)
- Mai Tram Vo
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Chang-Yong Choi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Young Bong Choi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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43
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Davey NE, Simonetti L, Ivarsson Y. The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome. Curr Opin Struct Biol 2023; 80:102593. [PMID: 37099901 DOI: 10.1016/j.sbi.2023.102593] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 04/28/2023]
Abstract
Short linear motifs (SLiMs) are a unique and ubiquitous class of protein interaction modules that perform key regulatory functions and drive dynamic complex formation. For decades, interactions mediated by SLiMs have accumulated through detailed low-throughput experiments. Recent methodological advances have opened this previously underexplored area of the human interactome to high-throughput protein-protein interaction discovery. In this article, we discuss that SLiM-based interactions represent a significant blind spot in the current interactomics data, introduce the key methods that are illuminating the elusive SLiM-mediated interactome of the human cell on a large scale, and discuss the implications for the field.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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44
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Farnung J, Muhar M, Liang JR, Tolmachova KA, Benoit RM, Corn JE, Bode JW. Semisynthetic LC3 Probes for Autophagy Pathways Reveal a Noncanonical LC3 Interacting Region Motif Crucial for the Enzymatic Activity of Human ATG3. ACS CENTRAL SCIENCE 2023; 9:1025-1034. [PMID: 37252361 PMCID: PMC10214526 DOI: 10.1021/acscentsci.3c00009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Indexed: 05/31/2023]
Abstract
Macroautophagy is one of two major degradation systems in eukaryotic cells. Regulation and control of autophagy are often achieved through the presence of short peptide sequences called LC3 interacting regions (LIR) in autophagy-involved proteins. Using a combination of new protein-derived activity-based probes prepared from recombinant LC3 proteins, along with protein modeling and X-ray crystallography of the ATG3-LIR peptide complex, we identified a noncanonical LIR motif in the human E2 enzyme responsible for LC3 lipidation, ATG3. The LIR motif is present in the flexible region of ATG3 and adopts an uncommon β-sheet structure binding to the backside of LC3. We show that the β-sheet conformation is crucial for its interaction with LC3 and used this insight to design synthetic macrocyclic peptide-binders to ATG3. CRISPR-enabled in cellulo studies provide evidence that LIRATG3 is required for LC3 lipidation and ATG3∼LC3 thioester formation. Removal of LIRATG3 negatively impacts the rate of thioester transfer from ATG7 to ATG3.
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Affiliation(s)
- Jakob Farnung
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zürich, CH-8093 Zürich, Switzerland
| | - Matthias Muhar
- Institute
of Molecular Health Sciences, Department of Biology ETH Zürich, CH-8093 Zürich, Switzerland
| | - Jin Rui Liang
- Institute
of Molecular Health Sciences, Department of Biology ETH Zürich, CH-8093 Zürich, Switzerland
| | - Kateryna A. Tolmachova
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zürich, CH-8093 Zürich, Switzerland
| | - Roger M. Benoit
- Laboratory
of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jacob E. Corn
- Institute
of Molecular Health Sciences, Department of Biology ETH Zürich, CH-8093 Zürich, Switzerland
| | - Jeffrey W. Bode
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zürich, CH-8093 Zürich, Switzerland
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45
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Abstract
Significance: Autophagy is a self-degrading process that determines cell fate in response to various environmental stresses. In contrast to autophagy-mediated cell survival, the signals, mechanisms, and effects of autophagy-dependent cell death remain obscure. The discovery of autophagy-dependent ferroptosis provides a paradigm for understanding the relationship between aberrant degradation pathways and excessive lipid peroxidation in driving regulated cell death. Recent Advances: Ferroptosis was originally described as an autophagy-independent and iron-mediated nonapoptotic cell death. Current studies reveal that the level of intracellular autophagy is positively correlated with ferroptosis sensitivity. Selective autophagic degradation of proteins (e.g., ferritin, SLC40A1, ARNTL, GPX4, and CDH2) or organelles (e.g., lipid droplets or mitochondria) promotes ferroptosis by inducing iron overload and/or lipid peroxidation. Several upstream autophagosome regulators (e.g., TMEM164), downstream autophagy receptors (e.g., HPCAL1), or danger signals (e.g., DCN) are selectively required for ferroptosis-related autophagy, but not for starvation-induced autophagy. The induction of autophagy-dependent ferroptosis is an effective approach to eliminate drug-resistant cancer cells. Critical Issues: How different organelles selectively activate autophagy to modulate ferroptosis sensitivity is not fully understood. Identifying direct protein effectors of ferroptotic cell death remains a challenge. Future Directions: Further understanding of the molecular mechanics and immune consequences of autophagy-dependent ferroptosis is critical for the development of precision antitumor therapies.
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Affiliation(s)
- Fangquan Chen
- DAMP Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, Guangzhou Medical University, Guangzhou, China
| | - Xiutao Cai
- DAMP Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, Guangzhou Medical University, Guangzhou, China
| | - Rui Kang
- Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Jiao Liu
- DAMP Laboratory, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, Guangzhou Medical University, Guangzhou, China
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, Texas, USA
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46
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Walczak M, Meister TR, Nguyen HM, Zhu Y, Besteiro S, Yeh E. Structure-Function Relationship for a Divergent Atg8 Protein Required for a Nonautophagic Function in Apicomplexan Parasites. mBio 2023; 14:e0364221. [PMID: 36625582 PMCID: PMC9973341 DOI: 10.1128/mbio.03642-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Atg8 family proteins are highly conserved eukaryotic proteins with diverse autophagy and nonautophagic functions in eukaryotes. While the structural features required for conserved autophagy functions of Atg8 are well established, little is known about the molecular changes that facilitated acquisition of divergent, nonautophagic functions of Atg8. The malaria parasite Plasmodium falciparum offers a unique opportunity to study nonautophagic functions of Atg8 family proteins because it encodes a single Atg8 homolog whose only essential function is in the inheritance of an unusual secondary plastid called the apicoplast. Here, we used functional complementation to investigate the structure-function relationship for this divergent Atg8 protein. We showed that the LC3-interacting region (LIR) docking site (LDS), the major interaction interface of the Atg8 protein family, is required for P. falciparum Atg8 (PfAtg8) apicoplast localization and function, likely via Atg8 lipidation. On the other hand, another region previously implicated in canonical Atg8 interactions, the N-terminal helix, is not required for apicoplast-specific PfAtg8 function. Finally, our investigations at the cellular level demonstrate that the unique apicomplexan-specific loop, previously implicated in interaction with membrane conjugation machinery in recombinant protein-based in vitro assays, is not required for membrane conjugation nor for the apicoplast-specific effector function of Atg8 in both P. falciparum and related Apicomplexa member Toxoplasma gondii. These results suggest that the effector function of apicomplexan Atg8 is mediated by structural features distinct from those previously identified for macroautophagy and selective autophagy functions. IMPORTANCE The most extensively studied role of Atg8 proteins is in autophagy. However, it is clear that they have other nonautophagic functions critical to cell function and disease pathogenesis that are so far understudied compared to their canonical role in autophagy. Mammalian cells contain multiple Atg8 paralogs that have diverse, specialized functions. Gaining molecular insight into their nonautophagic functions is difficult because of redundancy between the homologs and their role in both autophagy and nonautophagic pathways. Malaria parasites such as Plasmodium falciparum are a unique system to study a novel, nonautophagic function of Atg8 separate from its role in autophagy: they have only one Atg8 protein whose only essential function is in the inheritance of the apicoplast, a unique secondary plastid organelle. Insights into the molecular basis of PfAtg8's function in apicoplast biogenesis will have important implications for the evolution of diverse nonautophagic functions of the Atg8 protein family.
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Affiliation(s)
- Marta Walczak
- Department of Pathology, Stanford School of Medicine, Stanford, California, USA
| | - Thomas R. Meister
- Department of Molecular and Cellular Physiology, Stanford School of Medicine, Stanford, California, USA
| | - Hoa Mai Nguyen
- LPHI UMR5235, University of Montpellier, CNRS, Montpellier, France
| | - Yili Zhu
- Department of Pathology, Stanford School of Medicine, Stanford, California, USA
| | | | - Ellen Yeh
- Department of Pathology, Stanford School of Medicine, Stanford, California, USA
- Department of Microbiology & Immunology, Stanford School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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47
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Steffek M, Helgason E, Popovych N, Rougé L, Bruning JM, Li KS, Burdick DJ, Cai J, Crawford T, Xue J, Decurtins W, Fang C, Grubers F, Holliday MJ, Langley A, Petersen A, Satz AL, Song A, Stoffler D, Strebel Q, Tom JYK, Skelton N, Staben ST, Wichert M, Mulvihill MM, Dueber EC. A Multifaceted Hit-Finding Approach Reveals Novel LC3 Family Ligands. Biochemistry 2023; 62:633-644. [PMID: 34985287 DOI: 10.1021/acs.biochem.1c00682] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Autophagy-related proteins (Atgs) drive the lysosome-mediated degradation pathway, autophagy, to enable the clearance of dysfunctional cellular components and maintain homeostasis. In humans, this process is driven by the mammalian Atg8 (mAtg8) family of proteins comprising the LC3 and GABARAP subfamilies. The mAtg8 proteins play essential roles in the formation and maturation of autophagosomes and the capture of specific cargo through binding to the conserved LC3-interacting region (LIR) sequence within target proteins. Modulation of interactions of mAtg8 with its target proteins via small-molecule ligands would enable further interrogation of their function. Here we describe unbiased fragment and DNA-encoded library (DEL) screening approaches for discovering LC3 small-molecule ligands. Both strategies resulted in compounds that bind to LC3, with the fragment hits favoring a conserved hydrophobic pocket in mATG8 proteins, as detailed by LC3A-fragment complex crystal structures. Our findings demonstrate that the malleable LIR-binding surface can be readily targeted by fragments; however, rational design of additional interactions to drive increased affinity proved challenging. DEL libraries, which combine small, fragment-like building blocks into larger scaffolds, yielded higher-affinity binders and revealed an unexpected potential for reversible, covalent ligands. Moreover, DEL hits identified possible vectors for synthesizing fluorescent probes or bivalent molecules for engineering autophagic degradation of specific targets.
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Affiliation(s)
- Micah Steffek
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Elizabeth Helgason
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Nataliya Popovych
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Lionel Rougé
- Structure Biology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - John M Bruning
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Ke Sherry Li
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel J Burdick
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Jianping Cai
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Terry Crawford
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Jing Xue
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Willy Decurtins
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Chunlin Fang
- WuXi AppTec (Wuhan) Company, Ltd., No. 666 GaoXin Road, WuHan East Lake High-tech Development Zone, Hubei 430075, China
| | - Felix Grubers
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Michael J Holliday
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Allyson Langley
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Ann Petersen
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Alexander Lee Satz
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Aimin Song
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel Stoffler
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Quentin Strebel
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Jeffrey Y K Tom
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Nicholas Skelton
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Steven T Staben
- Chemistry Departments, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Moreno Wichert
- Roche Pharma Research and Early Development, Roche Innovation Center, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Melinda M Mulvihill
- Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
| | - Erin C Dueber
- Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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48
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Zhou J, Rasmussen NL, Olsvik HL, Akimov V, Hu Z, Evjen G, Kaeser-Pebernard S, Sankar DS, Roubaty C, Verlhac P, van de Beek N, Reggiori F, Abudu YP, Blagoev B, Lamark T, Johansen T, Dengjel J. TBK1 phosphorylation activates LIR-dependent degradation of the inflammation repressor TNIP1. J Cell Biol 2023; 222:e202108144. [PMID: 36574265 PMCID: PMC9797988 DOI: 10.1083/jcb.202108144] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 06/24/2022] [Accepted: 08/17/2022] [Indexed: 12/28/2022] Open
Abstract
Limitation of excessive inflammation due to selective degradation of pro-inflammatory proteins is one of the cytoprotective functions attributed to autophagy. In the current study, we highlight that selective autophagy also plays a vital role in promoting the establishment of a robust inflammatory response. Under inflammatory conditions, here TLR3-activation by poly(I:C) treatment, the inflammation repressor TNIP1 (TNFAIP3 interacting protein 1) is phosphorylated by Tank-binding kinase 1 (TBK1) activating an LIR motif that leads to the selective autophagy-dependent degradation of TNIP1, supporting the expression of pro-inflammatory genes and proteins. This selective autophagy efficiently reduces TNIP1 protein levels early (0-4 h) upon poly(I:C) treatment to allow efficient initiation of the inflammatory response. At 6 h, TNIP1 levels are restored due to increased transcription avoiding sustained inflammation. Thus, similarly as in cancer, autophagy may play a dual role in controlling inflammation depending on the exact state and timing of the inflammatory response.
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Affiliation(s)
- Jianwen Zhou
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Nikoline Lander Rasmussen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
| | - Hallvard Lauritz Olsvik
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
| | - Vyacheslav Akimov
- Department of Biochemistry and Molecular Biology, Center for Experimental BioInformatics, University of Southern Denmark, Odense, Denmark
| | - Zehan Hu
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Gry Evjen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
| | | | | | - Carole Roubaty
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Pauline Verlhac
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Nicole van de Beek
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Fulvio Reggiori
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus, Denmark
| | - Yakubu Princely Abudu
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, Center for Experimental BioInformatics, University of Southern Denmark, Odense, Denmark
| | - Trond Lamark
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
| | - Terje Johansen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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49
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Dutta SB, Linneweber GA, Andriatsilavo M, Hiesinger PR, Hassan BA. EGFR-dependent suppression of synaptic autophagy is required for neuronal circuit development. Curr Biol 2023; 33:517-532.e5. [PMID: 36640763 DOI: 10.1016/j.cub.2022.12.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/31/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023]
Abstract
The development of neuronal connectivity requires stabilization of dynamic axonal branches at sites of synapse formation. Models that explain how axonal branching is coupled to synaptogenesis postulate molecular regulators acting in a spatiotemporally restricted fashion to ensure branching toward future synaptic partners while also stabilizing the emerging synaptic contacts between such partners. We investigated this question using neuronal circuit development in the Drosophila brain as a model system. We report that epidermal growth factor receptor (EGFR) activity is required in presynaptic axonal branches during two distinct temporal intervals to regulate circuit wiring in the developing Drosophila visual system. EGFR is required early to regulate primary axonal branching. EGFR activity is then independently required at a later stage to prevent degradation of the synaptic active zone protein Bruchpilot (Brp). Inactivation of EGFR results in a local increase of autophagy in presynaptic branches and the translocation of active zone proteins into autophagic vesicles. The protection of synaptic material during this later interval of wiring ensures the stabilization of terminal branches, circuit connectivity, and appropriate visual behavior. Phenotypes of EGFR inactivation can be rescued by increasing Brp levels or downregulating autophagy. In summary, we identify a temporally restricted molecular mechanism required for coupling axonal branching and synaptic stabilization that contributes to the emergence of neuronal wiring specificity.
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Affiliation(s)
- Suchetana B Dutta
- Institut du Cerveau-Paris Brain Institute (ICM), Sorbonne Université, Inserm, CNRS, Hôpital Pitié Salpêtrière, 75013 Paris, France; Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany; Einstein-BIH, Charité Universitätsmedizin, 10117 Berlin, Germany
| | | | - Maheva Andriatsilavo
- Institut du Cerveau-Paris Brain Institute (ICM), Sorbonne Université, Inserm, CNRS, Hôpital Pitié Salpêtrière, 75013 Paris, France; Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany; Einstein-BIH, Charité Universitätsmedizin, 10117 Berlin, Germany
| | | | - Bassem A Hassan
- Institut du Cerveau-Paris Brain Institute (ICM), Sorbonne Université, Inserm, CNRS, Hôpital Pitié Salpêtrière, 75013 Paris, France; Division of Neurobiology, Free University of Berlin, 14195 Berlin, Germany; Einstein-BIH, Charité Universitätsmedizin, 10117 Berlin, Germany.
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50
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Abstract
In this issue of PLOS Biology, Ibrahim and colleagues demonstrate how AlphaFold-multimer, an artificial intelligence-based structure prediction tool, can be used to identify sequence motifs binding to the ATG8 family of proteins central to autophagy.
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Affiliation(s)
- Hallvard Lauritz Olsvik
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
| | - Terje Johansen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø—The Arctic University of Norway, Tromsø, Norway
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