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Helgoe J, Davy SK, Weis VM, Rodriguez-Lanetty M. Triggers, cascades, and endpoints: connecting the dots of coral bleaching mechanisms. Biol Rev Camb Philos Soc 2024; 99:715-752. [PMID: 38217089 DOI: 10.1111/brv.13042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/15/2024]
Abstract
The intracellular coral-dinoflagellate symbiosis is the engine that underpins the success of coral reefs, one of the most diverse ecosystems on the planet. However, the breakdown of the symbiosis and the loss of the microalgal symbiont (i.e. coral bleaching) due to environmental changes are resulting in the rapid degradation of coral reefs globally. There is an urgent need to understand the cellular physiology of coral bleaching at the mechanistic level to help develop solutions to mitigate the coral reef crisis. Here, at an unprecedented scope, we present novel models that integrate putative mechanisms of coral bleaching within a common framework according to the triggers (initiators of bleaching, e.g. heat, cold, light stress, hypoxia, hyposalinity), cascades (cellular pathways, e.g. photoinhibition, unfolded protein response, nitric oxide), and endpoints (mechanisms of symbiont loss, e.g. apoptosis, necrosis, exocytosis/vomocytosis). The models are supported by direct evidence from cnidarian systems, and indirectly through comparative evolutionary analyses from non-cnidarian systems. With this approach, new putative mechanisms have been established within and between cascades initiated by different bleaching triggers. In particular, the models provide new insights into the poorly understood connections between bleaching cascades and endpoints and highlight the role of a new mechanism of symbiont loss, i.e. 'symbiolysosomal digestion', which is different from symbiophagy. This review also increases the approachability of bleaching physiology for specialists and non-specialists by mapping the vast landscape of bleaching mechanisms in an atlas of comprehensible and detailed mechanistic models. We then discuss major knowledge gaps and how future research may improve the understanding of the connections between the diverse cascade of cellular pathways and the mechanisms of symbiont loss (endpoints).
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Affiliation(s)
- Joshua Helgoe
- Department of Biological Sciences, Institute of Environment, Florida International University, 11200 SW 8th Street, OE 167, Miami, FL, USA
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - Virginia M Weis
- Department of Integrative Biology, Oregon State University, 2701 SW Campus Way, 2403 Cordley Hall, Corvallis, OR, USA
| | - Mauricio Rodriguez-Lanetty
- Department of Biological Sciences, Institute of Environment, Florida International University, 11200 SW 8th Street, OE 167, Miami, FL, USA
- Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL, USA
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2
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Yang SY, Lin WY, Hsiao YM, Chiou TJ. Milestones in understanding transport, sensing, and signaling of the plant nutrient phosphorus. THE PLANT CELL 2024; 36:1504-1523. [PMID: 38163641 PMCID: PMC11062440 DOI: 10.1093/plcell/koad326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/03/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
As an essential nutrient element, phosphorus (P) is primarily acquired and translocated as inorganic phosphate (Pi) by plant roots. Pi is often sequestered in the soil and becomes limited for plant growth. Plants have developed a sophisticated array of adaptive responses, termed P starvation responses, to cope with P deficiency by improving its external acquisition and internal utilization. Over the past 2 to 3 decades, remarkable progress has been made toward understanding how plants sense and respond to changing environmental P. This review provides an overview of the molecular mechanisms that regulate or coordinate P starvation responses, emphasizing P transport, sensing, and signaling. We present the major players and regulators responsible for Pi uptake and translocation. We then introduce how P is perceived at the root tip, how systemic P signaling is operated, and the mechanisms by which the intracellular P status is sensed and conveyed. Additionally, the recent exciting findings about the influence of P on plant-microbe interactions are highlighted. Finally, the challenges and prospects concerning the interplay between P and other nutrients and strategies to enhance P utilization efficiency are discussed. Insights obtained from this knowledge may guide future research endeavors in sustainable agriculture.
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Affiliation(s)
- Shu-Yi Yang
- Institute of Plant Biology, National Taiwan University, Taipei 106319, Taiwan
| | - Wei-Yi Lin
- Department of Agronomy, National Taiwan University, Taipei 106319, Taiwan
| | - Yi-Min Hsiao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115201, Taiwan
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115201, Taiwan
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3
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Yagyu M, Yoshimoto K. New insights into plant autophagy: molecular mechanisms and roles in development and stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1234-1251. [PMID: 37978884 DOI: 10.1093/jxb/erad459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/17/2023] [Indexed: 11/19/2023]
Abstract
Autophagy is an evolutionarily conserved eukaryotic intracellular degradation process. Although the molecular mechanisms of plant autophagy share similarities with those in yeast and mammals, certain unique mechanisms have been identified. Recent studies have highlighted the importance of autophagy during vegetative growth stages as well as in plant-specific developmental processes, such as seed development, germination, flowering, and somatic reprogramming. Autophagy enables plants to adapt to and manage severe environmental conditions, such as nutrient starvation, high-intensity light stress, and heat stress, leading to intracellular remodeling and physiological changes in response to stress. In the past, plant autophagy research lagged behind similar studies in yeast and mammals; however, recent advances have greatly expanded our understanding of plant-specific autophagy mechanisms and functions. This review summarizes current knowledge and latest research findings on the mechanisms and roles of plant autophagy with the objective of improving our understanding of this vital process in plants.
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Affiliation(s)
- Mako Yagyu
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
- Life Sciences Program, Graduate School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
| | - Kohki Yoshimoto
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
- Life Sciences Program, Graduate School of Agriculture, Meiji University, 1-1-1 Higashimita, Tama-ku, Kawasaki, Kanagawa, 214-8571, Japan
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4
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Li DW, Tan JZ, Li ZF, Ou LJ. Membrane lipid remodeling and autophagy to cope with phosphorus deficiency in the dinoflagellate Prorocentrum shikokuense. CHEMOSPHERE 2024; 349:140844. [PMID: 38042419 DOI: 10.1016/j.chemosphere.2023.140844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023]
Abstract
Dinoflagellates, which are responsible for more than 80% of harmful algal blooms in coastal waters, are competitive in low-phosphate environments. However, the specific acclimated phosphorus strategies to adapt to phosphorus deficiency in dinoflagellates, particularly through intracellular phosphorus metabolism, remain largely unknown. Comprehensive physiological, biochemical, and transcriptomic analyses were conducted to investigate intracellular phosphorus modulation in a model dinoflagellate, Prorocentrum shikokuense, with a specific focus on membrane lipid remodeling and autophagy in response to phosphorus deficiency. Under phosphorus deficiency, P. shikokuense exhibited a preference to spare phospholipids with nonphospholipids. The major phospholipid classes of phosphatidylcholine and phosphatidylethanolamine decreased in content, whereas the betaine lipid class of diacylglyceryl carboxyhydroxymethylcholine increased in content. Furthermore, under phosphorus deficiency, P. shikokuense induced autophagy as a mechanism to conserve and recycle cellular phosphorus resources. The present study highlights the effective modulation of intracellular phosphorus in P. shikokuense through membrane phospholipid remodeling and autophagy and contributes to a comprehensive understanding of the acclimation strategies to low-phosphorus conditions in dinoflagellates.
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Affiliation(s)
- Da-Wei Li
- College of Life Science and Technology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, Guangzhou, China
| | - Jin-Zhou Tan
- College of Life Science and Technology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, Guangzhou, China
| | - Zhuo-Fan Li
- College of Life Science and Technology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, Guangzhou, China
| | - Lin-Jian Ou
- College of Life Science and Technology, and Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institute, Jinan University, Guangzhou, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
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5
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Agbemafle W, Wong MM, Bassham DC. Transcriptional and post-translational regulation of plant autophagy. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6006-6022. [PMID: 37358252 PMCID: PMC10575704 DOI: 10.1093/jxb/erad211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/09/2023] [Indexed: 06/27/2023]
Abstract
In response to changing environmental conditions, plants activate cellular responses to enable them to adapt. One such response is autophagy, in which cellular components, for example proteins and organelles, are delivered to the vacuole for degradation. Autophagy is activated by a wide range of conditions, and the regulatory pathways controlling this activation are now being elucidated. However, key aspects of how these factors may function together to properly modulate autophagy in response to specific internal or external signals are yet to be discovered. In this review we discuss mechanisms for regulation of autophagy in response to environmental stress and disruptions in cell homeostasis. These pathways include post-translational modification of proteins required for autophagy activation and progression, control of protein stability of the autophagy machinery, and transcriptional regulation, resulting in changes in transcription of genes involved in autophagy. In particular, we highlight potential connections between the roles of key regulators and explore gaps in research, the filling of which can further our understanding of the autophagy regulatory network in plants.
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Affiliation(s)
- William Agbemafle
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Min May Wong
- 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
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6
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Lei P, Yu F, Liu X. Recent advances in cellular degradation and nuclear control of leaf senescence. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5472-5486. [PMID: 37453102 DOI: 10.1093/jxb/erad273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Senescence is the final stage of plant growth and development, and is a highly regulated process at the molecular, cellular, and organismal levels. When triggered by age, hormonal, or environmental cues, plants actively adjust their metabolism and gene expression to execute the progression of senescence. Regulation of senescence is vital for the reallocation of nutrients to sink organs, to ensure reproductive success and adaptations to stresses. Identification and characterization of hallmarks of leaf senescence are of great importance for understanding the molecular regulatory mechanisms of plant senescence, and breeding future crops with more desirable senescence traits. Tremendous progress has been made in elucidating the genetic network underpinning the metabolic and cellular changes in leaf senescence. In this review, we focus on three hallmarks of leaf senescence - chlorophyll and chloroplast degradation, loss of proteostasis, and activation of senescence-associated genes (SAGs), and discuss recent findings of the molecular players and the crosstalk of senescence pathways.
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Affiliation(s)
- Pei Lei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fei Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiayan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
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7
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Barros JAS, Chatt EC, Augustine RC, McLoughlin F, Li F, Otegui MS, Vierstra RD. Autophagy during maize endosperm development dampens oxidative stress and promotes mitochondrial clearance. PLANT PHYSIOLOGY 2023; 193:1395-1415. [PMID: 37335933 PMCID: PMC10517192 DOI: 10.1093/plphys/kiad340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 06/21/2023]
Abstract
The selective turnover of macromolecules by autophagy provides a critical homeostatic mechanism for recycling cellular constituents and for removing superfluous and damaged organelles, membranes, and proteins. To better understand how autophagy impacts seed maturation and nutrient storage, we studied maize (Zea mays) endosperm in its early and middle developmental stages via an integrated multiomic approach using mutants impacting the core macroautophagy factor AUTOPHAGY (ATG)-12 required for autophagosome assembly. Surprisingly, the mutant endosperm in these developmental windows accumulated normal amounts of starch and Zein storage proteins. However, the tissue acquired a substantially altered metabolome, especially for compounds related to oxidative stress and sulfur metabolism, including increases in cystine, dehydroascorbate, cys-glutathione disulfide, glucarate, and galactarate, and decreases in peroxide and the antioxidant glutathione. While changes in the associated transcriptome were mild, the proteome was strongly altered in the atg12 endosperm, especially for increased levels of mitochondrial proteins without a concomitant increase in mRNA abundances. Although fewer mitochondria were seen cytologically, a heightened number appeared dysfunctional based on the accumulation of dilated cristae, consistent with attenuated mitophagy. Collectively, our results confirm that macroautophagy plays a minor role in the accumulation of starch and storage proteins during maize endosperm development but likely helps protect against oxidative stress and clears unneeded/dysfunctional mitochondria during tissue maturation.
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Affiliation(s)
- Jessica A S Barros
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Elizabeth C Chatt
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Robert C Augustine
- 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
| | - Faqiang Li
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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8
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Barreca F, Aventaggiato M, Vitiello L, Sansone L, Russo MA, Mai A, Valente S, Tafani M. SIRT5 Activation and Inorganic Phosphate Binding Reduce Cancer Cell Vitality by Modulating Autophagy/Mitophagy and ROS. Antioxidants (Basel) 2023; 12:1635. [PMID: 37627630 PMCID: PMC10451763 DOI: 10.3390/antiox12081635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/24/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Cancer cells show increased glutamine consumption. The glutaminase (GLS) enzyme controls a limiting step in glutamine catabolism. Breast tumors, especially the triple-negative subtype, have a high expression of GLS. Our recent study demonstrated that GLS activity and ammonia production are inhibited by sirtuin 5 (SIRT5). We developed MC3138, a selective SIRT5 activator. Treatment with MC3138 mimicked the deacetylation effect mediated by SIRT5 overexpression. Moreover, GLS activity was regulated by inorganic phosphate (Pi). Considering the interconnected roles of GLS, SIRT5 and Pi in cancer growth, our hypothesis is that activation of SIRT5 and reduction in Pi could represent a valid antitumoral strategy. Treating cells with MC3138 and lanthanum acetate, a Pi chelator, decreased cell viability and clonogenicity. We also observed a modulation of MAP1LC3B and ULK1 with MC3138 and lanthanum acetate. Interestingly, inhibition of the mitophagy marker BNIP3 was observed only in the presence of MC3138. Autophagy and mitophagy modulation were accompanied by an increase in cytosolic and mitochondrial reactive oxygen species (ROS). In conclusion, our results show how SIRT5 activation and/or Pi binding can represent a valid strategy to inhibit cell proliferation by reducing glutamine metabolism and mitophagy, leading to a deleterious accumulation of ROS.
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Affiliation(s)
- Federica Barreca
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (F.B.); (M.A.)
| | - Michele Aventaggiato
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (F.B.); (M.A.)
| | - Laura Vitiello
- Laboratory of Flow Cytometry, IRCCS San Raffaele Roma, Via di Val Cannuta 247, 00166 Rome, Italy;
| | - Luigi Sansone
- MEBIC Consortium, San Raffaele University, 00166 Rome, Italy; (L.S.); (M.A.R.)
- Cellular and Molecular Pathology, IRCCS San Raffaele Roma, Via di Val Cannuta 247, 00166 Rome, Italy
| | - Matteo Antonio Russo
- MEBIC Consortium, San Raffaele University, 00166 Rome, Italy; (L.S.); (M.A.R.)
- Cellular and Molecular Pathology, IRCCS San Raffaele Roma, Via di Val Cannuta 247, 00166 Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy; (A.M.); (S.V.)
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy; (A.M.); (S.V.)
| | - Marco Tafani
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy; (F.B.); (M.A.)
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9
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Lin LY, Chow HX, Chen CH, Mitsuda N, Chou WC, Liu TY. Role of autophagy-related proteins ATG8f and ATG8h in the maintenance of autophagic activity in Arabidopsis roots under phosphate starvation. FRONTIERS IN PLANT SCIENCE 2023; 14:1018984. [PMID: 37434600 PMCID: PMC10331476 DOI: 10.3389/fpls.2023.1018984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 05/23/2023] [Indexed: 07/13/2023]
Abstract
Nutrient starvation-induced autophagy is a conserved process in eukaryotes. Plants defective in autophagy show hypersensitivity to carbon and nitrogen limitation. However, the role of autophagy in plant phosphate (Pi) starvation response is relatively less explored. Among the core autophagy-related (ATG) genes, ATG8 encodes a ubiquitin-like protein involved in autophagosome formation and selective cargo recruitment. The Arabidopsis thaliana ATG8 genes, AtATG8f and AtATG8h, are notably induced in roots under low Pi. In this study, we show that such upregulation correlates with their promoter activities and can be suppressed in the phosphate response 1 (phr1) mutant. Yeast one-hybrid analysis failed to attest the binding of the AtPHR1 transcription factor to the promoter regions of AtATG8f and AtATG8h. Dual luciferase reporter assays in Arabidopsis mesophyll protoplasts also indicated that AtPHR1 could not transactivate the expression of both genes. Loss of AtATG8f and AtATG8h leads to decreased root microsomal-enriched ATG8 but increased ATG8 lipidation. Moreover, atg8f/atg8h mutants exhibit reduced autophagic flux estimated by the vacuolar degradation of ATG8 in the Pi-limited root but maintain normal cellular Pi homeostasis with reduced number of lateral roots. While the expression patterns of AtATG8f and AtATG8h overlap in the root stele, AtATG8f is more strongly expressed in the root apex and root hair and remarkably at sites where lateral root primordia develop. We hypothesize that Pi starvation-induction of AtATG8f and AtATG8h may not directly contribute to Pi recycling but rely on a second wave of transcriptional activation triggered by PHR1 that fine-tunes cell type-specific autophagic activity.
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Affiliation(s)
- Li-Yen Lin
- Institute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Hong-Xuan Chow
- Institute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Chih-Hao Chen
- Institute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Wen-Chun Chou
- Institute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Tzu-Yin Liu
- Institute of Bioinformatics and Structural Biology, College of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan
- Department of Life Science, College of Life Sciences and Medicine, National Tsing Hua University, Hsinchu, Taiwan
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10
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Chiu CY, Lung HF, Chou WC, Lin LY, Chow HX, Kuo YH, Chien PS, Chiou TJ, Liu TY. Autophagy-Mediated Phosphate Homeostasis in Arabidopsis Involves Modulation of Phosphate Transporters. PLANT & CELL PHYSIOLOGY 2023; 64:519-535. [PMID: 36943363 DOI: 10.1093/pcp/pcad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 01/31/2023] [Accepted: 03/01/2023] [Indexed: 05/17/2023]
Abstract
Autophagy in plants is regulated by diverse signaling cascades in response to environmental changes. Fine-tuning of its activity is critical for the maintenance of cellular homeostasis under basal and stressed conditions. In this study, we compared the Arabidopsis autophagy-related (ATG) system transcriptionally under inorganic phosphate (Pi) deficiency versus nitrogen deficiency and showed that most ATG genes are only moderately upregulated by Pi starvation, with relatively stronger induction of AtATG8f and AtATG8h among the AtATG8 family. We found that Pi shortage increased the formation of GFP-ATG8f-labeled autophagic structures and the autophagic flux in the differential zone of the Arabidopsis root. However, the proteolytic cleavage of GFP-ATG8f and the vacuolar degradation of endogenous ATG8 proteins indicated that Pi limitation does not drastically alter the autophagic flux in the whole roots, implying a cell type-dependent regulation of autophagic activities. At the organismal level, the Arabidopsis atg mutants exhibited decreased shoot Pi concentrations and smaller meristem sizes under Pi sufficiency. Under Pi limitation, these mutants showed enhanced Pi uptake and impaired root cell division and expansion. Despite a reduced steady-state level of several PHOSPHATE TRANSPORTER 1s (PHT1s) in the atg root, cycloheximide treatment analysis suggested that the protein stability of PHT1;1/2/3 is comparable in the Pi-replete wild type and atg5-1. By contrast, the degradation of PHT1;1/2/3 is enhanced in the Pi-deplete atg5-1. Our findings reveal that both basal autophagy and Pi starvation-induced autophagy are required for the maintenance of Pi homeostasis and may modulate the expression of PHT1s through different mechanisms.
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Affiliation(s)
- Chang-Yi Chiu
- Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd., East Dist., Hsinchu 30013, Taiwan
| | - Hui-Fang Lung
- Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd., East Dist., Hsinchu 30013, Taiwan
| | - Wen-Chun Chou
- Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd., East Dist., Hsinchu 30013, Taiwan
| | - Li-Yen Lin
- Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd., East Dist., Hsinchu 30013, Taiwan
| | - Hong-Xuan Chow
- Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd., East Dist., Hsinchu 30013, Taiwan
| | - Yu-Hao Kuo
- Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd., East Dist., Hsinchu 30013, Taiwan
| | - Pei-Shan Chien
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Tzyy-Jen Chiou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Tzu-Yin Liu
- Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd., East Dist., Hsinchu 30013, Taiwan
- Department of Life Science, College of Life Science, National Tsing Hua University, No. 101, Sec. 2, Guangfu Rd., East Dist., Hsinchu 30013, Taiwan
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Montpetit J, Clúa J, Hsieh YF, Vogiatzaki E, Müller J, Abel S, Strasser R, Poirier Y. Endoplasmic reticulum calnexins participate in the primary root growth response to phosphate deficiency. PLANT PHYSIOLOGY 2023; 191:1719-1733. [PMID: 36567484 PMCID: PMC10022610 DOI: 10.1093/plphys/kiac595] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Accumulation of incompletely folded proteins in the endoplasmic reticulum (ER) leads to ER stress, activates ER protein degradation pathways, and upregulates genes involved in protein folding. This process is known as the unfolded protein response (UPR). The role of ER protein folding in plant responses to nutrient deficiencies is unclear. We analyzed Arabidopsis (Arabidopsis thaliana) mutants affected in ER protein quality control and established that both CALNEXIN (CNX) genes function in the primary root response to phosphate (Pi) deficiency. CNX1 and CNX2 are homologous ER lectins promoting protein folding of N-glycosylated proteins via the recognition of the GlcMan9GlcNAc2 glycan. Growth of cnx1-1 and cnx2-2 single mutants was similar to that of the wild type under high and low Pi conditions, but the cnx1-1 cnx2-2 double mutant showed decreased primary root growth under low Pi conditions due to reduced meristematic cell division. This phenotype was specific to Pi deficiency; the double mutant responded normally to osmotic and salt stress. Expression of CNX2 mutated in amino acids involved in binding the GlcMan9GlcNAc2 glycan failed to complement the cnx1-1 cnx2-2 mutant. The root growth phenotype was Fe-dependent and was associated with root apoplastic Fe accumulation. Two genes involved in Fe-dependent inhibition of primary root growth under Pi deficiency, the ferroxidase LOW PHOSPHATE 1 (LPR1) and P5-type ATPase PLEIOTROPIC DRUG RESISTANCE 2 (PDR2) were epistatic to CNX1/CNX2. Overexpressing PDR2 failed to complement the cnx1-1 cnx2-2 root phenotype. The cnx1-1 cnx2-2 mutant showed no evidence of UPR activation, indicating a limited effect on ER protein folding. CNX might process a set of N-glycosylated proteins specifically involved in the response to Pi deficiency.
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Affiliation(s)
- Jonatan Montpetit
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland
| | - Joaquín Clúa
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland
| | - Yi-Fang Hsieh
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland
| | - Evangelia Vogiatzaki
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jens Müller
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Steffen Abel
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Yves Poirier
- Department of Plant Molecular Biology, Biophore Building, University of Lausanne, 1015 Lausanne, Switzerland
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12
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He Z, Chen M, Ling B, Cao T, Wang C, Li W, Tang W, Chen K, Zhou Y, Chen J, Xu Z, Wang D, Guo C, Ma Y. Overexpression of the autophagy-related gene SiATG8a from foxtail millet (Setaria italica L.) in transgenic wheat confers tolerance to phosphorus starvation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:580-586. [PMID: 36774913 DOI: 10.1016/j.plaphy.2023.01.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
In plants, autophagy plays an important role in regulating intracellular degradation and amino acid recycling in response to nutrient starvation, senescence, and other environmental stresses. Foxtail millet (Setaria italica) shows strong resistance to various abiotic stresses; however, current understanding of the regulation network of abiotic stress resistance in foxtail millet remains limited. In this study, we aimed to determine the autophagy-related gene SiATG8a in foxtail millet. We found that SiATG8a was mainly expressed in the stem and was induced by low-phosphorus (LP) stress. Overexpression of SiATG8a in wheat (Triticum aestivum) significantly increased the grain yield and spike number per m2 under LP treatment compared to those in the WT varieties S366 and S4056. There was no significant difference in the grain P content between SiATG8a-overexpressing wheat and WT wheat under normal phosphorus (NP) and LP treatments. However, the phosphorus (P) content in the roots, stems, and leaves of transgenic plants was significantly higher than that in WT plants under NP and LP conditions. Furthermore, the expression of P transporter genes, such as TaPHR1, TaPHR3, TaIPS1, and TaPT9, in SiATG8a-transgenic wheat was higher than that in WT under LP. Collectively, overexpression of SiATG8a increases the P content of roots, stems, and leaves of transgenic wheat under LP conditions by modulating the expression of P-related transporter gene, which may result in increased grain yield; thus, SiATG8a is a candidate gene for generating transgenic wheat with improved tolerance to LP stress in the field.
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Affiliation(s)
- Zhang He
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China.
| | - Ming Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Bingqi Ling
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Tao Cao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Chunxiao Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Weiwei Li
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China.
| | - Wensi Tang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Kai Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Yongbin Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Jun Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Zhaoshi Xu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Dan Wang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China.
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China.
| | - Youzhi Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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13
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Saeed B, Deligne F, Brillada C, Dünser K, Ditengou FA, Turek I, Allahham A, Grujic N, Dagdas Y, Ott T, Kleine-Vehn J, Vert G, Trujillo M. K63-linked ubiquitin chains are a global signal for endocytosis and contribute to selective autophagy in plants. Curr Biol 2023; 33:1337-1345.e5. [PMID: 36863341 DOI: 10.1016/j.cub.2023.02.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/08/2022] [Accepted: 02/07/2023] [Indexed: 03/04/2023]
Abstract
In contrast to other eukaryotic model organisms, the closely related ubiquitin (Ub)-conjugating enzymes UBC35 and UBC36 are the main sources of K63-linked Ub chains in Arabidopsis.1 Although K63-linked chains have been associated with the regulation of vesicle trafficking, definitive proof for their role in endocytosis was missing. We show that the ubc35 ubc36 mutant has pleiotropic phenotypes related to hormone and immune signaling. Specifically, we reveal that ubc35-1 ubc36-1 plants have altered turnover of integral membrane proteins including FLS2, BRI1, and PIN1 at the plasma membrane. Our data indicates that K63-Ub chains are generally required for endocytic trafficking in plants. In addition, we show that in plants K63-Ub chains are involved in selective autophagy through NBR1, the second major pathway delivering cargoes to the vacuole for degradation. Similar to autophagy-defective mutants, ubc35-1 ubc36-1 plants display an accumulation of autophagy markers. Moreover, autophagy receptor NBR1 interacts with K63-Ub chains, which are required for its delivery to the lytic vacuole.2 Together, we show that K63-Ub chains act as a general signal required for the two main pathways delivering cargo to the vacuole and thus, to maintain proteostasis.
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Affiliation(s)
- Bushra Saeed
- Albert-Ludwigs-University Freiburg, Institute for Biology II, Cell Biology, 79104 Freiburg, Germany
| | - Florian Deligne
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/University Toulouse 3, 31320 Auzeville Tolosane, France
| | - Carla Brillada
- Albert-Ludwigs-University Freiburg, Institute for Biology II, Cell Biology, 79104 Freiburg, Germany
| | - Kai Dünser
- Albert-Ludwigs-University Freiburg, Institute for Biology II, Cell Biology, 79104 Freiburg, Germany
| | - Franck Aniset Ditengou
- Albert-Ludwigs-University Freiburg, Institute for Biology II, Cell Biology, 79104 Freiburg, Germany; Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany; Bio Imaging Core Light Microscopy (BiMiC), Institute for Disease Modeling and Targeted Medicine (IMITATE), Medical Center University of Freiburg, Albert Ludwigs University Freiburg, Breisacher Str. 113, 79106 Freiburg, Germany
| | - Ilona Turek
- Department of Rural Clinical Sciences, La Trobe Rural Health School, La Trobe University, Bendigo, VIC 3552, Australia
| | - Alaa Allahham
- Albert-Ludwigs-University Freiburg, Institute for Biology II, Cell Biology, 79104 Freiburg, Germany
| | - Nenad Grujic
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna 1030, Austria
| | - Thomas Ott
- Albert-Ludwigs-University Freiburg, Institute for Biology II, Cell Biology, 79104 Freiburg, Germany; Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Jürgen Kleine-Vehn
- Albert-Ludwigs-University Freiburg, Institute for Biology II, Cell Biology, 79104 Freiburg, Germany; Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Grégory Vert
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/University Toulouse 3, 31320 Auzeville Tolosane, France.
| | - Marco Trujillo
- Albert-Ludwigs-University Freiburg, Institute for Biology II, Cell Biology, 79104 Freiburg, Germany.
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Yoshitake Y, Yoshimoto K. Intracellular phosphate recycling systems for survival during phosphate starvation in plants. FRONTIERS IN PLANT SCIENCE 2023; 13:1088211. [PMID: 36733584 PMCID: PMC9888252 DOI: 10.3389/fpls.2022.1088211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Phosphorus (P) is an essential nutrient for plant growth and plants use inorganic phosphate (Pi) as their P source, but its bioavailable form, orthophosphate, is often limited in soils. Hence, plants have several mechanisms for adaptation to Pi starvation. One of the most common response strategies is "Pi recycling" in which catabolic enzymes degrade intracellular constituents, such as phosphoesters, nucleic acids and glycerophospholipids to salvage Pi. Recently, several other intracellular degradation systems have been discovered that salvage Pi from organelles. Also, one of sphingolipids has recently been identified as a degradation target for Pi recycling. So, in this mini-review we summarize the current state of knowledge, including research findings, about the targets and degradation processes for Pi recycling under Pi starvation, in order to further our knowledge of the whole mechanism of Pi recycling.
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15
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Autophagic degradation of membrane-bound organelles in plants. Biosci Rep 2023; 43:232379. [PMID: 36562332 PMCID: PMC9842949 DOI: 10.1042/bsr20221204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022] Open
Abstract
Eukaryotic cells have evolved membrane-bound organelles, including the endoplasmic reticulum (ER), Golgi, mitochondria, peroxisomes, chloroplasts (in plants and green algae) and lysosomes/vacuoles, for specialized functions. Organelle quality control and their proper interactions are crucial both for normal cell homeostasis and function and for environmental adaption. Dynamic turnover of organelles is tightly controlled, with autophagy playing an essential role. Autophagy is a programmed process for efficient clearing of unwanted or damaged macromolecules or organelles, transporting them to vacuoles for degradation and recycling and thereby enhancing plant environmental plasticity. The specific autophagic engulfment of organelles requires activation of a selective autophagy pathway, recognition of the organelle by a receptor, and selective incorporation of the organelle into autophagosomes. While some of the autophagy machinery and mechanisms for autophagic removal of organelles is conserved across eukaryotes, plants have also developed unique mechanisms and machinery for these pathways. In this review, we discuss recent progress in understanding autophagy regulation in plants, with a focus on autophagic degradation of membrane-bound organelles. We also raise some important outstanding questions to be addressed in the future.
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16
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Ying S, Scheible WR, Lundquist PK. A stress-inducible protein regulates drought tolerance and flowering time in Brachypodium and Arabidopsis. PLANT PHYSIOLOGY 2023; 191:643-659. [PMID: 36264121 PMCID: PMC9806587 DOI: 10.1093/plphys/kiac486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
To cope with environmental stresses and ensure maximal reproductive success, plants have developed strategies to adjust the timing of their transition to reproductive growth. This has a substantial impact on the stress resilience of crops and ultimately on agricultural productivity. Here, we report a previously uncharacterized, plant-specific gene family designated as Regulator of Flowering and Stress (RFS). Overexpression of the BdRFS gene in Brachypodium distachyon delayed flowering, increased biomass accumulation, and promoted drought tolerance, whereas clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated knockout mutants exhibited opposite phenotypes. A double T-DNA insertional mutant in the two Arabidopsis (Arabidopsis thaliana) homologs replicated the effects on flowering and water deprivation seen in the B. distachyon CRISPR knockout lines, highlighting the functional conservation of the family between monocots and dicots. Lipid analysis of B. distachyon and Arabidopsis revealed that digalactosyldiacylglycerol (DGDG) and phosphatidylcholine (PC) contents were significantly, and reciprocally, altered in overexpressor and knockout mutants. Importantly, alteration of C16:0-containing PC, a Flowering Locus T-interacting lipid, associated with flowering phenotype, with elevated levels corresponding to earlier flowering. Co-immunoprecipitation analysis suggested that BdRFS interacts with phospholipase Dα1 as well as several other abscisic acid-related proteins. Furthermore, reduction of C18:3 fatty acids in DGDG corresponded with reduced jasmonic acid metabolites in CRISPR mutants. Collectively, we suggest that stress-inducible RFS proteins represent a regulatory component of lipid metabolism that impacts several agronomic traits of biotechnological importance.
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Affiliation(s)
- Sheng Ying
- Authors for correspondence: (P.K.L.) and (S.Y.)
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17
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Sharma I, Kirti PB, Pati PK. Autophagy: a game changer for plant development and crop improvement. PLANTA 2022; 256:103. [PMID: 36307739 DOI: 10.1007/s00425-022-04004-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Manipulation of autophagic pathway represents a tremendous opportunity for designing climate-smart crops with improved yield and better adaptability to changing environment. For exploiting autophagy to its full potential, identification and comprehensive characterization of adapters/receptor complex and elucidation of its regulatory network in crop plants is highly warranted. Autophagy is a major intracellular trafficking pathway in eukaryotes involved in vacuolar degradation of cytoplasmic constituents, mis-folded proteins, and defective organelles. Under optimum conditions, autophagy operates at a basal level to maintain cellular homeostasis, but under stressed conditions, it is induced further to provide temporal stress relief. Our understanding of this highly dynamic process has evolved exponentially in the past few years with special reference to several plant-specific roles of autophagy. Here, we review the most recent advances in the field of autophagy in plants and discuss its potential implications in designing crops with improved stress and disease-tolerance, enhanced yield potential, and improved capabilities for producing metabolites of high economic value. We also assess the current knowledge gaps and the possible strategies to develop a robust module for biotechnological application of autophagy to enhance bioeconomy and sustainability of agriculture.
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Affiliation(s)
- Isha Sharma
- AgriBiotech Foundation, PJTS Agriculture University, Rajendranagar, Hyderabad, Telangana, 500032, India.
- International Crops Research Institute for the Semi-Arid Tropics, 502324, Patancheru, Telangana, India.
| | | | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, 140301, India
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Li L, Lee CP, Ding X, Qin Y, Wijerathna-Yapa A, Broda M, Otegui MS, Millar AH. Defects in autophagy lead to selective in vivo changes in turnover of cytosolic and organelle proteins in Arabidopsis. THE PLANT CELL 2022; 34:3936-3960. [PMID: 35766863 PMCID: PMC9516138 DOI: 10.1093/plcell/koac185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/21/2022] [Indexed: 05/26/2023]
Abstract
Identification of autophagic protein cargo in plants in autophagy-related genes (ATG) mutants is complicated by changes in protein synthesis and protein degradation. To detect autophagic cargo, we measured protein degradation rate in shoots and roots of Arabidopsis (Arabidopsis thaliana) atg5 and atg11 mutants. These data show that less than a quarter of proteins changing in abundance are probable cargo and revealed roles of ATG11 and ATG5 in degradation of specific glycolytic enzymes and of other cytosol, chloroplast, and ER-resident proteins, and a specialized role for ATG11 in degradation of proteins from mitochondria and chloroplasts. Protein localization in transformed protoplasts and degradation assays in the presence of inhibitors confirm a role for autophagy in degrading glycolytic enzymes. Autophagy induction by phosphate (Pi) limitation changed metabolic profiles and the protein synthesis and degradation rates of atg5 and atg11 plants. A general decrease in the abundance of amino acids and increase in secondary metabolites in autophagy mutants was consistent with altered catabolism and changes in energy conversion caused by reduced degradation rate of specific proteins. Combining measures of changes in protein abundance and degradation rates, we also identify ATG11 and ATG5-associated protein cargo of low Pi-induced autophagy in chloroplasts and ER-resident proteins involved in secondary metabolism.
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Affiliation(s)
- Lei Li
- Authors for correspondence (L.L.) and (A.H.M)
| | - Chun Pong Lee
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, Crawley, WA 6009, Australia
| | - Xinxin Ding
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Yu Qin
- Frontiers Science Center for Cell Responses, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Akila Wijerathna-Yapa
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, Crawley, WA 6009, Australia
| | - Martyna Broda
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, Crawley, WA 6009, Australia
| | - Marisa S Otegui
- Department of Botany and Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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19
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Chien PS, Chao YT, Chou CH, Hsu YY, Chiang SF, Tung CW, Chiou TJ. Phosphate transporter PHT1;1 is a key determinant of phosphorus acquisition in Arabidopsis natural accessions. PLANT PHYSIOLOGY 2022; 190:682-697. [PMID: 35639954 PMCID: PMC9434223 DOI: 10.1093/plphys/kiac250] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/04/2022] [Indexed: 05/11/2023]
Abstract
Phosphorus (P) is a mineral nutrient essential for plant growth and development, but most P in the soil is unavailable for plants. To understand the genetic basis of P acquisition regulation, we performed genome-wide association studies (GWASs) on a diversity panel of Arabidopsis (Arabidopsis thaliana). Two primary determinants of P acquisition were considered, namely, phosphate (Pi)-uptake activity and PHOSPHATE TRANSPORTER 1 (PHT1) protein abundance. Association mapping revealed a shared significant peak on chromosome 5 (Chr5) where the PHT1;1/2/3 genes reside, suggesting a connection between the regulation of Pi-uptake activity and PHT1 protein abundance. Genes encoding transcription factors, kinases, and a metalloprotease associated with both traits were also identified. Conditional GWAS followed by statistical analysis of genotype-dependent PHT1;1 expression and transcriptional activity assays revealed an epistatic interaction between PHT1;1 and MYB DOMAIN PROTEIN 52 (MYB52) on Chr1. Further, analyses of F1 hybrids generated by crossing two subgroups of natural accessions carrying specific PHT1;1- and MYB52-associated single nucleotide polymorphisms (SNPs) revealed strong effects of these variants on PHT1;1 expression and Pi uptake activity. Notably, the soil P contents in Arabidopsis habitats coincided with PHT1;1 haplotype, emphasizing how fine-tuned P acquisition activity through natural variants allows environmental adaptation. This study sheds light on the complex regulation of P acquisition and offers a framework to systematically assess the effectiveness of GWAS approaches in the study of quantitative traits.
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Affiliation(s)
| | | | - Chia-Hui Chou
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
| | - Yu-Ying Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Su-Fen Chiang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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20
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Yoshitake Y, Shinozaki D, Yoshimoto K. Autophagy triggered by iron-mediated ER stress is an important stress response to the early phase of Pi starvation in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1370-1381. [PMID: 35306710 DOI: 10.1111/tpj.15743] [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: 09/06/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Inorganic phosphate (Pi) is essential for plant growth. However, Pi is often limiting in soil. Hence, plants have established several mechanisms of response to Pi starvation. One of the important mechanisms is Pi recycling, which includes membrane lipid remodeling and plastid DNA degradation via catabolic enzymes. However, the involvement of other degradation systems in Pi recycling remains unclear. Autophagy, a system for degradation of intracellular components, contributes to recycling of some nutrients, such as nitrogen, carbon, and zinc, under starvation. In the present study, we found that autophagy-deficient mutants depleted Pi early and exhibited severe leaf growth defects under Pi starvation. The main cargo of autophagy induced by early Pi depleted conditions was the endoplasmic reticulum (ER), indicating that ER-phagy, a type of autophagy that selectively degrades the ER, is involved in the response to the early phase of Pi starvation for contribution to Pi recycling. This ER-phagy was suppressed in an INOSITOL-REQUIRING ENZYME 1 double mutant, ire1a ire1b, in which ER stress responses are defective, suggesting that the early Pi starvation induced ER-phagy is induced by ER stress. Furthermore, iron limitation and inhibition of lipid-reactive oxygen species accumulation suppressed the ER-phagy. Interestingly, membrane lipid remodeling, a response to late Pi starvation, was accelerated in the ire1a ire1b under early Pi-depleted conditions. Our findings reveal the existence of two different phases of responses to Pi starvation (i.e. early and late) and indicate that ER stress-mediated ER-phagy is involved in Pi recycling in the early phase to suppress acceleration of the late phase.
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Affiliation(s)
- Yushi Yoshitake
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1, Tama-ku, Kawasaki-shi, Kanagawa, 214-8571, Japan
| | - Daiki Shinozaki
- Life Science Program, Graduate School of Agriculture, Meiji University, 1-1-1, Tama-ku, Kawasaki-shi, Kanagawa, 214-8571, Japan
| | - Kohki Yoshimoto
- Department of Life Sciences, School of Agriculture, Meiji University, 1-1-1, Tama-ku, Kawasaki-shi, Kanagawa, 214-8571, Japan
- Life Science Program, Graduate School of Agriculture, Meiji University, 1-1-1, Tama-ku, Kawasaki-shi, Kanagawa, 214-8571, Japan
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21
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Luong AM, Koestel J, Bhati KK, Batoko H. Cargo receptors and adaptors for selective autophagy in plant cells. FEBS Lett 2022; 596:2104-2132. [PMID: 35638898 DOI: 10.1002/1873-3468.14412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/08/2022] [Accepted: 05/23/2022] [Indexed: 11/06/2022]
Abstract
Plant selective (macro)autophagy is a highly regulated process whereby eukaryotic cells spatiotemporally degrade some of their constituents that have become superfluous or harmful. The identification and characterization of the factors determining this selectivity make it possible to integrate selective (macro)autophagy into plant cell physiology and homeostasis. The specific cargo receptors and/or scaffold proteins involved in this pathway are generally not structurally conserved, as are the biochemical mechanisms underlying recognition and integration of a given cargo into the autophagosome in different cell types. This review discusses the few specific cargo receptors described in plant cells to highlight key features of selective autophagy in the plant kingdom and its integration with plant physiology, so as to identify evolutionary convergence and knowledge gaps to be filled by future research.
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Affiliation(s)
- Ai My Luong
- Louvain Institute of Biomolecular Science and Technology, University of Louvain Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
| | - Jérôme Koestel
- Louvain Institute of Biomolecular Science and Technology, University of Louvain Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
| | - Kaushal Kumar Bhati
- Louvain Institute of Biomolecular Science and Technology, University of Louvain Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
| | - Henri Batoko
- Louvain Institute of Biomolecular Science and Technology, University of Louvain Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
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22
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Wang J, Miao S, Liu Y, Wang Y. Linking Autophagy to Potential Agronomic Trait Improvement in Crops. Int J Mol Sci 2022; 23:ijms23094793. [PMID: 35563184 PMCID: PMC9103229 DOI: 10.3390/ijms23094793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/18/2022] [Accepted: 04/25/2022] [Indexed: 12/10/2022] Open
Abstract
Autophagy is an evolutionarily conserved catabolic process in eukaryotic cells, by which the superfluous or damaged cytoplasmic components can be delivered into vacuoles or lysosomes for degradation and recycling. Two decades of autophagy research in plants uncovers the important roles of autophagy during diverse biological processes, including development, metabolism, and various stress responses. Additionally, molecular machineries contributing to plant autophagy onset and regulation have also gradually come into people’s sights. With the advancement of our knowledge of autophagy from model plants, autophagy research has expanded to include crops in recent years, for a better understanding of autophagy engagement in crop biology and its potentials in improving agricultural performance. In this review, we summarize the current research progress of autophagy in crops and discuss the autophagy-related approaches for potential agronomic trait improvement in crop plants.
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23
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Magen S, Seybold H, Laloum D, Avin-Wittenberg T. Metabolism and autophagy in plants - A perfect match. FEBS Lett 2022; 596:2133-2151. [PMID: 35470431 DOI: 10.1002/1873-3468.14359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 01/18/2023]
Abstract
Autophagy is a eukaryotic cellular transport mechanism that delivers intracellular macromolecules, proteins, and even organelles to a lytic organelle (vacuole in yeast and plants/lysosome in animals) for degradation and nutrient recycling. The process is mediated by highly conserved Autophagy-Related (ATG) proteins. In plants, autophagy maintains cellular homeostasis under favorable conditions, guaranteeing normal plant growth and fitness. Severe stress such as nutrient starvation and plant senescence further induce it, thus ensuring plant survival under unfavorable conditions by providing nutrients through the removal of damaged or aged proteins, or organelles. In this article, we examine the interplay between metabolism and autophagy, focusing on the different aspects of this reciprocal relationship. We show that autophagy has a strong influence on a range of metabolic processes, whereas, at the same time, even single metabolites can activate autophagy. We highlight the involvement of ATG genes in metabolism, examine the role of the macronutrients carbon and nitrogen, as well as various micronutrients, and take a closer look at how the interaction between autophagy and metabolism impacts on plant phenotypes and yield.
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Affiliation(s)
- Sahar Magen
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Israel
| | - Heike Seybold
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Israel
| | - Daniel Laloum
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Israel
| | - Tamar Avin-Wittenberg
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, the Hebrew University of Jerusalem, Israel
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Naumann C, Heisters M, Brandt W, Janitza P, Alfs C, Tang N, Toto Nienguesso A, Ziegler J, Imre R, Mechtler K, Dagdas Y, Hoehenwarter W, Sawers G, Quint M, Abel S. Bacterial-type ferroxidase tunes iron-dependent phosphate sensing during Arabidopsis root development. Curr Biol 2022; 32:2189-2205.e6. [PMID: 35472311 PMCID: PMC9168544 DOI: 10.1016/j.cub.2022.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 02/21/2022] [Accepted: 04/04/2022] [Indexed: 12/02/2022]
Abstract
Access to inorganic phosphate (Pi), a principal intermediate of energy and nucleotide metabolism, profoundly affects cellular activities and plant performance. In most soils, antagonistic Pi-metal interactions restrict Pi bioavailability, which guides local root development to maximize Pi interception. Growing root tips scout the essential but immobile mineral nutrient; however, the mechanisms monitoring external Pi status are unknown. Here, we show that Arabidopsis LOW PHOSPHATE ROOT 1 (LPR1), one key determinant of Fe-dependent Pi sensing in root meristems, encodes a novel ferroxidase of high substrate specificity and affinity (apparent KM ∼ 2 μM Fe2+). LPR1 typifies an ancient, Fe-oxidizing multicopper protein family that evolved early upon bacterial land colonization. The ancestor of streptophyte algae and embryophytes (land plants) acquired LPR1-type ferroxidase from soil bacteria via horizontal gene transfer, a hypothesis supported by phylogenomics, homology modeling, and biochemistry. Our molecular and kinetic data on LPR1 regulation indicate that Pi-dependent Fe substrate availability determines LPR1 activity and function. Guided by the metabolic lifestyle of extant sister bacterial genera, we propose that Arabidopsis LPR1 monitors subtle concentration differentials of external Fe availability as a Pi-dependent cue to adjust root meristem maintenance via Fe redox signaling and cell wall modification. We further hypothesize that the acquisition of bacterial LPR1-type ferroxidase by embryophyte progenitors facilitated the evolution of local Pi sensing and acquisition during plant terrestrialization. Arabidopsis thaliana LPR1 multicopper oxidase typifies a novel ferroxidase cohort Fe availability tunes LPR1-dependent root responses to phosphate (Pi) limitation LPR1 specificity links Fe-Pi interactions to root Pi sensing via redox cycling Streptophyte ancestors acquired LPR1-type ferroxidase from soil bacteria by HGT
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Hibbert L, Taylor G. Improving phosphate use efficiency in the aquatic crop watercress (Nasturtium officinale). HORTICULTURE RESEARCH 2022; 9:uhac011. [PMID: 35147194 PMCID: PMC8969064 DOI: 10.1093/hr/uhac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Watercress is a nutrient-dense leafy green crop, traditionally grown in aquatic outdoor systems and increasingly seen as well-suited for indoor hydroponic systems. However, there is concern that this crop has a detrimental impact on the environment through direct phosphate additions causing environmental pollution. Phosphate-based fertilisers are supplied to enhanced crop yield, but their use may contribute to eutrophication of waterways downstream of traditional watercress farms. One option is to develop a more phosphate use efficient (PUE) crop. This review identifies the key traits for this aquatic crop (the ideotype), for future selection, marker development and breeding. Traits identified as important for PUE are (i) increased root surface area through prolific root branching and adventitious root formation, (ii) aerenchyma formation and root hair growth. Functional genomic traits for improved PUE are (iii) efficacious phosphate remobilisation and scavenging strategies and (iv) the use of alternative metabolic pathways. Key genomic targets for this aquatic crop are identified as: PHT phosphate transporter genes, global transcriptional regulators such as those of the SPX family and genes involved in galactolipid and sulfolipid biosynthesis such as MGD2/3, PECP1, PSR2, PLDζ1/2 and SQD2. Breeding for enhanced PUE in watercress will be accelerated by improved molecular genetic resources such as a full reference genome sequence that is currently in development.
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Affiliation(s)
- Lauren Hibbert
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
| | - Gail Taylor
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
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26
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Lima KRP, Cavalcante FLP, Paula-Marinho SDO, Pereira IMC, Lopes LDS, Nunes JVS, Coutinho ÍAC, Gomes-Filho E, Carvalho HHD. Metabolomic profiles exhibit the influence of endoplasmic reticulum stress on sorghum seedling growth over time. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 170:192-205. [PMID: 34902782 DOI: 10.1016/j.plaphy.2021.11.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
Environmental stresses disturb the endoplasmic reticulum (ER) protein folding. However, primary metabolic responses induced by ER stress remain unclear. Thus, we investigated the morphophysiological and metabolomic changes under ER stress, induced by dithiothreitol (DTT) and tunicamycin (TM) treatments in sorghum seedlings from 24 to 96 h. The ER stress caused lipid peroxidation and increased the expression of SbBiP1, SbPDI, and SbIRE1. The development impairment was more pronounced in roots than in shoots as distinct metabolomic profiles were observed. DTT decreased root length, lateral roots, and root hair, while TM decreased mainly the root length. At 24 h, under ER stresses, the glutamic acid and o-acetyl-serine were biomarkers in the shoots. While homoserine, pyroglutamic acid, and phosphoric acid were candidates for roots. At the latest time (96 h), kestose and galactinol were key metabolites for shoots under DTT and TM, respectively. In roots, palatinose, trehalose, and alanine were common markers for DTT and TM late exposure. The accumulation of sugars such as arabinose and kestose occurred mainly in roots in the presence of DTT at a later time, which also inhibited glycolysis and the tricarboxylic acid cycle (TCA). Amino acid metabolism was induced, which also contributed TCA components decreasing, such as succinate in shoots and citrate in roots. Thus, our study may provide new insights into primary metabolism modulated by ER stress and seedling development.
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Affiliation(s)
- Karollyny Roger Pereira Lima
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, CEP-60440-554, Fortaleza, CE, Brazil
| | | | | | - Isabelle Mary Costa Pereira
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, CEP-60440-554, Fortaleza, CE, Brazil
| | - Lineker de Sousa Lopes
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, CEP-60440-554, Fortaleza, CE, Brazil
| | | | | | - Enéas Gomes-Filho
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, CEP-60440-554, Fortaleza, CE, Brazil
| | - Humberto Henrique de Carvalho
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, CEP-60440-554, Fortaleza, CE, Brazil.
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Gomez RE, Lupette J, Chambaud C, Castets J, Ducloy A, Cacas JL, Masclaux-Daubresse C, Bernard A. How Lipids Contribute to Autophagosome Biogenesis, a Critical Process in Plant Responses to Stresses. Cells 2021; 10:1272. [PMID: 34063958 PMCID: PMC8224036 DOI: 10.3390/cells10061272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/17/2021] [Indexed: 01/18/2023] Open
Abstract
Throughout their life cycle, plants face a tremendous number of environmental and developmental stresses. To respond to these different constraints, they have developed a set of refined intracellular systems including autophagy. This pathway, highly conserved among eukaryotes, is induced by a wide range of biotic and abiotic stresses upon which it mediates the degradation and recycling of cytoplasmic material. Central to autophagy is the formation of highly specialized double membrane vesicles called autophagosomes which select, engulf, and traffic cargo to the lytic vacuole for degradation. The biogenesis of these structures requires a series of membrane remodeling events during which both the quantity and quality of lipids are critical to sustain autophagy activity. This review highlights our knowledge, and raises current questions, regarding the mechanism of autophagy, and its induction and regulation upon environmental stresses with a particular focus on the fundamental contribution of lipids. How autophagy regulates metabolism and the recycling of resources, including lipids, to promote plant acclimation and resistance to stresses is further discussed.
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Affiliation(s)
- Rodrigo Enrique Gomez
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, F-33140 Villenave d’Ornon, France; (R.E.G.); (J.L.); (C.C.); (J.C.)
| | - Josselin Lupette
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, F-33140 Villenave d’Ornon, France; (R.E.G.); (J.L.); (C.C.); (J.C.)
| | - Clément Chambaud
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, F-33140 Villenave d’Ornon, France; (R.E.G.); (J.L.); (C.C.); (J.C.)
| | - Julie Castets
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, F-33140 Villenave d’Ornon, France; (R.E.G.); (J.L.); (C.C.); (J.C.)
| | - Amélie Ducloy
- Institut Jean-Pierre Bourgin, UMR 1318 AgroParisTech-INRAE, Université Paris-Saclay, 78000 Versailles, France; (A.D.); (J.-L.C.); (C.M.-D.)
| | - Jean-Luc Cacas
- Institut Jean-Pierre Bourgin, UMR 1318 AgroParisTech-INRAE, Université Paris-Saclay, 78000 Versailles, France; (A.D.); (J.-L.C.); (C.M.-D.)
| | - Céline Masclaux-Daubresse
- Institut Jean-Pierre Bourgin, UMR 1318 AgroParisTech-INRAE, Université Paris-Saclay, 78000 Versailles, France; (A.D.); (J.-L.C.); (C.M.-D.)
| | - Amélie Bernard
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, F-33140 Villenave d’Ornon, France; (R.E.G.); (J.L.); (C.C.); (J.C.)
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López-Marqués RL, Davis JA, Harper JF, Palmgren M. Dynamic membranes: the multiple roles of P4 and P5 ATPases. PLANT PHYSIOLOGY 2021; 185:619-631. [PMID: 33822217 PMCID: PMC8133672 DOI: 10.1093/plphys/kiaa065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/24/2020] [Indexed: 05/31/2023]
Abstract
The lipid bilayer of biological membranes has a complex composition, including high chemical heterogeneity, the presence of nanodomains of specific lipids, and asymmetry with respect to lipid composition between the two membrane leaflets. In membrane trafficking, membrane vesicles constantly bud off from one membrane compartment and fuse with another, and both budding and fusion events have been proposed to require membrane lipid asymmetry. One mechanism for generating asymmetry in lipid bilayers involves the action of the P4 ATPase family of lipid flippases; these are biological pumps that use ATP as an energy source to flip lipids from one leaflet to the other. The model plant Arabidopsis (Arabidopsis thaliana) contains 12 P4 ATPases (AMINOPHOSPHOLIPID ATPASE1-12; ALA1-12), many of which are functionally redundant. Studies of P4 ATPase mutants have confirmed the essential physiological functions of these pumps and pleiotropic mutant phenotypes have been observed, as expected when genes required for basal cellular functions are disrupted. For instance, phenotypes associated with ala3 (dwarfism, pollen defects, sensitivity to pathogens and cold, and reduced polar cell growth) can be related to membrane trafficking problems. P5 ATPases are evolutionarily related to P4 ATPases, and may be the counterpart of P4 ATPases in the endoplasmic reticulum. The absence of P4 and P5 ATPases from prokaryotes and their ubiquitous presence in eukaryotes make these biological pumps a defining feature of eukaryotic cells. Here, we review recent advances in the field of plant P4 and P5 ATPases.
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Affiliation(s)
- Rosa L López-Marqués
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - James A Davis
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV 89557, USA
| | - Jeffrey F Harper
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV 89557, USA
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
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29
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Molinari M. ER-phagy responses in yeast, plants, and mammalian cells and their crosstalk with UPR and ERAD. Dev Cell 2021; 56:949-966. [PMID: 33765438 DOI: 10.1016/j.devcel.2021.03.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/23/2021] [Accepted: 02/27/2021] [Indexed: 12/24/2022]
Abstract
ER-phagy, literally endoplasmic reticulum (ER)-eating, defines the constitutive or regulated clearance of ER portions within metazoan endolysosomes or yeast and plant vacuoles. The advent of electron microscopy led to the first observations of ER-phagy over 60 years ago, but only recently, with the discovery of a set of regulatory proteins named ER-phagy receptors, has it been dissected mechanistically. ER-phagy receptors are activated by a variety of pleiotropic and ER-centric stimuli. They promote ER fragmentation and engage luminal, membrane-bound, and cytosolic factors, eventually driving lysosomal clearance of select ER domains along with their content. After short historical notes, this review introduces the concept of ER-phagy responses (ERPRs). ERPRs ensure lysosomal clearance of ER portions expendable during nutrient shortage, nonfunctional, present in excess, or containing misfolded proteins. They cooperate with unfolded protein responses (UPRs) and with ER-associated degradation (ERAD) in determining ER size, function, and homeostasis.
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Affiliation(s)
- Maurizio Molinari
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland; School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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30
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Yoshitake Y, Nakamura S, Shinozaki D, Izumi M, Yoshimoto K, Ohta H, Shimojima M. RCB-mediated chlorophagy caused by oversupply of nitrogen suppresses phosphate-starvation stress in plants. PLANT PHYSIOLOGY 2021; 185:318-330. [PMID: 33721901 PMCID: PMC8133631 DOI: 10.1093/plphys/kiaa030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/28/2020] [Indexed: 05/26/2023]
Abstract
Inorganic phosphate (Pi) and nitrogen (N) are essential nutrients for plant growth. We found that a five-fold oversupply of nitrate rescues Arabidopsis (Arabidopsis thaliana) plants from Pi-starvation stress. Analyses of transgenic plants that overexpressed GFP-AUTOPHAGY8 showed that an oversupply of nitrate induced autophagy flux under Pi-depleted conditions. Expression of DIN6 and DIN10, the carbon (C) starvation-responsive genes, was upregulated when nitrate was oversupplied under Pi starvation, which suggested that the plants recognized the oversupply of nitrate as C starvation stress because of the reduction in the C/N ratio. Indeed, formation of Rubisco-containing bodies (RCBs), which contain chloroplast stroma and are induced by C starvation, was enhanced when nitrate was oversupplied under Pi starvation. Moreover, autophagy-deficient mutants did not release Pi (unlike wild-type plants), exhibited no RCB accumulation inside vacuoles, and were hypersensitive to Pi starvation, indicating that RCB-mediated chlorophagy is involved in Pi starvation tolerance. Thus, our results showed that the Arabidopsis response to Pi starvation is closely linked with N and C availability and that autophagy is a key factor that controls plant growth under Pi starvation.
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Affiliation(s)
- Yushi Yoshitake
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
- Department of Life Science, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Sakuya Nakamura
- Center for Sustainable Resource Science, RIKEN, Wako, Saitama 351-0198, Japan
| | - Daiki Shinozaki
- Department of Life Science, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
- Life Science Program, Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Masanori Izumi
- Center for Sustainable Resource Science, RIKEN, Wako, Saitama 351-0198, Japan
| | - Kohki Yoshimoto
- Department of Life Science, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
- Life Science Program, Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Hiroyuki Ohta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Mie Shimojima
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
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31
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Ma Y, Chen R. Nitrogen and Phosphorus Signaling and Transport During Legume-Rhizobium Symbiosis. FRONTIERS IN PLANT SCIENCE 2021; 12:683601. [PMID: 34239527 PMCID: PMC8258413 DOI: 10.3389/fpls.2021.683601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/25/2021] [Indexed: 05/11/2023]
Abstract
Nitrogen (N) and phosphorus (P) are the two predominant mineral elements, which are not only essential for plant growth and development in general but also play a key role in symbiotic N fixation in legumes. Legume plants have evolved complex signaling networks to respond to both external and internal levels of these macronutrients to optimize symbiotic N fixation in nodules. Inorganic phosphate (Pi) and nitrate (NO3 -) are the two major forms of P and N elements utilized by plants, respectively. Pi starvation and NO3 - application both reduce symbiotic N fixation via similar changes in the nodule gene expression and invoke local and long-distance, systemic responses, of which N-compound feedback regulation of rhizobial nitrogenase activity appears to operate under both conditions. Most of the N and P signaling and transport processes have been investigated in model organisms, such as Medicago truncatula, Lotus japonicus, Glycine max, Phaseolus vulgaris, Arabidopsis thaliana, Oryza sativa, etc. We attempted to discuss some of these processes wherever appropriate, to serve as references for a better understanding of the N and P signaling and transport during symbiosis.
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Affiliation(s)
- Yanlin Ma
- MOE Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Rujin Chen
- MOE Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
- School of Life Sciences, Lanzhou University, Lanzhou, China
- *Correspondence: Rujin Chen,
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32
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Wang P, Wang T, Han J, Li M, Zhao Y, Su T, Ma C. Plant Autophagy: An Intricate Process Controlled by Various Signaling Pathways. FRONTIERS IN PLANT SCIENCE 2021; 12:754982. [PMID: 34630498 PMCID: PMC8495024 DOI: 10.3389/fpls.2021.754982] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 08/31/2021] [Indexed: 05/17/2023]
Abstract
Autophagy is a ubiquitous process used widely across plant cells to degrade cellular material and is an important regulator of plant growth and various environmental stress responses in plants. The initiation and dynamics of autophagy in plant cells are precisely controlled according to the developmental stage of the plant and changes in the environment, which are transduced into intracellular signaling pathways. These signaling pathways often regulate autophagy by mediating TOR (Target of Rapamycin) kinase activity, an important regulator of autophagy initiation; however, some also act via TOR-independent pathways. Under nutrient starvation, TOR activity is suppressed through glucose or ROS (reactive oxygen species) signaling, thereby promoting the initiation of autophagy. Under stresses, autophagy can be regulated by the regulatory networks connecting stresses, ROS and plant hormones, and in turn, autophagy regulates ROS levels and hormone signaling. This review focuses on the latest research progress in the mechanism of different external signals regulating autophagy.
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33
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Bao Y, Bassham DC. ER-Phagy and Its Role in ER Homeostasis in Plants. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1771. [PMID: 33327515 PMCID: PMC7764954 DOI: 10.3390/plants9121771] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022]
Abstract
The endoplasmic reticulum (ER) is the largest continuous membrane-bound cellular organelle and plays a central role in the biosynthesis of lipids and proteins and their distribution to other organelles. Autophagy is a conserved process that is required for recycling unwanted cellular components. Recent studies have implicated the ER as a membrane source for the formation of autophagosomes, vesicles that transport material to the vacuole during autophagy. When unfolded proteins accumulate in the ER and/or the ER lipid bilayer is disrupted, a condition known as ER stress results. During ER stress, ER membranes can also be engulfed through autophagy in a process termed ER-phagy. An interplay between ER stress responses and autophagy thus maintains the functions of the ER to allow cellular survival. In this review, we discuss recent progress in understanding ER-phagy in plants, including identification of regulatory factors and selective autophagy receptors. We also identify key unanswered questions in plant ER-phagy for future study.
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Affiliation(s)
- Yan Bao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Diane C. Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
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Mugume Y, Kazibwe Z, Bassham DC. Target of Rapamycin in Control of Autophagy: Puppet Master and Signal Integrator. Int J Mol Sci 2020; 21:ijms21218259. [PMID: 33158137 PMCID: PMC7672647 DOI: 10.3390/ijms21218259] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
The target of rapamycin (TOR) is an evolutionarily-conserved serine/threonine kinase that senses and integrates signals from the environment to coordinate developmental and metabolic processes. TOR senses nutrients, hormones, metabolites, and stress signals to promote cell and organ growth when conditions are favorable. However, TOR is inhibited when conditions are unfavorable, promoting catabolic processes such as autophagy. Autophagy is a macromolecular degradation pathway by which cells degrade and recycle cytoplasmic materials. TOR negatively regulates autophagy through phosphorylation of ATG13, preventing activation of the autophagy-initiating ATG1-ATG13 kinase complex. Here we review TOR complex composition and function in photosynthetic and non-photosynthetic organisms. We also review recent developments in the identification of upstream TOR activators and downstream effectors of TOR. Finally, we discuss recent developments in our understanding of the regulation of autophagy by TOR in photosynthetic organisms.
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35
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Boycheva Woltering S, Isono E. Knowing When to Self-Eat - Fine-Tuning Autophagy Through ATG8 Iso-forms in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:579875. [PMID: 33224169 PMCID: PMC7669990 DOI: 10.3389/fpls.2020.579875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
Autophagy is a catabolic process that takes place under both normal and adverse conditions and is important for the degradation of various organelles and proteins that are no longer needed. Thus, it can be viewed as both a constitutive recycling machinery and an adaptation mechanism. Increase in the activity of autophagy can be caused by multiple biotic and abiotic stress factors. Though intensive research in the past decade has elucidated many molecular details of plant autophagy, the mechanisms of induction and regulation of the process remain understudied. Here, we discuss the role of ATG8 proteins in autophagic signaling and regulation with an emphasis on the significance of ATG8 diversification for adapting autophagy to the changing needs of plants.
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Affiliation(s)
- Svetlana Boycheva Woltering
- Department of Biology, University of Konstanz, Konstanz, Germany
- Zukunftskolleg, University of Konstanz, Konstanz, Germany
| | - Erika Isono
- Department of Biology, University of Konstanz, Konstanz, Germany
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36
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Stephani M, Picchianti L, Gajic A, Beveridge R, Skarwan E, Sanchez de Medina Hernandez V, Mohseni A, Clavel M, Zeng Y, Naumann C, Matuszkiewicz M, Turco E, Loefke C, Li B, Dürnberger G, Schutzbier M, Chen HT, Abdrakhmanov A, Savova A, Chia KS, Djamei A, Schaffner I, Abel S, Jiang L, Mechtler K, Ikeda F, Martens S, Clausen T, Dagdas Y. A cross-kingdom conserved ER-phagy receptor maintains endoplasmic reticulum homeostasis during stress. eLife 2020; 9:e58396. [PMID: 32851973 PMCID: PMC7515635 DOI: 10.7554/elife.58396] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022] Open
Abstract
Eukaryotes have evolved various quality control mechanisms to promote proteostasis in the endoplasmic reticulum (ER). Selective removal of certain ER domains via autophagy (termed as ER-phagy) has emerged as a major quality control mechanism. However, the degree to which ER-phagy is employed by other branches of ER-quality control remains largely elusive. Here, we identify a cytosolic protein, C53, that is specifically recruited to autophagosomes during ER-stress, in both plant and mammalian cells. C53 interacts with ATG8 via a distinct binding epitope, featuring a shuffled ATG8 interacting motif (sAIM). C53 senses proteotoxic stress in the ER lumen by forming a tripartite receptor complex with the ER-associated ufmylation ligase UFL1 and its membrane adaptor DDRGK1. The C53/UFL1/DDRGK1 receptor complex is activated by stalled ribosomes and induces the degradation of internal or passenger proteins in the ER. Consistently, the C53 receptor complex and ufmylation mutants are highly susceptible to ER stress. Thus, C53 forms an ancient quality control pathway that bridges selective autophagy with ribosome-associated quality control in the ER.
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Affiliation(s)
- Madlen Stephani
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Lorenzo Picchianti
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Alexander Gajic
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Rebecca Beveridge
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Emilio Skarwan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | | | - Azadeh Mohseni
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Marion Clavel
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Yonglun Zeng
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, School of Life Sciences, New TerritoriesShatinChina
| | - Christin Naumann
- Department of Molecular Signal Processing, Leibniz Institute of Plant BiochemistryHalleGermany
| | - Mateusz Matuszkiewicz
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences-SGGWWarsawPoland
| | - Eleonora Turco
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Christian Loefke
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Baiying Li
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, School of Life Sciences, New TerritoriesShatinChina
| | - Gerhard Dürnberger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Michael Schutzbier
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Hsiao Tieh Chen
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, School of Life Sciences, New TerritoriesShatinChina
| | - Alibek Abdrakhmanov
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Adriana Savova
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Khong-Sam Chia
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Armin Djamei
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
| | - Irene Schaffner
- BOKU Core Facility Biomolecular & Cellular Analysis, University of Natural Resources and Life SciencesViennaAustria
| | - Steffen Abel
- Department of Molecular Signal Processing, Leibniz Institute of Plant BiochemistryHalleGermany
| | - Liwen Jiang
- School of Life Sciences, Centre for Cell and Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, School of Life Sciences, New TerritoriesShatinChina
| | - Karl Mechtler
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Fumiyo Ikeda
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu UniversityFukuokaJapan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC)ViennaAustria
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC)ViennaAustria
| | - Tim Clausen
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
- Medical University of ViennaViennaAustria
| | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC)ViennaAustria
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37
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Autophagy Dances with Phytohormones upon Multiple Stresses. PLANTS 2020; 9:plants9081038. [PMID: 32824209 PMCID: PMC7463709 DOI: 10.3390/plants9081038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/11/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
Autophagy is an evolutionarily conserved process for turning over unwanted cellular components, thus promoting nutrient recycling and maintaining cellular homeostasis, which eventually enables plants to survive unfavorable growth conditions. In addition to plant growth and development, previous studies have demonstrated that autophagy is involved in the responses to various environmental challenges through interplaying with multiple phytohormones, including abscisic acid (ABA), jasmonic acid (JA), and salicylic acid (SA). In this review, we summarize the advances made in their synergistic interactions in response to multiple abiotic and biotic stresses; we also discuss the remaining issues and perspectives regarding their crosstalk.
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38
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Transcriptional and Epigenetic Regulation of Autophagy in Plants. Trends Genet 2020; 36:676-688. [PMID: 32674948 DOI: 10.1016/j.tig.2020.06.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 01/12/2023]
Abstract
Autophagy, a highly conserved quality control mechanism, is essential for maintaining cellular homeostasis and healthy growth of plants. Compared with extensive research in the cytoplasmic control of autophagy, studies regarding the nuclear events involved in the regulation of plant autophagy are just beginning to emerge. Accumulating evidence reveals a coordinated expression of plant autophagy genes in response to diverse developmental states and growth conditions. Here, we summarize recent progress in the identification of tightly controlled transcription factors and histone marks associated with the autophagic process in plants, and propose several modules, consisting of transcription regulators and epigenetic modifiers, as important nuclear players that could contribute to both short-term and long-term controls of plant autophagy at the transcriptional and post-transcriptional levels.
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39
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Blocking the Bromodomains Function Contributes to Disturbances in Alga Chara vulgaris Spermatids Differentiation. Cells 2020; 9:cells9061352. [PMID: 32486024 PMCID: PMC7349737 DOI: 10.3390/cells9061352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 12/04/2022] Open
Abstract
Bromodomain containing (BRD) proteins play an essential role in many cellular processes. The aim of this study was to estimate activity of bromodomains during alga Chara vulgaris spermatids differentiation. The effect of a bromodomain inhibitor, JQ1 (100 μM), on the distribution of individual stages of spermatids and their ultrastructure was studied. The material was Feulgen stained and analysed in an electron microscope. JQ1 caused shortening of the early stages of spermiogenesis and a reverse reaction at the later stages. Additionally, in the same antheridium, spermatids at distant developmental stages were present. On the ultrastructural level, chromatin fibril system disorders and significantly distended endoplasmic reticulum (ER) cisternae already at the early stages were observed. Many autolytic vacuoles were also visible. The ultrastructural disturbances intensified after prolonged treatment with JQ1. The obtained data show that JQ1 treatment led to changes in the spermatid number and disturbances in chromatin condensation and to cytoplasm reduction. The current studies show some similarities between C. vulgaris and mammals spermiogenesis. Taken together, these results suggest that JQ1 interferes with the spermatid differentiation on many interdependent levels and seems to induce ER stress, which leads to spermatid degeneration. Studies on the role of bromodomains in algae spermiogenesis have not been conducted so far.
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40
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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.
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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
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41
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Borek S, Stefaniak S, Śliwiński J, Garnczarska M, Pietrowska-Borek M. Autophagic Machinery of Plant Peroxisomes. Int J Mol Sci 2019; 20:E4754. [PMID: 31557865 PMCID: PMC6802006 DOI: 10.3390/ijms20194754] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/22/2019] [Accepted: 09/23/2019] [Indexed: 12/28/2022] Open
Abstract
Peroxisomes are cell organelles that play an important role in plants in many physiological and developmental processes. The plant peroxisomes harbor enzymes of the β-oxidation of fatty acids and the glyoxylate cycle; photorespiration; detoxification of reactive oxygen and nitrogen species; as well as biosynthesis of hormones and signal molecules. The function of peroxisomes in plant cells changes during plant growth and development. They are transformed from organelles involved in storage lipid breakdown during seed germination and seedling growth into leaf peroxisomes involved in photorespiration in green parts of the plant. Additionally, intensive oxidative metabolism of peroxisomes causes damage to their components. Therefore, unnecessary or damaged peroxisomes are degraded by selective autophagy, called pexophagy. This is an important element of the quality control system of peroxisomes in plant cells. Despite the fact that the mechanism of pexophagy has already been described for yeasts and mammals, the molecular mechanisms by which plant cells recognize peroxisomes that will be degraded via pexophagy still remain unclear. It seems that a plant-specific mechanism exists for the selective degradation of peroxisomes. In this review, we describe the physiological role of pexophagy in plant cells and the current hypotheses concerning the mechanism of plant pexophagy.
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Affiliation(s)
- Sławomir Borek
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Szymon Stefaniak
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Jan Śliwiński
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK.
| | - Małgorzata Garnczarska
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Małgorzata Pietrowska-Borek
- Department of Biochemistry and Biotechnology, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland.
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42
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Pan W, Wu Y, Xie Q. Regulation of Ubiquitination Is Central to the Phosphate Starvation Response. TRENDS IN PLANT SCIENCE 2019; 24:755-769. [PMID: 31176527 DOI: 10.1016/j.tplants.2019.05.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/02/2019] [Accepted: 05/08/2019] [Indexed: 05/22/2023]
Abstract
As sessile organisms, plants have developed numerous strategies to overcome the limiting availability of the essential nutrient phosphate in nature. Recent studies reveal that post-translational modification (PTM) by ubiquitination is an important and central regulation mechanism in the plant phosphate starvation response (PSR). Ubiquitination precisely modulates the stability and trafficking of proteins in response to the heterogeneous phosphate supplement. Induction of autophagy provides novel insights into the molecular mechanisms under phosphate starvation. In this review, we present and discuss novel findings on the regulation of diverse PSRs through ubiquitination. Resolving these regulation mechanisms will pave the way to improve phosphate acquisition and utilization efficiency in crops.
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Affiliation(s)
- Wenbo Pan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaorong Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Qi Xie
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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43
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Zeng Y, Li B, Zhang W, Jiang L. ER-Phagy and ER Stress Response (ERSR) in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:1192. [PMID: 31611901 PMCID: PMC6777540 DOI: 10.3389/fpls.2019.01192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/29/2019] [Indexed: 05/03/2023]
Abstract
The endoplasmic reticulum (ER) is the starting point for protein secretion and lipid biosynthesis in eukaryotes. ER homeostasis is precisely regulated by the unfolded protein response (UPR) to alleviate stress, involving both transcriptional and translational regulators. Autophagy is an intracellular self-eating process mediated by the double-membrane structure autophagosome for the degradation of cytosolic components and damaged organelles to regenerate nutrient supplies under nutrient-deficient or stress conditions. A recent study has revealed that besides serving as a membrane source for phagophore formation, the ER is also tightly regulated under stress conditions by a distinct type of autophagosome, namely ER-phagy. ER-phagy has been characterized with receptors clearly identified in mammals and yeast, yet relatively little is known about plant ER-phagy and its receptors. Here, we will summarize our current knowledge of ER-phagy in yeast and mammals and highlight recent progress in plant ER-phagy studies, pointing towards a possible interplay between ER-phagy and ER homeostasis under ER stress responses (ERSRs) in plants.
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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
- *Correspondence: Yonglun Zeng, ; Baiying Li, ; Liwen Jiang,
| | - 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
- *Correspondence: Yonglun Zeng, ; Baiying Li, ; Liwen Jiang,
| | - Wenxin Zhang
- 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
- *Correspondence: Yonglun Zeng, ; Baiying Li, ; Liwen Jiang,
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