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Yang MK, Zhu XJ, Chen CM, Guo X, Xu SX, Xu YR, Du SX, Xiao S, Mueller-Roeber B, Huang W, Chen L. The plant circadian clock regulates autophagy rhythm through transcription factor LUX ARRHYTHMO. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2135-2149. [PMID: 35962716 DOI: 10.1111/jipb.13343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Autophagy is an evolutionarily conserved degradation pathway in eukaryotes; it plays a critical role in nutritional stress tolerance. The circadian clock is an endogenous timekeeping system that generates biological rhythms to adapt to daily changes in the environment. Accumulating evidence indicates that the circadian clock and autophagy are intimately interwoven in animals. However, the role of the circadian clock in regulating autophagy has been poorly elucidated in plants. Here, we show that autophagy exhibits a robust circadian rhythm in both light/dark cycle (LD) and in constant light (LL) in Arabidopsis. However, autophagy rhythm showed a different pattern with a phase-advance shift and a lower amplitude in LL compared to LD. Moreover, mutation of the transcription factor LUX ARRHYTHMO (LUX) removed autophagy rhythm in LL and led to an enhanced amplitude in LD. LUX represses expression of the core autophagy genes ATG2, ATG8a, and ATG11 by directly binding to their promoters. Phenotypic analysis revealed that LUX is responsible for improved resistance of plants to carbon starvation, which is dependent on moderate autophagy activity. Comprehensive transcriptomic analysis revealed that the autophagy rhythm is ubiquitous in plants. Taken together, our findings demonstrate that the LUX-mediated circadian clock regulates plant autophagy rhythms.
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Affiliation(s)
- Ming-Kang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, 510642, China
| | - Xiao-Jie Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Chu-Min Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xu Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shu-Xuan Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Ya-Rou Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shen-Xiu Du
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Bernd Mueller-Roeber
- Department of Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam-Golm, Germany
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, 510642, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, 510642, China
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Degradation Mechanism of Autophagy-Related Proteins and Research Progress. Int J Mol Sci 2022; 23:ijms23137301. [PMID: 35806307 PMCID: PMC9266641 DOI: 10.3390/ijms23137301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 12/21/2022] Open
Abstract
In all eukaryotes, autophagy is the main pathway for nutrient recycling, which encapsulates parts of the cytoplasm and organelles in double-membrane vesicles, and then fuses with lysosomes/vacuoles to degrade them. Autophagy is a highly dynamic and relatively complex process influenced by multiple factors. Under normal growth conditions, it is maintained at basal levels. However, when plants are subjected to biotic and abiotic stresses, such as pathogens, drought, waterlogging, nutrient deficiencies, etc., autophagy is activated to help cells to survive under stress conditions. At present, the regulation of autophagy is mainly reflected in hormones, second messengers, post-transcriptional regulation, and protein post-translational modification. In recent years, the degradation mechanism of autophagy-related proteins has attracted much attention. In this review, we have summarized how autophagy-related proteins are degraded in yeast, animals, and plants, which will help us to have a more comprehensive and systematic understanding of the regulation mechanisms of autophagy. Moreover, research progress on the degradation of autophagy-related proteins in plants has been discussed.
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Wang Q, Hou S. The emerging roles of ATG1/ATG13 kinase complex in plants. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153653. [PMID: 35255243 DOI: 10.1016/j.jplph.2022.153653] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Autophagy is a conserved system from yeast to mammals that mediates the degradation and renovation of cellular components. This process is mainly driven by numerous autophagy-related (ATG) proteins. Among these components, the ATG1/ATG13 complex plays an essential role in initiating autophagy, sensing nutritional status signals, recruiting downstream ATG proteins to the autophagosome formation site, and governing autophagosome formation. In this review, we will focus on the ATG1/ATG13 kinase complex, summarizing and discussing the current views on the composition, structure, function, and regulation of this complex in plants.
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Affiliation(s)
- Qiuling Wang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Suiwen Hou
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, People's Republic of China.
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Lemke MD, Fisher KE, Kozlowska MA, Tano DW, Woodson JD. The core autophagy machinery is not required for chloroplast singlet oxygen-mediated cell death in the Arabidopsis thaliana plastid ferrochelatase two mutant. BMC PLANT BIOLOGY 2021; 21:342. [PMID: 34281507 PMCID: PMC8290626 DOI: 10.1186/s12870-021-03119-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Chloroplasts respond to stress and changes in the environment by producing reactive oxygen species (ROS) that have specific signaling abilities. The ROS singlet oxygen (1O2) is unique in that it can signal to initiate cellular degradation including the selective degradation of damaged chloroplasts. This chloroplast quality control pathway can be monitored in the Arabidopsis thaliana mutant plastid ferrochelatase two (fc2) that conditionally accumulates chloroplast 1O2 under diurnal light cycling conditions leading to rapid chloroplast degradation and eventual cell death. The cellular machinery involved in such degradation, however, remains unknown. Recently, it was demonstrated that whole damaged chloroplasts can be transported to the central vacuole via a process requiring autophagosomes and core components of the autophagy machinery. The relationship between this process, referred to as chlorophagy, and the degradation of 1O2-stressed chloroplasts and cells has remained unexplored. RESULTS To further understand 1O2-induced cellular degradation and determine what role autophagy may play, the expression of autophagy-related genes was monitored in 1O2-stressed fc2 seedlings and found to be induced. Although autophagosomes were present in fc2 cells, they did not associate with chloroplasts during 1O2 stress. Mutations affecting the core autophagy machinery (atg5, atg7, and atg10) were unable to suppress 1O2-induced cell death or chloroplast protrusion into the central vacuole, suggesting autophagosome formation is dispensable for such 1O2-mediated cellular degradation. However, both atg5 and atg7 led to specific defects in chloroplast ultrastructure and photosynthetic efficiencies, suggesting core autophagy machinery is involved in protecting chloroplasts from photo-oxidative damage. Finally, genes predicted to be involved in microautophagy were shown to be induced in stressed fc2 seedlings, indicating a possible role for an alternate form of autophagy in the dismantling of 1O2-damaged chloroplasts. CONCLUSIONS Our results support the hypothesis that 1O2-dependent cell death is independent from autophagosome formation, canonical autophagy, and chlorophagy. Furthermore, autophagosome-independent microautophagy may be involved in degrading 1O2-damaged chloroplasts. At the same time, canonical autophagy may still play a role in protecting chloroplasts from 1O2-induced photo-oxidative stress. Together, this suggests chloroplast function and degradation is a complex process utilizing multiple autophagy and degradation machineries, possibly depending on the type of stress or damage incurred.
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Affiliation(s)
- Matthew D. Lemke
- The School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036 USA
| | - Karen E. Fisher
- The School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036 USA
| | - Marta A. Kozlowska
- The School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036 USA
| | - David W. Tano
- The School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036 USA
| | - Jesse D. Woodson
- The School of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036 USA
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Rigault M, Citerne S, Masclaux-Daubresse C, Dellagi A. Salicylic acid is a key player of Arabidopsis autophagy mutant susceptibility to the necrotrophic bacterium Dickeya dadantii. Sci Rep 2021; 11:3624. [PMID: 33574453 PMCID: PMC7878789 DOI: 10.1038/s41598-021-83067-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/08/2021] [Indexed: 12/26/2022] Open
Abstract
Autophagy is a ubiquitous vesicular process for protein and organelle recycling in eukaryotes. In plant, autophagy is reported to play pivotal roles in nutrient recycling, adaptation to biotic and abiotic stresses. The role of autophagy in plant immunity remains poorly understood. Several reports showed enhanced susceptibility of different Arabidopsis autophagy mutants (atg) to necrotrophic fungal pathogens. Interaction of necrotrophic bacterial pathogens with autophagy is overlooked. We then investigated such interaction by inoculating the necrotrophic enterobacterium Dickeya dadantii in leaves of the atg2 and atg5 mutants and an ATG8a overexpressing line. Overexpressing ATG8a enhances plant tolerance to D. dadantii. While atg5 mutant displayed similar susceptibility to the WT, the atg2 mutant exhibited accelerated leaf senescence and enhanced susceptibility upon infection. Both phenotypes were reversed when the sid2 mutation, abolishing SA signaling, was introduced in the atg2 mutant. High levels of SA signaling in atg2 mutant resulted in repression of the jasmonic acid (JA) defense pathway known to limit D. dadantii progression in A. thaliana. We provide evidence that in atg2 mutant, the disturbed hormonal balance leading to higher SA signaling is the main factor causing increased susceptibility to the D. dadantii necrotroph by repressing the JA pathway and accelerating developmental senescence.
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Affiliation(s)
- Martine Rigault
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRAE Centre de Versailles-Grignon, Université Paris-Saclay, Route de St Cyr (RD 10), 78000, Versailles Cedex, France
| | - Sylvie Citerne
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRAE Centre de Versailles-Grignon, Université Paris-Saclay, Route de St Cyr (RD 10), 78000, Versailles Cedex, France
| | - Céline Masclaux-Daubresse
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRAE Centre de Versailles-Grignon, Université Paris-Saclay, Route de St Cyr (RD 10), 78000, Versailles Cedex, France
| | - Alia Dellagi
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRAE Centre de Versailles-Grignon, Université Paris-Saclay, Route de St Cyr (RD 10), 78000, Versailles Cedex, France.
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Stefaniak S, Wojtyla Ł, Pietrowska-Borek M, Borek S. Completing Autophagy: Formation and Degradation of the Autophagic Body and Metabolite Salvage in Plants. Int J Mol Sci 2020; 21:E2205. [PMID: 32210003 PMCID: PMC7139740 DOI: 10.3390/ijms21062205] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 12/12/2022] Open
Abstract
Autophagy is an evolutionarily conserved process that occurs in yeast, plants, and animals. Despite many years of research, some aspects of autophagy are still not fully explained. This mostly concerns the final stages of autophagy, which have not received as much interest from the scientific community as the initial stages of this process. The final stages of autophagy that we take into consideration in this review include the formation and degradation of the autophagic bodies as well as the efflux of metabolites from the vacuole to the cytoplasm. The autophagic bodies are formed through the fusion of an autophagosome and vacuole during macroautophagy and by vacuolar membrane invagination or protrusion during microautophagy. Then they are rapidly degraded by vacuolar lytic enzymes, and products of the degradation are reused. In this paper, we summarize the available information on the trafficking of the autophagosome towards the vacuole, the fusion of the autophagosome with the vacuole, the formation and decomposition of autophagic bodies inside the vacuole, and the efflux of metabolites to the cytoplasm. Special attention is given to the formation and degradation of autophagic bodies and metabolite salvage in plant cells.
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Affiliation(s)
- Szymon Stefaniak
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (S.S.); (Ł.W.)
| | - Łukasz Wojtyla
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (S.S.); (Ł.W.)
| | - Małgorzata Pietrowska-Borek
- Department of Biochemistry and Biotechnology, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland;
| | - Sławomir Borek
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (S.S.); (Ł.W.)
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Liao CY, Bassham DC. Combating stress: the interplay between hormone signaling and autophagy in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1723-1733. [PMID: 31725881 PMCID: PMC7067298 DOI: 10.1093/jxb/erz515] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/13/2019] [Indexed: 05/18/2023]
Abstract
Autophagy is a conserved recycling process in which cellular components are delivered to and degraded in the vacuole/lysosome for reuse. In plants, it assists in responding to dynamic environmental conditions and maintaining metabolite homeostasis under normal or stress conditions. Under stress, autophagy is activated to remove damaged components and to recycle nutrients for survival, and the energy sensor kinases target of rapamycin (TOR) and SNF-related kinase 1 (SnRK1) are key to this activation. Here, we discuss accumulating evidence that hormone signaling plays critical roles in regulating autophagy and plant stress responses, although the molecular mechanisms by which this occurs are often not clear. Several hormones have been shown to regulate TOR activity during stress, in turn controlling autophagy. Hormone signaling can also regulate autophagy gene expression, while, reciprocally, autophagy can regulate hormone synthesis and signaling pathways. We highlight how the interplay between major energy sensors, plant hormones, and autophagy under abiotic and biotic stress conditions can assist in plant stress tolerance.
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Affiliation(s)
- Ching-Yi Liao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
- Correspondence:
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