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Rogov VV, Nezis IP, Tsapras P, Zhang H, Dagdas Y, Noda NN, Nakatogawa H, Wirth M, Mouilleron S, McEwan DG, Behrends C, Deretic V, Elazar Z, Tooze SA, Dikic I, Lamark T, Johansen T. Atg8 family proteins, LIR/AIM motifs and other interaction modes. AUTOPHAGY REPORTS 2023; 2:27694127.2023.2188523. [PMID: 38214012 PMCID: PMC7615515 DOI: 10.1080/27694127.2023.2188523] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
The Atg8 family of ubiquitin-like proteins play pivotal roles in autophagy and other processes involving vesicle fusion and transport where the lysosome/vacuole is the end station. Nuclear roles of Atg8 proteins are also emerging. Here, we review the structural and functional features of Atg8 family proteins and their protein-protein interaction modes in model organisms such as yeast, Arabidopsis, C. elegans and Drosophila to humans. Although varying in number of homologs, from one in yeast to seven in humans, and more than ten in some plants, there is a strong evolutionary conservation of structural features and interaction modes. The most prominent interaction mode is between the LC3 interacting region (LIR), also called Atg8 interacting motif (AIM), binding to the LIR docking site (LDS) in Atg8 homologs. There are variants of these motifs like "half-LIRs" and helical LIRs. We discuss details of the binding modes and how selectivity is achieved as well as the role of multivalent LIR-LDS interactions in selective autophagy. A number of LIR-LDS interactions are known to be regulated by phosphorylation. New methods to predict LIR motifs in proteins have emerged that will aid in discovery and analyses. There are also other interaction surfaces than the LDS becoming known where we presently lack detailed structural information, like the N-terminal arm region and the UIM-docking site (UDS). More interaction modes are likely to be discovered in future studies.
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Affiliation(s)
- Vladimir V. Rogov
- Institute for Pharmaceutical Chemistry, Department of Biochemistry, Chemistry and Pharmacy, Goethe University, 60438 Frankfurt, am Main, and Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Ioannis P. Nezis
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | | | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China and College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yasin Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo 060-0815, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Martina Wirth
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Stephane Mouilleron
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | | | - Christian Behrends
- Munich Cluster of Systems Neurology, Ludwig-Maximilians-Universität München, München, Germany
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM and Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Zvulun Elazar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Ivan Dikic
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt am Main, and Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Trond Lamark
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Terje Johansen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
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2
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Norizuki T, Minamino N, Sato M, Ueda T. Autophagy regulates plastid reorganization during spermatogenesis in the liverwort Marchantia polymorpha. FRONTIERS IN PLANT SCIENCE 2023; 14:1101983. [PMID: 36844055 PMCID: PMC9947651 DOI: 10.3389/fpls.2023.1101983] [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: 11/18/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Autophagy is a highly conserved system that delivers cytoplasmic components to lysosomes/vacuoles. Plastids are also degraded through autophagy for nutrient recycling and quality control; however, the involvement of autophagic degradation of plastids in plant cellular differentiation remains unclear. Here, we investigated whether spermiogenesis, the differentiation of spermatids into spermatozoids, in the liverwort Marchantia polymorpha involves autophagic degradation of plastids. Spermatozoids of M. polymorpha possess one cylindrical plastid at the posterior end of the cell body. By fluorescently labeling and visualizing plastids, we detected dynamic morphological changes during spermiogenesis. We found that a portion of the plastid was degraded in the vacuole in an autophagy-dependent manner during spermiogenesis, and impaired autophagy resulted in defective morphological transformation and starch accumulation in the plastid. Furthermore, we found that autophagy was dispensable for the reduction in plastid number and plastid DNA elimination. These results demonstrate a critical but selective role of autophagy in plastid reorganization during spermiogenesis in M. polymorpha.
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Affiliation(s)
- Takuya Norizuki
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
- Laboratory of Molecular Membrane Biology, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Naoki Minamino
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
| | - Miyuki Sato
- Laboratory of Molecular Membrane Biology, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
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3
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Pettinari G, Finello J, Plaza Rojas M, Liberatore F, Robert G, Otaiza-González S, Velez P, Theumer M, Agudelo-Romero P, Enet A, González C, Lascano R, Saavedra L. Autophagy modulates growth and development in the moss Physcomitrium patens. FRONTIERS IN PLANT SCIENCE 2022; 13:1052358. [PMID: 36600927 PMCID: PMC9807217 DOI: 10.3389/fpls.2022.1052358] [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: 09/23/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Physcomitrium patens apical growing protonemal cells have the singularity that they continue to undergo cell divisions as the plant develops. This feature provides a valuable tool to study autophagy in the context of a multicellular apical growing tissue coupled to development. Herein, we showed that the core autophagy machinery is present in the moss P. patens, and characterized the 2D and 3D growth and development of atg5 and atg7 loss-of-function mutants under optimal and nutrient-deprived conditions. Our results showed that 2D growth of the different morphological and functional protonemata apical growing cells, chloronema and caulonema, is differentially modulated by this process. These differences depend on the protonema cell type and position along the protonemal filament, and growth condition. As a global plant response, the absence of autophagy favors the spread of the colony through protonemata growth at the expense of a reduction of the 3D growth, such as the buds and gametophore development, and thus the adult gametophytic and reproductive phases. Altogether this study provides valuable information suggesting that autophagy has roles during apical growth with differential responses within the cell types of the same tissue and contributes to life cycle progression and thus the growth and development of the 2D and 3D tissues of P. patens.
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Affiliation(s)
- Georgina Pettinari
- Unidad Ejecutora de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Juan Finello
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Macarena Plaza Rojas
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Franco Liberatore
- Unidad Ejecutora de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
| | - Germán Robert
- Unidad Ejecutora de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | | | - Pilar Velez
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Universidad Nacional de Córdoba-CONICET, Córdoba, Argentina
| | - Martin Theumer
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Universidad Nacional de Córdoba-CONICET, Córdoba, Argentina
| | | | - Alejandro Enet
- Unidad Ejecutora de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
| | - Claudio González
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Ramiro Lascano
- Unidad Ejecutora de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Laura Saavedra
- Unidad Ejecutora de Doble Dependencia INTA-CONICET (UDEA), Córdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, Argentina
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4
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Bowman JL, Arteaga-Vazquez M, Berger F, Briginshaw LN, Carella P, Aguilar-Cruz A, Davies KM, Dierschke T, Dolan L, Dorantes-Acosta AE, Fisher TJ, Flores-Sandoval E, Futagami K, Ishizaki K, Jibran R, Kanazawa T, Kato H, Kohchi T, Levins J, Lin SS, Nakagami H, Nishihama R, Romani F, Schornack S, Tanizawa Y, Tsuzuki M, Ueda T, Watanabe Y, Yamato KT, Zachgo S. The renaissance and enlightenment of Marchantia as a model system. THE PLANT CELL 2022; 34:3512-3542. [PMID: 35976122 PMCID: PMC9516144 DOI: 10.1093/plcell/koac219] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/21/2022] [Indexed: 05/07/2023]
Abstract
The liverwort Marchantia polymorpha has been utilized as a model for biological studies since the 18th century. In the past few decades, there has been a Renaissance in its utilization in genomic and genetic approaches to investigating physiological, developmental, and evolutionary aspects of land plant biology. The reasons for its adoption are similar to those of other genetic models, e.g. simple cultivation, ready access via its worldwide distribution, ease of crossing, facile genetics, and more recently, efficient transformation, genome editing, and genomic resources. The haploid gametophyte dominant life cycle of M. polymorpha is conducive to forward genetic approaches. The lack of ancient whole-genome duplications within liverworts facilitates reverse genetic approaches, and possibly related to this genomic stability, liverworts possess sex chromosomes that evolved in the ancestral liverwort. As a representative of one of the three bryophyte lineages, its phylogenetic position allows comparative approaches to provide insights into ancestral land plants. Given the karyotype and genome stability within liverworts, the resources developed for M. polymorpha have facilitated the development of related species as models for biological processes lacking in M. polymorpha.
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Affiliation(s)
| | - Mario Arteaga-Vazquez
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Frederic Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Liam N Briginshaw
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Philip Carella
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Adolfo Aguilar-Cruz
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Kevin M Davies
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North 4442, New Zealand
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Liam Dolan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna 1030, Austria
| | - Ana E Dorantes-Acosta
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa VER 91090, México
| | - Tom J Fisher
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Eduardo Flores-Sandoval
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne VIC 3800, Australia
| | - Kazutaka Futagami
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | | | - Rubina Jibran
- The New Zealand Institute for Plant & Food Research Limited, Auckland 1142, New Zealand
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Hirotaka Kato
- Graduate School of Science, Kobe University, Kobe 657-8501, Japan
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Jonathan Levins
- School of Biological Sciences, Monash University, Melbourne VIC 3800, Australia
| | - Shih-Shun Lin
- Institute of Biotechnology, National Taiwan University, Taipei 106, Taiwan
| | - Hirofumi Nakagami
- Basic Immune System of Plants, Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Ryuichi Nishihama
- Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | | | - Yasuhiro Tanizawa
- Department of Informatics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo 153-8902, Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama 649-6493, Japan
| | - Sabine Zachgo
- Division of Botany, School of Biology and Chemistry, Osnabrück University, Osnabrück 49076, Germany
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5
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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: 9] [Impact Index Per Article: 4.5] [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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6
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Goto-Yamada S, Oikawa K, Yamato KT, Kanai M, Hikino K, Nishimura M, Mano S. Image-Based Analysis Revealing the Molecular Mechanism of Peroxisome Dynamics in Plants. Front Cell Dev Biol 2022; 10:883491. [PMID: 35592252 PMCID: PMC9110829 DOI: 10.3389/fcell.2022.883491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/15/2022] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are present in eukaryotic cells and have essential roles in various biological processes. Plant peroxisomes proliferate by de novo biosynthesis or division of pre-existing peroxisomes, degrade, or replace metabolic enzymes, in response to developmental stages, environmental changes, or external stimuli. Defects of peroxisome functions and biogenesis alter a variety of biological processes and cause aberrant plant growth. Traditionally, peroxisomal function-based screening has been employed to isolate Arabidopsis thaliana mutants that are defective in peroxisomal metabolism, such as lipid degradation and photorespiration. These analyses have revealed that the number, subcellular localization, and activity of peroxisomes are closely related to their efficient function, and the molecular mechanisms underlying peroxisome dynamics including organelle biogenesis, protein transport, and organelle interactions must be understood. Various approaches have been adopted to identify factors involved in peroxisome dynamics. With the development of imaging techniques and fluorescent proteins, peroxisome research has been accelerated. Image-based analyses provide intriguing results concerning the movement, morphology, and number of peroxisomes that were hard to obtain by other approaches. This review addresses image-based analysis of peroxisome dynamics in plants, especially A. thaliana and Marchantia polymorpha.
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Affiliation(s)
- Shino Goto-Yamada
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Kazusato Oikawa
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Katsuyuki T. Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Masatake Kanai
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Kazumi Hikino
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Mikio Nishimura
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
- *Correspondence: Shoji Mano
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7
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Wang Q, Hou S. The emerging roles of ATG1/ATG13 kinase complex in plants. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153653. [PMID: 35255243 DOI: 10.1016/j.jplph.2022.153653] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Autophagy is a conserved system from yeast to mammals that mediates the degradation and renovation of cellular components. This process is mainly driven by numerous autophagy-related (ATG) proteins. Among these components, the ATG1/ATG13 complex plays an essential role in initiating autophagy, sensing nutritional status signals, recruiting downstream ATG proteins to the autophagosome formation site, and governing autophagosome formation. In this review, we will focus on the ATG1/ATG13 kinase complex, summarizing and discussing the current views on the composition, structure, function, and regulation of this complex in plants.
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Affiliation(s)
- Qiuling Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Suiwen Hou
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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8
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Zhou X, Zhao P, Sun MX. Autophagy in sexual plant reproduction: new insights. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7658-7667. [PMID: 34338297 DOI: 10.1093/jxb/erab366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/01/2021] [Indexed: 06/13/2023]
Abstract
Autophagy is a mechanism by which damaged or unwanted cells are degraded and their constituents recycled. Over the past decades, research focused on autophagy has expanded from yeast to mammals and plants, and the core machinery regulating autophagy appears to be conserved. In plants, autophagy has essential roles in responses to stressful conditions and also contributes to normal development, especially in the context of reproduction. Here, based on recent efforts to understand the roles and molecular mechanisms underlying autophagy, we highlight the specific roles of autophagy in plant reproduction and provide new insights for further studies.
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Affiliation(s)
- Xuemei Zhou
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Engineering Research Centre for the Protection and Utilization of Bioresource in Ethnic Area of Southern China, College of Life Sciences, South-Central University for Nationalities, Wuhan 430074, China
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Peng Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Meng-Xiang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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9
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Quezada-Rodríguez EH, Gómez-Velasco H, Arthikala MK, Lara M, Hernández-López A, Nanjareddy K. Exploration of Autophagy Families in Legumes and Dissection of the ATG18 Family with a Special Focus on Phaseolus vulgaris. PLANTS 2021; 10:plants10122619. [PMID: 34961093 PMCID: PMC8703869 DOI: 10.3390/plants10122619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 11/16/2022]
Abstract
Macroautophagy/autophagy is a fundamental catabolic pathway that maintains cellular homeostasis in eukaryotic cells by forming double-membrane-bound vesicles named autophagosomes. The autophagy family genes remain largely unexplored except in some model organisms. Legumes are a large family of economically important crops, and knowledge of their important cellular processes is essential. Here, to first address the knowledge gaps, we identified 17 ATG families in Phaseolus vulgaris, Medicago truncatula and Glycine max based on Arabidopsis sequences and elucidated their phylogenetic relationships. Second, we dissected ATG18 in subfamilies from early plant lineages, chlorophytes to higher plants, legumes, which included a total of 27 photosynthetic organisms. Third, we focused on the ATG18 family in P. vulgaris to understand the protein structure and developed a 3D model for PvATG18b. Our results identified ATG homologs in the chosen legumes and differential expression data revealed the nitrate-responsive nature of ATG genes. A multidimensional scaling analysis of 280 protein sequences from 27 photosynthetic organisms classified ATG18 homologs into three subfamilies that were not based on the BCAS3 domain alone. The domain structure, protein motifs (FRRG) and the stable folding conformation structure of PvATG18b revealing the possible lipid-binding sites and transmembrane helices led us to propose PvATG18b as the functional homolog of AtATG18b. The findings of this study contribute to an in-depth understanding of the autophagy process in legumes and improve our knowledge of ATG18 subfamilies.
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Affiliation(s)
- Elsa-Herminia Quezada-Rodríguez
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (UNAM), León C.P. 37684, Mexico; (E.-H.Q.-R.); (M.-K.A.); (A.H.-L.)
| | - Homero Gómez-Velasco
- Instituto de Química, Universidad Nacional Autónoma de México (UNAM), Cuidad Universitaria, Cuidad de Mexico C.P. 04510, Mexico;
| | - Manoj-Kumar Arthikala
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (UNAM), León C.P. 37684, Mexico; (E.-H.Q.-R.); (M.-K.A.); (A.H.-L.)
| | - Miguel Lara
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca C.P. 62271, Mexico;
| | - Antonio Hernández-López
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (UNAM), León C.P. 37684, Mexico; (E.-H.Q.-R.); (M.-K.A.); (A.H.-L.)
| | - Kalpana Nanjareddy
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México (UNAM), León C.P. 37684, Mexico; (E.-H.Q.-R.); (M.-K.A.); (A.H.-L.)
- Correspondence: ; Tel.: +52-477-1940800 (ext. 43462)
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Paul S, Bravo Vázquez LA, Márquez Nafarrate M, Gutiérrez Reséndiz AI, Srivastava A, Sharma A. The regulatory activities of microRNAs in non-vascular plants: a mini review. PLANTA 2021; 254:57. [PMID: 34424349 DOI: 10.1007/s00425-021-03707-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/14/2021] [Indexed: 05/21/2023]
Abstract
MicroRNA-mediated gene regulation in non-vascular plants is potentially involved in several unique biological functions, including biosynthesis of several highly valuable exclusive bioactive compounds, and those small RNAs could be manipulated for the overproduction of essential bioactive compounds in the future. MicroRNAs (miRNAs) are a class of endogenous, small (20-24 nucleotides), non-coding RNA molecules that regulate gene expression through the miRNA-mediated mechanisms of either translational inhibition or messenger RNA (mRNA) cleavage. In the past years, studies have mainly focused on elucidating the roles of miRNAs in vascular plants as compared to non-vascular plants. However, non-vascular plant miRNAs have been predicted to be involved in a wide variety of specific biological mechanisms; nevertheless, some of them have been demonstrated explicitly, thus showing that the research field of this plant group owns a noteworthy potential to develop novel investigations oriented towards the functional characterization of these miRNAs. Furthermore, the insights into the roles of miRNAs in non-vascular plants might be of great importance for designing the miRNA-based genetically modified plants for valuable secondary metabolites, active compounds, and biofuels in the future. Therefore, in this current review, we provide an overview of the potential roles of miRNAs in different groups of non-vascular plants such as algae and bryophytes.
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Affiliation(s)
- Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico.
| | - Luis Alberto Bravo Vázquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico
| | - Marilyn Márquez Nafarrate
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Av. Eugenio Garza Sada, No. 2501 Tecnologico, CP 64849, Monterrey, Mexico
| | - Ana Isabel Gutiérrez Reséndiz
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico
| | - Aashish Srivastava
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc. San Pablo, CP 76130, Querétaro, Mexico.
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Zhang S, Hama Y, Mizushima N. The evolution of autophagy proteins - diversification in eukaryotes and potential ancestors in prokaryotes. J Cell Sci 2021; 134:270774. [PMID: 34228793 DOI: 10.1242/jcs.233742] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Autophagy is a degradative pathway for cytoplasmic constituents, and is conserved across eukaryotes. Autophagy-related (ATG) genes have undergone extensive multiplications and losses in different eukaryotic lineages, resulting in functional diversification and specialization. Notably, even though bacteria and archaea do not possess an autophagy pathway, they do harbor some remote homologs of Atg proteins, suggesting that preexisting proteins were recruited when the autophagy pathway developed during eukaryogenesis. In this Review, we summarize our current knowledge on the distribution of Atg proteins within eukaryotes and outline the major multiplication and loss events within the eukaryotic tree. We also discuss the potential prokaryotic homologs of Atg proteins identified to date, emphasizing the evolutionary relationships and functional differences between prokaryotic and eukaryotic proteins.
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Affiliation(s)
- Sidi Zhang
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yutaro Hama
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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Huang X, Chen S, Yang X, Yang X, Zhang T, Zhou G. Friend or Enemy: A Dual Role of Autophagy in Plant Virus Infection. Front Microbiol 2020; 11:736. [PMID: 32373106 PMCID: PMC7186577 DOI: 10.3389/fmicb.2020.00736] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/30/2020] [Indexed: 11/20/2022] Open
Abstract
Autophagy is a primary protective process that involves removing damaged organelles or dysfunctional proteins in eukaryotes. The autophagy pathway not only maintains cellular homeostasis, but also modulates the host's cellular response to pathogen infection. Several studies proved that autophagy plays a dominant role in plant fitness and immunity. As intracellular parasites, the replication and spread of viruses entirely rely upon the molecular machinery of the host cell, including the autophagy process. Plant viruses severely affect crop yields and quality. During infection, complex interactions occur between viral proteins and host factors in relation to plant defense and virus counter-defense. An increasing number of studies demonstrated that plants use autophagy to eliminate and inhibit viruses; some viruses were shown to manipulate the process of autophagy to promote their own replication and survival in plant cells. In this review, we summarize recent advances in plant autophagy, with an emphasis on the role of autophagy in plant virus infection.
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Affiliation(s)
- Xiuqin Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Siping Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Xiaorong Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
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Norizuki T, Minamino N, Ueda T. Role of Autophagy in Male Reproductive Processes in Land Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:756. [PMID: 32625219 PMCID: PMC7311755 DOI: 10.3389/fpls.2020.00756] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/12/2020] [Indexed: 05/02/2023]
Abstract
Autophagy is a highly conserved system for degrading and recycling cytoplasmic components. The identification of autophagy-related (ATG) genes, required for autophagosome formation, has led to numerous studies using atg mutants. These studies have revealed the physiological significance of autophagy in various functions of diverse organisms. In land plants, autophagy is required for higher-order functions such as stress responses and development. Although defective autophagy does not result in any marked defect in the reproductive processes of Arabidopsis thaliana under laboratory conditions, several studies have shown that autophagy plays a pivotal role in male reproduction in several land plants. In this review, we aim to summarize information on the role of autophagy in male reproductive processes in land plants.
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Affiliation(s)
- Takuya Norizuki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
| | - Naoki Minamino
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
- The Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
- *Correspondence: Takashi Ueda,
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