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Degli Esposti M. Did mitophagy follow the origin of mitochondria? Autophagy 2024; 20:985-993. [PMID: 38361280 PMCID: PMC11135861 DOI: 10.1080/15548627.2024.2307215] [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: 09/20/2023] [Accepted: 01/13/2024] [Indexed: 02/17/2024] Open
Abstract
Mitophagy is the process of selective autophagy that removes superfluous and dysfunctional mitochondria. Mitophagy was first characterized in mammalian cells and is now recognized to follow several pathways including basal forms in specific organs. Mitophagy pathways are regulated by multiple, often interconnected factors. The present review aims to streamline this complexity and evaluate common elements that may define the evolutionary origin of mitophagy. Key issues surrounding mitophagy signaling at the mitochondrial surface may fundamentally derive from mitochondrial membrane dynamics. Elements of such membrane dynamics likely originated during the endosymbiosis of the alphaproteobacterial ancestor of our mitochondria but underwent an evolutionary leap forward in basal metazoa that determined the currently known variations in mitophagy signaling.Abbreviations: AGPAT, 1-acylglycerol-3-phosphate O-acyltransferase; ATG, autophagy related; BCL2L13, BCL2 like 13; BNIP3, BCL2 interacting protein 3; BNIP3L, BCL2 interacting protein 3 like; CALCOCO, calcium binding and coiled-coil domain; CL, cardiolipin; ER, endoplasmic reticulum; ERMES, ER-mitochondria encounter structure; FBXL4, F-box and leucine rich repeat protein 4; FUNDC1, FUN14 domain containing 1; GABARAPL1, GABA type A receptor associated protein like 1; HIF, hypoxia inducible factor; IMM, inner mitochondrial membrane; LBPA/BMP, lysobisphosphatidic acid; LIR, LC3-interacting region; LPA, lysophosphatidic acid; MAM, mitochondria-associated membranes; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MCL, monolysocardiolipin; ML, maximum likelihood; NBR1, NBR1 autophagy cargo receptor; OMM, outer mitochondrial membrane; PA, phosphatidic acid; PACS2, phosphofurin acidic cluster sorting protein 2; PC/PLC, phosphatidylcholine; PE, phosphatidylethanolamine; PHB2, prohibitin 2; PINK1, PTEN induced kinase 1; PtdIns, phosphatidylinositol; SAR, Stramenopiles, Apicomplexa and Rhizaria; TAX1BP1, Tax1 binding protein 1; ULK1, unc-51 like autophagy activating kinase 1; VDAC/porin, voltage dependent anion channel.
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Affiliation(s)
- Mauro Degli Esposti
- Center for Genomic Sciences, UNAM Campus de Morelos, Cuernavaca, Morelos, Mexico
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Tooze SA, Zhang W, Lazzeri G, Gahlot D, Thukral L, Covino R, Nishimura T. Membrane association of the ATG8 conjugation machinery emerges as a key regulatory feature for autophagosome biogenesis. FEBS Lett 2024; 598:107-113. [PMID: 37259601 PMCID: PMC10952647 DOI: 10.1002/1873-3468.14676] [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: 04/22/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023]
Abstract
Autophagy is a highly conserved intracellular pathway that is essential for survival in all eukaryotes. In healthy cells, autophagy is used to remove damaged intracellular components, which can be as simple as unfolded proteins or as complex as whole mitochondria. Once the damaged component is captured, the autophagosome engulfs it and closes, isolating the content from the cytoplasm. The autophagosome then fuses with the late endosome and/or lysosome to deliver its content to the lysosome for degradation. Formation of the autophagosome, sequestration or capture of content, and closure all require the ATG proteins, which constitute the essential core autophagy protein machinery. This brief 'nutshell' will highlight recent data revealing the importance of small membrane-associated domains in the ATG proteins. In particular, recent findings from two parallel studies reveal the unexpected key role of α-helical structures in the ATG8 conjugation machinery and ATG8s. These studies illustrate how unique membrane association modules can control the formation of autophagosomes.
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Affiliation(s)
- Sharon A. Tooze
- Molecular Cell Biology of Autophagy LaboratoryThe Francis Crick InstituteLondonUK
| | - Wenxin Zhang
- Molecular Cell Biology of Autophagy LaboratoryThe Francis Crick InstituteLondonUK
| | | | - Deepanshi Gahlot
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | - Lipi Thukral
- CSIR‐Institute of Genomics and Integrative BiologyNew DelhiIndia
- Academy of Scientific and Innovative Research (AcSIR)GhaziabadIndia
| | | | - Taki Nishimura
- PRESTO, Japan Science and Technology AgencyTokyoJapan
- Department of Biochemistry and Molecular Biology, Graduate School of MedicineThe University of TokyoJapan
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3
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Rivetta A, Allen K, Graham M, Potapova T, Slayman C, Liu X. Morphodynamics of non-canonical autophagic structures in Neurospora crassa. mSphere 2023; 8:e0046023. [PMID: 37847028 PMCID: PMC10732065 DOI: 10.1128/msphere.00460-23] [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: 08/14/2023] [Accepted: 09/08/2023] [Indexed: 10/18/2023] Open
Abstract
IMPORTANCE Neurospora is a quintessential tip-growing organism, which is well known for packaging and longitudinal transport of tip-building blocks. Thus far, however, little attention has been paid to the co-essential process of reclamation, that is-taking apart of upstream, older structural elements, otherwise known as "autophagy". We are not yet prepared to set out the chemistry of that elaborate process, but its morphological start alone is worthy of attention. Carbon starvation triggers significant autophagic changes, beginning with prolific vacuolation along the plasma membrane, and eventual filling of 70% (or more) of cytoplasmic volume. Additionally, the Neurospora plasma membrane elaborates a variety of phagophores which themselves often look lytic. These have either dual enclosing membranes, like the familiar autophagosomes, can be doubled and have four wrapping membranes, or can be compounded with multiple membrane layers. These reclamation processes must be accommodated by the mechanism of tip growth.
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Affiliation(s)
- Alberto Rivetta
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Kenneth Allen
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Morven Graham
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Tatiana Potapova
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, USA
- Belozersky Institute of Physicochemical Biology, Moscow State University, Moscow, Russia
| | - Clifford Slayman
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Xinran Liu
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut, USA
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4
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Tamargo-Gómez I, Martínez-García GG, Suárez MF, Mayoral P, Bretones G, Astudillo A, Prieto-Lloret J, Sveen C, Fueyo A, Engedal N, López-Otín C, Mariño G. Analysis of ATG4C function in vivo. Autophagy 2023; 19:2912-2933. [PMID: 37459465 PMCID: PMC10549197 DOI: 10.1080/15548627.2023.2234799] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 08/17/2023] Open
Abstract
ABBREVIATIONS ATG4 (autophagy related 4 cysteine peptidase); ATG4A (autophagy related 4A cysteine peptidase); ATG4B (autophagy related 4B cysteine peptidase); ATG4C (autophagy related 4C cysteine peptidase); ATG4D (autophagy related 4D cysteine peptidase); Atg8 (autophagy related 8); GABARAP (GABA type A receptor-associated protein); GABARAPL1(GABA type A receptor-associated protein like 1); GABARAPL2 (GABA type A receptor-associated protein like 2); MAP1LC3A/LC3A (microtubule associated protein 1 light chain 3 alpha); MAP1LC3B/LC3B (microtubule associated protein 1 light chain 3 beta); mATG8 (mammalian Atg8); PE (phosphatidylethanolamine); PS (phosphatydylserine); SQSTM1/p62 (sequestosome 1).
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Affiliation(s)
- Isaac Tamargo-Gómez
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
| | - Gemma G. Martínez-García
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
| | - María F. Suárez
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
| | - Pablo Mayoral
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Spain
| | - Gabriel Bretones
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Spain
| | - Aurora Astudillo
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
- Biobanco Del Principado de Asturias (BBPA_ISPA_IUOPA), Registro Nacional de Biobancos PT20/161, Oviedo, Spain
| | - Jesús Prieto-Lloret
- Departamento de Bioquímica y Biología Molecular y Fisiología, Facultad de Medicina, Universidad de Valladolid. Instituto de Biología y Genética Molecular-CSIC, Valladolid, Spain
| | - Christina Sveen
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, Norway
| | - Antonio Fueyo
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
| | - Nikolai Engedal
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Montebello, Norway
| | - Carlos López-Otín
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Spain
| | - Guillermo Mariño
- Departamento de Biología Funcional, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario de Oncología (IUOPA), Oviedo, Spain
- Instituto de Investigación Sanitaria Del Principado de Asturias (ISPA), Oviedo, Spain
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Raval PK, Martin WF, Gould SB. Mitochondrial evolution: Gene shuffling, endosymbiosis, and signaling. SCIENCE ADVANCES 2023; 9:eadj4493. [PMID: 37556561 PMCID: PMC10411874 DOI: 10.1126/sciadv.adj4493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Genes for cardiolipin and ceramide synthesis occur in some alphaproteobacterial genomes. They shed light on mitochondrial origin and signaling in the first eukaryotic cells.
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Affiliation(s)
- Parth K. Raval
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - William F. Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Sven B. Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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6
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Elander PH, Holla S, Sabljić I, Gutierrez-Beltran E, Willems P, Bozhkov PV, Minina EA. Interactome of Arabidopsis ATG5 Suggests Functions beyond Autophagy. Int J Mol Sci 2023; 24:12300. [PMID: 37569688 PMCID: PMC10418956 DOI: 10.3390/ijms241512300] [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: 07/05/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Autophagy is a catabolic pathway capable of degrading cellular components ranging from individual molecules to organelles. Autophagy helps cells cope with stress by removing superfluous or hazardous material. In a previous work, we demonstrated that transcriptional upregulation of two autophagy-related genes, ATG5 and ATG7, in Arabidopsis thaliana positively affected agronomically important traits: biomass, seed yield, tolerance to pathogens and oxidative stress. Although the occurrence of these traits correlated with enhanced autophagic activity, it is possible that autophagy-independent roles of ATG5 and ATG7 also contributed to the phenotypes. In this study, we employed affinity purification and LC-MS/MS to identify the interactome of wild-type ATG5 and its autophagy-inactive substitution mutant, ATG5K128R Here we present the first interactome of plant ATG5, encompassing not only known autophagy regulators but also stress-response factors, components of the ubiquitin-proteasome system, proteins involved in endomembrane trafficking, and potential partners of the nuclear fraction of ATG5. Furthermore, we discovered post-translational modifications, such as phosphorylation and acetylation present on ATG5 complex components that are likely to play regulatory functions. These results strongly indicate that plant ATG5 complex proteins have roles beyond autophagy itself, opening avenues for further investigations on the complex roles of autophagy in plant growth and stress responses.
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Affiliation(s)
- Pernilla H. Elander
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
| | - Sanjana Holla
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
| | - Igor Sabljić
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
| | - Emilio Gutierrez-Beltran
- Instituto de Bioquımica Vegetal y Fotosıntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Cientıficas, 41092 Sevilla, Spain;
- Departamento de Bioquimica Vegetal y Biologia Molecular, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Peter V. Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
| | - Elena A. Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 750-07 Uppsala, Sweden; (P.H.E.); (S.H.); (I.S.); (P.V.B.)
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7
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Siddique I, Kamble K, Gupta S, Solanki K, Bhola S, Ahsan N, Gupta S. ARL6IP5 Ameliorates α-Synuclein Burden by Inducing Autophagy via Preventing Ubiquitination and Degradation of ATG12. Int J Mol Sci 2023; 24:10499. [PMID: 37445677 DOI: 10.3390/ijms241310499] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/15/2023] Open
Abstract
Recent advanced studies in neurodegenerative diseases have revealed several links connecting autophagy and neurodegeneration. Autophagy is the major cellular degradation process for the removal of toxic protein aggregates responsible for neurodegenerative diseases. More than 30 autophagy-related proteins have been identified as directly participating in the autophagy process. Proteins regulating the process of autophagy are much more numerous and unknown. To address this, in our present study, we identified a novel regulator (ARL6IP5) of neuronal autophagy and showed that the level of ARL6IP5 decreases in the brain with age and in Parkinson's disease in mice and humans. Moreover, a cellular model of PD (Wild type and A53T mutant α-synuclein overexpression) has also shown decreased levels of ARL6IP5. ARL6IP5 overexpression reduces α-synuclein aggregate burden and improves cell survival in an A53T model of Parkinson's disease. Interestingly, detailed mechanistic studies revealed that ARL6IP5 is an autophagy inducer. ARL6IP5 enhances Rab1-dependent autophagosome initiation and elongation by stabilizing free ATG12. We report for the first time that α-synuclein downregulates ARL6IP5 to inhibit autophagy-dependent clearance of toxic aggregates that exacerbate neurodegeneration.
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Affiliation(s)
- Ibrar Siddique
- Molecular Science Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Kajal Kamble
- Molecular Science Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Sakshi Gupta
- Molecular Science Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Kavita Solanki
- Molecular Science Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Sumnil Bhola
- Molecular Science Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Nuzhat Ahsan
- Molecular Science Laboratory, National Institute of Immunology, New Delhi 110067, India
| | - Sarika Gupta
- Molecular Science Laboratory, National Institute of Immunology, New Delhi 110067, India
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8
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Ding G, Mugume Y, Dueñas ME, Lee YJ, Liu M, Nettleton DS, Zhao X, Li L, Bassham DC, Nikolau BJ. Biological insights from multi-omics analysis strategies: Complex pleotropic effects associated with autophagy. FRONTIERS IN PLANT SCIENCE 2023; 14:1093358. [PMID: 36875559 PMCID: PMC9978356 DOI: 10.3389/fpls.2023.1093358] [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: 11/08/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Research strategies that combine molecular data from multiple levels of genome expression (i.e., multi-omics data), often referred to as a systems biology strategy, has been advocated as a route to discovering gene functions. In this study we conducted an evaluation of this strategy by combining lipidomics, metabolite mass-spectral imaging and transcriptomics data from leaves and roots in response to mutations in two AuTophaGy-related (ATG) genes of Arabidopsis. Autophagy is an essential cellular process that degrades and recycles macromolecules and organelles, and this process is blocked in the atg7 and atg9 mutants that were the focus of this study. Specifically, we quantified abundances of ~100 lipids and imaged the cellular locations of ~15 lipid molecular species and the relative abundance of ~26,000 transcripts from leaf and root tissues of WT, atg7 and atg9 mutant plants, grown either in normal (nitrogen-replete) and autophagy-inducing conditions (nitrogen-deficient). The multi-omics data enabled detailed molecular depiction of the effect of each mutation, and a comprehensive physiological model to explain the consequence of these genetic and environmental changes in autophagy is greatly facilitated by the a priori knowledge of the exact biochemical function of the ATG7 and ATG9 proteins.
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Affiliation(s)
- Geng Ding
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Yosia Mugume
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | | | - Young Jin Lee
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Meiling Liu
- Department of Statistics, Iowa State University, Ames, IA, United States
| | | | - Xuefeng Zhao
- Research Information Technology, College of Liberal Arts & Sciences, Iowa State University, Ames, IA, United States
| | - Ling Li
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Diane C. Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Basil J. Nikolau
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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9
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Zhang S, Mizushima N. The autophagy pathway beyond model organisms: an evolutionary perspective. Autophagy 2023; 19:1-2. [PMID: 36448729 PMCID: PMC9809957 DOI: 10.1080/15548627.2022.2153568] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
In this issue, we answer a frequently asked question regarding the evolution of the macroautophagy/autophagy pathway.
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Affiliation(s)
- Sidi Zhang
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
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10
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Zhang S, Yazaki E, Sakamoto H, Yamamoto H, Mizushima N. Evolutionary diversification of the autophagy-related ubiquitin-like conjugation systems. Autophagy 2022; 18:2969-2984. [PMID: 35427200 PMCID: PMC9673942 DOI: 10.1080/15548627.2022.2059168] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Two autophagy-related (ATG) ubiquitin-like conjugation systems, the ATG12 and ATG8 systems, play important roles in macroautophagy. While multiple duplications and losses of the ATG conjugation system proteins are found in different lineages, the extent to which the underlying systems diversified across eukaryotes is not fully understood. Here, in order to understand the evolution of the ATG conjugation systems, we constructed a transcriptome database consisting of 94 eukaryotic species covering major eukaryotic clades and systematically identified ATG conjugation system components. Both ATG10 and the C-terminal glycine of ATG12 are essential for the canonical ubiquitin-like conjugation of ATG12 and ATG5. However, loss of ATG10 or the C-terminal glycine of ATG12 occurred at least 16 times in a wide range of lineages, suggesting that possible covalent-to-non-covalent transition is not limited to the species that we previously reported such as Alveolata and some yeast species. Some species have only the ATG8 system (with conjugation enzymes) or only ATG8 (without conjugation enzymes). More than 10 species have ATG8 homologs without the conserved C-terminal glycine, and Tetrahymena has an ATG8 homolog with a predicted transmembrane domain, which may be able to anchor to the membrane independent of the ATG conjugation systems. We discuss the possibility that the ancestor of the ATG12 and ATG8 systems is more similar to ATG8. Overall, our study offers a whole picture of the evolution and diversity of the ATG conjugation systems among eukaryotes, and provides evidence that functional diversifications of the systems are more common than previously thought.Abbreviations: APEAR: ATG8-PE association region; ATG: autophagy-related; LIR: LC3-interacting region; NEDD8: neural precursor cell expressed, developmentally down-regulated gene 8; PE: phosphatidylethanolamine; SAMP: small archaeal modifier protein; SAR: Stramenopiles, Alveolata, and Rhizaria; SMC: structural maintenance of chromosomes; SUMO: small ubiquitin like modifier; TACK: Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota; UBA: ubiquitin like modifier activating enzyme; UFM: ubiquitin fold modifier; URM: ubiquitin related modifier.
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Affiliation(s)
- Sidi Zhang
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Euki Yazaki
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), RIKEN, Saitama, Japan
| | - Hirokazu Sakamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hayashi Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,CONTACT Noboru Mizushima Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
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11
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Du Q, Schaap P. Autophagy of the somatic stalk cells likely nurses the propagating spores of Dictyostelid social amoebas. OPEN RESEARCH EUROPE 2022; 2:104. [PMID: 36860212 PMCID: PMC7614253 DOI: 10.12688/openreseurope.14947.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 11/14/2022] [Indexed: 11/24/2022]
Abstract
Background: Autophagy (self-feeding) assists survival of starving cells by partial self-digestion, while dormancy as cysts, spores or seeds enables long-term survival. Starving Dictyostelium amoebas construct multicellular fruiting bodies with spores and stalk cells, with many Dictyostelia still able to encyst individually like their single-celled ancestors. While autophagy mostly occurs in the somatic stalk cells, autophagy gene knock-outs in Dictyostelium discoideum ( D. discoideum) formed no spores and lacked cAMP induction of prespore gene expression. Methods: To investigate whether autophagy also prevents encystation, we knocked-out autophagy genes atg5 and atg7 in the dictyostelid Polysphondylium pallidum, which forms both spores and cysts. We measured spore and cyst differentiation and viability in the knock-out as well as stalk and spore gene expression and its regulation by cAMP. We tested a hypothesis that spores require materials derived from autophagy in stalk cells. Sporulation requires secreted cAMP acting on receptors and intracellular cAMP acting on PKA. We compared the morphology and viability of spores developed in fruiting bodies with spores induced from single cells by stimulation with cAMP and 8Br-cAMP, a membrane-permeant PKA agonist. Results: Loss of autophagy in P. pallidum reduced but did not prevent encystation. Stalk cells still differentiated but stalks were disorganised. However, no spores were formed at all and cAMP-induced prespore gene expression was lost. D. discoideum spores induced in vitro by cAMP and 8Br-cAMP were smaller and rounder than spores formed multicellularly and while they were not lysed by detergent they germinated not (strain Ax2) or poorly (strain NC4), unlike spores formed in fruiting bodies. Conclusions: The stringent requirement of sporulation on both multicellularity and autophagy, which occurs mostly in stalk cells, suggests that stalk cells nurse the spores through autophagy. This highlights autophagy as a major cause for somatic cell evolution in early multicellularity.
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Affiliation(s)
- Qingyou Du
- School of Life Sciences, University of Dundee, Dundee, Angus, DD15EH, UK
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee, Angus, DD15EH, UK
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12
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Rasmussen NL, Kournoutis A, Lamark T, Johansen T. NBR1: The archetypal selective autophagy receptor. J Cell Biol 2022; 221:213552. [PMID: 36255390 PMCID: PMC9582228 DOI: 10.1083/jcb.202208092] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/03/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
Abstract
NBR1 was discovered as an autophagy receptor not long after the first described vertebrate autophagy receptor p62/SQSTM1. Since then, p62 has currently been mentioned in >10,000 papers on PubMed, while NBR1 is mentioned in <350 papers. Nonetheless, evolutionary analysis reveals that NBR1, and likely also selective autophagy, was present already in the last eukaryotic common ancestor (LECA), while p62 appears first in the early Metazoan lineage. Furthermore, yeast-selective autophagy receptors Atg19 and Atg34 represent NBR1 homologs. NBR1 is the main autophagy receptor in plants that do not contain p62, while most animal taxa contain both NBR1 and p62. Mechanistic studies are starting to shed light on the collaboration between mammalian NBR1 and p62 in the autophagic degradation of protein aggregates (aggrephagy). Several domains of NBR1 are involved in cargo recognition, and the list of known substrates for NBR1-mediated selective autophagy is increasing. Lastly, roles of NBR1 in human diseases such as proteinopathies and cancer are emerging.
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Affiliation(s)
- Nikoline Lander Rasmussen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Athanasios Kournoutis
- Autophagy Research Group, Department of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - 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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13
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Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy. Cells 2022; 11:cells11203203. [PMID: 36291071 PMCID: PMC9601114 DOI: 10.3390/cells11203203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Autophagy plays an intricate role in paradigmatic human pathologies such as cancer, and neurodegenerative, cardiovascular, and autoimmune disorders. Autophagy regulation is performed by a set of autophagy-related (ATG) genes, first recognized in yeast genome and subsequently identified in other species, including humans. Several other genes have been identified to be involved in the process of autophagy either directly or indirectly. Studying the codon usage bias (CUB) of genes is crucial for understanding their genome biology and molecular evolution. Here, we examined the usage pattern of nucleotide and synonymous codons and the influence of evolutionary forces in genes involved in human autophagy. The coding sequences (CDS) of the protein coding human autophagy genes were retrieved from the NCBI nucleotide database and analyzed using various web tools and software to understand their nucleotide composition and codon usage pattern. The effective number of codons (ENC) in all genes involved in human autophagy ranges between 33.26 and 54.6 with a mean value of 45.05, indicating an overall low CUB. The nucleotide composition analysis of the autophagy genes revealed that the genes were marginally rich in GC content that significantly influenced the codon usage pattern. The relative synonymous codon usage (RSCU) revealed 3 over-represented and 10 under-represented codons. Both natural selection and mutational pressure were the key forces influencing the codon usage pattern of the genes involved in human autophagy.
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14
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Nakada-Tsukui K, Watanabe N, Shibata K, Wahyuni R, Miyamoto E, Nozaki T. Proteomic analysis of Atg8-dependent recruitment of phagosomal proteins in the enteric protozoan parasite Entamoeba histolytica. Front Cell Infect Microbiol 2022; 12:961645. [PMID: 36262186 PMCID: PMC9575557 DOI: 10.3389/fcimb.2022.961645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Autophagy is one of the bulk degradation systems and is conserved throughout eukaryotes. In the enteric protozoan parasite Entamoeba histolytica, the causative agent of human amebiasis, Atg8 is not exclusively involved in autophagy per se but also in other membrane traffic-related pathways such as phagosome biogenesis. We previously reported that repression of atg8 gene expression by antisense small RNA-mediated transcriptional gene silencing (gs) resulted in growth retardation, delayed endocytosis, and reduced acidification of endosomes and phagosomes. In this study, to better understand the role of Atg8 in phagocytosis and trogocytosis, we conducted a comparative proteomic analysis of phagosomes isolated from wild type and atg8-gs strains. We found that 127 and 107 proteins were detected >1.5-fold less or more abundantly, respectively, in phagosomes isolated from the atg8-gs strain, compared to the control strain. Among 127 proteins whose abundance was reduced in phagosomes from atg8-gs, a panel of proteins related to fatty acid metabolism, phagocytosis, and endoplasmic reticulum (ER) homeostasis was identified. Various lysosomal hydrolases and their receptors also tend to be excluded from phagosomes by atg8-gs, reinforcing the notion that Atg8 is involved in phagosomal acidification and digestion. On the contrary, among 107 proteins whose abundance increased in phagosomes from atg8-gs strain, ribosome-related proteins and metabolite interconversion enzymes are enriched. We further investigated the localization of several representative proteins, including adenylyl cyclase-associated protein and plasma membrane calcium pump, both of which were demonstrated to be recruited to phagosomes and trogosomes via an Atg8-dependent mechanism. Taken together, our study has provided the basis of the phagosome proteome to further elucidate molecular events in the Atg8-dependent regulatory network of phagosome/trogosome biogenesis in E. histolytica.
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Affiliation(s)
- Kumiko Nakada-Tsukui
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
- *Correspondence: Kumiko Nakada-Tsukui, ; Tomoyoshi Nozaki,
| | - Natsuki Watanabe
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kumiko Shibata
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ratna Wahyuni
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eri Miyamoto
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- *Correspondence: Kumiko Nakada-Tsukui, ; Tomoyoshi Nozaki,
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15
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To Die or Not to Die—Regulated Cell Death and Survival in Cyanobacteria. Microorganisms 2022; 10:microorganisms10081657. [PMID: 36014075 PMCID: PMC9415839 DOI: 10.3390/microorganisms10081657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/06/2022] [Accepted: 08/12/2022] [Indexed: 11/24/2022] Open
Abstract
Regulated cell death (RCD) is central to the development, integrity, and functionality of multicellular organisms. In the last decade, evidence has accumulated that RCD is a universal phenomenon in all life domains. Cyanobacteria are of specific interest due to their importance in aquatic and terrestrial habitats and their role as primary producers in global nutrient cycling. Current knowledge on cyanobacterial RCD is based mainly on biochemical and morphological observations, often by methods directly transferred from vertebrate research and with limited understanding of the molecular genetic basis. However, the metabolism of different cyanobacteria groups relies on photosynthesis and nitrogen fixation, whereas mitochondria are the central executioner of cell death in vertebrates. Moreover, cyanobacteria chosen as biological models in RCD studies are mainly colonial or filamentous multicellular organisms. On the other hand, unicellular cyanobacteria have regulated programs of cellular survival (RCS) such as chlorosis and post-chlorosis resuscitation. The co-existence of different genetically regulated programs in cyanobacterial populations may have been a top engine in life diversification. Development of cyanobacteria-specific methods for identification and characterization of RCD and wider use of single-cell analysis combined with intelligent image-based cell sorting and metagenomics would shed more light on the underlying molecular mechanisms and help us to address the complex colonial interactions during these events. In this review, we focus on the functional implications of RCD in cyanobacterial communities.
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16
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Norizuki T, Minamino N, Sato M, Tsukaya H, Ueda T. Dynamic rearrangement and autophagic degradation of mitochondria during spermiogenesis in the liverwort Marchantia polymorpha. Cell Rep 2022; 39:110975. [PMID: 35705033 DOI: 10.1016/j.celrep.2022.110975] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 04/22/2022] [Accepted: 05/26/2022] [Indexed: 11/24/2022] Open
Abstract
Mitochondria change their morphology in response to developmental and environmental cues. During sexual reproduction, bryophytes produce spermatozoids with two mitochondria in the cell body. Although intensive morphological analyses have been conducted, how this fixed number of mitochondria is realized remains poorly understood. Here, we investigate how mitochondria are reorganized during spermiogenesis in Marchantia polymorpha. We find that the mitochondrial number is reduced to one through fission followed by autophagic degradation during early spermiogenesis, and then the posterior mitochondrion arises by fission of the anterior mitochondrion. Autophagy is also responsible for the removal of other organelles, including peroxisomes, but these other organelles are removed at distinct developmental stages from mitochondrial degradation. We also find that spermiogenesis involves nonautophagic organelle degradation. Our findings highlight the dynamic reorganization of mitochondria, which is regulated distinctly from that of other organelles, and multiple degradation mechanisms operate in organelle remodeling during spermiogenesis in M. polymorpha.
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Affiliation(s)
- Takuya Norizuki
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan; Laboratory of Molecular Membrane Biology, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma 371-8512, Japan
| | - Naoki Minamino
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Miyuki Sato
- Laboratory of Molecular Membrane Biology, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma 371-8512, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan; Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan.
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17
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Deep conservation and co-option of programmed cell death facilitates evolution of alternative phenotypes at multiple biological levels. Semin Cell Dev Biol 2022; 145:28-41. [PMID: 35654666 DOI: 10.1016/j.semcdb.2022.05.024] [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: 08/29/2021] [Revised: 03/04/2022] [Accepted: 05/24/2022] [Indexed: 11/22/2022]
Abstract
Alternative phenotypes, such as polyphenisms and sexual dimorphisms, are widespread in nature and appear at all levels of biological organization, from genes and cells to morphology and behavior. Yet, our understanding of the mechanisms through which alternative phenotypes develop and how they evolve remains understudied. In this review, we explore the association between alternative phenotypes and programmed cell death, a mechanism responsible for the elimination of superfluous cells during development. We discuss the ancient origins and deep conservation of programmed cell death (its function, forms and underlying core regulatory gene networks), and propose that it was co-opted repeatedly to generate alternative phenotypes at the level of cells, tissues, organs, external morphology, and even individuals. We review several examples from across the tree of life to explore the conditions under which programmed cell death is likely to facilitate the evolution of alternative phenotypes.
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18
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Russell RC, Guan KL. The multifaceted role of autophagy in cancer. EMBO J 2022; 41:e110031. [PMID: 35535466 PMCID: PMC9251852 DOI: 10.15252/embj.2021110031] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/20/2022] [Accepted: 04/08/2022] [Indexed: 12/15/2022] Open
Abstract
Autophagy is a cellular degradative pathway that plays diverse roles in maintaining cellular homeostasis. Cellular stress caused by starvation, organelle damage, or proteotoxic aggregates can increase autophagy, which uses the degradative capacity of lysosomal enzymes to mitigate intracellular stresses. Early studies have shown a role for autophagy in the suppression of tumorigenesis. However, work in genetically engineered mouse models and in vitro cell studies have now shown that autophagy can be either cancer-promoting or inhibiting. Here, we summarize the effects of autophagy on cancer initiation, progression, immune infiltration, and metabolism. We also discuss the efforts to pharmacologically target autophagy in the clinic and highlight future areas for exploration.
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Affiliation(s)
- Ryan C Russell
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Center for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada.,Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
| | - Kun-Liang Guan
- Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
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19
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Liu R, Zhang R, Yang Y, Liu X, Gong Q. Monitoring Autophagy in Rice With GFP-ATG8 Marker Lines. FRONTIERS IN PLANT SCIENCE 2022; 13:866367. [PMID: 35548298 PMCID: PMC9083259 DOI: 10.3389/fpls.2022.866367] [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: 01/31/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Autophagy is a conserved intracellular trafficking pathway for bulk degradation and recycling of cellular components in eukaryotes. The hallmark of autophagy is the formation of double-membraned vesicles termed autophagosomes, which selectively or non-selectively pack up various macromolecules and organelles and deliver these cargoes into the vacuole/lysosome. Like all other membrane trafficking pathways, the observation of autophagy is largely dependent on marker lines. ATG8/LC3 is the only autophagy-related (ATG) protein that, through a covalent bond to phosphatidylethanolamine (PE), associates tightly with the isolation membrane/pre-autophagosomal structure (PAS), the growing phagophore, the mature autophagosome, and the autophagic bodies. Therefore, fluorescent protein (FP)-tagged ATG8 had been widely used for monitoring autophagosome formation and autophagic flux. In rice (Oryza sativa), FP-OsATG8 driven by Cauliflower mosaic virus (CaMV) 35S promoter had been used for imaging autophagosome and autophagic bodies. Here, we constructed three vectors carrying GFP-OsATG8a, driven by 35S, ubiquitin, and the endogenous ATG8a promoter, individually. Then, we compared them for their suitability in monitoring autophagy, by observing GFP-ATG8a puncta formation in transiently transformed rice protoplasts, and by tracking the autophagic flux with GFP-ATG8 cleavage assay in rice stable transgenic lines. GFP-Trap immunoprecipitation and mass spectrometry were also performed with the three marker lines to show that they can be used reliably for proteomic studies. We found out that the ubiquitin promoter is the best for protoplast imaging. Transgenic rice seedlings of the three marker lines showed comparable performance in autophagic flux measurement using the GFP-ATG8 cleavage assay. Surprisingly, the levels of GFP-ATG8a transcripts and protein contents were similar in all marker lines, indicating post-transcriptional regulation of the transgene expression by a yet unknown mechanism. These marker lines can serve as useful tools for autophagy studies in rice.
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Affiliation(s)
- Rui Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rongxue Zhang
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Agricultural University, Tianjin, China
| | - Yi Yang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xuejun Liu
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Agricultural University, Tianjin, China
| | - Qingqiu Gong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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20
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Locatelli AG, Cenci S. Autophagy and longevity: Evolutionary hints from hyper-longevous mammals. Front Endocrinol (Lausanne) 2022; 13:1085522. [PMID: 36605941 PMCID: PMC9807614 DOI: 10.3389/fendo.2022.1085522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Autophagy is a fundamental multi-tasking adaptive cellular degradation and recycling strategy. Following its causal implication in age-related decline, autophagy is currently among the most broadly studied and challenged mechanisms within aging research. Thanks to these efforts, new cellular nodes interconnected with this phylogenetically ancestral pathway and unexpected roles of autophagy-associated genetic products are unveiled daily, yet the history of functional adaptations of autophagy along its evolutive trail is poorly understood and documented. Autophagy is traditionally studied in canonical and research-wise convenient model organisms such as yeast and mice. However, unconventional animal models endowed with extended longevity and exemption from age-related diseases offer a privileged perspective to inquire into the role of autophagy in the evolution of longevity. In this mini review we retrace the appearance and functions evolved by autophagy in eukaryotic cells and its protective contribution in the pathophysiology of aging.
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Affiliation(s)
- Andrea G. Locatelli
- Age Related Diseases, San Raffaele Scientific Institute, Division of Genetics and Cell Biology, Milano, Italy
- *Correspondence: Andrea G. Locatelli, ; Simone Cenci,
| | - Simone Cenci
- Age Related Diseases, San Raffaele Scientific Institute, Division of Genetics and Cell Biology, Milano, Italy
- University Vita-Salute San Raffaele, Milano, Italy
- *Correspondence: Andrea G. Locatelli, ; Simone Cenci,
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21
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Ke PY. Autophagy and antiviral defense. IUBMB Life 2021; 74:317-338. [PMID: 34859938 DOI: 10.1002/iub.2582] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 12/14/2022]
Abstract
Targeting intracellular components for lysosomal degradation by autophagy not only maintains cellular homeostasis but also counteracts the effects of external stimuli, including invading pathogens. Among various kinds of pathogens, viruses have been extensively shown to induce autophagy to benefit viral growth in infected cells and to modulate host defense responses, such as innate antiviral immunity. Recently, numerous lines of evidence have implied that virus-induced autophagy triggers multilayer mechanisms to regulate the innate antiviral response of host cells, thus promoting a balance in virus-host cell interactions. In this review, the detailed mechanisms underlying autophagy and the innate antiviral immune response are first described. Then, I summarize the current information regarding the diverse functional role(s) of autophagy in the control of antiviral defenses against different types of viral infections. Moreover, the physiological significance of autophagy-regulated antiviral responses on the viral life cycle and the potential autophagy alterations induced by virus-associated antiviral signaling is further discussed.
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Affiliation(s)
- Po-Yuan Ke
- Department of Biochemistry & Molecular Biology and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan, ROC.,Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan, ROC
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22
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Yim WWY, Kurikawa Y, Mizushima N. An exploratory text analysis of the autophagy research field. Autophagy 2021; 18:1648-1661. [PMID: 34812110 PMCID: PMC9298454 DOI: 10.1080/15548627.2021.1995151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
After its discovery in the 1950 s, the autophagy research field has seen its annual number of publications climb from tens to thousands. The ever-growing number of autophagy publications is a wealth of information but presents a challenge to researchers, especially those new to the field, who are looking for a general overview of the field to, for example, determine current topics of the field or formulate new hypotheses. Here, we employed text mining tools to extract research trends in the autophagy field, including those of genes, terms, and topics. The publication trend of the field can be separated into three phases. The exponential rise in publication number began in the last phase and is most likely spurred by a series of highly cited research papers published in previous phases. The exponential increase in papers has resulted in a larger variety of research topics, with the majority involving those that are directly physiologically relevant, such as disease and modulating autophagy. Our findings provide researchers a summary of the history of the autophagy research field and perhaps hints of what is to come.Abbreviations: 5Y-IF: 5-year impact factor; AIS: article influence score; EM: electron microscopy; HGNC: HUGO gene nomenclature committee; LDA: latent Dirichlet allocation; MeSH: medical subject headings; ncRNA: non-coding RNA.
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Affiliation(s)
- Willa Wen-You Yim
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshitaka Kurikawa
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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