51
|
Abstract
In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
Collapse
|
52
|
Zhang YM, Guo P, Xia X, Guo H, Li Z. Multiple Layers of Regulation on Leaf Senescence: New Advances and Perspectives. FRONTIERS IN PLANT SCIENCE 2021; 12:788996. [PMID: 34938309 PMCID: PMC8685244 DOI: 10.3389/fpls.2021.788996] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/03/2021] [Indexed: 05/22/2023]
Abstract
Leaf senescence is the last stage of leaf development and is an orderly biological process accompanied by degradation of macromolecules and nutrient recycling, which contributes to plant fitness. Forward genetic mutant screening and reverse genetic studies of senescence-associated genes (SAGs) have revealed that leaf senescence is a genetically regulated process, and the initiation and progression of leaf senescence are influenced by an array of internal and external factors. Recently, multi-omics techniques have revealed that leaf senescence is subjected to multiple layers of regulation, including chromatin, transcriptional and post-transcriptional, as well as translational and post-translational levels. Although impressive progress has been made in plant senescence research, especially the identification and functional analysis of a large number of SAGs in crop plants, we still have not unraveled the mystery of plant senescence, and there are some urgent scientific questions in this field, such as when plant senescence is initiated and how senescence signals are transmitted. This paper reviews recent advances in the multiple layers of regulation on leaf senescence, especially in post-transcriptional regulation such as alternative splicing.
Collapse
Affiliation(s)
- Yue-Mei Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Pengru Guo
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Zhonghai Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Zhonghai Li,
| |
Collapse
|
53
|
Qi H, Xia FN, Xiao S. Autophagy in plants: Physiological roles and post-translational regulation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:161-179. [PMID: 32324339 DOI: 10.1111/jipb.12941] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/22/2020] [Indexed: 05/20/2023]
Abstract
In eukaryotes, autophagy helps maintain cellular homeostasis by degrading and recycling cytoplasmic materials via a tightly regulated pathway. Over the past few decades, significant progress has been made towards understanding the physiological functions and molecular regulation of autophagy in plant cells. Increasing evidence indicates that autophagy is essential for plant responses to several developmental and environmental cues, functioning in diverse processes such as senescence, male fertility, root meristem maintenance, responses to nutrient starvation, and biotic and abiotic stress. Recent studies have demonstrated that, similar to nonplant systems, the modulation of core proteins in the plant autophagy machinery by posttranslational modifications such as phosphorylation, ubiquitination, lipidation, S-sulfhydration, S-nitrosylation, and acetylation is widely involved in the initiation and progression of autophagy. Here, we provide an overview of the physiological roles and posttranslational regulation of autophagy in plants.
Collapse
Affiliation(s)
- Hua Qi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Fan-Nv Xia
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| |
Collapse
|
54
|
Liu F, Hu W, Li F, Marshall RS, Zarza X, Munnik T, Vierstra RD. AUTOPHAGY-RELATED14 and Its Associated Phosphatidylinositol 3-Kinase Complex Promote Autophagy in Arabidopsis. THE PLANT CELL 2020; 32:3939-3960. [PMID: 33004618 PMCID: PMC7721316 DOI: 10.1105/tpc.20.00285] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 08/24/2020] [Accepted: 09/29/2020] [Indexed: 05/20/2023]
Abstract
Phosphatidylinositol 3-phosphate (PI3P) is an essential membrane signature for both autophagy and endosomal sorting that is synthesized in plants by the class III phosphatidylinositol 3-kinase (PI3K) complex, consisting of the VPS34 kinase, together with ATG6, VPS15, and either VPS38 or ATG14 as the fourth subunit. Although Arabidopsis (Arabidopsis thaliana) plants missing the three core subunits are infertile, vps38 mutants are viable but have aberrant leaf, root, and seed development, Suc sensing, and endosomal trafficking, suggesting that VPS38 and ATG14 are nonredundant. Here, we evaluated the role of ATG14 through a collection of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 and T-DNA insertion mutants disrupting the two Arabidopsis paralogs. atg14a atg14b double mutants were relatively normal phenotypically but displayed pronounced autophagy defects, including reduced accumulation of autophagic bodies and cargo delivery during nutrient stress. Unexpectedly, homozygous atg14a atg14b vps38 triple mutants were viable but showed severely compromised rosette development and reduced fecundity, pollen germination, and autophagy, consistent with a need for both ATG14 and VPS38 to fully actuate PI3P biology. However, the triple mutants still accumulated PI3P, but they were hypersensitive to the PI3K inhibitor wortmannin, indicating that the ATG14/VPS38 component is not essential for PI3P synthesis. Collectively, the ATG14/VPS38 mutant collection now permits the study of plants altered in specific aspects of PI3P biology.
Collapse
Affiliation(s)
- Fen Liu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Weiming Hu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Faqiang Li
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Xavier Zarza
- Department of Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 Amsterdam, The Netherlands
| | - Teun Munnik
- Department of Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 Amsterdam, The Netherlands
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| |
Collapse
|
55
|
Laureano-Marín AM, Aroca Á, Pérez-Pérez ME, Yruela I, Jurado-Flores A, Moreno I, Crespo JL, Romero LC, Gotor C. Abscisic Acid-Triggered Persulfidation of the Cys Protease ATG4 Mediates Regulation of Autophagy by Sulfide. THE PLANT CELL 2020; 32:3902-3920. [PMID: 33037147 PMCID: PMC7721334 DOI: 10.1105/tpc.20.00766] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/08/2020] [Indexed: 05/16/2023]
Abstract
Hydrogen sulfide is a signaling molecule that regulates essential processes in plants, such as autophagy. In Arabidopsis (Arabidopsis thaliana), hydrogen sulfide negatively regulates autophagy independently of reactive oxygen species via an unknown mechanism. Comparative and quantitative proteomic analysis was used to detect abscisic acid-triggered persulfidation that reveals a main role in the control of autophagy mediated by the autophagy-related (ATG) Cys protease AtATG4a. This protease undergoes specific persulfidation of Cys170 that is a part of the characteristic catalytic Cys-His-Asp triad of Cys proteases. Regulation of the ATG4 activity by persulfidation was tested in a heterologous assay using the Chlamydomonas reinhardtii CrATG8 protein as a substrate. Sulfide significantly and reversibly inactivates AtATG4a. The biological significance of the reversible inhibition of the ATG4 by sulfide is supported by the results obtained in Arabidopsis leaves under basal and autophagy-activating conditions. A significant increase in the overall ATG4 proteolytic activity in Arabidopsis was detected under nitrogen starvation and osmotic stress and can be inhibited by sulfide. Therefore, the data strongly suggest that the negative regulation of autophagy by sulfide is mediated by specific persulfidation of the ATG4 protease.
Collapse
Affiliation(s)
- Ana M Laureano-Marín
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - Ángeles Aroca
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - M Esther Pérez-Pérez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - Inmaculada Yruela
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, 50059 Zaragoza, Spain
- Group of Biochemistry, Biophysics and Computational Biology (BIFI-Unizar) Joint Unit to Consejo Superior de Investigaciones Científicas, 50059 Zaragoza, Spain
| | - Ana Jurado-Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - Inmaculada Moreno
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - José L Crespo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| | - Cecilia Gotor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, 41092 Seville, Spain
| |
Collapse
|
56
|
Wijerathna-Yapa A, Stroeher E, Fenske R, Li L, Duncan O, Millar AH. Proteomics for Autophagy Receptor and Cargo Identification in Plants. J Proteome Res 2020; 20:129-138. [PMID: 33241938 DOI: 10.1021/acs.jproteome.0c00609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Autophagy is a catabolic process facilitating the degradation of cytoplasmic proteins and organelles in a lysosome- or vacuole-dependent manner in plants, animals, and fungi. Proteomic studies have demonstrated that autophagy controls and shapes the proteome and has identified both receptor and cargo proteins inside autophagosomes. In a smaller selection of studies, proteomics has been used for the analysis of post-translational modifications that target proteins for elimination and protein-protein interactions between receptors and cargo, providing a better understanding of the complex regulatory processes controlling autophagy. In this perspective, we highlight how proteomic studies have contributed to our understanding of autophagy in plants against the backdrop of yeast and animal studies. We then provide a framework for how the future application of proteomics in plant autophagy can uncover the mechanisms and outcomes of sculpting organelles during plant development, particularly through the identification of autophagy receptors and cargo in plants.
Collapse
Affiliation(s)
- Akila Wijerathna-Yapa
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - Elke Stroeher
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia.,Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| |
Collapse
|
57
|
Origin and adaptation to high altitude of Tibetan semi-wild wheat. Nat Commun 2020; 11:5085. [PMID: 33033250 PMCID: PMC7545183 DOI: 10.1038/s41467-020-18738-5] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Tibetan wheat is grown under environmental constraints at high-altitude conditions, but its underlying adaptation mechanism remains unknown. Here, we present a draft genome sequence of a Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao) accession Zang1817 and re-sequence 245 wheat accessions, including world-wide wheat landraces, cultivars as well as Tibetan landraces. We demonstrate that high-altitude environments can trigger extensive reshaping of wheat genomes, and also uncover that Tibetan wheat accessions accumulate high-altitude adapted haplotypes of related genes in response to harsh environmental constraints. Moreover, we find that Tibetan semi-wild wheat is a feral form of Tibetan landrace, and identify two associated loci, including a 0.8-Mb deletion region containing Brt1/2 homologs and a genomic region with TaQ-5A gene, responsible for rachis brittleness during the de-domestication episode. Our study provides confident evidence to support the hypothesis that Tibetan semi-wild wheat is de-domesticated from local landraces, in response to high-altitude extremes. Mechanism of high altitude adaptation of wheat remains unknown. Here, the authors assemble the draft genome of a Tibetan semi-wild wheat accession and resequence 245 wheat accessions to reveal that Tibetan semi-wild wheat has been de-domesticated from local landraces to adapt to high altitude.
Collapse
|
58
|
Su T, Yang M, Wang P, Zhao Y, Ma C. Interplay between the Ubiquitin Proteasome System and Ubiquitin-Mediated Autophagy in Plants. Cells 2020; 9:cells9102219. [PMID: 33019500 PMCID: PMC7600366 DOI: 10.3390/cells9102219] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 12/12/2022] Open
Abstract
All eukaryotes rely on the ubiquitin-proteasome system (UPS) and autophagy to control the abundance of key regulatory proteins and maintain a healthy intracellular environment. In the UPS, damaged or superfluous proteins are ubiquitinated and degraded in the proteasome, mediated by three types of ubiquitin enzymes: E1s (ubiquitin activating enzymes), E2s (ubiquitin conjugating enzymes), and E3s (ubiquitin protein ligases). Conversely, in autophagy, a vesicular autophagosome is formed that transfers damaged proteins and organelles to the vacuole, mediated by a series of ATGs (autophagy related genes). Despite the use of two completely different componential systems, the UPS and autophagy are closely interconnected and mutually regulated. During autophagy, ATG8 proteins, which are autophagosome markers, decorate the autophagosome membrane similarly to ubiquitination of damaged proteins. Ubiquitin is also involved in many selective autophagy processes and is thus a common factor of the UPS and autophagy. Additionally, the components of the UPS, such as the 26S proteasome, can be degraded via autophagy, and conversely, ATGs can be degraded by the UPS, indicating cross regulation between the two pathways. The UPS and autophagy cooperate and jointly regulate homeostasis of cellular components during plant development and stress response.
Collapse
Affiliation(s)
| | | | | | | | - Changle Ma
- Correspondence: ; Tel.: +86-0531-86180792
| |
Collapse
|
59
|
McLoughlin F, Marshall RS, Ding X, Chatt EC, Kirkpatrick LD, Augustine RC, Li F, Otegui MS, Vierstra RD. Autophagy Plays Prominent Roles in Amino Acid, Nucleotide, and Carbohydrate Metabolism during Fixed-Carbon Starvation in Maize. THE PLANT CELL 2020; 32:2699-2724. [PMID: 32616663 PMCID: PMC7474275 DOI: 10.1105/tpc.20.00226] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/04/2020] [Accepted: 06/27/2020] [Indexed: 05/31/2023]
Abstract
Autophagic recycling of proteins, lipids, nucleic acids, carbohydrates, and organelles is essential for cellular homeostasis and optimal health, especially under nutrient-limiting conditions. To better understand how this turnover affects plant growth, development, and survival upon nutrient stress, we applied an integrated multiomics approach to study maize (Zea mays) autophagy mutants subjected to fixed-carbon starvation induced by darkness. Broad metabolic alterations were evident in leaves missing the core autophagy component ATG12 under normal growth conditions (e.g., lipids and secondary metabolism), while changes in amino acid-, carbohydrate-, and nucleotide-related metabolites selectively emerged during fixed-carbon starvation. Through combined proteomic and transcriptomic analyses, we identified numerous autophagy-responsive proteins, which revealed processes underpinning the various metabolic changes seen during carbon stress as well as potential autophagic cargo. Strikingly, a strong upregulation of various catabolic processes was observed in the absence of autophagy, including increases in simple carbohydrate levels with a commensurate drop in starch levels, elevated free amino acid levels with a corresponding reduction in intact protein levels, and a strong increase in the abundance of several nitrogen-rich nucleotide catabolites. Altogether, this analysis showed that fixed-carbon starvation in the absence of autophagy adjusts the choice of respiratory substrates, promotes the transition of peroxisomes to glyoxysomes, and enhances the retention of assimilated nitrogen.
Collapse
Affiliation(s)
- Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Xinxin Ding
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, Wisconsin 53706
| | - Elizabeth C Chatt
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Liam D Kirkpatrick
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Robert C Augustine
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Faqiang Li
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, Wisconsin 53706
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| |
Collapse
|
60
|
Kikuchi Y, Nakamura S, Woodson JD, Ishida H, Ling Q, Hidema J, Jarvis RP, Hagihara S, Izumi M. Chloroplast Autophagy and Ubiquitination Combine to Manage Oxidative Damage and Starvation Responses. PLANT PHYSIOLOGY 2020; 183:1531-1544. [PMID: 32554506 PMCID: PMC7401110 DOI: 10.1104/pp.20.00237] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/04/2020] [Indexed: 05/18/2023]
Abstract
Autophagy and the ubiquitin-proteasome system are the major degradation processes for intracellular components in eukaryotes. Although ubiquitination acts as a signal inducing organelle-targeting autophagy, the interaction between ubiquitination and autophagy in chloroplast turnover has not been addressed. In this study, we found that two chloroplast-associated E3 enzymes, SUPPRESSOR OF PPI1 LOCUS1 and PLANT U-BOX4 (PUB4), are not necessary for the induction of either piecemeal autophagy of chloroplast stroma or chlorophagy of whole damaged chloroplasts in Arabidopsis (Arabidopsis thaliana). Double mutations of an autophagy gene and PUB4 caused synergistic phenotypes relative to single mutations. The double mutants developed accelerated leaf chlorosis linked to the overaccumulation of reactive oxygen species during senescence and had reduced seed production. Biochemical detection of ubiquitinated proteins indicated that both autophagy and PUB4-associated ubiquitination contributed to protein degradation in the senescing leaves. Furthermore, the double mutants had enhanced susceptibility to carbon or nitrogen starvation relative to single mutants. Together, these results indicate that autophagy and chloroplast-associated E3s cooperate for protein turnover, management of reactive oxygen species accumulation, and adaptation to starvation.
Collapse
Affiliation(s)
- Yuta Kikuchi
- Graduate School of Life Sciences, Tohoku University, 980-0845 Sendai, Japan
| | - Sakuya Nakamura
- Center for Sustainable Resource Science, RIKEN, 351-0198 Wako, Japan
| | - Jesse D Woodson
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721-0036
| | - Hiroyuki Ishida
- Graduate School of Agricultural Science, Tohoku University, 980-0845 Sendai, Japan
| | - Qihua Ling
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Jun Hidema
- Graduate School of Life Sciences, Tohoku University, 980-0845 Sendai, Japan
| | - R Paul Jarvis
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Shinya Hagihara
- Center for Sustainable Resource Science, RIKEN, 351-0198 Wako, Japan
| | - Masanori Izumi
- Center for Sustainable Resource Science, RIKEN, 351-0198 Wako, Japan
- PRESTO, Japan Science and Technology Agency, 322-0012 Kawaguchi, Japan
| |
Collapse
|
61
|
Abstract
Autophagy is a conserved vacuole/lysosome-mediated degradation pathway for clearing and recycling cellular components including cytosol, macromolecules, and dysfunctional organelles. In recent years, autophagy has emerged to play important roles in plant-pathogen interactions. It acts as an antiviral defense mechanism in plants. Moreover, increasing evidence shows that plant viruses can manipulate, hijack, or even exploit the autophagy pathway to promote pathogenesis, demonstrating the pivotal role of autophagy in the evolutionary arms race between hosts and viruses. In this review, we discuss recent findings about the antiviral and proviral roles of autophagy in plant-virus interactions.
Collapse
Affiliation(s)
- Meng Yang
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China;
| | - Asigul Ismayil
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China;
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China;
| |
Collapse
|
62
|
Bu F, Yang M, Guo X, Huang W, Chen L. Multiple Functions of ATG8 Family Proteins in Plant Autophagy. Front Cell Dev Biol 2020; 8:466. [PMID: 32596242 PMCID: PMC7301642 DOI: 10.3389/fcell.2020.00466] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/19/2020] [Indexed: 11/13/2022] Open
Abstract
Autophagy is a major degradation process of cytoplasmic components in eukaryotes, and executes both bulk and selective degradation of targeted cargos. A set of autophagy-related (ATG) proteins participate in various stages of the autophagic process. Among ATGs, ubiquitin-like protein ATG8 plays a central role in autophagy. The ATG8 protein is conjugated to the membrane lipid phosphatidylethanolamine in a ubiquitin-like conjugation reaction that is essential for autophagosome formation. In addition, ATG8 interacts with various adaptor/receptor proteins to recruit specific cargos for degradation by selective autophagy. The ATG8-interacting proteins usually contain the ATG8-interacting motif (AIM) or the ubiquitin-interacting motif (UIM) for ATG8 binding. Unlike a single ATG8 gene in yeast, multiple ATG8 orthologs have been identified in the plant kingdom. The large diversity within the ATG8 family may explain the various functions of selective autophagy in plants. Here, we discuss and summarize the current view of the structure and function of ATG8 proteins in plants.
Collapse
Affiliation(s)
- Fan Bu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Mingkang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xu Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| |
Collapse
|
63
|
Chen T, Tian M, Han Y. Hydrogen sulfide: a multi-tasking signal molecule in the regulation of oxidative stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2862-2869. [PMID: 32076713 DOI: 10.1093/jxb/eraa093] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/15/2020] [Indexed: 05/24/2023]
Abstract
Accumulating evidence suggests that hydrogen sulfide (H2S) is an important signaling molecule in plant environmental interactions. The consensus view amongst plant scientists is that environmental stress leads to enhanced production and accumulation of reactive oxygen species (ROS). H2S interacts with the ROS-mediated oxidative stress response network at multiple levels, including the regulation of ROS-processing systems by transcriptional or post-translational modifications. H2S-ROS crosstalk also involves other interacting factors, including nitric oxide, and can affect key cellular processes like autophagy. While H2S often functions to prevent ROS accumulation, it can also act synergistically with ROS signals in processes such as stomatal closure. In this review, we summarize the mechanisms of H2S action and the multifaceted roles of this molecule in plant stress responses. Emphasis is placed on the interactions between H2S, ROS, and the redox signaling network that is crucial for plant defense against environmental threats.
Collapse
Affiliation(s)
- Tao Chen
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, Anhui, China
| | - Mimi Tian
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, Anhui, China
| | - Yi Han
- School of Food and Biological Engineering, Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei, Anhui, China
| |
Collapse
|
64
|
Huo L, Guo Z, Jia X, Sun X, Wang P, Gong X, Ma F. Increased autophagic activity in roots caused by overexpression of the autophagy-related gene MdATG10 in apple enhances salt tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 294:110444. [PMID: 32234232 DOI: 10.1016/j.plantsci.2020.110444] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/12/2020] [Accepted: 02/12/2020] [Indexed: 05/27/2023]
Abstract
Autophagy is a conserved pathway to degrade and recycle damaged proteins and organelles, which has generally been reported to play an important role in plant adaption to various abiotic stressors. Here, we isolated a new apple autophagy-related gene, MdATG10, from Malus domestica. Expression of MdATG10 was induced by salt stress, particularly in roots. To investigate the effects of increased autophagic activity on salt tolerance of apple, we generated three MdATG10-overexpressing apple lines and exposed them to salt stress. The transgenic apple plants exhibited enhanced salt tolerance, accompanied by slightly damaged photosynthetic ability and a milder growth limitation under the salt treatment. In addition, damage to growth and vitality of the root system caused by the salt treatment was alleviated by overexpressing MdATG10. Furthermore, reduced accumulation of Na+ and a lower Na+: K+ ratio was detected in the MdATG10-overexpressing apple lines under salt stress. The salt treatment induced expression of genes involved in ion homeostasis in transgenic apple roots. These results demonstrate a promoting role of autophagy in ion transport when plants encounter salty conditions.
Collapse
Affiliation(s)
- Liuqing Huo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zijian Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xin Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xun Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ping Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoqing Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
65
|
Bedu M, Marmagne A, Masclaux-Daubresse C, Chardon F. Transcriptional Plasticity of Autophagy-Related Genes Correlates with the Genetic Response to Nitrate Starvation in Arabidopsis Thaliana. Cells 2020; 9:E1021. [PMID: 32326055 PMCID: PMC7226452 DOI: 10.3390/cells9041021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 01/22/2023] Open
Abstract
In eukaryotes, autophagy, a catabolic mechanism for macromolecule and protein recycling, allows the maintenance of amino acid pools and nutrient remobilization. For a better understanding of the relationship between autophagy and nitrogen metabolism, we studied the transcriptional plasticity of autophagy genes (ATG) in nine Arabidopsis accessions grown under normal and nitrate starvation conditions. The status of the N metabolism in accessions was monitored by measuring the relative expression of 11 genes related to N metabolism in rosette leaves. The transcriptional variation of the genes coding for enzymes involved in ammonium assimilation characterize the genetic diversity of the response to nitrate starvation. Starvation enhanced the expression of most of the autophagy genes tested, suggesting a control of autophagy at transcriptomic level by nitrogen. The diversity of the gene responses among natural accessions revealed the genetic variation existing for autophagy independently of the nutritive condition, and the degree of response to nitrate starvation. We showed here that the genetic diversity of the expression of N metabolism genes correlates with that of the ATG genes in the two nutritive conditions, suggesting that the basal autophagy activity is part of the integral response of the N metabolism to nitrate availability.
Collapse
Affiliation(s)
- Magali Bedu
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (M.B.); (A.M.); (C.M.-D.)
- Bureau International des Poids et Mesures (BIPM), Pavillon de Breteuil, F-92312 Sèvres, France
| | - Anne Marmagne
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (M.B.); (A.M.); (C.M.-D.)
| | - Céline Masclaux-Daubresse
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (M.B.); (A.M.); (C.M.-D.)
| | - Fabien Chardon
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (M.B.); (A.M.); (C.M.-D.)
| |
Collapse
|
66
|
Liang JR, Lingeman E, Luong T, Ahmed S, Muhar M, Nguyen T, Olzmann JA, Corn JE. A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation. Cell 2020; 180:1160-1177.e20. [PMID: 32160526 DOI: 10.1016/j.cell.2020.02.017] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 11/04/2019] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Selective autophagy of organelles is critical for cellular differentiation, homeostasis, and organismal health. Autophagy of the ER (ER-phagy) is implicated in human neuropathy but is poorly understood beyond a few autophagosomal receptors and remodelers. By using an ER-phagy reporter and genome-wide CRISPRi screening, we identified 200 high-confidence human ER-phagy factors. Two pathways were unexpectedly required for ER-phagy. First, reduced mitochondrial metabolism represses ER-phagy, which is opposite of general autophagy and is independent of AMPK. Second, ER-localized UFMylation is required for ER-phagy to repress the unfolded protein response via IRE1α. The UFL1 ligase is brought to the ER surface by DDRGK1 to UFMylate RPN1 and RPL26 and preferentially targets ER sheets for degradation, analogous to PINK1-Parkin regulation during mitophagy. Our data provide insight into the cellular logic of ER-phagy, reveal parallels between organelle autophagies, and provide an entry point to the relatively unexplored process of degrading the ER network.
Collapse
Affiliation(s)
- Jin Rui Liang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Emily Lingeman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thao Luong
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Saba Ahmed
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Matthias Muhar
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Truc Nguyen
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
| |
Collapse
|
67
|
Qi H, Li J, Xia FN, Chen JY, Lei X, Han MQ, Xie LJ, Zhou QM, Xiao S. Arabidopsis SINAT Proteins Control Autophagy by Mediating Ubiquitylation and Degradation of ATG13. THE PLANT CELL 2020; 32:263-284. [PMID: 31732704 PMCID: PMC6961628 DOI: 10.1105/tpc.19.00413] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/30/2019] [Accepted: 11/11/2019] [Indexed: 05/04/2023]
Abstract
In eukaryotes, autophagy maintains cellular homeostasis by recycling cytoplasmic components. The autophagy-related proteins (ATGs) ATG1 and ATG13 form a protein kinase complex that regulates autophagosome formation; however, mechanisms regulating ATG1 and ATG13 remain poorly understood. Here, we show that, under different nutrient conditions, the RING-type E3 ligases SEVEN IN ABSENTIA OF ARABIDOPSIS THALIANA1 (SINAT1), SINAT2, and SINAT6 control ATG1 and ATG13 stability and autophagy dynamics by modulating ATG13 ubiquitylation in Arabidopsis (Arabidopsis thaliana). During prolonged starvation and recovery, ATG1 and ATG13 were degraded through the 26S proteasome pathway. TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED FACTOR1a (TRAF1a) and TRAF1b interacted in planta with ATG13a and ATG13b and required SINAT1 and SINAT2 to ubiquitylate and degrade ATG13s in vivo. Moreover, lysines K607 and K609 of ATG13a protein contributed to K48-linked ubiquitylation and destabilization, and suppression of autophagy. Under starvation conditions, SINAT6 competitively interacted with ATG13 and induced autophagosome biogenesis. Furthermore, under starvation conditions, ATG1 promoted TRAF1a protein stability in vivo, suggesting feedback regulation of autophagy. Consistent with ATGs functioning in autophagy, the atg1a atg1b atg1c triple knockout mutants exhibited premature leaf senescence, hypersensitivity to nutrient starvation, and reduction in TRAF1a stability. Therefore, these findings demonstrate that SINAT family proteins facilitate ATG13 ubiquitylation and stability and thus regulate autophagy.
Collapse
Affiliation(s)
- Hua Qi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Juan Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128 China
| | - Fan-Nv Xia
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jin-Yu Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xue Lei
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Mu-Qian Han
- College of Agronomy, Hunan Agricultural University, Changsha, 410128 China
| | - Li-Juan Xie
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Qing-Ming Zhou
- College of Agronomy, Hunan Agricultural University, Changsha, 410128 China
| | - Shi Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| |
Collapse
|
68
|
Kokabi K, Gorelova O, Zorin B, Didi-Cohen S, Itkin M, Malitsky S, Solovchenko A, Boussiba S, Khozin-Goldberg I. Lipidome Remodeling and Autophagic Respose in the Arachidonic-Acid-Rich Microalga Lobosphaera incisa Under Nitrogen and Phosphorous Deprivation. FRONTIERS IN PLANT SCIENCE 2020; 11:614846. [PMID: 33329680 PMCID: PMC7728692 DOI: 10.3389/fpls.2020.614846] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 11/02/2020] [Indexed: 05/09/2023]
Abstract
The green microalga Lobosphaera incisa accumulates triacylglycerols (TAGs) with exceptionally high levels of long-chain polyunsaturated fatty acid (LC-PUFA) arachidonic acid (ARA) under nitrogen (N) deprivation. Phosphorous (P) deprivation induces milder changes in fatty acid composition, cell ultrastructure, and growth performance. We hypothesized that the resource-demanding biosynthesis and sequestration of ARA-rich TAG in lipid droplets (LDs) are associated with the enhancement of catabolic processes, including membrane lipid turnover and autophagic activity. Although this work focuses mainly on N deprivation, a comparative analysis of N and P deprivation responses is included. The results of lipidomic profiling showed a differential impact of N and P deprivation on the reorganization of glycerolipids. The formation of TAG under N deprivation was associated with the enhanced breakdown of chloroplast glycerolipids and the formation of lyso-lipids. N-deprived cells displayed a profound reorganization of cell ultrastructure, including internalization of cellular material into autophagic vacuoles, concomitant with the formation of LDs, while P-deprived cells showed better cellular ultrastructural integrity. The expression of the hallmark autophagy protein ATG8 and the major lipid droplet protein (MLDP) genes were coordinately upregulated, but to different extents under either N or P deprivation. The expression of the Δ5-desaturase gene, involved in the final step of ARA biosynthesis, was coordinated with ATG8 and MLDP, exclusively under N deprivation. Concanamycin A, the inhibitor of vacuolar proteolysis and autophagic flux, suppressed growth and enhanced levels of ATG8 and TAG in N-replete cells. The proportions of ARA in TAG decreased with a concomitant increase in oleic acid under both N-replete and N-deprived conditions. The photosynthetic apparatus's recovery from N deprivation was impaired in the presence of the inhibitor, along with the delayed LD degradation. The GFP-ATG8 processing assay showed the release of free GFP in N-replete and N-deprived cells, supporting the existence of autophagic flux. This study provides the first insight into the homeostatic role of autophagy in L. incisa and points to a possible metabolic link between autophagy and ARA-rich TAG biosynthesis.
Collapse
Affiliation(s)
- Kamilya Kokabi
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Olga Gorelova
- Department of Bioengineering, Faculty of Biology, Moscow State University, GSP-1, Moscow, Russia
| | - Boris Zorin
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Shoshana Didi-Cohen
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Maxim Itkin
- Metabolic Profiling Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- Metabolic Profiling Unit, Life Science Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Alexei Solovchenko
- Department of Bioengineering, Faculty of Biology, Moscow State University, GSP-1, Moscow, Russia
- Institute of Natural Sciences, Derzhavin Tambov State University, Tambov, Russia
- Peoples Friendship University of Russia (RUDN University), Moscow, Russia
| | - Sammy Boussiba
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Inna Khozin-Goldberg
- Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology of Drylands, The J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| |
Collapse
|
69
|
Su T, Li X, Yang M, Shao Q, Zhao Y, Ma C, Wang P. Autophagy: An Intracellular Degradation Pathway Regulating Plant Survival and Stress Response. FRONTIERS IN PLANT SCIENCE 2020; 11:164. [PMID: 32184795 PMCID: PMC7058704 DOI: 10.3389/fpls.2020.00164] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/03/2020] [Indexed: 05/18/2023]
Abstract
Autophagy is an intracellular process that facilitates the bulk degradation of cytoplasmic materials by the vacuole or lysosome in eukaryotes. This conserved process is achieved through the coordination of different autophagy-related genes (ATGs). Autophagy is essential for recycling cytoplasmic material and eliminating damaged or dysfunctional cell constituents, such as proteins, aggregates or even entire organelles. Plant autophagy is necessary for maintaining cellular homeostasis under normal conditions and is upregulated during abiotic and biotic stress to prolong cell life. In this review, we present recent advances on our understanding of the molecular mechanisms of autophagy in plants and how autophagy contributes to plant development and plants' adaptation to the environment.
Collapse
Affiliation(s)
| | | | | | | | | | - Changle Ma
- *Correspondence: Changle Ma, ; Pingping Wang,
| | | |
Collapse
|
70
|
Fan T, Yang W, Zeng X, Xu X, Xu Y, Fan X, Luo M, Tian C, Xia K, Zhang M. A Rice Autophagy Gene OsATG8b Is Involved in Nitrogen Remobilization and Control of Grain Quality. FRONTIERS IN PLANT SCIENCE 2020; 11:588. [PMID: 32582228 PMCID: PMC7287119 DOI: 10.3389/fpls.2020.00588] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/20/2020] [Indexed: 05/03/2023]
Abstract
Enhancing nitrogen (N) use efficiency is a potential way to reduce excessive nitrogen application and increase yield. Autophagy is a conserved degradation system in the evolution of eukaryotic cells and plays an important role in plant development and stress response. Autophagic cores have two conjugation pathways that attach the product of autophagy-related gene 8 (ATG8) to phosphatidylethanolamine (PE) and ATG5 to ATG12, respectively, which then help with vesicle elongation and enclosure. Rice has six ATG8 genes, which have not been functionally confirmed so far. We identified the rice gene OsATG8b and characterized its role in N remobilization to affect grain quality by generating transgenic plants with its over-expression and knockdown. Our study confirmed the autophagy activity of OsATG8b through the complementation of the yeast autophagy-defective mutant scatg8 and by observation of autophagosome formation in rice. The autophagy activity is higher in OsATG8b-OE lines and lower in OsATG8b-RNAi than that in wild type (ZH11). 15N pulse-chase analysis revealed that OsATG8b-OE plants conferred higher N recycling efficiency to grains, while OsATG8b-RNAi transgenic plants exhibited lower N recycling efficiency and poorer grain quality. The autophagic role of OsATG8b was experimentally confirmed, and it was concluded that OsATG8b-mediated autophagy is involved in N recycling to grains and contributes to the grain quality, indicating that OsATG8b may be a potential gene for molecular breeding and cultivation of rice.
Collapse
Affiliation(s)
- Tian Fan
- School of Life Sciences, Guangzhou University, Guangzhou, China
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Wu Yang
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xuan Zeng
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xinlan Xu
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yanling Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Xiaorong Fan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Ming Luo
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Changen Tian
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Kuaifei Xia
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
| | - Mingyong Zhang
- Innovation Academy for Seed Design, Guangdong Provincial Key Laboratory of Applied Botany, Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Mingyong Zhang,
| |
Collapse
|
71
|
Huo L, Guo Z, Zhang Z, Jia X, Sun Y, Sun X, Wang P, Gong X, Ma F. The Apple Autophagy-Related Gene MdATG9 Confers Tolerance to Low Nitrogen in Transgenic Apple Callus. FRONTIERS IN PLANT SCIENCE 2020; 11:423. [PMID: 32351530 PMCID: PMC7174617 DOI: 10.3389/fpls.2020.00423] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/24/2020] [Indexed: 05/21/2023]
Abstract
Autophagy is an efficient degradation system for maintaining cellular homeostasis when plants are under environmental stress. ATG9 is the only integral membrane protein within the core ATG machinery that provides a membrane source for autophagosome formation. In this study, we isolated an ATG9 homologs gene in apple, MdATG9, from Malus domestica. The analysis of its sequence, subcellular localization, promoter cis-elements, and expression patterns revealed the potential function of MdATG9 in response to abiotic stressors. Overexpression of MdATG9 in apple callus conferred enhanced tolerance to nitrogen depletion stress. During the treatment, other important MdATGs were expressed at higher levels in transgenic callus than in the wild type. Furthermore, more free amino acids and increased sucrose levels were found in MdATG9-overexpression apple callus compared with the wild type in response to nitrogen starvation, and the expression levels of MdNRT1.1, MdNRT2.5, MdNIA1, and MdNIA2 were all increased higher in transgenic lines. These data suggest that, as an important autophagy gene, MdATG9 plays an important role in the maintenance of amino acids and sugars in response to nutrient starvation in apple.
Collapse
|
72
|
Goto-Yamada S, Oikawa K, Bizan J, Shigenobu S, Yamaguchi K, Mano S, Hayashi M, Ueda H, Hara-Nishimura I, Nishimura M, Yamada K. Sucrose Starvation Induces Microautophagy in Plant Root Cells. FRONTIERS IN PLANT SCIENCE 2019; 10:1604. [PMID: 31850051 PMCID: PMC6901504 DOI: 10.3389/fpls.2019.01604] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/14/2019] [Indexed: 05/26/2023]
Abstract
Autophagy is an essential system for degrading and recycling cellular components for survival during starvation conditions. Under sucrose starvation, application of a papain protease inhibitor E-64d to the Arabidopsis root and tobacco BY-2 cells induced the accumulation of vesicles, labeled with a fluorescent membrane marker FM4-64. The E-64d-induced vesicle accumulation was reduced in the mutant defective in autophagy-related genes ATG2, ATG5, and ATG7, suggesting autophagy is involved in the formation of these vesicles. To clarify the formation of these vesicles in detail, we monitored time-dependent changes of tonoplast, and vesicle accumulation in sucrose-starved cells. We found that these vesicles were derived from the tonoplast and produced by microautophagic process. The tonoplast proteins were excluded from the vesicles, suggesting that the vesicles are generated from specific membrane domains. Concanamycin A treatment in GFP-ATG8a transgenic plants showed that not all FM4-64-labeled vesicles, which were derived from the tonoplast, contained the ATG8a-containing structure. These results suggest that ATG8a may not always be necessary for microautophagy.
Collapse
Affiliation(s)
- Shino Goto-Yamada
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Kazusato Oikawa
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
| | - Jakub Bizan
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Katsushi Yamaguchi
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Makoto Hayashi
- Department of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Japan
| | - Haruko Ueda
- Faculty of Science and Engineering, Konan University, Kobe, Japan
| | | | - Mikio Nishimura
- Faculty of Science and Engineering, Konan University, Kobe, Japan
| | - Kenji Yamada
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| |
Collapse
|
73
|
Zeng Y, Li B, Lin Y, Jiang L. The interplay between endomembranes and autophagy in plants. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:14-22. [PMID: 31344498 DOI: 10.1016/j.pbi.2019.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/08/2019] [Accepted: 05/22/2019] [Indexed: 06/10/2023]
Abstract
Autophagosomes are unique double-membrane organelles that enclose a portion of intracellular components for lysosome/vacuole delivery to maintain cellular homeostasis in eukaryotic cells. Genetic screening has revealed the requirement of autophagy-related proteins for autophagosome formation, although the origin of the autophagosome membrane remains elusive. The endomembrane system is a series of membranous organelles maintained by dynamic membrane flow between various compartments. In plants, there is accumulating evidence pointing to a link between autophagy and the endomembrane system, in particular between the endoplasmic reticulum and autophagosome. Here, we highlight and discuss about recent findings on plant autophagosome formation. We also look into the functional roles of endomembrane machineries in regard to the autophagy pathway in plants.
Collapse
Affiliation(s)
- Yonglun Zeng
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Baiying Li
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Youshun Lin
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong; The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China.
| |
Collapse
|
74
|
Huang X, Zheng C, Liu F, Yang C, Zheng P, Lu X, Tian J, Chung T, Otegui MS, Xiao S, Gao C, Vierstra RD, Li F. Genetic Analyses of the Arabidopsis ATG1 Kinase Complex Reveal Both Kinase-Dependent and Independent Autophagic Routes during Fixed-Carbon Starvation. THE PLANT CELL 2019; 31:2973-2995. [PMID: 31615848 PMCID: PMC6925010 DOI: 10.1105/tpc.19.00066] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 09/04/2019] [Accepted: 10/14/2019] [Indexed: 05/16/2023]
Abstract
Under nutrient and energy-limiting conditions, plants up-regulate sophisticated catabolic pathways such as autophagy to remobilize nutrients and restore energy homeostasis. Autophagic flux is tightly regulated under these circumstances through the AuTophaGy-related1 (ATG1) kinase complex, which relays upstream nutrient and energy signals to the downstream components that drive autophagy. Here, we investigated the role(s) of the Arabidopsis (Arabidopsis thaliana) ATG1 kinase during autophagy through an analysis of a quadruple mutant deficient in all four ATG1 isoforms. These isoforms appear to act redundantly, including the plant-specific, truncated ATG1t variant, and like other well-characterized atg mutants, homozygous atg1abct quadruple mutants display early leaf senescence and hypersensitivity to nitrogen and fixed-carbon starvations. Although ATG1 kinase is essential for up-regulating autophagy under nitrogen deprivation and short-term carbon starvation, it did not stimulate autophagy under prolonged carbon starvation. Instead, an ATG1-independent response arose requiring phosphatidylinositol-3-phosphate kinase (PI3K) and SUCROSE NONFERMENTING1-RELATED PROTEIN KINASE1 (SnRK1), possibly through phosphorylation of the ATG6 subunit within the PI3K complex by the catalytic KIN10 subunit of SnRK1. Together, our data connect ATG1 kinase to autophagy and reveal that plants engage multiple pathways to activate autophagy during nutrient stress, which include the ATG1 route as well as an alternative route requiring SnRK1 and ATG6 signaling.plantcell;31/12/2973/FX1F1fx1.
Collapse
Affiliation(s)
- Xiao Huang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Chunyan Zheng
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Fen Liu
- Department of Biology, Washington University, St. Louis, Missouri 63130
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Chao Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Ping Zheng
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xing Lu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Taijoon Chung
- Department of Biological Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706
- Laboratory of Cell and Molecular Biology, University of Wisconsin, Madison, Wisconsin 53706
| | - Shi Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | | | - Faqiang Li
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
75
|
Chen Q, Shinozaki D, Luo J, Pottier M, Havé M, Marmagne A, Reisdorf-Cren M, Chardon F, Thomine S, Yoshimoto K, Masclaux-Daubresse C. Autophagy and Nutrients Management in Plants. Cells 2019; 8:cells8111426. [PMID: 31726766 PMCID: PMC6912637 DOI: 10.3390/cells8111426] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/07/2019] [Accepted: 11/09/2019] [Indexed: 02/07/2023] Open
Abstract
Nutrient recycling and mobilization from organ to organ all along the plant lifespan is essential for plant survival under changing environments. Nutrient remobilization to the seeds is also essential for good seed production. In this review, we summarize the recent advances made to understand how plants manage nutrient remobilization from senescing organs to sink tissues and what is the contribution of autophagy in this process. Plant engineering manipulating autophagy for better yield and plant tolerance to stresses will be presented.
Collapse
Affiliation(s)
- Qinwu Chen
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France; (Q.C.); (J.L.); (M.H.); (A.M.); (M.R.-C.); (F.C.)
| | - Daiki Shinozaki
- Department of Life Science, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan; (D.S.); (K.Y.)
- Life Science Program, Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Jie Luo
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France; (Q.C.); (J.L.); (M.H.); (A.M.); (M.R.-C.); (F.C.)
| | - Mathieu Pottier
- Institut de Biologie Intégrative de la Cellule, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France; (M.P.); (S.T.)
| | - Marien Havé
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France; (Q.C.); (J.L.); (M.H.); (A.M.); (M.R.-C.); (F.C.)
| | - Anne Marmagne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France; (Q.C.); (J.L.); (M.H.); (A.M.); (M.R.-C.); (F.C.)
| | - Michèle Reisdorf-Cren
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France; (Q.C.); (J.L.); (M.H.); (A.M.); (M.R.-C.); (F.C.)
| | - Fabien Chardon
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France; (Q.C.); (J.L.); (M.H.); (A.M.); (M.R.-C.); (F.C.)
| | - Sébastien Thomine
- Institut de Biologie Intégrative de la Cellule, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France; (M.P.); (S.T.)
| | - Kohki Yoshimoto
- Department of Life Science, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan; (D.S.); (K.Y.)
- Life Science Program, Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Céline Masclaux-Daubresse
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France; (Q.C.); (J.L.); (M.H.); (A.M.); (M.R.-C.); (F.C.)
- Correspondence: ; Tel.: +33-13083-3088
| |
Collapse
|
76
|
Xu T, Yan W, Wu Q, Xu Q, Yuan J, Li Y, Li P, Pan H, Ni C. MiR-326 Inhibits Inflammation and Promotes Autophagy in Silica-Induced Pulmonary Fibrosis through Targeting TNFSF14 and PTBP1. Chem Res Toxicol 2019; 32:2192-2203. [DOI: 10.1021/acs.chemrestox.9b00194] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Tiantian Xu
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Weiwen Yan
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Qiuyun Wu
- School of Public Health, Xuzhou Medical University, Xuzhou 221004, China
| | - Qi Xu
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jiali Yuan
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Yan Li
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Ping Li
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Honghong Pan
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Chunhui Ni
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| |
Collapse
|
77
|
Shull TE, Kurepa J, Smalle JA. Anatase TiO 2 Nanoparticles Induce Autophagy and Chloroplast Degradation in Thale Cress ( Arabidopsis thaliana). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:9522-9532. [PMID: 31356742 DOI: 10.1021/acs.est.9b01648] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The extensive use of TiO2 nanoparticles and their subsequent release into the environment have posed an important question about the effects of this nanomaterial on ecosystems. Here, we analyzed the link between the damaging effects of reactive oxygen species generated by TiO2 nanoparticles and autophagy, a housekeeping mechanism that removes damaged cellular constituents. We show that TiO2 nanoparticles induce autophagy in the plant model system Arabidopsis thaliana and that autophagy is an important mechanism for managing TiO2 nanoparticle-induced oxidative stress. Additionally, we find that TiO2 nanoparticles induce oxidative stress predominantly in chloroplasts and that this chloroplastic stress is mitigated by autophagy. Collectively, our results suggest that photosynthetic organisms are particularly susceptible to TiO2 nanoparticle toxicity.
Collapse
Affiliation(s)
- Timothy E Shull
- Department of Plant and Soil Sciences , University of Kentucky , Lexington , Kentucky 40546 United States
| | - Jasmina Kurepa
- Department of Plant and Soil Sciences , University of Kentucky , Lexington , Kentucky 40546 United States
| | - Jan A Smalle
- Department of Plant and Soil Sciences , University of Kentucky , Lexington , Kentucky 40546 United States
| |
Collapse
|
78
|
Han Z, Wang W, Lv X, Zong Y, Liu S, Liu Z, Wang L, Song L. ATG10 (autophagy-related 10) regulates the formation of autophagosome in the anti-virus immune response of pacific oyster (Crassostrea gigas). FISH & SHELLFISH IMMUNOLOGY 2019; 91:325-332. [PMID: 31128297 DOI: 10.1016/j.fsi.2019.05.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
Autophagy, a highly conserved intracellular degradation system, is involved in numerous processes in vertebrate and invertebrate, such as cell survival, ageing, and immune responses. However, the detailed molecular mechanism of autophagy and its immune regulatory role in bivalves are still not well understood. In the present study, an autophagy-related protein ATG10 (designated as CgATG10) was identified from Pacific oyster Crassostrea gigas. The open reading frame of CgATG10 cDNA was of 621 bp, encoding a polypeptide of 206 amino acid residues with an Autophagy_act_C domain (from 96 to 123 amino acid), which shared high homology with that from C. virginica and Octopus bimaculoides. The mRNA transcripts of CgATG10 were widely expressed in all the tested tissues including mantle, gonad, gills, hemocytes and hepatopancreas, with the highest expression level in mantle. After the stimulation with poly (I:C), the mRNA expression level of CgATG10 in the mantle of oysters was significantly up-regulated (4.92-fold of that in Blank group, p < 0.05), and the LC3-conversion from LC3-I to LC3-II (LC3-II/LC3-I) also increased. After an additional injection of dsRNA to knock-down the expression of CgATG10 (0.33-fold and 0.10-fold compared respectively with Blank group and dsGFP group, p < 0.05), the downstream conversion of CgLC3 was inhibited significantly compared with that of the control dsGFP group, while the expression level of autophagy-initiator CgBeclin1 did not change significantly. In addition, the mRNA transcripts of interferon regulatory factor CgIRF-1 increased significantly in CgATG10-knockdown oysters at 12 h post poly (I:C) stimulation. All the results indicated that CgATG10 might participate in the immune response against poly (I:C) by regulating autophagosome formation and interferon system in oysters.
Collapse
Affiliation(s)
- Zirong Han
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Weilin Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
| | - Xiaojing Lv
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Yanan Zong
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Shujing Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Zhaoqun Liu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Functional Laboratory of Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China.
| |
Collapse
|
79
|
Buet A, Costa ML, Martínez DE, Guiamet JJ. Chloroplast Protein Degradation in Senescing Leaves: Proteases and Lytic Compartments. FRONTIERS IN PLANT SCIENCE 2019; 10:747. [PMID: 31275332 PMCID: PMC6593067 DOI: 10.3389/fpls.2019.00747] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/21/2019] [Indexed: 05/20/2023]
Abstract
Leaf senescence is characterized by massive degradation of chloroplast proteins, yet the protease(s) involved is(are) not completely known. Increased expression and/or activities of serine, cysteine, aspartic, and metalloproteases were detected in senescing leaves, but these studies have not provided information on the identities of the proteases responsible for chloroplast protein breakdown. Silencing some senescence-associated proteases has delayed progression of senescence symptoms, yet it is still unclear if these proteases are directly involved in chloroplast protein breakdown. At least four cellular pathways involved in the traffic of chloroplast proteins for degradation outside the chloroplast have been described (i.e., "Rubisco-containing bodies," "senescence-associated vacuoles," "ATI1-plastid associated bodies," and "CV-containing vesicles"), which differ in their dependence on the autophagic machinery, and the identity of the proteins transported and/or degraded. Finding out the proteases involved in, for example, the degradation of Rubisco, may require piling up mutations in several senescence-associated proteases. Alternatively, targeting a proteinaceous protein inhibitor to chloroplasts may allow the inhibitor to reach "Rubisco-containing bodies," "senescence-associated vacuoles," "ATI1-plastid associated bodies," and "CV-containing vesicles" in essentially the way as chloroplast-targeted fluorescent proteins re-localize to these vesicular structures. This might help to reduce proteolytic activity, thereby reducing or slowing down plastid protein degradation during senescence.
Collapse
Affiliation(s)
- Agustina Buet
- Instituto de Fisiología Vegetal (INFIVE, CONICET-UNLP), La Plata, Argentina
| | - M Lorenza Costa
- Instituto de Fisiología Vegetal (INFIVE, CONICET-UNLP), La Plata, Argentina
| | - Dana E Martínez
- Instituto de Fisiología Vegetal (INFIVE, CONICET-UNLP), La Plata, Argentina
| | - Juan J Guiamet
- Instituto de Fisiología Vegetal (INFIVE, CONICET-UNLP), La Plata, Argentina
| |
Collapse
|
80
|
Yang M, Bu F, Huang W, Chen L. Multiple Regulatory Levels Shape Autophagy Activity in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:532. [PMID: 31068964 PMCID: PMC6491747 DOI: 10.3389/fpls.2019.00532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/05/2019] [Indexed: 05/29/2023]
Abstract
Autophagy is a strictly regulated pathway involving the degradation of cytoplasmic organelles and proteins. Most autophagy-related genes have been identified in plants based on sequence similarity to homologues in yeast and mammals. In addition, the molecular mechanisms underlying plant autophagy have been extensively studied in the last decade. Plant autophagy plays an important role in various stress responses, pathogen defense, and developmental processes such as seed germination, pollen maturation, and leaf senescence. However, the regulatory mechanisms of autophagy in plants remain poorly understood. Recent studies have identified several plant autophagy regulators, which modify autophagy activity at transcriptional, post-transcriptional, and post-translational levels. In this review, we summarize recent advances in understanding regarding regulatory network of plant autophagy and future directions in autophagy research.
Collapse
|
81
|
Marshall RS, Hua Z, Mali S, McLoughlin F, Vierstra RD. ATG8-Binding UIM Proteins Define a New Class of Autophagy Adaptors and Receptors. Cell 2019; 177:766-781.e24. [PMID: 30955882 DOI: 10.1016/j.cell.2019.02.009] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/14/2019] [Accepted: 02/08/2019] [Indexed: 01/02/2023]
Abstract
During autophagy, vesicle dynamics and cargo recruitment are driven by numerous adaptors and receptors that become tethered to the phagophore through interactions with lipidated ATG8/LC3 decorating the expanding membrane. Most currently described ATG8-binding proteins exploit a well-defined ATG8-interacting motif (AIM, or LC3-interacting region [LIR]) that contacts a hydrophobic patch on ATG8 known as the LIR/AIM docking site (LDS). Here we describe a new class of ATG8 interactors that exploit ubiquitin-interacting motif (UIM)-like sequences for high-affinity binding to an alternative ATG8 interaction site. Assays with candidate UIM-containing proteins together with unbiased screens identified a large collection of UIM-based ATG8 interactors in plants, yeast, and humans. Analysis of a subset also harboring ubiquitin regulatory X (UBX) domains revealed a role for UIM-directed autophagy in clearing non-functional CDC48/p97 complexes, including some impaired in human disease. With this new class of adaptors and receptors, we greatly extend the reach of selective autophagy and identify new factors regulating autophagic vesicle dynamics.
Collapse
Affiliation(s)
- Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| | - Sujina Mali
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
| |
Collapse
|
82
|
Wang H, Schippers JHM. The Role and Regulation of Autophagy and the Proteasome During Aging and Senescence in Plants. Genes (Basel) 2019; 10:genes10040267. [PMID: 30987024 PMCID: PMC6523301 DOI: 10.3390/genes10040267] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/06/2019] [Accepted: 03/27/2019] [Indexed: 12/18/2022] Open
Abstract
Aging and senescence in plants has a major impact on agriculture, such as in crop yield, the value of ornamental crops, and the shelf life of vegetables and fruits. Senescence represents the final developmental phase of the leaf and inevitably results in the death of the organ. Still, the process is completely under the control of the plant. Plants use their protein degradation systems to maintain proteostasis and transport or salvage nutrients from senescing organs to develop reproductive parts. Herein, we present an overview of current knowledge about the main protein degradation pathways in plants during senescence: The proteasome and autophagy. Although both pathways degrade proteins, autophagy appears to prevent aging, while the proteasome functions as a positive regulator of senescence.
Collapse
Affiliation(s)
- Haojie Wang
- Institute of Biology I, RWTH Aachen University, 52074 Aachen, Germany.
| | - Jos H M Schippers
- Institute of Biology I, RWTH Aachen University, 52074 Aachen, Germany.
| |
Collapse
|
83
|
Chung T. How phosphoinositides shape autophagy in plant cells. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:146-158. [PMID: 30824047 DOI: 10.1016/j.plantsci.2019.01.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/10/2019] [Accepted: 01/19/2019] [Indexed: 05/06/2023]
Abstract
Plant cells use autophagy to degrade their own cytoplasm in vacuoles, thereby not only recycling their breakdown products, but also ensuring the homeostasis of essential cytoplasmic constituents and organelles. Plants and other eukaryotes have a conserved set of core Autophagy-related (ATG) genes involved in the biogenesis of the autophagosome, the main autophagic compartment destined for the lytic vacuole. In the past decade, the core ATG genes were isolated from several plant species. The core ATG proteins include the components of the VACUOLAR PROTEIN SORTING 34 (VPS34) complex that is responsible for the local production of phosphatidylinositol 3-phosphate (PI3P) at the site of autophagosome formation. Dissecting the roles of PI3P and its effectors in autophagy is challenging, because of the multi-faceted links between autophagosomal and endosomal systems. This review highlights recent studies on putative plant PI3P effectors involved in autophagosome dynamics. Molecular mechanisms underlying the requirement of PI3P for autophagosome biogenesis and trafficking are also discussed.
Collapse
Affiliation(s)
- Taijoon Chung
- Department of Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea.
| |
Collapse
|
84
|
Izumi M, Nakamura S, Li N. Autophagic Turnover of Chloroplasts: Its Roles and Regulatory Mechanisms in Response to Sugar Starvation. FRONTIERS IN PLANT SCIENCE 2019; 10:280. [PMID: 30967883 PMCID: PMC6439420 DOI: 10.3389/fpls.2019.00280] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 02/20/2019] [Indexed: 05/29/2023]
Abstract
Photosynthetic reactions in chloroplasts convert atmospheric carbon dioxide into starch and soluble sugars during the day. Starch, a transient storage form of sugar, is broken down into sugars as a source for respiratory energy production at night. Chloroplasts thus serve as the main sites of sugar production for photoautotrophic plant growth. Autophagy is an evolutionarily conserved intracellular process in eukaryotes that degrades organelles and proteins. Numerous studies have shown that autophagy is actively induced in sugar-starved plants. When photosynthetic sugar production is inhibited by environmental cues, chloroplasts themselves may become an attractive alternative energy source to sugars via their degradation. Here, we summarize the process of autophagic turnover of chloroplasts and its roles in plants in response to sugar starvation. We hypothesize that piecemeal-type chloroplast autophagy is specifically activated in plants in response to sugar starvation.
Collapse
Affiliation(s)
- Masanori Izumi
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Sakuya Nakamura
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Nan Li
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
- College of Life Sciences, Liaocheng University, Liaocheng, China
| |
Collapse
|
85
|
Young PG, Passalacqua MJ, Chappell K, Llinas RJ, Bartel B. A facile forward-genetic screen for Arabidopsis autophagy mutants reveals twenty-one loss-of-function mutations disrupting six ATG genes. Autophagy 2019; 15:941-959. [PMID: 30734619 PMCID: PMC6526838 DOI: 10.1080/15548627.2019.1569915] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Macroautophagy is a process through which eukaryotic cells degrade large substrates including organelles, protein aggregates, and invading pathogens. Over 40 autophagy-related (ATG) genes have been identified through forward-genetic screens in yeast. Although homology-based analyses have identified conserved ATG genes in plants, only a few atg mutants have emerged from forward-genetic screens in Arabidopsis thaliana. We developed a screen that consistently recovers Arabidopsis atg mutations by exploiting mutants with defective LON2/At5g47040, a protease implicated in peroxisomal quality control. Arabidopsis lon2 mutants exhibit reduced responsiveness to the peroxisomally-metabolized auxin precursor indole-3-butyric acid (IBA), heightened degradation of several peroxisomal matrix proteins, and impaired processing of proteins harboring N-terminal peroxisomal targeting signals; these defects are ameliorated by preventing autophagy. We optimized a lon2 suppressor screen to expedite recovery of additional atg mutants. After screening mutagenized lon2-2 seedlings for restored IBA responsiveness, we evaluated stabilization and processing of peroxisomal proteins, levels of several ATG proteins, and levels of the selective autophagy receptor NBR1/At4g24690, which accumulates when autophagy is impaired. We recovered 21 alleles disrupting 6 ATG genes: ATG2/At3g19190, ATG3/At5g61500, ATG5/At5g17290, ATG7/At5g45900, ATG16/At5g50230, and ATG18a/At3g62770. Twenty alleles were novel, and 3 of the mutated genes lack T-DNA insertional alleles in publicly available repositories. We also demonstrate that an insertional atg11/At4g30790 allele incompletely suppresses lon2 defects. Finally, we show that NBR1 is not necessary for autophagy of lon2 peroxisomes and that NBR1 overexpression is not sufficient to trigger autophagy of seedling peroxisomes, indicating that Arabidopsis can use an NBR1-independent mechanism to target peroxisomes for autophagic degradation. Abbreviations: ATG: autophagy-related; ATI: ATG8-interacting protein; Col-0: Columbia-0; DSK2: dominant suppressor of KAR2; EMS: ethyl methanesulfonate; GFP: green fluorescent protein; IAA: indole-3-acetic acid; IBA: indole-3-butyric acid; ICL: isocitrate lyase; MLS: malate synthase; NBR1: Next to BRCA1 gene 1; PEX: peroxin; PMDH: peroxisomal malate dehydrogenase; PTS: peroxisomal targeting signal; thiolase: 3-ketoacyl-CoA thiolase; UBA: ubiquitin-associated; WT: wild type
Collapse
Affiliation(s)
- Pierce G Young
- a Department of Biosciences , Rice University , Houston , TX , USA
| | | | - Kevin Chappell
- a Department of Biosciences , Rice University , Houston , TX , USA.,b Department of Biology , University of Mary Hardin-Baylor , Belton , TX , USA
| | - Roxanna J Llinas
- a Department of Biosciences , Rice University , Houston , TX , USA
| | - Bonnie Bartel
- a Department of Biosciences , Rice University , Houston , TX , USA
| |
Collapse
|
86
|
Jia M, Liu X, Xue H, Wu Y, Shi L, Wang R, Chen Y, Xu N, Zhao J, Shao J, Qi Y, An L, Sheen J, Yu F. Noncanonical ATG8-ABS3 interaction controls senescence in plants. NATURE PLANTS 2019; 5:212-224. [PMID: 30664732 PMCID: PMC6368864 DOI: 10.1038/s41477-018-0348-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 12/13/2018] [Indexed: 05/18/2023]
Abstract
Protein homeostasis is essential for cellular functions and longevity, and the loss of proteostasis is one of the hallmarks of senescence. Autophagy is an evolutionarily conserved cellular degradation pathway that is critical for the maintenance of proteostasis. Paradoxically, autophagy deficiency leads to accelerated protein loss by unknown mechanisms. We discover that the ABNORMAL SHOOT3 (ABS3) subfamily of multidrug and toxic compound extrusion transporters promote senescence under natural and carbon-deprivation conditions in Arabidopsis thaliana. The senescence-promoting ABS3 pathway functions in parallel with the longevity-promoting autophagy to balance plant senescence and survival. Surprisingly, ABS3 subfamily multidrug and toxic compound extrusion proteins interact with AUTOPHAGY-RELATED PROTEIN 8 (ATG8) at the late endosome to promote senescence and protein degradation without canonical cleavage and lipidation of ATG8. This non-autophagic ATG8-ABS3 interaction paradigm is probably conserved among dicots and monocots. Our findings uncover a previously unknown non-autophagic function of ATG8 and an unrecognized senescence regulatory pathway controlled by ATG8-ABS3-mediated proteostasis.
Collapse
Affiliation(s)
- Min Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiayan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Hui Xue
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yue Wu
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lin Shi
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Rui Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- Department of Molecular Genetics, Center for Applied Plant Science, Ohio State University, Columbus, OH, USA
| | - Yu Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ni Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Jun Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Jingxia Shao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yafei Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Lijun An
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Fei Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| |
Collapse
|
87
|
Wang Y, Cao JJ, Wang KX, Xia XJ, Shi K, Zhou YH, Yu JQ, Zhou J. BZR1 Mediates Brassinosteroid-Induced Autophagy and Nitrogen Starvation in Tomato. PLANT PHYSIOLOGY 2019; 179:671-685. [PMID: 30482787 PMCID: PMC6426427 DOI: 10.1104/pp.18.01028] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/13/2018] [Indexed: 05/10/2023]
Abstract
Autophagy, an innate cellular destructive mechanism, plays crucial roles in plant development and responses to stress. Autophagy is known to be stimulated or suppressed by multiple molecular processes, but the role of phytohormone signaling in autophagy is unclear. Here, we demonstrate that the transcripts of autophagy-related genes (ATGs) and the formation of autophagosomes are triggered by enhanced levels of brassinosteroid (BR). Furthermore, the BR-activated transcription factor brassinazole-resistant1 (BZR1), a positive regulator of the BR signaling pathway, is involved in BR-induced autophagy. Treatment with BR enhanced the formation of autophagosomes and the transcripts of ATGs in BZR1-overexpressing plants, while the effects of BR were compromised in BZR1-silenced plants. Yeast one-hybrid analysis and chromatin immunoprecipitation coupled with quantitative polymerase chain reaction revealed that BZR1 bound to the promoters of ATG2 and ATG6 The BR-induced formation of autophagosomes decreased in ATG2- and ATG6-silenced plants. Moreover, exogenous application of BR enhanced chlorophyll content and autophagosome formation and decreased the accumulation of ubiquitinated proteins under nitrogen starvation. Leaf chlorosis and chlorophyll degradation were exacerbated in BZR1-silenced plants and the BR biosynthetic mutant d^im but were alleviated in BZR1- and BZR1-1D-overexpressing plants under nitrogen starvation. Meanwhile, nitrogen starvation-induced expression of ATGs and autophagosome formation were compromised in both BZR1-silenced and d^im plants but were increased in BZR1- and BZR1-1D-overexpressing plants. Taken together, our results suggest that BZR1-dependent BR signaling up-regulates the expression of ATGs and autophagosome formation, which plays a critical role in the plant response to nitrogen starvation in tomato (Solanum lycopersicum).
Collapse
Affiliation(s)
- Yu Wang
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jia-Jian Cao
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
| | - Kai-Xin Wang
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
| | - Xiao-Jian Xia
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
| | - Kai Shi
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
| | - Yan-Hong Zhou
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
| | - Jing-Quan Yu
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Horticultural Plants Growth, Development, and Quality Improvement, Agricultural Ministry of China, Hangzhou 310058, China
| | - Jie Zhou
- Department of Horticulture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
88
|
Chen Q, Soulay F, Saudemont B, Elmayan T, Marmagne A, Masclaux-Daubresse CL. Overexpression of ATG8 in Arabidopsis Stimulates Autophagic Activity and Increases Nitrogen Remobilization Efficiency and Grain Filling. PLANT & CELL PHYSIOLOGY 2019; 60:343-352. [PMID: 30407574 DOI: 10.1093/pcp/pcy214] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/27/2018] [Indexed: 05/20/2023]
Abstract
Autophagy knock-out mutants in maize and in Arabidopsis are impaired in nitrogen (N) recycling and exhibit reduced levels of N remobilization to their seeds. It is thus impoortant to determine whether higher autophagy activity could, conversely, improve N remobilization efficiency and seed protein content, and under what circumstances. As the autophagy machinery involves many genes amongst which 18 are important for the core machinery, the choice of which AUTOPHAGY (ATG) gene to manipulate to increase autophagy was examined. We choose ATG8 overexpression since it has been shown that this gene could increase autophagosome size and autophagic activity in yeast. The results we report here are original as they show for the first time that increasing ATG8 gene expression in plants increases autophagosome number and promotes autophagy activity. More importantly, our data demonstrate that, when cultivated under full nitrate conditions, known to repress N remobilization due to sufficient N uptake from the soil, N remobilization efficiency can nevertheless be sharply and significantly increased by overexpressing ATG8 genomic sequences under the control of the ubiquitin promoter. We show that overexpressors have improved seed N% and at the same time reduced N waste in their dry remains. In addition, we show that overexpressing ATG8 does not modify vegetative biomass or harvest index, and thus does not affect plant development.
Collapse
Affiliation(s)
- Qinwu Chen
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Fabienne Soulay
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Baptiste Saudemont
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Taline Elmayan
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Anne Marmagne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | | |
Collapse
|
89
|
Janse van Rensburg HC, Van den Ende W, Signorelli S. Autophagy in Plants: Both a Puppet and a Puppet Master of Sugars. FRONTIERS IN PLANT SCIENCE 2019; 10:14. [PMID: 30723485 PMCID: PMC6349728 DOI: 10.3389/fpls.2019.00014] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/07/2019] [Indexed: 05/20/2023]
Abstract
Autophagy is a major pathway that recycles cellular components in eukaryotic cells both under stressed and non-stressed conditions. Sugars participate both metabolically and as signaling molecules in development and response to various environmental and nutritional conditions. It is therefore essential to maintain metabolic homeostasis of sugars during non-stressed conditions in cells, not only to provide energy, but also to ensure effective signaling when exposed to stress. In both plants and animals, autophagy is activated by the energy sensor SnRK1/AMPK and inhibited by TOR kinase. SnRK1/AMPK and TOR kinases are both important regulators of cellular metabolism and are controlled to a large extent by the availability of sugars and sugar-phosphates in plants whereas in animals AMP/ATP indirectly translate sugar status. In plants, during nutrient and sugar deficiency, SnRK1 is activated, and TOR is inhibited to allow activation of autophagy which in turn recycles cellular components in an attempt to provide stress relief. Autophagy is thus indirectly regulated by the nutrient/sugar status of cells, but also regulates the level of nutrients/sugars by recycling cellular components. In both plants and animals sugars such as trehalose induce autophagy and in animals this is independent of the TOR pathway. The glucose-activated G-protein signaling pathway has also been demonstrated to activate autophagy, although the exact mechanism is not completely clear. This mini-review will focus on the interplay between sugar signaling and autophagy.
Collapse
Affiliation(s)
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, KU Leuven, Leuven, Belgium
| | - Santiago Signorelli
- Laboratory of Molecular Plant Biology, KU Leuven, Leuven, Belgium
- Departamento de Biologiía Vegetal, Facultad de Agronomía, Universidad de la Repuíblica, Montevideo, Uruguay
| |
Collapse
|
90
|
Abstract
As a major intracellular degradation pathway, autophagy contributes to nutrient recycling and is indispensable during plant senescence. Here we describe methods used for investigating the autophagic process during leaf senescence. These include transcript analysis of core machinery autophagy genes, immunoblotting of ATG8, and microscopic observation of autophagosome formation.
Collapse
|
91
|
Guan B, Lin Z, Liu D, Li C, Zhou Z, Mei F, Li J, Deng X. Effect of Waterlogging-Induced Autophagy on Programmed Cell Death in Arabidopsis Roots. FRONTIERS IN PLANT SCIENCE 2019; 10:468. [PMID: 31031792 PMCID: PMC6470631 DOI: 10.3389/fpls.2019.00468] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 03/28/2019] [Indexed: 05/18/2023]
Abstract
Autophagy, a highly conserved process in eukaryotes that involves vacuolar degradation of intracellular components and decomposition of damaged or toxic constituents, is induced by endogenous reactive oxygen species (ROS) accumulation, endoplasmic reticulum stress, and other factors. In plants, the role of autophagy in the induction of programmed cell death (PCD) is still unclear. Here, we show that ROS contribute to the regulation of PCD during waterlogging (which results in oxygen depletion) via autophagy. In wild-type roots, waterlogging induces the transcription of hypoxia-responsive genes and respiratory burst oxidase homolog (RBOH)-mediated ROS production. It also altered the transcription level of alternative oxidase1a and the activity level of antioxidant enzymes. Moreover, waterlogging increased the transcription levels of autophagy-related (ATG) genes and the number of autophagosomes. Autophagy first occurred in the root stele, and then autophagosomes appeared at other locations in the root. In rboh mutants, upregulation of autophagosomes was less pronounced than in the wild type upon waterlogging. However, the accumulation of ROS and the level of cell death in the roots of atg mutants were higher than those in the wild type after waterlogging. In conclusion, our results suggest that autophagy induced in Arabidopsis roots during waterlogging has an attenuating effect on PCD in the roots.
Collapse
Affiliation(s)
- Bin Guan
- Laboratory of Cell Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ze Lin
- Laboratory of Cell Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dongcheng Liu
- Laboratory of Cell Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengyang Li
- Laboratory of Cell Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhuqing Zhou
- Laboratory of Cell Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Zhuqing Zhou,
| | - Fangzhu Mei
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiwei Li
- College of Food and Biological Science and Technology, Wuhan Institute of Design and Sciences, Wuhan, China
| | - Xiangyi Deng
- College of Food and Biological Science and Technology, Wuhan Institute of Design and Sciences, Wuhan, China
| |
Collapse
|
92
|
Norizuki T, Kanazawa T, Minamino N, Tsukaya H, Ueda T. Marchantia polymorpha, a New Model Plant for Autophagy Studies. FRONTIERS IN PLANT SCIENCE 2019; 10:935. [PMID: 31379911 PMCID: PMC6652269 DOI: 10.3389/fpls.2019.00935] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/03/2019] [Indexed: 05/18/2023]
Abstract
Autophagy is a catabolic process for bulk and selective degradation of cytoplasmic components in the vacuole/lysosome. In Saccharomyces cerevisiae, ATG genes were identified as essential genes for autophagy, and most ATG genes are highly conserved among eukaryotes, including plants. Although reverse genetic analyses have revealed that autophagy is involved in responses to abiotic and biotic stresses in land plants, our knowledge of its molecular mechanism remains limited. This limitation is partly because of the multiplication of some ATG genes, including ATG8, in widely used model plants such as Arabidopsis thaliana, which adds complexity to functional studies. Furthermore, due to limited information on the composition and functions of the ATG genes in basal land plants and charophytes, it remains unclear whether multiplication of ATG genes is associated with neofunctionalization of these genes. To gain insight into the diversification of ATG genes during plant evolution, we compared the composition of ATG genes in plants with a special focus on a liverwort and two charophytes, which have not previously been analyzed. Our results showed that the liverwort Marchantia polymorpha and the charophytes Klebsormidium nitens and Chara braunii harbor fundamental sets of ATG genes with low redundancy compared with those of A. thaliana and the moss Physcomitrella patens, suggesting that multiplication of ATG genes occurred during land plant evolution. We also attempted to establish an experimental system for analyzing autophagy in M. polymorpha. We generated transgenic plants expressing fluorescently tagged MpATG8 to observe its dynamics in M. polymorpha and produced autophagy-defective mutants by genome editing using the CRISPR/Cas9 system. These tools allowed us to demonstrate that MpATG8 is transported into the vacuole in an MpATG2-, MpATG5-, and MpATG7-dependent manner, suggesting that fluorescently tagged MpATG8 can be used as an autophagosome marker in M. polymorpha. M. polymorpha can provide a powerful system for studying the mechanisms and evolution of autophagy in plants.
Collapse
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
| | - Takehiko Kanazawa
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
| | - Naoki Minamino
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
- *Correspondence: Takashi Ueda,
| |
Collapse
|
93
|
Kajikawa M, Yamauchi M, Shinkawa H, Tanaka M, Hatano K, Nishimura Y, Kato M, Fukuzawa H. Isolation and Characterization of Chlamydomonas Autophagy-Related Mutants in Nutrient-Deficient Conditions. PLANT & CELL PHYSIOLOGY 2019; 60:126-138. [PMID: 30295899 DOI: 10.1093/pcp/pcy193] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 09/17/2018] [Indexed: 05/08/2023]
Abstract
Autophagy is a recycling system for amino acids and carbon- and nitrogen (N)-containing compounds. To date, the functional importance of autophagy in microalgae in nutrient-deficient conditions has not been evaluated by using autophagy-defective mutants. Here, we provide evidence which supports the following notions by characterizing an insertional mutant of the autophagy-related gene ATG8, encoding a ubiquitin-like protein necessary for the formation of the autophagosome in the green alga, Chlamydomonas reinhardtii. First, ATG8 is required for maintenance of cell survival and Chl content in N-, sulfur- and phosphate-deficient conditions. Secondly, ATG8 supports the degradation of triacylglycerol and lipid droplets after the resupply of N to cells cultured in N-limiting conditions. Thirdly, ATG8 is also necessary for accumulation of starch in phosphate-deficient conditions. Additionally, autophagy is not essential for maternal inheritance of the organelle genomes in gametogenesis.
Collapse
Affiliation(s)
| | - Marika Yamauchi
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Haruka Shinkawa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Manabu Tanaka
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Kyoko Hatano
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | | | - Misako Kato
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Hideya Fukuzawa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| |
Collapse
|
94
|
Tang J, Bassham DC. Autophagy in crop plants: what's new beyond Arabidopsis? Open Biol 2018; 8:180162. [PMID: 30518637 PMCID: PMC6303781 DOI: 10.1098/rsob.180162] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/08/2018] [Indexed: 12/19/2022] Open
Abstract
Autophagy is a major degradation and recycling pathway in plants. It functions to maintain cellular homeostasis and is induced by environmental cues and developmental stimuli. Over the past decade, the study of autophagy has expanded from model plants to crop species. Many features of the core machinery and physiological functions of autophagy are conserved among diverse organisms. However, several novel functions and regulators of autophagy have been characterized in individual plant species. In light of its critical role in development and stress responses, a better understanding of autophagy in crop plants may eventually lead to beneficial agricultural applications. Here, we review recent progress on understanding autophagy in crops and discuss potential future research directions.
Collapse
Affiliation(s)
- Jie Tang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| |
Collapse
|
95
|
Ding X, Zhang X, Otegui MS. Plant autophagy: new flavors on the menu. CURRENT OPINION IN PLANT BIOLOGY 2018; 46:113-121. [PMID: 30267997 DOI: 10.1016/j.pbi.2018.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 08/28/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Autophagy mediates the delivery of cytoplasmic content to vacuoles or lysosomes for degradation or storage. The best characterized autophagy route called macroautophagy involves the sequestration of cargo in double-membrane autophagosomes and is conserved in eukaryotes, including plants. Recently, several new receptors, some of them plant-specific, that select cargo for macroautophagy have been identified. Some of these receptors appear to participate in regulation of competing catabolic pathways, for example proteasome-mediated versus autophagic degradation under specific stress conditions. Vacuolar microautophagy, a process by which the vacuole directly engulf cytoplasmic material, also occurs in plants but its underlying molecular mechanisms are yet to be elucidated.
Collapse
Affiliation(s)
- Xinxin Ding
- Department of Botany, 430 Lincoln Drive, University of Wisconsin-Madison, WI 53706, United States; Laboratory of Molecular and Cellular Biology, 1525 Linden Drive, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Xiaoguo Zhang
- Department of Botany, 430 Lincoln Drive, University of Wisconsin-Madison, WI 53706, United States; Laboratory of Molecular and Cellular Biology, 1525 Linden Drive, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Marisa S Otegui
- Department of Botany, 430 Lincoln Drive, University of Wisconsin-Madison, WI 53706, United States; Laboratory of Molecular and Cellular Biology, 1525 Linden Drive, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Genetics, 405 Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, United States.
| |
Collapse
|
96
|
Soltabayeva A, Srivastava S, Kurmanbayeva A, Bekturova A, Fluhr R, Sagi M. Early Senescence in Older Leaves of Low Nitrate-Grown Atxdh1 Uncovers a Role for Purine Catabolism in N Supply. PLANT PHYSIOLOGY 2018; 178:1027-1044. [PMID: 30190419 PMCID: PMC6236613 DOI: 10.1104/pp.18.00795] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/25/2018] [Indexed: 05/19/2023]
Abstract
The nitrogen (N)-rich ureides allantoin and allantoate, which are products of purine catabolism, play a role in N delivery in Leguminosae. Here, we examined their role as an N source in nonlegume plants using Arabidopsis (Arabidopsis thaliana) plants mutated in XANTHINE DEHYDROGENASE1 (AtXDH1), a catalytic bottleneck in purine catabolism. Older leaves of the Atxdh1 mutant exhibited early senescence, lower soluble protein, and lower organic N levels as compared with wild-type older leaves when grown with 1 mm nitrate but were comparable to the wild type under 5 mm nitrate. Similar nitrate-dependent senescence phenotypes were evident in the older leaves of allantoinase (Ataln) and allantoate amidohydrolase (Ataah) mutants, which also are impaired in purine catabolism. Under low-nitrate conditions, xanthine accumulated in older leaves of Atxdh1, whereas allantoin accumulated in both older and younger leaves of Ataln but not in wild-type leaves, indicating the remobilization of xanthine-degraded products from older to younger leaves. Supporting this notion, ureide transporter expression was enhanced in older leaves of the wild type in low-nitrate as compared with high-nitrate conditions. Elevated transcripts and proteins of AtXDH and AtAAH were detected in low-nitrate-grown wild-type plants, indicating regulation at protein and transcript levels. The higher nitrate reductase activity in Atxdh1 leaves compared with wild-type leaves indicated a need for nitrate assimilation products. Together, these results indicate that the absence of remobilized purine-degraded N from older leaves of Atxdh1 caused senescence symptoms, a result of higher chloroplastic protein degradation in older leaves of low-nitrate-grown plants.
Collapse
Affiliation(s)
- Aigerim Soltabayeva
- Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Israel
| | - Sudhakar Srivastava
- Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Israel
| | - Assylay Kurmanbayeva
- Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Israel
| | - Aizat Bekturova
- Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Israel
| | - Robert Fluhr
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Moshe Sagi
- Plant Stress Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Israel
| |
Collapse
|
97
|
Biology in Bloom: A Primer on the Arabidopsis thaliana Model System. Genetics 2018; 208:1337-1349. [PMID: 29618591 DOI: 10.1534/genetics.118.300755] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/23/2018] [Indexed: 12/13/2022] Open
Abstract
Arabidopsis thaliana could have easily escaped human scrutiny. Instead, Arabidopsis has become the most widely studied plant in modern biology despite its absence from the dinner table. Pairing diminutive stature and genome with prodigious resources and tools, Arabidopsis offers a window into the molecular, cellular, and developmental mechanisms underlying life as a multicellular photoautotroph. Many basic discoveries made using this plant have spawned new research areas, even beyond the verdant fields of plant biology. With a suite of resources and tools unmatched among plants and rivaling other model systems, Arabidopsis research continues to offer novel insights and deepen our understanding of fundamental biological processes.
Collapse
|
98
|
Hirota T, Izumi M, Wada S, Makino A, Ishida H. Vacuolar Protein Degradation via Autophagy Provides Substrates to Amino Acid Catabolic Pathways as an Adaptive Response to Sugar Starvation in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2018; 59:1363-1376. [PMID: 29390157 DOI: 10.1093/pcp/pcy005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/04/2018] [Indexed: 05/28/2023]
Abstract
The vacuolar lytic degradation of proteins releases free amino acids that plants can use instead of sugars for respiratory energy production. Autophagy is a major cellular process leading to the transport of proteins into the vacuole for degradation. Here, we examine the contribution of autophagy to the amino acid metabolism response to sugar starvation in mature leaves of Arabidopsis thaliana. During sugar starvation arising from the exposure of wild-type (WT) plants to darkness, autophagic transport of chloroplast stroma, which contains most of the proteins in a leaf, into the vacuolar lumen was induced within 2 d. During this time, the level of soluble proteins, primarily Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase), decreased and the amount of free amino acid increased. In dark-treated autophagy-defective (atg) mutants, the decrease of soluble proteins was suppressed, which resulted in the compromised release of basic amino acids, branched-chain amino acids (BCAAs) and aromatic amino acids. The impairment of BCAA catabolic pathways in the knockout mutants of the electron transfer flavoprotein (ETF)/ETF:ubiquinone oxidoreductase (etfqo) complex and the electron donor protein isovaleryl-CoA dehydrogenase (ivdh) caused a reduced tolerance to dark treatment similar to that in the atg mutants. The enhanced accumulation of BCAAs in the ivdh and etfqo mutants during the dark treatment was reduced by additional autophagy deficiency. These results indicate that vacuolar protein degradation via autophagy serves as an adaptive response to disrupted photosynthesis by providing substrates to amino acid catabolic pathways, including BCAA catabolism mediated by IVDH and ETFQO.
Collapse
Affiliation(s)
- Takaaki Hirota
- Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, Aramaki Aza Aoba, Sendai, Japan
| | - Masanori Izumi
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramaki Aza Aoba, Sendai, Japan
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Katahira, Sendai, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Shinya Wada
- Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, Aramaki Aza Aoba, Sendai, Japan
| | - Amane Makino
- Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, Aramaki Aza Aoba, Sendai, Japan
| | - Hiroyuki Ishida
- Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, Aramaki Aza Aoba, Sendai, Japan
| |
Collapse
|
99
|
Abstract
Plants have evolved sophisticated mechanisms to recycle intracellular constituents, which are essential for developmental and metabolic transitions; for efficient nutrient reuse; and for the proper disposal of proteins, protein complexes, and even entire organelles that become obsolete or dysfunctional. One major route is autophagy, which employs specialized vesicles to encapsulate and deliver cytoplasmic material to the vacuole for breakdown. In the past decade, the mechanics of autophagy and the scores of components involved in autophagic vesicle assembly have been documented. Now emerging is the importance of dedicated receptors that help recruit appropriate cargo, which in many cases exploit ubiquitylation as a signal. Although operating at a low constitutive level in all plant cells, autophagy is upregulated during senescence and various environmental challenges and is essential for proper nutrient allocation. Its importance to plant metabolism and energy balance in particular places autophagy at the nexus of robust crop performance, especially under suboptimal conditions.
Collapse
Affiliation(s)
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA;
| |
Collapse
|
100
|
Di Berardino J, Marmagne A, Berger A, Yoshimoto K, Cueff G, Chardon F, Masclaux-Daubresse C, Reisdorf-Cren M. Autophagy controls resource allocation and protein storage accumulation in Arabidopsis seeds. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1403-1414. [PMID: 29378007 PMCID: PMC6018931 DOI: 10.1093/jxb/ery012] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 01/16/2018] [Indexed: 05/18/2023]
Abstract
Autophagy is essential for nutrient recycling and plays a fundamental role in seed production and grain filling in plants. Autophagy participates in nitrogen remobilization at the whole-plant level, and the seeds of autophagy mutants present abnormal C and N contents relative to wild-type (WT) plants. It is well known that autophagy (ATG) genes are induced in leaves during senescence; however, expression of such genes in seeds has not yet been reported. In this study we show that most of the ATG genes are induced during seed maturation in Arabidopsis siliques. Promoter-ATG8f::UIDA and promoter-ATG8f::GFP fusions showed the strong expression of ATG8f in the phloem companion cells of pericarps and the funiculus, and in the embryo. Expression was especially strong at the late stages of development. The presence of many GFP-ATG8 pre-autophagosomal structures and autophagosomes confirmed the presence of autophagic activity in WT seed embryos. Seeds of atg5 and WT plants grown under low- or high-nitrate conditions were analysed. Nitrate-independent phenotypes were found with higher seed abortion in atg5 and early browing, higher total protein concentrations in the viable seeds of this mutant as compared to the WT. The higher total protein accumulation in atg5 viable seeds was significant from early developmental stages onwards. In addition, relatively low and early accumulation of 12S globulins were found in atg5 seeds. These features led us to the conclusion that atg5 seed development is accelerated and that the protein storage deposition pathway is somehow abnormal or incomplete.
Collapse
Affiliation(s)
- Julien Di Berardino
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
- Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Anne Marmagne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Adeline Berger
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Kohki Yoshimoto
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Gwendal Cueff
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Fabien Chardon
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Céline Masclaux-Daubresse
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Michèle Reisdorf-Cren
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
- Université de Versailles Saint Quentin en Yvelines, Université Paris Saclay, Versailles, France
| |
Collapse
|