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Restrepo LJ, Baehrecke EH. Regulation and Functions of Autophagy During Animal Development. J Mol Biol 2024; 436:168473. [PMID: 38311234 PMCID: PMC11260256 DOI: 10.1016/j.jmb.2024.168473] [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: 12/12/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Autophagy is used to degrade cytoplasmic materials, and is critical to maintain cell and organismal health in diverse animals. Here we discuss the regulation, utilization and impact of autophagy on development, including roles in oogenesis, spermatogenesis and embryogenesis in animals. We also describe how autophagy influences postembryonic development in the context of neuronal and cardiac development, wound healing, and tissue regeneration. We describe recent studies of selective autophagy during development, including mitochondria-selective autophagy and endoplasmic reticulum (ER)-selective autophagy. Studies of developing model systems have also been used to discover novel regulators of autophagy, and we explain how studies of autophagy in these physiologically relevant systems are advancing our understanding of this important catabolic process.
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Affiliation(s)
- Lucas J Restrepo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Eric H Baehrecke
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA.
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2
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Li X, Yang JY, Hu WZ, Ruan Y, Chen HY, Zhang Q, Zhang Z, Ding ZS. Mitochondria-associated membranes contribution to exercise-mediated alleviation of hepatic insulin resistance: Contrasting high-intensity interval training with moderate-intensity continuous training in a high-fat diet mouse model. J Diabetes 2024; 16:e13540. [PMID: 38599845 PMCID: PMC11006604 DOI: 10.1111/1753-0407.13540] [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: 07/06/2023] [Revised: 12/18/2023] [Accepted: 02/03/2024] [Indexed: 04/12/2024] Open
Abstract
OBJECTIVE Mitochondria-associated membranes (MAMs) serve pivotal functions in hepatic insulin resistance (IR). Our aim was to explore the potential role of MAMs in mitigating hepatic IR through exercise and to compare the effects of different intensities of exercise on hepatic MAMs formation in high-fat diet (HFD) mice. METHODS Male C57BL/6J mice were fed an HFD and randomly assigned to undergo supervised high-intensity interval training (HIIT) or moderate-intensity continuous training (MICT). IR was evaluated using the serum triglyceride/high-density lipoprotein cholesterol ratio (TG/HDL-C), glucose tolerance test (GTT), and insulin tolerance test (ITT). Hepatic steatosis was observed using hematoxylin-eosin (H&E) and oil red O staining. The phosphatidylinositol 3-kinase/protein kinase B/glycogen synthase kinase 3 beta (PI3K-AKT-GSK3β) signaling pathway was assessed to determine hepatic IR. MAMs were evaluated through immunofluorescence (colocalization of voltage-dependent anion-selective channel 1 [VDAC1] and inositol 1,4,5-triphosphate receptor [IP3R]). RESULTS After 8 weeks on an HFD, there was notable inhibition of the hepatic PI3K/Akt/GSK3β signaling pathway, accompanied by a marked reduction in hepatic IP3R-VDAC1 colocalization levels. Both 8-week HIIT and MICT significantly enhanced the hepatic PI3K/Akt/GSK3β signaling and colocalization levels of IP3R-VDAC1 in HFD mice, with MICT exhibiting a stronger effect on hepatic MAMs formation. Furthermore, the colocalization of hepatic IP3R-VDAC1 positively correlated with the expression levels of phosphorylation of protein kinase B (p-AKT) and phosphorylation of glycogen synthase kinase 3 beta (p-GSK3β), while displaying a negative correlation with serum triglyceride/high-density lipoprotein cholesterol levels. CONCLUSION The reduction in hepatic MAMs formation induced by HFD correlates with the development of hepatic IR. Both HIIT and MICT effectively bolster hepatic MAMs formation in HFD mice, with MICT demonstrating superior efficacy. Thus, MAMs might wield a pivotal role in exercise-induced alleviation of hepatic IR.
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Affiliation(s)
- Xi Li
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of EducationEast China Normal UniversityShanghaiChina
- College of Physical Education & HealthEast China Normal UniversityShanghaiChina
| | - Jun Yang Yang
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of EducationEast China Normal UniversityShanghaiChina
- College of Physical Education & HealthEast China Normal UniversityShanghaiChina
| | - Wen Zhi Hu
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of EducationEast China Normal UniversityShanghaiChina
- College of Physical Education & HealthEast China Normal UniversityShanghaiChina
| | - YuXin Ruan
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of EducationEast China Normal UniversityShanghaiChina
- College of Physical Education & HealthEast China Normal UniversityShanghaiChina
| | - Hong Ying Chen
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of EducationEast China Normal UniversityShanghaiChina
- College of Physical Education & HealthEast China Normal UniversityShanghaiChina
| | - Qiang Zhang
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of EducationEast China Normal UniversityShanghaiChina
- College of Physical Education & HealthEast China Normal UniversityShanghaiChina
| | - Zhe Zhang
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of EducationEast China Normal UniversityShanghaiChina
- College of Physical Education & HealthEast China Normal UniversityShanghaiChina
| | - Zhe Shu Ding
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of EducationEast China Normal UniversityShanghaiChina
- College of Physical Education & HealthEast China Normal UniversityShanghaiChina
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3
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Mathur A, Ritu, Chandra P, Das A. Autophagy: a necessary evil in cancer and inflammation. 3 Biotech 2024; 14:87. [PMID: 38390576 PMCID: PMC10879063 DOI: 10.1007/s13205-023-03864-w] [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: 07/20/2023] [Accepted: 11/21/2023] [Indexed: 02/24/2024] Open
Abstract
Autophagy, a highly regulated cellular process, assumes a dual role in the context of cancer. On the one hand, it functions as a crucial homeostatic pathway, responsible for degrading malfunctioning molecules and organelles, thereby maintaining cellular health. On the other hand, its involvement in cancer development and regression is multifaceted, contingent upon a myriad of factors. This review meticulously examines the intricacies of autophagy, from its molecular machinery orchestrated by Autophagy-Related Genes (ATG) initially discovered in yeast to the various modes of autophagy operative within cells. Beyond its foundational role in cellular maintenance, autophagy reveals context-specific functions in processes like angiogenesis and inflammation. Our analysis delves into how autophagy-related factors directly impact inflammation, underscoring their profound implications for cancer dynamics. Additionally, we extend our inquiry to explore autophagy's associations with cardiovascular conditions, neurodegenerative disorders, and autoimmune diseases, illuminating the broader medical relevance of this process. Furthermore, this review elucidates how autophagy contributes to sustaining hallmark cancer features, including stem cell maintenance, proliferation, angiogenesis, metastasis, and metabolic reprogramming. Autophagy emerges as a pivotal process that necessitates careful consideration in cancer treatment strategies. To this end, we investigate innovative approaches, ranging from enzyme-based therapies to MTOR inhibitors, lysosomal blockers, and nanoparticle-enabled interventions, all aimed at optimizing cancer treatment outcomes by targeting autophagy pathways. In summary, this comprehensive review provides a nuanced perspective on the intricate and context-dependent role of autophagy in cancer biology. Our exploration not only deepens our understanding of this fundamental process but also highlights its potential as a therapeutic target. By unraveling the complex interplay between autophagy and cancer, we pave the way for more precise and effective cancer treatments, promising better outcomes for patients.
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Affiliation(s)
- Amit Mathur
- Department of Biotechnology, Delhi Technological University, Main Bawana Road, Delhi, 110042 India
| | - Ritu
- Department of Biotechnology, Delhi Technological University, Main Bawana Road, Delhi, 110042 India
| | - Prakash Chandra
- Department of Biotechnology, Delhi Technological University, Main Bawana Road, Delhi, 110042 India
| | - Asmita Das
- Department of Biotechnology, Delhi Technological University, Main Bawana Road, Delhi, 110042 India
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Lecordier L, Heo P, Graversen JH, Hennig D, Skytthe MK, Cornet d'Elzius A, Pincet F, Pérez-Morga D, Pays E. Apolipoproteins L1 and L3 control mitochondrial membrane dynamics. Cell Rep 2023; 42:113528. [PMID: 38041817 PMCID: PMC10765320 DOI: 10.1016/j.celrep.2023.113528] [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: 07/12/2023] [Revised: 11/08/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Apolipoproteins L1 and L3 (APOLs) are associated at the Golgi with the membrane fission factors phosphatidylinositol 4-kinase-IIIB (PI4KB) and non-muscular myosin 2A. Either APOL1 C-terminal truncation (APOL1Δ) or APOL3 deletion (APOL3-KO [knockout]) reduces PI4KB activity and triggers actomyosin reorganization. We report that APOL3, but not APOL1, controls PI4KB activity through interaction with PI4KB and neuronal calcium sensor-1 or calneuron-1. Both APOLs are present in Golgi-derived autophagy-related protein 9A vesicles, which are involved in PI4KB trafficking. Like APOL3-KO, APOL1Δ induces PI4KB dissociation from APOL3, linked to reduction of mitophagy flux and production of mitochondrial reactive oxygen species. APOL1 and APOL3, respectively, can interact with the mitophagy receptor prohibitin-2 and the mitophagosome membrane fusion factor vesicle-associated membrane protein-8 (VAMP8). While APOL1 conditions PI4KB and APOL3 involvement in mitochondrion fission and mitophagy, APOL3-VAMP8 interaction promotes fusion between mitophagosomal and endolysosomal membranes. We propose that APOL3 controls mitochondrial membrane dynamics through interactions with the fission factor PI4KB and the fusion factor VAMP8.
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Affiliation(s)
- Laurence Lecordier
- Laboratory of Molecular Parasitology, IBMM, Université Libre de Bruxelles, 6041 Gosselies, Belgium
| | - Paul Heo
- Laboratoire de Physique de l'Ecole Normale Supérieure, Ecole Normale Supérieure (ENS), Université Paris Sciences et Lettres (PSL), CNRS, Sorbonne Université, Université Paris-Cité, 75005 Paris, France; Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, 75014 Paris, France
| | - Jonas H Graversen
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense C, Denmark
| | - Dorle Hennig
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense C, Denmark
| | - Maria Kløjgaard Skytthe
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense C, Denmark
| | | | - Frédéric Pincet
- Laboratoire de Physique de l'Ecole Normale Supérieure, Ecole Normale Supérieure (ENS), Université Paris Sciences et Lettres (PSL), CNRS, Sorbonne Université, Université Paris-Cité, 75005 Paris, France
| | - David Pérez-Morga
- Laboratory of Molecular Parasitology, IBMM, Université Libre de Bruxelles, 6041 Gosselies, Belgium; Center for Microscopy and Molecular Imaging (CMMI), Université Libre de Bruxelles, 6041 Gosselies, Belgium
| | - Etienne Pays
- Laboratory of Molecular Parasitology, IBMM, Université Libre de Bruxelles, 6041 Gosselies, Belgium.
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Ke X, Pan ZH, Du HF, Shen Y, Shen JD, Liu ZQ, Zheng YG. Secretory production of 7-dehydrocholesterol by engineered Saccharomyces cerevisiae. Biotechnol J 2023; 18:e2300056. [PMID: 37688450 DOI: 10.1002/biot.202300056] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 08/02/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023]
Abstract
BACKGROUND 7-Dehydrocholesterol (7-DHC) can be directly converted to vitamin D3 by UV irradiation and de novo synthesis of 7-DHC in engineered Saccharomyces cerevisiae has been recognized as an attractive substitution to traditional chemical synthesis. Introduction of sterol extracellular transport pathway for the secretory production of 7-DHC is a promising approach to achieve higher titer and simplify the downstream purification processing. METHODS AND RESULTS A series of genes involved in ergosterol pathway were combined reinforced and reengineered in S. cerevisiae. A biphasic fermentation system was introduced and 7-DHC was found to be enriched in oil-phase with an increased titer by 1.5-folds. Quantitative PCR revealed that say1, atf2, pdr5, pry1-3 involved in sterol storage and transport were all significantly induced in sterol overproduced strain. To enhance the secretion capacity, lipid transporters of pathogen-related yeast proteins (Pry), Niemann-Pick disease type C2 (NPC2), ATP-binding cassette (ABC)-family, and their homologues were screened. Both individual and synergetic overexpression of Plant pathogenesis Related protein-1 (Pr-1) and Sterol transport1 (St1) largely increased the de novo biosynthesis and secretory productivity of 7-DHC, and the final titer reached 28.2 mg g-1 with a secretion ratio of 41.4%, which was 26.5-folds higher than the original strain. In addition, the cooperation between Pr-1 and St1 in sterol transport was further confirmed by confocal microscopy, molecular docking, and directed site-mutation. CONCLUSION Selective secretion of different sterol intermediates was characterized in sterol over-produced strain and the extracellular export of 7-DHC developed in present study significantly improved the cell biosynthetic capacity, which offered a novel modification idea for 7-DHC de novo biosynthesis by S. cerevisiae cell factory.
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Affiliation(s)
- Xia Ke
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Zi-Hao Pan
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Hong-Fei Du
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Yi Shen
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Ji-Dong Shen
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Zhi-Qiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Yu-Guo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
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6
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Oshchepkova A, Zenkova M, Vlassov V. Extracellular Vesicles for Therapeutic Nucleic Acid Delivery: Loading Strategies and Challenges. Int J Mol Sci 2023; 24:ijms24087287. [PMID: 37108446 PMCID: PMC10139028 DOI: 10.3390/ijms24087287] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Extracellular vesicles (EVs) are membrane vesicles released into the extracellular milieu by cells of various origins. They contain different biological cargoes, protecting them from degradation by environmental factors. There is an opinion that EVs have a number of advantages over synthetic carriers, creating new opportunities for drug delivery. In this review, we discuss the ability of EVs to function as carriers for therapeutic nucleic acids (tNAs), challenges associated with the use of such carriers in vivo, and various strategies for tNA loading into EVs.
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Affiliation(s)
- Anastasiya Oshchepkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
| | - Marina Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
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7
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Feline Calicivirus P39 Inhibits Innate Immune Responses by Autophagic Degradation of Retinoic Acid Inducible Gene I. Int J Mol Sci 2023; 24:ijms24065254. [PMID: 36982330 PMCID: PMC10048920 DOI: 10.3390/ijms24065254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
Feline calicivirus (FCV) is a feline pathogen that can cause severe upper respiratory tract disease in cats, thus posing a major threat to their health. The exact pathogenic mechanism of FCV is still unclear, although it has been identified as having the ability to induce immune depression. In this study, we discovered that FCV infection triggers autophagy and that its non-structural proteins, P30, P32, and P39, are responsible for initiating this process. Additionally, we observed that altering autophagy levels via chemical modulation resulted in different influences on FCV replication. Moreover, our findings indicate that autophagy can modify the innate immunity induced by FCV infection, with increased autophagy further suppressing FCV-induced RIG-I signal transduction. This research provides insights into the mechanism of FCV replication and has the potential to aid in the development of autophagy-targeted drugs to inhibit or prevent FCV infection.
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8
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Moghimianavval H, Patel C, Mohapatra S, Hwang SW, Kayikcioglu T, Bashirzadeh Y, Liu AP, Ha T. Engineering Functional Membrane-Membrane Interfaces by InterSpy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202104. [PMID: 35618485 PMCID: PMC9789529 DOI: 10.1002/smll.202202104] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Engineering synthetic interfaces between membranes has potential applications in designing non-native cellular communication pathways and creating synthetic tissues. Here, InterSpy is introduced as a synthetic biology tool consisting of a heterodimeric protein engineered to form and maintain membrane-membrane interfaces between apposing synthetic as well as cell membranes through the SpyTag/SpyCatcher interaction. The inclusion of split fluorescent protein fragments in InterSpy allows tracking of the formation of a membrane-membrane interface and reconstitution of functional fluorescent protein in the space between apposing membranes. First, InterSpy is demonstrated by testing split protein designs using a mammalian cell-free expression (CFE) system. By utilizing co-translational helix insertion, cell-free synthesized InterSpy fragments are incorporated into the membrane of liposomes and supported lipid bilayers with the desired topology. Functional reconstitution of split fluorescent protein between the membranes is strictly dependent on SpyTag/SpyCatcher. Finally, InterSpy is demonstrated in mammalian cells by detecting fluorescence reconstitution of split protein at the membrane-membrane interface between two cells each expressing a component of InterSpy. InterSpy demonstrates the power of CFE systems in the functional reconstitution of synthetic membrane interfaces via proximity-inducing proteins. This technology may also prove useful where cell-cell contacts and communication are recreated in a controlled manner using minimal components.
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Affiliation(s)
- Hossein Moghimianavval
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Chintan Patel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sonisilpa Mohapatra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sung-Won Hwang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Tunc Kayikcioglu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Baltimore, MD 21205, USA
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9
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Berlin I, Sapmaz A, Stévenin V, Neefjes J. Ubiquitin and its relatives as wizards of the endolysosomal system. J Cell Sci 2023; 136:288517. [PMID: 36825571 PMCID: PMC10022685 DOI: 10.1242/jcs.260101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The endolysosomal system comprises a dynamic constellation of vesicles working together to sense and interpret environmental cues and facilitate homeostasis. Integrating extracellular information with the internal affairs of the cell requires endosomes and lysosomes to be proficient in decision-making: fusion or fission; recycling or degradation; fast transport or contacts with other organelles. To effectively discriminate between these options, the endolysosomal system employs complex regulatory strategies that crucially rely on reversible post-translational modifications (PTMs) with ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. The cycle of conjugation, recognition and removal of different Ub- and Ubl-modified states informs cellular protein stability and behavior at spatial and temporal resolution and is thus well suited to finetune macromolecular complex assembly and function on endolysosomal membranes. Here, we discuss how ubiquitylation (also known as ubiquitination) and its biochemical relatives orchestrate endocytic traffic and designate cargo fate, influence membrane identity transitions and support formation of membrane contact sites (MCSs). Finally, we explore the opportunistic hijacking of Ub and Ubl modification cascades by intracellular bacteria that remodel host trafficking pathways to invade and prosper inside cells.
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Affiliation(s)
- Ilana Berlin
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Aysegul Sapmaz
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Virginie Stévenin
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Jacques Neefjes
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
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10
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Capitanio C, Bieber A, Wilfling F. How Membrane Contact Sites Shape the Phagophore. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231162495. [PMID: 37366413 PMCID: PMC10243513 DOI: 10.1177/25152564231162495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/15/2023] [Accepted: 02/18/2023] [Indexed: 06/28/2023]
Abstract
During macroautophagy, phagophores establish multiple membrane contact sites (MCSs) with other organelles that are pivotal for proper phagophore assembly and growth. In S. cerevisiae, phagophore contacts have been observed with the vacuole, the ER, and lipid droplets. In situ imaging studies have greatly advanced our understanding of the structure and function of these sites. Here, we discuss how in situ structural methods like cryo-CLEM can give unprecedented insights into MCSs, and how they help to elucidate the structural arrangements of MCSs within cells. We further summarize the current knowledge of the contact sites in autophagy, focusing on autophagosome biogenesis in the model organism S. cerevisiae.
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Affiliation(s)
- Cristina Capitanio
- Department of Molecular Machines and
Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Aligning Science Across Parkinson's (ASAP)
Collaborative Research Network, Chevy Chase, MD, USA
| | - Anna Bieber
- Department of Molecular Machines and
Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Aligning Science Across Parkinson's (ASAP)
Collaborative Research Network, Chevy Chase, MD, USA
| | - Florian Wilfling
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt a. M., Germany
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11
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Enrich C, Lu A, Tebar F, Rentero C, Grewal T. Ca 2+ and Annexins - Emerging Players for Sensing and Transferring Cholesterol and Phosphoinositides via Membrane Contact Sites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1422:393-438. [PMID: 36988890 DOI: 10.1007/978-3-031-21547-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Maintaining lipid composition diversity in membranes from different organelles is critical for numerous cellular processes. However, many lipids are synthesized in the endoplasmic reticulum (ER) and require delivery to other organelles. In this scenario, formation of membrane contact sites (MCS) between neighbouring organelles has emerged as a novel non-vesicular lipid transport mechanism. Dissecting the molecular composition of MCS identified phosphoinositides (PIs), cholesterol, scaffolding/tethering proteins as well as Ca2+ and Ca2+-binding proteins contributing to MCS functioning. Compelling evidence now exists for the shuttling of PIs and cholesterol across MCS, affecting their concentrations in distinct membrane domains and diverse roles in membrane trafficking. Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) at the plasma membrane (PM) not only controls endo-/exocytic membrane dynamics but is also critical in autophagy. Cholesterol is highly concentrated at the PM and enriched in recycling endosomes and Golgi membranes. MCS-mediated cholesterol transfer is intensely researched, identifying MCS dysfunction or altered MCS partnerships to correlate with de-regulated cellular cholesterol homeostasis and pathologies. Annexins, a conserved family of Ca2+-dependent phospholipid binding proteins, contribute to tethering and untethering events at MCS. In this chapter, we will discuss how Ca2+ homeostasis and annexins in the endocytic compartment affect the sensing and transfer of cholesterol and PIs across MCS.
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Affiliation(s)
- Carlos Enrich
- Departament de Biomedicina, Unitat de Biologia Cel⋅lular, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain.
| | - Albert Lu
- Departament de Biomedicina, Unitat de Biologia Cel⋅lular, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Tebar
- Departament de Biomedicina, Unitat de Biologia Cel⋅lular, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Carles Rentero
- Departament de Biomedicina, Unitat de Biologia Cel⋅lular, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Thomas Grewal
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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12
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Atakpa-Adaji P, Ivanova A. IP 3R at ER-Mitochondrial Contact Sites: Beyond the IP 3R-GRP75-VDAC1 Ca 2+ Funnel. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2023; 6:25152564231181020. [PMID: 37426575 PMCID: PMC10328019 DOI: 10.1177/25152564231181020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/23/2023] [Indexed: 07/11/2023]
Abstract
Membrane contact sites (MCS) circumvent the topological constraints of functional coupling between different membrane-bound organelles by providing a means of communication and exchange of materials. One of the most characterised contact sites in the cell is that between the endoplasmic reticulum and the mitochondrial (ERMCS) whose function is to couple cellular Ca2+ homeostasis and mitochondrial function. Inositol 1,4,5-trisphosphate receptors (IP3Rs) on the ER, glucose-regulated protein 75 (GRP 75) and voltage-dependent anion channel 1 (VDAC1) on the outer mitochondrial membrane are the canonical component of the Ca2+ transfer unit at ERMCS. These are often reported to form a Ca2+ funnel that fuels the mitochondrial low-affinity Ca2+ uptake system. We assess the available evidence on the IP3R subtype selectivity at the ERMCS and consider if IP3Rs have other roles at the ERMCS beyond providing Ca2+. Growing evidence suggests that all three IP3R subtypes can localise and regulate Ca2+ signalling at ERMCS. Furthermore, IP3Rs may be structurally important for assembly of the ERMCS in addition to their role in providing Ca2+ at these sites. Evidence that various binding partners regulate the assembly and Ca2+ transfer at ERMCS populated by IP3R-GRP75-VDAC1, suggesting that cells have evolved mechanisms that stabilise these junctions forming a Ca2+ microdomain that is required to fuel mitochondrial Ca2+ uptake.
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Affiliation(s)
- Peace Atakpa-Adaji
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Adelina Ivanova
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
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13
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Martelli A, Omrani M, Zarghooni M, Citi V, Brogi S, Calderone V, Sureda A, Lorzadeh S, da Silva Rosa SC, Grabarek BO, Staszkiewicz R, Los MJ, Nabavi SF, Nabavi SM, Mehrbod P, Klionsky DJ, Ghavami S. New Visions on Natural Products and Cancer Therapy: Autophagy and Related Regulatory Pathways. Cancers (Basel) 2022; 14:5839. [PMID: 36497321 PMCID: PMC9738256 DOI: 10.3390/cancers14235839] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/06/2022] [Accepted: 11/15/2022] [Indexed: 11/29/2022] Open
Abstract
Macroautophagy (autophagy) has been a highly conserved process throughout evolution and allows cells to degrade aggregated/misfolded proteins, dysfunctional or superfluous organelles and damaged macromolecules, in order to recycle them for biosynthetic and/or energetic purposes to preserve cellular homeostasis and health. Changes in autophagy are indeed correlated with several pathological disorders such as neurodegenerative and cardiovascular diseases, infections, cancer and inflammatory diseases. Conversely, autophagy controls both apoptosis and the unfolded protein response (UPR) in the cells. Therefore, any changes in the autophagy pathway will affect both the UPR and apoptosis. Recent evidence has shown that several natural products can modulate (induce or inhibit) the autophagy pathway. Natural products may target different regulatory components of the autophagy pathway, including specific kinases or phosphatases. In this review, we evaluated ~100 natural compounds and plant species and their impact on different types of cancers via the autophagy pathway. We also discuss the impact of these compounds on the UPR and apoptosis via the autophagy pathway. A multitude of preclinical findings have shown the function of botanicals in regulating cell autophagy and its potential impact on cancer therapy; however, the number of related clinical trials to date remains low. In this regard, further pre-clinical and clinical studies are warranted to better clarify the utility of natural compounds and their modulatory effects on autophagy, as fine-tuning of autophagy could be translated into therapeutic applications for several cancers.
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Affiliation(s)
- Alma Martelli
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Marzieh Omrani
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran 1983969411, Iran
| | - Maryam Zarghooni
- Department of Laboratory Medicine & Pathobiology, University of Toronto Alumna, Toronto, ON M5S 3J3, Canada
| | - Valentina Citi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Antoni Sureda
- Research Group in Community Nutrition, Oxidative Stress and Health Research Institute of the Balearic Islands (IdISBa), University of Balearic Islands, 07122 Palma de Mallorca, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Shahrokh Lorzadeh
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, 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 R3T 2N2, Canada
| | - Beniamin Oscar Grabarek
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine in Zabrze, Academy of Silesia, 41-800 Zabrze, Poland
- Department of Gynaecology and Obstetrics, Faculty of Medicine in Zabrze, Academy of Silesia, 41-800 Zabrze, Poland
- GynCentrum, Laboratory of Molecular Biology and Virology, 40-851 Katowice, Poland
| | - Rafał Staszkiewicz
- Department of Histology, Cytophysiology and Embryology, Faculty of Medicine in Zabrze, Academy of Silesia, 41-800 Zabrze, Poland
- Department of Neurosurgery, 5th Military Clinical Hospital with the SP ZOZ Polyclinic in Krakow, 30-901 Krakow, Poland
| | - Marek J. Los
- Biotechnology Centre, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Seyed Fazel Nabavi
- Nutringredientes Research Center, Federal Institute of Education, Science and Technology (IFCE), Baturite 62760-000, Brazil
| | - Seyed Mohammad Nabavi
- Advanced Medical Pharma (AMP-Biotec), Biopharmaceutical Innovation Centre, Via Cortenocera, 82030 San Salvatore Telesino, Italy
| | - Parvaneh Mehrbod
- Influenza and Respiratory Viruses Department, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Daniel J. Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Faculty of Medicine in Zabrze, Academia of Silesia, 41-800 Zabrze, Poland
- Research Institute of Oncology and Hematology, Cancer Care Manitoba, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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14
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Xu L, Qiu Y, Wang X, Shang W, Bai J, Shi K, Liu H, Liu JP, Wang L, Tong C. ER-mitochondrial contact protein Miga regulates autophagy through Atg14 and Uvrag. Cell Rep 2022; 41:111583. [DOI: 10.1016/j.celrep.2022.111583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 08/10/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
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15
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Perea-García A, Puig S, Peñarrubia L. The role of post-transcriptional modulators of metalloproteins in response to metal deficiencies. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1735-1750. [PMID: 34849747 DOI: 10.1093/jxb/erab521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Copper and iron proteins have a wide range of functions in living organisms. Metal assembly into metalloproteins is a complex process, where mismetalation is detrimental and energy consuming to cells. Under metal deficiency, metal distribution is expected to reach a metalation ranking, prioritizing essential versus dispensable metalloproteins, while avoiding interference with other metals and protecting metal-sensitive processes. In this review, we propose that post-transcriptional modulators of metalloprotein mRNA (ModMeR) are good candidates in metal prioritization under metal-limited conditions. ModMeR target high quota or redundant metalloproteins and, by adjusting their synthesis, ModMeR act as internal metal distribution valves. Inappropriate metalation of ModMeR targets could compete with metal delivery to essential metalloproteins and interfere with metal-sensitive processes, such as chloroplastic photosynthesis and mitochondrial respiration. Regulation of ModMeR targets could increase or decrease the metal flow through interconnected pathways in cellular metal distribution, helping to achieve adequate differential metal requirements. Here, we describe and compare ModMeR that function in response to copper and iron deficiencies. Specifically, we describe copper-miRNAs from Arabidopsis thaliana and diverse iron ModMeR from yeast, mammals, and bacteria under copper and iron deficiencies, as well as the influence of oxidative stress. Putative functions derived from their role as ModMeR are also discussed.
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Affiliation(s)
- Ana Perea-García
- Departament de Bioquímica i Biologia Molecular and Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, Burjassot, Valencia, Spain
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Lola Peñarrubia
- Departament de Bioquímica i Biologia Molecular and Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, Burjassot, Valencia, Spain
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16
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Visintin R, Ray SK. Specific microRNAs for Modulation of Autophagy in Spinal Cord Injury. Brain Sci 2022; 12:247. [PMID: 35204010 PMCID: PMC8870708 DOI: 10.3390/brainsci12020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/02/2022] [Accepted: 02/06/2022] [Indexed: 02/05/2023] Open
Abstract
The treatment of spinal cord injury (SCI) is currently a major challenge, with a severe lack of effective therapies for yielding meaningful improvements in function. Therefore, there is a great opportunity for the development of novel treatment strategies for SCI. The modulation of autophagy, a process by which a cell degrades and recycles unnecessary or harmful components (protein aggregates, organelles, etc.) to maintain cellular homeostasis and respond to a changing microenvironment, is thought to have potential for treating many neurodegenerative conditions, including SCI. The discovery of microRNAs (miRNAs), which are short ribonucleotide transcripts for targeting of specific messenger RNAs (mRNAs) for silencing, shows prevention of the translation of mRNAs to the corresponding proteins affecting various cellular processes, including autophagy. The number of known miRNAs and their targets continues to grow rapidly. This review article aims to explore the relationship between autophagy and SCI, specifically with the intent of identifying specific miRNAs that can be useful to modulate autophagy for neuroprotection and the improvement of functional recovery in SCI.
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Affiliation(s)
- Rhett Visintin
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA;
| | - Swapan K. Ray
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA
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17
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Dussouchaud A, Jacob J, Secq C, Verbavatz JM, Moras M, Larghero J, Fader CM, Ostuni MA, Lefevre SD. Transmission Electron Microscopy to Follow Ultrastructural Modifications of Erythroblasts Upon ex vivo Human Erythropoiesis. Front Physiol 2022; 12:791691. [PMID: 35222062 PMCID: PMC8864112 DOI: 10.3389/fphys.2021.791691] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/23/2021] [Indexed: 01/02/2023] Open
Abstract
Throughout mammal erythroid differentiation, erythroblasts undergo enucleation and organelle clearance becoming mature red blood cell. Organelles are cleared by autophagic pathways non-specifically targeting organelles and cytosolic content or by specific mitophagy targeting mitochondria. Mitochondrial functions are essential to coordinate metabolism reprogramming, cell death, and differentiation balance, and also synthesis of heme, the prosthetic group needed in hemoglobin assembly. In mammals, mitochondria subcellular localization and mitochondria interaction with other structures as endoplasmic reticulum and nucleus might be of importance for the removal of the nucleus, that is, the enucleation. Here, we aim to characterize by electron microscopy the changes in ultrastructure of cells over successive stages of human erythroblast differentiation. We focus on mitochondria to gain insights into intracellular localization, ultrastructure, and contact with other organelles. We found that mitochondria are progressively cleared with a significant switch between PolyE and OrthoE stages, acquiring a rounded shape and losing contact sites with both ER (MAM) and nucleus (NAM). We studied intracellular vesicle trafficking and found that endosomes and MVBs, known to be involved in iron traffic and heme synthesis, are increased during BasoE to PolyE transition; autophagic structures such as autophagosomes increase from ProE to OrthoE stages. Finally, consistent with metabolic switch, glycogen accumulation was observed in OrthoE stage.
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Affiliation(s)
- Alice Dussouchaud
- Université de Paris and Université des Antilles, INSERM, BIGR, Paris, France
| | - Julieta Jacob
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología, CONICET, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Charles Secq
- Université de Paris and Université des Antilles, INSERM, BIGR, Paris, France
| | | | - Martina Moras
- Université de Paris and Université des Antilles, INSERM, BIGR, Paris, France
| | - Jérôme Larghero
- CNRS, UMR 7592, Institut Jacques Monod, Université de Paris, Paris, France
| | - Claudio M. Fader
- Laboratorio de Biología Celular y Molecular, Instituto de Histología y Embriología, CONICET, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Mariano A. Ostuni
- Université de Paris and Université des Antilles, INSERM, BIGR, Paris, France
| | - Sophie D. Lefevre
- Université de Paris and Université des Antilles, INSERM, BIGR, Paris, France
- *Correspondence: Sophie D. Lefevre,
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18
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Poggio E, Brini M, Calì T. Get Closer to the World of Contact Sites: A Beginner's Guide to Proximity-Driven Fluorescent Probes. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:25152564221135748. [PMID: 37366505 PMCID: PMC10243574 DOI: 10.1177/25152564221135748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
To maintain cellular homeostasis and to coordinate the proper response to a specific stimulus, information must be integrated throughout the cell in a well-organized network, in which organelles are the crucial nodes and membrane contact sites are the main edges. Membrane contact sites are the cellular subdomains where two or more organelles come into close apposition and interact with each other. Even though many inter-organelle contacts have been identified, most of them are still not fully characterized, therefore their study is an appealing and expanding field of research. Thanks to significant technological progress, many tools are now available or are in rapid development, making it difficult to choose which one is the most suitable for answering a specific biological question. Here we distinguish two different experimental approaches for studying inter-organelle contact sites. The first one aims to morphologically characterize the sites of membrane contact and to identify the molecular players involved, relying mainly on the application of biochemical and electron microscopy (EM)-related methods. The second approach aims to understand the functional importance of a specific contact, focusing on spatio-temporal details. For this purpose, proximity-driven fluorescent probes are the experimental tools of choice, since they allow the monitoring and quantification of membrane contact sites and their dynamics in living cells under different cellular conditions or upon different stimuli. In this review, we focus on these tools with the purpose of highlighting their great versatility and how they can be applied in the study of membrane contacts. We will extensively describe all the different types of proximity-driven fluorescent tools, discussing their benefits and drawbacks, ultimately providing some suggestions to choose and apply the appropriate methods on a case-to-case basis and to obtain the best experimental outcomes.
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Affiliation(s)
- Elena Poggio
- Department of Biology (DiBio), University of
Padova, Padova, Italy
| | - Marisa Brini
- Department of Biology (DiBio), University of
Padova, Padova, Italy
- Study Center for Neurodegeneration (CESNE),
University of Padova, Padova, Italy
| | - Tito Calì
- Study Center for Neurodegeneration (CESNE),
University of Padova, Padova, Italy
- Department of Biomedical Sciences (DSB),
University of Padova, Padova, Italy
- Padova Neuroscience Center (PNC), University
of Padova, Padova, Italy
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19
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Winkler MBL, Nel L, Frain KM, Dedic E, Olesen E, Pedersen BP. Sterol uptake by the NPC system in eukaryotes: a Saccharomyces cerevisiae perspective. FEBS Lett 2022; 596:160-179. [PMID: 34897668 DOI: 10.1002/1873-3468.14253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022]
Abstract
Sterols are an essential component of membranes in all eukaryotic cells and the precursor of multiple indispensable cellular metabolites. After endocytotic uptake, sterols are integrated into the lysosomal membrane by the Niemann-Pick type C (NPC) system before redistribution to other membranes. The process is driven by two proteins that, together, compose the NPC system: the lysosomal sterol shuttle protein NPC2 and the membrane protein NPC1 (named NCR1 in fungi), which integrates sterols into the lysosomal membrane. The Saccharomyces cerevisiae NPC system provides a compelling model to study the molecular mechanism of sterol integration into membranes and sterol homeostasis. This review summarizes recent advances in the field, and by interpreting available structural data, we propose a unifying conceptual model for sterol loading, transfer and transport by NPC proteins.
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Affiliation(s)
- Mikael B L Winkler
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Lynette Nel
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Kelly M Frain
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Emil Dedic
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Esben Olesen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
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20
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Lei Y, Wen X, Klionsky DJ. Vps13 is required for efficient autophagy in Saccharomyces cerevisiae. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:25152564221136388. [PMID: 37151407 PMCID: PMC10162780 DOI: 10.1177/25152564221136388] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/14/2022] [Indexed: 05/09/2023]
Abstract
Vps13 is a large, conserved protein that transports lipids between membranes. Its localization at multiple organelle membranes and membrane contact sites suggests its important physiological roles. In addition, the high correlation of mutant VPS13 with certain diseases, especially those involving neurodegeneration, makes this protein of considerable biomedical interest. Taking advantage of the fact that yeasts only have one Vps13 protein, the roles of yeast Vps13 have been well studied. However, whether and how Vps13 functions in macroautophagy/autophagy, a process of degradation of cytoplasmic cargoes, have been elusive questions. In this paper, we investigated the role of Vps13 in both non-selective and selective autophagy and found that this protein participates in non-selective autophagy, reticulophagy and pexophagy, but not mitophagy, and that Vps13 plays a role in the late stage of autophagy.
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Affiliation(s)
- Yuchen Lei
- Life Sciences Institute, and the Department
of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xin Wen
- Life Sciences Institute, and the Department
of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J Klionsky
- Life Sciences Institute, and the Department
of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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21
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Egea PF. Mechanisms of Non-Vesicular Exchange of Lipids at Membrane Contact Sites: Of Shuttles, Tunnels and, Funnels. Front Cell Dev Biol 2021; 9:784367. [PMID: 34912813 PMCID: PMC8667587 DOI: 10.3389/fcell.2021.784367] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic cells are characterized by their exquisite compartmentalization resulting from a cornucopia of membrane-bound organelles. Each of these compartments hosts a flurry of biochemical reactions and supports biological functions such as genome storage, membrane protein and lipid biosynthesis/degradation and ATP synthesis, all essential to cellular life. Acting as hubs for the transfer of matter and signals between organelles and throughout the cell, membrane contacts sites (MCSs), sites of close apposition between membranes from different organelles, are essential to cellular homeostasis. One of the now well-acknowledged function of MCSs involves the non-vesicular trafficking of lipids; its characterization answered one long-standing question of eukaryotic cell biology revealing how some organelles receive and distribute their membrane lipids in absence of vesicular trafficking. The endoplasmic reticulum (ER) in synergy with the mitochondria, stands as the nexus for the biosynthesis and distribution of phospholipids (PLs) throughout the cell by contacting nearly all other organelle types. MCSs create and maintain lipid fluxes and gradients essential to the functional asymmetry and polarity of biological membranes throughout the cell. Membrane apposition is mediated by proteinaceous tethers some of which function as lipid transfer proteins (LTPs). We summarize here the current state of mechanistic knowledge of some of the major classes of LTPs and tethers based on the available atomic to near-atomic resolution structures of several "model" MCSs from yeast but also in Metazoans; we describe different models of lipid transfer at MCSs and analyze the determinants of their specificity and directionality. Each of these systems illustrate fundamental principles and mechanisms for the non-vesicular exchange of lipids between eukaryotic membrane-bound organelles essential to a wide range of cellular processes such as at PL biosynthesis and distribution, lipid storage, autophagy and organelle biogenesis.
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Affiliation(s)
- Pascal F Egea
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
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22
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Vallée A, Lecarpentier Y, Vallée JN. The Key Role of the WNT/β-Catenin Pathway in Metabolic Reprogramming in Cancers under Normoxic Conditions. Cancers (Basel) 2021; 13:cancers13215557. [PMID: 34771718 PMCID: PMC8582658 DOI: 10.3390/cancers13215557] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The canonical WNT/β-catenin pathway is upregulated in cancers and plays a major role in proliferation, invasion, apoptosis and angiogenesis. Recent studies have shown that cancer processes are involved under normoxic conditions. These findings completely change the way of approaching the study of the cancer process. In this review, we focus on the fact that, under normoxic conditions, the overstimulation of the WNT/β-catenin pathway leads to modifications in the tumor micro-environment and the activation of the Warburg effect, i.e., aerobic glycolysis, autophagy and glutaminolysis, which in turn participate in tumor growth. Abstract The canonical WNT/β-catenin pathway is upregulated in cancers and plays a major role in proliferation, invasion, apoptosis and angiogenesis. Nuclear β-catenin accumulation is associated with cancer. Hypoxic mechanisms lead to the activation of the hypoxia-inducible factor (HIF)-1α, promoting glycolytic and energetic metabolism and angiogenesis. However, HIF-1α is degraded by the HIF prolyl hydroxylase under normoxia, conditions under which the WNT/β-catenin pathway can activate HIF-1α. This review is therefore focused on the interaction between the upregulated WNT/β-catenin pathway and the metabolic processes underlying cancer mechanisms under normoxic conditions. The WNT pathway stimulates the PI3K/Akt pathway, the STAT3 pathway and the transduction of WNT/β-catenin target genes (such as c-Myc) to activate HIF-1α activity in a hypoxia-independent manner. In cancers, stimulation of the WNT/β-catenin pathway induces many glycolytic enzymes, which in turn induce metabolic reprogramming, known as the Warburg effect or aerobic glycolysis, leading to lactate overproduction. The activation of the Wnt/β-catenin pathway induces gene transactivation via WNT target genes, c-Myc and cyclin D1, or via HIF-1α. This in turn encodes aerobic glycolysis enzymes, including glucose transporter, hexokinase 2, pyruvate kinase M2, pyruvate dehydrogenase kinase 1 and lactate dehydrogenase-A, leading to lactate production. The increase in lactate production is associated with modifications to the tumor microenvironment and tumor growth under normoxic conditions. Moreover, increased lactate production is associated with overexpression of VEGF, a key inducer of angiogenesis. Thus, under normoxic conditions, overstimulation of the WNT/β-catenin pathway leads to modifications of the tumor microenvironment and activation of the Warburg effect, autophagy and glutaminolysis, which in turn participate in tumor growth.
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Affiliation(s)
- Alexandre Vallée
- Department of Clinical Research and Innovation (DRCI), Foch Hospital, 92150 Suresnes, France
- Correspondence:
| | - Yves Lecarpentier
- Centre de Recherche Clinique, Grand Hôpital de l’Est Francilien (GHEF), 6-8 Rue Saint-Fiacre, 77100 Meaux, France;
| | - Jean-Noël Vallée
- Centre Hospitalier Universitaire (CHU) Amiens Picardie, Université Picardie Jules Verne (UPJV), 80054 Amiens, France;
- Laboratoire de Mathématiques et Applications (LMA), UMR, CNRS 7348, Université de Poitiers, 86000 Poitiers, France
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23
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Struyfs C, Cammue BPA, Thevissen K. Membrane-Interacting Antifungal Peptides. Front Cell Dev Biol 2021; 9:649875. [PMID: 33912564 PMCID: PMC8074791 DOI: 10.3389/fcell.2021.649875] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/09/2021] [Indexed: 12/17/2022] Open
Abstract
The incidence of invasive fungal infections is increasing worldwide, resulting in more than 1.6 million deaths every year. Due to growing antifungal drug resistance and the limited number of currently used antimycotics, there is a clear need for novel antifungal strategies. In this context, great potential is attributed to antimicrobial peptides (AMPs) that are part of the innate immune system of organisms. These peptides are known for their broad-spectrum activity that can be directed toward bacteria, fungi, viruses, and/or even cancer cells. Some AMPs act via rapid physical disruption of microbial cell membranes at high concentrations causing cell leakage and cell death. However, more complex mechanisms are also observed, such as interaction with specific lipids, production of reactive oxygen species, programmed cell death, and autophagy. This review summarizes the structure and mode of action of antifungal AMPs, thereby focusing on their interaction with fungal membranes.
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Affiliation(s)
- Caroline Struyfs
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Karin Thevissen
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
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Tosal-Castano S, Peselj C, Kohler V, Habernig L, Berglund LL, Ebrahimi M, Vögtle FN, Höög J, Andréasson C, Büttner S. Snd3 controls nucleus-vacuole junctions in response to glucose signaling. Cell Rep 2021; 34:108637. [PMID: 33472077 DOI: 10.1016/j.celrep.2020.108637] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 12/08/2020] [Accepted: 12/21/2020] [Indexed: 12/29/2022] Open
Abstract
Membrane contact sites facilitate the exchange of metabolites between organelles to support interorganellar communication. The nucleus-vacuole junctions (NVJs) establish physical contact between the perinuclear endoplasmic reticulum (ER) and the vacuole. Although the NVJ tethers are known, how NVJ abundance and composition are controlled in response to metabolic cues remains elusive. Here, we identify the ER protein Snd3 as central factor for NVJ formation. Snd3 interacts with NVJ tethers, supports their targeting to the contacts, and is essential for NVJ formation. Upon glucose exhaustion, Snd3 relocalizes from the ER to NVJs and promotes contact expansion regulated by central glucose signaling pathways. Glucose replenishment induces the rapid dissociation of Snd3 from the NVJs, preceding the slow disassembly of the junctions. In sum, this study identifies a key factor required for formation and regulation of NVJs and provides a paradigm for metabolic control of membrane contact sites.
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Affiliation(s)
- Sergi Tosal-Castano
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Carlotta Peselj
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Lukas Habernig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Lisa Larsson Berglund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390 Gothenburg, Sweden
| | - Mahsa Ebrahimi
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Stefan-Meier-Straße 17, 79104 Freiburg, Germany; Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Johanna Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390 Gothenburg, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, 8010 Graz, Austria.
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Kohler V, Büttner S. Remodelling of Nucleus-Vacuole Junctions During Metabolic and Proteostatic Stress. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2021; 4:25152564211016608. [PMID: 34124572 PMCID: PMC7610967 DOI: 10.1177/25152564211016608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022]
Abstract
Cellular adaptation to stress and metabolic cues requires a coordinated response of different intracellular compartments, separated by semipermeable membranes. One way to facilitate interorganellar communication is via membrane contact sites, physical bridges between opposing organellar membranes formed by an array of tethering machineries. These contact sites are highly dynamic and establish an interconnected organellar network able to quickly respond to external and internal stress by changing size, abundance and molecular architecture. Here, we discuss recent work on nucleus-vacuole junctions, connecting yeast vacuoles with the nucleus. Appearing as small, single foci in mitotic cells, these contacts expand into one enlarged patch upon nutrient exhaustion and entry into quiescence or can be shaped into multiple large foci essential to sustain viability upon proteostatic stress at the nuclear envelope. We highlight the remarkable plasticity and rapid remodelling of these contact sites upon metabolic or proteostatic stress and their emerging importance for cellular fitness.
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Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner‐Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner‐Gren Institute, Stockholm University, Stockholm, Sweden
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
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26
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Cavinato M, Madreiter-Sokolowski CT, Büttner S, Schosserer M, Zwerschke W, Wedel S, Grillari J, Graier WF, Jansen-Dürr P. Targeting cellular senescence based on interorganelle communication, multilevel proteostasis, and metabolic control. FEBS J 2020; 288:3834-3854. [PMID: 33200494 PMCID: PMC7611050 DOI: 10.1111/febs.15631] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/02/2020] [Accepted: 11/13/2020] [Indexed: 02/06/2023]
Abstract
Cellular senescence, a stable cell division arrest caused by severe damage and stress, is a hallmark of aging in vertebrates including humans. With progressing age, senescent cells accumulate in a variety of mammalian tissues, where they contribute to tissue aging, identifying cellular senescence as a major target to delay or prevent aging. There is an increasing demand for the discovery of new classes of small molecules that would either avoid or postpone cellular senescence by selectively eliminating senescent cells from the body (i.e., ‘senolytics’) or inactivating/switching damage‐inducing properties of senescent cells (i.e., ‘senostatics/senomorphics’), such as the senescence‐associated secretory phenotype. Whereas compounds with senolytic or senostatic activity have already been described, their efficacy and specificity has not been fully established for clinical use yet. Here, we review mechanisms of senescence that are related to mitochondria and their interorganelle communication, and the involvement of proteostasis networks and metabolic control in the senescent phenotype. These cellular functions are associated with cellular senescence in in vitro and in vivo models but have not been fully exploited for the search of new compounds to counteract senescence yet. Therefore, we explore possibilities to target these mechanisms as new opportunities to selectively eliminate and/or disable senescent cells with the aim of tissue rejuvenation. We assume that this research will provide new compounds from the chemical space which act as mimetics of caloric restriction, modulators of calcium signaling and mitochondrial physiology, or as proteostasis optimizers, bearing the potential to counteract cellular senescence, thereby allowing healthy aging.
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Affiliation(s)
- Maria Cavinato
- Institute for Biomedical Aging Research, Leopold-Franzens Universität Innsbruck, Austria.,Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens Universität Innsbruck, Austria
| | - Corina T Madreiter-Sokolowski
- Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland.,Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Austria
| | - Sabrina Büttner
- Institute of Molecular Biosciences, University of Graz, Austria.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Markus Schosserer
- Christian Doppler Laboratory for Skin Multimodal Analytical Imaging of Aging and Senescence, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Austrian Cluster for Tissue Regeneration, Medical University of Vienna, Austria
| | - Werner Zwerschke
- Institute for Biomedical Aging Research, Leopold-Franzens Universität Innsbruck, Austria.,Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens Universität Innsbruck, Austria
| | - Sophia Wedel
- Institute for Biomedical Aging Research, Leopold-Franzens Universität Innsbruck, Austria.,Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens Universität Innsbruck, Austria
| | - Johannes Grillari
- Christian Doppler Laboratory for Skin Multimodal Analytical Imaging of Aging and Senescence, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Austrian Cluster for Tissue Regeneration, Medical University of Vienna, Austria.,Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Vienna, Austria
| | - Wolfgang F Graier
- Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Austria.,BioTechMed Graz, Austria
| | - Pidder Jansen-Dürr
- Institute for Biomedical Aging Research, Leopold-Franzens Universität Innsbruck, Austria.,Center for Molecular Biosciences Innsbruck (CMBI), Leopold-Franzens Universität Innsbruck, Austria
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