1
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Sharma I, Talakayala A, Tiwari M, Asinti S, Kirti PB. A synchronized symphony: Intersecting roles of ubiquitin proteasome system and autophagy in cellular degradation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108700. [PMID: 38781635 DOI: 10.1016/j.plaphy.2024.108700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/01/2024] [Indexed: 05/25/2024]
Abstract
Eukaryotic cells have evolved dynamic quality control pathways and recycling mechanisms for cellular homeostasis. We discuss here, the two major systems for quality control, the ubiquitin-proteasome system (UPS) and autophagy that regulate cellular protein and organelle turnover and ensure efficient nutrient management, cellular integrity and long-term wellbeing of the plant. Both the pathways rely on ubiquitination signal to identify the targets for proteasomal and autophagic degradation, yet they use distinct degradation machinery to process these cargoes. Nonetheless, both UPS and autophagy operate together as an interrelated quality control mechanism where they communicate with each other at multiple nodes to coordinate and/or compensate the recycling mechanism particularly under development and environmental cues. Here, we provide an update on the cellular machinery of autophagy and UPS, unravel the nodes of their crosstalk and particularly highlight the factors responsible for their differential deployment towards protein, macromolecular complexes and organelles.
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Affiliation(s)
- Isha Sharma
- International Crop Research Institute for Semi-Arid Tropics, Patancheru, Hyderabad, India, 502324.
| | - Ashwini Talakayala
- International Crop Research Institute for Semi-Arid Tropics, Patancheru, Hyderabad, India, 502324
| | - Manish Tiwari
- CSIR-National Botanical Research Institute, 435, Rana Pratap Marg, Lucknow, 226001, Uttar Pradesh, India
| | - Sarath Asinti
- Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, Uttar Pradesh, 211007, India
| | - P B Kirti
- Agri Biotech Foundation, Rajendranagar, 500030, Hyderabad, India
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2
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He L, Liu Q, Han S. Genome-Wide Analysis of Serine Carboxypeptidase-like Genes in Soybean and Their Roles in Stress Resistance. Int J Mol Sci 2024; 25:6712. [PMID: 38928417 PMCID: PMC11203753 DOI: 10.3390/ijms25126712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/11/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
The serine carboxypeptidase-like (SCPL) gene family plays a crucial role in the regulation of plant growth, development, and stress response through activities such as acyltransferases in plant secondary metabolism pathways. Although SCPL genes have been identified in various plant species, their specific functions and characteristics in soybean (Glycine max) have not yet been studied. We identified and characterized 73 SCPL genes, grouped into three subgroups based on gene structure and phylogenetic relationships. These genes are distributed unevenly across 20 soybean chromosomes and show varied codon usage patterns influenced by both mutation and selection pressures. Gene ontology (GO) enrichment suggests these genes are involved in plant cell wall regulation and stress responses. Expression analysis in various tissues and under stress conditions, including the presence of numerous stress-related cis-acting elements, indicated that these genes have varied expression patterns. This suggests that they play specialized roles such as modulating plant defense mechanisms against nematode infections, enhancing tolerance to drought and high salinity, and responding to cold stress, thereby helping soybean adapt to environmental stresses. Moreover, the expression of specific GmSCPLs was significantly affected following exposure to nematode infection, drought, high salt (NaCl), and cold stresses. Our findings underscore the potential of SCPL genes in enhancing stress resistance in soybean, providing a valuable resource for future genetic improvement and breeding strategies.
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Affiliation(s)
- Long He
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (L.H.); (Q.L.)
- Zhejiang Lab, Hangzhou 310058, China
| | - Qiannan Liu
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (L.H.); (Q.L.)
| | - Shaojie Han
- State Key Laboratory of Rice Biology and Breeding, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (L.H.); (Q.L.)
- Zhejiang Lab, Hangzhou 310058, China
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3
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Parra M, Coppola M, Hellmann H. PDX proteins from Arabidopsis thaliana as novel substrates of cathepsin B: implications for vitamin B 6 biosynthesis regulation. FEBS J 2024; 291:2372-2387. [PMID: 38431778 DOI: 10.1111/febs.17110] [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: 05/29/2023] [Revised: 12/18/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024]
Abstract
Vitamin B6 is a critical molecule for metabolism, development, and stress sensitivity in plants. It is a cofactor for numerous biochemical reactions, can serve as an antioxidant, and has the potential to increase tolerance against both biotic and abiotic stressors. Due to the importance of vitamin B6, its biosynthesis is likely tightly regulated. Plants can synthesize vitamin B6 de novo via the concerted activity of Pyridoxine Biosynthesis Protein 1 (PDX1) and PDX2. Previously, PDX proteins have been identified as targets for ubiquitination, indicating they could be marked for degradation by two highly conserved pathways: the Ubiquitin Proteasome Pathway (UPP) and the autophagy pathway. Initial experiments show that PDXs are in fact degraded, but surprisingly, in a ubiquitin-independent manner. Inhibitor studies pointed toward cathepsin B, a conserved lysosomal cysteine protease, which is implicated in both programed cell death and autophagy in humans and plants. In plants, cathepsin Bs are poorly described, and no confirmed substrates have been identified. Here, we present PDX proteins from Arabidopsis thaliana as interactors and substrates of a plant Cathepsin B. These findings not only describe a novel cathepsin B substrate in plants, but also provide new insights into how plants regulate de novo biosynthesis of vitamin B6.
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Affiliation(s)
- Marcelina Parra
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | | | - Hanjo Hellmann
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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Luo J, Havé M, Soulay F, Balliau T, Clément G, Tellier F, Zivy M, Avice JC, Masclaux-Daubresse C. Multi-omics analyses of sid2 mutant reflect the need of isochorismate synthase ICS1 to cope with sulfur limitation in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1635-1651. [PMID: 38498624 DOI: 10.1111/tpj.16702] [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: 10/27/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/20/2024]
Abstract
The SID2 (SA INDUCTION-DEFICIENT2) gene that encodes ICS1 (isochorismate synthase), plays a central role in salicylic acid biosynthesis in Arabidopsis. The sid2 and NahG (encoding a bacterial SA hydroxylase) overexpressing mutants (NahG-OE) have currently been shown to outperform wild type, presenting delayed leaf senescence, higher plant biomass and better seed yield. When grown under sulfate-limited conditions (low-S), sid2 mutants exhibited early leaf yellowing compared to the NahG-OE, the npr1 mutant affected in SA signaling pathway, and WT. This indicated that the hypersensitivity of sid2 to sulfate limitation was independent of the canonical npr1 SA-signaling pathway. Transcriptomic and proteomic analyses revealed that major changes occurred in sid2 when cultivated under low-S, changes that were in good accordance with early senescence phenotype and showed the exacerbation of stress responses. The sid2 mutants displayed a lower sulfate uptake capacity when cultivated under low-S and lower S concentrations in their rosettes. Higher glutathione concentrations in sid2 rosettes under low-S were in good accordance with the higher abundance of proteins involved in glutathione and ascorbate redox metabolism. Amino acid and lipid metabolisms were also strongly modified in sid2 under low-S. Depletion of total fatty acids in sid2 under low-S was consistent with the fact that S-metabolism plays a central role in lipid synthesis. Altogether, our results show that functional ICS1 is important for plants to cope with S limiting conditions.
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Affiliation(s)
- Jie Luo
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Marien Havé
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Fabienne Soulay
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Thierry Balliau
- UMR GQE- le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Gilles Clément
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Frédérique Tellier
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Michel Zivy
- UMR GQE- le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Jean-Christophe Avice
- UMR 950 EVA (Ecophysiologie Végétale & Agronomie), INRAE, Normandie Université (UNICAEN), Federation of Research Normandie Végétal (Fed4277 NORVEGE), 14032, Caen, France
| | - Céline Masclaux-Daubresse
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
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5
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Yang G, Chen T, Fan TT, Lin XY, Cui YQ, Dong WC, An LZ, Zhang H. Cathepsin B degrades RbcL during freezing-induced programmed cell death in Arabidopsis. PLANT CELL REPORTS 2024; 43:81. [PMID: 38418607 DOI: 10.1007/s00299-023-03099-2] [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: 08/16/2023] [Accepted: 10/20/2023] [Indexed: 03/01/2024]
Abstract
KEY MESSAGE Cathepsin B plays an important role that degrades the Rubisco large subunit RbcL in freezing stress. Programmed cell death (PCD) has been well documented in both development and in response to environmental stresses in plants, however, PCD induced by freezing stress and its molecular mechanisms remain poorly understood. In the present study, we characterized freezing-induced PCD and explored its mechanisms in Arabidopsis. PCD induced by freezing stress was similar to that induced by other stresses and senescence in Arabidopsis plants with cold acclimation. Inhibitor treatment assays and immunoblotting indicated that cathepsin B mainly contributed to increased caspase-3-like activity during freezing-induced PCD. Cathepsin B was involved in freezing-induced PCD and degraded the large subunit, RbcL, of Rubisco. Our results demonstrate an essential regulatory mechanism of cathepsin B for Rubisco degradation in freezing-induced PCD, improving our understanding of freezing-induced cell death and nitrogen and carbohydrate remobilisation in plants.
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Affiliation(s)
- Gang Yang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Tao Chen
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ting-Ting Fan
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiang-Yu Lin
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yu-Qiong Cui
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Wei-Chao Dong
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Li-Zhe An
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
- School of Forestry, Beijing Forestry University, Beijing, 100083, China.
| | - Hua Zhang
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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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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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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8
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Ebinezer LB, Battisti I, Sharma N, Ravazzolo L, Ravi L, Trentin AR, Barion G, Panozzo A, Dall'Acqua S, Vamerali T, Quaggiotti S, Arrigoni G, Masi A. Perfluorinated alkyl substances affect the growth, physiology and root proteome of hydroponically grown maize plants. JOURNAL OF HAZARDOUS MATERIALS 2022; 438:129512. [PMID: 35999737 DOI: 10.1016/j.jhazmat.2022.129512] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 06/14/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Poly- and perfluorinated alkyl substances (PFAS) are a group of persistent organic pollutants causing serious global concern. Plants can accumulate PFAS but their effect on plant physiology, especially at the molecular level is not very well understood. Hence, we used hydroponically-grown maize plants treated with a combination of eleven different PFAS (each at 100 μg L-1) to investigate their bioaccumulation and effects on the growth, physiology and their impact on the root proteome. A dose-dependent decrease in root growth parameters was evidenced with a significant reduction in the relative growth rate, fresh weight of leaves and roots and altered photosynthetic parameters in PFAS-treated plants. Higher concentration of shorter PFAS (C < 8) was detected in the leaves, while long-chain PFAS (C ≥ 8) were more retained in roots. From the root proteome analysis, we identified 75 differentially abundant proteins, mostly involved in cellular metabolic and biosynthetic processes, translation and cytoskeletal reorganization. Validating the altered protein abundance using quantitative real-time PCR, the results were further substantiated using amino acid and fatty acid profiling, thus, providing first insight into the altered metabolic state of plants exposed to PFAS from a proteomics perspective.
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Affiliation(s)
- Leonard Barnabas Ebinezer
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Ilaria Battisti
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy; Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, via G. Orus 2/B, 35129 Padova, Italy
| | - Nisha Sharma
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Laura Ravazzolo
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Lokesh Ravi
- Department of Botany, St. Joseph's College (Autonomous), Bengaluru, India
| | - Anna Rita Trentin
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Giuseppe Barion
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Anna Panozzo
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Stefano Dall'Acqua
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 PD, Italy
| | - Teofilo Vamerali
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Silvia Quaggiotti
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Giorgio Arrigoni
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, via G. Orus 2/B, 35129 Padova, Italy; Department of Biomedical Sciences, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy; CRIBI Biotechnology Center, University of Padova, via U. Bassi 58/B, 35131 Padova, Italy.
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
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9
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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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10
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Yip Delormel T, Avila-Ospina L, Davanture M, Zivy M, Lang J, Valentin N, Rayapuram N, Hirt H, Colcombet J, Boudsocq M. In vivo identification of putative CPK5 substrates in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 314:111121. [PMID: 34895550 DOI: 10.1016/j.plantsci.2021.111121] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Calcium signaling mediates most developmental processes and stress responses in plants. Among plant calcium sensors, the calcium-dependent protein kinases display a unique structure harboring both calcium sensing and kinase responding activities. AtCPK5 is an essential member of this family in Arabidopsis that regulates immunity and abiotic stress tolerance. To understand the underlying molecular mechanisms, we implemented a biochemical approach to identify in vivo substrates of AtCPK5. We generated transgenic lines expressing a constitutively active form of AtCPK5 under the control of a dexamethasone-inducible promoter. Lines expressing a kinase-dead version were used as a negative control. By comparing the phosphoproteome of the kinase-active and kinase-dead lines upon dexamethasone treatment, we identified 5 phosphopeptides whose abundance increased specifically in the kinase-active lines. Importantly, we showed that all 5 proteins were phosphorylated in vitro by AtCPK5 in a calcium-dependent manner, suggesting that they are direct targets of AtCPK5. We also detected several interaction patterns between the kinase and the candidates in the cytosol, membranes or nucleus, consistent with the ubiquitous localization of AtCPK5. Finally, we further validated the two phosphosites S245 and S280 targeted by AtCPK5 in the E3 ubiquitin ligase ATL31. Altogether, those results open new perspectives to decipher AtCPK5 biological functions.
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Affiliation(s)
- Tiffany Yip Delormel
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.
| | - Liliana Avila-Ospina
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.
| | - Marlène Davanture
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Évolution (GQE) - Le Moulon, 91190, Gif-sur-Yvette, France.
| | - Michel Zivy
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Évolution (GQE) - Le Moulon, 91190, Gif-sur-Yvette, France.
| | - Julien Lang
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.
| | - Nicolas Valentin
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.
| | - Naganand Rayapuram
- Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Heribert Hirt
- Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Jean Colcombet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.
| | - Marie Boudsocq
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.
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11
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Jin X, Liu Y, Hou Z, Zhang Y, Fang Y, Huang Y, Cai H, Qin Y, Cheng Y. Genome-Wide Investigation of SBT Family Genes in Pineapple and Functional Analysis of AcoSBT1.12 in Floral Transition. Front Genet 2021; 12:730821. [PMID: 34557223 PMCID: PMC8452990 DOI: 10.3389/fgene.2021.730821] [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: 06/25/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
SBT (Subtilisin-like serine protease), a clan of serine proteolytic enzymes, plays a versatile role in plant growth and defense. Although SBT family genes have been obtained from studies of dicots such as Arabidopsis, little is known about the potential functions of SBT in the monocots. In this study, 54 pineapple SBT genes (AcoSBTs) were divided into six subfamilies and then identified to be experienced strong purifying selective pressure and distributed on 25 chromosomes unevenly. Cis-acting element analysis indicated that almost all AcoSBTs promoters contain light-responsive elements. Further, the expression pattern via RNA-seq data showed that different AcoSBTs were preferentially expressed in different above-ground tissues. Transient expression in tobacco showed that AcoSBT1.12 was located in the plasma membrane. Moreover, Transgenic Arabidopsis ectopically overexpressing AcoSBT1.12 exhibited delayed flowering time. In addition, under the guidance of bioinformatic prediction, we found that AcoSBT1.12 could interact with AcoCWF19L, AcoPUF2, AcoCwfJL, Aco012905, and AcoSZF1 by yeast-two hybrid (Y2H). In summary, this study provided valuable information on pineapple SBT genes and illuminated the biological function of AcoSBT1.12 in floral transition.
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Affiliation(s)
- Xingyue Jin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanhui Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhimin Hou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunfei Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunying Fang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youmei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hanyang Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Cheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, College of Plant Protection, College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
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12
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Gems D, Kern CC, Nour J, Ezcurra M. Reproductive Suicide: Similar Mechanisms of Aging in C. elegans and Pacific Salmon. Front Cell Dev Biol 2021; 9:688788. [PMID: 34513830 PMCID: PMC8430333 DOI: 10.3389/fcell.2021.688788] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/21/2021] [Indexed: 12/17/2022] Open
Abstract
In some species of salmon, reproductive maturity triggers the development of massive pathology resulting from reproductive effort, leading to rapid post-reproductive death. Such reproductive death, which occurs in many semelparous organisms (with a single bout of reproduction), can be prevented by blocking reproductive maturation, and this can increase lifespan dramatically. Reproductive death is often viewed as distinct from senescence in iteroparous organisms (with multiple bouts of reproduction) such as humans. Here we review the evidence that reproductive death occurs in C. elegans and discuss what this means for its use as a model organism to study aging. Inhibiting insulin/IGF-1 signaling and germline removal suppresses reproductive death and greatly extends lifespan in C. elegans, but can also extend lifespan to a small extent in iteroparous organisms. We argue that mechanisms of senescence operative in reproductive death exist in a less catastrophic form in iteroparous organisms, particularly those that involve costly resource reallocation, and exhibit endocrine-regulated plasticity. Thus, mechanisms of senescence in semelparous organisms (including plants) and iteroparous ones form an etiological continuum. Therefore understanding mechanisms of reproductive death in C. elegans can teach us about some mechanisms of senescence that are operative in iteroparous organisms.
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Affiliation(s)
- David Gems
- Institute of Healthy Ageing, Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Carina C. Kern
- Institute of Healthy Ageing, Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Joseph Nour
- Institute of Healthy Ageing, Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Marina Ezcurra
- School of Biosciences, University of Kent, Canterbury, United Kingdom
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13
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Guo Y, Ren G, Zhang K, Li Z, Miao Y, Guo H. Leaf senescence: progression, regulation, and application. MOLECULAR HORTICULTURE 2021; 1:5. [PMID: 37789484 PMCID: PMC10509828 DOI: 10.1186/s43897-021-00006-9] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/11/2021] [Indexed: 05/24/2023]
Abstract
Leaf senescence, the last stage of leaf development, is a type of postmitotic senescence and is characterized by the functional transition from nutrient assimilation to nutrient remobilization which is essential for plants' fitness. The initiation and progression of leaf senescence are regulated by a variety of internal and external factors such as age, phytohormones, and environmental stresses. Significant breakthroughs in dissecting the molecular mechanisms underpinning leaf senescence have benefited from the identification of senescence-altered mutants through forward genetic screening and functional assessment of hundreds of senescence-associated genes (SAGs) via reverse genetic research in model plant Arabidopsis thaliana as well as in crop plants. Leaf senescence involves highly complex genetic programs that are tightly tuned by multiple layers of regulation, including chromatin and transcription regulation, post-transcriptional, translational and post-translational regulation. Due to the significant impact of leaf senescence on photosynthesis, nutrient remobilization, stress responses, and productivity, much effort has been made in devising strategies based on known senescence regulatory mechanisms to manipulate the initiation and progression of leaf senescence, aiming for higher yield, better quality, or improved horticultural performance in crop plants. This review aims to provide an overview of leaf senescence and discuss recent advances in multi-dimensional regulation of leaf senescence from genetic and molecular network perspectives. We also put forward the key issues that need to be addressed, including the nature of leaf age, functional stay-green trait, coordination between different regulatory pathways, source-sink relationship and nutrient remobilization, as well as translational researches on leaf senescence.
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Affiliation(s)
- Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101 Shandong China
| | - Guodong Ren
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Kewei Zhang
- Institute of Plant Genetics and Developmental Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, 321004 Zhejiang China
| | - Zhonghai Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Hongwei Guo
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, 518055 Guangdong China
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14
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Current Understanding of Leaf Senescence in Rice. Int J Mol Sci 2021; 22:ijms22094515. [PMID: 33925978 PMCID: PMC8123611 DOI: 10.3390/ijms22094515] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 11/17/2022] Open
Abstract
Leaf senescence, which is the last developmental phase of plant growth, is controlled by multiple genetic and environmental factors. Leaf yellowing is a visual indicator of senescence due to the loss of the green pigment chlorophyll. During senescence, the methodical disassembly of macromolecules occurs, facilitating nutrient recycling and translocation from the sink to the source organs, which is critical for plant fitness and productivity. Leaf senescence is a complex and tightly regulated process, with coordinated actions of multiple pathways, responding to a sophisticated integration of leaf age and various environmental signals. Many studies have been carried out to understand the leaf senescence-associated molecular mechanisms including the chlorophyll breakdown, phytohormonal and transcriptional regulation, interaction with environmental signals, and associated metabolic changes. The metabolic reprogramming and nutrient recycling occurring during leaf senescence highlight the fundamental role of this developmental stage for the nutrient economy at the whole plant level. The strong impact of the senescence-associated nutrient remobilization on cereal productivity and grain quality is of interest in many breeding programs. This review summarizes our current knowledge in rice on (i) the actors of chlorophyll degradation, (ii) the identification of stay-green genotypes, (iii) the identification of transcription factors involved in the regulation of leaf senescence, (iv) the roles of leaf-senescence-associated nitrogen enzymes on plant performance, and (v) stress-induced senescence. Compiling the different advances obtained on rice leaf senescence will provide a framework for future rice breeding strategies to improve grain yield.
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15
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Wang H, Ding Z, Gou M, Hu J, Wang Y, Wang L, Wang Y, Di T, Zhang X, Hao X, Wang X, Yang Y, Qian W. Genome-wide identification, characterization, and expression analysis of tea plant autophagy-related genes (CsARGs) demonstrates that they play diverse roles during development and under abiotic stress. BMC Genomics 2021; 22:121. [PMID: 33596831 PMCID: PMC7891152 DOI: 10.1186/s12864-021-07419-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/31/2021] [Indexed: 12/12/2022] Open
Abstract
Background Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay aging and longevity in eukaryotes. To date, the functions of autophagy have been heavily studied in yeast, mammals and model plants, but few studies have focused on economically important crops, especially tea plants (Camellia sinensis). The roles played by autophagy in coping with various environmental stimuli have not been fully elucidated to date. Therefore, investigating the functions of autophagy-related genes in tea plants may help to elucidate the mechanism governing autophagy in response to stresses in woody plants. Results In this study, we identified 35 C. sinensis autophagy-related genes (CsARGs). Each CsARG is highly conserved with its homologues from other plant species, except for CsATG14. Tissue-specific expression analysis demonstrated that the abundances of CsARGs varied across different tissues, but CsATG8c/i showed a degree of tissue specificity. Under hormone and abiotic stress conditions, most CsARGs were upregulated at different time points during the treatment. In addition, the expression levels of 10 CsARGs were higher in the cold-resistant cultivar ‘Longjing43’ than in the cold-susceptible cultivar ‘Damianbai’ during the CA period; however, the expression of CsATG101 showed the opposite tendency. Conclusions We performed a comprehensive bioinformatic and physiological analysis of CsARGs in tea plants, and these results may help to establish a foundation for further research investigating the molecular mechanisms governing autophagy in tea plant growth, development and response to stress. Meanwhile, some CsARGs could serve as putative molecular markers for the breeding of cold-resistant tea plants in future research. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07419-2.
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Affiliation(s)
- Huan Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhaotang Ding
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Mengjie Gou
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jianhui Hu
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yu Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lu Wang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.,Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Yuchun Wang
- College of Agriculture and Food Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Taimei Di
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.,Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Xinfu Zhang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xinyuan Hao
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.,Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Xinchao Wang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.,Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Yajun Yang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China.,Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Wenjun Qian
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
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16
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Wolff H, Jakoby M, Stephan L, Koebke E, Hülskamp M. Heat Stress-Dependent Association of Membrane Trafficking Proteins With mRNPs Is Selective. FRONTIERS IN PLANT SCIENCE 2021; 12:670499. [PMID: 34249042 PMCID: PMC8264791 DOI: 10.3389/fpls.2021.670499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/27/2021] [Indexed: 05/03/2023]
Abstract
The Arabidopsis AAA ATPase SKD1 is essential for ESCRT-dependent endosomal sorting by mediating the disassembly of the ESCRTIII complex in an ATP-dependent manner. In this study, we show that SKD1 localizes to messenger ribonucleoprotein complexes upon heat stress. Consistent with this, the interactome of SKD1 revealed differential interactions under normal and stress conditions and included membrane transport proteins as well as proteins associated with RNA metabolism. Localization studies with selected interactome proteins revealed that not only RNA associated proteins but also several ESCRTIII and membrane trafficking proteins were recruited to messenger ribonucleoprotein granules after heat stress.
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Affiliation(s)
- Heike Wolff
- Cluster of Excellence on Plant Sciences (CEPLAS), Botanical Institute, Cologne University, Cologne, Germany
| | - Marc Jakoby
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Lisa Stephan
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Eva Koebke
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
| | - Martin Hülskamp
- Botanical Institute, Biocenter, Cologne University, Cologne, Germany
- *Correspondence: Martin Hülskamp
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17
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Shi Z, Halaly-Basha T, Zheng C, Sharabi-Schwager M, Wang C, Galbraith DW, Ophir R, Pang X, Or E. Identification of potential post-ethylene events in the signaling cascade induced by stimuli of bud dormancy release in grapevine. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1251-1268. [PMID: 32989852 DOI: 10.1111/tpj.14997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 08/24/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
Ethylene signaling appears critical for grape bud dormancy release. We therefore focused on identification and characterization of potential downstream targets and events, assuming that they participate in the regulation of dormancy release. Because ethylene responding factors (ERF) are natural candidates for targets of ethylene signaling, we initially characterized the behavior of two VvERF-VIIs, which we identified within a gene set induced by dormancy release stimuli. As expected, these VvERF-VIIs are localized within the nucleus, and are stabilized upon decreases in oxygen availability within the dormant buds. Less expected, the proteins are also stabilized upon hydrogen cyanamide (HC) application under normoxic conditions, and their levels peak at deepest dormancy under vineyard conditions. We proceeded to catalog the response of all bud-expressed ERFs, and identified additional ERFs that respond similarly to ethylene, HC, azide and hypoxia. We also identified a core set of genes that are similarly affected by treatment with ethylene and with various dormancy release stimuli. Interestingly, the functional annotations of this core set center around response to energy crisis and renewal of energy resources via autophagy-mediated catabolism. Because ERF-VIIs are stabilized under energy shortage and reshape cell metabolism to allow energy regeneration, we propose that: (i) the availability of VvERF-VIIs is a consequence of an energy crisis within the bud; (ii) VvERF-VIIs function as part of an energy-regenerating mechanism, which activates anaerobic metabolism and autophagy-mediated macromolecule catabolism; and (iii) activation of catabolism serves as the mandatory switch and the driving force for activation of the growth-inhibited meristem during bud-break.
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Affiliation(s)
- Zhaowan Shi
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, 7528809, Israel
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Tamar Halaly-Basha
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, 7528809, Israel
| | - Chuanlin Zheng
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, 7528809, Israel
- Department of Fruit Tree Sciences, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Michal Sharabi-Schwager
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, 7528809, Israel
| | - Chen Wang
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, 7528809, Israel
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - David W Galbraith
- School of Plant Sciences and Bio5 Institute, University of Arizona, Tucson, AZ, 85721, USA
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Jin Ming Avenue, Kaifeng, 475004, China
- State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Jin Ming Avenue, Kaifeng, 475004, China
| | - Ron Ophir
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, 7528809, Israel
| | - Xuequn Pang
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Etti Or
- Department of Fruit Tree Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, 7528809, Israel
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18
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Wijerathna-Yapa A, Stroeher E, Fenske R, Li L, Duncan O, Millar AH. Proteomics for Autophagy Receptor and Cargo Identification in Plants. J Proteome Res 2020; 20:129-138. [PMID: 33241938 DOI: 10.1021/acs.jproteome.0c00609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Autophagy is a catabolic process facilitating the degradation of cytoplasmic proteins and organelles in a lysosome- or vacuole-dependent manner in plants, animals, and fungi. Proteomic studies have demonstrated that autophagy controls and shapes the proteome and has identified both receptor and cargo proteins inside autophagosomes. In a smaller selection of studies, proteomics has been used for the analysis of post-translational modifications that target proteins for elimination and protein-protein interactions between receptors and cargo, providing a better understanding of the complex regulatory processes controlling autophagy. In this perspective, we highlight how proteomic studies have contributed to our understanding of autophagy in plants against the backdrop of yeast and animal studies. We then provide a framework for how the future application of proteomics in plant autophagy can uncover the mechanisms and outcomes of sculpting organelles during plant development, particularly through the identification of autophagy receptors and cargo in plants.
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Affiliation(s)
- Akila Wijerathna-Yapa
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - Elke Stroeher
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia.,Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009 Crawley, Western Australia, Australia
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Luo J, Havé M, Clément G, Tellier F, Balliau T, Launay-Avon A, Guérard F, Zivy M, Masclaux-Daubresse C. Integrating multiple omics to identify common and specific molecular changes occurring in Arabidopsis under chronic nitrate and sulfate limitations. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6471-6490. [PMID: 32687580 DOI: 10.1093/jxb/eraa337] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Plants have fundamental dependences on nitrogen and sulfur and frequently have to cope with chronic limitations when their supply is sub-optimal. This study aimed at characterizing the metabolomic, proteomic, and transcriptomic changes occurring in Arabidopsis leaves under chronic nitrate (Low-N) and chronic sulfate (Low-S) limitations in order to compare their effects, determine interconnections, and examine strategies of adaptation. Metabolite profiling globally revealed opposite effects of Low-S and Low-N on carbohydrate and amino acid accumulations, whilst proteomic data showed that both treatments resulted in increases in catabolic processes, stimulation of mitochondrial and cytosolic metabolism, and decreases in chloroplast metabolism. Lower abundances of ribosomal proteins and translation factors under Low-N and Low-S corresponded with growth limitation. At the transcript level, the major and specific effect of Low-N was the enhancement of expression of defence and immunity genes. The main effect of chronic Low-S was a decrease in transcripts of genes involved in cell division, DNA replication, and cytoskeleton, and an increase in the expression of autophagy genes. This was consistent with a role of target-of-rapamycin kinase in the control of plant metabolism and cell growth and division under chronic Low-S. In addition, Low-S decreased the expression of several NLP transcription factors, which are master actors in nitrate sensing. Finally, both the transcriptome and proteome data indicated that Low-S repressed glucosinolate synthesis, and that Low-N exacerbated glucosinolate degradation. This showed the importance of glucosinolate as buffering molecules for N and S management.
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Affiliation(s)
- Jie Luo
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- College of Horticulture and Forestry Sciences, Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, China
| | - Marien Havé
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Gilles Clément
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Frédérique Tellier
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Thierry Balliau
- UMR GQE- le Moulon, INRAE, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alexandra Launay-Avon
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Florence Guérard
- Université Paris-Saclay, CNRS, INRAE, Université d'Évry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Michel Zivy
- UMR GQE- le Moulon, INRAE, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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20
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Masclaux-Daubresse C, d’Andrea S, Bouchez I, Cacas JL. Reserve lipids and plant autophagy. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2854-2861. [PMID: 32080724 PMCID: PMC7260719 DOI: 10.1093/jxb/eraa082] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/20/2020] [Indexed: 05/21/2023]
Abstract
Autophagy is a universal mechanism that facilitates the degradation of unwanted cytoplasmic components in eukaryotic cells. In this review, we highlight recent developments in the investigation of the role of autophagy in lipid homeostasis in plants by comparison with algae, yeast, and animals. We consider the storage compartments that form the sources of lipids in plants, and the roles that autophagy plays in the synthesis of triacylglycerols and in the formation and maintenance of lipid droplets. We also consider the relationship between lipids and the biogenesis of autophagosomes, and the role of autophagy in the degradation of lipids in plants.
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Affiliation(s)
| | - Sabine d’Andrea
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Isabelle Bouchez
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Jean-Luc Cacas
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
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21
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The Ins and Outs of Autophagic Ribosome Turnover. Cells 2019; 8:cells8121603. [PMID: 31835634 PMCID: PMC6952998 DOI: 10.3390/cells8121603] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/05/2019] [Accepted: 12/08/2019] [Indexed: 02/07/2023] Open
Abstract
Ribosomes are essential for protein synthesis in all organisms and their biogenesis and number are tightly controlled to maintain homeostasis in changing environmental conditions. While ribosome assembly and quality control mechanisms have been extensively studied, our understanding of ribosome degradation is limited. In yeast or animal cells, ribosomes are degraded after transfer into the vacuole or lysosome by ribophagy or nonselective autophagy, and ribosomal RNA can also be transferred directly across the lysosomal membrane by RNautophagy. In plants, ribosomal RNA is degraded by the vacuolar T2 ribonuclease RNS2 after transport by autophagy-related mechanisms, although it is unknown if a selective ribophagy pathway exists in plants. In this review, we describe mechanisms of turnover of ribosomal components in animals and yeast, and, then, discuss potential pathways for degradation of ribosomal RNA and protein within the vacuole in plants.
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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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Quantitative Proteome Analysis of Atg5-Deficient Mouse Embryonic Fibroblasts Reveals the Range of the Autophagy-Modulated Basal Cellular Proteome. mSystems 2019; 4:4/6/e00481-19. [PMID: 31690592 PMCID: PMC6832020 DOI: 10.1128/msystems.00481-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Autophagy performs housekeeping functions for cells and maintains a functional mode by degrading damaged proteins and organelles and providing energy under starvation conditions. The process is tightly regulated by the evolutionarily conserved Atg genes, of which Atg5 is one such crucial mediator. Here, we have done a comprehensive quantitative proteome analysis of mouse embryonic fibroblasts that lack a functional autophagy pathway (Atg5 knockout). We observe that 14% of the identified cellular proteome is remodeled, and several proteins distributed across diverse cellular processes with functions in signaling, cell adhesion, development, and immunity show either higher or lower levels under autophagy-deficient conditions. These cells have lower levels of crucial immune proteins that are required to mount a protective inflammatory response. This study will serve as a valuable resource to determine the role of autophagy in modulating specific protein levels in cells. Basal autophagy is crucial for maintenance of cellular homeostasis. ATG5 is an essential protein for autophagosome formation, and its depletion has been extensively used as a tool to disrupt autophagy. Here, we characterize the impact of Atg5 deficiency on the cellular proteome of mouse embryonic fibroblasts (MEFs). Using a tandem mass tagging (TMT)-based quantitative proteomics analysis, we observe that 14% of identified proteins show dysregulated levels in atg5−/− MEFs. These proteins were distributed across diverse biological processes, such as cell adhesion, development, differentiation, transport, metabolism, and immune responses. Several of the upregulated proteins were receptors involved in transforming growth factor β (TGF-β) signaling, JAK-STAT signaling, junction adhesion, and interferon/cytokine-receptor interactions and were validated as autophagy substrates. Nearly equal numbers of proteins, including several lysosomal proteins and enzymes, were downregulated, suggesting a complex role of autophagy/ATG5 in regulating their levels. The atg5−/− MEFs had lower levels of key immune sensors and effectors, including Toll-like receptor 2 (TLR2), interferon regulatory factor 3 (IRF3), IRF7, MLKL, and STAT1/3/5/6, which were restored by reexpression of ATG5. While these cells could efficiently mount a type I interferon response to the double-stranded RNA (dsRNA) mimic poly(I·C), they were compromised in their inflammatory response to the bacterial pathogen-associated molecular patterns (PAMPs) lipopolysaccharide (LPS) and Pam3CSK4. Transcriptional activation and secretion of interleukin-6 (IL-6) in these cells could be recovered by ATG5 expression, supporting the role of autophagy in the TLR2-induced inflammatory response. This study provides a key resource for understanding the effect of autophagy/ATG5 deficiency on the fibroblast proteome. IMPORTANCE Autophagy performs housekeeping functions for cells and maintains a functional mode by degrading damaged proteins and organelles and providing energy under starvation conditions. The process is tightly regulated by the evolutionarily conserved Atg genes, of which Atg5 is one such crucial mediator. Here, we have done a comprehensive quantitative proteome analysis of mouse embryonic fibroblasts that lack a functional autophagy pathway (Atg5 knockout). We observe that 14% of the identified cellular proteome is remodeled, and several proteins distributed across diverse cellular processes with functions in signaling, cell adhesion, development, and immunity show either higher or lower levels under autophagy-deficient conditions. These cells have lower levels of crucial immune proteins that are required to mount a protective inflammatory response. This study will serve as a valuable resource to determine the role of autophagy in modulating specific protein levels in cells. Author Video: An author video summary of this article is available.
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Decros G, Beauvoit B, Colombié S, Cabasson C, Bernillon S, Arrivault S, Guenther M, Belouah I, Prigent S, Baldet P, Gibon Y, Pétriacq P. Regulation of Pyridine Nucleotide Metabolism During Tomato Fruit Development Through Transcript and Protein Profiling. FRONTIERS IN PLANT SCIENCE 2019; 10:1201. [PMID: 31681351 PMCID: PMC6798084 DOI: 10.3389/fpls.2019.01201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/02/2019] [Indexed: 05/12/2023]
Abstract
Central metabolism is the engine of plant biomass, supplying fruit growth with building blocks, energy, and biochemical cofactors. Among metabolic cornerstones, nicotinamide adenine dinucleotide (NAD) is particularly pivotal for electron transfer through reduction-oxidation (redox) reactions, thus participating in a myriad of biochemical processes. Besides redox functions, NAD is now assumed to act as an integral regulator of signaling cascades involved in growth and environmental responses. However, the regulation of NAD metabolism and signaling during fruit development remains poorly studied and understood. Here, we benefit from RNAseq and proteomic data obtained from nine growth stages of tomato fruit (var. Moneymaker) to dissect mRNA and protein profiles that link to NAD metabolism, including de novo biosynthesis, recycling, utilization, and putative transport. As expected for a cofactor synthesis pathway, protein profiles failed to detect enzymes involved in NAD synthesis or utilization, except for nicotinic acid phosphoribosyltransferase (NaPT) and nicotinamidase (NIC), which suggested that most NAD metabolic enzymes were poorly represented quantitatively. Further investigations on transcript data unveiled differential expression patterns during fruit development. Interestingly, among specific NAD metabolism-related genes, early de novo biosynthetic genes were transcriptionally induced in very young fruits, in association with NAD kinase, while later stages of fruit growth rather showed an accumulation of transcripts involved in later stages of de novo synthesis and in NAD recycling, which agreed with augmented NAD(P) levels. In addition, a more global overview of 119 mRNA and 78 protein significant markers for NAD(P)-dependent enzymes revealed differential patterns during tomato growth that evidenced clear regulations of primary metabolism, notably with respect to mitochondrial functions. Overall, we propose that NAD metabolism and signaling are very dynamic in the developing tomato fruit and that its differential regulation is certainly critical to fuel central metabolism linking to growth mechanisms.
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Affiliation(s)
| | | | - Sophie Colombié
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Cécile Cabasson
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- MetaboHUB-Bordeaux, MetaboHUB, Phenome-Emphasis, Villenave d’Ornon, France
| | - Stéphane Bernillon
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- MetaboHUB-Bordeaux, MetaboHUB, Phenome-Emphasis, Villenave d’Ornon, France
| | - Stéphanie Arrivault
- Department 2, Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Manuela Guenther
- Department 2, Metabolic Networks, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Isma Belouah
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Sylvain Prigent
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- MetaboHUB-Bordeaux, MetaboHUB, Phenome-Emphasis, Villenave d’Ornon, France
| | - Pierre Baldet
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Yves Gibon
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- MetaboHUB-Bordeaux, MetaboHUB, Phenome-Emphasis, Villenave d’Ornon, France
| | - Pierre Pétriacq
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
- MetaboHUB-Bordeaux, MetaboHUB, Phenome-Emphasis, Villenave d’Ornon, France
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25
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Zhen X, Xu F, Zhang W, Li N, Li X. Overexpression of rice gene OsATG8b confers tolerance to nitrogen starvation and increases yield and nitrogen use efficiency (NUE) in Arabidopsis. PLoS One 2019; 14:e0223011. [PMID: 31553788 PMCID: PMC6760796 DOI: 10.1371/journal.pone.0223011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/11/2019] [Indexed: 12/11/2022] Open
Abstract
Nitrogen (N) is an important element required for plant growth and development, which also affects plant yield and quality. Autophagy, a conserved pathway in eukaryotes, degrades and recycles cellular components, thus playing an important role in N remobilization. However, only a few autophagy genes related to N remobilization in rice (Oryza sativa) have been reported. Here, we identified a core autophagy gene in rice, OsATG8b, with increased expression levels under N starvation conditions. It was investigated the function of OsATG8b by generating three independent homozygous 35S-OsATG8b transgenic Arabidopsis thaliana lines. The overexpression of OsATG8b significantly enhanced autophagic flux in the transgenic Arabidopsis plants. It was also showed that over-expressing OsATG8b promoted growth and development of Arabidopsis, in which the rosette leaves were larger than those of the wild type (WT), and the yield increased significantly by 25.25%. In addition, the transgenic lines accumulated more N in seeds than in the rosette leaves. Further examination revealed that overexpression of OsATG8b could effectively alleviate the growth inhibition of transgenic Arabidopsis under nitrogen (N) stress. N partitioning studies revealed that nitrogen-harvest index (NHI) and nitrogen use efficiency (NUE) were significantly increased in the transgenic Arabidopsis, as well as the 15N-tracer experiments revealing that the remobilization of N to seeds in the OsATG8b-overexpressing transgenic Arabidopsis was high and more than WT. Based on our findings, we consider OsATG8b to be a great candidate gene to increase NUE and yield, especially under suboptimal field conditions.
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Affiliation(s)
- Xiaoxi Zhen
- Rice Research Institute of Shenyang Agricultural University, Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Key Laboratory of Northeast Rice Biology and Genetics and Breeding, Ministry of Agriculture, Shenyang, China
| | - Fan Xu
- Rice Research Institute of Shenyang Agricultural University, Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Key Laboratory of Northeast Rice Biology and Genetics and Breeding, Ministry of Agriculture, Shenyang, China
- * E-mail: (FX); (WZ)
| | - Wenzhong Zhang
- Rice Research Institute of Shenyang Agricultural University, Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Key Laboratory of Northeast Rice Biology and Genetics and Breeding, Ministry of Agriculture, Shenyang, China
- * E-mail: (FX); (WZ)
| | - Nan Li
- Shen Yang Product Quality Supervision and Inspection Institute, Shenyang, China
| | - Xin Li
- Rice Research Institute of Shenyang Agricultural University, Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Key Laboratory of Northeast Rice Biology and Genetics and Breeding, Ministry of Agriculture, Shenyang, China
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26
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Calero-Muñoz N, Exposito-Rodriguez M, Collado-Arenal AM, Rodríguez-Serrano M, Laureano-Marín AM, Santamaría ME, Gotor C, Díaz I, Mullineaux PM, Romero-Puertas MC, Olmedilla A, Sandalio LM. Cadmium induces reactive oxygen species-dependent pexophagy in Arabidopsis leaves. PLANT, CELL & ENVIRONMENT 2019; 42:2696-2714. [PMID: 31152467 DOI: 10.1111/pce.13597] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 05/22/2023]
Abstract
Cadmium treatment induces transient peroxisome proliferation in Arabidopsis leaves. To determine whether this process is regulated by pexophagy and to identify the mechanisms involved, we analysed time course-dependent changes in ATG8, an autophagy marker, and the accumulation of peroxisomal marker PEX14a. After 3 hr of Cd exposure, the transcript levels of ATG8h, ATG8c, a, and i were slightly up-regulated and then returned to normal. ATG8 protein levels also increased after 3 hr of Cd treatment, although an opposite pattern was observed in PEX14. Arabidopsis lines expressing GFP-ATG8a and CFP-SKL enabled us to demonstrate the presence of pexophagic processes in leaves. The Cd-dependent induction of pexophagy was demonstrated by the accumulation of peroxisomes in autophagy gene (ATG)-related Arabidopsis knockout mutants atg5 and atg7. We show that ATG8a colocalizes with catalase and NBR1 in the electron-dense peroxisomal core, thus suggesting that NBR1 may be an autophagic receptor for peroxisomes, with catalase being possibly involved in targeting pexophagy. Protein carbonylation and peroxisomal redox state suggest that protein oxidation may trigger pexophagy. Cathepsine B, legumain, and caspase 6 may also be involved in the regulation of pexophagy. Our results suggest that pexophagy could be an important step in rapid cell responses to cadmium.
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Affiliation(s)
- Nieves Calero-Muñoz
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | | | - Aurelio M Collado-Arenal
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | - María Rodríguez-Serrano
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | - Ana M Laureano-Marín
- Institute of Plant Biochemistry and Photosynthesis, CSIC and Universidad de Sevilla, Seville, 41092, Spain
| | - M Estrella Santamaría
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM), The National Institute for Agricultural and Food Research and Technology (INIA), Madrid, 28223, Spain
| | - Cecilia Gotor
- Institute of Plant Biochemistry and Photosynthesis, CSIC and Universidad de Sevilla, Seville, 41092, Spain
| | - Isabel Díaz
- Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid (UPM), The National Institute for Agricultural and Food Research and Technology (INIA), Madrid, 28223, Spain
| | | | - María C Romero-Puertas
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | - Adela Olmedilla
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
| | - Luisa M Sandalio
- Department of Biochemistry and Molecular and Cellular Biology of Plants, Estación Experimental del Zaidín, CSIC, Granada, 18008, Spain
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Havé M, Luo J, Tellier F, Balliau T, Cueff G, Chardon F, Zivy M, Rajjou L, Cacas JL, Masclaux-Daubresse C. Proteomic and lipidomic analyses of the Arabidopsis atg5 autophagy mutant reveal major changes in endoplasmic reticulum and peroxisome metabolisms and in lipid composition. THE NEW PHYTOLOGIST 2019; 223:1461-1477. [PMID: 31077612 DOI: 10.1111/nph.15913] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/29/2019] [Indexed: 05/21/2023]
Abstract
Autophagy is a universal mechanism in eukaryotic cells that facilitates the degradation of unwanted cell constituents and is essential for cell homeostasis and nutrient recycling. The salicylic acid-independent effects of autophagy defects on leaf metabolism were determined through large-scale proteomic and lipidomic analyses of atg5 and atg5/sid2 mutants under different nitrogen and sulfur growth conditions. Results revealed that irrespective of the growth conditions, plants carrying the atg5 mutation presented all the characteristics of endoplasmic reticulum (ER) stress. Increases in peroxisome and ER proteins involved in very long chain fatty acid synthesis and β-oxidation indicated strong modifications of lipid metabolism. Lipidomic analyses revealed changes in the concentrations of sphingolipids, phospholipids and galactolipids. Significant accumulations of phospholipids and ceramides and changes in GIPCs (glycosyl-inositol-phosphoryl-ceramides) in atg5 mutants indicated large modifications in endomembrane-lipid and especially plasma membrane-lipid composition. Decreases in chloroplast proteins and galactolipids in atg5 under low nutrient conditions, indicated that chloroplasts were used as lipid reservoirs for β-oxidation in atg5 mutants. In conclusion, this report demonstrates the strong impact of autophagy defect on ER stress and reveals the role of autophagy in the control of plant lipid metabolism and catabolism, influencing both lipid homeostasis and endomembrane composition.
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Affiliation(s)
- Marien Havé
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Jie Luo
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Frédérique Tellier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Thierry Balliau
- UMR GQE- le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Gwendal Cueff
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Fabien Chardon
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Michel Zivy
- UMR GQE- le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190, Gif-sur-Yvette, France
| | - Loic Rajjou
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Jean-Luc Cacas
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Céline Masclaux-Daubresse
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
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Belouah I, Nazaret C, Pétriacq P, Prigent S, Bénard C, Mengin V, Blein-Nicolas M, Denton AK, Balliau T, Augé S, Bouchez O, Mazat JP, Stitt M, Usadel B, Zivy M, Beauvoit B, Gibon Y, Colombié S. Modeling Protein Destiny in Developing Fruit. PLANT PHYSIOLOGY 2019; 180:1709-1724. [PMID: 31015299 PMCID: PMC6752906 DOI: 10.1104/pp.19.00086] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/02/2019] [Indexed: 05/18/2023]
Abstract
Protein synthesis and degradation are essential processes that regulate cell status. Because labeling in bulky organs, such as fruits, is difficult, we developed a modeling approach to study protein turnover at the global scale in developing tomato (Solanum lycopersicum) fruit. Quantitative data were collected for transcripts and proteins during fruit development. Clustering analysis showed smaller changes in protein abundance compared to mRNA abundance. Furthermore, protein and transcript abundance were poorly correlated, and the coefficient of correlation decreased during fruit development and ripening, with transcript levels decreasing more than protein levels. A mathematical model with one ordinary differential equation was used to estimate translation (kt ) and degradation (kd ) rate constants for almost 2,400 detected transcript-protein pairs and was satisfactorily fitted for >1,000 pairs. The model predicted median values of ∼2 min for the translation of a protein, and a protein lifetime of ∼11 d. The constants were validated and inspected for biological relevance. Proteins involved in protein synthesis had higher kt and kd values, indicating that the protein machinery is particularly flexible. Our model also predicts that protein concentration is more strongly affected by the rate of translation than that of degradation.
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Affiliation(s)
- Isma Belouah
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université Bordeaux, F33883 Villenave d'Ornon, France
| | - Christine Nazaret
- Institut de Mathématiques de Bordeaux, Ecole Nationale Supérieure de Technologie des Biomolécules de Bordeaux-Institut Polytechnique de Bordeaux, 33400 Talence, France
| | - Pierre Pétriacq
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université Bordeaux, F33883 Villenave d'Ornon, France
| | - Sylvain Prigent
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université Bordeaux, F33883 Villenave d'Ornon, France
| | - Camille Bénard
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université Bordeaux, F33883 Villenave d'Ornon, France
| | - Virginie Mengin
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Mélisande Blein-Nicolas
- La Plateforme d'Analyse Protéomique de Paris Sud Ouest, Génétique Quantitative et Évolution-Le Moulon, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Alisandra K Denton
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen 52074, Germany
| | - Thierry Balliau
- La Plateforme d'Analyse Protéomique de Paris Sud Ouest, Génétique Quantitative et Évolution-Le Moulon, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Ségolène Augé
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université Bordeaux, F33883 Villenave d'Ornon, France
| | - Olivier Bouchez
- Institut National de la Recherche Agronomique, US1426, Service Génome et Transcriptome, Plateforme Génomique, Genotoul, 31326 Castanet-Tolosan, France
| | - Jean-Pierre Mazat
- Institute for Cellular Biochemistry and Genetics-Centre National de la Recherche Scientifique, F-33077 Bordeaux Cedex, France
| | - Mark Stitt
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Björn Usadel
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen 52074, Germany
| | - Michel Zivy
- La Plateforme d'Analyse Protéomique de Paris Sud Ouest, Génétique Quantitative et Évolution-Le Moulon, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Bertrand Beauvoit
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université Bordeaux, F33883 Villenave d'Ornon, France
| | - Yves Gibon
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université Bordeaux, F33883 Villenave d'Ornon, France
| | - Sophie Colombié
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université Bordeaux, F33883 Villenave d'Ornon, France
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Buet A, Costa ML, Martínez DE, Guiamet JJ. Chloroplast Protein Degradation in Senescing Leaves: Proteases and Lytic Compartments. FRONTIERS IN PLANT SCIENCE 2019; 10:747. [PMID: 31275332 PMCID: PMC6593067 DOI: 10.3389/fpls.2019.00747] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/21/2019] [Indexed: 05/20/2023]
Abstract
Leaf senescence is characterized by massive degradation of chloroplast proteins, yet the protease(s) involved is(are) not completely known. Increased expression and/or activities of serine, cysteine, aspartic, and metalloproteases were detected in senescing leaves, but these studies have not provided information on the identities of the proteases responsible for chloroplast protein breakdown. Silencing some senescence-associated proteases has delayed progression of senescence symptoms, yet it is still unclear if these proteases are directly involved in chloroplast protein breakdown. At least four cellular pathways involved in the traffic of chloroplast proteins for degradation outside the chloroplast have been described (i.e., "Rubisco-containing bodies," "senescence-associated vacuoles," "ATI1-plastid associated bodies," and "CV-containing vesicles"), which differ in their dependence on the autophagic machinery, and the identity of the proteins transported and/or degraded. Finding out the proteases involved in, for example, the degradation of Rubisco, may require piling up mutations in several senescence-associated proteases. Alternatively, targeting a proteinaceous protein inhibitor to chloroplasts may allow the inhibitor to reach "Rubisco-containing bodies," "senescence-associated vacuoles," "ATI1-plastid associated bodies," and "CV-containing vesicles" in essentially the way as chloroplast-targeted fluorescent proteins re-localize to these vesicular structures. This might help to reduce proteolytic activity, thereby reducing or slowing down plastid protein degradation during senescence.
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Affiliation(s)
- Agustina Buet
- Instituto de Fisiología Vegetal (INFIVE, CONICET-UNLP), La Plata, Argentina
| | - M Lorenza Costa
- Instituto de Fisiología Vegetal (INFIVE, CONICET-UNLP), La Plata, Argentina
| | - Dana E Martínez
- Instituto de Fisiología Vegetal (INFIVE, CONICET-UNLP), La Plata, Argentina
| | - Juan J Guiamet
- Instituto de Fisiología Vegetal (INFIVE, CONICET-UNLP), La Plata, Argentina
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Dissmeyer N. Conditional Protein Function via N-Degron Pathway-Mediated Proteostasis in Stress Physiology. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:83-117. [PMID: 30892918 DOI: 10.1146/annurev-arplant-050718-095937] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The N-degron pathway, formerly the N-end rule pathway, regulates functions of regulatory proteins. It impacts protein half-life and therefore directs the actual presence of target proteins in the cell. The current concept holds that the N-degron pathway depends on the identity of the amino (N)-terminal amino acid and many other factors, such as the follow-up sequence at the N terminus, conformation, flexibility, and protein localization. It is evolutionarily conserved throughout the kingdoms. One possible entry point for substrates of the N-degron pathway is oxidation of N-terminal Cys residues. Oxidation of N-terminal Cys is decisive for further enzymatic modification of various neo-N termini by arginylation that generates potentially neofunctionalized or instable proteoforms. Here, I focus on the posttranslational modifications that are encompassed by protein degradation via the Cys/Arg branch of the N-degron pathway-part of the PROTEOLYSIS 6 (PRT6)/N-degron pathway-as well as the underlying physiological principles of this branch and its biological significance in stress response.
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Affiliation(s)
- Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB) and ScienceCampus Halle-Plant-Based Bioeconomy, D-06120 Halle (Saale), Germany; ; Twitter: @NDissmeyer
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31
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Tornkvist A, Liu C, Moschou PN. Proteolysis and nitrogen: emerging insights. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2009-2019. [PMID: 30715465 DOI: 10.1093/jxb/erz024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/10/2019] [Indexed: 05/07/2023]
Abstract
Nitrogen (N) is a core component of fertilizers used in modern agriculture to increase yields and thus to help feed a growing global population. However, this comes at a cost to the environment, through run-off of excess N as a result of poor N-use efficiency (NUE) by crops. An obvious remedy to this problem would therefore be the improvement of NUE, which requires advancing our understanding on N homeostasis, sensing, and uptake. Proteolytic pathways are linked to N homeostasis as they recycle proteins that contain N and carbon; however, emerging data suggest that their functions extend beyond this simple recycling. Here, we highlight roles of proteolytic pathways in non-symbiotic and symbiotic N uptake and in systemic N sensing. We also offer a novel view in which we suggest that proteolytic pathways have roles in N homeostasis that differ from their accepted function in recycling.
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Affiliation(s)
- Anna Tornkvist
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Chen Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
- Department of Biology, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
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32
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Perrar A, Dissmeyer N, Huesgen PF. New beginnings and new ends: methods for large-scale characterization of protein termini and their use in plant biology. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2021-2038. [PMID: 30838411 PMCID: PMC6460961 DOI: 10.1093/jxb/erz104] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/27/2019] [Indexed: 05/17/2023]
Abstract
Dynamic regulation of protein function and abundance plays an important role in virtually every aspect of plant life. Diversifying mechanisms at the RNA and protein level result in many protein molecules with distinct sequence and modification, termed proteoforms, arising from a single gene. Distinct protein termini define proteoforms arising from translation of alternative transcripts, use of alternative translation initiation sites, and different co- and post-translational modifications of the protein termini. Also site-specific proteolytic processing by endo- and exoproteases generates truncated proteoforms, defined by distinct protease-generated neo-N- and neo-C-termini, that may exhibit altered activity, function, and localization compared with their precursor proteins. In eukaryotes, the N-degron pathway targets cytosolic proteins, exposing destabilizing N-terminal amino acids and/or destabilizing N-terminal modifications for proteasomal degradation. This enables rapid and selective removal not only of unfolded proteins, but also of substrate proteoforms generated by proteolytic processing or changes in N-terminal modifications. Here we summarize current protocols enabling proteome-wide analysis of protein termini, which have provided important new insights into N-terminal modifications and protein stability determinants, protein maturation pathways, and protease-substrate relationships in plants.
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Affiliation(s)
- Andreas Perrar
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg, Halle (Saale), Germany
- ScienceCampus Halle – Plant-based Bioeconomy, Halle (Saale), Germany
| | - Pitter F Huesgen
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
- Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
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33
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Buono RA, Hudecek R, Nowack MK. Plant proteases during developmental programmed cell death. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2097-2112. [PMID: 30793182 PMCID: PMC7612330 DOI: 10.1093/jxb/erz072] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/12/2019] [Indexed: 05/08/2023]
Abstract
Proteases are among the key regulators of most forms of programmed cell death (PCD) in animals. Many PCD processes have also been associated with protease expression or activation in plants, However, functional evidence for the roles and actual modes of action of plant proteases in PCD remains surprisingly limited. In this review, we provide an update on protease involvement in the context of developmentally regulated plant PCD. To illustrate the diversity of protease functions, we focus on several prominent developmental PCD processes, including xylem and tapetum maturation, suspensor elimination, endosperm degradation, and seed coat formation, as well as plant senescence processes. Despite the substantial advances in the field, protease functions are often only correlatively linked to developmental PCD, and the specific molecular roles of proteases in many developmental PCD processes remain to be elucidated.
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Affiliation(s)
- Rafael Andrade Buono
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Roman Hudecek
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Moritz K. Nowack
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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34
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Stael S, Van Breusegem F, Gevaert K, Nowack MK. Plant proteases and programmed cell death. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1991-1995. [PMID: 31222306 PMCID: PMC6460956 DOI: 10.1093/jxb/erz126] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
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35
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Wang H, Schippers JHM. The Role and Regulation of Autophagy and the Proteasome During Aging and Senescence in Plants. Genes (Basel) 2019; 10:genes10040267. [PMID: 30987024 PMCID: PMC6523301 DOI: 10.3390/genes10040267] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/06/2019] [Accepted: 03/27/2019] [Indexed: 12/18/2022] Open
Abstract
Aging and senescence in plants has a major impact on agriculture, such as in crop yield, the value of ornamental crops, and the shelf life of vegetables and fruits. Senescence represents the final developmental phase of the leaf and inevitably results in the death of the organ. Still, the process is completely under the control of the plant. Plants use their protein degradation systems to maintain proteostasis and transport or salvage nutrients from senescing organs to develop reproductive parts. Herein, we present an overview of current knowledge about the main protein degradation pathways in plants during senescence: The proteasome and autophagy. Although both pathways degrade proteins, autophagy appears to prevent aging, while the proteasome functions as a positive regulator of senescence.
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Affiliation(s)
- Haojie Wang
- Institute of Biology I, RWTH Aachen University, 52074 Aachen, Germany.
| | - Jos H M Schippers
- Institute of Biology I, RWTH Aachen University, 52074 Aachen, Germany.
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36
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Faden F, Mielke S, Dissmeyer N. Modulating Protein Stability to Switch Toxic Protein Function On and Off in Living Cells. PLANT PHYSIOLOGY 2019; 179:929-942. [PMID: 30679267 PMCID: PMC6393803 DOI: 10.1104/pp.18.01215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/10/2019] [Indexed: 05/02/2023]
Abstract
Toxic proteins are prime targets for molecular farming (the generation of pharmacologically active or biotechnologically usable compounds in plants) and are also efficient tools for targeted cell ablation in genetics, developmental biology, and biotechnology. However, achieving conditional activity of cytotoxins and maintaining the toxin-expressing plants as stably transformed lines remain challenging. Here, we produce a switchable version of the highly cytotoxic bacterial RNase barnase by fusing the protein to a portable protein degradation cassette, the low-temperature degron cassette. This method allows conditional genetics based on conditional protein degradation via the N-end rule or N-degron pathway and has been used to vice versa accumulate and/or deplete a diverse variety of highly active, unstable or stable target proteins in different living multicellular organisms and cell systems. Moreover, we expressed the barnase fusion under control of the trichome-specific TRIPTYCHON promoter. This enabled efficient temperature-dependent control of protein accumulation in Arabidopsis (Arabidopsis thaliana) leaf hairs (trichomes). By tuning the levels of the protein, we were able to control the fate of trichomes in vivo. The on-demand formation of trichomes through manipulating the balance between stabilization and destabilization of barnase provides proof of concept for a robust and powerful tool for conditional switchable cell arrest. We present this tool as a potential strategy for the manufacture and accumulation of cytotoxic proteins and toxic high-value products in plants or for conditional genetic cell ablation.
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Affiliation(s)
- Frederik Faden
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
- ScienceCampus Halle, Plant-Based Bioeconomy, D-06120 Halle (Saale), Germany
| | - Stefan Mielke
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
- ScienceCampus Halle, Plant-Based Bioeconomy, D-06120 Halle (Saale), Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany
- ScienceCampus Halle, Plant-Based Bioeconomy, D-06120 Halle (Saale), Germany
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37
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Chen Q, Soulay F, Saudemont B, Elmayan T, Marmagne A, Masclaux-Daubresse CL. Overexpression of ATG8 in Arabidopsis Stimulates Autophagic Activity and Increases Nitrogen Remobilization Efficiency and Grain Filling. PLANT & CELL PHYSIOLOGY 2019; 60:343-352. [PMID: 30407574 DOI: 10.1093/pcp/pcy214] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/27/2018] [Indexed: 05/20/2023]
Abstract
Autophagy knock-out mutants in maize and in Arabidopsis are impaired in nitrogen (N) recycling and exhibit reduced levels of N remobilization to their seeds. It is thus impoortant to determine whether higher autophagy activity could, conversely, improve N remobilization efficiency and seed protein content, and under what circumstances. As the autophagy machinery involves many genes amongst which 18 are important for the core machinery, the choice of which AUTOPHAGY (ATG) gene to manipulate to increase autophagy was examined. We choose ATG8 overexpression since it has been shown that this gene could increase autophagosome size and autophagic activity in yeast. The results we report here are original as they show for the first time that increasing ATG8 gene expression in plants increases autophagosome number and promotes autophagy activity. More importantly, our data demonstrate that, when cultivated under full nitrate conditions, known to repress N remobilization due to sufficient N uptake from the soil, N remobilization efficiency can nevertheless be sharply and significantly increased by overexpressing ATG8 genomic sequences under the control of the ubiquitin promoter. We show that overexpressors have improved seed N% and at the same time reduced N waste in their dry remains. In addition, we show that overexpressing ATG8 does not modify vegetative biomass or harvest index, and thus does not affect plant development.
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Affiliation(s)
- Qinwu Chen
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Fabienne Soulay
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Baptiste Saudemont
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Taline Elmayan
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
| | - Anne Marmagne
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles, France
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38
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McLoughlin F, Augustine RC, Marshall RS, Li F, Kirkpatrick LD, Otegui MS, Vierstra RD. Maize multi-omics reveal roles for autophagic recycling in proteome remodelling and lipid turnover. NATURE PLANTS 2018; 4:1056-1070. [PMID: 30478358 DOI: 10.1038/s41477-018-0299-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/10/2018] [Indexed: 05/21/2023]
Abstract
The turnover of cytoplasmic material by autophagic encapsulation and delivery to vacuoles is essential for recycling cellular constituents, especially under nutrient-limiting conditions. To determine how cells/tissues rely on autophagy, we applied in-depth multi-omic analyses to study maize (Zea mays) autophagy mutants grown under nitrogen-replete and -starvation conditions. Broad alterations in the leaf metabolome were evident in plants missing the core autophagy component ATG12, even in the absence of stress, particularly affecting products of lipid turnover and secondary metabolites, which were underpinned by substantial changes in the transcriptome and/or proteome. Cross-comparison of messenger RNA and protein abundances allowed for the identification of organelles, protein complexes and individual proteins targeted for selective autophagic clearance, and revealed several processes controlled by this catabolism. Collectively, we describe a facile multi-omic strategy to survey autophagic substrates, and show that autophagy has a remarkable influence in sculpting eukaryotic proteomes and membranes both before and during nutrient stress.
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Affiliation(s)
- Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Robert C Augustine
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Faqiang Li
- Department of Genetics, University of Wisconsin, Madison, WI, USA
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Liam D Kirkpatrick
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Marisa S Otegui
- Department of Genetics, University of Wisconsin, Madison, WI, USA
- Department of Botany, University of Wisconsin, Madison, WI, USA
- Laboratory of Cell and Molecular Biology, University of Wisconsin, Madison, WI, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Genetics, University of Wisconsin, Madison, WI, USA.
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39
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Liu F, Marshall RS, Li F. Understanding and exploiting the roles of autophagy in plants through multi-omics approaches. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:146-152. [PMID: 30080598 PMCID: PMC6082170 DOI: 10.1016/j.plantsci.2018.05.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 05/20/2023]
Abstract
Autophagy is a highly conserved pathway in eukaryotes that promotes nutrient recycling and cellular homeostasis through the degradation of excess or damaged cytoplasmic constituents. In plants, autophagy is increasingly recognized as a key contributor to development, reproduction, metabolism, leaf senescence, endosperm and grain development, pathogen defense, and tolerance to abiotic and biotic stresses. Characterizing the functional transcriptomic, proteomic, and metabolomic networks relating to autophagy in plants subjected to various extra- and intra-cellular stimuli may help to identify components associated with the pathway. As such, the integration of multi-omics approaches (i.e., transcriptomics, proteomics and metabolomics), along with cellular, genetic and functional analyses, could provide a global perspective regarding the effects of autophagy on plant metabolism, development and stress responses. In this mini-review, recent research progress in plant autophagy is discussed, highlighting the importance of high-throughput omics approaches for defining the underpinning molecular mechanisms of autophagy and understanding its associated regulatory network.
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Affiliation(s)
- Fen Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Faqiang Li
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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40
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Abstract
Plants have evolved sophisticated mechanisms to recycle intracellular constituents, which are essential for developmental and metabolic transitions; for efficient nutrient reuse; and for the proper disposal of proteins, protein complexes, and even entire organelles that become obsolete or dysfunctional. One major route is autophagy, which employs specialized vesicles to encapsulate and deliver cytoplasmic material to the vacuole for breakdown. In the past decade, the mechanics of autophagy and the scores of components involved in autophagic vesicle assembly have been documented. Now emerging is the importance of dedicated receptors that help recruit appropriate cargo, which in many cases exploit ubiquitylation as a signal. Although operating at a low constitutive level in all plant cells, autophagy is upregulated during senescence and various environmental challenges and is essential for proper nutrient allocation. Its importance to plant metabolism and energy balance in particular places autophagy at the nexus of robust crop performance, especially under suboptimal conditions.
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Affiliation(s)
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130, USA;
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41
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Affiliation(s)
- Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
- Correspondence:
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42
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Abstract
Most assimilated nutrients in the leaves of land plants are stored in chloroplasts as photosynthetic proteins, where they mediate CO2 assimilation during growth. During senescence or under suboptimal conditions, chloroplast proteins are degraded, and the amino acids released during this process are used to produce young tissues, seeds, or respiratory energy. Protein degradation machineries contribute to the quality control of chloroplasts by removing damaged proteins caused by excess energy from sunlight. Whereas previous studies revealed that chloroplasts contain several types of intraplastidic proteases that likely derived from an endosymbiosed prokaryotic ancestor of chloroplasts, recent reports have demonstrated that multiple extraplastidic pathways also contribute to chloroplast protein turnover in response to specific cues. One such pathway is autophagy, an evolutionarily conserved process that leads to the vacuolar or lysosomal degradation of cytoplasmic components in eukaryotic cells. Here, we describe and contrast the extraplastidic pathways that degrade chloroplasts. This review shows that diverse pathways participate in chloroplast turnover during sugar starvation, senescence, and oxidative stress. Elucidating the mechanisms that regulate these pathways will help decipher the relationship among the diverse pathways mediating chloroplast protein turnover.
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Affiliation(s)
- Masanori Izumi
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8578, Japan.
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan.
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi 332-0012, Japan.
| | - Sakuya Nakamura
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan.
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43
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Indispensable Role of Proteases in Plant Innate Immunity. Int J Mol Sci 2018; 19:ijms19020629. [PMID: 29473858 PMCID: PMC5855851 DOI: 10.3390/ijms19020629] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 02/14/2018] [Accepted: 02/19/2018] [Indexed: 12/13/2022] Open
Abstract
Plant defense is achieved mainly through the induction of microbe-associated molecular patterns (MAMP)-triggered immunity (MTI), effector-triggered immunity (ETI), systemic acquired resistance (SAR), induced systemic resistance (ISR), and RNA silencing. Plant immunity is a highly complex phenomenon with its own unique features that have emerged as a result of the arms race between plants and pathogens. However, the regulation of these processes is the same for all living organisms, including plants, and is controlled by proteases. Different families of plant proteases are involved in every type of immunity: some of the proteases that are covered in this review participate in MTI, affecting stomatal closure and callose deposition. A large number of proteases act in the apoplast, contributing to ETI by managing extracellular defense. A vast majority of the endogenous proteases discussed in this review are associated with the programmed cell death (PCD) of the infected cells and exhibit caspase-like activities. The synthesis of signal molecules, such as salicylic acid, jasmonic acid, and ethylene, and their signaling pathways, are regulated by endogenous proteases that affect the induction of pathogenesis-related genes and SAR or ISR establishment. A number of proteases are associated with herbivore defense. In this review, we summarize the data concerning identified plant endogenous proteases, their effect on plant-pathogen interactions, their subcellular localization, and their functional properties, if available, and we attribute a role in the different types and stages of innate immunity for each of the proteases covered.
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